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Cophylogenetic analyses reveal extensive host-shift speciation in a highly specialized and host-specific symbiont system
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... Triangular opisthosomal lobes well developed with slightly rounded lateral margins and straight median margins, length 55 (52-56), width at the base 46 (41)(42)(43). Interlobar cleft triangular, 55 (52-56) long, 48 (45)(46)(47)(48)(49)(50)(51)(52)(53)(54)(55)(56)(57)(58) wide at the level of setae ps1. Narrow interlobar membranes present along the whole cleft, rounded terminally. ...
... It has long been noted that feather mites exhibit high host specificity at different taxonomic levels [41], sometimes serving even as additional information to identify their hosts. Also, many previous phylogenetic analyses have shown that numerous feather mite taxa show significant parallelism with the evolutionary history of their hosts, making them an important model for cophylogenetic studies [42,43], but there are also cases where little evolutionary parallelism is found when comparing the phylogenies of birds and feather mites [44,45]. However, such analyses, which are fundamental to understanding the evolutionary strategy of different groups of feather mites and their hosts, require good taxonomic sampling of both partners. ...
... MALE (holotype, ranges for three paratypes in parentheses,Figures 1 and 3A-C). Gnathosoma trapezoid, length including palps 49(47)(48)(49), width at the base 42(40)(41)(42)(43)(44)(45). Body moderately elongated with well-developed opisthosomal lobes. ...
Feather mites of finfoots (Heliornithidae), a small gruiform family, are poorly and partly erroneously recognized. Grallolichus heliornisi sp. n. (Astigmata: Pterolichidae) is here described from the sungrebe Heliornis fulica as the first representative of the genus commonly found on close relatives of finfoots, Rallidae and Sarothuridae. This species belongs to the species group having ornamented dorsal shields and is morphologically most close to G. proctogamus inhabiting Eurasian coot (Fulica atra). Males of the new species differ from G. proctogamus mainly by the shape of opisthosomal lobes (triangular vs. rounded) and the aedeagus form (parallel sided vs. tapering distally). Females differ mainly by the shape of supranal concavity (open anteriorly vs. closed) and location of setae h1 in relation to supranal concavity (lateral vs. anterior). A key to known species of the genus Grallolichus is provided. The morphological analysis and descriptive characterization of this species, like much of the approximately 2500 feather mite species described to date, were based on mummified mite material preserved in 19th-century old museum bird specimens. These often-forgotten collections are the only source for the analysis of the acarofauna of many rare, unavailable wild or even extinct bird taxa.
... W ith the advance of cophylogenetic analytical and methodological frameworks, many host-symbiont systems have been assessed for the relative contribution of codiversification versus other types of events that shape coevolutionary histories of hosts and symbionts. The majority of studies have suggested that strict codiversification between hosts and symbionts (i.e., temporal and topological congruence of host and parasite phylogenetic branching pattern) is rare [1][2][3][4][5][6][7][8][9][10][11][12][13][14] , on average, being only 7% as common as other coevolutionary events 15 . Generally, cophylogenetic incongruence (i.e., the disagreement between host and symbiont phylogenetic branching patterns at the macroevolutionary scale) may be caused by several evolutionary events, such as duplication (speciation of a symbiont within a single-host species), sorting (extinction and missing the boat), failure of the symbiont to speciate, and host switching (or host shift) 16 . ...
... In contrast, conspecific vertical transmission, i.e., from biological parents to offspring ( Fig. 1: q vc ), is expected to maintain single-host symbionts (i.e., high host specificity) and produce congruent host and symbiont phylogenies (strict codiversification) 22,23 . Yet, despite the perceived dominance of vertical transmission and low horizontal transmission rates [24][25][26][27][28] , some host-symbiont systems may simultaneously display both incongruent cophylogenetic patterns and high host specificity 3,5,16,29,30 . This conundrum challenges the role of vertical conspecific transmission in promoting codiversification and maintaining host specificity. ...
... Consequently, the diversification of these symbionts is expected to be driven largely by host evolution. However, multiple cophylogenetic studies have shown that host switches are relatively common in feather mites 3,5,6,32,40 , suggesting that host switches are in fact one of the main drivers of feather mite diversification 3 . Thus, the current biological expectations are in conflict: one suggests that vertical transmission should be prevalent, leading to congruence between host and symbiont phylogenies, while observations show widespread phylogenetic incongruence among mites, despite their high host specificity. ...
In host-symbiont systems, interspecific transmissions create opportunities for host switches, potentially leading to cophylogenetic incongruence. In contrast, conspecific transmissions often result in high host specificity and congruent cophylogenies. In most bird-feather mite systems, conspecific transmission is considered dominant, while interspecific transmission is supposedly rare. However, while mites typically maintain high host specificity, incongruent cophylogenies are common. To explain this conundrum, we quantify the magnitude of conspecific vs. interspecific transmission in the brood parasitic shiny cowbird (Molothrus bonariensis). M. bonariensis lacks parental care, allowing the assessment of the role of horizontal transmission alone in maintaining host specificity. We found that despite frequent interspecific interactions via foster parental care, mite species dispersing via conspecific horizontal contacts are three times more likely to colonize M. bonariensis than mites transmitted vertically via foster parents. The results highlight the previously underappreciated rate of transmission via horizontal contacts in maintaining host specificity on a microevolutionary scale. On a macroevolutionary scale, however, host switches were estimated to have occurred as frequently as codivergences. This suggests that macroevolutionary patterns resulting from rare events cannot be easily generalized from short-term evolutionary trends.
... Sampling hosts at broad taxonomic scales poses the risk of underestimating symbiont host specificity and overlooking signatures of (co)evolutionary processes that occur at lower taxonomic levels, as has been documented in the fig-fig wasp mutualism (Machado et al. 2005) and avian lice parasitism (Sweet et al. 2016). For feather mites, previous studies have broadly sampled representative host species across a wide range of passerine families (Doña et al. 2017b;Klimov et al. 2017;Dabert et al. 2022). For example, Klimov et al. (2017) sampled mites across 140 host species of 100 genera from 56 families, and Dabert et al. (2022) sampled mites across 47 host species of 33 genera from 16 families. ...
... Thus, cox1 may A c c e p t e d M a n u s c r i p t misinform estimates of host specificity and biodiversity. Multilocus genetic studies on feather mites are rarer (Doña et al. 2017b;Klimov et al. 2017) and have been constrained for these small-bodied organisms due to the minimal yield of high-quality DNA usable for multilocus sequencing. An alternative solution is to conduct pooled sequencing (Pool-Seq). ...
... We targeted 13 mitochondrial protein-coding genes for assembly using aTRAM version 2.3.4. Specifically, we used translated amino acid sequences from Proctophyllodes miliariae (family Proctophyllodidae) as reference loci for aTRAM, which was the most closely related species to our collected mites with all 13 mitochondrial genes present in a reference dataset (Doña et al. 2017b). Although a published feather mite reference mitogenome exists (Esteban et al. ...
A fundamental aspect of symbiotic relationships is host specificity, ranging from extreme specialists associated with only a single host species to generalists associated with many different species. Although symbionts with limited dispersal capabilities are expected to be host specialists, some are able to associate with multiple hosts. Understanding the micro- and macroevolutionary causes of variations in host specificity is often hindered by sampling biases and the limited power of traditional evolutionary markers. Here, we studied feather mites to address the barriers associated with estimates of host specificity for dispersal-limited symbionts. We sampled feather mites (Proctophyllodidae) from a nearly comprehensive set of North American breeding warblers (Parulidae) to study mite phylogenetic relationships and host-symbiont codiversification. We used pooled-sequencing (Pool-Seq) and short-read Illumina technology to interpret results derived from a traditional barcoding gene (cytochrome c oxidase subunit 1) versus 11 protein-coding mitochondrial genes using concatenated and multispecies coalescent approaches. Despite the statistically significant congruence between mite and host phylogenies, mite-host specificity varies widely, and host switching is common regardless of the genetic marker resolution (i.e., barcode versus multilocus). However, the multilocus approach was more effective than the single barcode in detecting the presence of a heterogeneous Pool-Seq sample. These results suggest that presumed symbiont dispersal capabilities are not always strong indicators of host specificity or of historical host-symbiont coevolutionary events. Comprehensive sampling at fine phylogenetic scales may help to better elucidate the microevolutionary filters that impact macroevolutionary processes regulating symbioses, particularly for dispersal-limited symbionts.
... Thus, these dispersal events would sustain multi-host species in host-specific symbionts 2 . Indeed, some recent studies have indicated that colonisation opportunities may be underestimated for some of these symbionts with limited transmission capabilities, and clade-limited host-switching may occur frequently [25][26][27][28] . Alternatively, multi-host symbiont species from relatively host-specific symbionts could represent undiscovered cryptic species [29][30][31][32][33] . ...
... Feather mites are host-specific symbionts with limited dispersal capabilities, but also with some clade-limited host-switching [25][26][27][35][36][37][38][39] . Previous studies have documented multi-host species [35][36][37]40 and cases of morphologically-cryptic but genetically different mite species [35][36][37]40 . ...
... Notably, however, in all the symbiont species studied, we found evidence of population divergence manifested by a low but significant level of population genetic structure among symbionts populations inhabiting different host species. Altogether, these results add to previous findings suggesting that feather mites can potentially disperse among host species more than expected based on their known biology, and suggest the presence of small scale gene flow between populations of feather mites on different host species 24,25,27 . ...
Some symbiont species are highly host-specific, inhabiting only one or a very few host species, and typically have limited dispersal abilities. When they do occur on multiple host species, populations of such symbionts are expected to become genetically structured across these different host species, and this may eventually lead to new symbiont species over evolutionary timescales. However, a low number of dispersal events of symbionts between host species across time might be enough to prevent population structure and species divergence. Overall, processes of evolutionary divergence and the species status of most putative multi-host symbiont systems are yet to be investigated. Here, we used DNA metabarcoding data of 6,023 feather mites (a total of 2,225 OTU representative sequences) from 147 infracommunities (i.e., the assemblage consisting of all mites of different species collected from the same bird host individual) to investigate patterns of population genetic structure and species status of three different putative multi-host feather mite species Proctophyllodes macedo Vitzthum, 1922, Proctophyllodes motacillae Gaud, 1953, and Trouessartia jedliczkai (Zimmerman, 1894), each of which inhabits a variable number of different closely related wagtail host species (genus Motacilla). We show that mite populations from different host species represent a single species. This pattern was found in all the mite species, suggesting that each of these species is a multi-host species in which dispersal of mites among host species prevents species divergence. Also, we found evidence of limited evolutionary divergence manifested by a low but significant level of population genetic structure among symbiont populations inhabiting different host species. Our study agrees with previous studies showing a higher than expected colonization opportunities in host-specific symbionts. Indeed, our results support that these dispersal events would allow the persistence of multi-host species even in symbionts with limited dispersal capabilities, though additional factors such as the geographical structure of some bird populations may also play a role.
... Moreover, even for putatively highly host-specific symbionts such as feather mites on birds, they have been often described as multihost (or oligoxenous) symbionts (Dabert, Solarczyk, Badek, & Dabert, 2005;Doña, Proctor, Mironov, Serrano, & Jovani, 2018), and there are some evidence supporting that straggling and eventual host-switching to a new host may be a common phenomenon (Doña, Sweet, et al., 2017;Doña, Proctor, Mironov, et al., 2018;Gaud, 1992;Klimov, Mironov, & OConnor BM, 2017;Matthews et al., 2018). However, we are still far from quantifying the relevance of these processes and understanding the mechanisms governing them. ...
... Thus, such host-specific symbionts have all the ingredients to be diversifying mainly by cospeciation. Interestingly, and contrary to this expectation, there is also evidence of horizontal transfer within and between bird species (Dubinin, 1951;Gaud, 1992;Jovani & Blanco, 2000), and recent studies have inferred that host-switching with subsequent speciation is the primary process driving their evolutionary diversification (Doña, Sweet, et al., 2017;Doña, Proctor, Mironov, et al., 2018;Klimov et al., 2017;Matthews et al., 2018). These results suggest that host-switching, despite its apparent difficulty for feather mites, has left macroevolutionary fingerprints along millions of years (Doña, Proctor, Mironov, et al., 2018;Doña, Sweet, et al., 2017). ...
... Interestingly, and contrary to this expectation, there is also evidence of horizontal transfer within and between bird species (Dubinin, 1951;Gaud, 1992;Jovani & Blanco, 2000), and recent studies have inferred that host-switching with subsequent speciation is the primary process driving their evolutionary diversification (Doña, Sweet, et al., 2017;Doña, Proctor, Mironov, et al., 2018;Klimov et al., 2017;Matthews et al., 2018). These results suggest that host-switching, despite its apparent difficulty for feather mites, has left macroevolutionary fingerprints along millions of years (Doña, Proctor, Mironov, et al., 2018;Doña, Sweet, et al., 2017). Our specific aims here were (a) to quantify the extent of unexpected associations in feather mites; (b) to study their performance (abundance) and genetic differentiation in the atypical hosts; and (c) to gain insight on the host-symbiont and mite infracommunity-level interactions that govern host-switching. ...
The high relevance of host‐switching for the diversification of highly host‐specific symbionts (i.e., those commonly inhabiting a single host species) demands a better understanding of host‐switching dynamics at an ecological scale. Here we used DNA metabarcoding to study feather mites on passerine birds in Spain, sequencing mtDNA (COI) for 25,540 individual mites (representing 64 species) from 1,130 birds (representing 71 species). Surprisingly, 1,228 (4.8%) mites from 84 (7.4%) birds were found on host species that were not the expected to be a host according to a recent bird‐feather mite associations catalog. Unexpected associations were widespread across studied mite (40.6%) and bird (43.7%) species and showed smaller average infrapopulation sizes than typical associations. Unexpected mite species colonized hosts being distantly related to the set of their usual hosts, but with similar body size. The network of bird‐mite associations was modular (i.e., some groups of bird and mite species tended to be more associated with each other than with the others), with 75.9% of the unexpected associations appearing within the module of the typical hosts of the mite species. Lastly, 68.4% of mite species found on unexpected hosts showed signatures of genetic differentiation, and we found evidence for reproduction or the potential for it in many of the unexpected associations. Results show host colonization as a common phenomenon even for these putatively highly host‐specific symbionts. Thus, host‐switching by feather mites, rather than a rare phenomenon, appears as a relatively frequent phenomenon shaped by ecological filters such as host morphology and is revealed as a fundamental component for a dynamic coevolutionary and codiversification scenario
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... Although cospeciation between symbionts and their hosts has been inferred in some systems (Hafner and Nadler 1988, Light and Hafner 2007, the evolutionary processes related to host-symbiont associations may also be nuanced and quite complex (Paterson and Banks 2001, Marussich and Machado 2007, Hendricks et al. 2013, Fraija-Fernández et al. 2016, Doña et al. 2017c, Klimov et al. 2017). In addition to cospeciation, various other events and processes may occur over evolutionary time, including speciation within a host species (i.e. ...
... At least one study has found similar patterns of cospeciation between feather mites and hosts (Štefka et al. 2011), but these hosts (Galápagos mockingbirds; Mimidae: Mimus) were geographically isolated. However, a recent study (Doña et al. 2017c) explored feather mites on European passerines using mitochondrial molecular data and rigorous cophylogenetic tests. They found high incongruence between feather mite and host phylogenies, which strongly supports host-shift speciation, rather than strict cospeciation, as an explanation for the evolutionary relationships between feather mites and hosts (Doña et al. 2017c). ...
... However, a recent study (Doña et al. 2017c) explored feather mites on European passerines using mitochondrial molecular data and rigorous cophylogenetic tests. They found high incongruence between feather mite and host phylogenies, which strongly supports host-shift speciation, rather than strict cospeciation, as an explanation for the evolutionary relationships between feather mites and hosts (Doña et al. 2017c). Furthermore, another recent, nearly global analysis (Klimov et al. 2017) found that even though feather mite and host (Passeriformes) phylogenies were incongruent (in some cases due to host switches), several ancient synchronous codispersals of mites and birds (for example, from the Old World to the New World) could still be inferred using a double dating approach, where divergence times on both host and mite phylogenies are compared. ...
