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opencc-zeroDec 2013View details →

Data from: Genomic variation in a widespread Neotropical bird (Xenops minutus) reveals divergence, population expansion, and gene flow

The demographic and phylogeographic histories of species provide insight into the processes responsible for generating biological diversity, and genomic datasets are now permitting the estimation of species histories with unprecedented accuracy. We used a genomic single nucleotide polymorphism (SNP) dataset generated using a RAD-Seq method to investigate the historical demography and phylogeography of a widespread lowland Neotropical bird (Xenops minutus). As expected, we found that prominent landscape features that act as dispersal barriers, such as Amazonian rivers and the Andes Mountains, are associated with the deepest phylogeographic breaks, and also that isolation by distance is limited in areas between these barriers. In addition, we inferred positive population growth for most populations and detected evidence of historical gene flow between populations that are now physically isolated. Although we were able to reconstruct the history of Xenops minutus with unprecedented resolution, we had difficulty conclusively relating this history to the landscape events implicated in many Neotropical diversification hypotheses. We suggest that even if many traditional diversification hypotheses remain untestable, investigations using genomic datasets will provide greater resolution of species histories in the Neotropics and elsewhere.

opencc-zeroDec 2012View details →

Data from: Genetic structure, spatial organization, and dispersal in two populations of bat-eared foxes

We incorporated radio-telemetry data with genetic analysis of bat-eared foxes (Otocyon megalotis) from individuals in 32 different groups to examine relatedness and spatial organization in two populations in South Africa that differed in density, home-range sizes, and group sizes. Kin clustering occurred only for female dyads in the high-density population. Relatedness was negatively correlated with distance only for female dyads in the high-density population, and for male and mixed-sex dyads in the low-density population. Home-range overlap of neighboring female dyads was significantly greater in the high compared to low-density population, whereas overlap within other dyads was similar between populations. Amount of home-range overlap between neighbors was positively correlated with genetic relatedness for all dyad-site combinations, except for female and male dyads in the low-density population. Foxes from all age and sex classes dispersed, although females (mostly adults) dispersed farther than males. Yearlings dispersed later in the high-density population, and overall exhibited a male-biased dispersal pattern. Our results indicated that genetic structure within populations of bat-eared foxes was sex-biased, and was interrelated to density and group sizes, as well as sex-biases in philopatry and dispersal distances. We conclude that a combination of male-biased dispersal rates, adult dispersals, and sex-biased dispersal distances likely helped to facilitate inbreeding avoidance in this evolutionarily unique species of Canidae.

opencc-zeroDec 2018View details →

Data from: Historical population size change and differentiation of relict populations of the endangered giant kangaroo rat

From a conservation management perspective it is important to understand how genetic diversity is partitioned across a species' range, including (1) identification of evolutionarily distinct units versus those recently isolated through anthropogenic activities and (2) the relative genetic contributions among components of fragmented (meta)populations. To address these questions, we investigated the phylogeography and metapopulation structure among relict populations of the endangered giant kangaroo rat (Dipodomys ingens) in the highly altered San Joaquin Desert Ecosystem. This keystone species underwent a ~97% range reduction over the past century, resulting in a current range that is highly fragmented, with two dominant northern and southern populations occurring 150 km apart. We sequenced >800 bp of mitochondrial DNA and genotyped 17 nuclear microsatellites in >275 D. ingens to assess the evolutionary relationship of these populations as well as the genetic structure within the northern metapopulation. A Bayesian Skyline Plot indicated that the species experienced a demographic expansion toward the end of the Pleistocene, with a recent population decline. Northern and southern D. ingens split 1,857–13,443 years ago, prior to the massive conversion of the San Joaquin Valley to irrigated agriculture. We recommend that the northern and southern populations of D. ingens be re-classified as distinct population segments under the United States Endangered Species Act. We also observed population structure and asymmetrical migration within northern D. ingens where the Tumey Hills acted as a source contributing gene flow to all peripheral populations. This emphasized the importance of this location in the conservation of the metapopulation as a whole.

