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209 results for “Biogeographic history”
Data from: Multiple genomic ancestries in the broom hare mark the complex biogeographic history of hares in the Iberian Peninsula
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Genetic structure and biogeographic history of the Bicknell's Thrush/ Gray-cheeked Thrush species complex
Abstract We examined species limits, admixture, and genetic structure among populations in the Bicknell's Thrush (Catharus bicknelli)–Gray-cheeked Thrush (C. minimus) species complex to establish the geographic and temporal context of speciation in this group, which is a model system in ecology and a high conservation priority. We obtained mitochondrial ND2 sequences from 186 Bicknell's Thrushes, 77 Gray-cheeked Thrushes, and 55 individuals of their closest relative, the Veery (C. fuscescens), and genotyped a subset of individuals (n = 72) at 5,633 anonymous single nucleotide polymorphic (SNP) loci. Between-species sequence divergence was an order of magnitude greater than divergence within each species, divergence was dated to the late Pleistocene (420 kbp) based on Bayesian coalescence estimation, and a coalescent model (IMa) revealed almost no gene flow between species based on ND2. SNP data were consistent with mitochondrial results and revealed low levels of admixture among species (3 of 37 Bicknell's Thrushes, no Gray-cheeked Thrushes, and no Veeries were >2% admixed). Species distribution models projected to the Last Glacial Maximum suggest that Bicknell's Thrush and Gray-cheeked Thrush resided in primarily allopatric refugia in the late Pleistocene, consistent with the genetic data that support reproductive isolation over an extended period of time. Our genetic data suggest that both species underwent demographic expansions, possibly as they expanded out of Pleistocene refugia into their current ranges. We conclude that Bicknell's Thrush and Gray-cheeked Thrush are 2 distinct species-level lineages despite low levels of Gray-cheeked Thrush introgression in Bicknell's Thrushes, and divergence has been maintained by a long history of allopatry in subtly different habitats. Their unique phylogeography among boreal forest birds indicates that either cryptic species breaks in eastern North America are still undiscovered, or another factor, such as divergent natural selection, high migratory connectivity, or interspecific competition, played a role in their divergence.
Phylogenomic analysis of ultraconserved elements resolves the evolutionary and biogeographic history of Segmented Trapdoor Spiders
<p>The segmented trapdoor spiders (Liphistiidae) are the sole surviving family of the suborder Mesothelae, which forms the sister lineage to all other living spiders. Liphistiids have retained a number of plesiomorphic traits and their present-day distribution is limited to East and Southeast Asia. Studying this group has the potential to shed light on the deep evolutionary history of spiders, but the phylogeny and divergence times of the family have not been resolved with confidence. We performed phylogenomic and molecular dating analyses of 2,765 ultraconserved element loci from 185 liphistiid taxa. Our analyses show that the crown group of Liphistiidae appeared in the mid-Cretaceous at 102 Ma (95% credibility interval 92–113 Ma), but it was not until the Neogene that much of the diversification within the family occurred in mainland Southeast and East Asia. This diversification was coincident with tectonic events such as the extension of the East Asian continental margin, as well as geological upheavals in Indochina induced by the collision between India and Asia. Our study highlights the important role of major tectonic events in shaping the evolutionary history, present-day diversity, and geographical distribution of mesothele and liphistiid spiders.</p>
Data from: Crossing the uncrossable: novel trans-valley biogeographic patterns revealed in the genetic history of low dispersal mygalomorph spiders (Antrodiaetidae, Antrodiaetus) from California
Antrodiaetus riversi is a dispersal-limited, habitat specialized mygalomorph spider species endemic to mesic woodlands of northern and central California. Here we build upon prior phylogeographic research using a much larger geographic sample and include additional nuclear genes, providing more detailed biogeographic insights throughout the range of this complex. Of particular interest is the uncovering of unexpected and replicated trans-valley biogeographic patterns, where in two separate genetic clades western haplotypes in the California south Coast Ranges are phylogenetically closely-related to eastern haplotypes from central and northern Sierran foothills. In both instances, these trans-valley phylogenetic patterns are strongly supported by multiple genes. These western and eastern populations are currently separated by the Central Valley, a well-recognized modern-day and historical biogeographic barrier in California. For one clade the directionality is clearly northeast to southwest, and all available evidence is consistent with a jump dispersal event estimated at 1.2-1.3 million years ago. During this time period, paleogeographic data indicate that northern Sierran rivers emptied to the ocean in the south Coast Ranges, rather than at the San Francisco Bay. For the other trans-valley clade genetic evidence is less conclusive regarding the mechanism and directionality of biogeographic exchange, although the estimated timeframe is similar (approximately 1.8 Ma). Despite the large number of biogeographic studies previously conducted in central California, to the best of our knowledge no prior studies have discussed or revealed a northern Sierran to south Coast Range biogeographic connection. This uniqueness may reflect the low-dispersal biology of mygalomorph spiders, where "post-event" gene exchange rarely erases historical biogeographic signal.
