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Molecular phylogeny of pimoid spiders and the limits of Linyphiidae, with a reassessment of male palpal homologies (Araneae, Pimoidae)
Abstract
We address the phylogenetic relationships of pimoid spiders (Pimoidae) using a standard target-gene approach with an extensive taxonomic sample, which includes representatives of the four currently recognized pimoid genera, 26 linyphiid genera, a sample of Physoglenidae, Cyatholipidae and one Tetragnathidae species. We test the monophyly of Pimoidae and Linyphiidae and explore the biogeographic history of the group. Nanoa Hormiga, Buckle and Scharff, 2005 and Pimoa Chamberlin & Ivie, 1943 form a clade which is the sister group of a lineage that includes all Linyphiidae, Weintrauboa Hormiga, 2003 and Putaoa Hormiga and Tu, 2008. Weintrauboa, Putaoa, Pecado and Stemonyphantes form a clade (Stemonyphantinae) sister to all remaining linyphiids. We use the resulting optimal molecular phylogenetic tree to assess hypotheses on the male palp sclerite homologies of pimoids and linyphiids. Pimoidae is redelimited to only include Pimoa and Nanoa. We formalize the transfer from Pimoidae of the genera Weintrauboa and Putaoa to Linyphiidae, re-circumscribe the linyphiid subfamily Stemonyphantinae, and offer revised morphological diagnoses for Pimoidae and Linyphiidae.
... This clade was informally named by Hormiga (1994Hormiga ( , 2000 to group the families Linyphiidae and Pimoidae. The monophyly of linyphioids is supported by the following synapomorphies: cheliceral stridulatory striae, patella-tibia autospasy, enlargement of the peripheral cylindrical spigot base on the posterior lateral spinnerets, a 9+0 axonemal pattern in the sperm and an ectal cymbial process in the male palp (Hormiga, 1993(Hormiga, , 1994aMichalik and Hormiga, 2010;Hormiga et al., 2021). ...
... In the latter archipelago 15 endemic species of Laminacauda and ten species of Neomaso occur, suggesting their long dispersal abilities . Linyphiidae have been classified into several subfamilies (Mynogleninae, Dubiaraneinae, Erigoninae, Linyphiinae, Micronetinae, Ipainae and Stemonyphantinae) although no comprehensive phylogenetic classification exists for the family and only some of existing subfamilies have been corroborated as clades (e.g., Stemonyphantinae and Mynogleninae) while others have never been repeatedly shown not to be monophyletic (e.g., Dubiraneinae or Micronetinae) (Hormiga, 2000;Miller & Hormiga, 2004;Frick & Scharff, 2018;Wang et al., 2015;Hormiga et al., 2021;Moreira et al., in prep). In our combined analysis, Stemonyphantinae and Mynogleninae were monophyletic whereas Erigoninae, and Micronetinae were polyphyletic ( Figure 10A). ...
... More recently, Hormiga et al., (2021) addressed the placement of Weintrauboa and Putaoa using Sanger sequencing data and formalized the transfer of Weintrauboa and Putaoa to linyphiid subfamily Stemonyphantinae. The remaining two genera, Nanoa and Pimoa were hypothesized to be sister groups based on their male genitalic morphology (Hormiga et al., 2005), which was corroborated by the molecular data (Dimitrov et al., 2012Hormiga et al., 2021). ...
In the last decade and a half, advances in genetic sequencing technologies have revolutionized systematics, transforming the field as studying morphological characters; a few genetic markers have given way to genomic data sets in the phylogenomic era. A plethora of molecular phylogenetic studies on many taxonomic groups have come about, converging on, or refuting prevailing morphology or legacy-marker-based hypotheses about evolutionary affinities. Spider systematics has been no exception to this transformation and the interrelationships of several groups have now been studied using genomic data. About 50,500 extant spider species have been described so far, all with a conservative body plan, but innumerable morphological and behavioral peculiarities. Inferring the spider tree of life using morphological data has been a challenging task. Molecular data have corroborated many hypotheses of higher-level relationships, but also resulted in new groups that refute previous hypotheses. In this review, we discuss recent advances in the reconstruction of the Spider Tree of Life and highlight areas where additional effort is needed with potential solutions. We base this review on the most comprehensive spider phylogeny to date, representing 131 of the currently known 132 (99%) spider families. To achieve this sampling, we combined a legacy data set of six Sanger-based markers with newly generated and publicly available genome-scale data sets. We find that some inferred relationships between major lineages of spiders (such as Austrochiloidea, Palpimanoidea, Synspermiata, etc.) are robust across different classes of data. However, several surprising new hypotheses have emerged with different classes of molecular data. We identify and discuss the robust and controversial hypotheses and compile this blueprint to design future studies targeting systematic revisions of these problematic groups. We offer an evolutionary framework to explore comparative questions such as evolution of venoms, silk, webs, morphological traits, and reproductive strategies.
... It is common in systematics that a high-level molecular phylogeny may significantly conflict with the established taxonomic system based on morphological characters [1][2][3][4]. Understanding the evolutionary past that shaped the species diversity of lineages always attracts the interest of biologists [5][6][7][8]. Spiders are generalist predators, forming a successful terrestrial animal group, and their high species diversity is distributed unevenly across lineages [9], even extremely asymmetrically between sister groups [4,10]. Several hypotheses have been proposed to interpret the driving forces that promote spider diversification, such as co-diversification with insects [11][12][13], key innovations in silk structure and web architecture [10], repeated evolution of the respiratory system from book lungs to tracheae [14], and foraging changes from using capturing web to cursorial habits [15]. ...
... Four of them, Linyphiinae, Erigoninae, Micronetinae, and Ipainae, were not monophyletic groups; the representatives of Mynogleninae and Dubiaraneinae fell into Linyphiinae; the Stemonyphantinae taxa were often clustered with pimoids, the sister group of linyphiids [1,4,[19][20][21]. The subfamily Stemonyphantinae was newly revised by adding two ex-pimoid genera and another linyphiid genus in it [8]. However, the seven-clade topology of molecular phylogenies are robustly supported, and all of these seven major clades (clades A-F and S in [4]) are supported by some putative synapomorphic characters. ...
... Pimoidae is the sister group of Linyphiidae and often used as outgroups for rooting. Given the recent revision of Pimoidae having the formerly pimoid genera Putaoa and Weintrauboa transferred to Linyphiidae, and redelimited Pimoidae as including only Pimoa and Nanoa [8], we also added representatives of Pimoa and Putaoa into the dataset. The final data set consisted of 127 taxa, including 13 Solenysa taxa, 113 other linyphiids, and one pimoid. ...
A time scale of phylogenetic relationships contributes to a better understanding of the evolutionary history of organisms. Herein, we investigate the temporal divergence pattern that gave rise to the poor species diversity of the spider genus Solenysa in contrast with the other six major clades within linyphiids. We reconstructed a dated phylogeny of linyphiids based on multi-locus sequence data. We found that Solenysa diverged from other linyphiids early in the Cretaceous (79.29 mya), while its further diversification has been delayed until the middle Oligocene (28.62 mya). Its diversification trend is different from all of the other major lineages of linyphiids but is closely related to the Cenozoic ecosystem transition caused by global climate changes. Our results suggest that Solenysa is a Cretaceous relict group, which survived the mass extinction around the K-T boundary. Its low species diversity, extremely asymmetric with its sister group, is largely an evolutionary legacy of such a relict history, a long-time lag in its early evolutionary history that delayed its diversification. The limited distribution of Solenysa species might be related to their extreme dependence on highly humid environments.
... In their study, Putaoa was represented by a single species, which was nested in the Weintrauboa clade (represented by two species), thus rendering the latter genus paraphyletic. Because the relationship between Putaoa and Weintrauboa require additional work and new species remain to be described, Hormiga et al. (2021) did not provide a formal recircumscription of these two genera. ...
... All specimens examined in this study were deposited in the College of Life Sciences, Hunan Normal University (HNU). Terms and abbreviations used in the text and figures follow those of Hormiga and Tu (2008) and Hormiga et al. (2021). Etymology. ...
Two new species of the genus Putaoa Hormiga and Tu, 2008 from southern China are described, Putaoa annulata n. sp. (♂♀) and Putaoa titanoverpa n. sp. (♂♀), for a total number of five described species in this genus. Detailed descriptions and illustrations of the two new species are provided. A map of collecting localities is also provided for all five Putaoa species.
