Find research datasets worth reusing

Data from: Sun skink landscape genomics: assessing how microevolutionary processes shape genetic and phenotypic diversity across a heterogeneous and fragmented landscape

Incorporating genomic data sets into landscape genetic analyses allows for powerful insights into population genetics, explicitly geographical correlates of selection, and morphological diversification of organisms across the geographical template. Here, we utilize an integrative approach to examine gene flow and detect selection, and we relate these processes to genetic and phenotypic population differentiation across South-East Asia in the common sun skink, Eutropis multifasciata. We quantify the relative effects of geographic and ecological isolation in this system and find elevated genetic differentiation between populations from island archipelagos compared to those on the adjacent South-East Asian continent, which is consistent with expectations concerning landscape fragmentation in island archipelagos. We also identify a pattern of isolation by distance, but find no substantial effect of ecological/environmental variables on genetic differentiation. To assess whether morphological conservatism in skinks may result from stabilizing selection on morphological traits, we perform FST–PST comparisons, but observe that results are highly dependent on the method of comparison. Taken together, this work provides novel insights into the manner by which micro-evolutionary processes may impact macro-evolutionary scale biodiversity patterns across diverse landscapes, and provide genomewide confirmation of classic predictions from biogeographical and landscape ecological theory.

Data from: Node-based measures of connectivity in genetic networks

At-site environmental conditions can have strong influences on genetic connectivity, and in particular on the immigration and settlement phases of dispersal. However, at-site processes are rarely explored in landscape genetic analyses. Networks can facilitate the study of at-site processes, where network nodes are used to model site-level effects. We used simulated genetic networks to compare and contrast the performance of 7 node-based (as opposed to edge-based) genetic connectivity metrics. We simulated increasing node connectivity by varying migration in two ways: we increased the number of migrants moving between a focal node and a set number of recipient nodes, and we increased the number of recipient nodes receiving a set number of migrants. We found that two metrics in particular, the average edge weight and the average inverse edge weight, varied linearly with simulated connectivity. Conversely, node degree was not a good measure of connectivity. We demonstrated the use of average inverse edge weight to describe the influence of at-site habitat characteristics on genetic connectivity of 653 American martens (Martes americana) in Ontario, Canada. We found that highly connected nodes had high habitat quality for marten (deep snow and high proportions of coniferous and mature forest) and were farther from the range edge. We recommend the use of node-based genetic connectivity metrics, in particular, average edge weight or average inverse edge weight, to model the influences of at-site habitat conditions on the immigration and settlement phases of dispersal.

opencc-zeroDec 2013View details →

Data from: Testing for beneficial reversal of dominance during salinity shifts in the invasive copepod Eurytemora affinis, and implications for the maintenance of genetic variation

Maintenance of genetic variation at loci under selection has profound implications for adaptation under environmental change. In temporally and spatially varying habitats, non-neutral polymorphism could be maintained by heterozygote advantage across environments (marginal overdominance), which could be greatly increased by beneficial reversal of dominance across conditions. We tested for reversal of dominance and marginal overdominance in salinity tolerance in the salt-to-freshwater invading copepod Eurytemora affinis. We compared survival of F1 offspring generated by crossing saline and freshwater inbred lines (between-salinity F1 crosses) relative to within-salinity F1 crosses, across three salinities. We found evidence for both beneficial reversal of dominance and marginal overdominance in salinity tolerance. In support of reversal of dominance, survival of between-salinity F1 crosses was not different from that of freshwater F1 crosses under freshwater conditions and saltwater F1 crosses under saltwater conditions. In support of marginal overdominance, between-salinity F1 crosses exhibited significantly higher survival across salinities relative to both freshwater and saltwater F1 crosses. Our study provides a rare empirical example of complete beneficial reversal of dominance associated with environmental change. This mechanism might be crucial for maintaining genetic variation in salinity tolerance in E. affinis populations, allowing rapid adaptation to salinity changes during habitat invasions.

