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33 results for “biogeographical barriers”
Seascape genetics in a polychaete worm: Disentangling the roles of a biogeographic barrier and environmental factors
<p><strong>Aim:</strong> Seascape genomics studies aim to understand how environmental variables shape species diversity through genotype-environment associations. Identifying these effects on lecithotrophic larval species that live in intertidal zones is particularly challenging because they are subject to environmental heterogeneity and anthropogenic events. Here, we evaluate how biotic and abiotic features in the Southwest Atlantic littoral zone can affect a high dispersal species' present and historical demographic.</p> <p><strong>Taxon:</strong> <em>Perinereis ponteni.</em></p> <p><strong>Methods: </strong>We investigated population genetic diversity, connectivity, and past dynamics using 23,300 SNPs generated using Genotyping by sequencing. We tested whether environmental abiotic variables could explain the variance found in genotype frequencies using isolation-by-environment (IBE) and landscape association approaches. These data, combined with paleodistribution simulations and oceanic circulation modeling, were used to infer species demographic history and connectivity patterns.</p> <p><strong>Results:</strong> Along with high levels of connectivity detected, we found a genetic boundary in the southeastern region of Brazil around Cabo Frio (Rio de Janeiro) and a cline trend for some loci. The paleodistribution simulations reveal a spatial refuge in the southeast during the Last Glacial Maximum (21 kya), with the expansion of the northern region. We identified 1,421 SNPs with frequencies associated with eight environmental variables, most of which were related to temperature - the main environmental factor determining IBE.</p> <p><strong>Main conclusions:</strong> <em>Perinereis ponteni</em>, a polychaete with high gene flow capability responds to biogeographic barriers, highlighting the importance of biotic and abiotic factors in shaping population connectivity. Furthermore, the effect of temperature indicates that future climate change and ocean warming can hugely impact this species.</p>
Seascape genetics in a polychaete worm: Disentangling the roles of a biogeographic barrier and environmental factors
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Data from: The great rift valley is a greater biogeographic barrier than the blue Nile Valley for six Ethiopian highland passerines in the Eastern Afromontane biodiversity hotspot
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Genetic structures across a biogeographical barrier reflect dispersal potential of four Southeast Asian mangrove plant species
Aim Biogeographic barriers restrict the movement of individuals, resulting in population divergence, genetic differentiation, endemism and speciation. Yet, some barriers demonstrate unequal effect across species depending on species dispersal, which manifests in varying genetic structure. We test the hypotheses that the genetic structure of four coastal mangrove species would reflect differences in dispersal potential across the Malay Peninsula, a major biogeographic barrier in the Indo-West Pacific region. Location Twelve sites from the east and west coasts of the Malay Peninsula. Taxon Mangrove trees Avicennia alba, Sonneratia alba, Bruguiera gymnorhiza, and Rhizhophora mucronata. Methods For each species, we characterized genetic structure and gene flow using seven to 12 species-specific nuclear microsatellite markers. We tested for east-west genetic differentiation across the peninsula, a stepping-stone migration pattern, and assessed the proportion of recent dispersal and direction of historical migration along the Malacca Strait. Results Significant east-west genetic differentiation across the peninsula was observed in A. alba, S. alba and B. gymnorhiza, and the effect was most pronounced for the two species with lower dispersal potential (A. alba, S. alba). In contrast, the two species with higher dispersal potential (B. gymnorhiza and R. mucronata) exhibited much higher proportion of recent inter-population migration along the Malacca Strait. The signature of historical colonization from refugia in the Andaman Sea (north-to-south migration along the Malacca Strait) predominated for A. alba and S. alba. Historical south-north migration predominated for R. mucronata and B. gymnorhiza. Main conclusions This study is the first to implicate dispersal potential as a causal factor of varying mangrove species genetic structure across a biogeographic barrier. The Malay Peninsula functions as a filter to gene flow rather than a barrier. The genetic structure in mangrove species with a higher dispersal potential is more congruent with contemporary gene flow while that of species with a lower dispersal potential reflects historical processes.Our findings hint at the role of dispersal potential as a predictor of gene flow in mangroves.
