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opencc-zeroSep 2020View details →

Genome-wide SNPs detect no evidence of genetic population structure for reef manta rays (Mobula alfredi) in southern Mozambique

Little is known about the extent of genetic connectivity along continuous coastlines in manta rays or whether site visitation is influenced by relatedness. Such information is pertinent to defining population boundaries and understanding localised dispersal patterns and behaviour. Here, we use 3057 genome-wide single nucleotide polymorphisms (SNPs) to evaluate population genetic structure and assess levels of relatedness at aggregation sites of reef manta rays (Mobula alfredi) in southern Mozambique (n = 114). Contrary to indications of limited dispersal along the southern Mozambican coastline inferred from photo identification and telemetry studies, our results show no evidence of population structure (non-significant FST <0.001) for M. alfredi along this coast. We also found no evidence that individuals sampled at the same site were more related than expected by chance for males, females or across both sexes, suggesting kinship may not influence visitation pattern s at these sites. We estimated the effective population size (Ne) of this population to be 375 (95% CI = 369-380). Comparison to a distant eastern Indian Ocean site (Western Australia; n = 15) revealed strong genetic differentiation between Mozambique and Western Australia (FST = 0.377), identifying the Indian Ocean basin as a barrier to dispersal. Our findings show that genetic connectivity in M. alfredi extends for several hundred kilometres along continuous coastlines. We therefore recommend the population in Mozambique be considered a discrete management unit and future conservation plans should prioritize integrated strategies along the entire southern coastline.

opencc-zeroOct 2020View details →

Evolutionary rate and genetic load in an emblematic Mediterranean tree following an ancient and prolonged population collapse

Severe bottlenecks significantly diminish the amount of genetic diversity and the speed at which it accumulates (i.e. evolutionary rate). They further compromise the efficiency of natural selection to eliminate deleterious variants, which may reach fixation in the surviving populations. Consequently, expanding and adapting to new environments may pose a significant challenge when strong bottlenecks result in genetic pauperization. Herein, we surveyed the patterns of nucleotide diversity, molecular adaptation and genetic load across hundreds of loci in a circum-Mediterranean conifer (Pinus pinea L.) that represents one of the most extreme cases of genetic pauperization in widespread outbreeding taxa. We found very little genetic variation in both hypervariable non-coding (nuSSRs) and gene-coding loci, which translated into genetic diversity estimates one order of magnitude lower than those previously reported for pines. Such values were consistent with a strong population decline that began some ~1Ma. Comparisons with the related and partially parapatric maritime pine revealed reduced rates of adaptive evolution (α and ωa) and a significant accumulation of genetic load. These did not appear to result from differences in mutation rates or linkage disequilibrium between the two species; instead they are the likely outcome of contrasting demographic histories affecting both the speed at which these taxa accumulate genetic diversity, and the global efficacy of selection. Future studies, and programs for conservation and management, should thus start testing for the effects of genetic load on fitness and integrating such effects into predictive models.

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Taxus genotype data for "Trunk perimeter correlates with genetic bottleneck intensity and the level of genetic diversity in populations of Taxus baccata L."

The data set contains microsatellite genotypes (18 loci) of Taxus baccata trees, together with the information about sampling sites.

opencc-by-4.0Oct 2020View details →

opencc-zeroNov 2020View details →

Genetic diversity and structure of wild Vaccinium populations - V. myrtillus, V.vitis-idaea and V. uliginosum in the Baltic States

V. myrtillus L., V. vitis-idaea L. and V. uliginosum L. belong to the genus Vaccinium. These wild species are widely distributed and ecologically important within the Baltic countries but they have not been extensively studied using molecular markers. EST-SSR and cpSSR markers were used to investigate the population structure and genetic diversity of these species to obtain information useful for the development of in situ conservation strategies for these species. Wild Vaccinium species populations are moderately genetically differentiated, with some populations more highly differentiated, but without higher order clustering of groups of populations, indicating that there are no dispersal barriers for these species within the Baltic countries. Genetic diversity of populations growing in protected areas, managed forests and intensively utilised public recreational areas is similar.

opencc-zeroNov 2020View details →

The many population genetic and demographic routes to islands of genomic divergence