... Wang et al.'s (2015) analyses resulted in seven robustly supported clades within Linyphiidae, but the placements of four deep and long branches are sensitive to variations in both outgroup and ingroup sampling. Hormiga et al. (2021) confirmed that Weintrauboa Hormiga, 2003;Putaoa Hormiga & Tu, 2008;Pecado Hormiga & Scharff, 2005; and Stemonyphantes form a clade (Stemonyphantinae) sister to all remaining linyphiids, and they re-circumscribed Stemonyphantinae. Bifurcia Saaristo, Tu & Li, 2006 is classified as Micronetinae (Tanasevitch 2024), but no phylogenetic analysis has ever found Micronetinae to be a monophyletic group. ...
Five new species of the genus Bifurcia are described: B. kangding sp. nov. (♂♀), B. labahe sp. nov. (♂), B. luding sp. nov. (♂♀), B. shuangqiao sp. nov. (♂♀), and B. xiaojin sp. nov. (♂♀) from western Sichuan, China. A distribution map of the species and illustrations of genital characters are provided in this paper.
... The new species resembles Stemonyphantes lineatus (Linnaeus, 1758) in having the similar paracymbium ( Fig. 46B; Hormiga et al. 2021: fig. 8a) but can be distinguished by the radix with bifurcated anterior radical process (Fig. 46A); tegulum with three anterior tegular process (Fig. 46A-B, D). ...
An extensive survey of Linyphiidae spiders from Wulipo National Nature Reserve (NNR), Chongqing has been conducted, in which 24 species belonging to 16 genera are recorded including two new genera and eight new species described here as: Agyneta Hull, 1911, A. orthogonia sp. nov. (♂♀); Dicristatus gen. nov., D. minutus gen. et sp. nov. (♂♀); Dicymbium Menge, 1868, D. pingqianense sp. nov. (♂♀); Himalaphantes Tanasevitch, 1992, H. azumiensis (Oi, 1979) (♂♀); Indophantes Saaristo & Tanasevitch, 2003, I. wushanensis sp. nov. (♂♀); Ketambea Millidge & Russell-Smith, 1992, K. nigripectoris (Oi, 1960) (♂♀); Molestia Tu, Saaristo & Li, 2006, M. pollicaris sp. nov. (♂♀); Neriene Blackwall, 1833, N. calozonata Chen & Zhu, 1989 (♀), N. cavaleriei (Schenkel, 1963) (♂♀), N. emphana (Walckenaer, 1841) (♂♀), N. japonica (Oi, 1960) (♂♀), N. limbatinella (Bösenberg & Strand, 1906) (♀), N. longipedella (Bösenberg & Strand, 1906) (♂♀), N. oidedicata van Helsdingen, 1969 (♀); Prosoponoides Millidge & Russell-Smith, 1992, P. sinense (Chen, 1991) (♂♀); Ryojius Saito & Ono, 2001, R. simplex sp. nov. (♂♀); Stemonyphantes Menge, 1866, S. bifurcus sp. nov. (♂); Syedra Simon, 1884, S. oii Saito, 1983; Tapinopa Westring, 1851, T. guttata Komatsu, 1937 (♀); Tenuiphantes Saaristo & Tanasevitch, 1996, T. ancatus (Zhu, Li & Sha, 1986) (♂♀); Walckenaeria Blackwall, 1833, Walckenaeria asymmetrica Song & Li, 2011 (♂♀); Wuliphantes gen. nov., W. guanshan (Irfan, Wang & Zhang, 2022) gen. et comb. nov. (♂♀), W. tongluensis (Chen & Song, 1988) gen. et comb. nov. (♂♀), W. trigyrus gen. et sp. nov. (♂♀). Male of Tenuiphantes ancatus (Zhu, Li & Sha, 1986) is described here for the first time as new to science. The taxonomic status of Bathyphantes guanshan Irfan, Wang & Zhang, 2022 and Bathyphantes tongluensis (Chen & Song, 1988) is revised and proposed here as: Wuliphantes tongluensis (Chen& Song, 1988) gen. et comb. nov. (♂♀) and Wuliphantes guanshan (Irfan, Wang & Zhang, 2022) gen. et comb. nov. (♂♀), respectively. Morphological descriptions, photos of body and copulatory organs, as well as the locality map are provided.
... The spider family Pimoidae Wunderlich, 1986 includes 82 species belonging to two genera: Nanoa Hormiga, Buckle & Scharff, 2005 (one species from U.S.A.) and Pimoa Chamberlin & Ivie, 1943 (81 species from North America, Asia and South Europe) (World Spider Catalog 2021). Hormiga et al. (2021) revised the Pimoidae based on molecular phylogeny and transferred two genera (Putaoa Tu, 2008 andWeintrauboa Hormiga, 2003) to the family Linyphiidae. ...
Three new species of the spider genus Pimoa Chamberlin & Ivie, 1943 are described: P. pingwuensis n. sp. (♂♀) and P. yajiangensis n. sp. (♀) from Sichuan and P. zekogensis n. sp. (♂) from Qinghai. These new species are distinguished from other known Pimoa species by genital characters as well as by DNA barcodes. Detailed descriptions, photographs of genital characters and somatic features, a distribution map, comparisons to closely related species and DNA barcodes of the new species are presented. Illustrations of new species are provided and their phylogenetic relationships within the genus Pimoa are also discussed.
Photographs of the webs of approximately 113 species in 52 genera show that the web architecture of linyphioid spiders (Linyphiidae and Pimoidae) present many variations on a single basic pattern. Nearly all species built webs with a more or less horizontal, continuous sheet with an open space just below the sheet. However, the details in the designs showed great diversity; we recognized >50 web traits, including positions relative to the ground or large objects; sheet shapes and orientations; secondary sheets; “slime” on the sheet; patterns and densities of lines in sheets; visible droplets on sticky lines; upward and downward directed dimples in the sheet with tensor lines; primary and secondary frame lines; retreats; and the presence, location, and designs of associated tangles. This survey probably substantially underestimates both intraspecific and intrageneric diversity of web forms. Intrageneric comparisons in just over 20 genera documented varying degrees of intrageneric variation; some genera show striking differences. Several web designs were widely distributed: sheets with dense tangles above commonly had arrays of lines attached to the sheet's upper surface; downward dimples in sheets commonly occurred at sites where the sheet curved upward, but upward-directed dimples were rare and small; and sheets built next to the surface of the ground almost always lacked extensive tangles above them. New web patterns not previously reported for linyphiid webs include: sandwich webs (pairs of closely spaced, otherwise naked sheets); extensive vertical sheets next to tree trunks; tubular retreats at the edges of the sheet where the spider rests; trough-like sheets just above the upper surface of a curled leaf; sizeable, apparently sticky droplets densely covering many lines that were apparently placed in pairs in the sheet; long sheet lines that converge at one corner; runways to a sheltered site where the spider waits beyond the sheet's edge; and apparent skeleton lines in the sheet (probably from early stages of construction). Patterns of lines within the sheet may reflect patterns of movement during sheet construction behavior. We propose that some webs on the substrate function to extend the spider's sensory field rather than detain prey and that some tangles below and perhaps some above the sheet may function to defend the spider from enemies. A suite of linyphiid traits, including leg, chelicera, and spinneret morphology; details of web design, such as numerous small upward-directed dimples in dome-shaped sheets but fewer, large downward-directed dimples in cup-shaped sheets; and attack behavior, appears to function to increase the speed with which spiders attack prey. The functions of many architectural features remain obscure.
In the last decade and a half, advances in genetic sequencing technologies have revolutionized systematics, transforming the field from studying morphological characters or a few genetic markers, to genomic datasets in the phylogenomic era. A plethora of molecular phylogenetic studies on many taxonomic groups have come about, converging on, or refuting prevailing morphology or legacy-marker-based hypotheses about evolutionary affinities. Spider systematics has been no exception to this transformation and the interrelationships of several groups have now been studied using genomic data. About 51 500 extant spider species have been described, all with a conservative body plan, but innumerable morphological and behavioural peculiarities. Inferring the spider tree of life using morphological data has been a challenging task. Molecular data have corroborated many hypotheses of higher-level relationships, but also resulted in new groups that refute previous hypotheses. In this review, we discuss recent advances in the reconstruction of the spider tree of life and highlight areas where additional effort is needed with potential solutions. We base this review on the most comprehensive spider phylogeny to date, representing 131 of the 132 spider families. To achieve this sampling, we combined six Sanger-based markers with newly generated and publicly available genome-scale datasets. We find that some inferred relationships between major lineages of spiders (such as Austrochiloidea, Palpimanoi-dea and Synspermiata) are robust across different classes of data. However, several new hypotheses have emerged with different classes of molecular data. We identify and discuss the robust and controversial hypotheses and compile this blueprint to design future studies targeting systematic revisions of these problematic groups. We offer an evolutionary framework to explore comparative questions such as evolution of venoms, silk, webs, morphological traits and reproductive strategies.