Data from: Identification of the notothenioid sister lineage illuminates the biogeographic history of an Antarctic adaptive radiation
Background: Antarctic notothenioids are an impressive adaptive radiation. While they share recent common ancestry with several species-depauperate lineages that exhibit a relictual distribution in areas peripheral to the Southern Ocean, an understanding of their evolutionary origins and biogeographic history is limited as the sister lineage of notothenioids remains unidentified. The phylogenetic placement of notothenioids among major lineages of perciform fishes, which include sculpins, rockfishes, sticklebacks, eelpouts, scorpionfishes, perches, groupers and soapfishes, remains unresolved. We investigate the phylogenetic position of notothenioids using DNA sequences of 10 protein coding nuclear genes sampled from more than 650 percomorph species. The biogeographic history of notothenioids is reconstructed using a maximum likelihood method that integrates phylogenetic relationships, estimated divergence times, geographic distributions and paleogeographic history. Results: Percophis brasiliensis is resolved, with strong node support, as the notothenioid sister lineage. The species is endemic to the subtropical and temperate Atlantic coast of southern South America. Biogeographic reconstructions imply the initial diversification of notothenioids involved the western portion of the East Gondwanan Weddellian Province. The geographic disjunctions among the major lineages of notothenioids show biogeographic and temporal correspondence with the fragmentation of East Gondwana. Conclusions: The phylogenetic resolution of Percophis requires a change in the classification of percomorph fishes and provides evidence for a western Weddellian origin of notothenioids. The biogeographic reconstruction highlights the importance of the geographic and climatic isolation of Antarctica in driving the radiation of cold-adapted notothenioids.
Data from: Where did all the trees come from? A novel multispecies approach reveals the impacts of biogeographical history and functional diversity on rain forest assembly
Aim: We take advantage of next generation sequencing-based technology to assess how landscape-level dynamics, biogeographical history and functional factors shape the distribution of genetic diversity in rain forest trees. To achieve this, we explore chloroplast genomic diversity and divergence patterns across multiple, co-distributed species from three major centres of rain forest diversity. Location: Subtropical rain forests in south-eastern Australia: Nightcap–Border Ranges, Dorrigo and Washpool. Methods: We assembled chloroplast genomic data from whole-genome shotgun libraries for 71 species collected across three major centres of rain forest diversity. Chloroplast single nucleotide polymorphisms were used to measure genetic variation within and between multiple populations, species and locations, and we used this information to identify patterns related to landscape-level processes, biogeographical origins and functional characteristics. Results: We identified Nightcap–Border Ranges and Dorrigo as containing multiple refugia and Washpool as primarily a recolonized area. We found that rapidly expanding lineages of Indo-Malesian origin exhibit significantly lower levels of genetic diversity than Gondwanan lineages with longer local histories. Functional traits related to persistence and dispersal were the most important in regulating the distribution of genetic diversity. Main conclusions: The distribution and assembly of species reflect interactions and competition between different floristic elements at different stages of continental occupation. Additionally, given the multiple evolutionary origins and histories of the Australian rain forest flora, it is important to avoid treating rain forest communities as single management units.