<ol> <li>The way that organisms diverge into reproductively isolated species is a major question in biology. The recent accumulation of genomic data provides promising opportunities to understand the genomic landscape of divergence, which describes the distribution of differences across genomes. Genomic areas of unusually high differentiation have been called genomic islands of divergence. Their formation has been attributed to a variety of mechanisms, but a prominent hypothesis is that they result from divergent selection over a small portion of the genome, with surrounding areas homogenised by gene flow. Such islands have often been interpreted as being associated with divergence with gene flow. However other mechanisms related to genomic structure and population history can also contribute to the formation of genomic islands of divergence.</li> <li>We currently lack a quantitative framework to examine the dynamics of genomic landscapes under the complex and nuanced conditions that are found in natural systems. Here, we develop an individual-based simulation to explore the dynamics of diverging genomes under various scenarios of gene flow, selection and genotype-phenotype maps.</li> <li>Our modelling results are consistent with empirical observations demonstrating the formation of genomic islands under genetic isolation. Importantly, we have quantified the range of conditions that produce genomic islands. We demonstrate that the initial level of genetic diversity, drift, time since divergence, linkage disequilibrium, strength of selection and gene flow are all important factors that can influence the formation of genomic islands. Because the accumulation of genomic differentiation over time tends to erode the signal of genomic islands, genomic islands are more likely to be observed in recently divergent taxa, although not all recently diverged taxa will necessarily exhibit islands of genomic divergence. Gene flow primarily slows the swamping of islands of divergence with time.</li> <li>By using this framework, further studies may explore the relative influence of particular suites of events that contribute to the emergence of genomic islands under sympatric, parapatric and allopatric conditions. This approach represents a novel tool to explore quantitative expectations of the speciation process, and should prove useful in elucidating past and projecting future genomic evolution of any taxa.</li> </ol>

opencc-zeroNov 2020View details →

Genetic population structure constrains local adaptation in sticklebacks

Repeated and independent adaptation to specific environmental conditions from standing genetic variation is common. However, if genetic variation is limited, the evolution of similar locally adapted traits may be restricted to genetically different and potentially less optimal solutions or prevented from happening altogether. Using a quantitative trait locus (QTL) mapping approach, we identified the genomic regions responsible for the repeated pelvic reduction (PR) in three crosses between nine-spined stickleback populations expressing full and reduced pelvic structures. In one cross, PR mapped to linkage group 7 (LG7) containing the gene Pitx1, known to control pelvic reduction also in the three-spined stickleback. In the two other crosses, PR was polygenic and attributed to ten novel QTL, of which 90% were unique to specific crosses. When screening the genomes from 27 different populations for deletions in the Pitx1 regulatory element, these were only found in the population in which PR mapped to LG7, even though the morphological data indicated large effect QTL for PR in several other populations as well. Consistent with the available theory and simulations parameterised on empirical data, we hypothesise that the observed variability in genetic architecture of PR is due to heterogeneity in the spatial distribution of standing genetic variation caused by >2x stronger population structuring among freshwater populations and >10x stronger genetic isolation by distance in the sea in nine-spined sticklebacks as compared to three-spined sticklebacks.

opencc-zeroNov 2021View details →

Intraspecific genetic variation and spectral data of a Fagus sylvatica population in a temperate forest

This dataset contain genetic variation and multi-annual conopy level spectral responses of 77 Fagus sylvatica individuals from Laegern temperate forest (47°28'N, 8°21'E) population.

Ancestral genetic variation in phenotypic plasticity underlies rapid evolutionary changes in resurrected populations of waterfleas

The role that phenotypic plasticity plays in adaptive evolution has been debated for decades. This is because the strength of natural selection is dependent upon the direction and magnitude of phenotypic responses to environmental signals. Therefore, the connection between plasticity and adaptation will depend on the patterns of plasticity harbored by ancestral populations prior to a change in the environment. Yet, few studies have directly assessed ancestral variation in plasticity and tracked phenotypic changes over time. Here we resurrected historic propagules of Daphnia spanning multiple species and lakes in Wisconsin following the invasion and proliferation of a novel predator (spiny waterflea, Bythotrephes longimanus). This approach revealed extensive genetic variation in predator-induced plasticity in ancestral populations of Daphnia. It is unlikely that the standing patterns of plasticity shielded Daphnia from selection to permit long-term coexistence with a novel predator. Instead, this variation in plasticity provided the raw materials for Bythotrephes-mediated selection to drive rapid shifts in Daphnia behavior and life history. Surprisingly, there was little evidence for the evolution of trait plasticity as genetic variation in plasticity was maintained in the face of a novel predator. Such results provide new insights into the link between plasticity and adaptation and highlight the importance of quantifying genetic variation in plasticity when evaluating the drivers of evolutionary change in the wild.