Data from: Environmental heterogeneity and not vicariant biogeographic barriers generate community wide population structure in desert adapted snakes
Genetic structure can be influenced by local adaptation to environmental heterogeneity and biogeographic barriers, resulting in discrete population clusters. Geographic distance among populations, however, can result in continuous clines of genetic divergence that appear as structured populations. Here we evaluate the relevant importance of these three factors over a landscape characterized by environmental heterogeneity and the presence of a hypothesized biogeographic barrier in producing population genetic structure within 13 codistributed snake species using a genomic dataset. We demonstrate that geographic distance and environmental heterogeneity across western North America contribute to population genomic divergence. Surprisingly, landscape features long thought to contribute to biogeographic barriers play little role in divergence community wide. Our results suggest that isolation by environment is the most important contributor to genomic divergence. Furthermore, we show that models of population clustering that incorporate spatial information consistently outperform nonspatial models, demonstrating the importance of considering geographic distances in population clustering. We argue that environmental and geographic distances as drivers of community-wide divergence should be explored before assuming the role of biogeographic barriers.
Data for study on the permeability of biogeographic barriers to marine species on the east and west coasts of North America
<p><strong>Aim</strong>: We assess the role of contemporary oceanography and species traits in shaping observed patterns of biogeography over broad spatial scales.</p> <p><strong>Location</strong>: Our study domain covers the east and west coasts of North America, from 30° to 73° on the east coast and 33° to 73° on the west coast.</p> <p><strong>Time Period</strong>: Hydrodynamic models use climatological fields from 1990 to 2015 on the east coast, and 1993 to 2018 on the west coast.</p> <p><strong>Major Taxa Studied:</strong> Model simulations represent larval dispersal for generalized benthic invertebrate species distributed in the subtidal zone from 10 m to 100 m depth, with planktonic larval durations ranging from 21–60 days.</p> <p><strong>Methods</strong>: We conducted a literature review to identify major biogeographic barriers along the east and west coasts of North America, and then assessed the permeability of these barriers to larval dispersal using Lagrangian Particle Tracking. We ran a series of simulations in which we varied the suitable habitat distribution, planktonic larval duration, and spawning seasonality of simulated larvae (i.e. particles) to assess the role of species traits on biogeography.</p> <p><strong>Results</strong>: Our results showed a strong alignment of observed biogeographic barriers with larval dispersal patterns, with high variation in barrier permeability depending on the traits of the species considered. The location of suitable habitat and the season during which particle release occurred were the biological traits that drove much of the variation in barrier permeability among simulations on both coasts.</p> <p><strong>Main Conclusions</strong>: Our results indicate an important role of contemporary oceanographic and geographic features in determining the biogeography of species whose primary dispersal is during larval stages, suggesting that climate change is likely to alter patterns of species biogeography. Our results also demonstrate that species traits play a strong role in determining the location and strength of biogeographic barriers.</p>
Data from: Diversification processes in Gerp's mouse lemur demonstrate the importance of rivers and altitude as biogeographic barriers in Madagascar's humid rainforests
<p><span>Madagascar exhibits exceptionally high levels of biodiversity and endemism. Models to explain the diversification and distribution of species in Madagascar stress the importance of historical variability in climate conditions which may have led to the formation of geographic barriers by changing water and habitat availability. The relative importance of these models for the diversification of the various forest-adapted taxa of Madagascar has yet to be understood. Here, we reconstructed the phylogeographic history of Gerp's mouse lemur (<em>Microcebus gerpi</em>) to identify relevant mechanisms and drivers of diversification in Madagascar's humid rainforests. We used restriction site associated DNA (RAD) markers and applied population genomic and coalescent-based techniques to estimate genetic diversity, population structure, gene flow and divergence times among <em>M. gerpi</em> populations and its two sister species <em>M. jollyae</em> and <em>M. marohita</em>. Genomic results were complemented with ecological niche models to better understand the relative barrier function of rivers and altitude. We show that <em>M. gerpi</em> diversified during the late Pleistocene. The inferred ecological niche, patterns of gene flow and genetic differentiation in <em>M. gerpi</em> suggest that the potential for rivers to act as biogeographic barriers depended on both size and elevation of headwaters. Populations on opposite sides of the largest river in the area with headwaters that extend far into the highlands show particularly high genetic differentiation, whereas rivers with lower elevation headwaters have weaker barrier functions, indicated by higher migration rates and admixture. We conclude that<em> M. gerpi</em> likely diversified through repeated cycles of dispersal punctuated by isolation to refugia as a result of paleoclimatic fluctuations during the Pleistocene. We argue that this diversification scenario serves as a model of diversification for other rainforest taxa that are similarly limited by geographic factors. In addition, we highlight conservation implications for this critically endangered species, which faces extreme habitat loss and fragmentation. </span></p>
