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209 results for “Biogeographic history”

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zenodo36/100

An exploration of the complex biogeographical history of the Neotropical banner-wing damselflies (Odonata: Polythoridae)

Here you will find .zip files for all the Time divergence and Biogeographical Analyses for the paper.  Within each you will fine a README file with the explanation for each file. Time Divergence BEAST_2020_05.zip Biogeographical BioGeo_2020_05.zip                             RASP_2020_05.zip

opencc-by-4.0Dec 2019View details →

dryad36/100

Data from: Bayesian estimation of the global biogeographical history of the Solanaceae

Aim: The tomato family Solanaceae is distributed on all major continents except Antarctica and has its centre of diversity in South America. Its worldwide distribution suggests multiple long-distance dispersals within and between the New and Old Worlds. Here, we apply maximum likelihood (ML) methods and newly developed biogeographical stochastic mapping (BSM) to infer the ancestral range of the family and to estimate the frequency of dispersal and vicariance events resulting in its present-day distribution. Location: Worldwide. Methods: Building on a recently inferred megaphylogeny of Solanaceae, we conducted ML model fitting of a range of biogeographical models with the program 'BioGeoBEARS'. We used the parameters from the best fitting model to estimate ancestral range probabilities and conduct stochastic mapping, from which we estimated the number and type of biogeographical events. Results: Our best model supported South America as the ancestral area for the Solanaceae and its major clades. The BSM analyses showed that dispersal events, particularly range expansions, are the principal mode by which members of the family have spread beyond South America. Main conclusions: For Solanaceae, South America is not only the family's current centre of diversity but also its ancestral range, and dispersal was the principal driver of range evolution. The most common dispersal patterns involved range expansions from South America into North and Central America, while dispersal in the reverse direction was less common. This directionality may be due to the early build-up of species richness in South America, resulting in large pool of potential migrants. These results demonstrate the utility of BSM not only for estimating ancestral ranges but also in inferring the frequency, direction and timing of biogeographical events in a statistically rigorous framework.

opencc-zeroDec 2015View details →

dryad36/100

Palaearctic origin and repeated dispersal over the world shaped the biogeographic history of the saprophytic genus Coprinopsis (Psathyrellaceae, Basidiomycota)

Aim: The biogeographic history of most fungi is still poorly known, as well as the patterns and processes responsible for their diversification. Recent studies uncovered that most fungi have originated and present higher diversification rates in the temperate zone. The distributional pattern known for fungi is also different from many plants, animals and microbes. Using the most comprehensive phylogeny of the saprotrophic genus Coprinopsis, we aim to infer the biogeographic history and test evolutionary hypotheses in the genus. Location: Worldwide Taxon: Fungi, Basidiomycota, Psathyrellaceae, Coprinopsis Methods: We used a four-gene alignment with 100 species to estimate divergence times using two fossil calibrations within Agaricales. The chronograms were used to estimate diversification rates and geographic state-dependent models were applied. We further reconstructed the ancestral range history of the genus. Results: Molecular dating estimated that the genus has diverged ca. 41 Ma (Eocene) and originated in the Palaearctic region. Diversification rates showed a decreasing pattern towards the present across Coprinopsis, especially after the Miocene (ca. 14 Ma). The diversification models dependent on distribution showed cosmopolitan lineages with higher net-diversification rates. When we compared temperate and tropical regions, we found that temperate lineages have higher net-diversification rates. The biogeographic history of Coprinopsis estimated different routes of dispersal. The most common dispersal route was from the Palaearctic to the Nearctic (15 times), followed by the Palaeartic to the Neotropics (14 times). Main Conclusions: The study is the first to estimate the diversification rates and the historical biogeography of the coprinoid genus Coprinopsis. The diversification dynamics estimates in Coprinopsis are in agreement with the "generalized diversification rates model", where we found higher diversification rates in temperate regions compared to tropical regions. In general, the ancestral area and major dispersal routes recovered in the genus are similar to findings in other groups of fungi.

opencc-zeroJan 2024View details →

zenodo36/100

Figure 1 in An update on the phylogeny and biogeographical history of Rhipicephalus sanguineus complex

Figure 1. Map of collecting sites. (The map was generated using QGIS 3.22.2 software.)

opencc-by-4.0Dec 2023View details →

dryad36/100

Biogeographic history of pigeons and doves drives the origin and diversification of their parasitic body lice

