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Concerted Pleistocene dispersal and genetic differentiation in passerine birds from the Tres Marías Archipelago, Mexico
Abstract
Studies in evolutionary biology have commonly been focused on insular systems because of their natural geographic isolation and relatively simpler biotas. Using mitochondrial DNA sequences of 4 passerine bird species distributed in the Tres Marías Archipelago (TMA) and the nearby mainland of western Mexico-Cardinalis cardinalis, Turdus rufopalliatus, Vireo hypochryseus, and Icterus pustulatus-we determined interspecific and intraspecific phylogenetic relationships between insular and mainland populations, conducted insular age-based time calibration for the estimation of divergence times, and used Bayesian analyses to examine the colonization history of islands. Specifically, we tested whether the study species from the TMA share the same colonization history since the emergence of the islands ∼120 kya, taking advantage of the reduced isolation due to sea-level fluctuations during the Pleistocene, or whether there were independent colonization events. We also looked for evidence in the genetic structure of the island populations that would support the idea of colonization by a small number of individuals. Phylogenetic relationships consistently recovered lineage divergence between the TMA and mainland populations, with strong support in 3 of the 4 species. Our estimates for the sea level and coastline of the west coast of Mexico during the Pleistocene showed that the distance between the TMA and the mainland was ∼25 km. We tested several island colonization scenarios according to the phylogenetic relationships, haplotype networks, divergence time estimates, historical demography, and different glaciation dates. The most supported scenario of colonization of the TMA suggests that a single event occurred ∼120 kya when the islands emerged, which is highly concordant with geological evidence, and simultaneously affected the 4 species.
... Although we consider that this could have resulted from an extraordinary random event, which led a group of parrots to end up more than six thousand kilometers from Panama to the TMI, it does not rule out other colonization scenarios (from mainland to TMI) with vicariance processes, dispersions, extinctions and recolonization that could also explain the origin of this lineage, as has been presented for other species that inhabit the TMI and the Mexican continental area such as Cardinalis cardinalis (Smith and Klicka, 2013), Turdus rufopalliatus, or others (Ortiz-Ramírez et al., 2018). ...
... Taking into account the probable scenario by assisted dispersal, we deduce that after the arrival at the TMI, A. o. oratrix diverged from tresmariae about 358 kya, at the end of the Pleistocene (Node 5; Fig. 3), possibly when sea level was ~100 m below the current level (Yokoyama et al., 2000;Ortiz-Ramírez et al., 2018), and the distance separating the TMI from the Mexican mainland was only ~25 km (Ortiz-Ramírez et al., 2018). Therefore, other founder effects were possibly carried out by reducing genetic diversity, which we have documented for this lineage (Table 2). ...
... Taking into account the probable scenario by assisted dispersal, we deduce that after the arrival at the TMI, A. o. oratrix diverged from tresmariae about 358 kya, at the end of the Pleistocene (Node 5; Fig. 3), possibly when sea level was ~100 m below the current level (Yokoyama et al., 2000;Ortiz-Ramírez et al., 2018), and the distance separating the TMI from the Mexican mainland was only ~25 km (Ortiz-Ramírez et al., 2018). Therefore, other founder effects were possibly carried out by reducing genetic diversity, which we have documented for this lineage (Table 2). ...
Elucidating the historical processes that led populations to their current spatial and genetic arrangement is
relevant in conserving threatened species. We interpreted the phylogeographic structure of the threatened
Yellow-headed Parrot (Amazona oratrix) with mitochondrial markers and analyzed 98 samples from Mexico,
Guatemala, and Belize. We performed analyses of genetic structure, genealogical relationships, demographic
history, and divergence times and illustrated the phenotypic variation qualitatively of the sampled individuals.
The studies revealed that 92% of the genetic variation is explained between the Mexican Tres Marías Islands, the
Mexican Pacific Coast, and the Atlantic groups. These three groups were segregated into two main lineages
(Pacific and Atlantic), separated by 26 mutations, leaving A. auropalliata within the Atlantic. We found that both
lineages diverged 0.55 million years ago, from which the Atlantic lineage experienced population expansion,
high levels of genetic diversity, and a low genetic structure with two phenotypes. The Pacific experienced demographic
stability, low levels of diversity, and a genetic structure marked with two phenotypes. Our estimates
indicate that this separation occurred in the Pleistocene when the Atlantic clade diverged from Panama and
dispersed overland to the Gulf of Mexico. Simultaneously, the Pacific clade departed from the same area to Tres
Marías Islands and the Mexican Pacific coast. We deduce that this long-distance event was probably produced by
assisted dispersal, but other scenarios appear more parsimonious. We conclude that there is no gene flow between
both lineages and that the phylogeographic structure resulted significantly from historical events and
climatic changes during the Pleistocene. We propose undertaking other analyses in the future to compare our
results and the paraphyletic relationships in A. oratrix.
... Additionally, recent phylogeographic studies on birds and other vertebrates (e.g. Devitt, 2006;Arbeláez-Cortés et al., 2014;Arcangeli et al., 2018;Ortiz-Ramírez et al., 2018) show similar genetic structure among faunas within the Mesoamerican SDTF. This suggests a history of population isolation, which may explain the observed biodiversity patterns. ...
... In our study, demographic results, including high levels of genetic divergence (F ST ) in all species, support the hypothesis that the apparently continuous distribution in the taxa was probably fragmented into allopatric populations during the Pleistocene. Although complex demographic inferences based only on mtDNA markers should be treated with caution, they are highly informative, especially when shared patterns are found in multiple phylogenetically and ecologically distict taxa (Arbeláez-Cortés et al., 2014;Ortiz-Ramírez et al., 2018). ...
... The pacific slope of The mesoamerican sdTf as a climaTic sTabiliTy region P h y l o g e n e t i c a n d d e m o g r a p h i c a n a l y s e s o f mitochondrial genes revealed divergence and isolation of populations in different lineages, as seen in other Mesoamerican highland and lowland bird taxa (Sánchez-González et al., 2008;Arbeláez-Cortés et al., 2014;Ortiz-Ramírez et al., 2018). Other SDTFassociated taxa, such as the snake Trimorphodon biscutatus (Devitt, 2006) and the marsupial Tlacuatzin canescens (Arcangeli et al., 2018) have similarly shown genetic structure in areas without apparent physical barriers limiting dispersion. ...
We analysed the phylogeographic structure of five resident bird lineages distributed in the seasonally dry tropical forests (SDTF) of Mesoamerica to test whether they show patterns of synchronous and geographically coincident genetic divergence during the Quaternary. We generated phylogenetic trees, estimated divergence times and analysed the genetic structure of populations (based on sequences of mitochondrial genes), as well as estimating historical distributions (range extension and areas of long-term climate stability) during the Late Pleistocene. We tested and selected the phylogeographic divergence scenarios that best explain the current divergence patterns of taxa using the Approximate Bayesian Computation (ABC) approach. For most species, phylogenetic trees and haplotype networks showed a clear genetic structure associated with geographical distribution. Overall, the divergence times ranged from 0.29–2.0 Mya, suggesting that diversification of populations occurred at different times during the Pleistocene. The palaeodistribution models predicted at least two areas of climatic stability within the current SDTF that probably allowed glacial-interglacial persistence of isolated bird populations along the Mexican Pacific, thus promoting their genetic divergence. The results provide information relevant to the identification of diversification hotspots for the Mesoamerican SDTF avifauna.
... Additional information. -Cortés-Rodríguez et al. (2008) and Ortiz-Ramírez et al. (2018) found reciprocal monophyly but shallow genetic divergence between graysonii and mainland specimens. Shallow genetic divergence is also seen in other sister species of orioles even when they possess distinctly different plumage features (e.g. ...
... - Montaño-Rendón et al. (2015) and Ortiz-Ramírez et al. (2018) found reciprocal monophyly and deep genetic divergence between graysoni and rufopalliatus. ...
... The absence of clear distinctions in plumage between some graysoni and other races (see above) makes it particularly difficult to identify potential hybrids based on plumage, and there is slight overlap in morphometrics, especially bill length of females (Grant 1965a). Montaño-Rendón et al. (2015) and Ortiz-Ramírez et al. (2018) apparently did not include DNA of graysoni from the mainland, nor indeed of any rufopalliatus from the Nayarit coastal plain, where hybrids, if any, would be expected (all of their Nayarit rufopalliatus were from a single locality in the foothills). Because the extent of hybridisation, if any, is presently unknown, we recommend further studies before concluding whether graysoni represents a species. ...
