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Figure 4 in Genetic variation within and among asexual populations of Porphyra umbilicalis Kützing (Bangiales, Rhodophyta) in the Gulf of Maine, USA
Figure 4: Four possible scenarios that explain colonization of the NW Atlantic from the NE Atlantic that attempt to reconcile data from this study and others that find no sexual reproduction in the NW Atlantic.
Figure 1 in Genetic variation within and among asexual populations of Porphyra umbilicalis Kützing (Bangiales, Rhodophyta) in the Gulf of Maine, USA
Figure 1: Collection localities of Porphyra umbilicalis populations in New Hampshire and Maine, USA. Pie charts show frequencies of genotypes in each population collection. The sum of genotype frequencies among all populations is also given.
Figure 2 in Genetic variation within and among asexual populations of Porphyra umbilicalis Kützing (Bangiales, Rhodophyta) in the Gulf of Maine, USA
Figure 2: Principal Components Analysis based on Nei's genetic distances among Porphyra umbilicalis genotypes. The genotypes as well as the individuals assayed with the genotype are given (DP =Dover Point, FS=Fort Stark, NL= Nubble Light, QH =Quoddy Head, RSP=Reid State Park, and W =Wiscasset).
Figure 3 in Genetic variation within and among asexual populations of Porphyra umbilicalis Kützing (Bangiales, Rhodophyta) in the Gulf of Maine, USA
Figure 3: Principal components analysis based on Nei's unbiased genetic distances among populations of Porphyra umbilicalis in the Gulf of Maine, USA.
Contrasting clonal and population genetic structure in two endangered Costa Rican Vanilla species of commercial interest
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Data files for: Hazardous loss of genetic diversity through selective sweeps in asexual populations
<p>With the two-fold cost of sex, derived asexual organisms have an immediate reproductive advantage over their sexual sisters. Yet the "twiggy'' phylogenetic distribution of asexual lineages implies that they go extinct relatively quickly over evolutionary time. Meanwhile, bacteria and archaea have persisted for billions of years without requiring sexual reproduction. A simple explanation for this difference is that prokaryotes have very large population sizes that are not subject to the accumulation of deleterious mutations, but this implies that drift and mutational meltdown dominate derived asexual populations. </p> <p>We explored a different hazard, quantifying the degree to which genetic variation is lost in asexual populations experiencing selective sweeps. Even though large populations generate diversity by mutation during sweeps, we find that populations that are safe from mutational meltdown may still be reduced to dangerous effective population sizes by sweeps. Thus, ironically, adaptation itself reduces further adaptive potential and may predispose asexual populations to extinction. Our data give results for the probability of mutational meltdown across various population sizes, the critical population size required to avoid meltdown, and the effect of selective sweeps on heterozygosity. Analytical predictions are confirmed by simulation.</p> <p>We also derive a simple approximation for the effective population size after a hard sweep, and quantify the impact of recent sweeps on evolutionary rescue. These factors may help to explain the phylogenetic twigginess of asexuals, the maintenance of sex and recombination, and the evolutionary persistence of prokaryotes.</p>
Figure 1 in Effects of islanding on the genetics of Niviventer confucianus (Mamalia: Rodentia: Muridae) populations in the Thousand Island Lake region
Figure 1. Distribution of 13 islands and three peninsulas in the study. There are 16 populations in total. We collected samples from 5 to 10 points randomly on each island. Here, we have not shown the collection points in Figure 1 because of the different sizes of islands (i.e. collection points cannot be plotted clearly enough on small islands in Figure 1).
