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59 results for “gene dispersal”
Data from: Rampant dispersal without gene-flow: Reproductively and geographically isolated lineages of the Supertramp lizard Lamprolepis smaragdina permeate the lesser Sunda Archipelago
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Analysing landscape effects on dispersal networks and gene flow with genetic graphs
<p>Graph-theoretic approaches have relevant applications in landscape genetic analyses. When species form populations in discrete habitat patches, genetic graphs can be used i) to identify direct dispersal paths followed by propagules or ii) to quantify landscape effects on multigenerational gene flow. However, the influence of their construction parameters remains to be explored. Using a simulation approach, we constructed genetic graphs using several pruning methods (geographical distance thresholds, topological constraints, statistical inference) and genetic distances to weight graph links (F<sub>ST</sub>, D<sub>PS</sub>, Euclidean genetic distances). We then compared the capacity of these different graphs to i) identify the precise topology of the dispersal network and ii) to infer landscape resistance to gene flow from the relationship between cost-distances and genetic distances. Although not always clear-cut, our results showed that methods based on geographical distance thresholds seem to better identify dispersal networks in most cases. More interestingly, our study demonstrates that a subselection of pairwise distances through graph pruning (thereby reducing the number of data points) can counter-intuitively lead to improved inferences of landscape effects on dispersal. Finally, we showed that genetic distances such as the D<sub>PS</sub> or Euclidean genetic distances should be preferred over the F<sub>ST</sub> for landscape effect inference as they respond faster to landscape changes.</p>
Data from: Gene expression shifts in yellow-bellied marmots prior to natal dispersal
The causes and consequences of vertebrate natal dispersal have been studied extensively, yet little is known about the molecular mechanisms involved. We used RNA-seq to quantify transcriptomic gene expression in blood of wild yellow-bellied marmots (Marmota flaviventer) prior to dispersing from or remaining philopatric to their natal colony. We tested three predictions. First, we hypothesized dispersers and residents will differentially express genes and gene networks since dispersal is physiologically demanding. Second, we expected differentially expressed genes to be involved in metabolism, circadian processes, and immune function. Finally, in dispersing individuals, we predicted differentially expressed genes would change as a function of sampling date relative to dispersal date. We detected 150 differentially expressed genes, including genes that have critical roles in lipid metabolism and antigen defense. Gene network analysis revealed a module of 126 co-expressed genes associated with dispersal that was enriched for extra-cellular immune function. Of the dispersal-associated genes, 22 altered expression as a function of days until dispersal, suggesting that dispersal-associated genes do not initiate transcription on the same time scale. Our results provide novel insights into the fundamental molecular changes required for dispersal and suggest evolutionary conservation of functional pathways during this behavioral process.
Male dispersal drives gene flow in Timber Rattlesnakes (Crotalus horridus)
<p class="MsoNormal">Threatened across much of their range, timber rattlesnakes (<em>Crotalus horridus</em>) exhibit patterns in movement and genetic diversity that are shaped by many aspects of their environments in ways that may foster or constrain conservation. We combine movement data with nuclear and mitochondrial population genetic data to understand the population structure of snakes in four overwintering sites (hibernacula) in central Pennsylvania. Our analyses support the conclusion that hibernacula separated by only a few kilometers can represent genetically distinct populations. In addition, as the first dataset to compare nuclear and mitochondrial patterns in<em> C. horridus</em>, we provide novel evidence for how likely asymmetry in gene flow (with males responsible for inter-hibernaculum matings) shapes timber rattlesnake population genetics.</p>
Fine-scale spatial genetic structure, mating and gene flow dispersal patterns in Parkia biglobosa populations under different levels of habitat fragmentation
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Data from: Gene expression shifts in yellow-bellied marmots prior to natal dispersal
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Analysing landscape effects on dispersal networks and gene flow with genetic graphs
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Phylogenomic analysis reveals dispersal-driven speciation and divergence with gene flow in Lesser Sunda Flying Lizards (Genus Draco)
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Male dispersal drives gene flow in Timber Rattlesnakes (Crotalus horridus)
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Data from: Asymmetric contributions of seed and pollen to gene dispersal in the marsh orchid Dactylorhiza umbrosa in Asia Minor
