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76 results for “comparative phylogeography”
Data from: Full Bayesian comparative phylogeography from genomic data
A challenge to understanding biological diversification is accounting for community-scale processes that cause multiple, co-distributed lineages to co-speciate. Such processes predict non-independent, temporally clustered divergences across taxa. Approximate-likelihood Bayesian computation (ABC) approaches to inferring such patterns from comparative genetic data are very sensitive to prior assumptions and often biased toward estimating shared divergences. We introduce a full-likelihood Bayesian approach, ecoevolity, which takes full advantage of information in genomic data. By analytically integrating over gene trees, we are able to directly calculate the likelihood of the population history from genomic data, and efficiently sample the model-averaged posterior via Markov chain Monte Carlo algorithms. Using simulations, we find that the new method is much more accurate and precise at estimating the number and timing of divergence events across pairs of populations than existing approximate-likelihood methods. Our full Bayesian approach also requires several orders of magnitude less computational time than existing ABC approaches. We find that despite assuming unlinked characters (e.g., unlinked single-nucleotide polymorphisms), the new method performs better if this assumption is violated in order to retain the constant characters of whole linked loci. In fact, retaining constant characters allows the new method to robustly estimate the correct number of divergence events with high posterior probability in the face of character-acquisition biases, which commonly plague loci assembled from reduced-representation genomic libraries. We apply our method to genomic data from four pairs of insular populations of Gekko lizards from the Philippines that are not expected to have co-diverged. Despite all four pairs diverging very recently, our method strongly supports that they diverged independently, and these results are robust to very disparate prior assumptions.
Fig. 6 in Comparative phylogeography of bamboo bats of the genus Tylonycteris (Chiroptera, Vespertilionidae) in Southeast Asia
Fig. 6. Distribution and species richness for the eight genera of woody bamboo forests currently found in Asia (adapted and modified from Bystriakova et al. 2003b) and putative geographic range areas of the species of Tylonycteris. During glacial periods of the Pleistocene, the highlighted biogeographic regions may have acted as bamboo refugia for Tylonycteris spp. Moreover, sea level falls (at around 120 m below present) exposed land bridges, such as the entire Sunda Shelf (adapted from Voris 2000), connecting the islands to the continent.
Fig. 5 in Comparative phylogeography of bamboo bats of the genus Tylonycteris (Chiroptera, Vespertilionidae) in Southeast Asia
Fig. 5. Morphological characteristics of the two nominal species of the genus Tylonycteris Peters, 1872. A. T. pachypus (Temminck, 1840) (corrected taxon name is T. fulvida (Blyth, 1859)), IEBR-VN11- 0015. B. T. robustula Thomas, 1915 (corrected taxon name is T. tonkinensis Tu, Csorba, Ruedi & Hassanin sp. nov.), holotype, IEBR-VN11-0055. Head profiles, ventral and dorsal views, fleshy pads at the base of the thumb and on the sole of the foot, and different views of the skull (dorsal, ventral and lateral). Scale = 10 mm.
Fig. 4 in Comparative phylogeography of bamboo bats of the genus Tylonycteris (Chiroptera, Vespertilionidae) in Southeast Asia
Fig. 4. Scatter plots obtained from morphological analyses of Tylonycteris spp. A. Range of GLS measurements of specimens within each group of Tylonycteris spp. B. Range of PC*1 scores of specimens of Tylonycteris spp. obtained from PCA of log-transformed raw data of craniodental measurements. C. Plot of PC 1 against PC 2 obtained from PCA on log-transformed standardized data. Triangles and circles refer to T. pachypus s. lat. and T. robustula s. lat., respectively. Colour patterns indicate the mtDNA haplogroups: green for Tp3 and Tr3 (northern Indochina); blue for Tp2 and Tr2 (other regions of the Southeast Asian mainland); red for Tp1 and Tr1 (Sundaland).