opencc-zeroDec 2011View details →

Data from: Range-wide population genetic structure of the Caribbean sea fan coral, Gorgonia ventalina

The population structure of benthic marine organisms is of central relevance for the conservation and management of these often threatened species as well as an accurate understanding of their ecological and evolutionary dynamics. A growing body of evidence suggests that marine populations can be structured over short distances despite theoretically high dispersal potential. Yet the proposed mechanisms governing this structure vary, and existing empirical population genetic evidence is of insufficient taxonomic and geographic scope to allow strong general inferences. Here we describe the range-wide population genetic structure of an ecologically important Caribbean octocoral, Gorgonia ventalina. Genetic differentiation was positively correlated with geographic distance and negatively correlated with oceanographically-modeled dispersal probability throughout the range. Although we observed admixture across hundreds of kilometers, estimated dispersal is low, and populations can be differentiated across distances <2km. These results suggest that populations of G. ventalina may be evolutionarily coupled via gene flow but are largely demographically independent. Observed patterns of differentiation corroborate biogeographic breaks identified in other taxa (e.g. an east/west divide near Puerto Rico) and also identify population divides not discussed in previous studies (e.g. the Yucatan Channel). Across the range, diversity was positively correlated with latitude, consistent with a source/sink dynamic driven by ocean currents. High genotypic diversity and absence of clonemates indicate that sex is the primary reproductive mode for G. ventalina. A comparative analysis of the population structure of G. ventalina and its dinoflagellate symbiont, Symbiodinium, indicates that the dispersal of these symbiotic partners is not coupled, and symbiont transmission occurs horizontally.

opencc-zeroJul 2019View details →

Data from: Assortative mating frames establishment in a young island bird population

Successful island colonizations are key events to understand range dynamic processes, but studying a young population right after it reaches establishment is a rare opportunity in natural systems. However, the genetic structure of a recently established population may offer unique insights into its colonization history and demographic processes important for a successful colonization. Here, we studied the population genetics of a recently established island population of Eurasian blackbirds (Aves: Turdus merula) located on the island of Heligoland in the German North Sea. Using microsatellites, we genotyped the majority of the island population, including the nestlings, over a four-year period between 2004 and 2007. We also genotyped high numbers of migrants on stopover and mainland individuals, as they are potential founders of the island population. We identified two genetic clusters that comply with the migrating and mainland birds respectively. While most of the island birds belong to the mainland cluster, some breeding individuals and a low fraction of the offspring belong to the genetic cluster found in migrating individuals with almost no admixture between the two, pointing to assortative mating acting on the island population. We did not find any evidence for founder events and detected deviations from Hardy-Weinberg equilibrium that disappeared in cohorts of older age that coincide with a lower number of siblings in older cohorts. The observed genetic patterns unravel a complex colonization history to which migratory and mainland birds have contributed and which is characterized by assortative mating. Further research will be directed towards habitat selection and phenotypic differences as potential drivers of assortative mating in this island population.

opencc-zeroDec 2013View details →

Data from: Introduction beyond a species range: a relationship between population origin, adaptive potential and plant performance

The adaptive potential of a population defines its importance for species survival in changing environmental conditions such as global climate change. Very few empirical studies have examined adaptive potential across species' ranges, namely, of edge vs core populations, and we are unaware of a study that has tested adaptive potential (namely, variation in adaptive traits) and measured performance of such populations in conditions not currently experienced by the species but expected in the future. Here we report the results of a Triticum dicoccoides population study that employed transplant experiments and analysis of quantitative trait variation. Two populations at the opposite edges of the species range (1) were locally adapted; (2) had lower adaptive potential (inferred from the extent of genetic quantitative trait variation) than the two core populations; and (3) were outperformed by the plants from the core population in the novel environment. The fact that plants from the species arid edge performed worse than plants from the more mesic core in extreme drought conditions beyond the present climatic envelope of the species implies that usage of peripheral populations for conservation purposes must be based on intensive sampling of among-population variation.

