Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
1,271
datasets available to search
ShareScore release 0.9.0
Dataset results
1,271 results for “Data Flow”
Data from: Intercontinental genetic structure and gene flow in Dunlin (Calidris alpina), a potential vector of avian influenza
Waterfowl (Anseriformes) and shorebirds (Charadriiformes) are the most common wild vectors of influenza A viruses. Due to their migratory behavior, some may transmit disease over long distances. Migratory connectivity studies can link breeding and nonbreeding grounds while illustrating potential interactions among populations that may spread diseases. We investigated Dunlin (Calidris alpina), a shorebird with a subspecies (C. a. arcticola) that migrates from nonbreeding areas endemic to avian influenza in eastern Asia to breeding grounds in northern Alaska. Using microsatellites and mitochondrial DNA, we illustrate genetic structure among six subspecies: C. a. arcticola, C. a. pacifica, C. a. hudsonia, C. a. sakhalina, C. a. kistchinski, and C. a. actites. We demonstrate that mitochondrial DNA can help distinguish C. a. arcticola on the Asian nonbreeding grounds with >70% accuracy depending on their relative abundance, indicating that genetics can help determine if C. a. arcticola occurs where they may be exposed to highly pathogenic avian influenza (HPAI) during outbreaks. Our data reveal asymmetric intercontinental gene flow, with some C. a. arcticola short-stopping migration to breed with C. a. pacifica in western Alaska. Because C. a. pacifica migrates along the Pacific Coast of North America, interactions between these subspecies and other taxa provides route for transmission of HPAI into other parts of North America.
Data from: Estimating the impact of divergent mating phenology between residents and migrants on the potential for gene flow
Gene flow between populations can allow the spread of beneficial alleles and genetic diversity between populations, with importance to conservation, invasion biology, and agriculture. Levels of gene flow between populations vary not only with distance, but also with divergence in reproductive phenology. Since phenology is often locally adapted, arriving migrants may be reproductively out of synch with residents, which can depress realized gene flow. In flowering plants, the potential impact of phenological divergence on hybridization between populations can be predicted from overlap in flowering schedules—the daily count of flowers capable of pollen exchange—between a resident and migrant population. The accuracy of this prospective hybridization estimate, based on parental phenotypes, rests upon the assumptions of unbiased pollen transfer between resident and migrant active flowers. We tested the impact of phenological divergence on resident–migrant mating frequencies in experiments that mimicked a single large gene flow event. We first prospectively estimated mating frequencies two lines of Brassica rapaselected or early and late flowering. We then estimated realized mating frequencies retrospectively through progeny testing. The two estimates strongly agreed in a greenhouse experiment, where procedures ensured saturating, unbiased pollination. Under natural pollination in the field, the rate of resident–migrant mating, was lower than estimated by phenological divergence alone, although prospective and retrospective estimates were correlated. In both experiments, differences between residents and migrants in flowering schedule shape led to asymmetric hybridization. Results suggest that a prospective estimate of hybridization based on mating schedules can be a useful, although imperfect, tool for evaluating potential gene flow. They also illustrate the impact of mating phenology on the magnitude and symmetry of reproductive isolation.
Data from: Fragmentation can increase spatial genetic structure without decreasing pollen-mediated gene flow in a wind-pollinated tree
Fragmentation reduces population sizes, increases isolation between habitats, and can result in restricted dispersal of pollen and seeds. Given that diploid seed dispersal contributes more to shaping fine-scale spatial genetic structure than haploid pollen flow, we tested whether fine-scale SGS can be sensitive to fragmentation even if extensive pollen dispersal is maintained. Castanopsis sclerophylla (Lindley & Paxton) Schottky (Fagaceae), a wind-pollinated and gravity seed-dispersed tree, was studied in an area of Southeast China where its populations have been fragmented to varying extents by human activity. Using different age classes of trees in areas subject to varying extents of fragmentation, we found no significant difference in genetic diversity between pre- and post-fragmentation C. sclerophylla subpopulations. Genetic differentiation among post-fragmentation subpopulations was also only slightly lower than among post-fragmentation subpopulations. In the most fragmented habitat, selfing rates were significantly higher than zero in pre-fragmentation, but not post-fragmentation, cohorts. These results suggest that fragmentation had not decreased gene flow among these populations and that pollen flow remains extensive. However, significantly greater fine-scale SGS was found in post-fragmentation subpopulations in the most fragmented habitat, but not in less fragmented habitats. This alteration in SGS reflected more restricted seed dispersal, induced by changes in the physical environments and the prevention of secondary seed dispersal by rodents. An increase in SGS can therefore result from more restricted seed dispersal, even in the face of extensive pollen flow, making it a sensitive indicator of the negative consequences of population fragmentation.