Data from: Multiple loci and complete taxonomic sampling resolve the phylogeny and biogeographic history of tenrecs (Mammalia: Tenrecidae) and reveal higher speciation rates in Madagascar's humid forests
The family Tenrecidae (tenrecs) is one of only four extant terrestrial mammal lineages to have colonized and diversified on Madagascar. Over the past 15 years, several studies have disagreed on relationships among major tenrec lineages, resulting in multiple reinterpretations of the number and timing of historical transoceanic dispersal events between Africa and Madagascar. We reconstructed the phylogeny of Tenrecidae using multiple loci from all recognized extant species and estimated divergence timing using six fossil calibrations within Afrotheria. All phylogenetic analyses strongly support monophyly of the Malagasy tenrecs, and our divergence timing analysis places their colonization of the island at 30-56 Ma. Our comprehensive phylogeny supports three important taxonomic revisions that reflect the evolutionary history of tenrecs: (1) we formally elevate the African otter shrews to their own family Potamogalidae, thereby rendering extant Tenrecidae entirely endemic to Madagascar, (2) we subsume the semiaquatic genus Limnogale within the shrew-tenrec genus Microgale, and (3) we re-elevate the two largest-bodied shrew tenrecs, Microgale dobsoni and M. talazaci, to the genus Nesogale Thomas 1918. Finally, we use recently summarized habitat data to test the hypothesis that diversification rates differ between humid and arid habitats on Madagascar, and we compare three common methods for ancestral biogeographic reconstruction. These analyses suggest higher speciation rates in humid habitats and reveal a minimum of three and more likely five independent transitions to arid habitats. Our results resolve the relationships among previously recalcitrant taxa, illuminate the timing and mechanisms of major biogeographic patterns in an extraordinary example of an island radiation, and permit the first comprehensive, phylogenetically consistent taxonomy of Madagascar's tenrecs.
FIGURES 11–14. M in The genus Magia Distant (Hemiptera: Lophopidae): review and biogeographic history
FIGURES 11–14. M. stuarti, male, lateral view. 11. Pygofer, anal tube and gonostyli. 12. Phallic complex. 13. Edeagus. 14. Periandrium.
FIGURES 7–9. M. subocellata, fifth instar nymph. 7 in The genus Magia Distant (Hemiptera: Lophopidae): review and biogeographic history
FIGURES 7–9. M. subocellata, fifth instar nymph. 7. picture of the habitus. 8. Drawing of the habitus. 9. Posterior view of the apex of the abdomen.
FIGURES 2–6. M in The genus Magia Distant (Hemiptera: Lophopidae): review and biogeographic history
FIGURES 2–6. M. subocellata, male, lateral view. 2. Pygofer, anal tube and gonostyli. 3. Phallic complex. 4. Dorsal part of the periandrium. 5. Edeagus. 6. Ventral part of the periandrium.
FIGURES 53–60 in A new lophopid genus as another piece in the biogeographical history puzzle of the family in the Sunda Shelf (Hemiptera: Fulgoromorpha: Lophopidae)
FIGURES 53–60. Binaluana emarginata gen. et sp. nov., female. (53–55) Pregenital sternite: (53) ventral view, (54) ventroposterior view, (55) posterior view; (56) anal tube, dorsal view; (57) gonoplac and gonapophysis VIII, external view (lateral); (58) bursa copulatrix, lateral view; (59–60) spermatheca.
FIGURES 61 in A new lophopid genus as another piece in the biogeographical history puzzle of the family in the Sunda Shelf (Hemiptera: Fulgoromorpha: Lophopidae)
FIGURES 61. Lophopidae Phylogeny. Strict consensus of the seventeen cladograms obtained with the Bremer support (or Decay index) indicated for each node.