Host-symbiont relationships are ubiquitous in nature, yet evolutionary and ecological processes that shape these intricate associations are often poorly understood. All orders of birds engage in symbioses with feather mites, which are ectosymbiotic arthropods that spend their entire life on hosts. Due to their permanent obligatory association with hosts, limited dispersal, and primarily vertical transmission, we hypothesized that the cospeciation between feather mites and hosts within one avian family (Parulidae) would be perfect (strict cospeciation). We assessed cophylogenetic patterns and tested for congruence between species in two confamiliar feather mite genera (Proctophyllodidae: Proctophyllodes, Amerodectes) found on 13 species of migratory warblers (and one other closely related migratory species) in the eastern United States. Based on COI sequence data, we found three Proctophyllodes lineages and six Amerodectes lineages. Distance- and event-based cophylogenetic analyses suggested different cophylogenetic trajectories of the two mite genera, and although some associations were significant, there was little overall evidence supporting strict cospeciation. Host switching is likely responsible for incongruent phylogenies. In one case, we documented Prairie Warblers (Setophaga discolor) harboring two mite species of the same genus. Most interestingly, we found strong evidence that host ecology may influence the likelihood of host switching occurring. For example, we documented relatively distantly related ground-nesting hosts (Ovenbird, Seiurus aurocapilla, and Kentucky Warbler, Geothlypis formosa) sharing a single mite species, while other birds are shrub/canopy or cavity nesters. Overall, our results suggest that cospeciation is not the case for feather mites and parulid hosts at this fine phylogenetic scale, and raise the question if cospeciation applies for other symbiotic systems involving hosts that have complex life histories. We also provide preliminary evidence that incorporating host ecological traits into cophylogenetic analyses may be useful for understanding how symbiotic systems have evolved.
... Contrary to Harrison's rule (Harrison, 1915), we did not find a significant correlation between the body size of the bird species studied here and the size of their feather mites. This may be because feather mite species show a complex co-evolutionary history with their hosts, with host-switching being as frequent as cospeciation Doña, Sweet, et al., 2017), and relevant at both micro-and macroevolutionary scales (Doña, Sweet, et al., 2017;Matthews et al., 2023). In other words, mites currently found on one bird species may have speciated on another host species (typically from the same genus or family). ...
... Contrary to Harrison's rule (Harrison, 1915), we did not find a significant correlation between the body size of the bird species studied here and the size of their feather mites. This may be because feather mite species show a complex co-evolutionary history with their hosts, with host-switching being as frequent as cospeciation Doña, Sweet, et al., 2017), and relevant at both micro-and macroevolutionary scales (Doña, Sweet, et al., 2017;Matthews et al., 2023). In other words, mites currently found on one bird species may have speciated on another host species (typically from the same genus or family). ...
Comprehending symbiont abundance among host species is a major ecological endeavour, and the metabolic theory of ecology has been proposed to understand what constrains symbiont populations.
We parameterized metabolic theory equations to investigate how bird species' body size and the body size of their feather mites relate to mite abundance according to four potential energy (uropygial gland size) and space constraints (wing area, total length of barbs and number of feather barbs). Predictions were compared with the empirical scaling of feather mite abundance across 106 passerine bird species (26,604 individual birds sampled), using phylogenetic modelling and quantile regression.
Feather mite abundance was strongly constrained by host space (number of feather barbs) but not by energy. Moreover, feather mite species' body size was unrelated to the body size of their host species.
We discuss the implications of our results for our understanding of the bird–feather mite system and for symbiont abundance in general.
... Co-phylogenetic analyses performed on Amerodectes Valim & Hernandes, 2010 and Proctophyllodes Robin, 1868 species (both from Proctophyllodidae) did not reveal co-speciation as the main factor determining their host-symbiont associations with New World warblers (Parulidae) and discovered numerous hostswitching events (Matthews et al., 2018). Similarly, the phylogenies of Proctophyllodes and Trouessartia Canestrini & Kramer, 1899 (Trouessartiidae) and their hosts, represented by European passerines, showed high incongruence as a result of the same mechanisms (Doña et al., 2017). In contrast, the incongruence observed between phylogenies of Neumannella Trouessart, 1916 (Dermoglyphidae) species and tinamous (Tinamidae) was because of numerous lineage-sorting events (extinction or 'missing the boat') but not to host-switching (Dabert, 2014). ...
... predation, flock sharing or aggressive behaviour) or intermediate contact (e.g. sand-bath sharing, sharing or stealing nest cavities or nests) (Dabert et al., 2015;Doña et al., 2017Doña et al., , 2018. Regarding the use of foreign nests or nest cavities by birds, it should be noted that live Analges mites are not found in these localities. ...
Mites of the genus Analges (Acariformes: Analgidae) inhabit the down feathers of passeriform birds. The evolutionary history of Analges and the co-phylogentic relationships between these mites and their hosts are unknown. Our phylogenetic analysis supported the monophyly of the genus, but it did not support previous taxonomic hypotheses subdividing the genus into the subgenera Analges and Analgopsis or arranging some species into the A. chelopus and A. passerinus species groups. Molecular data reveal seven new species inhabiting Eurasian passerines and support the existence of several multi-host species. According to molecular dating, the origin of the Analges (c. 41 Mya) coincided with the Eocene diversification of Passerida into Sylvioidea and Muscicapoidea–Passeroidea. The initial diversification of Analges took place on the Muscicapoidea clade, while remaining passerine superfamilies appear to have been colonized because of host-switching. Co-speciation appears to be relatively common among Analges species and their hosts, but the most striking pattern in the co-phylogenetic scenario involves numerous complete host-switches, spreads and several failures to speciate. The mechanism of long-term gene-flow among different populations of multi-host Analges species is enigmatic and difficult to resolve. Probably, in some cases mites could be transferred between birds via feathers used as nest material.
... Co-phylogenetic analyses performed on Amerodectes Valim & Hernandes, 2010 and Proctophyllodes Robin, 1868 species (both from Proctophyllodidae) did not reveal co-speciation as the main factor determining their host-symbiont associations with New World warblers (Parulidae) and discovered numerous hostswitching events (Matthews et al., 2018). Similarly, the phylogenies of Proctophyllodes and Trouessartia Canestrini & Kramer, 1899 (Trouessartiidae) and their hosts, represented by European passerines, showed high incongruence as a result of the same mechanisms (Doña et al., 2017). In contrast, the incongruence observed between phylogenies of Neumannella Trouessart, 1916 (Dermoglyphidae) species and tinamous (Tinamidae) was because of numerous lineage-sorting events (extinction or 'missing the boat') but not to host-switching (Dabert, 2014). ...
... predation, flock sharing or aggressive behaviour) or intermediate contact (e.g. sand-bath sharing, sharing or stealing nest cavities or nests) (Dabert et al., 2015;Doña et al., 2017Doña et al., , 2018. Regarding the use of foreign nests or nest cavities by birds, it should be noted that live Analges mites are not found in these localities. ...
Mites of the genus Analges (Acariformes: Analgidae) inhabit the down feathers of passeriform birds. The evolutionary history of Analges and the co-phylogentic relationships between these mites and their hosts are unknown. Our phylogenetic analysis supported the monophyly of the genus, but it did not support previous taxonomic hypotheses subdividing the genus into the subgenera Analges and Analgopsis or arranging some species into the A. chelopus and A. passerinus species groups. Molecular data reveal seven new species inhabiting Eurasian passerines and support the existence of several multi-host species. According to molecular dating, the origin of the Analges (c. 41 Mya) coincided with the Eocene diversification of Passerida into Sylvioidea and Muscicapoidea–Passeroidea. The initial diversification of Analges took place on the Muscicapoidea clade, while remaining passerine superfamilies appear to have been colonized because of host-switching. Co-speciation appears to be relatively common among Analges species and their hosts, but the most striking pattern in the co-phylogenetic scenario involves numerous complete host-switches, spreads and several failures to speciate. The mechanism of long-term gene-flow among different populations of multi-host Analges species is enigmatic and difficult to resolve. Probably, in some cases mites could be transferred between birds via feathers used as nest material.
... In particular, the close association between host and parasite in these systems can result in cospeciation, i.e. simultaneous divergence of host and parasite lineages (Brooks, 1979). However, even in these tightly interacting systems, hostswitching can also be a common process (Boyd et al., 2021;Doña et al., 2017;Johnson et al., 2002). Host-switching involves parasite colonization (i.e. ...
... One advantage of this software is that it summarizes events across equally parsimonious (MPR) cophylogenetic reconstructions. To facilitate comparisons with prior cophylogenetic studies, we used costs of duplication: 1, sorting: 1, and host-switching: 2. This is the cost scheme used by most published cophyogenetic studies of lice, as well as other groups of ectosymbionts (Sweet et al., 2016;Doña et al., 2017;Matthews et al., 2018;de Moya et al., 2019a) because duplication + sorting is given an equal total weight to host-switching as alternative ways of reconstructing conflicting host and parasite nodes. Cospeciation always has a zero cost in cophylogenetic reconstruction techniques. ...
Parasite diversification is influenced by many of the same factors that affect speciation of free-living organisms, such as biogeographic barriers. However, the ecology and evolution of the host lineage also has a major impact on parasite speciation. Here we explore the interplay between biogeography and host-association on the pattern of diversification in a group of ectoparasitic lice (Insecta: Phthiraptera: Penenirmus) that feeds on the feathers of woodpeckers, barbets, and honeyguides (Piciformes) and some songbirds (Passeriformes). We use whole genome sequencing of 41 ingroup and 12 outgroup samples to develop a phylogenomic dataset of DNA sequences from a reference set of 2,395 single copy ortholog genes, for a total of nearly four million aligned base positions. The phylogenetic trees resulting from both concatenated and gene-tree/species-tree coalescent analyses were nearly identical and highly supported. These trees recovered the genus Penenirmus as monophyletic and identified several major clades, which tended to be associated with one major host group. However, cophylogenetic analysis revealed that host-switching was a prominent process in the diversification of this group. This host-switching generally occurred within single major biogeographic regions. We did, however, find one case in which it appears that a rare dispersal event by a woodpecker lineage from North America to Africa allowed its associated louse to colonize a woodpecker in Africa, even though the woodpecker lineage from North America never became established there.
... host-switching among major avian host lineages is similar to patterns seen on smaller cophylogenetic scales between feather mites and their avian hosts [18][19][20] . Extensive host-switching has been inferred in this mite system, which has a similar transmission ecology 18,19 to that of lice, despite ecological specialization 20 . ...
... host-switching among major avian host lineages is similar to patterns seen on smaller cophylogenetic scales between feather mites and their avian hosts [18][19][20] . Extensive host-switching has been inferred in this mite system, which has a similar transmission ecology 18,19 to that of lice, despite ecological specialization 20 . Extensive host-switching has also been detected in the malaria endoparasites that infect birds 21 . ...
Nearly all lineages of birds host parasitic feather lice. Based on recent phylogenomic studies, the three major lineages of modern birds diverged from each other before the Cretaceous-Paleogene (K-Pg) mass extinction event. In contrast, studies of the phylogeny of feather lice on birds, indicate that these parasites diversified largely after this event. However, these studies were unable to reconstruct the ancestral avian host lineage for feather lice. Here we use genome sequences of a broad diversity of lice to reconstruct a phylogeny based on 1,075 genes. By comparing this louse evolutionary tree to the avian host tree, we show that feather lice began diversifying on the common ancestor of waterfowl and landfowl, then radiated onto other avian lineages by extensive host-switching. Dating analyses and cophylogenetic comparisons revealed that two of three lineages of birds that diverged before the K-Pg boundary acquired their feather lice after this event via host-switching. Robert de Moya et al. use comparative genomics of avian lice to reconstruct the phylogeny of these parasites. They show that feather lice diversified on the common ancestor of waterfowl and landfowl, and then radiated onto other avian lineages through host-switching.
... Cophylogenetic methods have been 98 useful to disentangle which ecological and evolutionary traits drive the evolutionary history of 99 symbionts ( Clayton et al., 2015, and references therein). For instance, from cophylogenetics, we 100 know that at an evolutionary scale, lower dispersal capabilities are associated with higher 101 cospeciation rates and lower host-switching rates (Clayton et al., 2015;Doña et al., 2017b;Sweet 102 and Johnson, 2018). Similarly, cophylogenetic methods could be used to increase our knowledge 103 of which symbiont traits are behind particular extinction rates (e.g., transmission, aggregation, or 104 geographic patchiness, see Box 1). ...
... In short, highly host-specific symbionts are expected to have a higher extinction 134 risk. However, Strona et al., (2013) found that host-stability instead of host-specificity was the 135 main determinant of the risk of becoming extinct. is associated with major ecological and evolutionary aspects that may be relevant to consider in 139 symbiont extinction risk assessments ( Lipsitch et al., 1995;Whiteman et al., 2004;Huyse et al., 140 2005; Barrett et al., 2008;Clayton et al., 2015;Doña et al., 2017b;Sweet and Johnson, 2018;141 Poulin, 2011;Antonovics et al., 2017;Fisher et al., 2017;Doña et al., 2019c). All else being equal, 142 vertically-transmitted symbionts would be predicted to have a higher probability of extinction 143 given their level of specialization and other relevant features that increase extinction risk (e.g., 144 high virulence or low levels of genetic diversity). ...
Symbionts have a unique mode of life that has attracted the attention of ecologists and evolutionary biologists for centuries. As a result of this attention, these disciplines have produced a mature body of literature on host-symbiont interactions. In contrast, the discipline of symbiont conservation is still in a foundational stage. Here, we aim to integrate methodologies on symbiont coevolutionary biology with the perspective of conservation. We focus on host-symbiont cophylogenies, because they have been widely used to study symbiont diversification history and contain information on symbiont extinction. However, cophylogenetic information has never been used nor adapted to the perspective of conservation. Here, we propose a new statistic, “cophylogenetic extinction rate” (Ec), based on coevolutionary knowledge, that uses data from event-based cophylogenetic analyses, and which could be informative to assess relative symbiont extinction risks. Finally, we propose potential future research to further develop estimation of symbiont extinction risk from cophylogenetic analyses and continue the integration of this existing knowledge of coevolutionary biology and cophylogenetics into future symbiont conservation studies and practices.
... The number of primer mismatches (i.e., the number of bases that did not match between the primer and the target annealing site) was also taken into account to investigate whether this affected the accuracy of the abundance estimates (see Table 2). This was done using previously published mitogenomes or sequences from the species under study (Doña et al. 2015a(Doña et al. , 2017b. ...
... Accordingly, we did not include congeneric comparisons, as congeneric species of feather mites usually do not co-occur in the same host. However, recent results on the relevance of host-switching for feather mites may suggest revisiting this, as coexistence between congeneric may have been underestimated (e.g., Doña et al. 2017b). Nevertheless, estimates when dealing 94 Experimental and Applied Acarology (2018) 76:81-97 with congeneric species are likely to perform similarly, as, in a similar protocol, Diaz-Real et al. (2015) also obtained good quantitative estimates when working with congeneric comparisons. ...
Feather mites are among the most common and diverse ectosymbionts of birds, yet basic questions such as the nature of their relationship remain largely unanswered. One reason for feather mites being understudied is that their morphological identification is often virtually impossible when using female or young individuals. Even for adult male specimens this task is tedious and requires advanced taxonomic expertise, thus hampering large-scale studies. In addition, molecular-based methods are challenging because the low DNA amounts usually obtained from these tiny mites do not reach the levels required for high-throughput sequencing. This work aims to overcome these issues by using a DNA metabarcoding approach to accurately identify and quantify the feather mite species present in a sample. DNA metabarcoding is a widely used molecular technique that takes advantage of high-throughput sequencing methodologies to assign the taxonomic identity to all the organisms present in a complex sample (i.e., a sample made up of multiple specimens that are hard or impossible to individualise). We present a high-throughput method for feather mite identification using a fragment of the COI gene as marker and Illumina Miseq technology. We tested this method by performing two experiments plus a field test over a total of 11,861 individual mites (5360 of which were also morphologically identified). In the first experiment, we tested the probability of detecting a single feather mite in a heterogeneous pool of non-conspecific individuals. In the second experiment, we made 2 × 2 combinations of species and studied the relationship between the proportion of individuals of a given species in a sample and the proportion of sequences retrieved to test whether DNA metabarcoding can reliably quantify the relative abundance of mites in a sample. Here we also tested the efficacy of degenerate primers (i.e., a mixture of similar primers that differ in one or several bases that are designed to increase the chance of annealing) and investigated the relationship between the number of mismatches and PCR success. Finally, we applied our DNA metabarcoding pipeline to a total of 6501 unidentified and unsorted feather mite individuals sampled from 380 European passerine birds belonging to 10 bird species (field test). Our results show that this proposed pipeline is suitable for correct identification and quantitative estimation of the relative abundance of feather mite species in complex samples, especially when dealing with a moderate number (> 30) of individuals per sample.
... Given this biology, it is surprising that a recent cophylogenetic study between two genera of feather mites and European passerine birds (Doña, Sweet, Johnson, Serrano, & Jovani, 2017) showed that host switching, rather than host-parasite cospeciation (i.e., symbiont speciation after host speciation), may be the main driver of diversification. In fact, cophylogenetic reconstructions showed that speciation after host switching was more prevalent by far than cospeciation in the passerine feather mites studied. ...
... However, the number of examples is few, and the role of infrequent major host switches on the development of symbiont specialization requires further study. Finally, a recent cophylogenetic study (Doña, Sweet et al., 2017) carried out at a clade-limited scale for hosts (between passerine species) recovered many more host switches (70-75% of the events for Proctophyllodes and Trouessartia mites, respectively) than it did cospeciation events. Altogether, this supports diversification of the feather mites as the consequence of a history of both clade-limited and major host switches, with a potentially more minor role of cospeciation. ...