Data from: Integrating genetic analysis of mixed populations with a spatially-explicit population dynamics model

Inferring the dynamics of populations in time and space is a central challenge in ecology. Intra-specific structure (for example genetically distinct sub-populations or meta-populations) may require methods that can jointly infer the dynamics of multiple populations. This is of particular importance for harvested species, for which management must balance utilization of productive populations with protection of weak ones. Here we present a novel method for simultaneous learning about the spatio-temporal dynamics of multiple populations that combines genetic data with prior information about abundance and movement in an integrated population modelling approach. We apply the Bayesian genetic mixed stock analysis to 17 wild and 10 hatchery-reared Baltic salmon (S. salar) stocks, quantifying uncertainty in stock composition in time and space, and in population dynamics parameters such as migration timing and speed. Our results indicate that the commonly used "equal prior probabilities" assumption may not be appropriate for all mixed stock analyses. Incorporation of prior information about stock abundance and movement resulted in more precise and plausible estimates of mixture compositions in time and space. Inclusion of a population dynamics model also allowed robust interpolation of expected catch composition at areas and times with no genetic observations. The genetic data were informative about stock-specific movement patterns, updating priors for migration path, timing and speed. The model we present here forms the basis for optimizing the spatial and temporal allocation of harvest to support the management of mixed populations of migratory species.

Data from: Genome sequence and population declines in the critically endangered greater bamboo lemur (Prolemur simus) and implications for conservation

Background: The greater bamboo lemur (Prolemur simus) is a member of the Family Lemuridae that is unique in their dependency on bamboo as a primary food source. This Critically Endangered species lives in small forest patches in eastern Madagascar, occupying a fraction of its historical range. Here we sequence the genome of the greater bamboo lemur for the first time, and provide genome resources for future studies of this species that can be applied across its distribution. Results: Following whole genome sequencing of five individuals we identified over 152,000 polymorphic single nucleotide variants (SNVs), and evaluated geographic structuring across nearly 19k SNVs. We characterized a stronger signal associated with a north-south divide than across elevations for our limited samples. We also evaluated the demographic history of this species, and infer a dramatic population crash. This species had the largest effective population size (estimated between ~900,000 to one million individuals) between approximately 60,000-90,000 years before present (ybp), during a time in which global climate change affected terrestrial mammals worldwide. We also note the single sample from the northern portion of the extant range had the largest effective population size around 35,000 ybp. Conclusions: From our whole genome sequencing we recovered an average genomic heterozygosity of 0.0037%, comparable to other lemurs. Our demographic history reconstructions recovered a probable climate-related decline (60-90,000 ybp), followed by a second population decrease following human colonization, which has reduced the species to a census size of approximately 1,000 individuals. The historical distribution was likely a vast portion of Madagascar, minimally estimated at 44,259 km2, while the contemporary distribution is only ~1,700 km2. The decline in effective population size of 89-99.9% corresponded to a vast range retraction. Conservation management of this species is crucial to retain genetic diversity across the remaining isolated populations.

Data from: Impact of sexually antagonistic genital morphologies on female reproduction and wild population demography

Sexual conflict is a strong driver of evolution. The evolutionary outcomes of sexual conflict can, in turn, influence ecological processes within populations, e.g., demography. However, evidence for the latter hypothesis is scarce, especially in the wild. Here, we show that sexual conflict is associated with demographic processes determining population size in the ground beetle Carabus insulicola with elaborate male and female genitalia, based on individual- and population-level analyses. We found that sexually antagonistic selection can operate on the genitalia: longer male genitalia can be beneficial in sperm competition but decrease female reproductive success with increased egg dumping, while longer female genitalia are resistant to this male harassment via decreased egg dumping and increased fertilization rate. As expected from sexually antagonistic coevolution due to sexual conflict, we detected coevolutionary divergence between male and female genital sizes among populations. In parallel with decrease in female reproductive success, more harmful males with longer genitalia and less resistant females with shorter genitalia were related to small effective population sizes. Thus, sexual conflict may promote coevolutionary diversification between sexual traits, and this was associated with a demographic process. Our findings provide an insight into sex-driven eco-evolutionary dynamics in the wild.