Fig. 1. A–B in Comparative phylogeography of bamboo bats of the genus Tylonycteris (Chiroptera, Vespertilionidae) in Southeast Asia
Fig. 1. A–B. Maps of Asia showing the distribution range (shaded) and type localities of described subspecies of T. pachypus (Temminck, 1840) and T. robustula Thomas, 1915 (Bates et al. 2008a, 2008b). C. Localities of Tylonycteris specimens included in this study. Triangles and circles refer to T. pachypus and T. robustula, respectively; the colours indicate the mtDNA haplogroups found in the Bayesian analyses of COI and Cytb sequences (see Fig. 2 for details).
Data from: Full Bayesian comparative phylogeography from genomic data
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Comparative phylogeography of phrynosomatid lizards in Baja California: Asynchronous divergences and expansion of <em>Callisaurus draconoides</em> across the North American deserts
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Data from: Comparative phylogeography, genetic differentiation, and contrasting reproductive modes in three fungal symbionts of a multipartite bark beetle symbiosis
Multipartite symbioses are complex symbiotic relationships involving multiple interacting partners. These types of partnerships provide excellent opportunities in which to apply a comparative approach to identify common historical patterns of population differentiation and species-specific life history traits. Using three symbiotic blue stain fungal species (Ophiostomatacea) associated with outbreaking populations of the mountain pine beetle (Dendroctonus ponderosae Hopkins) in western Canada, we applied phylogenetic, population genetic, and demographic approaches to clarify phylogeographic patterns among the three fungal species. Broadly, the three species showed significant population differentiation, forming northern and southern populations, despite dramatic differences in haplotype diversity. Finer scale structuring and population demographic patterns were less consistent, showing some interspecific incongruence. By contrasting these species simultaneously, we were able to identify differences in recombination rate and ecological traits that can explain the observed patterns of incongruence among the fungal species. By applying a comparative approach to partners of a multipartite symbiosis we were able to distinguish congruent population structuring and species-specific differences that help us to understand the complexity and evolution of this symbiotic system.
Data from: Comparative phylogeography biogeography of forest-dependent mammals reveals paleo-forest corridors throughout Sundaland
The evolutionary history of the colugo, a gliding arboreal mammal distributed throughout Sundaland, was influenced by the location of and connections between forest habitats. By comparing colugo phylogenetic patterns, species ecology, sample distributions, and times of divergence to those of other Sundaic taxa with different life history traits and dispersal capabilities, we inferred the probable distribution of paleo-forest corridors. We identified a consistent pattern of early diversification between east and west Bornean lineages in colugos, lesser mouse deer, and Sunda pangolins. This phylogenetic pattern has not been commonly described in mammals, and we found no evidence for this pattern in the greater mouse deer. Colugos on West Borneo diverged from colugos in Peninsular Malaysia and Sumatra in the late Pliocene, however most other mammalian populations distributed across these same geographic regions diverged from a common ancestor more recently in the Pleistocene. Low genetic divergence between colugos on large landmasses and their neighboring satellite islands indicated that past forest distributions were recently much larger than present refugial distributions. Our analysis of colugo evolutionary history reveals dynamic forested connections throughout Sundaland, and reconstructs Borneo as the most likely ancestral area of origin for Sunda colugos.
Fig. 2 in Comparative phylogeography of bamboo bats of the genus Tylonycteris (Chiroptera, Vespertilionidae) in Southeast Asia
Fig. 2. Bayesian tree obtained from the analyses of COI and Cytb genes. The values on the nodes indicate posterior probabilities (PP). In the COI tree, PPs were calculated from two DNA alignments of CO1 sequences (728 nt or 291 nt; see text for details). The sequence HM914921 was obtained from a specimen originally identified as T. robustula. In the Cytb tree, the sequence EU521635 was obtained from a specimen originally identified as T. robustula.