Heterogeneous microgeographic genetic structure of the common cockle (Cerastoderma edule) in the Northeast Atlantic Ocean: biogeographic barriers and environmental factors
<p>Knowledge of genetic structure at the finest level is essential for conservation of genetic resources. Despite no visible barriers limiting gene flow, significant genetic structure has been shown in marine species. The common cockle (<em>Cerastoderma</em> <em>edule</em>) is a bivalve of great commercial and ecological value inhabiting the Northeast Atlantic Ocean. Previous population genomics studies demonstrated significant structure both across the Northeast Atlantic, but also within small geographic areas, highlighting the need to investigate fine-scale structuring. Here, we analysed two geographic areas that could represent opposite models of structure for the species: 1) the SW British Isles region, highly fragmented due to biogeographic barriers, and 2) Galicia (NW Spain), a putative homogeneous region. 9,250 SNPs genotyped by 2b-RAD on 599 individuals from 22 natural beds were used for the analysis. The entire SNP dataset mostly confirmed previous observations related to genetic diversity and differentiation, however, neutral and divergent SNP outlier datasets enabled disentangling physical barriers from abiotic environmental factors structuring both regions. While Galicia showed a homogeneous structure, the SW British Isles region was split into four reliable genetic regions related to oceanographic features and abiotic factors, such as sea surface salinity and temperature. The information gathered supports specific management policies of cockle resources in SW British and Galician regions also considering their particular socio-economic characteristics; further, these new data will be added to those recently reported in the Northeast Atlantic to define sustainable management actions across the whole distribution range of the species.</p>
Biogeographic barriers and historical climate affect phylogeographic structure and demographic history of the common gartersnake
<p><strong>Aim</strong>: 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. </p> <p><strong>Location</strong>: North America</p> <p><strong>Taxon</strong>: Common gartersnake, <em>Thamnophis sirtalis</em></p> <p><strong>Methods</strong>: 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.</p> <p><strong>Results</strong>: 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.</p> <p><strong>Main Conclusion</strong>: Our results provide strong evidence for a Middle Pliocene origin for <em>Thamnophis</em> <em>sirtalis</em> 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.</p>
Data from: Environmental heterogeneity and not vicariant biogeographic barriers generate community wide population structure in desert adapted snakes
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Biogeographic barriers and historical climate affect phylogeographic structure and demographic history of the common gartersnake
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Data from: Diversification processes in Gerp's mouse lemur demonstrate the importance of rivers and altitude as biogeographic barriers in Madagascar's humid rainforests
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Data from: Plio-Pleistocene diversification and biogeographic barriers in southern Australia reflected in the phylogeography of a widespread and common lizard species
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Data for study on the permeability of biogeographic barriers to marine species on the east and west coasts of North America
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Genetic structures across a biogeographical barrier reflect dispersal potential of four Southeast Asian mangrove plant species
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Heterogeneous microgeographic genetic structure of the common cockle (Cerastoderma edule) in the Northeast Atlantic Ocean: biogeographic barriers and environmental factors
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Data from: The hidden side of a major marine biogeographic boundary: a wide mosaic hybrid zone at the Atlantic–Mediterranean divide reveals the complex interaction between natural and genetic barriers in mussels
The Almeria-Oran Front (AOF) is a recognised hotspot of genetic differentiation in the sea. It is a barrier to dispersal and an ecological boundary, which explain the position of genetic breaks. However, the maintenance of genetic differentiation is likely reinforced by genetic barriers. A general drawback of previous studies is an insufficient density of sampling sites at the transition zone with a conspicuous lack of samples from the southern coastline. We analysed the genetic structure in the mussel Mytilus galloprovincialis with ancestry-informative loci. We discovered a 600 km wide mosaic hybrid zone eastward of the AOF along the Algerian coasts. This mosaic zone provides a new twist to our understanding of the Atlantic-Mediterranean transition because it demonstrates the two lineages can live in sympatry but hardly interbreed. This implies some form of reproductive isolation must exist to maintain the two genetic backgrounds locally cohesive. The zone ends with an abrupt genetic shift at a barrier to dispersal in the Gulf of Bejaia. Simulations in models that account for hydrodynamic features of the region support the hypothesis that sister hybrid zones could have been differentially trapped at two alternative barriers to dispersal or environmental boundaries. A preponderantly unidirectional north-south gene flow next to the AOF can also maintain a patch of an intrinsically maintained genetic background in the south and the mosaic structure. Our results concur with the coupling hypothesis that suggests natural barriers mostly explain the position of genetic breaks while their maintenance must additionally require genetic barriers.