The Tres Marías archipelago off western Mexico, rarely visited by ornithologists, is currently considered to have 24 endemic subspecies of landbirds. Using both new and previously overlooked information, we evaluate some of the better-marked taxa by applying recently proposed criteria for determining whether they merit recognition at species level. We propose that six of these be elevated to species (Cynanthus lawrencei, Amazilia graysoni, Forpus insularis, Pheugopedius lawrencii, Icterus graysonii and Granatellus francescae) although for some there is evidence that they occasionally interbreed with close relatives on the adjacent mainland. These taxa are threatened by introduced goats, cats and rats, and we hope that by recognising them as endemic species, greater awareness of their plight might stimulate increased conservation action to preserve them and their ecosystem.
... Because the modern landscape of the Mesoamerican lowlands is semihomogeneous, environmental heterogeneity or physical barriers are less likely explanations for the high diversity in the region. This gives way to other explanations, such as environmental changes throughout the Pleistocene, which promoted range contractions, isolation, and differentiation, followed by range expansions that modified geographical distributions (Arbeláez-Cortés et al. 2014, Hernández-Canchola and León-Paniagua 2017, Ortiz-Ramírez et al. 2018, Castillo-Chora et al. 2021a. Although processes of range expansion have been described, few analyses have explicitly focused on niche requirements in currently widely distributed taxa (e.g. ...
... For example, several studies indicate shared structure of geographical patterns and, in some cases, synchronic Pleistocene divergence times for intraspecific lineages (e.g. Arbeláez-Cortés et al. 2014, Mastretta-Yanes et al. 2015, Ortiz-Ramírez et al. 2018, Castillo-Chora et al. 2021a. Haffer's general model for population differentiation indicates that climatic shifts led to shrinking, allopatric distributions of populations in the past, which may have promoted local adaptation and differentiation. ...
Here, we aimed to assess the role of historical (climate events) and the current geographical and ecological features in the evolutionary history of a clade of New World jays. Using an ellipsoid-based approach relying on environmental climatic layers and occurrence data, we tested whether closely related taxa in the clade Cyanocorax colliei + C. formosus + C. morio occupy ecologically different environmental spaces throughout their mostly allopatric distribution in a semihomogeneous landscape, and whether they have been influenced by similar processes given the geographical and ecological context of the Mesoamerican lowland tropical forests. We reconstructed palaeo-distributions to assess the effects of climate shifts on their current patterns of distribution. Additionally, we assess the importance of areas that could function as environmental barriers between taxa. Our results at the species level show evidence for niche divergence for two of the three species pairs. Geographical transferences (areas of suitability inferred by the model) seem to have good explanatory power for current subspecies distribution and variation. At the subspecies level, we find no evidence for niche divergence; the observed parapatric and allopatric distributions seem instead associated with historical environmental differences and ecological barriers limiting the connection between populations with similar niche requirements.
... In the group west of the IT, within the NA clade, all individuals from Tres Marías islands (currently in subspecies capitalis) were grouped, showing a genetic structure consistent with simple paraphyly (Omland et al., 2006), in which lineage sorting seems to be incomplete. Simple paraphyly in this case may be the result of a small number of founders that likely dispersed to the islands (180-40 kya), which is consistent with islands emergence (McCloy et al., 1988) and with dispersal times in other insular bird species (Ortiz-Ramírez et al., 2018). In the group east of IT, genetic differentiation between sister clades YUC and NCA is relatively low (0.7%), also suggesting a recent divergence event. ...
Due to a complex geological and biotic history, the Isthmus of Tehuantepec (IT), has been long recognized as a driver for the evolutionary divergence of numerous lowland and highland taxa. Widely distributed in the lowlands of the American continent, the White-Tipped Dove (Leptotila verreauxi) is a polytypic species with 13 recognized subspecies. Four of these have been recorded in Mexico, and the distribution of three abuts at the IT, suggesting a contact zone. To estimate phylogenetic patterns, divergence times and genetic differentiation, we examined two mtDNA (ND2 and COI) and one nDNA (β-fibint 7) markers. We also used correlative ecological niche models (ENM) to assess whether ecological differences across the IT may have acted as a biogeographical boundary. We estimated paleodistributions during the Middle Holocene, Last Glacial Maximum and Last Interglacial, to evaluate the influence of climate changes on the distribution and demographic changes. Our results showed genetically distinct lineages that diverged approximately 2.5 million years ago. Climatic and ecological factors may have played a dual role in promoting differentiation, but also in the formation of a secondary contact zone in the southern IT. Our ecological niche comparisons indicated that the ecological niche of sympatric lineages at the IT are not identical, suggesting niches divergence; in addition, environmental niche models across the region indicated no abrupt biogeographic barriers, but the presence of regions with low suitability. These results suggest that genetic differentiation originated by a vicariant event probably related to environmental factors favored the evolution of different ecological niches. Also, the absence of a biogeographic barrier but the presence of less suitable areas in the contact regions, suggest that secondary contact zones may be also maintained by climatic factors for the eastern group, but also by biotic interactions for the western group.
... Global FST or ΦST values in seabirds are usually lower than the maximal theoretical (FST or ΦST = 1) [5,75], and we interpreted their values as low (0 to 0.05), moderate (0.05 to 0.15), high (0.15 to 0.25), and very high (>0.25) [96]. Thus, the lower the value, the higher the gene flow. ...
Philopatry can promote genetic differentiation among populations but remains undescribed in many seabirds. Hence, we explored such associations in Heermann’s Gull. Philopatry was observed monitoring 998 gulls in Rasa Island, while genetic differences were examined in the Cardonosa, Rasa, and Isabel islands using the cytochrome b of 296 gulls. Adults returned repeatedly to its natal valley or to a very close distance from it under different modelled hypotheses. Likewise, the interaction between sex and distance indicated significant male-biased philopatry. Besides, low to high genetic differentiation was observed between the Rasa and Cardonosa islands (ΦST = 0–0.22) (both in the Midriff Islands Region), but higher genetic differentiation against Isabel Island (ΦST > 0.25) (in the Mexican Province region). Consistently, genetic structure among regions was observed using different approaches (AMOVA: ΦCT = 0.49; SAMOVA: FCT = 0.49; and BAPS: K = 2). Similarly, a pattern of isolation by distance (rM = 0.82, p = 0.03), agrees with lower estimates of scaled migration rates between regions than among islands of the same region. Overall, it is suggested that the genetic structure found in Heermann’s Gull has been promoted by physical and behavioral barriers.
... pygmaeus), the Tres Marias raccoon (Procyon lotor insularis), and the Cozumel island coati (Nasua narica nelsoni) (Helgen and Wilson 2005;McFadden et al. 2008;Cuaron et al. 2009). The Tres Marias raccoon demonstrates that procyonids are capable of dispersing over at least 25 km of open water, the shortest distance between the Tres Marias archipelago and the mainland during the Pleistocene (Ortiz-Ramírez et al. 2018) In addition to dispersing to a new environment, successful colonization requires establishing a viable population. In this regard, the ecological uniqueness of procyonids relative to the endemic South American biota may have favored their establishment in South America long before other carnivores. ...
It was once thought that the endemic carnivorous mammals of South America, the metatherian sparassodonts, were driven extinct by North American carnivorans through competitive exclusion. However, sparassodonts went extinct before most groups of carnivorans entered South America; only the endemic Cyonasua-group procyonids (Cyonasua and Chapalmalania), which immigrated to South America nearly 4 million years earlier than other carnivorans, significantly overlapped with sparassodonts in time. In this study, we examine the functional morphology of the dentition of Cyonasua and Chapalmalania through quantitative analysis to determine the dietary habits of these taxa and the degree to which they may have ecologically overlapped sparassodonts and large predatory Neogene didelphimorphians. We find Cyonasua and Chapalmalania to be more carnivorous than extant procyonids, other than Bassariscus, in agreement with previous studies, but more omnivorous than most other carnivorans and all meat-eating South American metatherians, including sparassodonts. The extreme ecological dissimilarity between Cyonasua-group procyonids and members of the endemic South American predator guild may explain why procyonids were able to successfully establish themselves in South America several million years earlier than most other northern mammals (including all other carnivorans): they moved into a previously unoccupied ecological niche (large omnivore) and avoided direct competition with incumbent native species, a situation similar to that documented in historical cases of biological invasion. The omnivorous diets and climbing/swimming abilities of procyonids may have increased their chances for a successful over-water dispersal relative to other carnivorans, further favoring their successful establishment in South America.