Figure 2 in Effects of islanding on the genetics of Niviventer confucianus (Mamalia: Rodentia: Muridae) populations in the Thousand Island Lake region
Figure 2. Bayesian clustering assignment of individual Niviventer confucianus to three clusters based on nuclear (microsatellite) genetic data. Each vertical column represents one individual, with the length of coloured segments proportional to the assignment strength of that individual to each of the three clusters. Most individuals of populations CS, G, D, DM, LW, L and TS are assigned to Cluster 1 (light grey); most individuals of populations Q, Y, JS and ZD are assigned to Cluster 2 (grey); and most individuals of populations WS, WT, ZD and CF are assigned to Cluster 3 (dark). Combined with the island distribution (Figure 1), a reasonable dispersion history of populations could be postulated: population L and TS might be the dispersion centre of Cluster 1, population Y might be the dispersion centre of Cluster 2, and population WT might be the dispersion centre of Cluster 3. Populations in Clusters 1 and 2 are more closely related based on the value of allele frequency divergence (0.0145).
Microsatellite markers for assessing genetic diversity and kinship relationships in one of the largest South American fur seal (Arctocephalus australis) populations of the Pacific Ocean
<p class="CuerpoAA">The genetic diversity of a population is the foundation of its adaptability to environmental challenges. The South American fur seal is a widely distributed pinniped in the south cone of South America. However, a large gap in the Pacific coast separates two distinct evolutionary units for the species: the Peruvian and the Southern Pacific/Atlantic populations. Throughout the Pacific, one of the main breeding colonies is located in Guafo Island, in the southern Chilean Patagonia. As the closest reproductive population to the isolated Peruvian group, Guafo's colony may potentially facilitate gene flow, contribute with new alleles and increase genetic variability to Peruvian populations', connecting the entire Pacific's distribution of the species. In this study, Guafo's Island South American fur seal population was characterized by the identification and genotyping of species-specific microsatellite markers. As a result, we confirm that Guafo's colony is a diverse group with mild evidence of genetic structure. Although a couple of family groups among seasons were observed, results indicate that half-siblings are rare and suggest that polygyny in this species is more relaxed than previously thought. Additionally, three full-sibling pairs were genetically identified within the 2017 season, which is the first genetic support that describes the presence of twins for the species. These attributes suggest that the colony at Guafo is a panmictic large group, and could serve as a potential genetic source for other isolated populations.</p>
The population genetics of non-migratory Allen's Hummingbird (Selasphorus sasin sedentarius) following a recent mainland colonization
<p>Allen's Hummingbird comprises two subspecies, one migratory (<i>Selasphorus sasin sasin</i>) and one non-migratory (<i>S. s. sedentarius</i>). The non-migratory subspecies, previously endemic to the California Channel Islands, apparently colonized the California mainland on the Palos Verdes Peninsula some time before 1970, and now breeds throughout coastal southern California. We sequenced and compared populations of mainland non-migratory Allen's Hummingbird to Channel Island populations from Santa Catalina, San Clemente, and Santa Cruz Island. We found no evidence of founder effects on the mainland population. Values of nucleotide diversity on the Channel Islands were lower than those on the mainland. There were low levels of divergence between the Channel Islands and the mainland, although Santa Cruz Island was the most genetically distinct. Ecological niche models showed that rainfall and temperature variables on the Channel Islands are similar in the Los Angeles basin, and predicted continued expansion of non-migratory Allen's Hummingbird north along the coast and inland. We also reviewed previous genetic studies of vertebrate species found on the Channel Islands and mainland, and showed that broad conclusions regarding island-mainland patterns remain elusive. Challenges include the idiosyncratic nature of colonization itself as well as the lack of a comprehensive approach that incorporates similar markers and sampling strategies across taxa, which, within the context of a comparative study of island-mainland relationships, may lead to inconsistent results.</p>
Genetic diversity, differentiation and historical origin of the isolated population of rooksCorvus frugilegusin Iberia