Comparative and predictive phylogeography in the South American diagonal of open formations: Unravelling the biological and environmental influences on multitaxon demography
<p><span><span>Phylogeography investigates historical drivers of species' geographic distribution. Special attention has been given to ecological, climatic, and geological processes in the diversification of the Neotropical biota. Several species sampled across the dry diagonal of South America (DDSA, comprising the Caatinga, Cerrado, and Chaco biomes) experienced range shifts coincident with Quaternary climatic changes. However, studies across different spatial, temporal, and biological scales on species from South America's dry biomes are still poorly represented. Here, we combine phylogeographic model selection and machine learning predictive frameworks to investigate the influence of Pleistocene climatic changes on both plant and animal species from the DDSA. We assembled mitochondrial/chloroplastic DNA sequences in public repositories and inferred the historical demographic responses of 70 lineages. We then built a random forest model using both biotic and abiotic information to identify potential traits for predicting whether species underwent population expansion, contraction, or stasis during the Pleistocene. Finally, we estimated the temporal synchrony of species demographic responses using hierarchical approximate Bayesian computation (hABC). Biotic variables largely predicted how species responded to Pleistocene climatic changes, and demographic changes were mostly synchronous during the Middle Pleistocene. Although many DDSA species underwent demographic expansion, presumably associated with the spread of aridity during glacial Pleistocene periods, our findings suggest that some species exhibited the opposite response and that species-specific attributes might have been related to these differences.</span></span></p>
Data from: Between the Cape Fold Mountains and the deep blue sea: comparative phylogeography of selected codistributed ectotherms reveals asynchronous cladogenesis. Sampling locations and MaxEnt input files
<p><span>We compare the phylogeographic structure of thirteen codistributed ectotherms including four reptiles (a snake, a legless skink and two tortoise species) and nine invertebrates (six freshwater crabs and three velvet worm species) to test the presence of congruent evolutionary histories. </span><span>Phylogenies were estimated and dated using maximum likelihood and Bayesian methods with combined mitochondrial and nuclear DNA sequence datasets. </span><span>All taxa demonstrated a marked east/west phylogeographic division, separated by the Cape Fold Mountain range.</span><span> <span>Phylogeographic concordance factors were calculated to assess the degree of evolutionary congruence among the study species and </span></span><span>generally supported a shared pattern of diversification along the east/west longitudinal axis</span><span>. Testing simultaneous divergence between the eastern and western phylogeographic regions indicated </span><span>pseudo-congruent evolutionary histories among the study taxa, with at least three separate divergence events throughout the Mio/Plio/Pleistocene epochs.</span><span> <span>Climatic refugia were identified for each species using climatic niche modeling, </span></span><span>demonstrating taxon-specific responses to climatic fluctuations. Climate and the Cape Fold Mountain barrier explained the highest proportion of genetic diversity in all taxa, while climate was the most significant individual abiotic variable. </span><span>This study highlights the complex interactions between the Cape Fold Mountains and past climatic oscillations during the Mio/Plio/Pleistocene. The congruent east/west phylogeographic division observed in all taxa lends support to the conclusion that the longitudinal climatic gradient within the Greater Cape Floristic Region, mediated in part by the barrier to dispersal posed by the Cape Fold Mountains, plays a major role in lineage diversification and population differentiation.</span></p>
Comparative phylogeography of two commensal rat species (Rattus tanezumi and R. norvegicus) in China: Insights from mitochondiral DNA, microsatellite and RADseq