Data from: Biogeographic barriers drive co-diversification within associated eukaryotes of the Sarracenia alata pitcher plant system
Understanding if the members of an ecological community have co-diversified is a central concern of evolutionary biology, as co-diversification suggests prolonged association and possible coevolution. By sampling associated species from an ecosystem, researchers can better understand how abiotic and biotic factors influence diversification in a region. In particular, studies of co-distributed species that interact ecologically can allow us to disentangle the effect of how historical processes have helped shape community level structure and interactions. Here we investigate the Sarracenia alata pitcher plant system, an ecological community where many species from disparate taxonomic groups live inside the fluid-filled pitcher leaves. Direct sequencing of the eukaryotes present in the pitcher plant fluid enables us to better understand how a host plant can shape and contribute to the genetic structure of its associated inquilines, and to ask whether genetic variation in the taxa are structured in a similar manner to the host plant. We used 454 amplicon-based metagenomics to demonstrate that the pattern of genetic diversity in many, but not all, of the eukaryotic community is similar to that of S. alata, providing evidence that associated eukaryotes share an evolutionary history with the host pitcher plant. Our work provides further evidence that a host plant can influence the evolution of its associated commensals.
Subspecies and Distribution. S.m.murinaWaterhouse,1838—E&SEAustralia,EQueensland(includingFraserI),NewSouthWales,Victoria,andE&SESouthAustralia. S. m. tate: Troughton, 1965 — NE Queensland. The subspecies are probably allopatric, with neither form apparently occurring in mideastern Queensland, a known biogeographical barrier to many terrestrial vertebrates. in Dasyuridae
Subspecies and Distribution. S.m.murinaWaterhouse,1838—E&SEAustralia,EQueensland(includingFraserI),NewSouthWales,Victoria,andE&SESouthAustralia. S. m. tate: Troughton, 1965 — NE Queensland. The subspecies are probably allopatric, with neither form apparently occurring in mideastern Queensland, a known biogeographical barrier to many terrestrial vertebrates.
Major biogeographic barriers in eastern Australia have shaped population structure of widely distributed Eucalyptus moluccana and its four putative subspecies
<p>We have investigated the impact of recognized biogeographic barriers on genetic differentiation of grey box (<i>Eucalyptus moluccana</i>), a common and widespread tree species of the family Myrtaceae in eastern Australian woodlands, and its previously proposed four subspecies <i>moluccana</i>, <i>pedicellata</i>, <i>queenslandica</i> and <i>crassifolia</i>.<b> </b>A range of phylogeographic analyses were conducted to examine the population genetic differentiation and subspecies genetic structure in <i>E. moluccana </i>in relation to biogeographic barriers. Slow evolving markers uncovering long term processes (chloroplast DNA) were used to generate a haplotype network and infer phylogeographic barriers. Additionally, fast evolving, hypervariable markers (microsatellites) were used to estimate demographic processes and genetic structure among five geographic regions (29 populations) across the entire distribution of <i>E. moluccana</i>. Morphological features of seedlings, such as leaf and stem traits were assessed to evaluate population clusters and test differentiation of the putative subspecies.</p> <p>Haplotype network analysis revealed twenty chloroplast haplotypes with a main haplotype in a central position shared by individuals belonging to the regions containing the four putative subspecies. Microsatellite analysis detected genetic structure between Queensland (QLD) and New South Wales (NSW) populations consistent with the McPherson Range barrier, an east-west spur of the Great Dividing Range. Substructure was detected within QLD and NSW in line with other barriers in eastern Australia. The morphological analyses supported differentiation between QLD and NSW populations, with no difference within QLD, yet some differentiation within NSW populations.</p> <p>Our molecular and morphological analyses provide evidence that several geographic barriers in eastern Australia, including the Burdekin Gap and the McPherson Range have contributed to the genetic structure of <i>E. moluccana</i>. Genetic differentiation among <i>E. moluccana </i>populations supports the recognition of some but not all the four previously proposed subspecies, with<i> crassifolia </i>being the most differentiated.</p>
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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.