The controversial taxonomy of the Artibeus lituratus-intermedius complex and the lack of genetic studies in the Artibeus specimens reported in the Tres Marias Islands (TMI) have caused the taxonomic identity of these specimens to remain ambiguous. During an expedition carried out in May 2022, we captured four specimens of Artibeus in the Maria Madre and Maria Cleophas islands. The specimens were assigned by external morphological characters and traditional morphometrics, and were compared with the data available in the taxonomic descriptions of A. lituratus and A. intermedius. Additionally, we performed a phylogenetic analysis of cytochrome b sequences. Our genetic data suggest that the Artibeus populations are a lineage of the Artibeus lituratus-intermedius complex. In addition, the morphometric data suggest the presence of two morphotypes that, according to the literature, would correspond to A. lituratus palmarum and A. intermedius koopmani. With these results, we propose that both species of Artibeus are present and therefore the bat community of TMI is composed of ten species. However, future more detailed genetic studies are needed to elucidate the true taxonomic diversity of the archipelago.
The Tres Marías archipelago in the central Mexican Pacific is a protected area that has a complex geological history due to its tectonic setting. This study describes an integrative analysis of the biogeographical affinities of the biota inhabiting the islands. A biotic component analysis showed a close relationship between the islands and the Pacific Lowlands and Veracruzan biogeographical provinces, whereas a cladistic biogeographical analysis additionally showed a Nearctic affinity with the Sonoran biogeographical province. The biogeographical affinity patterns, based on the distribution of the sister group of each endemic species, revealed three distinct patterns: Neotropical, Sonoran-Neotropical and Nearctic-Neotropical. The study recognized that the Tres Marías Islands are a region of great biological complexity where the biota of the Pacific Lowlands and the Veracruzan provinces intersect, with a predominantly Neotropical affinity. In this biogeographical analysis, information on the biotic assemblage and the geological history of the Tres Marías Islands are integrated and discussed. The biotic assembly of the islands must have occurred via both vicariance and dispersal at different geological times, related to opening of the Gulf of California (Miocene–Pleistocene) as well as to periods of glaciation (Pleistocene).
Islands have been characterized as natural laboratories because of their distinct and often identifiable role in promoting genetic variation and population differentiation, but they have also been considered as evolutionary sinks of biodiversity. Here, we extend classical studies of island biogeography based in the Eastern Mediterranean to compare genetic divergences and population structure among birds in insular and continental populations. We focused on populations of six passerine species (Short‐toed Treecreeper, Great Tit, Eurasian Wren, Eurasian Blackbird, Common Chaffinch and Sardinian Warbler) with breeding populations on the islands of Cyprus and Crete and compared those with a continental population from mainland Greece. We sampled 172 individuals from six species and used double‐digest RAD sequencing to examine population‐level genetic divergence and structure. Population structure analyses using single nucleotide polymorphisms (SNPs) revealed structure between the islands and mainland for all six species, and this was most pronounced in Short‐toed Treecreeper, Great Tit and Eurasian Wren. For all species with the exception of the Sardinian Warbler, the populations from the two islands were more differentiated from each other than either was from mainland Greece, reflecting variation in island colonization dynamics. Patterns ranged from pronounced population differentiation among populations, e.g. in Short‐toed Treecreeper, where taxonomic revisions are potentially warranted, to others with weak structure among insular and continental populations, such as in Common Chaffinch and Sardinian Warbler. Although some patterns are consistent with increased rates of genetic drift in smaller populations explaining greater differences among the island populations than either insular population has from continental source populations, in others, including in Eurasian Blackbird and Common Chaffinch, higher nucleotide diversity in Cyprus may reflect a demographic pattern of post‐glacial north‐westward expansion.
Background
The Mesoamerican dominion is a biogeographic area of great interest due to its complex topography and distinctive climatic history. This area has a large diversity of habitats, including tropical deciduous forests, which house a large number of endemic species. Here, we assess phylogeographic pattern, genetic and morphometric variation in the Cinnamon Hummingbird complex Amazilia rutila , which prefers habitats in this region. This resident species is distributed along the Pacific coast from Sinaloa—including the Tres Marías Islands in Mexico to Costa Rica, and from the coastal plain of the Yucatán Peninsula of Mexico south to Belize.
Methods
We obtained genetic data from 85 samples of A. rutila , using 4 different molecular markers (mtDNA: ND2, COI; nDNA: ODC, MUSK) on which we performed analyses of population structure (median-joining network, STRUCTURE, F ST , AMOVA), Bayesian and Maximum Likelihood phylogenetic analyses, and divergence time estimates. In order to evaluate the historic suitability of environmental conditions, we constructed projection models using past scenarios (Pleistocene periods), and conducted Bayesian Skyline Plots (BSP) to visualize changes in population sizes over time. To analyze morphometric variation, we took measurements of 5 morphological traits from 210 study skins. We tested for differences between sexes, differences among geographic groups (defined based on genetic results), and used PCA to examine the variation in multivariate space.
Results
Using mtDNA, we recovered four main geographic groups: the Pacific coast, the Tres Marías Islands, the Chiapas region, and the Yucatán Peninsula together with Central America. These same groups were recovered by the phylogenetic results based on the multilocus dataset. Demography based on BSP results showed constant population size over time throughout the A. rutila complex and within each geographic group. Ecological niche model projections onto past scenarios revealed no drastic changes in suitable conditions, but revealed some possible refuges. Morphometric results showed minor sexual dimorphism in this species and statistically significant differences between geographic groups. The Tres Marías Islands population was the most differentiated, having larger body size than the remaining groups.
Conclusions
The best supported evolutionary hypothesis of diversification within this group corresponds to geographic isolation (limited gene flow), differences in current environmental conditions, and historical habitat fragmentation promoted by past events (Pleistocene refugia). Four well-defined clades comprise the A. rutila complex, and we assess the importance of a taxonomic reevaluation. Our data suggest that both of A. r. graysoni (Tres Marías Islands) and A. r. rutila (Pacific coast) should be considered full species. The other two strongly supported clades are: (a) the Chiapas group (southern Mexico), and (b) the populations from Yucatán Peninsula and Central America. These clades belong to the corallirostris taxon, which needs to be split and properly named.
Abstract Historical events, habitat preferences, and geographic barriers might result in distinct genetic patterns in insular versus mainland populations. Comparison between these two biogeographic systems provides an opportunity to investigate the relative role of isolation in phylogeographic patterns and to elucidate the importance of evolution and demographic history in population structure. Herein, we use a genotype‐by‐sequencing approach (GBS) to explore population structure within three species of mastiff bats (Molossus molossus, M. coibensis, and M. milleri), which represent different ecological histories and geographical distributions in the genus. We tested the hypotheses that oceanic straits serve as barriers to dispersal in Caribbean bats and that isolated island populations are more likely to experience genetic drift and bottlenecks in comparison with highly connected ones, thus leading to different phylogeographic patterns. We show that population structures vary according to general habitat preferences, levels of population isolation, and historical fluctuations in climate. In our dataset, mainland geographic barriers played only a small role in isolation of lineages. However, oceanic straits posed a partial barrier to the dispersal for some populations within some species (M. milleri), but do not seem to disrupt gene flow in others (M. molossus). Lineages on distant islands undergo genetic bottlenecks more frequently than island lineages closer to the mainland, which have a greater exchange of haplotypes.