Data from: A tight balance between natural selection and gene flow in a southern African arid-zone endemic bird
Gene flow is traditionally thought to be antagonistic to population differentiation and local adaptation. However, recent studies have demonstrated that local adaptation can proceed provided that selection is greater than the homogenising effects of gene flow. We extend these initial studies by combining ecology (climate), phenotype (body size), physiological genetics (oxidative phosphorylation genes) and neutral loci (nuclear microsatellites and introns) to test whether selection can counter-balance gene flow and hence promote local adaptation in a bird whose distribution spans an aridity gradient. Our results show that the Karoo scrub-robin's climatic niche is spatially structured, providing the potential for local adaptation to develop. We found remarkably discordant patterns of divergence among mtDNA, morphology and neutral loci. For the mitochondrial genes, two amino acid replacements, strong population structure and reduced gene flow were associated with the environmental gradient separating western coastal sites from the interior of southern Africa. In contrast, morphology and the neutral loci exhibited variation independent of environmental variables, and revealed extensive levels of gene flow across the aridity gradient, 50 times larger than the estimates for mitochondrial genes. Together, our results suggest that selective pressures on physiology, mediated by the mitochondrial genome, may well be a common mechanism for facilitating local adaptation to new climatic conditions.
Data from: Local selection modifies phenotypic divergence among Rana temporaria populations in the presence of gene flow
In ectotherms, variation in life-history traits among populations is common and suggests local adaptation. However, geographic variation itself is not a proof for local adaptation, since genetic drift and gene flow may also shape patterns of quantitative variation. We studied local and regional variation in means and phenotypic plasticity of larval life history traits in the common frog Rana temporaria using six populations from central Sweden, breeding in either open canopy or partially closed canopy ponds. To separate local adaptation from genetic drift we compared differentiation in quantitative genetic traits (QST) obtained from a common garden experiment with differentiation in presumably neutral microsatellite markers (FST). We found that R. temporaria populations differ in means and plasticities of life-history traits in different temperatures at local, and in Fst at regional scale. Comparisons of differentiation in quantitative traits and in molecular markers suggested that natural selection was responsible for the divergence in growth and development rates as well as in temperature-induced plasticity, indicating local adaptation. However, at low temperature the role of genetic drift could not be separated from selection. Phenotypes were correlated with forest canopy closure but not with geographical or genetic distance. These results indicate that local adaptation can evolve in the presence of ongoing gene flow among populations, and that natural selection is strong in this system.
Data from: Genetic divergence with ongoing gene flow is maintained by the use of different hosts in phytophagous ladybird beetles genus Henosepilachna
Adaptation to different environments can promote population divergence via natural selection even in the presence of gene flow–a phenomenon that typically occurs during ecological speciation. To elucidate how natural selection promotes and maintains population divergence during speciation, we investigated the population genetic structure, degree of gene flow and heterogeneous genomic divergence in three closely related Japanese phytophagous ladybird beetles: Henosepilachna pustulosa, H. niponica and H. yasutomii. These species act as a generalist, a wild thistle (Cirsium spp.) specialist and a blue cohosh (Caulophyllum robustum) specialist, respectively, and their ranges differ accordingly. The two specialist species widely co-occur but are reproductively isolated solely due to their high specialisation to a particular host plant. Genome-wide amplified fragment-length polymorphism (AFLP) markers and mitochondrial cytochrome c oxidase subunit I (COI) gene sequences demonstrated obvious genome-wide divergence associated with both geographic distance and ecological divergence. However, a hybridisation assessment for both AFLP loci and the mitochondrial sequences revealed a certain degree of unidirectional gene flow between the two sympatric specialist species. Principal coordinates analysis (PCoA) based on all of the variable AFLP loci demonstrated that there are genetic similarities between populations from adjacent localities irrespective of the species (i.e. host range). However, a further comparative genome scan identified a few fractions of loci representing approximately 1% of all loci as different-host associated outliers. These results suggest that these three species had a complex origin, which could be obscured by current gene flow, and that ecological divergence can be maintained with only a small fraction of the genome is related to different host use even when there is a certain degree of gene flow between sympatric species pairs.