Data from: Squamate Conserved Loci (SqCL): a unified set of conserved loci for phylogenomics and population genetics of squamate reptiles

The identification of conserved loci across genomes, along with advances in target capture methods and high-throughput sequencing, has helped spur a phylogenomics revolution by enabling researchers to gather large numbers of homologous loci across clades of interest with minimal upfront investment in locus design. Target capture for vertebrate animals is currently dominated by two approaches – anchored hybrid enrichment (AHE) and ultraconserved elements (UCE) – and both approaches have proven useful for addressing questions in phylogenomics, phylogeography, and population genomics. However, these two sets of loci have minimal overlap with each other; moreover, they do not include many traditional loci that that have been used for phylogenetics. Here, we combine across UCE, AHE, and traditional phylogenetic gene locus sets to generate the Squamate Conserved Loci (SqCL) set, a single integrated probe set that can generate high-quality and highly complete data across all three loci types. We use these probes to generate data for 44 phylogenetically-disparate taxa that collectively span approximately 33% of terrestrial vertebrate diversity. Our results generated an average of 4.29 Mb across 4709 loci per individual, of which an average of 2.99 Mb was sequenced to high enough coverage (≥10×) to use for population genetic analyses. We validate the utility of these loci for both phylogenomic and population genomic questions, provide a comparison among these locus sets of their relative usefulness, and suggest areas for future improvement.

Data from: Intermediate habitat associations by hybrids may facilitate genetic introgression in a songbird

Hybridization or the interbreeding of genetically discrete populations or species can occur where ranges of genetically distinct units overlap. Golden-winged warblers Vermivora chrysoptera, a species that has been in steady decline for decades, highlight the potential population-level consequences of hybridization. A major factor implicated in their decline is hybridization with their sister species, the blue-winged warbler Vermivora cyanoptera, which has likely been exacerbated by historic and current land-use practices. We examined habitat associations of golden-winged and blue-winged warblers, phenotypic hybrids, and cryptic hybrids (i.e. mismatch between plumage phenotype and genotype as identified by mitochondrial DNA) in an area of relatively recent range overlap and hybridization in northern New York, USA. To explore the robustness of these results, we then compared the patterns from New York with habitat associations from the central Pennsylvanian Appalachian Mountains where blue-winged warblers either do not occur or are in very low abundance, yet cryptic golden-winged warbler hybrids are present. From 2008 to 2011, we captured 122 birds in New York and 28 in Pennsylvania and collected blood samples, which we used to determine maternal ancestry. For each bird captured, we measured territory-level (50-m radius circles) habitat, and later used remote-sensing data to quantify habitat on the territories and in surrounding areas (100-, 250-, and 500-m radius circles). In New York, golden-winged warblers occupied structurally heterogeneous territories surrounded by homogeneously structured, contiguous deciduous forest, far from urban areas. Blue-winged warblers showed opposite associations, and hybrids' habitat associations were typically intermediate. In Pennsylvania, the habitat associations of golden-winged warblers and their cryptic hybrids were remarkably similar to those in New York. These findings suggest that patterns of habitat occupancy by hybrids may promote contact with golden-winged warblers and thus likely facilitate genetic introgression, even in areas where the parental species are not sympatric.

opencc-zeroDec 2015View details →

Data from: Estimation of genetic purging under competitive conditions

Inbreeding depression for fitness traits is a key issue in evolutionary biology and conservation genetics. The magnitude of inbreeding depression, though, may critically depend on the efficiency of genetic purging, the elimination or recessive deleterious mutations by natural selection after they are exposed by inbreeding. However, the detection and quantification of genetic purging for nonlethal mutations is a rather difficult task. Here, we present two comprehensive sets of experiments with Drosophila aimed at detecting genetic purging in competitive conditions and quantifying its magnitude. We obtain, for the first time in competitive conditions, an estimate for the predictive parameter, the purging coefficient (d), that quantifies the magnitude of genetic purging, either against overall inbreeding depression (d ≈ 0.3), or against the component ascribed to nonlethal alleles (dNL ≈ 0.2). We find that competitive fitness declines at a high rate when inbreeding increases in the absence of purging. However, in moderate size populations under competitive conditions, inbreeding depression need not be too dramatic in the medium to short term, as the efficiency of purging is also very high. Furthermore, we find that purging occurred under competitive conditions also reduced the inbreeding depression that is expressed in the absence of competition.

opencc-zeroDec 2013View details →

Data from: Genetic structure of an introduced paper wasp, Polistes chinensis antennalis (Hymenoptera, Vespidae) in New Zealand