opencc-zeroDec 2008View details →

Data from: A worldwide perspective on the population structure and genetic diversity of bottlenose dolphins (Tursiops truncatus) in New Zealand

Bottlenose dolphins (Tursiops truncatus) occupy a wide range of coastal and pelagic habitats throughout tropical and temperate waters worldwide. In some regions, "inshore" and "offshore" forms or ecotypes differ genetically and morphologically, despite no obvious boundaries to interchange. Around New Zealand, bottlenose dolphins inhabit 3 coastal regions: Northland, Marlborough Sounds, and Fiordland. Previous demographic studies showed no interchange of individuals among these populations. Here, we describe the genetic structure and diversity of these populations using skin samples collected with a remote biopsy dart. Analysis of the molecular variance from mitochondrial DNA (mtDNA) control region sequences (n = 193) showed considerable differentiation among populations (Fst = 0.17, Φst = 0.21, P < 0.001) suggesting little or no female gene flow or interchange. All 3 populations showed higher mtDNA diversity than expected given their small population sizes and isolation. To explain the source of this variation, 22 control region haplotypes from New Zealand were compared with 108 haplotypes worldwide representing 586 individuals from 19 populations and including both inshore and offshore ecotypes as described in the Western North Atlantic. All haplotypes found in the Pacific, regardless of population habitat use (i.e., coastal or pelagic), are more divergent from populations described as inshore ecotype in the Western North Atlantic than from populations described as offshore ecotype. Analysis of gene flow indicated long-distance dispersal among coastal and pelagic populations worldwide (except for those haplotypes described as inshore ecotype in the Western North Atlantic), suggesting that these populations are interconnected on an evolutionary timescale. This finding suggests that habitat specialization has occurred independently in different ocean basins, perhaps with Tursiops aduncus filling the ecological niche of the inshore ecotype in some coastal regions of the Indian and Western Pacific Oceans.

opencc-zeroDec 2013View details →

Data from: Eliminating variation in age at spawning leads to genetic divergence within a single salmon population

Most coho salmon Oncorhynchus kisutch in Washington state spawn at 3 y of age, creating the potential for three temporal populations or "broodlines" at each spawning site. This is generally prevented by a portion of males in each site that mature and reproduce at 2 y of age, resulting in population structure in which the geographic component is stronger than the temporal component. The Quilcene National Fish Hatchery, located on Big Quilcene River in the Hood Canal region of Washington state, selected against late returning coho salmon by excluding all but the earliest returning fish from its broodstock for an unknown number of generations, and restricted gene flow among broodlines by excluding 2-y-old males for 27 generations. The resulting hatchery population exhibited three distinct broodlines that returned in alternating years: an "early" broodline that arrived 1 mo before the wild fish, a "late" broodline that arrived at the same time as the wild fish, and a "middle" broodline that arrived in between these two broodlines. We evaluated temporal and geographic components of population genetic structure in coho salmon from the Quilcene National Fish Hatchery and nine other sites from Puget Sound and the Strait of Juan de Fuca using 10 microsatellite loci. Genetic diversity at the Quilcene National Fish Hatchery was lowest in the early broodline and highest in the late broodline. Divergence among broodlines was generally much lower than divergence among sites, rendering the term broodline irrelevant for most sites. Divergence among broodlines at the Quilcene National Fish Hatchery, however was greater than that observed at any other site, and was also greater than that observed between any of the sites. This apparent reversal of the relative magnitudes of temporal and geographic components for this species emphasizes the importance of variable age-at-maturity in shaping population genetic structure.

opencc-zeroSep 2019View details →

Data from: Widespread infection of Areospora rohanae in southern king crab (Lithodes santolla) populations across south Chilean Patagonia