Data from: Flow-ecology relationships are spatially structured and differ among flow regimes
1. In streams, hydrology is a predominant driver of ecological structure and function. Providing adequate flows to support aquatic life, or environmental flows, is therefore a top management priority in stream systems. 2. Flow regime classification is a widely accepted approach for establishing environmental flow guidelines. However, it is surprisingly difficult to quantify relationships between hydrology and ecology (flow-ecology relationships) while describing how these relationships vary across classified flow regimes. Developing such relationships is complicated by several sources of spatial bias, such as autocorrelation due to spatial design, flow regime classification, and other environmental or ecological sources of spatial bias. 3. We used mixed moving-average spatial stream network models to develop flow-ecology relationships across classified flow regimes and to assess spatial patterns of these relationships. We compared relationships between fish traits and life-history strategies with hydrologic metrics across flow regimes and assessed whether spatial autocorrelation influenced these relationships. 4. Trait-hydrology relationships varied between flow regimes and across all streams combined. Some relationships between traits and hydrologic metrics fit predictions based on life-history theory, while others exhibited unexpected relationships with hydrology. Spatial factors described a large proportion of variability in fish traits and different patterns of spatial autocorrelation were observed in different flow regimes. Synthesis and Applications. Further work is needed to understand why flow-ecology relationships vary across classified flow regimes and why these relationships may not fit predictions based on life-history theories. Managers determining environmental flow standards need to be aware that different hydrologic metrics are often important drivers of fish trait diversity in different flow-regimes. Flow-ecology relationships may therefore be confounded by spatial structure that is inherent in flow regime classification and much existing biological data. Complex patterns of spatial bias should be considered when managing stream systems within an environmental flows framework.
Data from: Considering gene flow when using coalescent methods to delimit lineages of North American pitvipers of the genus Agkistrodon
Examining species diversity and mechanisms of speciation using coalescent models provides a framework for how regional diversity is accrued, even in well-studied areas such as the Nearctic. It is likely, that gene flow among closely-related species with adjacent distributions may be common. However, the absence of gene flow is a primary assumption of many phylogeographical methods that produce species trees and delimit species using Bayesian or likelihood functions in a coalescent framework. In the present study, we examine delimitation when gene flow between species is present using empirical datasets from two species of North American pitvipers of the genus Agkistrodon. We also use niche modelling to determine whether these young lineages occur in distinct environmental niches. To manage the problem of gene flow between species, we first identify admixed individuals, demonstrate that gene flow has occurred, and then identify the impact of alternative population assignments of admixed individuals on delimitation posterior probabilities. In addition, we examine the influence of mitochondrial genes relative to other loci combined in coalescent analyses that delimit species. Here, we find that the copperheads (Agkistrodon contortrix) and the cottonmouths (Agkistrodon piscivorus) are each composed of two distinct species, with each occupying different niches. Importantly, we find that species can be delimited when the amount of gene flow between lineages is low, although the methods are acutely sensitive to population assignment of individuals.
Data from: Gene flow among wild and domesticated almond species: insights from chloroplast and nuclear markers
Hybridization has played a central role in the evolutionary history of domesticated plants. Notably, several breeding programs relying on gene introgression from the wild compartment have been performed in fruit tree species within the genus Prunus but few studies investigated spontaneous gene flow among wild and domesticated Prunus species. Consequently, a comprehensive understanding of genetic relationships and levels of gene flow between domesticated and wild Prunus species is needed. Combining nuclear and chloroplastic microsatellites, we investigated the gene flow and hybridization among two key almond tree species, the cultivated Prunus dulcis and one of the most widespread wild relative Prunus orientalis in the Fertile Crescent. We detected high genetic diversity levels in both species along with substantial and symmetric gene flow between the domesticated P. dulcis and the wild P. orientalis. These results were discussed in light of the cultivated species diversity, by outlining the frequent spontaneous genetic contributions of wild species to the domesticated compartment. In addition, crop-to-wild gene flow suggests that ad hoc transgene containment strategies would be required if genetically modified cultivars were introduced in the northwestern Mediterranean.
