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149 results for “species connectivity”
Data from: Genetic variation and seasonal migratory connectivity in Wilson's warblers (Wilsonia pusilla): species-level differences in nuclear DNA between western and eastern populations
There is growing interest in understanding patterns of seasonal migratory connectivity between breeding and wintering sites, both because differences in migratory behavior can be associated with population differentiation and because knowledge of migratory connectivity is essential for understanding the ecology, evolution, and conservation of migratory species. We present the first broad survey of geographic variation in the nuclear genome of breeding and wintering Wilson's warblers (Wilsonia pusilla), which have previously served as a research system for the study of whether genetic markers and isotopes can reveal patterns of migratory connectivity. Using 153 samples surveyed at up to 257 variable amplified fragment length polymorphism (AFLP) markers, we show that Wilson's warblers consist of highly distinct western and eastern breeding groups, with all winter samples grouping with the western breeding group. Within the west there is weak geographic differentiation, at a level insufficient for use in assignment of wintering samples to specific areas. The distinctiveness of western and eastern genetic groups, with no known intermediates, strongly suggests that these two groups are cryptic species. Analysis of mitochondrial cytochrome b sequence variation shows that the estimated coalescence time between western and eastern clades is roughly 2.3 million years ago, a surprisingly old time of divergence that is more typical of distinct species than of subspecies. Given their morphological similarity but strong genetic differences, western and eastern Wilson's warblers present a likely case of association between divergence in migratory behavior and the process of speciation.
Data from: Adaptive evolution and segregating load contribute to the genomic landscape of divergence in two tree species connected by episodic gene flow
Speciation often involves repeated episodes of genetic contact between divergent populations before reproductive isolation (RI) is complete. Whole-genome sequencing (WGS) holds great promise for unravelling the genomic bases of speciation. We have studied two ecologically divergent, hybridizing species of the 'model tree' genus Populus (poplars, aspens, cottonwoods), Populus alba and P. tremula, using >8.6 million single nucleotide polymorphisms (SNPs) from WGS of population pools. We used the genomic data to (i) scan these species' genomes for regions of elevated and reduced divergence, (ii) assess key aspects of their joint demographic history based on genomewide site frequency spectra (SFS) and (iii) infer the potential roles of adaptive and deleterious coding mutations in shaping the genomic landscape of divergence. We identified numerous small, unevenly distributed genome regions without fixed polymorphisms despite high overall genomic differentiation. The joint SFS was best explained by ancient and repeated gene flow and allowed pinpointing candidate interspecific migrant tracts. The direction of selection (DoS) differed between genes in putative migrant tracts and the remainder of the genome, thus indicating the potential roles of adaptive divergence and segregating deleterious mutations on the evolution and breakdown of RI. Genes affected by positive selection during divergence were enriched for several functionally interesting groups, including well-known candidate 'speciation genes' involved in plant innate immunity. Our results suggest that adaptive divergence affects RI in these hybridizing species mainly through intrinsic and demographic processes. Integrating genomic with molecular data holds great promise for revealing the effects of particular genetic pathways on speciation.
Data from: Divergent landscape effects on population connectivity in two co-occurring amphibian species
The physical and environmental attributes of landscapes often shape patterns of population connectivity by influencing dispersal and gene flow. Landscape effects on movement are typically evaluated for single species. However, inferences from multiple species are required for multi-species management strategies increasingly being applied in conservation. In this study, I compared the spatial genetic patterns of two amphibian species across the northeastern U.S. and estimated the influence of specific landscape features on observed genetic patterns. The spotted salamander (Ambystoma maculatum) and wood frog (Rana sylvatica) share many ecological attributes related to habitat use, phenology and site fidelity. However, I hypothesized that important differences in their movement patterns and life history would create distinct genetic patterns for each species. Using 14 microsatellite loci, I tested for differences in the level of genetic differentiation between the two species across 22 breeding ponds. The effects of eight landscape features were also estimated by evaluating 32 landscape resistance models. Spotted salamanders exhibited significantly higher genetic differentiation than wood frogs. Different landscape features were also identified as potential drivers of the genetic patterns in each species, with little overlap in model support between species. Collectively, these results provide strong evidence that these two amphibian species interact with the landscape in measurably different ways. The distinct genetic patterns observed are consistent with key differences in movement ability and life history between A. maculatum and R. sylvatica. These results highlight the importance of considering more than one species when assessing the impacts of the landscape matrix on population connectivity, even for ecologically similar species within the same habitats.