Several eusocial wasps are prominent invaders to remote islands. The paper wasp Polistes chinensis antennalis is native to East Asia, was introduced to New Zealand in 1979, and has expanded its distribution there. This provides an excellent opportunity to examine the impacts of an initial bottleneck and subsequent expansion on genetic structure. We analysed and compared the genetic population structures of the native (Japan and South Korea) and invasive New Zealand populations. Although 94% of individuals had shared haplotypes detected across both populations, the remaining 6% had private haplotypes identified in only one of the three countries. The genetic variation at microsatellite loci was lower in New Zealand than in native countries, and the genetic structure in New Zealand was clearly distinct from that in its native range. Higher frequencies of diploid male and triploid female producing colonies were detected in New Zealand than in the native countries, showing the reduction of genetic variation via a genetic bottleneck. At least two independent introductions were suggested, and the putative source regions for New Zealand were assigned as Kanto (central island) and Kyushu (south island) in Japan. Serial founder events following the initial introduction were also indicated. The estimated dispersal distance between mother and daughter in New Zealand was twice that in Japan. Thus, the introduction history of P. chinensis antennalis in New Zealand is likely the result of at least two independent introductions, passing through a bottleneck during introduction, followed by population expansion from the point of introduction.

opencc-zeroDec 2017View details →

Data from: Urbanization drives genetic differentiation in physiology and structures the evolution of pace-of-life syndromes in the water flea Daphnia magna

Natural and human-induced stressors elicit changes in energy metabolism and stress physiology in populations of a wide array of species. Cities are stressful environments that may lead to differential selection on stress-coping mechanisms. Given that city ponds are exposed to the urban heat island effect and receive polluted run-off, organisms inhabiting these ecosystems might show genetic differentiation for physiological traits enabling them to better cope with higher overall stress levels. A common garden study with 62 Daphnia magna genotypes from replicated urban and rural populations revealed that urban Daphnia have significantly higher concentrations of total body fat, proteins, and sugars. Baseline activity levels of the antioxidant defense enzymes superoxide dismutase (SOD) and glutathione-S-transferase (GST) were higher in rural compared to city populations, yet urban animals were equally well protected against lipid peroxidation. Our results add to the recent evidence of urbanisation-driven changes in stress physiology and energy metabolism in terrestrial organisms. Combining our results with data on urban life history evolution in Daphnia revealed that urban genotypes show a structured pace-of-life syndrome involving both life history and physiological traits, whereas this is absent in rural populations.

Data from: Aneuploidy causes non-genetic individuality

Phenotypic variability is a hallmark of diseases involving chromosome gains and losses, such as Down syndrome and cancer. Allelic variances have been thought to be the sole cause of this heterogeneity. Here, we systematically examine the consequences of gaining and losing single or multiple chromosomes to show that the aneuploid state causes non-genetic phenotypic variability. Yeast cell populations harboring the same defined aneuploidy exhibit heterogeneity in cell-cycle progression and response to environmental perturbations. Variability increases with degree of aneuploidy and is partly due to gene copy number imbalances, suggesting that subtle changes in gene expression impact the robustness of biological networks and cause alternate behaviors when they occur across many genes. As inbred trisomic mice also exhibit variable phenotypes, we further propose that non-genetic individuality is a universal characteristic of the aneuploid state that may contribute to variability in presentation and treatment responses of diseases caused by aneuploidy.

opencc-zeroDec 2015View details →

Data from: Understanding the spatial scale of genetic connectivity at sea: unique insights from a land fish and a meta-analysis

Quantifying the spatial scale of population connectivity is important for understanding the evolutionary potential of ecologically divergent populations and for designing conservation strategies to preserve those populations. For marine organisms like fish, the spatial scale of connectivity is generally set by a pelagic larval phase. This has complicated past estimates of connectivity because detailed information on larval movements are difficult to obtain. Genetic approaches provide a tractable alternative and have the added benefit of estimating directly the reproductive isolation of populations. In this study, we leveraged empirical estimates of genetic differentiation among populations with simulations and a meta-analysis to provide a general estimate of the spatial scale of genetic connectivity in marine environments. We used neutral genetic markers to first quantify the genetic differentiation of ecologically-isolated adult populations of a land dwelling fish, the Pacific leaping blenny (Alticus arnoldorum), where marine larval dispersal is the only probable means of connectivity among populations. We then compared these estimates to simulations of a range of marine dispersal scenarios and to collated FST and distance data from the literature for marine fish across diverse spatial scales. We found genetic connectivity at sea was extensive among marine populations and in the case of A. arnoldorum, apparently little affected by the presence of ecological barriers. We estimated that ~5000 km (with broad confidence intervals ranging from 810 - 11,692 km) was the spatial scale at which evolutionarily meaningful barriers to gene flow start to occur at sea, although substantially shorter distances are also possible for some taxa. In general, however, such a large estimate of connectivity has important implications for the evolutionary and conservation potential of many marine fish communities.