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: Spatial variation in climate mediates gene flow across an island archipelago
High levels of gene flow among partially isolated populations can overwhelm selection and limit local adaptation. This process, known as "gene swamping," can homogenize genetic diversity among populations and reduce the capacity of a species to withstand rapid environmental change. We studied brown anole lizards (Anolis sagrei) distributed across seven islands in The Bahamas. We used microsatellite markers to estimate gene flow among islands and then examined the correlation between thermal performance and island temperature. The thermal optimum for sprint performance was correlated with both mean and maximum island temperature whereas performance breadth was not correlated with any measure of temperature variation. Gene flow between islands decreased as the difference between mean island temperatures increased, even when those islands were adjacent to one another. These data suggest that phenotypic variation is the result of either 1) local genetic adaptation with selection against immigrants maintaining variation in the thermal optimum, 2) irreversible forms of adaptive plasticity such that immigrants have reduced fitness, or 3) an interaction between fixed genetic differences and plasticity. In general, the patterns of gene flow we observed suggest that local thermal environments represent important ecological filters that can mediate gene flow on relatively fine geographic scales.
Data from: A rangewide herbarium-derived dataset indicates high levels of gene flow in black cherry (Prunus serotina)
Aim: Isolation by Distance (IBD) is a genetic pattern in which populations geographically closer to one another are more genetically similar to each other than populations which are farther apart. Black cherry (Prunus serotina Ehrh.) (Rosaceae) is a forest tree species widespread in eastern North America, and found sporadically in the southwestern United States, Mexico, and Guatemala. IBD has been studied in relatively few North American plant taxa, and no study has rigorously sampled across the range of such a widespread species. In this study, IBD and overall genetic structure were assessed in eastern black cherry (P. serotina Ehrh. subsp. serotina), the widespread subspecies of eastern North America. Location: Eastern North America Taxon: Prunus serotina Ehrh. Rosaceae Methods: Dense sampling across the entire range of eastern black cherry was made possible by genotyping 15 microsatellite loci in 439 herbarium samples from all portions of the range. Mantel tests and STRUCTURE analyses were performed to evaluate the hypothesis of IBD and genetic structure. Results: Mantel tests demonstrated significant but weak IBD, while STRUCTURE analyses revealed no clear geographic pattern of genetic groups. Main conclusions: The modest geographic/genetic structure across the eastern black cherry range suggests widespread gene flow in this taxon. This is consistent with P. serotina's status as a disturbance-associated species. Further studies should similarly evaluate IBD in species characteristic of low-disturbance forests.
Data from: The walk is never random: subtle landscape effects shape gene flow in a continuous white-tailed deer population in the Midwestern United States
One of the pervasive challenges in landscape genetics is detecting gene flow patterns within continuous populations of highly mobile wildlife. Understanding population genetic structure within a continuous population can give insights into social structure, movement across the landscape and contact between populations, which influence ecological interactions, reproductive dynamics, or pathogen transmission. We investigated the genetic structure of a large population of deer spanning the area of Wisconsin and Illinois, USA, affected by chronic wasting disease. We combined multi-scale investigation, landscape genetic techniques and spatial statistical modeling to address the complex questions of landscape factors influencing population structure. We sampled over 2,000 deer and used spatial autocorrelation and a spatial principal components analysis to describe the population genetic structure. We evaluated landscape effects on this pattern using a spatial auto-regressive model within a model selection framework to test alternative hypotheses about gene flow. We found high levels of genetic connectivity, with gradients of variation across the large continuous population of white-tailed deer. At the fine scale, spatial clustering of related animals was correlated with the amount and arrangement of forested habitat. At the broader scale, impediments to dispersal were important to shaping genetic connectivity within the population. We found significant barrier effects of individual state and interstate highways and rivers. Our results offer an important understanding of deer biology and movement that will help inform the management of this species in an area where over-abundance and disease spread are primary concerns.
Data from: Genome-wide evidence for speciation with gene flow in Heliconius butterflies
Most speciation events probably occur gradually, without complete and immediate reproductive isolation, but the full extent of gene flow between diverging species has rarely been characterized on a genome-wide scale. Documenting the extent and timing of admixture between diverging species can clarify the role of geographic isolation in speciation. Here we use new methodology to quantify admixture at different stages of divergence in Heliconius butterflies, based on whole genome sequences of 31 individuals. Comparisons between sympatric and allopatric populations of H. melpomene, H. cydno and H. timareta revealed a genome-wide trend of increased shared variation in sympatry, indicative of pervasive interspecific gene flow. Up to 40% of 100 kb genomic windows clustered by geography rather than by species, demonstrating that a very substantial fraction of the genome has been shared between sympatric species. Analyses of genetic variation shared over different time intervals suggested that admixture between these species has continued since early in speciation. Alleles shared between species during recent time intervals displayed higher levels of linkage disequilibrium than those shared over longer time intervals, suggesting that this admixture took place at multiple points during divergence and is probably ongoing. The signal of admixture was significantly reduced around loci controlling divergent wing patterns, as well as throughout the Z chromosome, consistent with strong selection for Müllerian mimicry and with known Z-linked hybrid incompatibility. Overall these results show that species divergence can occur in the face of persistent and genome-wide admixture over long periods of time.