Aim
Highly host‐specific symbionts are very rarely found except with their typical host species. Although switches to new hosts are rare and difficult to detect, a switch to a host phylogenetically distant from the original one (a ‘major host switch’) could allow diversification of the symbionts onto the new host lineage. The consequences of such major host switches on the diversification of highly host‐specific symbionts of animals have rarely been explored. Here, we examine the host specificity of vane‐dwelling feather mites, a group that shows strong specificity, together with their host‐switching dynamics and the consequences of major host switches for their diversification.
Location
Global.
Time period
From 1882 to 2015.
Major taxa studied
Feather mites and birds.
Methods
Using the largest published dataset of feather mite–bird associations, we analysed raw, phylogenetic and geographical host specificity of feather mites. We studied host‐switching dynamics by describing the sharing by feather mites of bird species with different phylogenetic distances. For three of the most species‐rich feather mite families, we quantified the consequences of major host switches for feather mite diversification.
Results
Most feather mite species (84%) inhabit one to three very closely related host species. Assemblages of feather mites on birds do not show a geographical signature, but rather show strong host‐driven structuring. The probability that a mite species occurs on two host species decays sharply with host phylogenetic distance, with only one instance of a feather mite species occupying distantly related hosts from different orders. However, results suggest that despite the strong host specificity, a few major host switches triggered the origin of 21% of the species and 38% of the genera of the mite families studied.
Main conclusions
We show that feather mites are highly host‐specific symbionts, whose assemblages do not show geographical structure, even at a continental scale. We conclude that major host switches are very rare events with strong macroevolutionary consequences for feather mite diversity.
... For instance, a metabarcoding study found ca 5% of feather mite individuals studied were carried by unexpected bird species according to the taxonomic literature (Doña et al. 2019b). Also, several authors have found host-switching to be more common than cospeciation in feather mite evolution (Doña et al. 2017b, Matthews et al. 2018, Dabert et al. 2022. Despite so, most feather mite species occur on one or few bird species, often in the same bird genus (Doña et al. 2018). ...
Symbionts are key elements of ecosystems, by playing important roles in shaping the biology and ecology of their hosts. However, the factors determining symbiont loads across host species are still unclear. Nowadays, we know that the intensity and prevalence of feather mites, the most diverse group of avian ectosymbionts, differ strongly between species. To understand those differences, we studied 17 bird species traits and two feather mite community features (species richness and composition in bird species) potentially related to interspecific differences in feather mite intensity and prevalence across bird species. We analyzed a large dataset of feather mite occurrence across European passerines: for feather mite intensity a sample of 27 424 birds from 119 bird species, and 1 805 566 feather mites counted, and for prevalence a sample of 76 126 birds from 122 bird species. Feather mite intensity and prevalence covaried positively across bird species, reinforcing the previous observation that species differ in feather mite load. Comparative analyses of the association of bird traits and feather mite richness with feather mite intensity or prevalence showed a moderate explanatory power, high model selection uncertainty, inconsistent results for both prevalence and intensity data, and contrasting results with previous comparative studies on feather mite occurrence. Furthermore, even though closely related bird species had similar feather mite communities, there was a low evolutionary conservatism of both the prevalence and intensity of feather mites across bird species (i.e. low phylogenetic signal). Finally, feather mite community composition did not explain feather mite intensity or prevalence across bird species. Overall, our large number of host and mite traits failed to satisfactorily explain the high variability in feather mite occurrence across bird species. We discuss that this difficult‐to‐understand apparent idiosyncrasy of bird species in their feather mite intensity and prevalence may be the outcome of the interaction between host and symbiont traits.
... Although they are dispersallimited and typically vertically transmitted [29,30], macroevolutionary (i.e., species level) studies have demonstrated that they often do not perfectly coevolve with their hosts. Instead, there is evidence for clade-limited host switching and a wide range of host specificity, which could be associated with the differential life histories of mites [31] or hosts [32][33][34]. Microevolutionary studies (i.e., infrapopulation level) are rare and have been restricted to barcoding markers [35,36], limiting our understanding of their infrapopulation genetic diversity to a small number of conserved loci instead of genome-wide. This is at least partly due to their minute size (0.3-0.7 mm in length [37]), which makes obtaining sufficient amounts of high-quality DNA for whole-genome HTS endeavors challenging, particularly for individual mites. ...
Microscopic symbionts represent crucial links in biological communities. However, they present technical challenges in high-throughput sequencing (HTS) studies due to their small size and minimal high-quality DNA yields, hindering our understanding of host–symbiont coevolution at microevolutionary and macroevolutionary scales. One approach to overcome those barriers is to pool multiple individuals from the same infrapopulation (i.e., individual host) and sequence them together (Pool-Seq), but individual-level information is then compromised. To simultaneously address both issues (i.e., minimal DNA yields and loss of individual-level information), we implemented a strategic Pool-Seq approach to assess variation in sequencing performance and categorize genetic diversity (single nucleotide polymorphisms (SNPs)) at both the individual-level and infrapopulation-level for microscopic feather mites. To do so, we collected feathers harboring mites (Proctophyllodidae: Amerodectes protonotaria) from four individual Prothonotary Warblers (Parulidae: Protonotaria citrea). From each of the four hosts (i.e., four mite infrapopulations), we conducted whole-genome sequencing on three extraction pools consisting of different numbers of mites (1 mite, 5 mites, and 20 mites). We found that samples containing pools of multiple mites had more sequencing reads map to the feather mite reference genome than did the samples containing only a single mite. Mite infrapopulations were primarily genetically structured by their associated individual hosts (not pool size) and the majority of SNPs were shared by all pools within an infrapopulation. Together, these results suggest that the patterns observed are driven by evolutionary processes occurring at the infrapopulation level and are not technical signals due to pool size. In total, despite the challenges presented by microscopic symbionts in HTS studies, this work highlights the value of both individual-level and infrapopulation-level sequencing toward our understanding of host–symbiont coevolution at multiple evolutionary scales.
... Allen et al., 2018). We used open reading frames of 13 mitochondrial protein-coding genes from Proctophyllodes miliariae (family Proctophyllodidae) as reference loci for aTRAM (Doña, Sweet, et al., 2017) and selected SPAdes (Bankevich et al., 2012) for the de novo assembler parameter in aTRAM. ...
Researchers often examine symbiont host specificity as a species-level pattern, but it can also be key to understanding processes occurring at the population level, which are not as well understood. The specialist-generalist variation hypothesis (SGVH) attempts to explain how host specificity influences population-level processes, stating that single-host symbionts (specialists) exhibit stronger population genetic structure than multi-host symbionts (generalists) because of fewer opportunities for dispersal and more restricted gene flow between populations. However, this hypothesis has not been tested in systems with highly mobile hosts, in which population connectivity may vary temporally and spatially. To address this gap, we tested the SGVH on proctophyllodid feather mites found on migratory warblers (family Parulidae) with contrasting host specificities, Amerodectes protonotaria (a host specialist of Protonotaria citrea) and A. ischyros (a host generalist of 17 parulid species). We used a pooled-sequencing approach and a novel workflow to analyse genetic variants obtained from whole genome data. Both mite species exhibited fairly weak population structure overall, and contrary to predictions of the SGVH, the generalist was more strongly structured than the specialist. These results may suggest that specialists disperse more freely among conspecifics, whereas generalists sort according to geography. Furthermore, our results may reflect an unexpected period for mite transmission - during the nonbreeding season of migratory hosts - as mite population structure more closely reflects the distributions of hosts during the nonbreeding season. Our findings alter our current understanding of feather mite biology and highlight the potential for studies to explore factors driving symbiont diversification at multiple evolutionary scales.
... We used eMPRess v1.0 (Santichaivekin et al., 2020) to compare host and parasite trees based on their topology. As in prior cophylogenetic studies, we used costs of duplication: 1, sorting: 1, and host-switching: 2. This is the cost scheme used by most published cophylogenetic studies of lice, as well as other groups of ectosymbionts (Boyd et al., 2022;Doña et al., 2017;Johnson et al., 2021Johnson et al., , 2022Matthews et al., 2018;Sweet & Johnson, 2018). For the host tree, we obtained phylogenetic information from a prior phylogenomic study (Boyd et al., 2022). ...
The effective population size (Ne) of an organism is expected to be generally proportional to the total number of individuals in a population. In parasites, we might expect the effective population size to be proportional to host population size and host body size, because both are expected to increase the number of parasite individuals. However, among other factors, parasite populations are sometimes so extremely subdivided that high levels of inbreeding may distort these predicted relationships. Here, we used whole-ge-nome sequence data from dove parasites (71 feather louse species of the genus Columbicola) and phylogenetic comparative methods to study the relationship between parasite effective population size and host population size and body size. We found that parasite effective population size is largely explained by host body size but not host population size. These results suggest the potential local population size (infrapopulation or deme size) is more predictive of the long-term effective population size of parasites than is the total number of potential parasite infrapopulations (i.e., host individuals).
... In contrast, phylogenetic relationships within the genus remain almost unexplored. The relationships between small numbers of species-mainly from a few species groups of European passerines-were recently analyzed based on molecular data (Doña et al. 2015(Doña et al. , 2017Constantinescu et al. 2018b). ...
The paper provides major references to Trouessartia species described since Santana’s (1976) world revision of this genus, unified diagnoses of 11 currently recognized species groups (africana, appendiculata, capensis, crucifera, estrildae, minutipes, picumni, rosterii, stelgidopteryx, tenuipilata and viduae), and a world checklist of currently known species. The updated checklist includes 147 valid species and is supplemented with data on type hosts, distribution and references to most useful descriptions.
... Specifically, we identified orthologous 1:1 single copy protein coding genes (PCGs; Acari: Sarcoptes scabiei ), consisting of 1,692 target nuclear PCGs, using OrthoDB version 10.1 [14] . To target the 13 PCGs of the mitochondria, we used data from Proctophyllodes miliariae , which was the most closely related species to A. protonotaria with all 13 mitochondrial genes present in a reference dataset [15] . With amino acid translated nuclear and mitochondrial genes as targets, we ran aTRAM using SPAdes for five iterations. ...
Feather mites are ubiquitous, permanent, obligate ectosymbionts of avian hosts and are a valuable natural system for studying host-symbiont evolutionary and ecological dynamics at multiple levels of biological organization. However, a lack of a sequenced genome impedes molecular studies using this system. Therefore, we present the first draft genome of a symbiotic feather mite, Amerodectes protonotaria Hernandes 2018. The genome sequence data presented here were derived from an individual female mite that was collected in the field from Protonotaria citrea, its only known host species. Short read sequence data were obtained using an Illumina NovaSeq 6000 platform. From these data, we assembled a 59,665,063 bp draft genome consisting of 2,399 contigs. Raw short reads and the assembled genome sequence are available at the National Center for Biotechnology Information (NCBI)’s Sequence Read Archive (SRA) under BioProject PRJNA884722. The data presented here are beneficial for future research on the biology and evolution of closely related mites and the genomics of host-symbiont interactions.
... However, there is some evidence for negative impacts of high mite densities on bird fitness Sanz 2006, Galván et al. 2008), but mite densities appear not to influence the host immune system (Lindstrom et al. 2004). Feather mites harbour many morphological adaptations to live in the feather environment (Proctor 2003) and there is evidence for both co-evolution (Proctor and Owens 2000, Proctor 2003, Doña et al. 2017b and host switching (Doña et al. 2017a, b) between avian hosts and their mite symbionts. Contrary to feather lice (which feed on the feathers themselves), feather mites tend to feed on dead skin and uropygial gland secretions from the hosts (Proctor 2003), and recent work demonstrated that mites clean feathers by feeding on bacteria and fungi (Doña et al. 2019). ...
Birds host a diversity of ectosymbionts including feather‐dwelling arthropods such as feather mites and lice that they have co‐evolved and speciated with. Among these ectosymbionts, feather mites have evolved more mutualistic to commensal associations with birds than other groups. However, our understanding of the biological and ecological drivers that shape the associations between avian hosts and feather mites in tropical communities is poor. Thus, to help fill this knowledge gap we investigated the factors that govern feather mite abundances at host community, host species and individual levels in bird communities from different elevations on the tropical island of New Guinea. We examined the effects of abiotic factors, such as temperature and precipitation, the influence of host species, feeding guilds, bill morphology, body region, body conditions and infections with haemosporidian blood parasites on feather mite abundance. We found that feather mites were very prevalent among New Guinean birds and that mite abundance was not significantly different between elevations. Bird species with curved bills experienced significantly lower number of mites compared to species with straight bills. Feather mite abundance was significantly higher on flight feathers than on the rest of the body and mite abundance was not strongly associated with the body condition of individuals in most host species, except for a significant negative relationships in three species. Moreover, we did not find an association between feather mite abundance and blood parasite infections, potentially indicating a non‐synergistic association of these two symbionts. Overall, our study demonstrates that tropical avian‐feather mite associations are driven by different biotic and abiotic factors at host community, species and individual levels, highlighting the importance of examining these associations at both broad and fine scales to thoroughly understand the evolution of these symbioses.
... All four cospeciation, duplication, host switch and partial extinction events are necessary to explain many observed parasite-host associations. [2][3][4][5][6][7][8][9] Even though many host-parasite interactions have been studied from this cophylogenetic viewpoint, studies of the changes in molecular host-parasite interactions during coevolution are scarce. ...
Over one hundred Mastadenovirus types infect seven orders of mammals. Virus-host coevolution may involve cospeciation, duplication, host switch and partial extinction events. We reconstruct Mastadenovirus diversification, finding that while cospeciation is dominant, the other three events are also common in Mastadenovirus evolution. Linear motifs are fast-evolving protein functional elements and key mediators of virus-host interactions, thus likely to partake in adaptive viral evolution. We study the evolution of eleven linear motifs in the Mastadenovirus E1A protein, a hub of virus-host protein-protein interactions, in the context of host diversification. The reconstruction of linear motif gain and loss events shows fast linear motif turnover, corresponding a virus-host protein-protein interaction turnover orders of magnitude faster than in model host proteomes. Evolution of E1A linear motifs is coupled, indicating functional coordination at the protein scale, yet presents motif-specific patterns suggestive of convergent evolution. We report a pervasive association between Mastadenovirus host diversification events and the evolution of E1A linear motifs. Eight of 17 host switches associate with the gain of one linear motif and the loss of four different linear motifs, while five of nine partial extinctions associate with the loss of one linear motif. The specific changes in E1A linear motifs during a host switch or a partial extinction suggest that changes in the host molecular environment lead to modulation of the interactions with the retinoblastoma protein and host transcriptional regulators. Altogether, changes in the linear motif repertoire of a viral hub protein are associated with adaptive evolution events during Mastadenovirus evolution.
... However, the phylogenetic relationships within the genus remain almost unexplored. Relationships between very limited numbers of Trouessartia species, mainly from European passerines, have recently been studied based on molecular data (Doña et al. 2017). ...
Two new species of the feather mite genus Trouessartia (Analgoidea: Trouessartiidae) are described from passerine birds in Primorsky Krai (Russian Far East): Trouessartia calliope sp. n. from the Siberian Rubythroat Calliope calliope (Linnaeus) and T. larvivorae sp. n. from the Rufous-tailed Robin Larvivora sibilans (Swinhoe) (Passeriformes: Muscicapidae: Saxicolinae). Both new species are close to T. swidwiensis Jablonska, 1968 associated with nightingales of the genus Luscinia (Linnaeus) (Muscicapidae) in having the prohysteronotal and lobar parts of the hysteronotal shield not separated in males and in having setae h1 situated on large ovate non-sclerotized areas and in the absence of the external copulatory tube in females.
... Although a significant number of known Trouessartia species are now arranged into species groups, the phylogenetic relationships within the genus remain almost unexplored. Relationships between a very limited number of species (mainly from European passerines and representing only a few species groups) were recently tested based on molecular data (Doña et al. 2017;Constantinescu et al. 2018b). ...
A new feather mite species, Trouessartia emberizae sp. n., is described from the Tristram’s Bunting, Emberiza tristrami Swinhoe (Passeriformes: Emberizidae) in the Primorye Territory (Russian Far East). The new species is close to T. jedliczkai (Zimmermann) and T. motacillae Dubinin, associated with wagtails (Motacillidae: Motacilla) and most clearly differs from them in the following features: in males, the hysteronotal shield is entire and the genital apparatus is narrow, parallel-sided and strongly convex dorsally; in females, the external copulatory tube is stylet-like and extends beyond the level of setae h3, and the head of the spermatheca has a short smooth collar. This is the first description of a Trouessartia species from a host of the family of buntings (Emberizidae).