Analyses of genetic variation allow understanding the origin, diversification and genetic resources of cultivated plants. Domesticated taxa and their wild relatives are ideal systems for studying genetic processes of plant domestication and their joint is important to evaluate the distribution of their genetic resources. Such is the case of the domesticated subspecies C. argyrosperma ssp. argyrosperma, known in Mexico as calabaza pipiana, and its wild relative C. argyrosperma ssp. sororia. The main aim of this study was to use molecular data (microsatellites) to assess the levels of genetic variation and genetic differentiation within and among populations of domesticated argyrosperma across its distribution in Mexico in comparison to its wild relative, sororia, and to identify environmental suitability in previously proposed centers of domestication. We analyzed nine unlinked nuclear microsatellite loci to assess levels of diversity and distribution of genetic variation within and among populations in 440 individuals from 19 populations of cultivated landraces of argyrosperma and from six wild populations of sororia, in order to conduct a first systematic analysis of their genetic resources. We also used species distribution models (SDMs) for sororia to identify changes in this wild subspecies’ distribution from the Holocene (∼6,000 years ago) to the present, and to assess the presence of suitable environmental conditions in previously proposed domestication sites. Genetic variation was similar among subspecies (HE = 0.428 in sororia, and HE = 0.410 in argyrosperma). Nine argyrosperma populations showed significant levels of inbreeding. Both subspecies are well differentiated, and genetic differentiation (FST) among populations within each subspecies ranged from 0.152 to 0.652. Within argyrosperma we found three genetic groups (Northern Mexico, Yucatan Peninsula, including Michoacan and Veracruz, and Pacific coast plus Durango). We detected low levels of gene flow among populations at a regional scale (<0.01), except for the Yucatan Peninsula, and the northern portion of the Pacific Coast. Our analyses suggested that the Isthmus of Tehuantepec is an effective barrier isolating southern populations. Our SDM results indicate that environmental characteristics in the Balsas-Jalisco region, a potential center of domestication, were suitable for the presence of sororia during the Holocene.
Crop wild relatives represent an important agronomic resource for crop improvement and biodiversity conservation. The wild squash Cucurbita argyrosperma subsp. sororia. (Cucurbitaceae) has been considered the wild ancestor of cultivated forms of C. argyrosperma. In order to characterise the geographic patterns of genetic variation in this wild cucurbit and to identify priority areas for conservation, we analysed the genetic diversity and structure of natural populations along the Mexican Pacific coast. By using 14 polymorphic microsatellites, we genotyped 378 individuals sampled from 61 locations. Standard population genetics analyses and group testing were conducted on the genotypes with the aid of principal coordinate analysis and Bayesian analysis. Overall, we found an average of 12.3 alleles per locus and an expected heterozygosity of 0.756. We found greater genetic diversity in southern populations. The fixation index was 0.113, suggesting a mixed mating system. The Mantel test revealed a minor distance effect on genetic differentiation between individuals (r = 0.321). Finally, we found three main groups of populations arranged in a mostly latitudinal pattern, from Sinaloa (north-west) to Oaxaca–Guerrero (south-east). The greater genetic diversity and heterogeneity among southern populations (Guerrero–Oaxaca), suggests that this region is an important centre of diversity of this wild squash with important implications for conservation.
p>Background: The domestication process has left signatures in the genomes of domesticated species. Before the existence of molecular markers, only phenotypic traits could be used in domestication studies and breeding programs, but these approaches required long time and effort. In the last decades, the use of molecular markers dramatically increased, and the development of massive sequencing tools have enable to obtain thousands or even millions of molecular markers. This work focuses on domesticated plants and the main goal is to bring a general and an integrative perspective of the data, approaches and questions that can be answered using massive sequencing tools, compared to classic genetic data.
Results: The use of molecular markers in the last decades has increased the efficiency and accuracy of plant breeding, allowing to access information about domestication history and to identify genes affected by domestication. Some patterns have been identified: (1) genetic diversity reduction due to demographic bottlenecks and artificial selection; (2) frequently, mutations related with domestication syndrome preexisted at low frequency in natural populations; (3) accumulation of deleterious mutation; (4) gene flow between wild and cultivated populations. There are several approaches that can be used in massive sequencing tools: de novo genome sequencing, whole genome resequencing, reduction of genome complexity using restriction enzymes, transcriptome analysis and epigenetic studies.
Conclusions: Despite the progress made, enormous challenges still remain: storage of large databases; development of fast, accurate and high throughput strategies to phenotype; identification of paralogous genes in polyploid species; and the analysis of large and highly diverse genomes.
Aim
We studied the gecko genus Ebenavia to reconstruct its colonization history, test for anthropogenic versus natural dispersal out of Madagascar, and correlate divergence date estimates of our phylogeny with geological age estimates of islands in the region.
Location
Madagascar and surrounding islands of the Western Indian Ocean (Comoros, Mayotte, Mauritius, Pemba).
Methods
We reconstructed the phylogeny of Ebenavia covering its entire geographical range using a molecular data set of three mitochondrial and two nuclear markers. We estimated divergence times based on calibrations using (1) previously calculated mutation rates of mitochondrial markers, (2) a combination of these rates with old or (3) young geological age estimates for some of the islands inhabited by the genus, and (4) an independent data set with fossil outgroup calibration points.
Results
Ebenavia inunguis , one of two recognized species of the genus, comprises multiple ancient evolutionary lineages. The earliest divergence within this complex (Miocene, 13–20 Ma; 95% credibility interval [ CI ]: 4–29 Ma) separates the population of the Comoros Islands, excluding Mayotte, from all other lineages. The age estimates for island lineages coincide with the geological age estimates of the islands except for Grand Comoro, where the age of the local clade (3–5 Ma; 95% CI : 2–7 Ma) significantly predates the estimated island age (0·5 Ma). A clade from north Madagascar + Mayotte + Pemba is estimated to have diverged from an eastern Malagasy clade in the Miocene.
Main Conclusions
Our results suggest that Grand Comoro Island is geologically older than previously estimated. The islands of the Comoros and Pemba were probably colonized via natural dispersal out of Madagascar (> 1000 km in the case of Pemba). Mauritius was most likely colonized only recently from eastern Madagascar via human translocation.
Background
One of the biggest challenges in avian taxonomy is the delimitation of allopatric species because their reproductive incompatibility cannot be directly studied in the wild. Instead, reproductive incompatibility has to be inferred from multiple, divergent character sets that indicate a low likelihood of allopatric populations amalgamating upon secondary contact. A set of quantitative criteria for species delimitation has been developed for avian taxonomy. ResultsHere, we report a broad multi-trait comparison of the two insular subspecies of the Blue Chaffinch Fringilla teydea, endemic to the pine forests of Tenerife (ssp. teydea) and Gran Canaria (ssp. polatzeki) in the Canary Islands. We found that the two taxa were reciprocally monophyletic in their whole mitogenomes and two Z chromosome introns. The genetic distance in mitogenomes indicates around 1 Mya of allopatric evolution. There were diagnostic differences in body morphometrics, song and plumage reflectance spectra, whose combined divergence score (=11) exceeds the threshold level (=7) set for species delimitation by Tobias et al. (Ibis 152:724–746, 2010). Moreover, we found a marked divergence in sperm lengths with little range overlap. Relatively long sperm with low intra- and intermale CV compared to other passerines suggest a mating system with high levels of sperm competition (extrapair paternity) in these taxa. Conclusion
The large and diagnostic divergences in multiple functional traits qualify for species rank, i.e., Tenerife Blue Chaffinch (Fringilla teydea) and Gran Canaria Blue Chaffinch (Fringilla polatzeki). We encourage a wider use of sperm traits in avian taxonomy because sperm divergences might signal reproductive incompatibility at the postcopulatory prezygotic stage, especially in species with sperm competition.
Aim
The history of Agave lechuguilla , a characteristic and dominant plant of the Chihuahuan Desert, was reconstructed in order to determine the importance of the Neogene orogenic uplift and the Quaternary glacial–interglacial climatic changes on the genetic patterns of a native Chihuahuan Desert species.
Location
Chihuahuan Desert, Mexico and United States.
Methods
Chloroplast DNA data from A. lechuguilla were analysed to describe levels of genetic diversity and structure and to infer the species’ demographic history, using traditional methods and approximate Bayesian computation (ABC). The time of divergence of the different haplogroups was estimated with a Bayesian approach. In addition, ecological niche modelling was used to identify possible refugia.
Results
Molecular dating analyses showed that A. lechuguilla originated 4.46 Ma and later differentiated into four haplogroups. The average chloroplast genetic diversity was low ( Hd , 0.24), with high levels of genetic differentiation ( G ST , 0.780). Demographic analysis, niche modelling and ABC indicated a recent expansion from at least five glacial refugia located south of the species’ current distribution.