Data from: Genome divergence and the genetic architecture of barriers to gene flow between Lycaeides idas and L. melissa
Genome divergence during speciation is a dynamic process that is affected by various factors, including the genetic architecture of barriers to gene flow. Herein we quantitatively describe aspects of the genetic architecture of two sets of traits, male genitalic morphology and oviposition preference, that putatively function as barriers to gene flow between the butterfly species Lycaeides idas and L. melissa. Our analyses are based on unmapped DNA sequence data and a recently developed Bayesian regression approach that includes variable selection and explicit parameters for the genetic architecture of traits. A modest number of nucleotide polymorphisms explained a small to large proportion of the variation in each trait, and average genetic variant effects were non-negligible. Several genetic regions were associated with variation in multiple traits or with trait variation within- and among-populations. In some instances genetic regions associated with trait variation also exhibited exceptional genetic differentiation between speices or exceptional introgression in hybrids. These results are consistent with the hypothesis that divergent selection on male genitalia has contributed to heterogeneous genetic differentiation, and that both sets of traits affect fitness in hybrids. Although these results are encouraging, we highlight several difficulties related to understanding the genetics of speciation.
Data from: Adaptive genetic markers discriminate migratory runs of Chinook salmon (Oncorhynchus tshawytscha) amid continued gene flow
Neutral genetic markers are routinely used to define distinct units within species that warrant discrete management. Human-induced changes to gene flow however may reduce the power of such an approach. We tested the efficiency of adaptive vs. neutral genetic markers in differentiating temporally divergent migratory runs of Chinook salmon (Oncorhynchus tshawytscha) amid high gene flow owing to artificial propagation and habitat alteration. We compared seven putative migration timing genes to ten microsatellite loci in delineating three migratory groups of Chinook in the Feather River, CA: offspring of fall run hatchery broodstock that returned as adults to freshwater in fall (fall run), spring run offspring that returned in spring (spring run), and fall run offspring that returned in spring (FRS). We found evidence for significant differentiation between the fall and federally-listed threatened spring groups based on divergence at three circadian clock genes (OtsClock1b, OmyFbxw11 and Omy1009UW), but not neutral markers. We thus demonstrate the importance of genetic marker choice in resolving complex life history types. These findings directly impact conservation management strategies and add to previous evidence from Pacific and Atlantic salmon indicating that circadian clock genes influence migration timing.
Data from: Patterns of gene flow in Encholirium horridum L.B.Sm., a monocarpic species of Bromeliaceae from Brazil
Encholirium horridum is a bromeliad that occurs exclusively on inselbergs in the Atlantic Forest biome of Brazil. These rock outcrops form natural islands that isolate populations from each other. We investigated gene flow by pollen through paternity analyses of a bromeliad population in an area of approximately 2 ha in Espírito Santo State, Brazil. To that end, seed rosettes and seedlings were genotyped using nuclear microsatellite loci. A plot was also established from the same population and specimens were genotyped to evaluate their fine-scale spatial genetic structure (SGS) through analyses of spatial autocorrelation and clonal growth. Paternity analysis indicated that 80% of the attributed progenitors of the genotyped seedlings were from inside the study area. The pollen dispersal distances within the area were restricted (mean distance of 45.5 m, varying from 3 to 156 m) and fine-scale SGS was weak (F ij = 0.0122, P < 0.001; Sp = 0.009). Clonal growth was found to be a rare event, supporting the monocarpy of this species.