<p>Orchids differ from other plants in their extremely small and partly air-filled seeds that can be transported long distances by wind. Seed dispersal in orchids is expected to contribute strongly to overall gene flow, and orchids generally express low levels of genetic differentiation between populations and low pollen to seed flow ratios. However, studies in orchids distributed in northern Europe have often found a poor geographic structuring of genetic variation. Here, we studied geographic differentiation in the marsh orchid <i>Dactylorhiza umbrosa</i>, which is widely distributed in upland regions from Asia Minor to Central Asia. These areas were less affected by Pleistocene ice ages than northern Europe and the orchid should have been able to survive the last ice age in local refugia. In the plastid genome, which is dispersed by seeds, populations at close distance were clearly divergent, but the differentiation still increased with geographic distance, and a significant phylogeographic structure had developed. In the nuclear genome, which is dispersed by both seeds and pollen, populations showed an even stronger correlation between genetic and geographic distance, but average levels of differentiation were lower than in the plastid genome, and no phylogeographic structure was evident. Combining plastid and nuclear data, we found that the ratio of pollen to seed dispersal (<i>mp/ms</i>) decreases with physical distance. Comparison with orchids that grow in parts of Europe that were glaciated during the last ice suggests that a balanced structure of genetic diversity develops only slowly in many terrestrial orchids, despite of efficient seed dispersal.</p>
Data from: Estimating the molecular evolutionary rates of mitochondrial genes referring to Quaternary Ice Age events with inferred population expansions and dispersals in Japanese Apodemus
Background: Determining reliable evolutionary rates of molecular markers is essential in illustrating historical episodes with phylogenetic inferences. Although emerging evidence has suggested a high evolutionary rate for intraspecific genetic variation, it is unclear how long such high evolutionary rates persist because a recent calibration point is rarely available. Other than using fossil evidence, it is possible to estimate evolutionary rates by relying on the well-established temporal framework of the Quaternary glacial cycles that would likely have promoted both rapid expansion events and interisland dispersal events. Results: We examined mitochondrial cytochrome b (Cytb) and control region (CR) gene sequences in two Japanese wood mouse species, Apodemus argenteus and A. speciosus, of temperate origin and found signs of rapid expansion in the population from Hokkaido, the northern island of Japan. Assuming that global warming after the last glacial period 7–10 thousand years before present (kyr BP) was associated with the expansion, the evolutionary rates (sites per million years, myr) of Cytb and CR were estimated as 11–16% and 22–32%, respectively, for A. argenteus, and 12–17% and 17–24%, respectively, for A. speciosus. Additionally, the significant signature of rapid expansion detected in the mtDNA sequences of A. speciosus from the remaining southern main islands, Honshu, Shikoku, and Kyushu, provided an estimated Cytb evolutionary rate of 3.1%/site/myr under the assumption of a postglacial population expansion event long ago, most probably at 130 kyr BP. Bayesian analyses using the higher evolutionary rate of 11–17%/site/myr for Cytb supported the recent demographic or divergence events associated with the Last Glacial Maximum. However, the slower evolutionary rate of 3.1%/site/myr would be reasonable for several divergence events that were associated with glacial periods older than 130 kyr BP. Conclusions: The faster and slower evolutionary rates of Cytb can account for divergences associated with the last and earlier glacial maxima, respectively, in the phylogenetic inference of murine rodents. The elevated evolutionary rate seemed to decline within 100,000 years.
Data from: Return of the ghosts of dispersal past: historical spread and contemporary gene flow in the blue sea star Linckia laevigata
Marine animals inhabiting the Indian and Pacific oceans have some of the most extensive species ranges in the world, sometimes spanning over half the globe. These Indo-Pacific species present a challenge for study with both geographic scope and sampling density as limiting factors. Here, we augment and aggregate phylogeographic sampling of the iconic blue sea star, Linckia laevigata Linnaeus, 1758, and present one of the most geographically comprehensive genetic studies of any Indo-Pacific species to date, sequencing 392 base pairs of mitochondrial COI from 791 individuals from 38 locations spanning over 14,000 km. We first use a permutation based multiple-regression approach to simultaneously evaluate the relative influence of historical and contemporary gene flow together with putative barriers to dispersal. We then use a discrete diffusion model of phylogeography to infer the historical migration and colonization routes most likely used by L. laevigata across the Indo-Pacific. We show that estimates of genetic structure have a stronger correlation to geographic distances than to "oceanographic" distances from a biophysical model of larval dispersal, reminding us that population genetic estimates of gene flow and genetic structure are often shaped by historical processes. While the diffusion model was equivocal about the location of the mitochondrial most recent common ancestor (MRCA), we show that gene flow has generally proceeded in a step-wise manner across the Indian and Pacific oceans. We do not find support for previously described barriers at the Sunda Shelf and within Cenderwasih Bay. Rather, the strongest genetic disjunction is found to the east of Cenderwasih Bay along northern New Guinea. These results underscore the importance of comprehensive range-wide sampling in marine phylogeography.