opencc-zeroDec 2011View details →

Data from: Rapid genetic assimilation of native wall lizard populations (Podarcis muralis) through extensive hybridization with introduced lineages

The Common Wall Lizard (Podarcis muralis) has established more than 150 non-native populations in Central Europe, stemming from eight geographically distinct evolutionary lineages. While the majority of these introduced populations are found outside the native range, some of these populations also exist at the northern range margin in south-western Germany. In order to a) infer the level of hybridization in contact zones of alien and native lineages and b) compare the genetic diversity among purebred introduced, native and hybrid populations we used a combination of maternally inherited markers (mtDNA: cytb) and Mendelian markers (microsatellites). Our results suggest a rapid genetic assimilation of native populations by strong introgression from introduced lineages. Discordant patterns of mtDNA and nDNA variation within hybrid populations may be explained by directed mate choice of females towards males of alien lineages. In contrast to previous studies we found a non-linear relationship between genetic diversity and admixture level. The genetic diversity of hybrid populations was substantially higher than in introduced and native populations belonging to a single lineage, but rapidly reaching a plateau of high genetic diversity at an admixture level of two. However, even introduced populations with low founder sizes and from one source population retained moderate levels of genetic diversity and no evidence for a genetic bottleneck was found. The extent of introgression and the dominance of alien haplotypes in mixed populations indicate that introductions of non-native lineages represent a serious threat to the genetic integrity of native populations due to the rapid creation of hybrid swarms.

Data from: Genetic and genomic evidence of niche partitioning and adaptive radiation in mountain pine beetle fungal symbionts

Bark beetles form multipartite symbiotic associations with blue stain fungi (Ophiostomatales, Ascomycota). These fungal symbionts play an important role during the beetle's life cycle by providing nutritional supplementation, overcoming tree defences and modifying host tissues to favour brood development. The maintenance of stable multipartite symbioses with seemingly less competitive symbionts in similar habitats is of fundamental interest to ecology and evolution. We tested the hypothesis that the coexistence of three fungal species associated with the mountain pine beetle is the result of niche partitioning and adaptive radiation using SNP genotyping coupled with genotype–environment association analysis and phenotypic characterization of growth rate under different temperatures. We found that genetic variation and population structure within each species is best explained by distinct spatial and environmental variables. We observed both common (temperature seasonality and the host species) and distinct (drought, cold stress, precipitation) environmental and spatial factors that shaped the genomes of these fungi resulting in contrasting outcomes. Phenotypic intraspecific variations in Grosmannia clavigera and Leptographium longiclavatum, together with high heritability, suggest potential for adaptive selection in these species. By contrast, Ophiostoma montium displayed narrower intraspecific variation but greater tolerance to extreme high temperatures. Our study highlights unique phenotypic and genotypic characteristics in these symbionts that are consistent with our hypothesis. By maintaining this multipartite relationship, the bark beetles have a greater likelihood of obtaining the benefits afforded by the fungi and reduce the risk of being left aposymbiotic. Complementarity among species could facilitate colonization of new habitats and survival under adverse conditions.

opencc-zeroDec 2012View details →

Data from: Phylogeographic and population genetic analyses reveal Pleistocene isolation followed by high gene flow in a wide- ranging, but endangered, freshwater mussel