Spiders of the genus Troglohyphantes (Araneae: Linyphiidae) exemplify one of the largest subterranean adaptive radiation across European mountain ranges, counting over 130 species and representing about one fifth of total species richness of cave spiders in Europe. Despite the emerging potential of Troglohyphantes as a biogeographical model, no attempt has been made to reconstruct the geological events underlying the current distribution patterns of the genus. By coupling traditional taxonomy with target gene sequence data and comparative functional trait analyses, we describe a new species of Troglohyphantes, the first reported from the island of Corsica (France). The species is characterized by a high level of subterranean adaptation and distinct morphological affinities with geographically distant congenerics. By means of time-stamped phylogenies, we tested contrasting hypotheses about the origin of the new species. The most parsimonious explanation suggests that the species diverged from an ancestral group of species originating in the Adriatic plate in the lower Miocene (~19 Ma), colonizing Corsica from the east. In the absence of relevant fossil records, the well-known geochronology of Corsica and the Western Mediterranean basin can be used in future studies to reconstruct the biogeography of the whole genus and for inferring the timeline of its diversification.
Nesticidae is a small family of spiders with a worldwide distribution that includes 15 genera and 272 described species. Seven genera and 56 species are known from Europe, distributed from the Iberian Peninsula to the Caucasus and the Ural Mountains. Most of these European species are cave dwellers and many of them are troglobites. In this study we present the first molecular phylogeny of the family Nesticidae in Europe with a wide geographical sampling across the continent. In our analysis the European nesticid fauna is well represented, including six genera and 40 of the 56 currently accepted species including the type species of all sampled genera. We have included in the analysis representatives of the North American and Asian fauna to test the monophyly of the European species and the phylogenetic relationships of European lineages. Phylogenetic relationships were reconstructed using maximum likelihood and Bayesian inference. As part of our Bayesian analyses, we also dated the phylogeny using two approaches, one based only on fossil calibrations and one that included an additional biogeographical constraint.
Our results show paraphyly of the European nesticids with respect to the Asian and North American taxa. We recover four main lineages within Europe. These four European lineages and all European genera have 100% bootstrap support and high posterior probability support in the BEAST2 analysis. The Typhlonesticus lineage is the earliest branching clade present in Europe and includes seven species, the five currently accepted species plus T. parvus from Bosnia and Herzegovina and T. silvestrii from western North America. The Eastern lineage includes the genus Aituaria and is the sister group of the Asian genera Nesticella and Wraios. The Domitius lineage is likely the sister group of the Central European lineage and spreads over the Iberian and Italian peninsulas. Finally, the Central European lineage includes three genera: Kryptonesticus, distributed from the karstic massifs of the Balkan Peninsula to Turkey, Nesticus with a single synanthropic species N. cellulanus and Carpathonesticus, exclusive to the Carpathian Mountains. With the exception of the genus Typhlonesticus, all European genera show an allopatric distribution (except for the two European synanthropic species). The results obtained in this study together with the revision of the original descriptions, redescriptions, and illustrations, lead us to propose 11 nomenclatural changes (new combinations) concerning the genera Typhlonesticus, Nesticus and Carpathonesticus.
The Mounded Posterior Median Eyes (MPME) clade is a group of linyphiid spiders characterized by having posterior median eyes (PME) on a mound. The species diversity of this lineage, especially in the Neotropical region, is still largely unknown. In this study, we tackled one of the MPME groups, the genus Diplothyron Millidge, 1991. We have studied numerous specimens from both museums and freshly collected specimens to monograph Diplothyron. We also compiled both morphological and behavioral data from Diplothyron and representatives of higher-level lineages within Linyphiidae and several potential MPME groups to infer the phylogenetic relationships. We redescribed the type species, Diplothyron fuscus Millidge, 1991 and described the previously unknown male, and six new species: Diplothyron ballesterosi sp. nov., D. dianae sp. nov., D. monteverde sp. nov., D. nubilosus sp. nov., D. sandrae sp. nov. and D. solitarius sp. nov. We also transferred the following species from Linyphia to Diplothyron based on the study of the type material: D. chiapasia (Gertsch & Davies, 1946) comb. nov., D. linguatulus (F.O. Pickard-Cambridge, 1902) comb. nov., D. nigritus (F.O. Pickard-Cambridge, 1902) comb. nov., D. simplicatus (F.O. Pickard-Cambridge, 1902) comb. nov. and D. trifalcatus (F.O. Pickard-Cambridge, 1902) comb. nov. Diplothyron species are mainly found in the cloud forests of Central and South America, with the distribution stretching from the Colombian Andes to the Mexican Sierra Madre across the Central American mountain chains. We also provide a detailed morphological comparison between Diplothyron and closely related genera in the MPME clade, focusing on the genital morphology, including identification keys to both the MPME genera and species of Diplothyron. Our cladistic analyses recovered Diplothyron as a monophyletic group placed within the MPME clade. A newly circumscribed lineage now includes the genera Diplothyron, Dubiaranea Mello-Leitão, 1943; Linyphia Latreille, 1804; Lomaita Bryant, 1948; Microlinyphia Gerhardt, 1928; Neriene Blackwall, 1833; Notiohyphantes Millidge, 1985; Novafrontina Millidge, 1991 and Pityohyphantes Simon, 1929.
Genome-scale data sets are converging on robust, stable phylogenetic hypotheses for many lineages; however, some nodes have shown disagreement across classes of data. We use spiders (Araneae) as a system to identify the causes of incongruence in phylogenetic signal between three classes of data: exons (as in phylotranscriptomics), non-coding regions (included in ultraconserved elements [UCE] analyses), and a combination of both (as in UCE analyses). Gene orthologs, coded as amino acids and nucleotides (with and without third codon positions), were generated by querying published transcriptomes for UCEs, recovering 1,931 UCE loci (codingUCEs). We expected that congeners represented in the codingUCE and UCEs data would form clades in the presence of phylogenetic signal. Non-coding regions derived from UCE sequences were recovered to test the stability of relationships. Phylogenetic relationships resulting from all analyses were largely congruent. All nucleotide data sets from transcriptomes, UCEs, or a combination of both recovered similar topologies in contrast with results from transcriptomes analyzed as amino acids. Most relationships inferred from low occupancy data sets, containing several hundreds of loci, were congruent across Araneae, as opposed to high occupancy data matrices with fewer loci, which showed more variation. Furthermore, we found that low occupancy data sets analyzed as nucleotides (as is typical of UCE data sets) can result in more congruent relationships than high occupancy data sets analyzed as amino acids (as in phylotranscriptomics). Thus, omitting data, through amino acid translation or via retention of only high occupancy loci, may have a deleterious effect in phylogenetic reconstruction.
Eight new species of the spider genus Pimoa Chamberlin & Ivie, 1943 are described from Tibet, China: P. cona Zhang & Li, sp. nov. (♂♀), P. duiba Zhang & Li, sp. nov. (♂♀), P. lemenba Zhang & Li, sp. nov. (♀), P. mainling Zhang & Li, sp. nov. (♂♀), P. nyingchi Zhang & Li, sp. nov. (♂♀), P. rongxar Zhang & Li, sp. nov. (♂♀), P. samyai Zhang & Li, sp. nov. (♂♀), and P. yadong Zhang & Li, sp. nov. (♂♀). The DNA barcodes of the eight new species are documented.
The withdrawal of the Tethys Sea and the formation of the Alpine‐Himalayan orogenic belt profoundly impacted the distribution and composition of terrestrial biota in Eurasia. However, studies that have explicitly addressed the potential links between the series of tectonic activities in the Tethyan region and the formation of extratropical biodiversity hotspots in the Alpine‐Himalayan belt are rare. Spiders in the genus Pireneitega (Agelenidae) are found throughout Eurasia and show high species richness in these hotspots. Thus, Pireneitega spiders may serve as a model group to shed light on how past tectonic events shaped Eurasian hotspots. To reconstruct the spatial and temporal evolution of Pireneitega spp., we conducted an integrative historical biogeographical analysis using thousands of novel DNA sequences and five novel transcriptome sequences from different species. Species distribution modelling based on complete geographical distribution information was used to assess the ecological preferences and the potential ecological interchangeability of Pireneitega species. Our study suggests that the rapid expansion of Pireneitega in Eurasia benefitted from regression of the Tethys Sea in the early Oligocene. Most Pireneitega species are distributed allopatrically, but in similar niches. The diversification of Pireneitega species relied on invading numerous new isolated habitats created by the uplift of Alpine‐Himalayan mountains during the Miocene (wet valley model). These results imply that the formation of Alpine‐Himalayan hotspots was driven by the series of tectonic events in the Tethyan region during the Oligocene–Miocene.