Despite their extensive diversity and ecological importance, the history of diversification for most groups of parasitic organisms remains relatively understudied. Elucidating broad macroevolutionary patterns of parasites is challenging, often limited by the availability of samples, genetic resources, and knowledge about ecological relationships with their hosts. In this study, we explore the macroevolutionary history of parasites by focusing on parasitic body lice from doves. Building on extensive knowledge of ecological relationships and previous phylogenomic studies of their avian hosts, we tested specific questions about the evolutionary origins of the body lice of doves, leveraging whole genome data sets for phylogenomics. Specifically, we sequenced whole genomes from 68 samples of dove body lice, including representatives of all body louse genera from 51 host taxa. From these data, we assembled >2,300 nuclear genes to estimate dated phylogenetic relationships among body lice and several outgroup taxa. The resulting phylogeny of body lice was well supported, although some branches had conflicting signal across the genome. We then reconstructed ancestral biogeographic ranges of body lice and compared the body louse phylogeny to phylogeny of doves, and also to a previously published phylogeny of the wing lice of doves. Divergence estimates placed the origin of body lice in the late Oligocene. Body lice likely originated in Australasia and dispersed with their hosts during the early Miocene, with subsequent codivergence and host switching throughout the world. Notably, this evolutionary history is very similar to that of dove wing lice, despite the stronger dispersal capabilities of wing lice compared to body lice. Our results highlight the central role of the biogeographic history of host organisms in driving the evolutionary history of their parasites across time and geographic space.

opencc-zeroJul 2024View details →

zenodo36/100

Figure 1 in Phylogenetic relationships and biogeographical history of the genus Rhinoclemmys Fitzinger, 1835 and the monophyly of the turtle family Geoemydidae (Testudines: Testudinoidea)

Figure 1. Distribution of the family Geoemydidae (data compiled from Iverson, 1992).

opencc-by-4.0Aug 2008View details →

dryad36/100

The missing link in biogeographic reconstruction: Accounting for lineage extinction rewrites history

Aim In the most widely used family of methods for ancestral range estimation (ARE), dispersal, speciation and extirpation events are estimated from information on extant lineages. However, this approach fails to consider the geographic distribution of extinct species and their position on the phylogenetic tree, an omission that could compromise reconstruction. Here, we present a method that models the geographic distribution of extinct species and we quantify the potential inaccuracy in ancestral range estimation when extinction rates are above zero. Location Global applications, with an example from the Americas. Taxon All taxa, with an example from hummingbirds (Amazilia). Methods Methods capable of explicitly modelling extinct branches along with their reconstructed geographic information (GeoSSE) have been overlooked in ARE analysis, perhaps due to the inherent complexity of implementation. We develop a user-friendly platform, which we term LEMAD (Lineage Extinction Model of Ancestral Distribution) that generalizes the likelihood described in GeoSSE for any number of areas and under several sets of geographic assumptions. We compare LEMAD and extinction-free approaches using extensive simulations under different macroevolutionary scenarios. We apply our method to revisit the historical biogeography of Amazilia hummingbirds. Results We find that accounting for the lineages removed from a tree by extinction improves reconstructions of ancestral distributions, especially when rates of vicariant speciation are higher than rates of in situ speciation, and when rates of extinction and range evolution are high. Rates of in situ and vicariant speciation are accurately estimated by LEMAD in all scenarios. North America as the most likely region for the common ancestor of hummingbirds. Main conclusions Methods that neglect lineage extinction are less likely to accurately reconstruct true biogeographic histories of extant clades. Our findings on an empirical dataset reconcile the Eurasian origin of Amazilia with biogeographic reconstructions when lineage extinction is considered.

opencc-zeroDec 2022View details →

dryad36/100

Data from: Ultraconserved elements improve resolution of marmot phylogeny and offer insights into biogeographic history