Data from: Ancestral gene flow and parallel organellar genome capture result in extreme phylogenomic discord in a lineage of angiosperms
While hybridization has recently received a resurgence of attention from systematists and evolutionary biologists, there remains a dearth of case studies on ancient, diversified hybrid lineages-clades of organisms that originated through reticulation. Studies on these groups are valuable in that they would speak to the long-term phylogenetic success of lineages following gene flow between species. We present a phylogenomic view of Heuchera, long known for frequent hybridization, incorporating all three independent genomes: targeted nuclear (~400,000 bp), plastid (~160,000 bp), and mitochondrial (~470,000 bp) data. We analyze these data using multiple concatenation and coalescence strategies. The nuclear phylogeny is consistent with previous work and with morphology, confidently suggesting a monophyletic Heuchera. By contrast, analyses of both organellar genomes recover a grossly polyphyletic Heuchera,consisting of three primary clades with relationships extensively rearranged within these as well. A minority of nuclear loci also exhibit phylogenetic discord; yet these topologies remarkably never resemble the pattern of organellar loci and largely present low levels of discord inter alia. Two independent estimates of the coalescent branch length of the ancestor of Heuchera using nuclear data suggest rare or nonexistent incomplete lineage sorting with related clades, inconsistent with the observed gross polyphyly of organellar genomes (confirmed by simulation of gene trees under the coalescent). These observations, in combination with previous work, strongly suggest hybridization as the cause of this phylogenetic discord.
Data from: Examining the role of parasites in limiting unidirectional gene flow between lake and river sticklebacks
1. Parasites are important selective agents with the potential to limit gene flow between host populations by shaping local host immunocompetence. 2. We report on a contact zone between lake and river three-spined sticklebacks (Gasterosteus aculeatus) that offers the ideal biogeographic setting to explore the role of parasite-mediated selection on reproductive isolation. A waterfall acts as a natural barrier and enforces unidirectional migration from the upstream river stickleback population to the downstream river and lake populations. 3. We assessed population genetic structure and parasite communities over four years. In a set of controlled experimental infections, we compared parasite susceptibility of upstream and downstream fish by exposing laboratory-bred upstream river and lake fish, as well as hybrids, to two common lake parasite species: a generalist trematode parasite, Diplostomum pseudospathaceum and a host-specific cestode, Schistocephalus solidus. 4. We found consistent genetic differentiation between upstream and downstream populations across four sampling years, even though the downstream river consisted of ~10% first-generation migrants from the upstream population as detected by parentage analysis. Fish in the upstream population had lower genetic diversity and were strikingly devoid of macroparasites. Through experimental infections, we demonstrated that upstream fish and their hybrids had higher susceptibility to parasite infections than downstream fish. Despite this, naturally-sampled upstream migrants were less infected than downstream residents. Thus, migrants coming from a parasite-free environment may enjoy an initial fitness advantage, but their descendants seem likely to suffer from higher parasite loads. 5. Our results suggest that adaptation to distinct parasite communities can influence stickleback invasion success and may represent a barrier to gene flow, even between close and connected populations.
Data from: The genetic architecture of reproductive isolation during speciation-with-gene-flow in lake whitefish species pairs assessed by RAD sequencing
During speciation-with-gene-flow, effective migration varies across the genome as a function of several factors, including proximity of selected loci, recombination rate, strength of selection, and number of selected loci. Genome scans may provide better empirical understanding of the genome-wide patterns of genetic differentiation, especially if the variance due to the previously mentioned factors is partitioned. In North American lake whitefish (Coregonus clupeaformis), glacial lineages that diverged in allopatry about 60,000 years ago and came into contact 12,000 years ago have independently evolved in several lakes into two sympatric species pairs (a normal benthic and a dwarf limnetic). Variable degrees of reproductive isolation between species pairs across lakes offer a continuum of genetic and phenotypic divergence associated with adaptation to distinct ecological niches. To disentangle the complex array of genetically based barriers that locally reduce the effective migration rate between whitefish species pairs, we compared genome-wide patterns of divergence across five lakes distributed along this divergence continuum. Using restriction site associated DNA (RAD) sequencing, we combined genetic mapping and population genetics approaches to identify genomic regions resistant to introgression and derive empirical measures of the barrier strength as a function of recombination distance. We found that the size of the genomic islands of differentiation was influenced by the joint effects of linkage disequilibrium maintained by selection on many loci, the strength of ecological niche divergence, as well as demographic characteristics unique to each lake. Partial parallelism in divergent genomic regions likely reflected the combined effects of polygenic adaptation from standing variation and independent changes in the genetic architecture of postzygotic isolation. This study illustrates how integrating genetic mapping and population genomics of multiple sympatric species pairs provide a window on the speciation-with-gene-flow mechanism.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.