Freshwater organisms of North America have had their contemporary genetic structure shaped by vicariant events, especially Pleistocene glaciations. Life history traits promoting dispersal and gene flow continue to shape population genetic structure. Cumberlandia monodonta, a widespread but imperiled (IUCN listed as endangered) freshwater mussel, was examined to determine genetic diversity and population genetic structure range-wide. MtDNA sequences and microsatellite loci were used to measure genetic diversity and simulate demographic events during the Pleistocene using approximate Bayesian computation (ABC) to test explicit hypotheses explaining the evolutionary history of current populations. A phylogeny and molecular clock suggested past isolation created two mtDNA lineages during the Pleistocene that are now widespread. Two distinct groups were also detected with microsatellites. ABC simulations indicated the presence of two glacial refugia and post-glacial admixture of them followed by simultaneous dispersal throughout the current range of the species. The Ouachita population is distinct from others and has the lowest genetic diversity, indicating that this is a peripheral population of the species. Gene flow within this species has maintained high levels of genetic diversity in northern populations, however, all population have experienced fragmentation. Extirpation from the center of its range likely has isolated remaining populations due to the geographic distances among them.

opencc-zeroDec 2013View details →

Data from: Genetic architecture of a hormonal response to gene knockdown in honey bees

Variation in endocrine signaling is proposed to underlie the evolution and regulation of social life histories, but the genetic architecture of endocrine signaling is still poorly understood. An excellent example of a hormonally influenced set of social traits is found in the honey bee (Apis mellifera): a dynamic and mutually suppressive relationship between juvenile hormone (JH) and the yolk precursor protein vitellogenin (Vg) regulates behavioral maturation and foraging of workers. Several other traits cosegregate with these behavioral phenotypes, comprising the pollen hoarding syndrome (PHS) one of the best-described animal behavioral syndromes. Genotype differences in responsiveness of JH to Vg are a potential mechanistic basis for the PHS. Here, we reduced Vg expression via RNA interference in progeny from a backcross between 2 selected lines of honey bees that differ in JH responsiveness to Vg reduction and measured JH response and ovary size, which represents another key aspect of the PHS. Genetic mapping based on restriction site-associated DNA tag sequencing identified suggestive quantitative trait loci (QTL) for ovary size and JH responsiveness. We confirmed genetic effects on both traits near many QTL that had been identified previously for their effect on various PHS traits. Thus, our results support a role for endocrine control of complex traits at a genetic level. Furthermore, this first example of a genetic map of a hormonal response to gene knockdown in a social insect helps to refine the genetic understanding of complex behaviors and the physiology that may underlie behavioral control in general.

opencc-zeroDec 2019View details →

Seedling traits from root to shoot exhibit genetic diversity and distinct responses to environmental heterogeneity within a tree population

<p>Phenotypic diversity within plant species is crucial to shaping evolutionary responses of populations and interactions among species, yet intraspecific genetic variability notably in roots has attracted little attention. Further, evidence for the root−shoot trait synchronisation remains inconclusive, narrowing our understanding of the role that belowground traits play in local adaptation. We applied broad 'top-to-toe' phenotyping to a model system whose native environmental conditions were simulated in experimental settings. Fifteen maternal families of Norway spruce <i>Picea abies </i>from southern Finland grew in six combinations of two simulated growing seasons and three soil treatments. We scored variation in 25 functional traits, including size, architecture and morphology of intact root systems, and shoot growth and phenology. Careful phenotyping of roots uncovered five trait dimensions, with root size, architecture and morphology forming the three largest axes of variation. Dimensions varied in their treatment responses. We observed among-family differences in all trait dimensions, marking substantial within-population genetic diversity. For example, average total root length varied almost twofold among families, but family × soil interactions indicated treatment-specific estimates of genetic variance. Mirroring root traits, phenotypic plasticity and genetic variation characterised shoot growth and phenology. In all, the complete phenotypic dataset yielded six trait dimensions, with assorted measures of root system and shoot size composing the main axis of variation. Although plastic and genetically variable, root architecture and morphology were not associated with shoot growth in any treatment. Also phenology and root-to-shoot ratio were detached from the primary axis of trait variability. Our results demonstrate that complex within-species patterns of trait covariation can be observed even locally and that phenotypic variation in independent trait dimensions reflecting divergent growth strategies is under genetic control. More accurate predictions of population and species responses to changes in the environment can be achieved when such intraspecific diversity is taken into account.</p>

Data from: Genetic assignment of large seizures of elephant ivory reveals Africa's major poaching hotspots

Poaching of elephants is now occurring at rates that threaten African populations with extinction. Identifying the number and location of Africa's major poaching hotspots may assist efforts to end poaching and facilitate recovery of elephant populations. We genetically assign origin to 28 large ivory seizures (≥0.5 tons) made between 1996-2014, also testing assignment accuracy. Results suggest that the major poaching hotspots in Africa may be currently concentrated in as few as two areas. Increasing law enforcement in these two hotspots could help curtail future elephant losses across Africa and disrupt this organized transnational crime.