... The sterilization of instruments prior to carrying out a new host analysis and the meticulousness during mounting, together with the fact that this species appears least frequently, leads us to think that it is not due to contamination. Thus, three possible explanations could account for this result: (i) this relationship could be common in nature but the scarce epidemiological surveys together with its low prevalence have precluded its detection; (ii) this is an incipient event of host switching, which has been found to possibly have important evolutionary consequences in other groups of avian mites [51]; (iii) this encounter is a consequence of the sampling method, which could lead to the infection of doves with mites from pigeons. Some authors have found that indirect transmission can take place via water, perches and other contaminated surfaces [15], so the sampling method of employing traps with water and food to catch individuals could lead to this event. ...
Rhynonyssidae is a family of endoparasitic hematophagous mites, which are still largely unknown even though they could act as vector or reservoir of different pathogens like dermanyssids. Sampling requirements have prevented deeper analysis. Rhinonyssids have been explored in a few host specimens per species, leading to undetailed morphological descriptions and inaccurate epidemiology. We explore the relationships established between these parasites in two Columbiformes urban birds (domestic pigeon (Columba livia domestica) and Eurasian collared dove (Streptopelia decaocto)), assesing 250 individuals of each type in Seville (Spain). As expected, Mesonyssus melloi (Castro, 1948) and Mesonyssus columbae (Crossley, 1950) were found in domestic pigeons, and Mesonyssus streptopeliae (Fain, 1962) in Eurasian collared doves. However, M. columbae was found for the first time in Eurasian collared doves. This relationship could be common in nature, but sampling methodology or host switching could also account for this result. An additional unknown specimen was found in a Eurasian collared dove, which could be a new species or an aberrant individual. We also provide an epidemiological survey of the three mite species, with M. melloi being the most common one followed by M. streptopeliae and M. columbae. High variation between previous epidemiological measurements and ours highlights the importance of developing deeper studies to uncover the factors regulating mite prevalence and intensities of infection.
... Cophylogeny analysis identifies the effect of evolution on diversification patterns of two or more ecologically associated species [60,61]. To date, cophylogeny studies have been mainly used to study host-parasite relationships or vertically transmitted symbionts [62]. In this study, we established the use of cophylogeny assessment to study the coevolution of seed microbiota from wild progenitors to modern cultivars of wheat and barley. ...
Introduction
The seed-associated microbiome has a strong influence on plant ecology, fitness, and productivity. Plant microbiota could be exploited for a more responsible crop management in sustainable agriculture. However, the relationships between seed microbiota and hosts related to the changes from ancestor species to breeded crops still remain poor understood.
Objectives
Our aims were i) to understand the effect of cereal domestication on seed endophytes in terms of diversity, structure and co-occurrence, by comparing four cereal crops and the respective ancestor species; ii) to test the phylogenetic coherence between cereals and their seed microbiota (clue of co-evolution).
Methods
We investigated the seed microbiota of four cereal crops (Triticum aestivum, Triticum monococcum, Triticum durum, and Hordeum vulgare), along with their respective ancestors (Aegilops tauschii, Triticum baeoticum, Triticum dicoccoides, and Hordeum spontaneum, respectively) using 16S rRNA gene metabarcoding, Randomly Amplified Polymorphic DNA (RAPD) profiling of host plants and co-evolution analysis.
Results
The diversity of seed microbiota was generally higher in cultivated cereals than in wild ancestors, suggesting that domestication lead to a bacterial diversification. On the other hand, more microbe-microbe interactions were detected in wild species, indicating a better-structured, mature community. Typical human-associated taxa, such as Cutibacterium, dominated in cultivated cereals, suggesting an interkingdom transfers of microbes from human to plants during domestication. Co-evolution analysis revealed a significant phylogenetic congruence between seed endophytes and host plants, indicating clues of co-evolution between hosts and seed-associated microbes during domestication.
Conclusion
This study demonstrates a diversification of the seed microbiome as a consequence of domestication, and provides clues of co-evolution between cereals and their seed microbiota. This knowledge is useful to develop effective strategies of microbiome exploitation for sustainable agriculture.
... Despite their tight association with their avian hosts, feather mites are known to switch hosts at an ecological and evolutionary scale (±100 generations, 200 to 400 years), a process that has been found to be the main driver of diversification in this group Doña, Sweet, et al., 2017;Matthews et al., 2018). Nevertheless, attempts to colonize new hosts are often unsuccessful because of feather mites' high level of specialization to the habitat (host) conditions (Doña et al., 2019). ...
Aim
The simultaneous influence of abiotic and biotic factors as main drivers of global species distributions remains poorly understood, especially in host‐dependent groups. In this study, we diverge from traditional macroecological approaches by considering both biotic (avian species diversity) and abiotic (climatic) factors in determining the global distribution pattern of feather mite species richness, one of the most abundant and diverse bird ectosymbionts.
Location
Global.
Methods
We used a global dataset of feather mite–bird interactions published in 2016, complemented with an up‐to‐date literature survey. We created statistical models designed to explain the effect of abiotic (i.e., temperature, precipitation and energy‐related variables) and biotic factors (bird species richness) on the species richness of feather mites. We used these models to predict global distribution patterns of mites and estimate each explanatory variable's relative importance in temperate and tropical regions.
Results
According to our models, bird species richness accounts for ~63% of the global distribution pattern of mites, which is ten times more relevant than climatic variables. Among abiotic drivers, precipitation intensity and seasonality were the most important variables, accounting for 10% of mite species richness. This figure is lower in tropical regions, where biotic factors are seven times more important than in temperate regions.
Main conclusions
We demonstrate that global mite diversity was primarily determined by biotic and, to a lesser extent, abiotic factors. The relative importance of the predictive variables, however, varied between tropical and temperate regions. The strong association between bird species richness and feather mite species diversity at a global scale raises concerns about the potential for future co‐extinctions.
... These mites have been shown to be useful models in co-evolutionary and co-biogeography studies. Particularly, in mites associated with passerines, ancient bird/mite intercontinental co-dispersals and co-divergence events have been demonstrated (Klimov et al. 2017), but overall co-evolutionary patterns appear to be influenced by host shifts (Doña et al. 2017). Host shifts may be driven by similarities in hosts' ecologies (Matthews et al. 2018) or faunal admixtures, which were frequent events in the evolution of passerines on different continents (Ericson et al. 2002;Fjeldsa 2013;Oliveros et al. 2019). ...
A new feather mite genus Bernierinyssus gen. n. (Analgoidea: Pteronyssidae), associated with endemic Malagasy warblers (Passeriformes: Bernieridae), is proposed based on morphological evidence and DNA sequence data. Within this genus, we detected six mite species, including five new species described here: Bernierinyssus angulatus sp. n. from Crossleyia xanthophrys, B. bernieriae sp. n. from Bernieria madagascariensis, B. bifenestratus sp. n. from Hartertula flavoviridis, B. randiae sp. n. from Randia pseudozosterops, B. xanthomixis sp. n. from Xanthomixis zosterops (type host) and X. cinereiceps, and B. oxylabis (Mironov and Wauthy 2005) comb. n. (transferred from Pteronyssoides Hull). Phylogenetic relationships of these mites were nearly perfectly congruent with those of their hosts, indicating that ancestral Bernierinyssus probably co-dispersed to Madagascar on the common ancestor of Malagasy warblers and then cospeciated with their hosts. Species of Bernierinyssus are well-delimited based on several lines of evidence: morphology (clear among-specific differences in discrete characters), host associations (one mite species per one host species, except for B. xanthomixis), genetic distances (large COX1 barcoding gap between among-and within-species K2P distances: 8.22-12.38% vs 0-2.9%, respectively), and molecular phylogenetics (all species are well-supported, monophyletic clades). Our study suggests that species of the genus Bernierinyssus have evolved slower than their avian hosts or co-associated feather lice. Despite the discordance in the mitochondrial DNA evolutionary rates, speciation events in mites largely corresponded to bird species divergences, resulting in a nearly perfect correlation between mite and bird species richness (Eichler's Rule). The mite B. xanthomixis was associated with two avian species, but still formed two distinct shallow lineages (COX1 distance: 1.65%) separated by the host species. The nearly strict host-specificity pattern found in Bernierinyssus contrasts with that of continental feather mites, which tend to be less host-specific and have nearly equal proportions of single-host vs multi-host species.
... Byers (2013) addressed a similar set of questions with the same morphological data set and used host bird phylogeny as a proxy for mite phylogeny. The phylogenetic approach showed the same patterns as the simpler correlational approach that we employ in the present work; however, it is risky to assume that patterns of feather mite speciation precisely follow those of their hosts (e.g., Doña et al. 2017), so the corroborating results of Byers (2013) should be viewed with caution. ...
Positive correlations between the shapes of male and female sexual structures can be interpreted as cooperative or as combative. In the feather mite genus Trouessartia Canestrini, 1899, the spermaducts of females range from entirely internal to extending externally for varying lengths, whereas male primary genitalia range from gracile to massive. Males also possess a pair of adanal suckers used to hold onto the dorsal surface of the female during copulation. In the area of this attachment, females exhibit ornamentation and have strongly developed dorsal setae (setae h1), which we hypothesized serve to weaken the male’s hold during copulation. In male and female Trouessartia from 51 bird species, we compared female external spermaduct length and male genitalic “massiveness” and explored whether patterns of female dorsal ornamentation and (or) h1 seta size correlate with male adanal sucker size. Our results indicate that females with longer external spermaducts are associated with males with relatively massive genitalia. However, we found no significant relationship between male adanal sucker size and female ornamentation or h1 seta size. Further information regarding how the genitalia interact during sperm transfer is necessary to interpret correlations in genitalia size and strong intersexual differences in dorsal ornamentation and seta size in Trouessartia.
... However, this does not undermine the role of horizontal transmission (which could lead to host-shift speciation) in parasite diversification. A large body of evidence suggests that host-shift speciation is a common process even for specialized symbionts or vertically transmitted parasites (Bailly-Bechet et al., 2017;Doña et al., 2017;de Vienne et al., 2013). Microsporidians show similar patterns. ...
In parasites that strongly rely on a host for dispersal, geographic barriers that act on the host will simultaneously influence parasite distribution as well. If their association persists over macroevolutionary time it may result in congruent phylogenetic and phylogeographic patterns due to shared geographic histories. Here, we investigated the level of congruent evolutionary history at a regional and global scale in a highly specialised parasite taxon infecting hosts with limited dispersal abilities: the microsporidians Dictyocoela spp. and their amphipod hosts. Dictyocoela can be transmitted both vertically and horizontally and is the most common microsporidian genus occurring in amphipods in Eurasia. However, little is known about its distribution elsewhere. We started by conducting molecular screening to detect microsporidian parasites in endemic amphipod species in New Zealand; based on phylogenetic analyses, we identified nine species‐level microsporidian taxa including six belonging to Dictyocoela. With a distance‐based cophylogenetic analysis at the regional scale, we identified overall congruent phylogenies between Paracalliope, the most common New Zealand freshwater amphipod taxon, and their Dictyocoela parasites. Also, hosts and parasites showed similar phylogeographic patterns suggesting shared biogeographic histories. Similarly, at a global scale, phylogenies of amphipod hosts and their Dictyocoela parasites showed broadly congruent phylogenies. The observed patterns may have resulted from covicariance and/or codispersal, suggesting that the intimate association between amphipods and Dictyocoela may have persisted over macroevolutionary time. We highlight that shared biogeographic histories could play a role in the codiversification of hosts and parasites at a macroevolutionary scale.
... Similar work even proposed that parasite phylogenies could be used as a proxy for their hosts' phylogeny (Harrison, 1914;Hopkins, 1942). Although subsequent research has shown that Fahrenholz's Rule and related predictions are infrequently demonstrated in natural systems (Braga, Razzolini, & Boeger, 2014;Doña et al., 2017;Fecchio et al., 2018;Hoberg & Brooks, 2008;Johnson, Williams, Drown, Adams, & Clayton, 2002;de Vienne et al., 2013), the concept of using host-parasite comparisons to understand the evolutionary and ecological history of the hosts and, more generally, the evolutionary history of host-parasite interactions remains a useful approach. ...
Understanding both sides of host–parasite relationships can provide more complete insights into host and parasite biology in natural systems. For example, phylogenetic and population genetic comparisons between a group of hosts and their closely associated parasites can reveal patterns of host dispersal, interspecies interactions, and population structure that might not be evident from host data alone. These comparisons are also useful for understanding factors that drive host–parasite coevolutionary patterns (e.g., codivergence or host switching) over different periods of time. However, few studies have compared the evolutionary histories between multiple groups of parasites from the same group of hosts at a regional geographic scale. Here, we used genomic data to compare phylogenomic and population genomic patterns of Alaska ptarmigan and grouse species (Aves: Tetraoninae) and two genera of their associated feather lice: Lagopoecus and Goniodes . We used whole‐genome sequencing to obtain hundreds of genes and thousands of single‐nucleotide polymorphisms (SNPs) for the lice and double‐digest restriction‐associated DNA sequences to obtain SNPs from Alaska populations of two species of ptarmigan. We found that both genera of lice have some codivergence with their galliform hosts, but these relationships are primarily characterized by host switching and phylogenetic incongruence. Population structure was also uncorrelated between the hosts and lice. These patterns suggest that grouse, and ptarmigan in particular, share habitats and have likely had historical and ongoing dispersal within Alaska. However, the two genera of lice also have sufficient dissimilarities in the relationships with their hosts to suggest there are other factors, such as differences in louse dispersal ability, that shape the evolutionary patterns with their hosts.
... Moreover, the relative number of schemes showed no significant cost reconstruction than randomization in Jane 4.0, which suggests the outcome of possible co-evolutionary scenarios may vary according to the cost assignment. However, the best cost schemes that have been found in the Core-PA analysis, did not detect any significant global co-speciation; the signal is largely used to evaluate coevolution (Charleston and Perkins 2006;Doña et al. 2017). These analyses support no coevolution between anemones and anemonefish. ...
The association between anemonefish and anemone is a classical example of mutualism in coral reefs. Although mutualism is probably the key innovation that triggered the adaptive radiation of anemonefish into a wide range of habitats, the coevolutionary history between the groups has not been thoroughly tested in a phylogenetic framework. We examined the evolutionary history of the association via distance-based (Parafit and PACo) and event-based methods (Core-PA, Jane). Mitochondrial DNA sequences (COI mtDNA, Cytb, 16S rDNA and 12S rDNA) were used to reconstruct the phylogenies of tropical Amphiprion species and their host anemones by using maximum likelihood with best-fit models selected. Neither distance-based analyses nor event-based analyses revealed global significant congruence between the phylogenies of the hosts and the symbionts, and thus no evidence for coevolution between anemone-anemonefish. However, at the individual pair level, the fish showed some dependence on anemone hosts. Even though living in close association and benefiting from each other, the change of genetic composition of one species (anemonefish) does not always evolve in response to changes in the other (anemones). These findings expand our understanding of the pattern and the role of evolutionary events to allow a better prediction of the future of the anemonefish-anemone relationship.
... Strauss, White & Boots, 2012;Lymbery et al., 2014) strongly support that host switching is a common phenomenon across symbiont taxa on evolutionary as well as ecological timescales, suggesting that evolutionary constraints are generally not strong enough to act as overwhelming barriers against symbiont population niche expansion. Indeed, host switching is relevant even in vertically transmitted, highly specialist symbionts (Millanes et al., 2014;Doña et al., 2017). The classic version of the concept of ecological fitting (Janzen, 1985) has developed as a mechanism to explain the apparent evolutionary lability of symbionts, and their ability to colonise novel unsuitable or suboptimal hosts (Agosta & Klemens, 2008;Araujo et al., 2015). ...
Range expansion results from complex eco-evolutionary processes where range dynamics and niche shifts interact in a novel physical space and/or environment, with scale playing a major role. Obligate symbionts (i.e. organisms permanently living on hosts) differ from free-living organisms in that they depend on strong biotic interactions with their hosts which alter their niche and spatial dynamics. A symbiotic lifestyle modifies organism-environment relationships across levels of organisation, from individuals to geographical ranges. These changes influence how symbionts experience colonisation and, by extension, range expansion. Here, we investigate the potential implications of a symbiotic lifestyle on range expansion capacity. We present a unified conceptual overview on range expansion of symbionts that integrates concepts grounded in niche and metapopulation theories. Overall, we explain how niche-driven and dispersal-driven processes govern symbiont range dynamics through their interaction across scales, from host switching to geographical range shifts. First, we describe a background framework for range dynamics based on metapopulation concepts applied to symbiont organisation levels. Then, we integrate metapopulation processes operating in the physical space with niche dynamics grounded in the environmental arena. For this purpose, we provide a definition of the biotope (i.e. living place) specific to symbionts as a hinge concept to link the physical and environmental spaces, wherein the biotope unit is a metapopulation patch (either a host individual or a land fragment). Further, we highlight the dual nature of the symbionts' niche, which is characterised by both host traits and the external environment, and define proper conceptual variants to provide a meaningful unification of niche, biotope and symbiont organisation levels. We also explore variation across systems in the relative relevance of both external environment and host traits to the symbiont's niche and their potential implications on range expansion. We describe in detail the potential mechanisms by which hosts, through their function as biotopes, could influence how some symbionts expand their range - depending on the life history and traits of both associates. From the spatial point of view, hosts can extend symbiont dispersal range via host-mediated dispersal, although the requirement for among-host dispersal can challenge symbiont range expansion. From the niche point of view, homeostatic properties of host bodies may allow symbiont populations to become insensitive to off-host environmental gradients during host-mediated dispersal. These two potential benefits of the symbiont-host interaction can enhance symbiont range expansion capacity. On the other hand, the central role of hosts governing the symbiont niche makes symbionts strongly dependent on the availability of suitable hosts. Thus, environmental, dispersal and biotic barriers faced by suitable hosts apply also to the symbiont, unless eventual opportunities for host switching allow the symbiont to expand its repertoire of suitable hosts (thus expanding its fundamental niche). Finally, symbionts can also improve their range expansion capacity through their impacts on hosts, via protecting their affiliated hosts from environmental harshness through biotic facilitation.