Data from: Variation at phenological candidate genes correlates with timing of dispersal and plumage morph in a sedentary bird of prey
Polymorphic genes involved in the conserved molecular signalling of circadian and circannual clocks may play important roles in governing the timing of breeding and dispersal and thereby affect fitness in vertebrates. However, relatively few studies have explored associations between phenological candidate genes and behaviour, and these are somewhat biased towards particular taxonomic groups such as passerine birds and salmonid fish. Consequently, we assayed microsatellite polymorphisms within the exonic and 3' untranslated regions of the regulatory genes CLOCK, NPAS2, ADCYAP1 and CREB1 in the common buzzard (Buteo buteo), a polymorphic raptor species with three plumage morphs that differ in key life history traits including lifetime reproductive success. In contrast to studies of passerines, CLOCK poly-glutamine (poly-Q) was found to be monomorphic in 976 common buzzard nestlings as well as in three other Buteo species. Moreover, none of the candidate genes were significantly associated with fledging dates, although intermediately melanised females were found to lay earlier on average than light or dark morph individuals, and their offspring carried longer ADCYAP1 alleles. In contrast, all three candidate genes explained significant variation in one or more measures of juvenile buzzard dispersal (resighting probability, timing of dispersal and distance dispersed). Our findings contribute towards a broader body of work on the adaptive significance of CLOCK polymorphism, while also building upon previous studies that have documented links between ADCYAP1 variability and the timing of migration.
Data from: Walking in a heterogeneous landscape: dispersal, gene-flow and conservation implications for the giant panda in the Qinling Mountains
Understanding the interaction between life history, demography and population genetics in threatened species is critical for the conservations of viable populations. In the context of habitat loss and fragmentation, identifying the factors that underpin the structuring of genetic variation within populations can allow conservationists to evaluate habitat quality and connectivity and help to design dispersal corridors effectively. In this study, we carried out a detailed, fine-scale landscape genetic investigation of a giant panda population for the first time, using a large microsatellite data set and examined the role of isolation-by-barriers (IBB), isolation-by-distance (IBD) and isolation-by-resistance (IBR) in shaping the genetic variation pattern of giant pandas in the Qinling Mountains. We found that the Qinling population comprises one continuous genetic cluster, and among the landscape hypotheses tested, gene flow was found to be correlated with resistance gradients for two topographic factors, rather than geographical distance or barriers. Gene-flow was inferred to be facilitated by easterly slope aspect and to be constrained by land surface with high topographic complexity. These factors are related to benign micro-climatic conditions for both the pandas and the food resources they rely on and more accessible topographic conditions for movement, respectively. We identified optimal corridors based on these results, aiming to promote gene flow between human-induced habitat fragments. These findings provide insight into the permeability and affinities of the giant panda habitat and offer important reference for the conservation of the giant panda and its habitat.