Cottage cheese disease is caused by microsporidian parasites that infect a wide range of animal populations. Despite its potential to affect economically important activities, the spatial patterns of prevalence of this disease are still not well understood. Here, we analyze the occurrence of the microsporidian Areospora rohanae in populations of the king crab Lithodes santolla over ca. 800 km of the southeastern Pacific shore. In winter 2011, conical pots were deployed between 50 and 200 m depth to capture crabs of a wide range of sizes. The infection was widely distributed along the region, with a mean prevalence of 16 %, and no significant association between prevalence and geographic location was detected. Males, females, and ovigerous females showed similar prevalence values of 16.5 (13 – 18.9), 15 (9.2 – 15), and 16.7 % (10 – 19 %), respectively. These patterns of prevalence were consistent across crab body sizes, despite the ontogenetic and sex-dependent variations in feeding behavior and bathymetric migrations previously reported for king crabs. This study provided the first report of the geographic distribution of A. rohanae infecting southern king crabs.

opencc-zeroDec 2015View details →

Data from: A genome scan for selection signatures comparing farmed Atlantic salmon with two wild populations: testing co-localization among outlier markers, candidate genes, and QTLs for production traits

Comparative genome scans can be used to identify chromosome regions, but not traits, that are putatively under selection. Identification of targeted traits may be more likely in recently domesticated populations under strong artificial selection for increased production. We used a North American Atlantic salmon 6K SNP dataset to locate genome regions of an aquaculture strain (Saint John River) that were highly diverged from that of its putative wild founder population (Tobique River). First, admixed individuals with partial European ancestry were detected using STRUCTURE and removed from the dataset. Outlier loci were then identified as those showing extreme differentiation between the aquaculture population and the founder population. All Arlequin methods identified an overlapping subset of 17 outlier loci, 3 of which were also identified by BayeScan. Many outlier loci were near candidate genes and some were near published quantitative trait loci (QTLs) for growth, appetite, maturity, or disease-resistance. Parallel comparisons using a wild, non-founder population (Stewiacke River) yielded only one overlapping outlier locus as well as a known maturity QTL. We conclude that genome scans comparing a recently domesticated strain with its wild founder population can facilitate identification of candidate genes for traits known to have been under strong artificial selection.

Data from: A parallel population genomic and hydrodynamic approach to fishery management of highly-dispersive marine invertebrates: the case of the Fijian black-lip pearl oyster Pinctada margaritifera

Fishery management and conservation of marine species increasingly relies on genetic data to delineate biologically relevant stock boundaries. Unfortunately for high gene flow species which may display low, but statistically significant population structure, there is no clear consensus on the level of differentiation required to resolve distinct stocks. The use of fine-scale neutral and adaptive variation, considered together with environmental data can offer additional insights to this problem. Genome-wide genetic data (4,123 SNPs), together with an independent hydrodynamic particle dispersal model were used to inform farm and fishery management in the Fijian black-lip pearl oyster Pinctada margaritifera, where comprehensive fishery management is lacking, and the sustainability of exploitation uncertain. Weak fine-scale patterns of population structure were detected, indicative of broad-scale panmixia among wild oysters, while a hatchery-sourced farmed population exhibited a higher degree of genetic divergence (Fst = 0.0850–0.102). This hatchery-produced population had also experienced a bottleneck (NeLD = 5.1; 95% C.I. = [5.1–5.3]); compared to infinite NeLD estimates for all wild oysters. Simulation of larval transport pathways confirmed the existence of broad-scale mixture by surface ocean currents, correlating well with fine-scale patterns of population structuring. Fst outlier tests failed to detect large numbers of loci supportive of selection, with 2–5 directional outlier SNPs identified (average Fst = 0.116). The lack of biologically significant population genetic structure, absence of evidence for local adaptation and larval dispersal simulation, all indicate the existence of a single genetic stock of P. margaritifera in the Fiji Islands. This approach using independent genomic and oceanographic tools has allowed fundamental insights into stock structure in this species, with transferability to other highly-dispersive marine taxa for their conservation and management.