Main conclusion
Agave lechuguilla originated in the Neogene, and the glacial–interglacial events of the Pleistocene resulted in the expansion and contraction of its range, playing an important role in its intraspecific diversification. These contraction–expansion events are consistent with biogeographical regions previously identified in the Chihuahuan Desert.
We implemented a temporally dynamic approach to the cladistic biogeographic analysis of 13 areas of North American deserts and several plant and animal taxa. We undertook a parsimony analysis of paralogy-free subtrees based on 43 phylogenetic hypotheses of arthropod, vertebrate and plant taxa, assigning their nodes to three different time slices based on their estimated minimum ages: Early-Mid-Miocene (23−7 Ma), Late Miocene/Pliocene (6.9−2.5 Ma) and Pleistocene (2.4−0.011 Ma). The analyses resulted in three general area cladograms, one for each time slice, showing different area relationships. They allowed us to detect influences of different geological and palaeoclimatological events of the Early-Mid-Miocene, Late Miocene/Pliocene and Pleistocene that might have affected the diversification of the desert biota. Several diversification events in the deserts of North America might have been driven by Neogene uplift, marine incursion and the opening of the California Gulf during the Miocene–Pliocene, whereas climatic fluctuations had the highest impact during the Pleistocene.
Squash was first domesticated in Mexico and is now found throughout North America (NA) along with Peponapis pruinosa, a pollen specialist bee species of the squash genus Cucurbita. The origin and spread of squash cultivation is well-studied archaeologically and phylogenetically; however, no study has documented how cultivation of this or any other crop has influenced species in mutualistic interactions. We used molecular markers to reconstruct the demographic range expansion and colonization routes of P. pruinosa from its native range into temperate NA. Populations east of the Rocky Mountains expanded from the wild host plant’s range in Mexico and were established by a series of founder events. Eastern NorthAmericawas most likely colonized from squash bee populations in the present-day continental Midwest USA and not from routes that followed the Gulf and Atlantic coasts from Mexico. Populations of P. pruinosa west of the Rockies spread north from the warm deserts much more recently, showing two genetically differentiated populations with no admixture: one in California and the other one in eastern Great Basin. These bees have repeatedly endured severe bottlenecks as they colonized NA, following human spread of their Cucurbita pollen hosts during the Holocene. © 2016 The Author(s) Published by the Royal Society. All rights reserved.
Premise of the study:
Genetic data suggest that three lineages of Phragmites australis are found in North America: the Native North American lineage, the Gulf Coast lineage, and the Invasive lineage. In Mexico, P. australis is a common species, but nothing is known about the distribution or ecology of these lineages. We examined the phylogeography of P. australis to analyze the current geographic distribution of genetic variation, demographic history, and dispersal patterns to better understand its evolutionary history in Mexico.
Methods:
We sampled 427 individuals from 28 populations. We used two noncoding regions of chloroplast DNA to estimate the levels of genetic variation and identified the genetic groups across the species' geographical range in Mexico. We compared the genealogical relationships among haplotypes with those previously reported. A hypothesis of demographic expansion was also tested for the Mexican P. australis lineages.
Key results:
We found 13 new haplotypes native to Mexico that might be undergoing an active process of expansion and diversification. Genealogical analyses provided evidence that two independent lineages of P. australis are present in Mexico. The invasive lineage was not detected with our sampling. Our estimates of population expansions in Mexico ranged from 0.202 to 0.726 mya.
Conclusions:
Phragmites australis is a native species that has been in Mexico for thousands of years. Genetic data suggest that climatic changes during the Pleistocene played an important role in the demographic expansion of the populations that constitute the different genetic groups of P. australis in Mexico.
Cucurbita are monoecious and creeping plants including 20 taxa and 15 species. In Mesoamerica, four species were domesticated or diversified after domestication in other geographic areas: C. argyrosperma C. pepo, C. moschata, and C. ficifolia. The earliest evidences of the domestication of Cucurbita date 9000 BP from Southwestern Mesoamerica and 10,000 BP from Southwestern Ecuador. The main targets of human selection were the seeds contained in larger and less bitter and toxic fruits (due to cucurbitacins), without vine detachment. C. argyrosperma ssp. sororia from México to Central America warm-humid and subhumid climates is considered the wild ancestor of the domesticated C. argyrosperma ssp. argyrosperma. For C. pepo, the proposed ancestor of the domesticated populations of México is C. pepo ssp. fraterna from northeastern Mexico, while the putative progenitor of the cultivars from in North America is C. pepo ssp. texana from eastern United States. For C moschata, there are two hypotheses as to its domestication region: southern Mesoamerica, or from the lowlands of Colombia and southern Ecuador. Cultivated C. ficifolia is found from the Mexican highlands south to Chile and Argentina, its center of domestication is either Central America or southern Mexico/Central America, as supported by linguistic evidence, or the Andes, as indicated by archaeological evidences from Peru dated at 3000 BC. Humans spread cultivated Cucurbita inside and out of Mesoamerica, structuring a complex agricultural system along with corn (Zea mays), and different species of beans (Phaseolus spp.) called “milpa,” that were established in a wide range of environments.
Oceanic islands are excellent systems for allowing biologists to test evolutionary hypotheses due to their relative simplicity of habitats, naturally replicated study design and high levels of endemic taxa with conspicuous variation in form, colour and behaviour. Over the last two decades the Canary Islands archipelago has proved an ideal system for evolutionary biologists who seek to unravel how biodiversity arises and disappears. In this review we have evaluated the contribution of the study of Canarian birds to our understanding of how and why species occur and change over time. We focus our attention on both extant and extinct Canarian taxa, and describe how research on these species has filled gaps in our understanding of avian speciation and extinction. In addition, we discuss the necessity of revising the current taxonomy in the Canarian avian taxa, especially the status of the endemic subspecies, some of which might be better treated as full species. An accurate classification of Canarian birds is not only necessary for testing evolutionary, biogeographic and ecological hypotheses, but also for effective decision making about conservation and environmental management. Finally we introduce future avenues of research that we feel will yield the most exciting and promising findings on island evolution in the coming years.
Hybrid zones have been promoted as windows on the evolutionary process and as laboratories for studying divergence and speciation. Patterns of divergence between hybridizing species can now be characterized on a genome-wide scale, and recent genome scans have focused on the presence of "islands" of divergence. Patterns of heterogeneous genomic divergence may reflect differential introgression following secondary contact and provide insights into which genome regions contribute to local adaptation, hybrid unfitness, and positive assortative mating. However, heterogeneous genome divergence can also arise in the absence of any gene flow, as a result of variation in selection and recombination across the genome. We suggest that to understand hybrid zone origins and dynamics, it is essential to distinguish between genome regions that are divergent between pure parental populations and regions that show restricted introgression where these populations interact in hybrid zones. The latter, more so than the former, reveal the likely genetic architecture of reproductive isolation. Mosaic hybrid zones, because of their complex structure and multiple contacts, are particularly good subjects for distinguishing primary intergradation from secondary contact. Comparisons among independent hybrid zones or transects that involve the "same" species pair can also help to distinguish between divergence with gene flow and secondary contact. However, data from replicate hybrid zones or replicate transects do not reveal consistent patterns; in a few cases, patterns of introgression are similar across independent transects, but for many taxa, there is distinct lack of concordance, presumably due to variation in environmental context and/or variation in the genetics of the interacting populations. This article is protected by copyright. All rights reserved.
During a recent visit to María Madre Island, in the Tres Marías Island archipelago, 2 specimens of Hypopachus variolosus were found. This new record of the sheep frog from Tres Marías Island archipelago represents the first island record for this species. Due to the uncertainty about its conservation status in this locality, we consider necessary to improve the information about this species in the island.
We present a phylogenetic analysis of relationships among members of the Amazona ochrocephala species complex of parrots, a broadly distributed group in Middle and South America that has been a "taxonomic headache." Mitochondrial DNA sequence data are used to infer phylogenetic relationships among most of the named subspecies in the complex. Sequence-based phylogenies show that Middle American subspecies included in the analysis are reciprocally monophyletic, but subspecies described for South America do not reflect patterns of genetic variation. Samples from the lower Amazon cluster with samples collected in western Amazonia - not with samples from Colombia and Venezuela, as was predicted by subspecies classification. All subspecies of the complex are more closely related to one another than to other Amazona species, and division of the complex into three species (A. ochrocephala, A. auropalliata, and A. oratrix) is not supported by our data. Divergence-date estimates suggest that these parrots arrived in Middle America after the Panama land-bridge formed, and then expanded and diversified rapidly. As in Middle America, diversification of the group in South America occurred during the Pleistocene, possibly driven by changes in distribution of forest habitat.