Data from: Genetic correlations among developmental and contextual behavioral plasticity in Drosophila melanogaster

Correlations among traits, including behaviors, are important because traits that are genetically correlated may not evolve independently. Recently, behavioral correlations research has expanded to include correlations not only in mean-level behaviors, but also in behavioral plasticity, i.e., the degree to which individuals change their behavior in response to environmental stimuli. Positive correlations among behavioral plasticities would imply that individuals or genotypes that are behaviorally plastic in one way may also be plastic in other ways; negative correlations could imply tradeoffs. Here, we examine aversive odor conditioning (learning) at two time points, and plasticity in pupation site selection behavior across substrates, in a panel of Drosophila genotypes. These behaviors represent different types of behavioral plasticity: contextual plasticity describes behavioral responses to stimuli that are currently present, while developmental plasticity describes behavioral responses to remembered experiences with stimuli in the recent past. We find that learning scores and plasticity in pupation site selection behavior are positively genetically correlated, representing the first example of a genetic correlation between developmental and contextual plasticity. These findings imply that ecological and evolutionary theories focusing on variation in a single dimension of behavioral plasticity may be incomplete.

opencc-zeroDec 2018View details →

Data from: Effect of plant chemical variation and mutualistic ants on the local population genetic structure of an aphid herbivore

1.Plants exhibit impressive genetic and chemical diversity, not just between species but also within species, and the importance of plant intraspecific variation for structuring ecological communities is well known. When there is variation at the local population level, this can create a spatially‐heterogeneous habitat for specialized herbivores potentially leading to non‐random distribution of individuals across host‐plants. 2.Plant variation can affect herbivores directly and indirectly via a third species, resulting in variable herbivore growth rates across different host plants. Herbivores also exhibit within‐species variation, with some genotypes better adapted to some plant variants than others. 3.We genotyped aphids collected across two years from a field site containing ~200 patchily‐distributed host plants that exhibit high chemical diversity. The distribution of aphid genotypes, their ant mutualists, and other predators was assessed across the plants. 4.We present evidence that the local distribution of aphid (Metopeurum fuscoviride) genotypes across host‐plant individuals is associated with variation in the plant volatiles (chemotypes) and non‐volatile metabolites (metabotypes) of their host plant tansy (Tanacetum vulgare). Furthermore, these interactions in the field were influenced by plant‐host preferences of aphid‐mutualist ants. 5.Our results emphasize that plant intraspecific variation can structure ecological communities not only at the species level but also at the genetic level within species, and that this effect can be enhanced through indirect interactions with a third species.

Data from: High genetic variation and moderate to high values for genetic parameters of Picea abies resistance to Pissodes strobi

Genetic parameters of Picea abies resistance to the white pine weevil (Pissodes strobi Peck) were estimated from 193 full-sib and 166 half-sib families in six 10-year-old progeny trials. The estimated family and individual heritability values for the cumulative weevil attack rate between ages 6 and 10 (CWA6–10) were high and moderate for both full-sib families (0.61 and 0.28, respectively) and half-sib families (0.85 and 0.40, respectively), indicating strong genetic control for this trait in Norway spruce. The fact that specific combining ability (SCA) variance represents 35 % of the general combining ability (GCA) variance suggests that non-additive (dominant) effects are weak. The strong type B correlations found for CWA6–10 (rˆB=0.96 for full-sib families and rˆB=0.81 for half-sib families) indicate that family ranks were stable across sites. For three of the five sites with high attack levels, genetic correlations were not significant between CWA6–10 and tree height at age 5. Moderate positive genetic correlations were detected between CWA6–10 and tree diameter at age 10 (rˆA from 0.29 to 0.60), but specific families showing both high resistance and good diameter growth can be found. These results suggest that the genetic improvement of Norway spruce for resistance to white pine weevil can be achieved successfully without adversely affecting growth.