<p>Current bird populations in southern temperate latitudes often represent relicts of glacial refugia from which northern populations expanded as the climate became suitable following the last glacial maximum, 18 000 years before present. Alternatively, these southern populations could be the result of the fragmentation of large distributions and other processes not related to glaciations, like recent recolonization from northern populations and human impact in historical times. Here, we investigate the origin of a small, isolated population of rooks Corvus frugilegus in north-western Iberia. We use genetic data from mitochondrial sequence markers and seven microsatellite loci to assess levels of genetic diversity, structure and gene flow among extant populations in Iberia and its broad distribution across western Europe. Microsatellite markers revealed the existence of two genetic clusters corresponding to Iberia and the remaining European populations, respectively. Haplotype networks based on mtDNA markers revealed a marked star-like phylogenetic pattern and evidence of a recent population expansion in northern Europe, but not in the Iberian population. Our results suggest that contemporary gene flow between Iberia and western Europe is restricted, and that breeding recruitment over recent generations in the Iberian population is local. The results are consistent with a relatively recent post-glacial colonization of Europe and western Siberia by rooks surviving the last glacial maximum in an Iberian refugium, and likely from refugia in other southern peninsulas. The unique ecological features and genetic differentiation of the Iberian rooks underscore the importance of ensuring the long-term conservation of this declining population.</p>
Assessing the population genetic structure of introduced rainbow trout (Oncorhynchus mykiss) in the Lake Tahoe basin: A case for understanding hybridization potential during the reintroduction of the native Endangered Species Act listed Lahontan cutthroat trout (O. clarkii henshawi)
<p class="MsoNormal">Hybridization with introduced or invasive species is a major threat and driver of population declines in native salmonids. The rainbow trout (<em>Oncorhynchus mykiss</em>, RBT) has been widely introduced globally and represents an important invasive species, often establishing entrenched naturalized populations. The cutthroat trout (<em>Oncorhynchus clarkii</em>, CT), a close congener, is particularly susceptible to competition and hybridization from RBT introductions which has led to range-wide population declines and loss of CT genetic variation. The Lahontan CT (<em>O. c. henshawi</em>, LCT) whose historic distribution included the Lake Tahoe basin, was extirpated by the 1940s due to overfishing and introduction of nonnative salmonids, including now naturalized RBT. Here, we characterize genetic variation of RBT in a subset of Lake Tahoe tributaries to assess potential homing of RBT to streams for spawning, thereby informing LCT reintroduction. Diploid reproductively viable RBT were stocked annually into Lake Tahoe from the late 1800s until the mid-2000s by California and Nevada fish and wildlife agencies, planting the same commonly raised hatchery strains over time. Since 2007, triploid RBT comprise the bulk of RBT planted. Despite extensive dispersal from stocking locations, our analyses revealed variation in population differentiation among tributaries, with individuals from spatially proximate streams clustering across multiple population genetic analyses. Although subtle, we detected evidence for genetic differentiation among tributaries from the southern, western, and northern regions, including surprising structure involving a single tributary. These results illustrate the extent of differentiation within and among streams and could inform possibilities for and implications of RBT removal and LCT reintroduction.</p>
Conserving on the edge: genetic variation and structure in northern populations of the endangered plant Dracocephalum ruyschiana L. (Lamiaceae)
<p>Loss of biodiversity is accelerating, including the loss of genetic diversity. Conservation of small, isolated populations may be important, as they can provide valuable contributions to overall genetic variation and long-term viability of species. Furthermore, such populations may play an essential role in adaptation to new environments following changes in e.g. land-use and climate. <em>Dracocephalum ruyschiana</em> is a threatened plant species throughout its European distribution, but 25% of the European populations are situated within Norway. Therefore, the species has its own action plan in Norway, which includes demographic monitoring. However, this monitoring does not cover genetic variation nor is the selection of monitored populations based on genetic differentiation, therefore this fundamental level of biodiversity is overlooked. We analyzed 43 sites using 96 SNPs developed for <em>D. ruyschiana</em>, to investigate whether the monitored populations cover the genetic variation and differentiation found within the Norwegian distribution. The results show structuring and differentiation between populations and indicate that there are at least four distinct genetic groups, of which only two are covered extensively by current demographic monitoring. We suggest that two sites representing the two other genetic groups should be included in the national monitoring program to better conserve the genetic variation found in the Norwegian population of <em>D. ruyschiana</em>. Overall, our results highlight the importance of an integrated, interdisciplinary framework to better monitor and conserve biodiversity at several levels.</p>