Studies in evolutionary biology and biogeography increasingly rely on the estimation of dated phylogenetic trees using molecular clocks. In turn, the calibration of such clocks is critically dependent on external evidence (i.e. fossils) anchoring the ages of particular nodes to known absolute ages. In recent years, a plethora of new fossil spiders, especially from the Mesozoic, have been described, while the number of studies presenting dated spider phylogenies based on fossil calibrations increased sharply. We critically evaluate 44 of these studies, which collectively employed 67 unique fossils in 180 calibrations. Approximately 54% of these calibrations are problematic, particularly regarding unsupported assignment of fossils to extant clades (44%) and crown (rather than stem) dating (9%). Most of these cases result from an assumed equivalence between taxonomic placement of fossils and their phylogenetic position. To overcome this limitation, we extensively review the literature on fossil spiders, with a special focus on putative synapomorphies and the phylogenetic placement of fossil species with regard to their importance for calibrating higher taxa (families and above) in the spider tree of life. We provide a curated list including 41 key fossils intended to be a basis for future estimations of dated spider phylogenies. In a second step, we use a revised set of 23 calibrations to estimate a new dated spider tree of life based on transcriptomic data. The revised placement of key fossils and the new calibrated tree are used to resolve a long‐standing debate in spider evolution – we tested whether there has been a major turnover in the spider fauna between the Mesozoic and Cenozoic. At least 17 (out of 117) extant families have been recorded from the Cretaceous, implying that at least 41 spider lineages in the family level or above crossed the Cretaeous–Paleogene (K–Pg) boundary. The putative phylogenetic affinities of families known only from the Mesozoic suggest that at least seven Cretaceous families appear to have no close living relatives and might represent extinct lineages. There is no unambiguous fossil evidence of the retrolateral tibial apophysis clade (RTA‐clade) in the Mesozoic, although molecular clock analyses estimated the major lineages within this clade to be at least ∼100 million years old. Our review of the fossil record supports a major turnover showing that the spider faunas in the Mesozoic and the Cenozoic are very distinct at high taxonomic levels, with the Mesozoic dominated by Palpimanoidea and Synspermiata, while the Cenozoic is dominated by Araneoidea and RTA‐clade spiders.
With the continual progress of sequencing techniques, genome-scale data are increasingly used in phylogenetic studies. With more data from throughout the genome, the relationship between genes and different kinds of characters is receiving more attention. Here, we present version 4 of RASP, a software to reconstruct ancestral states through phylogenetic trees. RASP can apply generalized statistical ancestral reconstruction methods to phylogenies, explore the phylogenetic signal of characters to particular trees, calculate distances between trees, and cluster trees into groups. RASP 4 has an improved graphic user interface and is freely available from http://mnh.scu.edu.cn/soft/blog/RASP (program) and https://github.com/sculab/RASP (source code).
Phylogenetic studies of geographic range evolution are increasingly using statistical model selection methods to choose among variants of the dispersal-extinction-cladogenesis (DEC) model, especially between DEC and DEC+J, a variant that emphasizes “jump dispersal,” or founder-event speciation, as a type of cladogenetic range inheritance scenario. Unfortunately, DEC+J is a poor model of founder-event speciation, and statistical comparisons of its likelihood with DEC are inappropriate. DEC and DEC+J share a conceptual flaw: cladogenetic events of range inheritance at ancestral nodes, unlike anagenetic events of dispersal and local extinction along branches, are not modelled as being probabilistic with respect to time. Ignoring this probability factor artificially inflates the contribution of cladogenetic events to the likelihood, and leads to underestimates of anagenetic, time-dependent range evolution. The flaw is exacerbated in DEC+J because not only is jump dispersal allowed, expanding the set of cladogenetic events, its probability relative to non-jump events is assigned a free parameter, j, that when maximized precludes the possibility of non-jump events at ancestral nodes. DEC+J thus parameterizes the mode of speciation, but like DEC, it does not parameterize the rate of speciation. This inconsistency has undesirable consequences, such as a greater tendency towards degenerate inferences in which the data are explained entirely by cladogenetic events (at which point branch lengths become irrelevant, with estimated anagenetic rates of 0). Inferences with DEC+J can in some cases depart dramatically from intuition, e.g. when highly unparsimonious numbers of jump dispersal events are required solely because j is maximized. Statistical comparison with DEC is inappropriate because a higher DEC+J likelihood does not reflect a more close approximation of the “true” model of range evolution, which surely must include time-dependent processes; instead, it is simply due to more weight being allocated (via j) to jump dispersal events whose time-dependent probabilities are ignored. In testing hypotheses about the geographic mode of speciation, jump dispersal can and should instead be modelled using existing frameworks for state-dependent lineage diversification in continuous time, taking appropriate cautions against Type I errors associated with such methods. For simple inference of ancestral ranges on a fixed phylogeny, a DEC-based model may be defensible if statistical model selection is not used to justify the choice, and it is understood that inferences about cladogenetic range inheritance lack any relation to time, normally a fundamental axis of evolutionary models.
The standard bootstrap (SBS), despite being computationally intensive, is widely used in maximum likelihood phylogenetic analyses. We recently proposed the ultrafast bootstrap approximation (UFBoot) to reduce computing time while achieving more unbiased branch supports than SBS under mild model violations. UFBoot has been steadily adopted as an efficient alternative to SBS and other bootstrap approaches.
Here, we present UFBoot2, which substantially accelerates UFBoot and reduces the risk of overestimating branch supports due to polytomies or severe model violations. Additionally, UFBoot2 provides suitable bootstrap resampling strategies for phylogenomic data. UFBoot2 is 778 times (median) faster than SBS and 8.4 times (median) faster than RAxML rapid bootstrap on tested datasets. UFBoot2 is implemented in the IQ-TREE software package version 1.6 and freely available at http://www.iqtree.org.
Pimoa delphinica Mammola, Hormiga & Isaia, 2016 is a troglophile araneoid spider endemic of the high Varaita valley (Western Alps, Province of Cuneo, NW Italy). In spite of relatively intense field research and examination of museum collections, the species is restricted to ten localities, thus showing a reduced extent of occurrence (EOO; 26 km) and area of occupancy (AOO; 12 km). Although the habitat and the subpopulations of P. delphinica are not currently threatened, the species is potentially exposed due to its extremely narrow geographic distribution range, subdivision in subpopulations and low dispersal capacity.