Data from: Gene flow by larval dispersal in the Antarctic notothenioid fish Gobionotothen gibberifrons
The diversification of the teleost suborder Notothenioidei (Perciformes) in Antarctic waters provides one of the most striking examples of a marine adaptive radiation. Along with a number of adaptations to the cold environment, such as the evolution of antifreeze glycoproteins, notothenioids diversified into eight families and at least 130 species. Here, we investigate the genetic population structure of the humped rockcod (Gobionotothen gibberifrons), a benthic notothenioid fish. Six populations were sampled at different locations around the Scotia Sea, comprising a large part of the species' distribution range (N=165). Our analyses based on mitochondrial DNA sequence data (352 bp) and eight microsatellite markers reveal a lack of genetic structuring over large geographic distances (ΦST≤0.058, F ST≤0.005, p-values nonsignificant). In order to test whether this was due to passive larval dispersal, we used GPS-tracked drifter trajectories, which approximate movement of passive surface particles with ocean currents. The drifter data indicate that the Antarctic Circumpolar Current (ACC) connects the sampling locations in one direction only (West-East), and that passive transport is possible within the four-months larval period of G. gibberifrons. Indeed, when applying the isolation-with-migration model in IMA, strong unidirectional West-East migration rates are detected in the humped rockcod. This leads us to conclude that, in G. gibberifrons, genetic differentiation is prevented by gene flow via larval dispersal with the ACC.
Data from: Maintaining genetic diversity and population panmixia through dispersal and not gene flow in a holocyclic heteroecious aphid species
Heteroecious holocyclic aphids exhibit both sexual and asexual reproduction and alternate among primary and secondary hosts. Most of these aphids can feed on several related hosts, and invasions to new habitats may limit the number of suitable hosts. For example, the aphid specialist Aphis glycines survives only on the primary host buckthorn (Rhamnus spp.) and the secondary host soybean (Glycine max) in North America where it is invasive. Owing to this specialization and sparse primary host distribution, host colonization events could be localized and involve founder effects, impacting genetic diversity, population structure and adaptation. We characterized changes in the genetic diversity and structure across time among A. glycines populations. Populations were sampled from secondary hosts twice in the same geographical location: once after secondary colonization (early season), and again immediately before primary host colonization (late season). We tested for evidence of founder effects and genetic isolation in early season populations, and whether or not late-season dispersal restored genetic diversity and reduced fragmentation. A total of 24 single-nucleotide polymorphisms and 6 microsatellites were used for population genetic statistics. We found significantly lower levels of genotypic diversity and more genetic isolation among early season collections, indicating secondary host colonization occurred locally and involved founder effects. Pairwise FST decreased from 0.046 to 0.017 in early and late collections, respectively, and while genetic relatedness significantly decreased with geographical distance in early season collections, no spatial structure was observed in late-season collections. Thus, late-season dispersal counteracts the secondary host colonization through homogenization and increases genetic diversity before primary host colonization.
Data from: Fire-induced population reduction and landscape opening increases gene flow via pollen dispersal in Pinus halepensis
Population reduction and disturbances may alter dispersal, mating patterns and gene flow. Rather than taking the common approach of comparing different populations or sites, here we studied gene flow via wind-mediated effective pollen dispersal on the same plant individuals before and after a fire-induced population drop, in a natural stand of Pinus halepensis. The fire killed 96% of the pine trees in the stand and cleared the vegetation in the area. Thirteen trees survived in two groups separated by ~80 m, and seven of these trees had serotinous (closed) pre-fire cones that did not open despite the fire. We analyzed pollen from closed pre- and post-fire cones using microsatellites. The two groups of surviving trees were highly genetically differentiated, and the pollen they produced also showed strong among-group differentiation and very high kinship both before and after the fire, indicating limited and very local pollen dispersal. The pollen not produced by the survivors also showed significant pre-fire spatial genetic structure and high kinship, indicating mainly within-population origin and limited gene flow from outside, but became spatially homogeneous with random kinship after the fire. We suggest that post-fire gene flow via wind-mediated pollen dispersal increased by two putative mechanisms: 1) a drastic reduction in local pollen production due to population thinning, effectively increasing pollen immigration; 2) an increase in wind speeds in the vegetation-free post-fire landscape. This research shows that dispersal can alleviate negative genetic effects of population size reduction, and that disturbances might enhance gene flow, rather than reduce it.