Population genetics reveal that the western Tianshan Mountains populations of Agrilus mali (Coleoptera: Buprestidae) may not be introduced recently
<p>Supplementary charts and haplotype sequences for all genes in the article are included in this zip file.</p>
Data from: Genetic analysis of life-history constraint and evolution in a wild ungulate population
Trade-offs among life-history traits are central to evolutionary theory. In quantitative genetic terms, trade-offs may be manifested as negative genetic covariances relative to the direction of selection on phenotypic traits. Although the expression and selection of ecologically important phenotypic variation are fundamentally multivariate phenomena, the in situ quantification of genetic covariances is challenging. Even for life-history traits, where well-developed theory exists with which to relate phenotypic variation to fitness variation, little evidence exists from in situ studies that negative genetic covariances are an important aspect of the genetic architecture of life-history traits. In fact, the majority of reported estimates of genetic covariances among life-history traits are positive. Here we apply theory of the genetics and selection of life histories in organisms with complex life cycles to provide a framework for quantifying the contribution of multivariate genetically based relationships among traits to evolutionary constraint. We use a Bayesian framework to link pedigree-based inference of the genetic basis of variation in life-history traits to evolutionary demography theory regarding how life histories are selected. Our results suggest that genetic covariances may be acting to constrain the evolution of female life-history traits in a wild population of red deer Cervus elaphus: genetic covariances are estimated to reduce the rate of adaptation by about 40%, relative to predicted evolutionary change in the absence of genetic covariances. Furthermore, multivariate phenotypic (rather than genetic) relationships among female life-history traits do not reveal this constraint.
Genetic insights into the range expansion of the cattle egret (Pelecaniformes: Ardeidae) in Brazil and population differentiation between the native and colonized areas
<p>Gnotypes of Cattle Egrets (Bubulcus ibis) at 14 microsatellite loci amplified using the primers in Table S1 of the article. The protocols are described in Appendix S1 of the Supplementary Material of Miño et al. 2022.</p> <p>Bubulcus ibis ibis naturally expanded its range by flying over the Atlantic Ocean from Africa or Europe (native range) to South America, being first reported in Suriname towards the end of the 19th century. However, the source populations of the birds colonising South America still remains unclear. Here, to o gain insights into the possible source and routes of colonisation, we characterize the levels of diversity at nuclear microsatellites and assessed the genetic structure of populations from central and southern Africa (n = 129, 13 sites, five countries) and from different latitudes along Brazil (n = 166, six sites). We found overall high levels of genetic diversity in the colonised range, which fit the expectations for organisms with long-distance dispersal potential, rapid growth rates and feeding plasticity. Noteworthy, the results from population-genetic analyses based on different assumptions concurrently agree in indicating that cattle egrets from Brazil harbour a genetic pool distinct from populations from Africa, suggesting restricted contemporary gene flow between these ranges. The lack of genetic differentiation among the African populations did not enable us to identify the source of Brazilian cattle egrets. Fernando de Noronha Archipelago, off the Brazilian northeastern coast, had the highest proportion of the African allelic ancestry. Approximate Bayesian computation analyses supported a scenario of population growth in Africa with subsequent expansion to Brazil and migration from Africa to Brazil at the time of colonisation. We discuss our findings in light of the anthropogenic changes that may have promoted the range expansion of this egret into Brazil.</p>
Population differences in Chinook salmon (Oncorhynchus tshawytscha) DNA methylation: genetic drift and environmental factors