Marmots (Marmota spp.) comprise a lineage of large-bodied ground squirrels that diversified rapidly in the Pleistocene, when the planet quickly transitioned to a drier, colder, and highly seasonal climate—particularly at high latitudes. Fossil evidence indicates the genus spread from North America, across Beringia, and into the European Alps over the course of only a few million years, beginning in the late Pliocene. Marmots are highly adapted to survive long and severely cold winters, and this likely favored their expansion and diversification over this time period. Previous phylogenetic studies have identified two major subgenera of marmots, but the timing of important speciation events and some species relationships have been difficult to resolve. Here we use ultraconserved elements and mitogenomes, with samples from all 15 extant species, to more precisely retrace how and when marmots came to inhabit a vast Holarctic range. Our results indicate marmots arose in North America in the mid Miocene (~16.3 Mya) and dispersed across the Bering Land Bridge in the late Pliocene (~3-4 Mya); in addition, our fossil-calibrated timeline is suggestive of the rise and spread of open grasslands as being particularly important to marmot diversification. The woodchuck (M. monax) and the Alaska marmot (M. broweri) are found to be more closely related to the Eurasian species than to the other North American species. Paraphyly is evident in the bobak marmot (M. bobak) and the hoary marmot (M. caligata), and in the case of the latter the data are highly suggestive of a second, cryptic species in the Cascade Mountains of Washington.

opencc-zeroMar 2023View details →

dryad36/100

Phylogenomic conflict analyses in the apple genus Malus s.l. reveal widespread hybridization and allopolyploidy driving diversification, with insights into the complex biogeographic history in the Northern Hemisphere

Phylogenomic evidence from an increasing number of studies has demonstrated that different data sets and analytical approaches often reconstruct strongly supported but conflicting relationships. In this study, 785 single-copy nuclear genes and 75 complete plastomes were used to infer the phylogenetic relationships and estimate the historical biogeography of the apple genus Malus sensu lato, an economically important lineage disjunctly distributed in the Northern Hemisphere and involved in known and suspected hybridization and allopolyploidy events. The nuclear phylogeny recovered the monophyly of Malus s.l. (including Docynia); however, the genus was supported to be biphyletic in the plastid phylogeny. An ancient chloroplast capture event in the Eocene in western North America best explains the cytonuclear discordance. Our conflict analysis demonstrated that ILS, hybridization, and allopolyploidy could explain the widespread nuclear gene tree discordance. One deep hybridization event (Malus doumeri) and one recent event (Malus coronaria) were detected in Malus s.l. Furthermore, our historical biogeographic analysis integrating living and fossil data supported a widespread East Asian-western North American origin of Malus s.l. in the Eocene, followed by several extinction and dispersal events in the Northern Hemisphere. We also propose a general workflow for assessing phylogenomic discordance and biogeographic analysis using deep genome skimming datasets.

opencc-zeroMay 2023View details →

dryad36/100

Biogeographic barriers and historical climate affect phylogeographic structure and demographic history of the common gartersnake

Aim: Current distributions of widespread North American (NA) species have been shaped by Pleistocene glacial cycles, latitudinal temperature gradients, sharp longitudinal habitat transitions, and the vicariant effects of major mountain and river systems that subdivide the continent. Within these transcontinental species, genetic diversity patterns might not conform to established biogeographic breaks compared to more spatially restricted taxa due to intrinsic differences (e.g., greater dispersal ability in generalist species) or spatiotemporal differences (e.g., wide-ranging species predate younger barriers). In this study, we highlight the effects of these extrinsic variables on genetic structuring by investigating the phylogeographic history of a widespread generalist squamate found throughout NA. Location: North America Taxon: Common gartersnake, Thamnophis sirtalis Methods: We evaluate the effects of major river basins and the forest-grassland transition into the Interior Plains on genetic structure patterns using phylogenetic, spatially informed population structure, and demographic analyses of SNP data, and address range expansion history with ecological niche modeling using locality and historic climate data. Results: We identify four phylogeographic lineages with varying degrees of connectivity between them. We find discordant population structure patterns between sex-linked and autosomal loci with respect to the relationship between the central NA lineage relative to coastal lineages. We find support for southeast Pleistocene refugia where recent secondary contact occurred during the Last Glacial Maximum and evidence for both northern and southern refugia in western NA. Main Conclusion: Our results provide strong evidence for a Middle Pliocene origin for Thamnophis sirtalis in central-southeastern NA preceding its rapid expansion across the continent prior to middle Pleistocene climate-mediated lineage formation. We implicate major riverine networks within the Mississippi watershed in likely repeated westward expansion events across the Interior Plains. Finally, we corroborate prior conclusions that phenotypic differences between subspecies do not reflect shared evolutionary history and note that the degree of separation between inferred lineages warrants further investigation before any taxonomic revisions are proposed.

opencc-zeroAug 2023View details →

dryad36/100