We present a phylogenetic analysis of spiders using a dataset of 932 spider species, representing 115 families (only the family Synaphridae is unrepresented), 700 known genera, and additional representatives of 26 unidentified or undescribed genera. Eleven genera of the orders Amblypygi, Palpigradi, Schizomida and Uropygi are included as outgroups. The dataset includes six markers from the mitochondrial (12S, 16S, COI) and nuclear (histone H3, 18S, 28S) genomes, and was analysed by multiple methods, including constrained analyses using a highly supported backbone tree from transcriptomic data. We recover most of the higher-level structure of the spider tree with good support, including Mesothelae, Opisthothelae, Mygalomorphae and Araneomorphae. Several of our analyses recover Hypochilidae and Filistatidae as sister groups, as suggested by previous transcriptomic analyses. The Synspermiata are robustly supported, and the families Trogloraptoridae and Caponiidae are found as sister to the Dysderoidea. Our results support the Lost Tracheae clade, including Pholcidae, Tetrablemmidae, Diguetidae, Plectreuridae and the family Pacullidae (restored status) separate from Tetrablemmidae. The Scytodoidea include Ochyroceratidae along with Sicariidae, Scytodidae, Drymusidae and Periegopidae; our results are inconclusive about the separation of these last two families. We did not recover monophyletic Austrochiloidea and Leptonetidae, but our data suggest that both groups are more closely related to the Cylindrical Gland Spigot clade rather than to Synspermiata. Palpimanoidea is not recovered by our analyses, but also not strongly contradicted. We find support for Entelegynae and Oecobioidea (Oecobiidae plus Hersiliidae), and ambiguous placement of cribellate orb-weavers, compatible with their non-monophyly. Nicodamoidea (Nicodamidae plus Megadictynidae) and Araneoidea composition and relationships are consistent with recent analyses. We did not obtain resolution for the titanoecoids (Titanoecidae and Phyxelididae), but the Retrolateral Tibial Apophysis clade is well supported. Penestomidae, and probably Homalonychidae, are part of Zodarioidea, although the latter family was set apart by recent transcriptomic analyses. Our data support a large group that we call the marronoid clade (including the families Amaurobiidae, Desidae, Dictynidae, Hahniidae, Stiphidiidae, Agelenidae and Toxopidae). The circumscription of most marronoid families is redefined here. Amaurobiidae include the Amaurobiinae and provisionally Macrobuninae. We transfer Malenellinae (Malenella, from Anyphaenidae), Chummidae (Chumma) (new syn.) and Tasmarubriinae (Tasmarubrius, Tasmabrochus and Teeatta, from Amphinectidae) to Macrobuninae. Cybaeidae are redefined to include Calymmaria, Cryphoeca, Ethobuella and Willisius (transferred from Hahniidae), and Blabomma and Yorima (transferred from Dictynidae). Cycloctenidae are redefined to include Orepukia (transferred from Agelenidae) and Pakeha and Paravoca (transferred from Amaurobiidae). Desidae are redefined to include five subfamilies: Amphinectinae, with Amphinecta, Mamoea, Maniho, Paramamoea and Rangitata (transferred from Amphinectidae); Ischaleinae, with Bakala and Manjala (transferred from Amaurobiidae) and Ischalea (transferred from Stiphidiidae); Metaltellinae, with Austmusia, Buyina, Calacadia, Cunnawarra, Jalkaraburra, Keera, Magua, Metaltella, Penaoola and Quemusia; Porteriinae (new rank), with Baiami, Cambridgea, Corasoides and Nanocambridgea (transferred from Stiphidiidae); and Desinae, with Desis, and provisionally Poaka (transferred from Amaurobiidae) and Barahna (transferred from Stiphidiidae). Argyroneta is transferred from Cybaeidae to Dictynidae. Cicurina is transferred from Dictynidae to Hahniidae. The genera Neoramia (from Agelenidae) and Aorangia, Marplesia and Neolana (from Amphinectidae) are transferred to Stiphidiidae. The family Toxopidae (restored status) includes two subfamilies: Myroinae, with Gasparia, Gohia, Hulua, Neomyro, Myro, Ommatauxesis and Otagoa (transferred from Desidae); and Toxopinae, with Midgee and Jamara, formerly Midgeeinae, new syn. (transferred from Amaurobiidae) and Hapona, Laestrygones, Lamina, Toxops and Toxopsoides (transferred from Desidae). We obtain a monophyletic Oval Calamistrum clade and Dionycha; Sparassidae, however, are not dionychans, but probably the sister group of those two clades. The composition of the Oval Calamistrum clade is confirmed (including Zoropsidae, Udubidae, Ctenidae, Oxyopidae, Senoculidae, Pisauridae, Trechaleidae, Lycosidae, Psechridae and Thomisidae), affirming previous findings on the uncertain relationships of the “ctenids” Ancylometes and Cupiennius, although a core group of Ctenidae are well supported. Our data were ambiguous as to the monophyly of Oxyopidae. In Dionycha, we found a first split of core Prodidomidae, excluding the Australian Molycriinae, which fall distantly from core prodidomids, among gnaphosoids. The rest of the dionychans form two main groups, Dionycha part A and part B. The former includes much of the Oblique Median Tapetum clade (Trochanteriidae, Gnaphosidae, Gallieniellidae, Phrurolithidae, Trachelidae, Gnaphosidae, Ammoxenidae, Lamponidae and the Molycriinae), and also Anyphaenidae and Clubionidae. Orthobula is transferred from Phrurolithidae to Trachelidae. Our data did not allow for complete resolution for the gnaphosoid families. Dionycha part B includes the families Salticidae, Eutichuridae, Miturgidae, Philodromidae, Viridasiidae, Selenopidae, Corinnidae and Xenoctenidae (new fam., including Xenoctenus, Paravulsor and Odo, transferred from Miturgidae, as well as Incasoctenus from Ctenidae). We confirm the inclusion of Zora (formerly Zoridae) within Miturgidae.
We test the limits of the spider superfamily Araneoidea and reconstruct its interfamilial relationships using standard molecular markers. The taxon sample (363 terminals) comprises for the first time representatives of all araneoid families, including the first molecular data of the family Synaphridae. We use the resulting phylogenetic framework to study web evolution in araneoids. Araneoidea is monophyletic and sister to Nicodamoidea rank. n. Orbiculariae are not monophyletic and also include the RTA clade, Oecobiidae and Hersiliidae. Deinopoidea is paraphyletic with respect to a lineage that includes the RTA clade, Hersiliidae and Oecobiidae. The cribellate orb-weaving family Uloboridae is monophyletic and is sister group to a lineage that includes the RTA Clade, Hersiliidae and Oecobiidae. The monophyly of most Araneoidea families is well supported, with a few exceptions. Anapidae includes holarchaeids but the family remains diphyletic even if Holarchaea is considered an anapid. The orb-web is ancient, having evolved by the early Jurassic; a single origin of the orb with multiple “losses” is implied by our analyses. By the late Jurassic, the orb-web had already been transformed into different architectures, but the ancestors of the RTA clade probably built orb-webs. We also find further support for a single origin of the cribellum and multiple independent losses. The following taxonomic and nomenclatural changes are proposed: the cribellate and ecribellate nicodamids are grouped in the superfamily Nicodamoidea rank n. (Megadictynidae rank res. and Nicodamidae stat. n.). Araneoidea includes 17 families with the following changes: Araneidae is re-circumscribed to include nephilines, Nephilinae rank res., Arkyidae rank n., Physoglenidae rank n., Synotaxidae is limited to the genus Synotaxus, Pararchaeidae is a junior synonym of Malkaridae (syn. n.), Holarchaeidae of Anapidae (syn. n.) and Sinopimoidae of Linyphiidae (syn. n.).
Phylogenies provide a useful way to understand the evolutionary history of genetic samples, and data sets with more than a thousand taxa are becoming increasingly common, notably with viruses (e.g. HIV). Dating ancestral events is one of the first, essential goals with such data. However, current sophisticated probabilistic approaches struggle to handle data sets of this size. Here we present very fast dating algorithms, based on a Gaussian model closely related to the Langley-Fitch molecular-clock model. We show that this model is robust to uncorrelated violations of the molecular clock. Our algorithms apply to serial data, where the tips of the tree have been sampled through times. They estimate the substitution rate and the dates of all ancestral nodes. When the input tree is unrooted, they can provide an estimate for the root position, thus representing a new, practical alternative to the standard rooting methods (e.g. mid-point). Our algorithms exploit the tree (recursive) structure of the problem at hand, and the close relationships between least-squares and linear algebra. We distinguish between an unconstrained setting and the case where the temporal precedence constraint (i.e. an ancestral node must be older that its daughter nodes) is accounted for. With rooted trees, the former is solved using linear algebra in linear computing time (i.e. proportional to the number of taxa), while the resolution of the latter, constrained setting, is based on an active-set method that runs in nearly linear time. With unrooted trees the computing time becomes (nearly) quadratic (i.e. proportional to the square of the number of taxa). In all cases very large input trees (>10,000 taxa) can easily be processed and transformed into time-scaled trees. We compare these algorithms to standard methods (root-to-tip, r8s version of Langley-Fitch method, and BEAST). Using simulated data, we show that their estimation accuracy is similar to that of the most sophisticated methods, while their computing time is much faster. We apply these algorithms on a large data set comprising 1,195 strains of Influenza virus from the pdm09 H1N1 Human pandemic. Again the results show that these algorithms provide a very fast alternative with results similar to those of other computer programs. These algorithms are implemented in the LSD software (Least-Squares Dating), which can be downloaded from http://www.atgc-montpellier.fr/LSD/, along with all our data sets and detailed results. An Online Appendix, providing additional algorithm descriptions, tables and figures can be found in the Dryad data repository*.
Abstract. Male secondary genitalia (pedipalps) are useful characters for species discrimination in most spider families.
Although efforts have been made to establish pedipalp sclerite homologies, there are still many inconsistencies in their use.
The majority of the morphological characters used to reconstruct the linyphiid phylogeny address male genitalic variation;
these inconsistencies may affect the phylogeny and our understanding of linyphiid evolution. Stemonyphantes Menge, 1866,
has been hypothesised to be sister to all remaining Linyphiidae. However, despite the basal position of Stemonyphantes,
its pedipalp sclerite homologies are not well understood and, along with its monophyly, have never been thoroughly
tested in a phylogenetic context. We tested the homology of tegular and radical structures of five Stemonyphantes species to
the known linyphioid and araneoid sclerites. All minimum-length trees found under all analytical methods used support
Stemonyphantes monophyly and its placement as the sister group to all other Linyphiidae. Our study suggests that
Stemonyphantes, unlike any other linyphiids, does have homologues of the araneoid median apophysis and conductor.
As Stemonyphantes is the sister group of all other linyphiids, resolving its pedipalp sclerite homologies is critical for
understanding sclerite homologies and the phylogeny of the entire family.