Data from: Population genetic analysis of a global collection of Fragaria vesca using microsatellite markers

The woodland strawberry, Fragaria vesca, holds great promise as a model organism. It not only represents the important Rosaceae family that includes economically important species such as apples, pears, peaches and roses, but it also complements the well-known model organism Arabidopsis thaliana in key areas such as perennial life cycle and the development of fleshy fruit. Analysis of wild populations of A. thaliana has shed light on several important developmental pathways controlling, for example, flowering time and plant growth, suggesting that a similar approach using F. vesca might add to our understanding on the development of rosaceous species and perennials in general. As a first step, 298 F. vesca plants were analyzed using microsatellite markers with the primary aim of analyzing population structure and distribution of genetic diversity. Of the 68 markers tested, 56 were polymorphic, with an average of 4.46 alleles per locus. Our analysis partly confirms previous classification of F. vesca subspecies in North America and suggests two groups within the subsp. bracteata. In addition, F. vesca subsp. vesca forms a single global population with evidence that the Icelandic group is a separate cluster from the main Eurasian population.

Data from: SNP-skimming: a fast approach to map loci generating quantitative variation in natural populations

Genome-wide association mapping (GWAS) is a method to estimate the contribution of segregating genetic loci to trait variation. A major challenge for applying GWAS to non-model species has been generating dense genome-wide markers that satisfy the key requirement that marker data is error-free. Here we present an approach to map loci within natural populations using inexpensive shallow genome sequencing. This 'SNP skimming' approach involves two steps: an initial genome-wide scan to identify putative targets followed by deep sequencing for confirmation of targeted loci. We apply our method to a test dataset of floral dimension variation in the plant Penstemon virgatus, a member of a genus that has experienced dynamic floral adaptation that reflects repeated transitions in primary pollinator. The ability to detect SNPs that generate phenotypic variation depends on population genetic factors such as population allele frequency, effect size, and epistasis as well as sampling effects contingent on missing data and genotype uncertainty. However, both simulations and the Penstemon data suggest that the most significant tests from the initial SNP skim are likely to be true positives – loci with subtle but significant quantitative effects on phenotype. We discuss the promise and limitations of this method and consider optimal experimental design for a given sequencing effort. Simulations demonstrate that sampling a larger number of individual at the expense of average read depth per individual maximizes the power to detect loci.

Data from: Genetic diversity and population divergences of an indigenous tree (Coffea mauritiana) in Reunion Island: role of climatic and geographical factors

Oceanic islands are commonly considered as natural laboratories for studies on evolution and speciation. The evolutionary specificities of islands associated with species biology provide unique scenarios to study the role of geography and climate in driving population divergence. However, few studies have addressed this subject in small oceanic islands with heterogeneous climates. Being widely distributed in Reunion Island forest, Coffea mauritiana represents an interesting model case for investigating patterns of within-island differentiation at small spatial scale. In this study, we examined the genetic diversity and population divergences of C. mauritiana using SNP markers obtained from 323 individuals across 34 locations in Reunion Island. Using redundancy analysis, we further evaluated the contribution of geographic and climatic factors to shaping genetic divergence among populations. Genetic diversity analyses revealed that accessions clustered according to the source population, with further grouping in regional clusters. Genetic relationships among the regional clusters underlined a recent process of expansion in the form of step-by-step colonization on both sides of the island. Divergence among source populations was mostly driven by the joint effect of geographic distance and climatic heterogeneity. The pattern of isolation-by-geography was in accordance with the dispersal characteristics of the species, while isolation-by-environment was mostly explained by the heterogeneous rainfall patterns, probably associated with an asynchronous flowering among populations. These findings advance our knowledge on the patterns of genetic diversity and factors of population differentiation of species native to Reunion Island, and will also usefully guide forest management for conservation.

Data from: Population differentiation or species formation across the Indian and the Pacific Oceans? An example from the brooding marine hydrozoan Macrorhynchia phoenicea