... endoparasitic nematodes and stick insect hosts [23]) and in highly specialized symbionts (e.g. feather mites and birds [37,38]), demonstrating that these obligate hostparasite systems do not always follow strict cospeciation and synchronous evolution [39]. Host-switching events are thought to be of central importance in driving parasite diversity (e.g. ...
Background:
Marine invertebrates are abundant and diverse on the continental shelf in Antarctica, but little is known about their parasitic counterparts. Endoparasites are especially understudied because they often possess highly modified body plans that pose problems for their identification. Asterophila, a genus of endoparasitic gastropod in the family Eulimidae, forms cysts in the arms and central discs of asteroid sea stars. There are currently four known species in this genus, one of which has been described from the Antarctic Peninsula (A. perknasteri). This study employs molecular and morphological data to investigate the diversity of Asterophila in Antarctica and explore cophylogenetic patterns between host and parasite.
Results:
A maximum-likelihood phylogeny of Asterophila and subsequent species-delimitation analysis uncovered nine well-supported putative species, eight of which are new to science. Most Asterophila species were found on a single host species, but four species were found on multiple hosts from one or two closely related genera, showing phylogenetic conservatism of host use. Both distance-based and event-based cophylogenetic analyses uncovered a strong signal of coevolution in this system, but most associations were explained by non-cospeciation events.
Discussion:
The prevalence of duplication and host-switching events in Asterophila and its asteroid hosts suggests that synchronous evolution may be rare even in obligate endoparasitic systems. The apparent restricted distribution of Asterophila from around the Scotia Arc may be an artefact of concentrated sampling in the area and a low obvious prevalence of infection. Given the richness of parasites on a global scale, their role in promoting host diversification, and the threat of their loss through coextinction, future work should continue to investigate parasite diversity and coevolution in vulnerable ecosystems.
... The prevalence host switching could reflect two nonexclusive influences. It should arise if hosts respond to diverse sets of specialized antagonists with batteries of defences (Jermy, 1984;Janz, 2011;Hardy & Otto, 2014), and is commonly observed for figs and galling wasps (Cook & Segar, 2010) and other antagonistic associations (Doña et al., 2017;Hsu et al., 2018;Purcell et al., 2018). Host switching could also be promoted by competition among multiple galling species contesting for access to ovules of the same fig species (e.g. ...
Interactions between mutualists, competitors, and antagonists have contrasting ecological effects that, sustained over generations, can influence micro‐ and macroevolution. Dissimilar benefits and costs for these interactions should cause contrasting co‐diversification patterns between interacting clades, with prevalent co‐speciation by mutualists, association loss by competitors, and host switching by antagonists.
We assessed these expectations for a local assemblage of 26 fig species (Moraceae: Ficus), 26 species of mutualistic (pollinating), and 33 species of parasitic (galling) wasps (Chalcidoidea). Using newly acquired gene sequences, we inferred the phylogenies for all three clades. We then compared the three possible pairs of phylogenies to assess phylogenetic congruence and the relative frequencies of co‐speciation, association duplication, switching, and loss.
The paired phylogenies of pollinators with their mutualists and competitors were significantly congruent, unlike that of figs and their parasites. The distributions of macroevolutionary events largely agreed with expectations for mutualists and antagonists. By contrast, that for competitors involved relatively frequent association switching, as expected, but also unexpectedly frequent co‐speciation. The latter result likely reflects the heterogeneous nature of competition among fig wasps.
These results illustrate the influence of different interspecific interactions on co‐diversification, while also revealing its dependence on specific characteristics of those interactions.
... Given rising threats from anthropogenic climate and land-use changes, it has never been more important to understand biodiversity (Pereira et al., 2010) and the extinction and speciation processes that drive its origin and maintenance (Hewitt, 2001). Cryptic speciation, the process of evolutionary divergence in the absence of morphological differentiation, has been described in a variety of organisms and ecosystems and has important implications not only for biodiversity estimates but also for habitat conservation, wildlife management (Bickford et al., 2007), pest control, and epidemiology (Doña et al., 2017;de Vienne et al., 2013). Nevertheless, the genetic and ecological interactions between sibling species are not well understood (Struck et al., 2017), particularly when they are found in sympatry. ...
Cryptic speciation and hybridization are two key processes that affect the origin and maintenance of biodiversity and our ability to understand and estimate it. To determine how these two processes interact, we studied allopatric and sympatric colonies of two cryptic bat species (Eptesicus serotinus and E. isabellinus) with parapatric distribution in the Iberian Peninsula. These species are the main reservoir for the most commonly rabies virus found in bats in Europe: the European Bat Lyssavirus type 1 (EBLV-1). We used mtDNA and nuclear microsatellite markers to confirm the taxonomic status of both species and to show a more pronounced and geographically-based genetic structure in E. isabellinus than in its sibling E. serotinus. Using Approximate Bayesian Computation (ABC) we inferred rapid range expansion in both species after the Last Glacial Maximum until reaching their present distributions. ABC analysis also supported interspecific differences in genetic diversity and structure, pointing to an earlier expansion of E. isabellinus northwards. We found no evidence of mitochondrial introgression between species, but nuclear markers identified a male-mediated ongoing asymmetric hybridization from E. isabellinus to E. serotinus (28% hybrids in E. serotinus and 5% in E. isabellinus) in the contact zone. Although none of the bats studied tested positive for Lyssavirus RNA, the asymmetric hybridization supports the potential for the recently suggested interspecific transmission of EBLV-1 from E. isabellinus into E. serotinus.
... Moreover, we suggest that environmental shifts might also act as a key driver for the variability observed in symbiotic species with free-living juvenile or early-adult phases. To date, animal symbionts most studied in terms of divergence caused by their symbiotic mode of life are parasitic insects like fleas, mites or louses (Whiting et al., 2008;Bruyndonckx et al., 2009;Bush et al., 2016;Doña et al., 2017) and phytoparasites like aphids, beetles or nematodes (Messina, 2004;Picard et al., 2007;Bass et al., 2013). These groups are highly abundant and diverse in terrestrial ecosystems and, particularly in the case of phytoparasites, host/parasite evolutionary relationships may play a key role in the emergence of new crop pests. ...
The polychaete Oxydromus okupa lives in association with the bivalves Scrobicularia plana and Maco-mopsis pellucida in the intertidal of Río San Pedro (CI = Cádiz Intertidal) and adjacent to CHipiona (CH) harbour, and in the subtidal of the Bay of Cádiz (CS = Cádiz Subtidal). We analyse these populations morphometrically, ecologically (including infestation characteristics) and genetically (intertidal populations , 16S and ITS-1 genes). We consider "host", "environment" and the combined "host and environment" as possible factors of interpopulation variability. Morphometry revealed three well-defined clusters for CI, CH and CS, showing intergroup phenotypic differences ranging from 35 to 50%. Hosts shell lengths ranged between 26 and 36 mm for S. plana and 20 and 28 mm for M. pellucida. The infestation of small M. pellucida by juvenile O. okupa suggests they show an active size segregation behaviour. The intertidal seems to be less favourable (infestation rate <25% vs. up to 65% in the subtidal), and did not show recent bottleneck events. Overall, CI and CH were genetically homogeneous, but showed a significant divergence (one dominant haplotype in each host species), suggesting host shift as being a soft barrier to gene flow. Most characters related with host-entering varied among populations, suggesting symbiotic behaviour to play a key role in reducing panmixia and leading to the initial phases of a speciation process in sympatric symbiotic populations. Polyxeny and symbiotic behaviour in O. okupa seem thus to be underlying mechanisms contributing to its great phenotypic variety, marked ecological differences, and genetic divergence.
... On the other hand, a recent cophylogenetic study on feather mites of the genera Proctophyllodes Robin, 1877 and Trouessartia Canestrini, 1899 (Analgoidea: Proctophyllodidae and Trouessartiidae) concluded that horizontal transfer -i.e. between different host species -is probably the main cause for speciation in these mites, suggesting that interspecific transfer can occur more commonly in nature than what was previously estimated (Doña et al. 2017). ...
The psoroptidian mite Myocoptes musculinus (Koch, 1844) is the most common species of the family Myocoptidae (Sarcoptoidea), along with its main host, the house mouse Mus musculus Linnaeus. The present article reports the first recorded confirmation of M. musculinus on a bird - the tropical screech-owl Megascops choliba (Vieillot). Finding myocoptid mites on a non-rodent host is an additional case of predator-prey contamination.
... However, the integration of molecular and morphological (and other) evidence can also inform us about underlying evolutionary processes at play (Struck et al. 2018). In this sense, the two cryptic Tinaminyssus species studied here showed strong differentiation for the two molecular markers studied, displaying genetic distances similar (and even larger) to those from clearly morphologically distinct Tinaminyssus species (de Rojas et al. 2002), feather mites (Doña et al. 2015(Doña et al. , 2017, tetranychid mites (Navajas and Boursot 2003), Demodex species (de Rojas et al. 2012;Zhao et al. 2013Zhao et al. , 2014 or ticks (Hornok et al. 2015). This suggests that the cryptic species found here may be an example of evolutionary stasis, likely because the morphological similarity between close bird host species does not impose strong selection pressures for morphological differentiation in these mite species. ...
The study of cryptic species allows to describe and to understand biodiversity, and the evolutionary processes shaping it. Mites of the family Rhinonyssidae are permanent parasites of the nasal cavities of birds, currently including about 500 described species and 12 genera. Here, we tested the hypothesis that mites from five populations of the genus Tinaminyssus—three isolated from European turtle doves (Streptopelia turtur), and two from Eurasian collared doves (Streptopelia decaocto; Aves: Columbiformes)—are, in fact, two cryptic species inhabiting different hosts. First, we performed a morphometrical study on 16 traits. Then, we used the ITS1-5.8S rDNA-ITS2 nuclear region (ITS region), and a fragment of the mitochondrial cytochrome c-oxidase 1 (COI) to carry out phylogenetic and species delimitation analyses on Tinaminyssus species. Morphological analyses revealed a lack of biometric differentiation among Tinaminyssus populations from the two host species. However, molecular analyses indicated a high degree of genetic differentiation between populations of Tinaminyssus sp. from S. turtur and S. decaocto. Overall, results show that they can be considered as different cryptic species, suggesting a case of evolutionary stasis, likely because of the anatomical similarity between closely-related bird host species.
... Feather mite species are relatively host-specific and (presumably) of switching to new host species (Doña, Proctor, et al., 2017;Doña, Sweet, et al., 2017;Gaud 1992;Klimov, Mironov, & O'Connor, 2017;Matthews et al., 2018). These switches mostly involve closely related hosts, but major-host switches (e.g., between bird orders) have been revealed as a major driver of their diversification (Doña, Proctor, et al., 2017). ...
Parasites and other symbionts are crucial components of ecosystems, regulating host populations and supporting food webs. However, most symbiont systems, especially those involving commensals and mutualists, are relatively poorly understood. In this study, we have investigated the nature of the symbiotic relationship between birds and their most abundant and diverse ectosymbionts: the vane‐dwelling feather mites. For this purpose, we studied the diet of feather mites using two complementary methods. First, we used light microscopy to examine the gut contents of 1,300 individual feather mites representing 100 mite genera (18 families) from 190 bird species belonging to 72 families and 19 orders. Second, we used high‐throughput sequencing (HTS) and DNA metabarcoding to determine gut contents from 1,833 individual mites of 18 species inhabiting 18 bird species. Results showed fungi and potentially bacteria as the main food resources for feather mites (apart from potential bird uropygial gland oil). Diatoms and plant matter appeared as rare food resources for feather mites. Importantly, we did not find any evidence of feather mites feeding upon bird resources (e.g., blood, skin) other than potentially uropygial gland oil. In addition, we found a high prevalence of both keratinophilic and pathogenic fungal taxa in the feather mite species examined. Altogether, our results shed light on the long‐standing question of the nature of the relationship between birds and their vane‐dwelling feather mites, supporting previous evidence for a commensalistic–mutualistic role of feather mites, which are revealed as likely fungivore–microbivore–detritivore symbionts of bird feathers.
... A second feature shared by the three systems is that duplications and host-switching were well represented in the coevolutionary histories. The importance of these events, specially host-switching, has been highlighted in a wide variety of models, including viruses (Bellec et al. 2014), microsporidians (Shafer et al. 2009), fungal mycoparasites (Millanes et al. 2014), digeneans (Cribb et al. 2001), feather mites of passerine birds (Doña et al. 2017), and monogeneans , Huyse & Volckaert 2005, Blasco-Costa et al. 2012. In addition, the number of duplications was relatively high, particularly in dactylogyrus. ...
The study of host-parasite associations has attracted much attention in the quest of unveiling the mechanisms behind the coevolutionary relationships of tightly associated organisms. We studied the cophylogeny of species of three genera of Monopisthocotylea, Lamellodiscus, Dactylogyrus and Gyrodactylus, and their fish hosts to determine which evolutionary events determine speciation and identify a common set of principles driving coevolution in the three host-monogenean systems studied. We used an event-based method (Jane) and a distance-base method (PACo) for cophylogenetic analysis. PACo revealed a significant coevolution signal in all three systems. In the significant coevolutionary scenarios retrieved by Jane, the number of cospeciations was always low, the number of failures to diverge was always high and relatively constant, and the number of losses was always the highest. The number of duplications and duplications with host-switching was more variable, but relatively high in most situations. These results suggest that speciation in the three host-monogenean systems is not driven primarily by the classical synchronic cospeciation process postulated for terrestrial host-parasite systems. Instead, pseudocospeciation (associated to host-switches), duplication and failure to diverge seemed to play a major role in shaping the current diversity and relationships to their hosts of the monogeneans studied. Therefore, evolutionary mechanisms leading to host specificity do not seem to primarily result from cospeciation.
During the evolution of parasites, co‐speciation and host‐range expansion are thought to play roles in establishing associations with hosts, while sorting events can lead to dissolution of those associations. To address the roles of these processes, we focus on avian haemosporidian parasites infecting hosts of the intensively studied great tit species complex. We estimated the phylogeography of lineages detected in the species complex, and quantified their transition probabilities among hosts. Lineages detected in different host species presented a strong geographical signal but did not form monophyletic groups. Yet, distributions of lineages are not merely the result of their dispersal limitations, as many lineages that infect only one focal species can be found in birds sympatric with other focal species. Besides, closely related lineages that infect the same host species reach more similar rates of infection than expected by chance. Finally, Haemoproteus and Leucocytozoon lineages infecting P. major, the most recently dispersed species, were more generalized than others, consistent with a pattern of generalist parasites expanding their host ranges by infecting newly encountered host species. Our results suggest that host–parasite associations in this system are mainly the result of sorting events and host‐range expansion of parasites, rather than co‐speciation.
Insect diversification has been catalyzed by widespread specialization on novel hosts - a process underlying exceptional radiations of phytophagous beetles, lepidopterans, parasitoid wasps, and inordinate lineages of symbionts, predators and other trophic specialists. The strict fidelity of many such interspecies associations is posited to hinge on sensory tuning to host-derived cues, a model supported by studies of neural function in host-specific model species. Here, we investigated the sensory basis of symbiotic interactions between a myrmecophile rove beetle and its single, natural host ant species. We show that host cues trigger analogous behaviors in both ant and symbiont. Cuticular hydrocarbons - the ant's nestmate recognition pheromones - elicit partner recognition by the beetle and execution of ant grooming behavior, integrating the beetle into the colony via chemical mimicry. The beetle also follows host trail pheromones, permitting inter-colony dispersal. Remarkably, the rove beetle also performs its symbiotic behaviors with ant species separated by ~95 million years, and shows minimal preference for its natural host over non-host ants. Experimentally validated agent-based modeling supports a scenario in which specificity is enforced by physiological constraints on symbiont dispersal, and negative fitness interactions with alternative hosts, rather than via sensory tuning. Enforced specificity may be a pervasive mechanism of host range restriction of specialists embedded within host niches. Chance realization of latent compatibilities with alternative hosts may facilitate host switching, enabling deep-time persistence of obligately symbiotic lineages.