Data from: One species for one island? Unexpected diversity and weak connectivity in a widely distributed tropical hydrozoan
Isolation by distance (IBD) is one of the main modes of differentiation in marine species, above all in species presenting low dispersal capacities. This study reports the genetic structuring in the tropical hydrozoan Lytocarpia brevirostris α (sensu Postaire et al, 2016b), a brooding species, from 13 populations in the Western Indian Ocean (WIO) and one from New Caledonia (Tropical Southwestern Pacific). At the local scale, populations rely on asexual propagation at short distance, which was not found at larger scales; identical genotypes were restricted to single populations. After the removal of repeated genotypes, all populations presented significant positive FIS values (between 0.094*** and 0.335***). Gene flow was extremely low at all spatial scales, between sites within islands (<10 km distance) and among islands (100 to>11 000 km distance), with significant pairwise FST values (between 0.012*** and 0.560***). A general pattern of IBD was found at the Indo-Pacific scale, but also within sampled ecoregions of the WIO province. Clustering analyses identified each sampled island as an independent population, whereas analysis of molecular variance indicated that population genetic differentiation was significant at small (within island) and intermediate (among islands within province) spatial scales. The high population differentiation might reflect the life cycle of this brooding hydrozoan, possibly preventing regular dispersal at distances more than a few kilometres and probably leading to high cryptic diversity, each island housing an independent evolutionary lineage.
Data from: Genetic connectivity for two bear species at wildlife crossing structures in Banff National Park
Roads can fragment and isolate wildlife populations, which will eventually decrease genetic diversity within populations. Wildlife crossing structures may counteract these impacts, but most crossings are relatively new, and there is little evidence that they facilitate gene flow. We conducted a three-year research project in Banff National Park, Alberta, to evaluate the effectiveness of wildlife crossings to provide genetic connectivity. Our main objective was to determine how the Trans-Canada Highway and crossing structures along it affect gene flow in grizzly (Ursus arctos) and black bears (Ursus americanus). We compared genetic data generated from wildlife crossings with data collected from greater bear populations. We detected a genetic discontinuity at the highway in grizzly bears but not in black bears. We assigned grizzly bears that used crossings to populations north and south of the highway, providing evidence of bidirectional gene flow and genetic admixture. Parentage tests showed that 47% of black bears and 27% of grizzly bears that used crossings successfully bred, including multiple males and females of both species. Differentiating between dispersal and gene flow is difficult, but we documented gene flow by showing migration, reproduction and genetic admixture. We conclude that wildlife crossings allow sufficient gene flow to prevent genetic isolation.
Data from: Tracking climate change in a dispersal-limited species: reduced spatial and genetic connectivity in a montane salamander
Tropical montane taxa are often locally adapted to very specific climatic conditions, contributing to their lower dispersal potential across complex landscapes. Climate and landscape features in montane regions affect population genetic structure in predictable ways, yet few empirical studies quantify the effects of both factors in shaping genetic structure of montane-adapted taxa. Here, we considered temporal and spatial variability in climate to explain contemporary genetic differentiation between populations of the montane salamander, Pseudoeurycea leprosa. Specifically, we used ecological niche modelling (ENM) and measured spatial connectivity and gene flow (using both mtDNA and microsatellite markers) across extant populations of P. leprosa in the Trans-Mexican Volcanic Belt (TVB). Our results indicate significant spatial and genetic isolation among populations, but we cannot distinguish between isolation by distance over time or current landscape barriers as mechanisms shaping population genetic divergences. Combining ecological niche modelling, spatial connectivity analyses, and historical and contemporary genetic signatures from different classes of genetic markers allows for inference of historical evolutionary processes and predictions of the impacts future climate change will have on the genetic diversity of montane taxa with low dispersal rates. Pseudoeurycea leprosa is one montane species among many endemic to this region and thus is a case study for the continued persistence of spatially and genetically isolated populations in the highly biodiverse TVB of central Mexico.
Data from: Using citizen science monitoring data in species distribution models to inform isotopic assignment of migratory connectivity in wetland birds
Stable isotopes have been used to estimate migratory connectivity in many species. Estimates are often greatly improved when coupled with species distribution models (SDMs), which temper estimates in relation to occurrence. SDMs can be constructed using from point locality data from a variety of sources including extensive monitoring data typically collected by citizen scientists. However, one potential issue with SDM is that these data oven have sampling bias. To avoid this potential bias, an approach using SDMs based on marsh bird monitoring program data collected by citizen scientists and other participants following protocols specifically designed to maximize detections of species of interest at locations representative of the species range. We then used the SDMs to refine isotopic assignments of breeding areas of autumn-migrating and wintering Sora (Porzana carolina), Virginia Rails (Rallus limicola), and Yellow Rails (Coturnicops noveboracensis) based on feathers collected from individuals caught at various locations in the United States from Minnesota south to Louisiana and South Carolina. Sora were assigned to an area that included much of the western U.S. and prairie Canada, covering parts of the Pacific, Central, and Mississippi Flyways. Yellow Rails were assigned to a broad area along Hudson and James Bay in northern Manitoba and Ontario, as well as smaller parts of Quebec, Minnesota, Wisconsin, and Michigan, including parts of the Mississippi and Atlantic Flyways. Virginia Rails were from several discrete areas, including parts of Colorado, New Mexico, the central valley of California, and southern Saskatchewan and Manitoba in the Pacific and Central Flyways. Our study demonstrates extensive data from organized citizen science monitoring programs are especially useful for improving isotopic assignments of migratory connectivity in birds, which can ultimately lead to better informed management decisions and conservation actions.