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.
Although most data suggest that the India-Eurasia continental collision began 45-55 Myr ago, the architecture of the Himalayan-Tibetan orogen is dominated by deformational structures developed in the Neogene period (<23 Myr ago). The stratigraphic record and thermochronometric data indicate that erosion of the Himalaya intensified as this constructional phase began and reached a peak around 15 Myr ago. It remained high until 10.5 Myr ago and subsequently slowed gradually to 3.5 Myr ago, but then began to increase once again in the Late Pliocene and Pleistocene epochs. Here we present weathering records from the South China Sea, Bay of Bengal and Arabian Sea that permit Asian monsoon climate to be reconstructed back to the earliest Neogene. These indicate a correlation between the rate of Himalayan exhumation as inferred from published thermochronometric data and monsoon intensity over the past 23 Myr. We interpret this correlation as indicating dynamic coupling between Neogene climate and both erosion and deformation in the Himalaya.
Modern attempts to produce biogeographic maps focus on the distribution of species, and the maps are typically drawn without
phylogenetic considerations. Here, we generate a global map of zoogeographic regions by combining data on the distributions
and phylogenetic relationships of 21,037 species of amphibians, birds, and mammals. We identify 20 distinct zoogeographic
regions, which are grouped into 11 larger realms. We document the lack of support for several regions previously defined based
on distributional data and show that spatial turnover in the phylogenetic composition of vertebrate assemblages is higher
in the Southern than in the Northern Hemisphere. We further show that the integration of phylogenetic information provides
valuable insight on historical relationships among regions, permitting the identification of evolutionarily unique regions
of the world.
We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including
options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained
alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples
to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to
clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
Ever larger phylogenies are being constructed due to the explosion of genetic data and development of high-performance phylogenetic reconstruction algorithms. However, most methods for calculating divergence times are limited to datasets that are orders of magnitude smaller than recently published large phylogenies. Here, we present an algorithm and implementation of a divergence time method using penalized likelihood that can handle datasets of thousands of taxa. We implement a method that combines the standard derivative-based optimization with a stochastic simulated annealing approach to overcome optimization challenges. We compare this approach with existing software including r8s, PATHd8 and BEAST.
Source code, example files, binaries and documentation for treePL are available at https://github.com/blackrim/treePL.
eebsmith@umich.edu
Supplementary data are available at Bioinformatics online.
The spermatozoa of spiders (Araneae) show a high structural diversity, resulting in several potential phylogenetic characters. In the present paper, we describe the spermatozoa of the spider family Pimoidae for the first time. We investigate four species of the genus Pimoa (P. altioculata, P. curvata, P. laurae, and P. edenticulata) by means of light and transmission electron microscopy. The male reproductive system consists of paired testes and long convoluted paired deferent ducts. The spermatozoa are generally characterized by: (1) a cylindrical acrosomal vacuole, (2) an acrosomal filament restricted to the precentriolar part of the nucleus, (3) a nuclear canal running in the periphery but projecting towards the posterior portion of the nucleus, (4) a short postcentriolar elongation of the nucleus, (5) a 9+0 axonemal pattern, and (6) cleistospermia as transfer form. The organization of the axoneme is of particular phylogenetic interest, since a 9+0 axonemal pattern was described within spiders only for the megadiverse family Linyphiidae, the sister group of Pimoidae. We have reconstructed the evolution of the axoneme using comparative spermatozoal data for 54 orbicularian species representing 11 families. We propose that the 9+0 axonemal pattern is a new synapomorphy for Pimoidae + Linyphiidae. The phylogenetic and evolutionary implications of other potential sperm characters (e.g., length of the postcentriolar elongation of the nucleus) are discussed.
This phylogenetic analysis of 31 exemplar taxa treats the 12 families of Araneoidea (Anapidae, Araneidae, Cyatholipidae, Linyphiidae, Mysmenidae, Nesticidae, Pimoidae, Symphytognathidae, Synotaxidae, Tetragnathidae, Theridiidae, and Theridiosomatidae). The data set comprises 93 characters: 23 from male genitalia, 3 from female genitalia, 18 from cephalothorax morphology, 6 from abdomen morphology, 14 from limb morphology, 15 from the spinnerets, and 14 from web architecture and other behaviour. Criteria for tree choice were minimum length parsimony and parsimony under implied weights. The outgroup for Araneoidea is Deinopoidea (Deinopidae and Uloboridae). The preferred shortest tree specifies the relationships ((Uloboridae, Deinopidae) (Araneidae (Tetragnathidae ((Theridiosomatidae (Mysmenidae (Symphytognathidae, Anapidae))) ((Linyphiidae, Pimoidae) ((Theridiidae, Nesticidae) (Cyatholipidae, Synotaxidae))))))). The monophyly of Tetragnathidae (including metines and nephilines), the symphytognathoids, theridiid-nesticid lineage, and Synotaxidae are confirmed. Cyatholipidae are sister to Synotaxidae, not closely related to either the Araneidae or Linyphiidae, as previously suggested. Four new clades are proposed: the cyatholipoids (Cyatholipidae plus Synotaxidae), the ‘spineless femur clade’ (theridioid lineage plus cyatholipoids), the ‘araneoid sheet web builders' (linyphioids plus the spineless femur clade), and the ‘reduced piriform clade’ (symphytognathoids plus araneoid sheet web builders). The results imply a coherent scenario for web evolution in which the monophyletic orb gives rise to the monophyletic araneoid sheet, which in turn gives rise to the gumfoot web of the theridiid-nesticid lineage. While the spinning complement of single pairs of glands does not change much over the evolution of the group, multiple sets of glands are dramatically reduced in number, implying that derived araneoids are incapable of spinning many silk fibers at the same time.
High throughput sequencing and phylogenomic analyses focusing on relationships among spiders have both reinforced and upturned long‐standing hypotheses. Likewise, the evolution of spider webs—perhaps their most emblematic attribute—is being understood in new ways. With a matrix including 272 spider species and close arachnid relatives, we analyze and evaluate the relationships among these lineages using a variety of orthology assessment methods, occupancy thresholds, tree inference methods and support metrics. Our analyses include families not previously sampled in transcriptomic analyses, such as Symphytognathidae, the only araneoid family absent in such prior works. We find support for the major established spider lineages, including Mygalomorphae, Araneomorphae, Synspermiata, Palpimanoidea, Araneoidea and the Retrolateral Tibial Apophysis Clade, as well as the uloborids, deinopids, oecobiids and hersiliids Grade. Resulting trees are evaluated using bootstrapping, Shimodaira–Hasegawa approximate likelihood ratio test, local posterior probabilities and concordance factors. Using structured Markov models to assess the evolution of spider webs while accounting for hierarchically nested traits, we find multiple convergent occurrences of the orb web across the spider tree‐of‐life. Overall, we provide the most comprehensive spider tree‐of‐life to date using transcriptomic data and use new methods to explore controversial issues of web evolution, including the origins and multiple losses of the orb web.
Phylogenomic methods have proven useful for resolving deep nodes and recalcitrant groups in the spider tree of life. Across arachnids, transcriptomic approaches may generate thousands of loci, and target‐capture methods, using the previously designed arachnid‐specific probe‐set, can target a maximum of about 1,000 loci. Here, we develop a specialized target‐capture probe set for spiders that contains over 2,000 ultraconserved elements (UCEs) and then demonstrate the utility of this probe set through sequencing and phylogenetic analysis. We designed the “spider‐specific” probe set using three spider genomes (Loxosceles, Parasteatoda and Stegodyphus) and ensured that the newly designed probe‐set include UCEs from the previously designed Arachnida probe set. The new “spider‐specific” probes were used to sequence UCE loci in 51 specimens. The remaining samples included five spider genomes and taxa that were enriched using Arachnida probe set. The “spider‐specific” probes were also used to gather loci from a total of 84 representative taxa across Araneae. On mapping these 84 taxa to the Arachnida probe set, we captured at most 710 UCE loci, while the spider specific probe set captured up to 1,547 UCE loci from the same taxon sample. Phylogenetic analyses using Maximum Likelihood and coalescent methods corroborate most nodes resolved by recent transcriptomic analyses, but not all (e.g., UCE data suggests monophyly of “symphytognathoids”). Our preferred analysis based on topology tests, suggests monophyly of the “symphytognathoids” (the miniature orb‐weavers), which in previous studies has only been supported by a combination of morphological and behavioral characters.