Cucurbita pepo (pumpkin, squash, gourd) is extremely variable in fruit characteristics. According to recent botanical and cultivated-plant taxonomical treatments that were based on variations in allozymes and fruit shape, C. pepo consists of three subspecies containing wild and cultivated, inedible, small-fruited sorts (gourds) and eight groups of edible, large-fruited cultivars (pumpkins and squash). Our objective was to determine if these treatments reflect genetic relationships as viewed at the DNA level, through the use AFLP, ISSR, and SSR markers. Forty-five accessions were compared for presence or absence of 448 AFLP, 147 ISSR, and 20 SSR bands, their genetic distances (GDs) were estimated, and UPGMA cluster analysis was conducted. Correlation coefficients were 0.95 between AFLPs and ISSRs, 0.78 between AFLPs and SSRs, and 0.77 between ISSRs and SSRs, all three comparisons with P << 0.001. Overall, clustering and sub-clustering were much in accordance with two highly polygenic characteristics, fruit shape and size. Clustering occurred in accordance with subspecies and sub-clustering in accordance with cultivar-groups. Within-group GDs were less than corresponding between-group GDs in nearly all comparisons. The smallest-fruited accession, 'Miniature Ball', occupied a central position within C. pepo.
Cucurbita pepo is extremely diverse in fruit characteristics. Native to semi-arid and temperate regions of North America, C. pepo was domesticated at least twice, in Mexico over 10,000 years ago and in the United States over 4000 years ago. There is no evidence for the existence of Cucurbita in the Old World prior to 1492. Pumpkins and squash of C. pepo are today found in countries on all continents. Pumpkins are valued for their fruit flesh and seeds, as well as for ornament. Squash, especially zucchini, are an increasingly popular, short-season, high-value crop. Plant resource allocation is fundamentally different for plants on which fruits are allowed to mature, the pumpkins and winter squash, as compared with those on which the fruits are continually removed when young, the summer squash. C. pepo contains a wealth of genetic variation that could be further exploited to enhance the fruit-flesh quality of pumpkins and the flavor of summer squash. Genomic tools can be expected to aid in this effort and, especially, facilitate the introgression of disease resistance from other species of Cucurbita. Fruit quality and flavor enhancements of pumpkins and squash have been and are being accomplished largely by the consumer-oriented breeders at research and academic institutions. However, lack of support for these breeding programs is jeopardizing the continued consumer-oriented fruit-quality enhancement of C. pepo germplasm.
Significance
Squashes, pumpkins, and gourds belonging to the genus Cucurbita were domesticated on several occasions throughout the Americas, beginning around 10,000 years ago. The wild forms of these species are unpalatably bitter to humans and other extant mammals, but their seeds are present in mastodon dung deposits, demonstrating that they may have been dispersed by large-bodied herbivores undeterred by their bitterness. However, Cucurbita may have been poorly adapted to a landscape lacking these large dispersal partners. Our study proposes a link between the disappearance of megafaunal mammals from the landscape, the decline of wild Cucurbita populations, and, ultimately, the evolution of domesticated Cucurbita alongside human cultivators.
Molecular estimates of evolutionary timescales have an important role in a range of biological studies. Such estimates can be made using methods based on molecular clocks, including models that are able to account for rate variation across lineages. All clock models share a dependence on calibrations, which enable estimates to be given in absolute time units. There are many available methods for incorporating fossil calibrations, but geological and climatic data can also provide useful calibrations for molecular clocks. However, a number of strong assumptions need to be made when using these biogeographic calibrations, leading to wide variation in their reliability and precision. In this review, we describe the nature of biogeographic calibrations and the assumptions that they involve. We present an overview of the different geological and climatic events that can provide informative calibrations, and explain how such temporal information can be incorporated into dating analyses.
© 2015 The Author(s).
Global climate fluctuations have significantly influenced the distribution and abundance of biodiversity [1]. During unfavorable glacial periods, many species experienced range contraction and fragmentation, expanding again during interglacials [2-4]. An understanding of the evolutionary consequences of both historical and ongoing climate changes requires knowledge of the temporal dynamics of population numbers during such climate cycles. Variation in abundance should have left clear signatures in the patterns of intraspecific genetic variation in extant species, from which historical effective population sizes (Ne) can be estimated [3]. We analyzed whole-genome sequences of 38 avian species in a pairwise sequentially Markovian coalescent (PSMC, [5]) framework to quantitatively reveal changes in Ne from approximately 10 million to 10 thousand years ago. Significant fluctuations in Ne over time were evident for most species. The most pronounced pattern observed in many species was a severe reduction in Ne coinciding with the beginning of the last glacial period (LGP). Among species, Ne varied by at least three orders of magnitude, exceeding 1 million in the most abundant species. Several species on the IUCN Red List of Threatened Species showed long-term reduction in population size, predating recent declines. We conclude that cycles of population expansions and contractions have been a common feature of many bird species during the Quaternary period, likely coinciding with climate cycles. Population size reduction should have increased the risk of extinction but may also have promoted speciation. Species that have experienced long-term declines may be especially vulnerable to recent anthropogenic threats.
Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.
Following an isolation gradient in West-Mexico the avifauna of three study areas is investigated, on mainland reserve and two island groups. The avifaunas are described and analysed regarding species richness, environmental attributes, ende-mism, broader ecological niches, and brood status. The taxonomical composition is determined on different hierarchy levels. Most species records come from mainland Chamela (262), followed by the coastal Marias (191) and the oceanic Revilla-gigedos (148). Thereof 139 bird species breed in Chamela, 61 on Marias and only 29 on the Revillagigedos. In total, in the three study areas 364 species were recorded, which belong to 22 orders. On island groups generally less taxa per hierarchy level are present than on the mainland, especially on the remote Revillagigedos. Here, on average 1.7 species are found per genus, 2.2 genera per family, and 2.5 families per order. In the analysis of the taxonomical hierarchy relations to each other an isolation gradient is identified: from mainland Chamela via the coastal Marias to the oceanic Revillagigedos the degree of relatedness decreases on average. The results support the theoretical hypothesis that on islands closely related taxa tend to exclude each other and that one generalist tends to replace several specialists. Small ecological niches are often not occupied by specialist species on islands, but are used by generalists.
Cucurbita pepo is a highly diverse, economically important member of the Cucurbitaceae. C. pepo encompasses hundreds of cultivars of pumpkins, squash, and gourds. Although C. pepo has been scrutinized with various types of DNA markers, the relationships among the cultivar-groups of C. pepo subsp. pepo, the more widely grown subspecies, have not heretofore been adequately resolved. We assessed genetic relationships among 68 accessions of Cucurbita pepo, including 48 from C. pepo subsp. pepo, using polymorphisms in 539 high frequency oligonucleotide–targeting active gene (HFO–TAG) fragments, that preferably represent coding regions of the genome. Dissimilarities among accessions were calculated, a dendrogram was constructed, and principal component analyses were conducted. Dissimilarities demarcated the four edible-fruited cultivar-groups of C. pepo subsp. pepo, Cocozelle, Pumpkin, Vegetable Marrow, and Zucchini. Furthermore, the results indicate that the Old World pumpkins as well as the long-fruited cultivar-groups of C. pepo subsp. pepo (cocozelle, vegetable marrow, and zucchini) evolved from spontaneous crossing and gene exchange between pumpkins derived from northern North America and pumpkins derived from southern North America. Consistent with pictorial and narrative historical records, such crossing appears to have occurred in Renaissance Europe within the first decades of the European contact with North America. The Old World pumpkins are more closely related to the long-fruited cultivar-groups than are the native North American pumpkins.