<p><em><span>Rattus norvegicus</span></em><span> and </span><em><span>Rattus tanezumi</span></em><span> are dominant species of Chinese house rats, but the colonization and demographic history of two species in China have not been thoroughly explored.</span><span> Phylogenetic analyses with mitochondrial DNA including 486 individuals from 31 localities revealed that </span><span><em>R</em>. <em>norvegicus</em></span><span> is widely distributed in China, </span><span>R. <em>tanezumi</em></span><span> is mainly distributed in southern China with currently invading northward; northeast China was the natal region of </span><span><em>R</em>. <em>norvegicus</em></span><span>, while the spread of </span><span><em>R</em>. <em>tanezumi</em></span><span> in China most likely started from the southeast coast. A total of 123 individuals from 18 localities were subjected to 2b‐RAD analyses. In the neighbor‐joining tree, individuals of </span><span><em>R</em>. <em>tanezumi</em></span><span> grouped into geographic‐specific branches, and populations from the southeast coast were ancestral groups, which confirmed the colonization route from the southeast coast to central and western China. However, individuals of </span><span><em>R</em>. <em>norvegicus</em></span><span> were generally grouped into two clusters instead of geographic‐specific branches. One cluster comprised inland populations, and another cluster included both southeast coast and inland populations, which indicated that the spread history of </span><span><em>R</em>. <em>norvegicus</em></span><span> in China was complex; in addition to on‐land colonization, shipping transportation also played a great role. ADMIXTURE and principal component analyses provided further supports for the colonization history. Demographic analyses revealed that climate changes at ~40,000 to 18,000 years ago and ~4000 years ago had led to population declines of both species; the </span><span>R<em>.</em> <em>norvegicus</em></span><span> declined rapidly while the population of </span><span><em>R</em>. <em>tanezumi</em></span><span> continuously expanded since ~1500 years ago, indicating the importance of interspecies' competition in their population size changes. Our study provided a valuable framework for further investigation of phylogeography of two species in China.</span></p>
Data from: Comparing phylogeographies to reveal incompatible geographical histories within genomes
<p>Modern phylogeography aims at reconstructing the geographic movement of organisms based on their genomic sequences and spatial information. Phylogeographic approaches are often applied to pathogen sequences and therefore tend to neglect the possibility of recombination, which decouples the evolutionary and geographic histories of different parts of the genome. Genomic regions of recombining or reassorting pathogens often originate and evolve at different times and locations, which characterise their unique spatial histories. Measuring the extent of these differences requires new methods to compare geographic information on phylogenetic trees reconstructed from different parts of the genome. Here we develop for the first time a set of measures of phylogeographic incompatibility, aimed at detecting differences between geographical histories in terms of distances between phylogeographies. We study the effect of varying demography and recombination on phylogeographic incompatibilities using coalescent simulations. We further apply these measures to the evolutionary history of human and livestock pathogens, either reassorting or recombining, such as the Victoria and Yamagata lineages of influenza B and the O/ME-SA/Ind-2001 foot-and-mouth disease virus strain. Our results reveal diverse geographical paths of migration that characterise the origins and evolutionary histories of different viral genes and genomic segments. These incompatibility measures can be applied to any phylogeography, and more generally to any phylogeny where each tip has been assigned either a continuous or discrete "trait" independent of the sequence. We illustrate this flexibility with an analysis of the interplay between the phylogeography and phylolinguistics of Uralic-speaking human populations, hinting at patrilinear language transmission.</p>
Phylogeography of Limia vittata (Cyprinodontiformes: Poeciliidae): geographical distribution of mitochondrial haplotypes is comparable to other Cuban poeciliids
<p>This is the supplementary material associated with the article "Phylogeography of <em>Limia vittata</em> (Cyprinodontiformes: Poeciliidae): geographical distribution of mitochondrial haplotypes is comparable to other Cuban poeciliids", published by the Biological Journal of the Linnean Society (<a href="https://doi.org/10.1093/biolinnean/blad040">https://doi.org/10.1093/biolinnean/blad040</a>). The following documents (pdf format) are included:</p> <p><strong>Supporting Information 1 </strong></p> <p><strong>Table S1.</strong> Sampling size (n) and haplotype (<em>COI</em>+<em>CR</em>) information for each sampling locality of <em>L. vittata</em> included in this study. Numbers correspond to those indicated in Figure 1. A star (*) represents a new locality record for <em>L. vittata</em>. ANC: acronym of the Acuario Nacional de Cuba Collection, La Habana, Cuba.