Increasing empirical evidence has revealed that host-switching is more common than cospeciation in the history of parasites. Here, we investigated how the intensity of host-switching, mediated by opportunity and compatibility, affects the phylogenetic history and ecology of the parasites. We developed a theoretical model to simulate the evolution of populations of parasites that can explore and colonize new hosts under variable host-switching intensities. Eco-evolutionary patterns (beta diversity/normalized Sackin index) obtained from parasite simulations were compared to nine empirical cases. Our model reproduced the empirical patterns, and such simulations varied in host-switching intensity according to the analysed case. This intensity does not differ among cases of ecto and endoparasites, but it was stronger in local cases when compared to a regional scale. Our results highlight the importance of contact opportunity, and suggest that host-switching intensity mediates the exploration and colonization of new hosts promoting variation in the eco-evolutionary patterns.
Speciation via host-switching is a macroevolutionary process that emerges from a microevolutionary dynamic where individual parasites switch hosts, establish a new association, and reduce reproductive contact with the original parasite lineage. Phylogenetic distance and geographic distribution of the hosts have been shown to be determinants of the capacity and opportunity of the parasite to change hosts. Although speciation via host-switching has been reported in many host-parasite systems, its dynamic on the individual, population and community levels is poorly understood. Here we propose a theoretical model to simulate parasite evolution considering host-switching events on the microevolutionary scale, taking into account the macroevolutionary history of the hosts, to evaluate how host-switching can affect ecological and evolutionary patterns of parasites in empirical communities at regional and local scales. In the model, parasite individuals can switch hosts under variable intensity and have their evolution driven by mutation and genetic drift. Mating is sexual and only individuals that are sufficiently similar can produce offspring. We assumed that parasite evolution occurs at the same evolutionary time scale as their hosts, and that the intensity of host-switching decreases as the host species differentiate. Ecological and evolutionary patterns were characterised by the turnover of parasite species among host species, and parasite evolutionary tree imbalance respectively. We found a range of host-switching intensity that reproduces ecological and evolutionary patterns observed in empirical communities. Our results showed that turnover decreased as host-switching intensity increased, with low variation among the model replications. On the other hand, tree imbalance showed wide variation and non-monotonic tendency. We concluded that tree imbalance was sensitive to stochastic events, whereas turnover may be a good indicator of host-switching. We found that local communities corresponded to higher host-switching intensity when compared to regional communities, highlighting that spatial scale is a limitation for host-switching.
Myriad branches in the tree of life are intertwined through ecological relationships. Biologists have long hypothesized that intimate symbioses between lineages can influence diversification patterns to the extent that it leaves a topological imprint on the phylogenetic trees of interacting clades. Over the past few decades, cophylogenetic methods development has provided a toolkit for identifying such histories of codiversification, yet it is often difficult to determine which tools best suit the task at hand. In this review, we organize currently available cophylogenetic methods into three categories—pattern-based statistics, event-scoring methods, and more recently developed generative model–based methods—and discuss their assumptions and appropriateness for different types of cophylogenetic questions. We classify cophylogenetic systems based on their biological properties to provide a framework for empiricists investigating the macroevolution of symbioses. In addition, we provide recommendations for the next generation of cophylogenetic models that we hope will facilitate further methods development.
Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 53 is November 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Symbionts have a unique mode of life that has attracted the attention of ecologists and evolutionary biologists for centuries. As a result of this attention, these disciplines have produced a mature body of literature on host-symbiont interactions. In contrast, the discipline of symbiont conservation is still in a foundational stage. Here, we aim to integrate methodologies for symbiont coevolutionary biology with symbiont conservation. We focus on host-symbiont cophylogenies, because they have been widely used to study symbiont diversification history and contain information on symbiont extinction. However, cophylogenetic information has never been used nor adapted to the perspective of conservation. Here, we propose a new statistic, “cophylogenetic extinction rate” (Ec), which is based on coevolutionary knowledge from event-based cophylogenetic analyses and could be informative to assess relative symbiont extinction risks. Finally, we propose potential future research to further develop methods to estimate symbiont extinction risk from cophylogenetic analyses, and to continue the integration of this existing knowledge of coevolutionary biology and cophylogenetics into future symbiont conservation studies and practices.
Feather mites are useful models for studying speciation due to their high diversity and strong degree of host specialization. However, studies to date have focused on the evolution of higher-level mite taxa while much hidden diversity likely occurs at the level of host genera and species. In this study, we examined the diversity and evolution of feather mites infesting six sympatric seabird species from six genera, breeding in the Cape Verde archipelago. We report 32 feather mite morphospecies categorized into 10 genera and three families, of which nine correspond to new, undescribed species. Molecular data corroborated morphological species descriptions, except for two morphologically-cryptic, but genetically distinct mite lineages related to Zachvatkinia oceanodromae and Laminalloptes simplex. Using these communities, we then applied a co-structure approach to test the contribution of ectosymbiont and host factors in driving feather mite evolution. Most seabird species hosted specific and unique feather mite species, even under sympatric conditions, and in general, feather mite species exhibited strong host-driven genetic structure. However, patterns of genetic differentiation were variable. That is, some mite species are more generalist than others and mite lineages/haplotypes can be shared by related seabird species. Interestingly, host-specific mites (e.g., Zachvatkinia spp.) tend to display much higher intra-specific diversity compared to more generalist mites (e.g., Microspalax and Plicatalloptes spp.). We discuss ectosymbiont and host life-history traits that might generate these patterns, such as host dispersal and breeding behavior and/or mite spatial and trophic specialization. Our findings highlight both the vast and largely unrecognized diversity of avian feather mites on seabirds, and the intrinsic complexity of the ecological processes underlying the evolution of these ectosymbionts.
Obligate symbionts may be genetically structured among host individuals and among phenotypically distinct host populations. Such processes may in turn determine within-host genetic diversity of symbionts, which is relevant for understanding symbiont population dynamics. We analysed the population genetic structure of two species of feather mites ( Proctophyllodes sylviae and Trouessartia bifurcata ) in migratory and resident blackcaps Sylvia atricapilla that winter sympatrically. Resident and migratory hosts may provide mites with habitats of different qualities, what might promote specialization of mite populations. We found high genetic diversity of within-host populations for both mite species, but no sign of genetic structure of mites between migratory and resident hosts. Our results suggest that, although dispersal mechanisms between hosts during the non-breeding season are unclear, mite populations are not limited by transmission bottlenecks that would reduce genetic diversity among individuals that share a host. Additionally, there is no evidence that host phenotypic divergence (associated with the evolution of migration and residency) has promoted the evolution of host-specialist mite populations. Unrestricted dispersal among host types may allow symbiotic organisms to avoid inbreeding and to persist in the face of habitat heterogeneity in phenotypically diverse host populations.
Inferring co-phylogeographic events requires matching the timing of these events on both host and symbiont (e.g., parasites) phylogenies because divergences of hosts and their symbionts may not temporally coincide, and host switches may occur. We investigate a large radiation of birds (Passeriformes) and their permanent symbionts, the proctophyllodid feather mites (117 species from 116 bird species; 6 genes, 11,468 nt aligned) using two time-calibration strategies for mites: fossils only and host phylogeography only. Out of 10 putative co-phylogeographic events 4 agree in timing for both symbiont and host events being synchronous co-origins or co-dispersals; 3 were based on host shifts, but agree in timing being very close to the origin of modern hosts; 2 disagree; and 1 large basal mite split was seemingly independent from host phylogeography. Among these events was an ancient (21-25.3 Mya), synchronous co-dispersal from the Old World leading to the origin and diversifications of New World emberizoid passerids and their mites, the thraupis+quadratus species groups of Proctophyllodes. Our framework offers a more robust detection of host and symbiont co-phylogeographic events (as compared to host-symbiont reconciliation analysis and using host phylogeography for time-calibration) and provides independent data for testing alternative hypotheses on timing of host diversification and dispersal. This article is protected by copyright. All rights reserved
DNA barcoding was intended as a means to provide species-level identifications through associating DNA sequences from unknown specimens to those from curated reference specimens. Although barcodes were not designed for phylogenetics, they can be beneficial to the completion of the Tree of Life. The barcode database for Trichoptera is relatively comprehensive, with data from every family, approximately two-thirds of the genera, and one-third of the described species. Most Trichoptera, as with most of life's species, have never been subjected to any formal phylogenetic analysis. Here, we present a phylogeny with over 16 000 unique haplotypes as a working hypothesis that can be updated as our estimates improve. We suggest a strategy of implementing constrained tree searches, which allow larger datasets to dictate the backbone phylogeny, while the barcode data fill out the tips of the tree. We also discuss how this phylogeny could be used to focus taxonomic attention on ambiguous species boundaries and hidden biodiversity. We suggest that systematists continue to differentiate between ‘Barcode Index Numbers’ (BINs) and ‘species’ that have been formally described. Each has utility, but they are not synonyms. We highlight examples of integrative taxonomy, using both barcodes and morphology for species description.
This article is part of the themed issue ‘From DNA barcodes to biomes’.
Even though feather mites are arthropod ectosymbionts widely distributed on almost all orders of birds, the nature and functional relationship of the interaction between feather mites and birds remain unclear. In this paper, we analyzed factors determining the distribution of feather mites at the individual as well as at the flock level, searching for correlates with bird characteristics such as body size and fat accumulation during winter. Long-tailed tits, Aegithalos caudatus (L.), live in family flocks during winter. Foraging, roosting and territory defence are done in groups. Communal roosting facilitates direct body contact among flock members, which may enhance the transmission of feather mites. Feather mites abundance was more similar within than among flocks; Within flocks, those individuals with longer wings and better body condition as determined by fat scores had larger numbers of feather mites. At the flock level, no relationship was found between mean mite intensity and any of the considered variables. We show that the distribution of feather mites among long-tailed tits is not random, but is shaped by individual features and flock ownership.
According to classic niche theory, species can coexist in heterogeneous environments by reducing interspecific competition via niche partitioning, e.g. trophic or spatial partitioning. However, support for the role of competition on niche partitioning remains controversial. Here, we tested for spatial and trophic partitioning in feather mites, a diverse and abundant group of arthropods. We focused on the two dominant mite species, Microspalax brevipes and Zachvatkinia ovata, inhabiting flight feathers of the Cory's shearwater, Calonectris borealis. We performed mite counts across and within primary and tail feathers on free-living shearwaters breeding on an oceanic island (Gran Canaria, Canary Islands). We then investigated trophic relationships between the two mite species and the host using stable isotope analyses of carbon and nitrogen on mite tissues and potential host food sources. The distribution of the two mite species showed clear spatial segregation among feathers; M. brevipes showed high preference for the central wing primary feathers, whereas Z. ovata was restricted to the two outermost primaries. Morphological differences between M. brevipes and Z. ovata support an adaptive basis for the spatial segregation of the two mite species. However, the two mites overlap in some central primaries and statistical modeling showed that Z. ovata tends to outcompete M. brevipes. Isotopic analyses indicated similar isotopic values for the two mite species and a strong correlation in carbon signatures between mites inhabiting the same individual host suggesting that diet is mainly based on shared host-associated resources. Among the four candidate tissues examined (blood, feather remains, skin remains and preen gland oil), we conclude that the diet is most likely dominated by preen gland oil, while the contribution of exogenous material to mite diets is less marked. Our results indicate that ongoing competition for space and resources plays a central role in structuring feather mite communities. They also illustrate that symbiotic infracommunities are excellent model systems to study trophic ecology, and can improve our understanding of mechanisms of niche differentiation and species coexistence.
Understanding what shapes variation in genetic diversity among species remains a major challenge in evolutionary ecology, and it has been seldom studied in parasites and other host-symbiont systems. Here, we studied mtDNA variation in a host-symbiont non-model system: 418 individual feather mites from 17 feather mite species living on 17 different passerine bird species. We explored how a surrogate of census size, the median infrapopulation size (i.e., the median number of individual parasites per infected host individual), explains mtDNA genetic diversity. Feather mite species genetic diversity was positively correlated with mean infrapopulation size, explaining 34% of the variation. As expected from the biology of feather mites, we found bottleneck signatures for most of the species studied but, in particular, three species presented extremely low mtDNA diversity values given their infrapopulation size. Their star-like haplotype networks (in contrast with more reticulated networks for the other species) suggested that their low genetic diversity was the consequence of severe bottlenecks or selective sweeps. Our study shows for the first time that mtDNA diversity can be explained by infrapopulation sizes, and suggests that departures from this relationship could be informative of underlying ecological and evolutionary processes.
The chemical composition of preen gland secretions of antbirds (Thamnophilidae and Formicaridae) and phylogenetically closely related Dendrocolaptidae, Tyrannidae and Pipridae were investigated to understand the role of environment in secretion components. The secretions of Thamnophilidae consisted of long chain acids, alcohols, esters, unsaturated hydrocarbons, and isoprenoids. Formicaridae secretions contained exclusively squalene and its derivatives. In Pipridae, secretions were made up of complex long chain esters. In Dendrocolaptidae, the secretions consisted of long chain esters of both saturated and monounsaturated acids combined with mono-alcohols and those of Tyrannidae consisted of long chain esters of saturated, mono-and tri-unsaturated acids with mono-and di-ols that were less complex. Higher molecular weight saturated and unsaturated components in tropical species suggest that the volatility of the secretion components is correlated to environmental temperatures experienced by the birds. Squalene is a precursor in steroid biosynthesis, but higher amounts in Formicaridae secretions suggest that it may have some additional functions.
Climatological variation and ecological perturbation have been pervasive drivers of faunal assembly, structure and diversification for parasites and pathogens through recurrent events of geographical and host colonization at varying spatial and temporal scales of Earth history. Episodic shifts in climate and environmental settings, in conjunction with ecological mechanisms and host switching, are often critical determinants of parasite diversification, a view counter to more than a century of coevolutionary thinking about the nature of complex host-parasite assemblages. Parasites are resource specialists with restricted host ranges, yet shifts onto relatively unrelated hosts are common during phylogenetic diversification of parasite lineages and directly observable in real time. The emerging Stockholm Paradigm resolves this paradox: Ecological Fitting (EF)-phenotypic flexibility and phylogenetic conservatism in traits related to resource use, most notably host preference-provides many opportunities for rapid host switching in changing environments, without the evolution of novel host-utilization capabilities. Host shifts via EF fuel the expansion phase of the Oscillation Hypothesis of host range and speciation and, more generally, the generation of novel combinations of interacting species within the Geographic Mosaic Theory of Coevolution. In synergy, an environmental dynamic of Taxon Pulses establishes an episodic context for host and geographical colonization.
© 2015 The Author(s) Published by the Royal Society. All rights reserved.
Summary
1. The functional significance of intra- and inter-specific structural variations in the flight feathers of birds is poorly understood. Here, a phylogenetic comparative analysis of four structural features (rachis width, barb and barbule density, and porosity) of proximal and distal primary feathers of 137 European bird species was conducted.
2. Flight type (flapping and soaring, flapping and gliding, continuous flapping or passerine type), habitat (terrestrial, riparian or aquatic), wing characteristics (wing area, S and aspect ratio, AR), and moult strategy were all found to affect feather structure to some extent. Species characterized by low wing-beat frequency flight (soaring and gliding) have broader feather rachises (shafts) and feather vanes with lower barb density than birds associated with more active flapping modes of flight. However, the effect of flying mode on rachis width disappeared after controlling for S and AR, suggesting that rachis width is primarily determined by wing morphology.
3. Rachis width and feather vane density are likely related to differences in force distribution across the wingspan during different flight modes. An increase in shaft diameter, barb density and porosity from the proximal to distal wing feathers was found, and was highest in species with flapping flight indicating that aerodynamic forces are more biased toward the distal feathers in flapping flyers than soarers, and gliders.
4. Habitat affected barb and barbule density, which was greatest in aquatic species, and within this group, barb density was greater in divers than non-divers, suggesting that the need for water repellency and resistance to water penetration may influence feather structure. However, we found little support for the importance of porosity in water repellency and water penetration, because porosity was similar in aquatic, riparian and terrestrial species, and among the aquatic birds (divers and non-divers). We also found that barb density was affected by moult pattern.
5. Our results have broad implications for the understanding of the selection pressures driving flight feather functional morphology. Specifically, the large sample size relative to any previous studies has emphasised that the morphology of flight feathers is the result of a suite of selection pressures. As well as routine flight needs, nutrition, habitat (particularly aquatic) and migratory requirements also affect flight feather morphology. Identifying the exact nature of these trade-offs will perhaps inform the reconstruction of the flying modes of extinct birds.