In this paper, we take a closer look into the evolution of Acrocephalus warblers on islands in the Atlantic, Indian and Pacific Oceans. The shape‐related morphological evolution of island species is characterized by changes in the hind limb, flight, and feeding apparatus. Birds on islands converged to a morphology with strong legs, shorter rictal bristles, and rounder, more slotted and broader wings. Because of their high variance among islands, body size and bill dimensions did not contribute to the separation of continental and island forms, although bills tend to be longer on islands. The wings of island birds hardly vary among islands, unsurprisingly due to a lack of the adaptive features associated with long distance flights. The tendency towards shorter rictal bristles in the island warblers can be explained by the diminished role of aerial feeding, and closer contact with various substrates in the course of extractive foraging. The shift towards stronger legs in several insular species is remarkable because reed warblers on continents have even stronger legs than other passerines of comparable size. This trait correlates with diverse, acrobatic feeding techniques that are typically associated with broad habitat use. Bills reach extreme lengths on some islands. However, short bills occur as frequently, rendering this character highly variable among islands. Short bills indicate gleaning feeding techniques, whereas long bills are typical for species that pursue hidden and difficult‐to‐access prey. Body sizes differ greatly from island to island. On average, the sizes of island birds do not differ from continental ones, however. We suggest that vegetation clutter is the major driving force for this variation.
The main conclusion following from our results is that evolution on islands pertains to all functional complexes, and not only the hitherto studied body size and bill dimensions.
Cucurbita pepo belongs to the genus Cucurbita with 22 taxa commonly known as
"pumpkins". Cucurbita is the species with the highest economic and cultural importance in the world. It is part of the Mexican “milpa” and it is a plant genetic resource. Mesoamerica is its center of origin and domestication. Cucurbita pepo has three recognized subspecies. The
subspecies fraterna, texana, which includes var. ovifera and var. ozarkana and finally the
domesticated pepo, which is cultivated worldwide. The aim of the present study is to increase our knowledge on the evolutionary history of C. pepo, through a phylogeographic approach. DNA was extracted from the three subspecies and five commercial varieties and archaeological sequences obtained from the literature of these subsp. With a total of 338 accessions, two chloroplast regions (psbD-trnT, psbJ-petA), and one region of the mitochondria trnL-trnF were amplified. We found 11 total haplotypes, with a single haplotype shared between the subsp. pepo and fraterna. The highest variation is found in in the wild taxon subspecie. fraterna Hd = 0.512 and π =0.00006, while the domesticated taxon subsp. pepo showed lower genetic variation Hd = 0.305 and π =0.00065. In contrast, in the trnL-F marker we found very low genetic variation with a total of Hd = 0.142 and π = 0.00108. Most genetic diversity and genetic pools were found in the central-western area of our country, which suggest that the center of diversification of this species may be found in this area. The time of divergence between the two lineages that constitute C. pepo, one endemic to the USA (subsp. texana) and another endemic to Mexico (subsp. pepo and fraterna), was 1.54 Ma (0.18- 6.43 95% HDP), which supports the existence of two independent domestication events.
Aim
We sought to assess different megafaunal species responses to the intense climatic changes that characterized the end of the Quaternary.
Location
Eurasia.
Methods
We used species distribution modelling, niche overlap tests and co‐occurrence analysis to model climatic niche evolution and change in six different megafauna species, including three extinct (woolly mammoth, woolly rhino and steppe bison) and three extant (red deer, wolf and reindeer) species.
Results
Co‐occurrence analysis indicates mammoth, rhino, reindeer and steppe bison to be significantly associated to each other in the fossil record in cold, arid environments. In contrast, red deer and wolf show no evidence for strong habitat requirements, although they both tended to be associated with more humid conditions than the other megafauna. Woolly mammoth and the woolly rhino were the best adapted to the cold, arid conditions dominating the Eurasian landscapes during the Last Glacial Maximum ( LGM ). Extant species did not exhibit larger climatic niches than extinct species, but changed more from one period to the next than those of extinct species.
Main conclusions
Although they did not have wider climatic niches, and were the least adapted to cold climates, red deer and the wolf were able to withstand the harsh climatic conditions of the LGM . Conversely, the now extinct mammoth and woolly rhino did not survive the demise of the LGM environment. Although “cold‐adapted”, reindeer survived the LGM by occupying a northerly distribution similar to today. Independent evidence indicates the steppe bison lineage might have survived in North America. Our data are consistent with a strong climatic control on the fate of late Quaternary megafauna species in Eurasia. We were unable to exclude a sizeable effect of human intervention by overhunting.
Allopatric divergence following the formation of geographical features has been implicated as a major driver of evolutionary diversification. Widespread species complexes provide opportunities to examine allopatric divergence across varying degrees of isolation in both time and space. In North America, several geographical features may play such a role in diversification, including the Mississippi River, Pecos River, Rocky Mountains, Cochise Filter Barrier, Gulf of California, and Isthmus of Tehuantepec. We used thousands of nuclear single nucleotide polymorphisms (SNPs) and mitochondrial DNA from several species of whipsnakes (genera Masticophis and Coluber) distributed across North and Central America to investigate the role that these geographical features have played on lineage divergence. We hypothesize that these features restrict gene flow and separate whipsnakes into diagnosable genomic clusters. We performed genomic clustering and phylogenetic reconstructions at the species and population levels using Bayesian and likelihood analyses, and quantified migration levels across geographical features to assess the degree of genetic isolation due to allopatry. Our analyses suggest that (i) major genetic divisions are often consistent with isolation by geographical features, (ii) migration rates between clusters are asymmetrical across major geographical features, and (iii) areas that receive proportionally more migrants possess higher levels of genetic diversity. Collectively, our findings suggest that multiple features of the North American landscape contributed to allopatric divergence in this widely-distributed snake group. This article is protected by copyright. All rights reserved.
Populations of common mynas introduced to Australia, New Zealand, Fiji, Hawaii, and South Africa from India during the last century were compared genetically with the extant native population using isozyme electrophoresis of 39 presumptive loci. Average heterozygosity, mean number of alleles/locus, and the percentage of polymorphic loci are lower in the introduced populations, and the 18% loss of alleles involves only alleles that are rare in the native population. The native population is only weakly subdivided genetically (FST = 0.032) whereas the introduced populations are much more differentiated (FST = 0.123), and the mean genetic distance among them is significantly greater than among native samples. The reduction in mean number of alleles/locus and average heterozygosity is greatest in the South African population, consistent with a very small effective size in the founder population. In the introduced populations, random drift is implicated by the different subsets of polymorphic loci they possess, by their greater variance in allele frequencies, and by shifts either side of the native means. It is concluded that in the evolutionarily short period of 100-120 years, bottlenecks and random drift have promoted genetic shifts equal to those between different subspecies of birds.
Episodes of population growth and decline leave characteristic signatures in the distribution of nucleotide (or restriction) site differences between pairs of individuals. These signatures appear in histograms showing the relative frequencies of pairs of individuals who differ by i sites, where i = 0, 1, .... In this distribution an episode of growth generates a wave that travels to the right, traversing 1 unit of the horizontal axis in each 1/2u generations, where u is the mutation rate. The smaller the initial population, the steeper will be the leading face of the wave. The larger the increase in population size, the smaller will be the distribution's vertical intercept. The implications of continued exponential growth are indistinguishable from those of a sudden burst of population growth Bottlenecks in population size also generate waves similar to those produced by a sudden expansion, but with elevated uppertail probabilities. Reductions in population size initially generate L-shaped distributions with high probability of identity, but these converge rapidly to a new equilibrium. In equilibrium populations the theoretical curves are free of waves. However, computer simulations of such populations generate empirical distributions with many peaks and little resemblance to the theory. On the other hand, agreement is better in the transient (nonequilibrium) case, where simulated empirical distributions typically exhibit waves very similar to those predicted by theory. Thus, waves in empirical distributions may be rich in information about the history of population dynamics.
Phylogenetics can facilitate the study of plant domestication by resolving sister relationships between crops and their wild relatives, thereby identifying the ancestors of cultivated plants. Previous phylogenetic studies of the six Cucurbita crop lineages (pumpkins and squashes) and their wild relatives suggest histories of deep coalescence that complicate uncovering the genetic origins of the six crop taxa. We investigated the evolution of wild and domesticated Cucurbita using the most comprehensive and robust molecular-based phylogeny for Cucurbita to date based on 44 loci derived from introns of single-copy nuclear genes. We discovered novel relationships among Cucurbita species and recovered the first Cucurbita tree with well-supported resolution within species. Cucurbita comprises a clade of mesophytic annual species that includes all six crop taxa and a grade of xerophytic perennial species that represent the ancestral xerophytic habit of the genus. Based on phylogenetic resolution within-species we hypothesize that the magnitude of domestication bottlenecks varies among Cucurbita crop lineages. Our phylogeny clarifies how wild Cucurbita species are related to the domesticated taxa. We find close relationships between two wild species and crop lineages not previously identified. Expanded geographic sampling of key wild species is needed for improved understanding of the evolution of domesticated Cucurbita.