<p>Local adaptation and phenotypic differences among populations have been reported in many species, though most studies focus on either neutral or adaptive genetic differentiation. With the discovery of DNA methylation, questions have arisen about its contribution to individual variation in and among natural populations. Previous studies have identified differences in methylation among populations of organisms, although most to date have been in plants and model animal species. Here we obtained eyed eggs from eight populations of Chinook salmon (<i>Oncorhynchus tshawytscha</i>) and assayed DNA methylation at 23 genes involved in development, immune function, stress response, and metabolism using a gene-targeted PCR-based assay for next-generation sequencing. Evidence for population differences in methylation was found at eight out of 23 gene loci after controlling for developmental timing in each individual. However, we found no correlation between freshwater environmental parameters and methylation variation among populations at those eight genes. A weak correlation was identified between pairwise DNA methylation dissimilarity among populations and pairwise F<sub>ST</sub> based on 15 microsatellite loci, indicating weak effects of genetic drift or geographic distance on methylation. The weak correlation was primarily driven by two genes, GTIIBS and Nkef. However, single-gene Mantel tests comparing methylation and pairwise F<sub>ST</sub> were not significant after Bonferroni correction. Thus, population differences in DNA methylation are more likely related to unmeasured oceanic environmental conditions, local adaptation, and/or genetic drift. DNA methylation is an additional mechanism that contributes to among population variation, with potential influences on organism phenotype, adaptive potential, and population resilience.</p>
Data from: Traces of Genetic but Not Epigenetic Adaptation in the Invasive Goldenrod Solidago canadensis Despite the Absence of Population Structure
<p><strong>General information</strong></p> <p>This deposition contains the datasets that were used in the statistical analysis of the manuscript entitled <strong>Traces of genetic but not epigenetic adaptation in the invasive goldenrod <em>Solidago canadensis</em> despite the absence of population structure </strong>published in Frontiers in Ecology and Evolution (doi: <a href="https://doi.org/10.3389/fevo.2022.856453">10.3389/fevo.2022.856453</a>).</p> <p><strong>Uploaded files</strong></p> <ul> <li><strong>README</strong> file to explain the datasets</li> <li><strong>AFLP/MSAP metadata</strong> called EckertHerdenStiftDurkavanKleunenJoshi_2022_FrontEcolEvol_AFLPMSAP_meta_data.txt</li> <li><strong>AFLP scoring dataset</strong> called EckertHerdenStiftDurkavanKleunenJoshi_2022_FrontEcolEvol_AFLP_scoring_data.txt</li> <li><strong>MSAP scoring dataset</strong> called EckertHerdenStiftDurkavanKleunenJoshi_2022_FrontEcolEvol_MSAP_scoring_data.txt</li> <li><strong>MSAP mix1-scoring dataset</strong> called EckertHerdenStiftDurkavanKleunenJoshi_2022_FrontEcolEvol_MSAP_scoring_data_mix1.txt</li> <li>All files were combined in a <strong>.zip file</strong></li> </ul>
Genetic Control of Reproductive Traits under Different Temperature Regimes in Inbred Line Populations Derived from Crosses between S. pimpinellifolium and S. lycopersicum Accessions
<p>Marker genotypes, linkage map and phenotypic data used for QTL analysis included in the manuscript by Gonzalo et al. <em>in press "</em>Genetic Control of Reproductive Traits under Different Temperature Regimes in Inbred Line Populations Derived from Crosses between <em>S. pimpinellifolium</em> and <em>S. lycopersicum</em> Accessions".</p>
Dispersal ability and its consequences for population genetic differentiation and diversification
<p><span>Dispersal ability is known to influence geographic structuring of genetic variation within species, with a direct relationship between low vagility and population genetic structure, which can potentially give rise to allopatric speciation. However, our general understanding of the relationship between dispersal ability, population differentiation and lineage diversification is limited. To address this issue, we sampled mitochondrial DNA variation within lineages of beetles and spiders across the Canary Islands to explore the relationships between dispersal ability, differentiation within lineages and diversification. We found positive relationships between population genetic structure and diversification for both beetles and spiders. Comparisons between dispersive and non-dispersive lineages revealed significant differences for both lineage differentiation and diversification. For both taxa, non-dispersive lineages had stronger population genetic structure. Genus-level endemic species richness and proxies for diversification rate within genera were higher in non-dispersive taxa for both beetles and spiders. Comparisons of average and maximum node divergences within genera suggest that species turnover may be higher in non-dispersive genera. Our results reveal a model where dispersal limitation may shape the diversity of lineages across evolutionary time scales by positively influencing intraspecific and species diversity, moderated by higher extinction rates compared to more dispersive lineages.</span></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.