Key-words: barb density, barbule density, flight feathers, flight, functional morphology, moult, vane porosity, rachis width, water repellence, wing morphology
In phylogenomics the analysis of concatenated gene alignments, the so-called supermatrix, is commonly accompanied by the assumption
of partition models. Under such models each gene, or more generally partition, is allowed to evolve under its own evolutionary
model. Though partition models provide a more comprehensive analysis of supermatrices, missing data may hamper the tree search
algorithms due to the existence of phylogenetic (partial) terraces. Here we introduce the phylogenetic terrace aware (PTA)
data structure for the efficient analysis under partition models. In the presence of missing data PTA exploits (partial) terraces
and induced partition trees to save computation time. We show that an implementation of PTA in IQ-TREE leads to a substantial
speedup of up to 4.5 and 8 times compared with the standard IQ-TREE and RAxML implementations, respectively. PTA is generally
applicable to all types of partition models and common topological rearrangements thus can be employed by all phylogenomic
inference software.
Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast
programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus,
there is need for additional approaches that employ different search strategies to find ML trees and that are at the same
time as fast as currently available ML programs. We show that a combination of hill-climbing approaches and a stochastic perturbation
method can be time-efficiently implemented. If we allow the same CPU time as RAxML and PhyML, then our software IQ-TREE found
higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. If we use
the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein
alignments, respectively. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3–97.1%. IQ-TREE
is freely available at http://www.cibiv.at/software/iqtree.
Recent molecular phylogenetic analyses have revealed that some apparently oligoxenous feather mite species are in fact monoxenous cryptic species with little morphological differentiation. In this study we analyzed two species, Zachvatkinia isolata (Avenzoariidae) and Alloptes (Sternalloptes) stercorarii (Alloptidae) which prefer different parts of the plumage of two sister species of birds: arctic skua (Stercorarius parasiticus) and long-tailed skua (S. longicaudus) breeding on tundra in the High Arctic archipelago of Svalbard. Given that there are no reports about hybridization events between the host species, we expected that both skuas would have a species-specific acarofauna. The genetic distances among DNA-barcode sequences (COI and 28S rDNA), phylogenetic tree topologies, and haplotype networks of the COI sequences of mites suggested extensive gene flow in Z. isolata between and within populations inhabiting both skua species, whereas the Alloptes populations were host specific and sufficiently genetically separated as to warrant species-level status. The discrepancy in the genetic structure of Alloptes and Zachvatkinia populations suggests frequent but transient contacts between the two skua species in which the probability of mite exchange is much higher for Zachvatkinia, which is present in high numbers and inhabits exposed parts of primary flight feathers, than for the less abundant Alloptes that lives primarily in more protected and inaccessible parts of the plumage. We discuss the possible nature of these contacts between host species and the area(s) where they might take place. The star-like structures in the haplotype network as well as high haplotype diversity and low nucleotide diversity observed in Z. isolata are concordant with the known dispersal strategy of feather mites: vertical colonization of new host individuals followed by rapid growth of founder populations.
Because host–parasite interactions are so ubiquitous, it is of primary interest for ecologists to understand the factors that generate, maintain and constrain these associations. Phylogenetic comparative studies have found abundant evidence for host‐switching to relatively unrelated hosts, sometimes related to diversification events, in a variety of host–parasite systems. For Monogenoidea (Platyhelminthes) parasites, it has been suggested that the co‐speciation model alone cannot explain host occurrences, hence host‐switching and/or non‐vicariant modes of speciation should be associated with the origins and diversification of several monogenoid taxa.
The factors that shape broad patterns of parasite sharing were investigated using path analysis as a way to generate hypotheses about the origins of host–parasite interactions between monogenoid gill parasites and Neotropical freshwater fishes.
Parasite sharing was assessed from an interaction matrix, and explanatory variables included phylogenetic relationships, environmental preferences, biological traits and geographic distribution for each host species.
Although geographic distribution of hosts and host ecology are important factors to understand host–parasite interactions, especially within host lineages that share a relatively recent evolutionary history, phylogeny had the strongest overall direct effect on parasite sharing.
Phylogenetic contiguity of host communities may allow a ‘stepping‐stone’ mode of host‐switching, which increases parasite sharing. Our results reinforce the importance of including evolutionary history in the study of ecological associations, including emerging infectious diseases risk assessment.
Significance
Emerging infectious diseases pose threats to humans and livestock, but little is known about the general propensity of parasitic organisms to shift between hosts or the role of host shifting in the diversification of parasite lineages. The malaria parasites of contemporary vertebrate species descended from a common ancestor, likely after the diversification of their major host taxa, requiring rapid speciation and shifting between hosts across large host–taxonomic distances. Examination of sister lineages of avian malaria parasites in the New World suggests that such host shifting is common and often leads to the origin of new evolutionary lineages of parasites.
Dominant/subordinate interspecific relationships of seven passerine species nesting in the high-mountain of the Sierra Nevada (S. Spain) were studied. The dominant species was Oenanthe oenanthe, and the subordinates Phoenicurus ochruros, Anthus campestris, Emberiza cia, Alauda arvensis, Carduelis cannabina and Sylvia communis. The degree of subordination was not related to population size, body size or foraging substrate overlap, although the dominant species' aggression was mainly directed at the two species more ecologically similar to it, viz. P. ochruros and, to a lesser degree, A. campestris. Aggressive encounters were more frequent during the reproductive period. P. ochruros was attacked by O. oenanthe five times as often as A. campestris, and this difference was attributed to their different foraging strategies.
Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community.
I present some of the most notable new features and extensions of RAxML, such as, a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX, and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date, 50 page user manual covering all new RAxML options is available.
The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML.
Alexandros.Stamatakis@h-its.org.
Dog Domestication
The precise details of the domestication and origins of domestic dogs are unclear. Thalmann et al. (p. 871 ; see the cover) analyzed complete mitochondrial genomes from present-day dogs and wolves, as well as 18 fossil canids dating from 1000 to 36,000 years ago from the Old and New Worlds. The data suggest that an ancient, now extinct, central European population of wolves was directly ancestral to domestic dogs. Furthermore, several ancient dogs may represent failed domestication events.
The parasite paradox arises from the dual observations that parasites (broadly construed, including phytophagous insects) are resource specialists with restricted host ranges, and yet shifts onto relatively unrelated hosts are common in the phylogenetic diversification of parasite lineages and directly observable in ecological time. We synthesize the emerging solution to this paradox: phenotypic flexibility and phylogenetic conservatism in traits related to resource use, grouped under the term ecological fitting, provide substantial opportunities for rapid host switching in changing environments, in the absence of the evolution of novel host-utilization capabilities. We discuss mechanisms behind ecological fitting, its implications for defining specialists and generalists, and briefly review empirical examples of host shifts in the context of ecological fitting. We conclude that host shifts via ecological fitting provide the fuel for the expansion phase of the recently proposed oscillation hypothesis of host range and speciation, and, more generally, the generation of novel combinations of interacting species within the geographic mosaic theory of coevolution. Finally, we conclude that taxon pulses, driven by climate change and large-scale ecological perturbation are drivers of biotic mixing and resultant ecological fitting, which leads to increased rates of rapid host switching, including the agents of Emerging Infectious Disease.
We present an in silico approach for the reconstruction of complete mitochondrial genomes of non-model organisms directly from next-generation sequencing
(NGS) data—mitochondrial baiting and iterative mapping (MITObim). The method is straightforward even if only (i) distantly
related mitochondrial genomes or (ii) mitochondrial barcode sequences are available as starting-reference sequences or seeds,
respectively. We demonstrate the efficiency of the approach in case studies using real NGS data sets of the two monogenean
ectoparasites species Gyrodactylus thymalli and Gyrodactylus derjavinoides including their respective teleost hosts European grayling (Thymallus thymallus) and Rainbow trout (Oncorhynchus mykiss). MITObim appeared superior to existing tools in terms of accuracy, runtime and memory requirements and fully automatically
recovered mitochondrial genomes exceeding 99.5% accuracy from total genomic DNA derived NGS data sets in <24 h using a standard
desktop computer. The approach overcomes the limitations of traditional strategies for obtaining mitochondrial genomes for
species with little or no mitochondrial sequence information at hand and represents a fast and highly efficient in silico alternative to laborious conventional strategies relying on initial long-range PCR. We furthermore demonstrate the applicability
of MITObim for metagenomic/pooled data sets using simulated data. MITObim is an easy to use tool even for biologists with
modest bioinformatics experience. The software is made available as open source pipeline under the MIT license at https://github.com/chrishah/MITObim.
We present Procrustean Approach to Cophylogeny (PACo), a novel statistical tool to test for congruence between phylogenetic trees, or between phylogenetic distance matrices of associated taxa. Unlike previous tests, PACo evaluates the dependence of one phylogeny upon the other. This makes it especially appropriate to test the classical coevolutionary model that assumes that parasites that spend part of their life in or on their hosts track the phylogeny of their hosts. The new method does not require fully resolved phylogenies and allows for multiple host-parasite associations. PACo produces a Procrustes superimposition plot enabling a graphical assessment of the fit of the parasite phylogeny onto the host phylogeny and a goodness-of-fit statistic, whose significance is established by randomization of the host-parasite association data. The contribution of each individual host-parasite association to the global fit is measured by means of jackknife estimation of their respective squared residuals and confidence intervals associated to each host-parasite link. We carried out different simulations to evaluate the performance of PACo in terms of Type I and Type II errors with respect to two similar published tests. In most instances, PACo performed at least as well as the other tests and showed higher overall statistical power. In addition, the jackknife estimation of squared residuals enabled more elaborate validations about the nature of individual links than the ParaFitLink1 test of the program ParaFit. In order to demonstrate how it can be used in real biological situations, we applied PACo to two published studies using a script written in the public-domain statistical software R.
After almost 50 years of scrutiny, the ideas that Ehrlich and Raven presented in their classical paper on the coevolution between butterflies and plants are still very much alive. Much of this interest has involved the potential for codiversification, both in how the interaction itself diversifies and how the interaction affects modes and rates of speciation. Despite high levels of conservatism and specialization, diversification of the interaction appears to be mainly a consequence of host shifts, but this somewhat paradoxical conclusion can be understood by an appreciation of the ecological as well as genetic mechanisms behind host shifts. There are several ways that the interaction can influence speciation, with or without host-plant-based divergent selection on reproductive barriers. One current debate is over the relative importance of radiations following shifts to new adaptive zones and elevated rates of speciation in groups with plastic and diverse host use.
Proctophyllodid feather mites (400+ species) are permanent (full-time) symbionts commonly occurring on passerine birds. Phenotypic evolution of these mites appears to be greatly influenced by characters related to reproduction (>87.5% of a total of 32 taxonomically important discrete characters) and male genitalic characters (21.9%). Because sexual selection could the major evolutionary driver in this system, we test the theoretical expectation that genitalic or sexually dimorphic characters should evolve more rapidly and divergently then other characters. We inferred a time-calibrated molecular phylogeny (6 genes, 8571 nt aligned, no missing data) for 133 taxa of proctophyllodid mites and 40 outgroups. Comparisons of the average number of character state changes inferred on 10,696 Bayesian stationary trees indicate that male genitalic or sexually dimorphic characters do not evolve significantly faster than other characters (p = 0.537 and p=0.819, respectively). However, among the male genitalic characters, a trait related to the relative length of the aedeagus experienced extremely fast rates of evolution and was detected as a statistical outlier. In this character, the transitions between short, long, and several intermediate states occurred in both directions. In contrast, the evolution of extremely long aedeagi (nearly as long as the body) occurred unidirectionally and irreversibly. This surprising result may be due to constraints imposed by the female spermathecal canal, which, in species where males have extremely long aedeagi, is also very long and may impede pumping sperm by short aedeagi. In proctophyllodid mites, extremely long aedeagi evolved independently five times in five different monophyletic lineages. Several of these lineages were lumped together by taxonomists to form easy-to-distinguish but apparently artificial species-groups. Male genitalic characters, thus, can introduce false synapomorphies that could affect morphology-based phylogenetic inference. For the most species-rich genus, Proctophyllodes, we develop a predictive classification of species-groups that reconciles molecular and morphological data.
An accurately resolved gene tree may not be congruent with the species tree because of lineage sorting of ancestral polymorphisms. DNA sequences from the mitochondrially encoded genes (mtDNA) are attractive sources of characters for estimating the phylogenies of recently evolved taxa because mtDNA evolves rapidly, but its utility is limited because the mitochondrial genes are inherited as a single linkage group (haplotype) and provide only one independent estimate of the species tree. In contrast, a set of nuclear genes can be selected from distinct chromosomes, such that each gene tree provides an independent estimate of the species tree. Another aspect of the gene-tree versus species-tree problem, however, favors the use of mtDNA for inferring species trees. For a three-species segment of a phylogeny, the branching order of a gene tree will correspond to that of the species tree if coalescence of the alleles or haplotypes occurred in the internode between the first and second bifurcation. From neutral theory, it is apparent that the probability of coalescence increases as effective population size decreases. Because the mitochondrial genome is maternally inherited and effectively haploid, its effective population size is one-fourth that of a nuclear-autosomal gene. Thus, the mitochondrial-haplotype tree has a substantially higher probability of accurately tracking a short internode than does a nuclear-autosomal-gene tree. When an internode is sufficiently long that the probability that the mitochondrial-haplotype tree will be congruent with the species tree is 0.95, the probability that a nuclear-autosomalgene tree will be congruent is only 0.62. If each of k independently sampled nuclear-gene trees has a probability of congruence with the species tree of 0.62, then a sample of 16 such trees would be required to be as confident of the inference based on the mitochondrial-haplotype tree. A survey of mtDNA-haplotype diversity in 34 species of birds indicates that coalescence is generally very recent, which suggests that coalescence times are typically much shorter than internodal branch lengths of the species tree, and that sorting of mtDNA lineages is not likely to confound the species tree. Hybridization resulting in transfer of mtDNA haplotypes among branches could also result in a haplotype tree that is incongruent with the species tree; if undetected, this could confound the species tree. However, hybridization is usually easy to detect and should be incorporated in the historical narrative of the group, because reticulation, as well as cladistic events, contributed to the evolution of the group.
1. The consequences of symbiont transmission strategies are better understood than their adaptive causes.
2. Feather mites are permanent ectosymbionts of birds assumed to be transmitted mainly vertically from parents to offspring. The transmission of Proctophyllodes doleophyes G aud ( A stigmata, P roctophyllodidae) was studied in two E uropean populations of pied flycatchers, Ficedula hypoleuca P allas ( P asseriformes, M uscicapidae).
3. The vertical transmission of this mite species is demonstrated here with an acaricide experiment. This study also compared (for two distant populations during 4 years) patterns in reductions in mite intensity in adult birds, from egg incubation to chick‐rearing periods, with the predictions of three hypotheses on how host survival prospects and mite intraspecific competition might drive feather mites' transmission strategy.
4. The results are in agreement with previous studies and show that feather mites transmit massively from parents to chicks.
5. The magnitude of the transmission was closer to that predicted by the hypothesis based on intraspecific competition, while a bet‐hedging strategy is also partially supported.
Understanding host–symbiont networks is a major question in evolutionary ecology. Birds host a great diversity of endo- and ectosymbiotic organisms, with feather mites (Arachnida: Acariformes: Analgoidea, Pterolichoidea) being among the most diverse of avian symbionts. A global approach to the ecology and evolution of bird–feather-mite associations has been hampered because of the absence of a centralized data repository. Here we present the most extensive data set of associations between feather mites and birds. Data include 12 036 records of 1887 feather mite species located on the flight feathers of 2234 bird species from 147 countries. Feather mites typically located inside quills, on the skin, or on downy body feathers are not included. Data were extracted from 493 published sources dating from 1882 to 2015. Data exploration shows that although most continents and bird families are represented, most bird species remain unexplored for feather mites. Nevertheless, this is the most comprehensive data set available for enabling global macroecological analyses of feather mites and their hosts, such as ecological network analyses. This metadata file outlines the structure of these data and provides primary references for all records used.
Hosts-parasite interactions are plentiful and diverse, and understanding the patterns of these interactions can provide great insight into the evolutionary history of the organisms involved. Estimating the phylogenetic relationships of a group of parasites and comparing them to that of their hosts can indicate how factors such as host or parasite life history, biogeography, or climate affect evolutionary patterns. In this study we compare the phylogeny generated for a clade of parasitic chewing lice (Insecta: Phthiraptera) within the genus Columbicola to that of their hosts, the small New World ground-doves (Aves: Columbidae). We sampled lice from the majority of host species, including samples from multiple geographic locations. From these samples we sequenced mitochondrial and nuclear loci for the lice, and used these data to estimate phylogenetic trees and population networks. After estimating the appropriate number of operational taxonomic units (OTUs) for the lice, we used cophylogenetic analyses to compare the louse phylogeny to an existing host phylogeny. Our phylogenetic analysis recovered significant structure within the louse clade, including evidence for potentially cryptic species. All cophylogenetic analyses indicated an overall congruence between the host and parasite trees. However, we only recovered a single cospeciation event. This finding suggests that certain branches in the trees are driving the signal of congruence. In particular, lice with the highest levels of congruence are associated with high Andean species of ground-doves that are well separated altitudinally from other related taxa. Other host-parasite associations are not as congruent, and these often involved widespread louse taxa. These widespread lice did, however, have significant phylogeographic structure, and their phylogenetic relationships are perhaps best explained by biogeographic patterns. Overall these results indicate that both host phylogeny and biogeography can be simultaneously important in influencing the patterns of diversification of parasites.