FIGURES 1–5 in The Australia-New Zealand connection re-visited, with two new species of Cartomothrips (Thysanoptera, Phlaeothripinae)
FIGURES 1–5. Cartomothrips species. (1) tofti, pro, meso & metanota, pelta and tergite II. (2) tofti, head of holotype. (3) abrsi, meso & metanota, pelta and tergite II. (4) abrsi, head & pronotum. (5) tofti, female with fustis internally on segment IX. (6) neboissi, male with genital complex internally on segment IX.
FIGURES 7–15. Cartomothrips species. Thoracic sternites 7–10 in The Australia-New Zealand connection re-visited, with two new species of Cartomothrips (Thysanoptera, Phlaeothripinae)
FIGURES 7–15. Cartomothrips species. Thoracic sternites 7–10: (7) abrsi; (8) tofti; (9) browni; (10) neboissi. (11) browni, head showing postoccipital apophyses. (12) abrsi, male head with weak occipital apophyses. Male sternite VIII with pore plate 13–14: (13) tofti; (14) abrsi. (15) tofti, tergites VII–IX and tube of female [S1 & S2—major setae (S3 arises ventro-laterally); Int—intermediate setae].
FIGURE 4. Dorsal connective, lateral view. A–B in Review of the leafhopper genus Oncopsis Burmeister (Hemiptera: Cicadellidae: Macropsinae) in China with descriptions of two new species
FIGURE 4. Dorsal connective, lateral view. A–B, Oncopsis alni (in part); C, O. anchorous; D, O. aurantiala; E, O. convexus; F, O. cuneiforma; G, O. latusoid; H, O. flavovirens; I, O. fumosa; J, O. furca; K, O. fusca; L, O. kangdingensis; M, O. kuluensis; N, O. melichari; O, O. nigrofaciala; P, O. nigrofaciatus; Q-R, O. obstructa (in part); S, O. odontoidea; T, O. serrulota; U, O. spinosa; V, O. taibaiensis; W, O. testacea; X, O. trimaculata; Y, O. tristis.
Fig. 5 in Across mountains and ocean: species delimitation and historical connectivity in Holarctic and Arctic-Alpine wolf spiders (Lycosidae, Pardosa)
Fig. 5. Introgression in P. saltuaria species group, n = 84, m = 43 datasets. P.hyper.FIN—Finnish P. hyperborea, P.hyper.GR—Greenland P. hyperborea; (a, c, e) de novo assembly; (b, d, f) reference assembly. (a, b) Fbranch D-statistics summary: dotted lines indicate internal node branches, fb—f-branch estimates of admixture; (c, d) fastsimcoal2 scenarios with the highest support: Ne effective population size of corresponding species/population (see fastsimcoal2 section in Supplementary Material for details about codes in brackets); tm—time of population/species merge (split) in generations; tadm—time of admixture in generations; adm—admixture fraction; (e, f) PhyloNetworks: colored lines and numbers indicate direction and proportion of admixture.
Fig. 2 in Across mountains and ocean: species delimitation and historical connectivity in Holarctic and Arctic-Alpine wolf spiders (Lycosidae, Pardosa)
Fig. 2. Maximum likelihood trees: (a) COI, 426 specimens; (b) ddRADseq, 91 specimens, 43,873 SNPs, de novo assembly; (c) ddRADseq, 84 specimens, 113,479 SNPs, de novo assembly; (d) ddRADseq, 84 specimens, 109,247 SNPs. CA—Canada, FI—Finland, FR—France, GL—Greenland, NO—Norway, SL—Slovakia, US—United States of America, n—number of specimens, m—minimum taxon coverage in ipyrad assembly.
Fig. 1 in Across mountains and ocean: species delimitation and historical connectivity in Holarctic and Arctic-Alpine wolf spiders (Lycosidae, Pardosa)
Fig. 1. Distribution map of P. hyperborea based on current literature review. Filled squares—approximate locations of P. hyperborea records in Palearctic; empty square—dubious record of P. hyperborea in Siberia; filled circles—approximate locations of P. hyperborea records in Nearctic.The references on which the map is based are in Supplementary Material.