</p> <p><strong>Supporting Information 2</strong></p> <p><strong>Table S1.</strong> Prior distribution of parameters used for the analysis of the <em>L. vittata</em> data based on the ABC approach using DIYABC v.2.1.0 (<a href="#CIT0008">Cornuet <em>et al</em>., 2014</a>). Time is in generations. W-PR: Western Pinar del Río population, W-C: Western-Central population, C-E: Central-Eastern population.</p> <p><strong>Table S2.</strong> Summary statistics between <em>L. vittata</em> haplogroups for each scenario based on 3 × 10<sup>6</sup> simulated datasets. NHA: number of alleles, NSS: number of segregating sites, MPD: mean of pairwise differences, VPD: variance of pairwise differences, MP2: mean pairwise differences within samples, MPB: mean pairwise differences between samples, HST: F<sub><em>ST</em></sub> between samples.</p> <p><strong>Table S3.</strong> Posterior distributions of the parameters based on scenario B for <em>L. vittata</em>. Data were obtained from 1% of the simulated dataset (1 × 10<sup>6</sup>). Time is in generations. W-PR: Western Pinar del Río population, W-C: Western-Central population, C-E: Central-Eastern population. RMAE: relative median of absolute error.</p> <p><strong>Figure S1.</strong> PCA of the summary statistics of the observed dataset and the dataset generated from the prior distribution of parameters to evaluate the three biogeographic scenarios explaining the current distribution of <em>L. vittata</em>. The analysis was performed using DIYABC v.2.1.0 (<a href="#CIT0008">Cornuet <em>et al.</em>, 2014</a>).</p> <p><strong>Figure S2.</strong> Posterior probability of the biogeographic scenarios tested to explain the current distribution of <em>L. vittata</em>. Logistic regression was used to compute the posterior probability using the ABC approach as implemented in DIYABC v.2.1.0 (<a href="#CIT0008">Cornuet <em>et al.</em>, 2014</a>).</p> <p><strong>Supporting Information 3</strong></p> <p><strong>Figure S1.</strong> Bayesian tree depicting the relationships of 160 partial <em>COI</em>+<em>CR</em> sequences of <em>L. vittata</em>. The red dots depict samples from eastern localities (Yateras, Sabanalamar, and Yacabo Abajo) sharing the W-C haplogroups (H9 and H10). Bootstrap support (≥ 93) and Bayesian posterior probabilities (≥ 0.95) are shown for the main clades.</p> <p><strong>Supporting Information 4</strong></p> <p><strong>Figure S1.</strong> Mismatch distribution of pairwise haplotype differences from partial <em>COI</em> and <em>CR</em> sequences for the three haplogroups recovered in <em>L. vittata</em>. Dashed lines represent the distribution of the observed pairwise nucleotide differences, whereas solid lines represent the values expected after a population growth or decline model.</p> <p><strong>Supporting Information 5</strong></p> <p><strong>Figure S1.</strong> Maximum Likelihood tree and haplotype network of <em>Girardinus falcatus</em>, <em>Girardinus metallicus,</em> and the <em>Gambusia punctata</em> species complex based on <em>cytb</em> partial sequences. Each colour represents a geographic region in Cuba. Green: westernmost Cuba, blue: western Cuba, orange: central Cuba, red: eastern Cuba. Numbers on tree branches are bootstrap values ≥ 95% and hatch marks on the networks are the number of mutations. n: number of individuals, H: number of haplotypes, <em>h</em>: haplotype diversity, π: nucleotide diversity, SD: standard deviation.</p> <p><strong>Table S1.</strong> Sampling size (n), GenBank accession numbers, and studies that made available the sequences of cytochrome <em>b</em> used for the phylogeographic comparisons of the different poeciliids in Cuba.</p>
Data from: Comparing phylogeographies to reveal incompatible geographical histories within genomes
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Comparative and predictive phylogeography in the South American diagonal of open formations: Unravelling the biological and environmental influences on multitaxon demography
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Data from: Comparative phylogeography, genetic differentiation, and contrasting reproductive modes in three fungal symbionts of a multipartite bark beetle symbiosis
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Data from: Comparative phylogeography of trans-Andean freshwater fishes based on genome-wide nuclear and mitochondrial markers
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Comparative phylogeography of two commensal rat species (Rattus tanezumi and R. norvegicus) in China: Insights from mitochondiral DNA, microsatellite and RADseq
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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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.