Data from: Estimates of gene flow and dispersal in wild riverine Brook Trout (Salvelinus fontinalis) populations reveal ongoing migration and introgression from stocked fish
As anthropogenic impacts accelerate changes to landscapes across the globe, understanding how genetic population structure is influenced by habitat features and dispersal is key to preserving evolutionary potential at the species level. Furthermore, knowledge of these interactions is essential to identifying potential constraints on local adaptation and for the development of effective management strategies. We examined these issues in Brook Trout (Salvelinus fontinalis) populations residing in the Upper Hudson River watershed of New York State by investigating the spatial genetic structure of over 350 fish collected from 14 different sampling locations encompassing three river systems. Population genetic analyses of microsatellite data suggest that fish in the area exhibit varying degrees of introgression from nearby State-directed supplementation activities. Levels of introgression in these populations correlate with water-way distance to stocking sites, although genetic population structure at the level of individual tributaries as well as their larger, parent river systems is also detectable and is dictated by migration and influenced by habitat connectivity. These findings represent a significant contribution to the current literature surrounding Brook Trout migration and dispersal, especially as it relates to larger interconnected systems. This work also suggests that stocking activities may have far-reaching consequences that are not directly limited to the immediate area where stocking occurs. The framework and data presented here may aid in the development of other local aquatic species-focused conservation plans that incorporate molecular tools to answer complex questions regarding diversity mapping, and genetically important conservation units.
Data from: Combined genetic and telemetry data reveal high rates of gene flow, migration, and long-distance dispersal potential in Arctic ringed seals (Pusa hispida)
Ringed seals (Pusa hispida) are broadly distributed in seasonally ice covered seas, and their survival and reproductive success is intricately linked to sea ice and snow. Climatic warming is diminishing Arctic snow and sea ice and threatens to endanger ringed seals in the foreseeable future. We investigated the population structure and connectedness within and among three subspecies: Arctic (P. hispida hispida), Baltic (P. hispida botnica), and Lake Saimaa (P. hispida saimensis) ringed seals to assess their capacity to respond to rapid environmental changes. We consider (a) the geographical scale of migration, (b) use of sea ice, and (c) the amount of gene flow between subspecies. Seasonal movements and use of sea ice were determined for 27 seals tracked via satellite telemetry. Additionally, population genetic analyses were conducted using 354 seals representative of each subspecies and 11 breeding sites. Genetic analyses included sequences from two mitochondrial regions and genotypes of 9 microsatellite loci. We found that ringed seals disperse on a pan-Arctic scale and both males and females may migrate long distances during the summer months when sea ice extent is minimal. Gene flow among Arctic breeding sites and between the Arctic and the Baltic Sea subspecies was high; these two subspecies are interconnected as are breeding sites within the Arctic subspecies.
Anthropogenic disturbance drives dispersal syndromes, demography, and gene flow in amphibian populations
<p>There is growing evidence that anthropogenic landscapes can strongly influence the evolution of dispersal, particularly through fragmentation, and may drive organisms into an evolutionary trap by suppressing dispersal. However, the influence on dispersal evolution of anthropogenic variation in habitat patch turnover has so far been largely overlooked. In this study, we examined how human-driven variation in patch persistence affects dispersal rates and distances, determines dispersal-related phenotypic specialization, and drives neutral genetic structure in spatially structured populations. We addressed this issue in an amphibian, Bombina variegata, using an integrative approach combining capture-recapture modeling, demographic simulation, common garden experiments, and population genetics. B. variegata reproduces in small ponds that occur either in habitat patches that are persistent (i.e. several decades or more), located in riverine environments with negligible human activity, or in patches that are highly temporary (i.e. a few years), created by logging operations in intensively harvested woodland. Our capture-recapture models revealed that natal and breeding dispersal rates and distances were drastically higher in spatially structured populations (SSPs) in logging environments than in riverine SSPs. Population simulations additionally showed that dispersal costs and benefits drive the fate of logging SSPs, which cannot persist without dispersal. The common garden experiments revealed that toadlets reared in laboratory conditions have morphological and behavioral specialization that depends on their habitat of origin. Toadlets from logging SSPs were found to have higher boldness and exploration propensity than those from riverine SSPs, indicating transgenerationally transmitted dispersal syndromes. We also found contrasting patterns of neutral genetic diversity and gene flow in riverine and logging SSPs, with genetic diversity and effective population size considerably higher in logging than in riverine SSPs. In parallel, intra-patch inbreeding and relatedness levels were lower in logging SSPs. Controlling for the effect of genetic drift and landscape connectivity, gene flow was found to be higher in logging than in riverine SSPs. Taken together, these results indicate that anthropogenic variation in habitat patch turnover may have an effect at least as important as landscape fragmentation on dispersal evolution and the long-term viability and genetic structure of wild populations.</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.