Fig. 3. Haplotype network for 419 in Across mountains and ocean: species delimitation and historical connectivity in Holarctic and Arctic-Alpine wolf spiders (Lycosidae, Pardosa)
Fig. 3. Haplotype network for 419 specimens of P. saltuaria species group based on mitochondrial COI data. Haplotypes are colored based on morphological identification. Each line is 1 mutation step.
FIGURE 6 in Molecular phylogeny of Aplosporella abexaminans: a novel species revealing the second report of sexual-asexual connection in Aplosporellaceae (Botryosphaeriales) from India
FIGURE 6. Phylogram generated from Maximum likelihood analysis based on combined genes of ITS and LSU of botryosphaerialean taxa. ML and MP bootstrap support values above 50% and BPP support above 0.50 are indicated above the branches. The newly sequenced collection is in red.
FIGURE 5 in Molecular phylogeny of Aplosporella abexaminans: a novel species revealing the second report of sexual-asexual connection in Aplosporellaceae (Botryosphaeriales) from India
FIGURE 5. Phylogram generated from Maximum likelihood analysis based on ITS region and LSU gene of strains belong to Aplosporellaceae. Kellermania dasylirionicola (CBS 131720) was chosen as outgroup. Bootstrap values for ML and MP above 50% and BPP support above 0.50 are indicated. Red names indicate Aplosporella abexaminans.
FIGURE 4 in Molecular phylogeny of Aplosporella abexaminans: a novel species revealing the second report of sexual-asexual connection in Aplosporellaceae (Botryosphaeriales) from India
FIGURE 4. Asexual morph of Aplosporella abexaminans on PDA (NFCCI 5010, ex-type culture). a. Colony on PDA from above. b. Colony on PDA from below. c, d. Initial stage of germinated ascospores on PDA. e, f. Development of hyphae from germinated ascospores on PDA. g. Verruculose hyphae. h. Smooth hyphae. i–m. Conidia. n, o. Chlamydospores (yellow arrows). Scale bars a, b = 20 mm, c–o = 10 µm.
FIGURE 2 in Molecular phylogeny of Aplosporella abexaminans: a novel species revealing the second report of sexual-asexual connection in Aplosporellaceae (Botryosphaeriales) from India
FIGURE 2. Sexual morph of Aplosporella abexaminans (AMH 10212, holotype). a–e Vertical sections through ascostromata. f. Released asci from ascostromata. g, h. Ascus released from an additional sac like structure (blue arrows). Scale bars a, b = 200 µm, c = 100 µm, d–h = 50 µm.
FIGURE 1 in Molecular phylogeny of Aplosporella abexaminans: a novel species revealing the second report of sexual-asexual connection in Aplosporellaceae (Botryosphaeriales) from India
FIGURE 1. Stem of Murraya koenigii. a, b. Habit of ascostromata on the bark of host stem. Scale bars a, b = 5 mm.
Combining population genomics with demographic analyses highlights habitat patchiness and larval dispersal as determinants of connectivity in coastal fish species
<p>Gene flow shapes spatial genetic structure as well as the potential for local adaptation of populations. Among marine animals with non-migratory adults, the presence or absence of a pelagic larval stage is thought to be a key determinant in shaping gene flow and the genetic structure of populations. In addition, the spatial distribution of suitable habitats will influence the distribution of biological populations and their pattern of gene flow. We used whole genome sequencing to study demographic history and reduced representation (ddRAD) sequencing data to analyze spatial genetic structure in the broadnosed pipefish (<em>Syngnathus typhle</em>). Its main habitat are seagrass meadows, which along the study coast (SW Norway) have a patchy distribution. Combining the results from several analyses including scans for selection, suggests that stochastic genetic drift has shaped the observed population structure largely due to its patchy habitat distribution. The restricted gene flow is further driven by life history traits such as the presence of parental care combined with no pelagic life stages, resulting in a clear isolation-by-distance pattern spanning 100s of kilometers.</p> <p>The spatial scale of demographic connectivity was inferred from long-term (~30 year) census population counts that uncovered a sharp decline in spatial correlations in abundance with distance (37% decorrelation over 2 km). These findings were contrasted with data from two other fish species sampled along the same coastline, both having pelagic larval stages lasting ~20 days (corkwing wrasse, <em>Symphodus melops</em>, and black goby, <em>Gobus niger</em>) where the population structure is not that evident. For these species, we found a wider spatial scale of demographic connectivity (decorrelation distances of 14 and 28 km, respectively), and weaker isolation-by-distance except at one point along the coast where both species revealed a strong barrier to gene flow, seemingly due to a lack of suitable habitat. Combined, these findings suggest that habitat fragmentation and absence of a pelagic larval stage in pipefish strongly increases geographic structuring, while the pelagic larvae of wrasse and goby increase genetic and demographic connectivity, except over extensive habitat shifts.</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.