Weintrauboa yele new species (Pimoidae) is described and illustrated based on specimens collected in China. The taxonomic status and distribution of Weintrauboa insularis (Saito, 1935) new combination and of W. chikunii (Oi, 1979) are discussed and the former species is illustrated based on specimens from the Sakhalin islands. Parsimony analysis of morphological characters provides support for the monophyly of Weintrauboa and for its sister group relationship to the genus Putaoa Hormiga and Tu, 2008. Some comments on the phylogenetic placement of the recently erected family “Sinopimoidae” are provided.
The spider genus Putaoa new genus (Araneae, Pimoidae) is described to place two species of pimoids from China, Putaoa huaping new species (the type species) and P. megacantha (Xu & Li, 2007) new combination. Parsimony analysis of morphological characters provides support for the monophyly of Putaoa and for its sister group relationship to the genus Weintrauboa Hormiga, 2003 and corroborates the monophyly of Pimoidae.
Dating back to almost 400 mya, spiders are among the most diverse terrestrial predators [1]. However, despite considerable effort [1-9], their phylogenetic relationships and diversification dynamics remain poorly understood. Here, we use a synergistic approach to study spider evolution through phylogenomics, comparative transcriptomics, and lineage diversification analyses. Our analyses, based on ca. 2,500 genes from 159 spider species, reject a single origin of the orb web (the "ancient orb-web hypothesis") and suggest that orb webs evolved multiple times since the late Triassic-Jurassic. We find no significant association between the loss of foraging webs and increases in diversification rates, suggesting that other factors (e.g., habitat heterogeneity or biotic interactions) potentially played a key role in spider diversification. Finally, we report notable genomic differences in the main spider lineages: while araneoids (ecribellate orb-weavers and their allies) reveal an enrichment in genes related to behavior and sensory reception, the retrolateral tibial apophysis (RTA) clade-the most diverse araneomorph spider lineage-shows enrichment in genes related to immune responses and polyphenic determination. This study, one of the largest invertebrate phylogenomic analyses to date, highlights the usefulness of transcriptomic data not only to build a robust backbone for the Spider Tree of Life, but also to address the genetic basis of diversification in the spider evolutionary chronicle.
The boreotropics hypothesis postulates a preferential tropical biotic interchange between North America and Eurasia during the early Tertiary that was directed by Eocene thermal maxima and the close proximity of these two continental plates. This preferential interchange occurred at a time when South America was geologically and biotically isolated. A prediction of this hypothesis posits that a taxon with a present-day center of diversity in tropical North America, and with an early Tertiary fossil record from any region there, has a high probability of having sister-group relatives in the Paleotropics and derived relatives in South America. We propose a test of this prediction with phylogenetic studies of two pantropical taxa of Leguminosae that have early Tertiary North American fossil records. Our findings are consistent with the boreotropics hypothesis, and additional evidence suggests that many tropical elements in North America could be descendants of northern tropical progenitors. Ramifications of this hypothesis include the importance of integrating the fossil record with cladistic biogeographic studies, theoretical bases for recognizing tropical taxa with such disjunct distributions as Mexico and Madagascar, identification of taxa that may be most useful for testing vicariance models of Caribbean biogeography, and integrating the study of disjunct distributions in temperate regions of the northern hemisphere with those in the neo- and paleotropics.
Model-based molecular phylogenetics plays an important role in comparisons of genomic data, and model selection is a key step in all such analyses. We present ModelFinder, a fast model-selection method that greatly improves the accuracy of phylogenetic estimates by incorporating a model of rate heterogeneity across sites not previously considered in this context and by allowing concurrent searches of model space and tree space.
Pimoidae is a small family of araneoid spiders, hitherto represented in Europe by two species with disjunct distribution in the Alps and in the Cantabrian Mountains of northern Spain. Here we report the description of two additional European species of Pimoa, discovered within the range of the only former alpine species, P. rupicola: P. graphitica sp. nov. and P. delphinica sp. nov. The new species are distinguished from the latter by genitalic characters as well as by molecular characters. On the basis of the re-examination of old and recent abundant material collected in caves and other subterranean habitats, we revise the distribution patterns of the genus Pimoa in the Alps and outline the species distribution ranges. Molecular data suggest the existence of gene flow between populations of the two new species when in sympatry. The different species probably originated in the alpine region as a result of range contractions following dramatic climatic changes in the Alps since the mid Miocene. We interpreted the present-day overlapping distribution in light of a possible postglacial expansion. Finally, we provide insights on the natural history and life cycles of the new species and discuss their phylogenetic relationships within Pimoidae.
For high-level molecular phylogenies, a comprehensive sampling design is a key factor for not only improving inferential accuracy, but also for maximizing the explanatory power of the resulting phylogeny. Two standing problems in molecular phylogenies are the unstable placements of some deep and long branches, and the phylogenetic relationships shown by robust supported clades conflict with recognized knowledge. Empirical and theoretical studies suggest that increasing taxon sampling is expected to ameliorate, if not resolve, both problems; however, neither the current taxonomic system nor the established phylogeny provides sufficient information to guide additional sampling design. We examined the phylogeny of the spider family Linyphiidae, and selected ingroup species based on epigynal morphology, which can be reconstructed in a phylogenetic context. Our analyses resulted in seven robustly supported clades within linyphiids. The placements of four deep and long branches are sensitive to variations in both outgroup and ingroup sampling, suggesting the possibility of long branch attraction artifacts. Results of ancestral state reconstruction indicate that successive state transformations of the epigynal plate are associated with early cladogenetic events in linyphiid diversification. Representatives of different subfamilies were mixed together within well supported clades and examination revealed that their defining characters, as per traditional taxonomy, are homoplastic. Furthermore, our results demonstrated that increased taxon sampling produced a more informative framework, which in turn helps to study character evolution and interpret the relationships among linyphiid lineages. Additional defining characters are needed to revise the linyphiid taxonomic system based on our phylogenetic hypothesis.
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This is the first genus‐level phylogeny of the subfamily Mynogleninae. It is based on 190 morphological characters scored for 44 taxa: 37 mynoglenine taxa (ingroup) representing 15 of the 17 known genera and seven outgroup taxa representing the subfamilies Stemonyphantinae, Linyphiinae (Linyphiini and Micronetini), and Erigoninae, and a representative of the family Pimoidae, the sister‐group to Linyphiidae. No fewer than 147 of the morphological characters used in this study are new and defined for this study, and come mainly from male and female genitalia. Parsimony analysis with equal weights resulted in three most parsimonious trees of length 871. The monophyly of the subfamily Mynogleninae and the genera Novafroneta, Parafroneta, Laminafroneta, Afroneta, Promynoglenes, Metamynoglenes, and Haplinis are supported, whereas Pseudafroneta is paraphyletic. The remaining seven mynoglenine genera are either monotypic or represented by only one taxon. Diagnoses are given for all genera included in the analysis. The evolution of morphological traits is discussed and we summarize the diversity and distribution patterns of the 124 known species of mynoglenines. The preferred topology suggests a single origin of mynoglenines in New Zealand with two dispersal events to Africa, and does not support Gondwana origin.
True rosefinches (Aves: Carpodacus) are restricted to Eurasia, and 19 out of 25 species occur in the Sino-
Himalayas, making this the likely centre of origin. To test this hypothesis, suggested species splits had to be
evaluated and potential further cryptic diversity unravelled. A taxon-complete dated molecular phylogeny was
reconstructed using maximum-likelihood and Bayesian methods. Maximum-parsimony and likelihood approaches
were applied to deduce ancestral areas. Rosefinches, including the widespread Carpodacus erythrinus (Pallas,
1770), originated in south-west China (and the Himalayas) 14 Mya, and gave rise to a smaller clade consisting of
C. erythrinus, Haematospiza sipahi (Hodgson, 1836), and Chaunoproctus ferreorostris (Vigors, 1829), and a larger
clade with 22 species. The latter split into four major lineages through vicariance during the uplift of the
Himalayas. The suggested species splits of dubius from Carpodacus thura Bonaparte & Schlegel, 1850, formosanus
from Carpodacus vinaceus Verreaux, 1871, grandis from Carpodacus rhodochlamys Brandt, 1843, verreauxii from
Carpodacus rodopeplus (Vigors, 1831) (even polyphyletic) could be supported, whereas the suggested split of
severtzovi from Carpodacus rubicilla (Güldenstädt, 1775) appears to be too young, and should be considered
intraspecific. On the other hand, the central Asian lineage of Carpodacus synoicus Temminck, 1825 deserves
species rank [Carpodacus stolickae (Hume, 1874)]. The Carpodacus eos/pulcherrimus complex consists of four
lineages, pulcherrimus/argyrophrys and davidianus [Carpodacus pulcherrimus s.s. (Moore, 1856)], and eos and
waltoni [Carpodacus waltoni (Sharpe, 1905)].