Host shifts by specialist insects can lead to reproductive isolation between insect populations that use different hosts, promoting diversification. When both a phytophagous insect and its ancestrally-associated parasitoid shift to the same novel host plant, they may cospeciate. However, because adult parasitoids are free-living, they can also colonize novel host insects and diversify independent of their ancestral host insect. Though shifts of parasitoids to new insect hosts have been documented in ecological time, the long-term importance of such shifts to parasitoid diversity has not been evaluated. We used a genus of flies with a history of speciation via host-shifting (Rhagoletis [Diptera: Tephritidae]) and three associated hymenopteran parasitoid genera (Diachasma, Coptera and Utetes) to examine cophylogenetic relationships between parasitoids and their host insects. We inferred phylogenies of Rhagoletis, Diachasma, Coptera, and Utetes and used distance-based cophylogenetic methods (ParaFit and PACo) to assess congruence between fly and parasitoid trees. We used an event-based method with a free-living parasitoid cost model to reconstruct cophylogenetic histories of each parasitoid genus and Rhagoletis. We found that the current species diversity and host-parasitoid associations between the Rhagoletis flies and parasitoids are the primary result of ancient cospeciation events. Parasitoid shifts to ancestrally unrelated hosts primarily occur near the branch tips, suggesting that host shifts contribute to recent parasitoid species diversity but that these lineages may not persist over longer time periods. Our analyses also stress the importance of biologically informed cost models when investigating the coevolutionary histories of hosts and free-living parasitoids. This article is protected by copyright. All rights reserved.
Free-living organisms are often host to multiple lineages of closely related parasites. Different lineages of obligate parasites living on the same hosts might potentially be expected to display similar cophylogenetic patterns. However, there are also reasons why these lineages might have different evolutionary histories (e.g. host switching, host geography). In the present study, we use mitochondrial and nuclear DNA sequence data to evaluate the cophylogenetic patterns between doves and their wing and body lice. Previous studies have found that the wing and body lice of doves have different levels of congruence between their phylogenetic histories. However, these studies are limited in scope, either taxonomically or geographically. We used both new and existing data to generate a worldwide and taxonomically diverse data set for doves and two independent groups of lice: wing and body lice. Using event and topology-based methods, we found that cophylogenetic patterns were not correlated between wing and body lice, even though both groups showed evidence of cospeciation with their hosts. These results indicate that external factors vary in their impact on different groups of parasites and also that broad sampling is critical for identifying patterns in cophylogenetic analyses.
Comparative studies of trait evolution require accounting for the shared evolutionary history. This is done by including phylogenetic hypotheses into statistical analyses of species’ traits, for which birds often serve as excellent models. The online publication of the most complete molecular phylogeny of extant bird species (www.birdtree.org, BirdTree hereafter) now allows evolutionary biologists to rapidly obtain sets of equally plausible phylogenetic trees for any set of species to be incorporated as a phylogenetic hypothesis in comparative analyses. We discuss methods to use BirdTree tree sets for comparative studies, either by building a consensus tree that can be incorporated into standard comparative analyses, or by using tree sets to account for the ef- fect of phylogenetic uncertainty. Methods accounting for phylogenetic uncertainty should be preferred whenever possible because they should provide more reliable parameter estimates and realistic confidence intervals around them. Based on a real compara- tive dataset, we ran simulations to investigate the effect of variation in the size of the random tree sets downloaded from BirdTree on the variability of parameter estimates from a bivariate relationship between mass-specific productivity and body mass. Irre- spective of the method of analysis, using at least 1,000 trees allows obtaining parameter estimates with very small (< 0.15%) co- efficients of variation. We argue that BirdTree, due to the ease of use and the major advantages over previous ‘traditional’ meth- ods to obtain phylogenetic hypotheses of bird species (e.g. supertrees or manual coding of published phylogenies), will become the standard reference in avian comparative studies for years to come.
A systematic revision is presented for the genus Proctophyllodes. Data on the bionomics, morphology, and host-parasite relationships are included.
Obligate symbionts (including parasites, commensals and mutualists) often share host species and host-based food resources. Such symbionts are frequently distributed unequally among hosts with different phenotypic features, or occupy different regions on a host. However, the processes leading to distinct within-host symbiont distributions remain obscure. We aimed to test whether distinct in-host symbiont distributions arise as the outcome of species-specific habitat preferences or interspecific competition, and how host phenotype influences such processes. To this end, we studied the distribution within and among individual bird hosts of two feather mites (Proctophyllodes sylviae and Trouessartia bifurcata) of migratory and sedentary European blackcaps, Sylvia atricapilla, wintering in sympatry. Trouessartia bifurcata was mostly restricted to resident blackcaps, while P. sylviae was abundant on both host types. Within hosts, each species tended to settle on different feather sectors (proximal or distal, respectively), which they filled by spreading on the wing following ordered but opposite patterns, thereby supporting the view that spatial segregation was primarily the outcome of dissimilar space preferences. However, we also found evidence of competition finely tuning mite distributions: when P. sylviae increased abundance and expanded onto the range of T. bifurcata, abundances of the two species were negatively correlated in the shared areas. In addition, the presence of T. bifurcata on a host was associated with a more restricted distribution of P. sylviae. Our results show that both species-specific preferences and interspecific interactions contribute to shaping mite distributions among and on individual hosts, a situation likely mirrored by other host-multi-symbiont systems.
Copyright © 2015. Published by Elsevier Ltd.
The biodiversity of mixed‐species samples of arthropods can be characterized by shotgun sequencing of bulk genomic DNA and subsequent bioinformatics assembly of mitochondrial genomes. Here, we tested the power of mitochondrial metagenomics by conducting Illumina sequencing on mixtures of >2600 individuals of leaf beetles (Chrysomelidae) from 10 communities.
Patterns of species richness, community dissimilarity and biomass were assessed from matches of reads against three reference databases, including (i) a custom set of mitogenomes generated for 156 species (89% of species in the study); (ii) mitogenomes obtained by the de novo assembly of sequence reads from the real‐world communities; and (iii) a custom set of DNA barcode ( cox1 ‐5′) sequences.
Species detection against the custom‐built reference genomes was very high (>90%). False presences were rare against mitogenomes but slightly higher against the barcode references. False absences were mainly due to the incompleteness of the reference databases and, thus, more prevalent in the de novo data set. Biomass (abundance × body length) and read numbers were strongly correlated, demonstrating the potential of mitochondrial metagenomics for studies of species abundance.
A phylogenetic tree from the mitogenomes showed high congruence with known relationships in Chrysomelidae. Patterns of taxonomic and phylogenetic dissimilarity between sites were highly consistent with data from morphological identifications.
The power of mitochondrial metagenomics results from the possibility of rapid assembly of mitogenomes from mixtures of specimens and the use of read counts for accurate estimates of key parameters of biodiversity directly from community samples.
Feather mites (Astigmata: Analgoidea, Pterolichoidea) are among the most abundantand commonly occurring bird ectosymbionts. Basic questions on the ecology and evolution of feather mites remain unanswered because feather mite species identification is often only possible for adult males and it is laborious even for specialised taxonomists, thus precluding large-scale identifications. Here, we tested DNA barcoding as a useful molecular tool to identify feather mites from passerine birds. 361 specimens of 72 species of feather mites from 68 species of European passerine birds from Russia and Spain were barcoded. The accuracy of barcoding and mini-barcoding was tested. Moreover, threshold choice (a controversial issue in barcoding studies) was also explored in a new way, by calculating through simulations the effect of sampling effort (in species number and species composition) on threshold calculations. We found one 200 bp mini-barcode region that showed the same accuracy as the full-length barcode (602 bp) and was surrounded by conserved regions potentially useful for group-specific degenerate primers. Species identification accuracy was perfect (100%) but decreased when singletons or species of the Proctophyllodes pinnatus group were included. In fact, barcoding confirmed previous taxonomic issues within the Proctophyllodes pinnatus group. Following an integrative taxonomy approach, we compared our barcode study with previous taxonomic knowledge on feather mites, discovering three new putative cryptic species and validating three previous morphologically different (but still undescribed) new species.
Mutualisms structure ecosystems and mediate their functioning. They also enhance invasions of many alien species. Invasions disrupt native mutu-alisms, often leading to population declines, reduced biodiversity, and al-tered ecosystem functioning. Focusing on three main types of mutualisms (pollination, seed dispersal, and plant-microbial symbioses) and drawing on examples from different ecosystems and from species-and community-level studies, we review the key mechanisms whereby such positive interactions mediate invasions and are in turn influenced by invasions. High interac-tion generalization is "the norm" in most systems, allowing alien species to infiltrate recipient communities. We identify traits that influence invasive-ness (e.g., selfing capacity in plants, animal behavioral traits) or invasibility (e.g., partner choice in mycorrhizas/rhizobia) through mutualistic interac-tions. Mutualistic disruptions due to invasions are pervasive, and subsequent cascading effects are also widespread. Ecological networks provide a useful framework for predicting tipping points for community collapse in response to invasions and other synergistic drivers of global change. Facilitation: an interaction in which the presence of one species benefits the performance of a second, neighboring species
Coevolutionary diversification is cited as a major mechanism driving the evolution of diversity, particularly in plants and insects. However, tests of coevolutionary diversification have focused on elucidating macroevolutionary patterns rather than the processes giving rise to such patterns. Hence, there is weak evidence that coevolution promotes diversification. This is in part due to a lack of understanding about the mechanisms by which coevolution can cause speciation and the difficulty of integrating results across micro- and macroevolutionary scales. In this review, we highlight potential mechanisms of coevolutionary diversification, outline approaches to examine this process across temporal scales, and propose a set of minimal requirements for demonstrating coevolutionary diversification. Our aim is to stimulate research that tests more rigorously for coevolutionary diversification.
The mitochondrial (mt) genome is, to date, the most extensively studied genomic system in insects, outnumbering nuclear genomes by tenfold and representing all orders versus very few. Phylogenomic analysis methods have been tested extensively, identifying compositional bias and rate variation, both within and between lineages, as the principal issues confronting accurate analyses. Major studies at both inter- and intraordinal levels have contributed to our understanding of phylogenetic relationships within many groups. Genome rearrangements are an additional data type for defining relationships, with rearrangement synapomorphies identified across multiple orders and at many different taxonomic levels. Hymenoptera and Psocodea have greatly elevated rates of rearrangement offering both opportunities and pitfalls for identifying rearrangement synapomorphies in each group. Finally, insects are model systems for studying aberrant mt genomes, including truncated tRNAs and multichromosomal genomes. Greater integration of nuclear and mt genomic studies is necessary to further our understanding of insect genomic evolution. Expected final online publication date for the Annual Review of Entomology Volume 59 is January 07, 2014. Please see http://www.annualreviews.org/catalog/pubdates.aspx for revised estimates.
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Interspecific competition for nest sites between tits (Parus spp.) and Collared Flycatchers (Ficedula albicollis) was responsible for the death of 23 flycatchers during one breeding season. Eighteen (78%) of the killed flycatchers were males, and nineteen (83%) of the kills took place in nest boxes occupied by Great Tits (Parus major), and two (9%) in boxes occupied by Blue Tits (P. caeruleus). The number of casualties in different plots increased with increasing proportion of nest boxes occupied by tits (r = 0.76), and decreased with increasing density of nest boxes (r = -0.43). The number of casualties equalled up to 17% of all flycatcher individuals breeding in a given plot, indicating that interspecific competition for nest sites may constitute a significant source of adult mortality in the Collared Flycatcher population studied.
Hosts and their symbionts are involved in intimate physiological and ecological interactions. The impact of these interactions on the evolution of each partner depends on the time‐scale considered. Short‐term dynamics – ‘coevolution’ in the narrow sense – has been reviewed elsewhere. We focus here on the long‐term evolutionary dynamics of cospeciation and speciation following host shifts. Whether hosts and their symbionts speciate in parallel, by cospeciation, or through host shifts, is a key issue in host–symbiont evolution. In this review, we first outline approaches to compare divergence between pairwise associated groups of species, their advantages and pitfalls. We then consider recent insights into the long‐term evolution of host–parasite and host–mutualist associations by critically reviewing the literature. We show that convincing cases of cospeciation are rare (7%) and that cophylogenetic methods overestimate the occurrence of such events. Finally, we examine the relationships between short‐term coevolutionary dynamics and long‐term patterns of diversification in host–symbiont associations. We review theoretical and experimental studies showing that short‐term dynamics can foster parasite specialization, but that these events can occur following host shifts and do not necessarily involve cospeciation. Overall, there is now substantial evidence to suggest that coevolutionary dynamics of hosts and parasites do not favor long‐term cospeciation.
Contents
Summary
347
I.
Introduction
348
II.
Origin of the cospeciation concept
349
III.
Theoretical framework and methods for testing for cospeciation
349
IV.
Studies of natural associations reveal the prevalence of host shifts
355
V.
Relationship between host–symbiont coevolution and symbiont speciation
378
VI.
Conclusion
381
Acknowledgements
381
References
381
Glossary
379
Long-term specialization may limit the ability of a species to respond to new environmental conditions and lead to a higher likelihood of extinction. For permanent parasites and other symbionts, the most intriguing question is whether these organisms can return to a free-living lifestyle and, thus, escape an evolutionary 'dead end'. This question is directly related to Dollo's law, which stipulates that a complex trait (such as being free-living vs. parasitic) cannot re-evolve again in the same form. Here we present conclusive evidence that house dust mites, a group of medically important free-living organisms, evolved from permanent parasites of warm-blooded vertebrates. A robust, multigene topology (315 taxa, 8,942 nt), ancestral character state reconstruction, and a test for irreversible evolution (Dollo's law) demonstrate that house dust mites have abandoned a parasitic lifestyle, secondarily becoming free-living, and then speciated in several habitats. Hence, as exemplified by this model system, highly specialized permanent parasites may drastically de-specialize to the extent of becoming free-living and, thus escape from dead-end evolution. Our phylogenetic and historical ecological framework explains the limited cross-reactivity between allergens from the house dust mites and 'storage' mites and the ability of the dust mites to inhibit host immune responses. It also provides insights into how ancestral features related to parasitism (frequent ancestral shifts to unrelated hosts, tolerance to lower humidity, and preexisting enzymes targeting skin and keratinous materials) played a major role in reversal to the free-living state. We propose that parasitic ancestors of pyroglyphids shifted to nests of vertebrates. Later the nest-inhabiting pyroglyphids expanded into human dwellings to become a major source of allergens.
A multiple sequence alignment program, MAFFT, has been developed. The CPU time is drastically reduced as compared with existing methods. MAFFT includes two novel techniques. (i) Homo logous regions are rapidly identified by the fast Fourier transform (FFT), in which an amino acid sequence is converted to a sequence composed of volume and polarity values of each amino acid residue. (ii) We propose a simplified scoring system that performs well for reducing CPU time and increasing the accuracy of alignments even for sequences having large insertions or extensions as well as distantly related sequences of similar length. Two different heuristics, the progressive method (FFT-NS-2) and the iterative refinement method (FFT-NS-i), are implemented in MAFFT. The performances of FFT-NS-2 and FFT-NS-i were compared with other methods by computer simulations and benchmark tests; the CPU time of FFT-NS-2 is drastically reduced as compared with CLUSTALW with comparable accuracy. FFT-NS-i is over 100 times faster than T-COFFEE, when the number of input sequences exceeds 60, without sacrificing the accuracy.
Current global patterns of biodiversity result from processes that operate over both space and time and thus require an integrated macroecological and macroevolutionary perspective. Molecular time trees have advanced our understanding of the tempo and mode of diversification and have identified remarkable adaptive radiations across the tree of life. However, incomplete joint phylogenetic and geographic sampling has limited broad-scale inference. Thus, the relative prevalence of rapid radiations and the importance of their geographic settings in shaping global biodiversity patterns remain unclear. Here we present, analyse and map the first complete dated phylogeny of all 9,993 extant species of birds, a widely studied group showing many unique adaptations. We find that birds have undergone a strong increase in diversification rate from about 50 million years ago to the near present. This acceleration is due to a number of significant rate increases, both within songbirds and within other young and mostly temperate radiations including the waterfowl, gulls and woodpeckers. Importantly, species characterized with very high past diversification rates are interspersed throughout the avian tree and across geographic space. Geographically, the major differences in diversification rates are hemispheric rather than latitudinal, with bird assemblages in Asia, North America and southern South America containing a disproportionate number of species from recent rapid radiations. The contribution of rapidly radiating lineages to both temporal diversification dynamics and spatial distributions of species diversity illustrates the benefits of an inclusive geographical and taxonomical perspective. Overall, whereas constituent clades may exhibit slowdowns, the adaptive zone into which modern birds have diversified since the Cretaceous may still offer opportunities for diversification.