Assessing population connectivity is necessary to construct effective marine protected areas. This connectivity depends, among other parameters, inherently on species dispersal capacities. Isolation by distance (IBD) is one of the main modes of differentiation in marine species, above all in species presenting low dispersal abilities. This study reports the genetic structuring in the tropical hydrozoan Macrorhynchia phoenicea α (sensu Postaire et al., 2016a), a brooding species, from 30 sampling sites in the Western Indian Ocean and the Tropical Southwestern Pacific, using 15 microsatellite loci. At the local scale, genet dispersal relied on asexual propagation at short distance, which was not found at larger scales. Considering one representative per clone, significant positive FIS values (from −0.327*** to 0.411***) were found within almost all sites. Gene flow was extremely low at all spatial scales, among sites within islands (<10 km distance) and among islands (100 to >11,000 km distance), with significant pairwise FST values (from 0.035*** to 0.645***). A general pattern of IBD was found at the Indo-Pacific scale, but also within ecoregions in the Western Indian Ocean province. Clustering and network analyses identified each island as a potential independent population, while analysis of molecular variance indicated that population genetic differentiation was significant at small (within island) and intermediate (among islands within province) spatial scales. As shown by this species, a brooding life cycle might be corollary of the high population differentiation found in some coastal marine species, thwarting regular dispersal at distances more than a few kilometers and probably leading to high cryptic diversity, each island housing independent evolutionary lineages.

opencc-zeroDec 2010View details →

Data from: Deep phylogeographic structuring of populations of the trapdoor spider Moggridgea tingle (Migidae) from southwestern Australia: evidence for long-term refugia within refugia

Southwestern Australia has been recognized as a biodiversity hotspot of global significance, and it is particularly well known for its considerable diversity of flowering plant species. Questions of interest are how this region became so diverse and whether its fauna show similarly diverse patterns of speciation. Here we have carried out a phylogeographic study of trapdoor spiders (Migidae: Moggridgea), a presumed Gondwanan lineage found in wet forest localities across southwestern Australia. Phylogenetic, molecular clock and population genetic analyses of mitochondrial (mtDNA) COI gene and ITS rRNA (internal transcribed spacer) data revealed considerable phylogeographic structuring of Moggridgea populations, with evidence for long-term (> 3 million years) isolation of at least nine populations in different geographic locations, including upland regions of the Stirling and Porongurup Ranges. High levels of mtDNA divergence and no evidence of recent mitochondrial gene flow among valley populations of the Stirling Range suggest that individual valleys have acted as refugia for the spiders throughout the Pleistocene. Our findings support the hypothesis that climate change, particularly the aridification of Australia after the late Miocene, and the topography of the landscape, which allowed persistence of moist habitats, have been major drivers of speciation in southwestern Australia.

Data from: Estimating the relative fitness of escaped farmed salmon offspring in the wild and modeling the consequences of invasion for wild populations

Throughout their native range, wild Atlantic salmon populations are threatened by hybridization and introgression with escapees from net-pen salmon aquaculture. Although domestic-wild hybrid offspring have shown reduced fitness in lab and field experiments, consequential impacts on population abundance and genetic integrity remain difficult to predict in the field, in part because the strength of selection against domestic offspring is often unknown and context-dependent. Here we follow a single large escape event of farmed Atlantic salmon in southern Newfoundland and monitor changes in the in-river proportions of hybrids and feral individuals over time using genetically-based hybrid identification. Over a three-year period following the escape, the overall proportion of wild parr increased consistently (total wild proportion of 71.6%, 75.1%, 87.5% each year, respectively), with subsequent declines in feral (genetically pure farmed individuals originating from escaped, farmed adults) and hybrid parr. We quantify the strength of selection against parr of aquaculture ancestry and explore the genetic and demographic consequences for populations in the region. Within-cohort changes in the relative proportions of feral and F1 parr suggest reduced relative survival compared to wild individuals over the first (0.15 and 0.81 for feral and F1, respectively), and second years of life (0.26, 0.83). These relative survivorship estimates were used to inform an individual-based salmon eco-genetic model to project changes in adult abundance and overall allele frequency across three invasion scenarios ranging from short-term to long-term invasion and three relative survival scenarios. Modeling results indicate that total population abundance and time to recovery were greatly affected by relative survivorship and predict significant declines in wild population abundance under continued large escape events and calculated survivorship. Overall this work demonstrates the importance of estimating the strength of selection against domestic offspring in the wild to predict the long-term impact of farmed salmon escape events on wild populations.