We investigate a neutral model for speciation and extinction, the constant rate birth-death process. The process is conditioned to have n extant species today, we look at the tree distribution of the reconstructed trees-- i.e. the trees without the extinct species. Whereas the tree shape distribution is well-known and actually the same as under the pure birth process, no analytic results for the speciation times were known. We provide the distribution for the speciation times and calculate the expectations analytically. This characterizes the reconstructed trees completely. We will show how the results can be used to date phylogenies.
At a time when historical biogeography appears to be again expanding its scope after a period of focusing primarily on discerning area relationships using cladograms, new inference methods are needed to bring more kinds of data to bear on questions about the geographic history of lineages. Here we describe a likelihood framework for inferring the evolution of geographic range on phylogenies that models lineage dispersal and local extinction in a set of discrete areas as stochastic events in continuous time. Unlike existing methods for estimating ancestral areas, such as dispersal-vicariance analysis, this approach incorporates information on the timing of both lineage divergences and the availability of connections between areas (dispersal routes). Monte Carlo methods are used to estimate branch-specific transition probabilities for geographic ranges, enabling the likelihood of the data (observed species distributions) to be evaluated for a given phylogeny and parameterized paleogeographic model. We demonstrate how the method can be used to address two biogeographic questions: What were the ancestral geographic ranges on a phylogenetic tree? How were those ancestral ranges affected by speciation and inherited by the daughter lineages at cladogenesis events? For illustration we use hypothetical examples and an analysis of a Northern Hemisphere plant clade (Cercis), comparing and contrasting inferences to those obtained from dispersal-vicariance analysis. Although the particular model we implement is somewhat simplistic, the framework itself is flexible and could readily be modified to incorporate additional sources of information and also be extended to address other aspects of historical biogeography.
This book had its origin when, about five years ago, an ecologist (MacArthur) and a taxonomist and zoogeographer (Wilson) began a dialogue about common interests in biogeography. The ideas and the language of the two specialties seemed initially so different as to cast doubt on the usefulness of the endeavor. But we had faith in the ultimate unity of population biology, and this book is the result. Now we both call ourselves biogeographers and are unable to see any real distinction between biogeography and ecology.
The Rufous-backed Robin (Turdus rufopalliatus) is endemic to deciduous and semideciduous tropical forests of western Mexico. Of the currently recognized subspecies, T. r. graysoni, from the Tres Marías Islands and nearby coastal Nayarit, has been considered a separate species; however, this treatment has been challenged due to an apparent contact zone on the mainland, although no hybrids have ever been recorded. Here, we use mitochondrial DNA sequences from individuals sampled across the species' range to assess their phylogeographic relationships. We found reciprocal monophyly between Tres Marías Islands and mainland populations, which share no haplotypes between them. Evolutionary divergence detected within T. rufopalliatus suggests that mainland and island populations have been isolated from each other, and divergence decreases if insular populations are excluded. Demographic parameters suggest that populations are in the process of a rapid expansion from ancestral populations with a lower population size. These results are consistent with morphometric and plumage differences that have been used to recognize the Tres Marías Islands populations from the mainland ones, thus suggesting species status of the island form.
The hypothesis that endemic species could have originated by the isolation and divergence of peripheral populations of widespread species can be tested through the use of ecological niche models (ENMs) and statistical phylogeography. The joint use of these tools provides complementary perspectives on historical dynamics and allows testing hypotheses regarding the origin of endemic taxa. We used this approach to infer the historical processes that have influenced the origin of a species endemic to the Mexican Plateau (Cynomys mexicanus) and its divergence from a widespread ancestor (Cynomys ludovicianus), and to test whether this endemic species originated through peripatric speciation. We obtained genetic data for 295 individuals for two species of black-tailed prairie dogs (C. ludovicianus and C. mexicanus). Genetic data consisted of mitochondrial DNA sequences (cytochrome b and control region), and 10 nuclear microsatellite loci. We estimated dates of divergence between species and between lineages within each species and performed ecological niche modelling (Present, Last Glacial Maximum and Last Interglacial) to determine changes in the distribution range of both species during the Pleistocene. Finally, we used Bayesian inference methods (DIYABC) to test different hypotheses regarding the divergence and demographic history of these species. Data supported the hypothesis of the origin of C. mexicanus from a peripheral population isolated during the Pleistocene [∼230,000 years ago (0.1 – 0.43 Ma 95% HPD)], with a Pleistocene-Holocene (∼9,000 − 11,000 years ago) population expansion (∼10-fold increase in population size). We identified the presence of two possible refugia in the southern area of the distribution range of C. ludovicianus and another, consistent with the distribution range of C. mexicanus. Our analyses suggest that Pleistocene climate change had a strong impact in the distribution of these species, promoting peripatric speciation for the origin of C. mexicanus and lineage divergence within C. ludovicianus.
At the end of the Cretaceous there was a possibility for relatively direct floristic interchange between South America and tropical North America via island hopping along the proto- Antilles. Uplift of the Andes, mostly in Neogene time, led to an incredible burst of speciation in a number of Gondwanan families. A similar evolutionary explosion in the same taxa also took place in Costa Rica and Panama. The taxonomic groups that have undergone this evolutionary explosion have distributional centers in the N Andean region and S Central America, are poorly represented in Amazonia, and consist mostly of epiphytes, shrubs, and palmettos; their pollination systems suggest that coevolutionary relationships with hummingbirds, nectar-feeding bats, and perhaps such specialized bees as euglossines, have played a prominent role in their evolution. The evolutionary phenomena associated with the Andean uplift account for almost half of the total Neotropical flora and are thus largely responsible for the excess floristic richness of the Neotropics. Closing of the Panamanian isthmus in the Pliocene led to 1) southward migration of some Laurasian taxa into the Andes where they have become ecologically dominant despite undergoing little speciation, at least in woody taxa, and 2) northward invasion of lowland Gondwanan taxa of canopy trees and lianas into Central America, leading to their ecological dominance in lowland tropical forests throughout the region, despite little significant speciation in Central America.-from Author
Aim
(1) To synthesize data on the physical and phylogeographical history of the Mexican highlands, with a focus on the Trans-Mexican Volcanic Belt (TMVB), and (2) to propose approaches and analyses needed for examining the interaction of climate and volcanism.
Location
Mexico.
Methods
We performed a literature and data survey of the climatic, geological and phylogeographical history of the Mexican highlands. We then assessed how the expected effects of topographic isolation, co-occurring palaeoclimatic fluctuations and volcanism can be tested against the distribution of genetic diversity of high-elevation taxa.
Results
The Mexican highlands present a complex biogeographical, climatic and geological history. Montane taxa have been exposed to a sky-island dynamic through climate fluctuations, allowing for long-term in situ population persistence, while also promoting recent divergence and speciation events. Volcanic activity transformed part of the Mexican highlands during the Pleistocene, mainly in the TMVB, leading to co-occurring climate and topographical changes. The TMVB highlands provide a suitable template to examine how low-latitude mountains can facilitate both the long-term persistence of biodiversity as well as allopatric and parapatric speciation driven by climatic and geological events.
Main conclusions
Climate fluctuations, together with recent volcanism, have driven the diversification and local persistence of biodiversity within the Mexican highlands. The climate–volcanism interaction is challenging to study; however, this can be overcome by coupling genomic data with landscape analyses that integrate the geological and climatic history of the region.
THE bird life of the Tres Marias Islands, off the west coast of Mexico, has been of interest to ornithologists since the time it was first brought to their attention by Andrew Jackson Grayson in 1865. Known historically since early in the 16th century, the islands were visited by early maritime explorers and served as a base for buccaneers operating along the Pacific coast of Mexico. In spite of this long period of contact by seafaring men, the islands even today are rather poorly charted and there exists a great deal of erroneous information regarding the immediate waters surrounding this insular chain.