This study presents a new phylogeny of erigonine spiders with emphasis on genera from the Neotropics. Thirty-nine exemplar taxa representing mostly Neotropical genera were added to a global sample of 31 erigonine and 12 outgroup exemplar taxa analyzed in a previous study. These 82 taxa were coded for 176 (172 informative) mostly morphological characters. Eighty-one characters were identical to or modified from the 73 (67 informative) characters included in a previous study; the remaining 95 characters are new. The complete data set includes 70 erigonine exemplars representing 65 genera, seven nonerigonine linyphiid exemplars, and five exemplars representing four araneoid families in the outgroup. Cladistic analysis resulted in a single most parsimonious tree (L =904, CI = 0.23, RI = 0.58; uninformative characters excluded: L = 900, CI = 0.23). This paper explores the implications of the new topology for the evolution of several characters of interest in erigonine evolution. The phylogeny implies that the desmitracheate condition is a synapomorphy of erigonines, with a reversal to the haplotracheate condition in one large clade within Erigoninae. We infer that the loss of the paracymbium in Neotropical erigonines occurred twice and may have progressed by different evolutionary pathways. Our phylogeny differs markedly from the previous cladistic hypothesis of erigonine relationships. We investigate how the addition of characters and taxa (alone and together) have altered the earlier hypothesis of erigonine phylogeny. We conclude that topological changes from the previous study to the current one are largely the result of adding and modifying characters, not adding taxa. Continuous Jackknife Function (CJF) analysis predicts that the inclusion of additional character data will continue to imply changes in the relationships among taxa in our analysis.
INTRODUCTION The very small genus Stemonyphantes up to our present knowledge is restricted to the temperate regions of Europe, Asia and North America. It was created by Menge (1866) for the European species Aranea trilineata Linnaeus, 1767, which, among others, appeared to be a junior synonym of Aranea lineata Linnaeus, 1758. The species was recorded also from North America (Emerton, 1876, 1882; Keyserling, 1886; and others). For nearly seventy years the nearctic population was thought to be conspecific with the palaearctic population. Keyserling (1886) even supposed the species to have been imported by ship from Europe and to have spread from there. A detailed description of S. lineatus, furnished with excellent figures of the genitalia of the species, was given by Blauvelt (1936) still without any indication of differences between European and North American specimens, although she states to have seen them from both regions. Gertsch (1951) was first in drawing attention to differences between the two populations; he created the new name Stemonyphantes blauveltae for the nearctic population. In Europe a new variety S. bucculentus [ = lineatus] pictus was described by Schenkel (1930) from the Riesengebirge on the Polish-Czechoslovakian frontier. Schenkel only possessed a female specimen, which differed from the nominate form mainly in the colour of the cephalothorax and abdomen. More specimens, including a male, were recorded by Buchar (1967) from the Böhmerwald in Czechoslovakia near the German frontier. Buchar examined the genitalia of these specimens and decided to raise Schenkel's variety to specific rank. He redescribed the species and listed the main differences with S. lineatus.
Using the most up-to-the-date information available, we present a considerably revised plate tectonic and paleogeographic model for the Indian Ocean bordering continents, from Gondwana's Middle Jurassic break-up through to India's collision with Asia in the middle Cenozoic. The landmass framework is then used to explore the sometimes complex and occasionally counter-intuitive patterns that have been observed in the fossil and extant biological records of India, Madagascar, Africa and eastern Eurasia, as well those of the more distal continents.
A new fossil Linyphiidae: Linyphiinae is described from 125–135 Ma old (Upper Neocomian–basal Lower Aptian) Cretaceous amber from the Kdeirji/Hammana outcrop, Lebanon. This is the oldest known linyphiid as well as the oldest described amber spider. The first major radiation of the linyphiid subfamilies occurred in the early Cretaceous, if not before, and the presence of Linyphiidae in this period predicts the presence of Pimoidae then too. Current evidence, which suggests the higher araneoids did not radiate and diversify until after the end-Cretaceous mass extinction event may be an artefact of sample size.
The male palpal organs of 124 British species of linyphiid spiders are described in detai, by reference to two basic types of palp structure (simple and complex).
The history of the taxonomy of the family is described, with reference especially to the work of Simon, Hull, Petrunkevitch, Locket & Millidge, and Wiehle.
This paper provides the first quantitative cladistic analysis of linyphiid morphology. Classical and novel homology hypotheses for a variety of character systems (male and female genitalia, somatic morphology, spinneret silk spigot morphology, etc.) are critically examined and studied within a phylogenetic context. Critical characters have been illustrated. A sample of linyphiid taxa (nine genera in four subfamilies), five species of Pimoa (Pimoidae), and two other araneoid families (Tetragnathidae and Araneidae, represented by Tetragnatha and Zygiella, respectively) were used to study the implications of the phylogeny of Pimoidae for the systematics of linyphiids. The phylogenetic relationships of these 16 exemplar taxa, as coded for the 47 characters studied, were analysed using numerical cladistic methods. In the preferred cladogram Pimoidae and Linyphiidae are sister groups, Stemonyphantinae are sister group to the remaining linyphiids, and Mynogleninae are sister group to the clade composed of Erigoninae plus Linyphiinae. These results agree with the relationships recently proposed by Wunderlich, except by finding erigonines as the sister group to linyphiines rather than to mynoglenines.
The genus Labulla Simon is circumscribed in phylogenetic terms to include the species Labulla thoracica (Wider), L. flahaulti Simon and L. machadoi sp. nov. The genital anatomy of the genus is described in detail and the taxonomy of the genus is reviewed. The monophyly of Labulla is supported by numerous morphological apomorphies of the male palp and female epigynum. Based on a cladistic analysis, a new genus, Pecado gen. nov., is erected to place Labulla impudica Denis, from Northern Africa. Lepthyphantes insularis Saito and ‘Labulla’nepula Tikader, both formerly included in Labulla, are not congeneric with the type species of Labulla. © 2005 The Linnean Society of London, Zoological Journal of the Linnean Society, 2005, 143, 359–404.
The spider genus Weintrauboa new genus (Araneae, Pimoidae) is described to place two species of pimoids from Japan and adjacent islands that were formerly classified in the linyphiid genus Labulla. Weintrauboa contortipes (Karsch) new comb., the type species, and W. chikunii (Oi) new comb. are redescribed. Parsimony analysis of morphological characters provides robust support for the monophyly of the genus Weintrauboa and corroborates the monophyly of Pimoa, Pimoidae, and the clade Linyphiidae plus Pimoidae. New diagnoses for Pimoa and Pimoidae are provided. © 2003 The Linnean Society of London, Zoological Journal of the Linnean Society, 2003, 139, 261–281
The spider genus Nanoa gen. nov. (Araneae, Pimoidae) is described to place Nanoa enana, a new species of pimoids from Western North America. Parsimony analysis of morphological characters provides support for the monophyly of Pimoa plus Nanoa and corroborates the monophyly of Pimoidae and of the clade Linyphiidae plus Pimoidae. © 2005 The Linnean Society of London, Zoological Journal of the Linnean Society, 2005, 145, 249–262.
This study infers the higher‐level cladistic relationships of linyphiid spiders from five genes (mitochondrial CO1, 16S; nuclear 28S, 18S, histone H3) and morphological data. In total, the character matrix includes 47 taxa: 35 linyphiids representing the currently used subfamilies of Linyphiidae (Stemonyphantinae, Mynogleninae, Erigoninae, and Linyphiinae (Micronetini plus Linyphiini)) and 12 outgroup species representing nine araneoid families (Pimoidae, Theridiidae, Nesticidae, Synotaxidae, Cyatholipidae, Mysmenidae, Theridiosomatidae, Tetragnathidae, and Araneidae). The morphological characters include those used in recent studies of linyphiid phylogenetics, covering both genitalic and somatic morphology. Different sequence alignments and analytical methods produce different cladistic hypotheses. Lack of congruence among different analyses is, in part, due to the shifting placement of Labulla , Pityohyphantes , Notholepthyphantes , and Pocobletus . Almost all combined analyses agree on the monophyly of linyphioids, Pimoidae, Linyphiidae, Erigoninae, Mynogleninae, as well as Stemonyphantes as a basal lineage within Linyphiidae. Our results suggest independent origins of the desmitracheate tracheal system in micronetines and erigonines, and that erigonines were primitively haplotracheate. Cephalothoracic glandular specializations of erigonines and mynoglenines apparently evolved independently. Subocular sulci of mynoglenines and lateral sulci (e.g. Bathyphantes ) evolved independently but glandular pores in the prosoma proliferated once. The contribution of different character partitions and their sensitivity to changes in traditional analytical parameters is explored and quantified.
© The Willi Hennig Society 2009.