FIGURES 42–47 in A new lophopid genus as another piece in the biogeographical history puzzle of the family in the Sunda Shelf (Hemiptera: Fulgoromorpha: Lophopidae)
FIGURES 42–47. Binaluana emarginata gen. et sp. nov., female, SEM images. (42–43) Abdomen: (42) dorso-lateral view, (43) lateral view; (44–45) terminalia: (44) dorso-lateral view, (45) lateral view; (46) anal tube, posterior view; (47) median part of anal tube, dorso-lateral view.
FIGURES 48–52 in A new lophopid genus as another piece in the biogeographical history puzzle of the family in the Sunda Shelf (Hemiptera: Fulgoromorpha: Lophopidae)
FIGURES 48–52. Binaluana emarginata gen. et sp. nov., female, SEM images. (48) Abdomen, ventral view; (50) terminalia, ventral view; (49) same, lateral view; (50–51) gonapophysis VIII: (50) ventral view, (51) posterior view; (52) gonoplac with wax secretion, lateral view.
FIGURES 36–41 in A new lophopid genus as another piece in the biogeographical history puzzle of the family in the Sunda Shelf (Hemiptera: Fulgoromorpha: Lophopidae)
FIGURES 36–41. Binaluana emarginata gen. et sp. nov., female, SEM images. (36) Fore femur and tibia, ventral view; (37– 40) hind tibia and tarsal segments; (41) rostrum, ventral view.
FIGURES 24–29 in A new lophopid genus as another piece in the biogeographical history puzzle of the family in the Sunda Shelf (Hemiptera: Fulgoromorpha: Lophopidae)
FIGURES 24–29. Binaluana emarginata gen. et sp. nov., female, SEM images. (24–27) Antenna: (24–25) dorsal view, (26) dorso-lateral view, (27) apical view; (28–29) plate organs.
FIGURES 1–5 in A new lophopid genus as another piece in the biogeographical history puzzle of the family in the Sunda Shelf (Hemiptera: Fulgoromorpha: Lophopidae)
FIGURES 1–5. Binaluana emarginata gen. et sp. nov., female. (1) Habitus, lateral view; (2) same, dorsal view; (3) anterior part of body, lateral view; (4) anterior part, frontal view; (5) anterior part of body, dorsal view.
FIGURES 12–17 in A new lophopid genus as another piece in the biogeographical history puzzle of the family in the Sunda Shelf (Hemiptera: Fulgoromorpha: Lophopidae)
FIGURES 12–17. Binaluana emarginata gen. et sp. nov., female, SEM images. (12–13) Anterior part of body: (12) dorsal view, (13) dorso-lateral view; (14) vertex, dorsal view; (15) head, frontal view; (16–17) frons, frontal view.
FIGURES 6–11 in A new lophopid genus as another piece in the biogeographical history puzzle of the family in the Sunda Shelf (Hemiptera: Fulgoromorpha: Lophopidae)
FIGURES 6–11. Binaluana emarginata gen. et sp. nov., female. (6) Head, rostrum and legs, ventral view; (7) abdomen and hind legs, ventral view; (8) labels; (9–11) abdomen: (9) dorsal view, (10) ventral view, (11) posterior view.
FIGURES 18–23 in A new lophopid genus as another piece in the biogeographical history puzzle of the family in the Sunda Shelf (Hemiptera: Fulgoromorpha: Lophopidae)
FIGURES 18–23. Binaluana emarginata gen. et sp. nov., female, SEM images. (18) Anterior part of body, lateral view; (19) head and pronotum, lateral view; (20) upper part of head, lateral view; (21) pronotum and mesonotum, lateral view; (22) lower part of head and pronotum, lateral view; (23) upper part of pronotum and mesonotum, lateral view.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.