Genetic and phenotypic diversity of guppy population pre- and post-flood disturbance

Rare extreme "black swan" disturbances can impact ecosystems in many ways, such as destroying habitats, depleting resources, and causing high mortality. In rivers, for instance, exceptional floods that occur infrequently (e.g., so-called "50-year floods") can strongly impact the abundance of fishes and other aquatic organisms. Beyond such ecological effects, these floods could also impact intraspecific diversity by elevating genetic drift or dispersal and by imposing strong selection, which could then influence the population's ability to recover from disturbance. And yet, natural systems might be resistant (show little change) or resilient (show rapid recovery) even to rare extreme events – perhaps as a result of selection due to past events. We considered these possibilities in two rivers where native guppies experienced two extreme floods - one in 2005 and another in 2016. For each river, we selected four sites and used archived "historical" samples to compare levels of genetic diversity and phenotypic mean traits before versus after floods. Genetic diversity was represented by 33 neutral microsatellite markers, and phenotypic diversity was represented by body length and male melanic (black) color. We found that genetic diversity and population structure was mostly resistant to even these extreme floods; whereas the larger impacts on phenotypic diversity were short-lived, suggesting additional resilience. We discuss the determinants of these two outcomes for guppies facing floods, and then consider the general implications for the resistance and resilience of intraspecific variation to black swan disturbances.

Data from: The genetic architecture of fitness drives population viability during rapid environmental change

The rapid global loss of biodiversity calls for improved predictions of how populations will evolve and respond demographically to ongoing environmental change. The heritability (h2) of selected traits has long been known to affect evolutionary and demographic responses to environmental change. However, effects of the genetic architecture underlying the h2 of a selected trait on population responses to selection are less well understood. We use deterministic models and stochastic simulations to show that the genetic architecture underlying h2 can dramatically affect population viability during environmental change. Polygenic trait architectures (many loci, each with a small phenotypic effect) conferred higher population viability than genetic architectures with the same initial h2 and large-effect loci under a wide range of scenarios. Population viability also depended strongly on the initial frequency of large-effect beneficial alleles, with moderately low initial allele frequencies conferring higher viability than rare or already-frequent large-effect alleles. Greater population viability associated with polygenic architectures appears to be due to higher short term evolutionary potential compared to architectures with large-effect loci. These results suggest that integrating information on the trait genetic architecture into quantitiative genetic analysis will substantially improve our understanding and prediction of evolutionary and demographic responses to environmental change.

Evolutionary stability, landscape heterogeneity, and human land-usage shape population genetic connectivity in the Cape Floristic Region biodiversity hotspot

As human-induced change eliminates natural habitats, it impacts genetic diversity and population connectivity for local biodiversity. The South African Cape Floristic Region (CFR) is the most diverse extratropical area for plant biodiversity, and much of its habitat is protected as a UNESCO World Heritage site. There has long been great interest in explaining the underlying factors driving this unique diversity, especially as much of the CFR is endangered by urbanization and other anthropogenic activity. Here, we use a population and landscape genetic analysis of SNP data from the CFR endemic plant Leucadendron salignum or "common sunshine conebush" as a model to address the evolutionary and environmental factors shaping the vast CFR diversity. We found that high population structure, along with relatively deeper and older genealogies, are characteristic of the southwestern CFR, whereas, low population structure and more recent lineage coalescence depicts the eastern CFR. Population network analyses show genetic connectivity is facilitated in areas of lower elevation and higher seasonal precipitation. These population genetic signatures corroborate CFR species-level patterns consistent with high Pleistocene biome stability and landscape heterogeneity in the southwest, but with coincident instability in the east. Finally, we also find evidence of human land-usage as a significant gene flow barrier, especially in severely-threatened lowlands where genetic connectivity has been historically the highest. These results help identify areas where conservation plans can prioritize protecting high genetic diversity threatened by contemporary human activities within this unique cultural UNESCO site.

Data from: Plasticity matches phenotype to local conditions despite genetic homogeneity across 13 snake populations

In a widespread species, a matching of phenotypic traits to local environmental optima is generally attributed to site-specific adaptation. However, the same matching can occur via adaptive plasticity, without requiring genetic differences among populations. Adult sea kraits (Laticauda saintgironsi) are highly philopatric to small islands, but the entire population within the Neo-Caledonian lagoon is genetically homogenous because females migrate to the mainland to lay their eggs at communal sites; recruits disperse before settling, mixing up alleles. Consequently, any adaptive matching between local environments (e.g., prey sizes) and snake phenotypes (e.g., body sizes and relative jaw sizes) must be achieved via phenotypic plasticity rather than spatial heterogeneity in gene frequencies. We sampled 13 snake colonies spread along a ~200km northwest-southeast gradient (N>4,500 individuals) to measure two morphological features that affect maximum ingestible prey size in gape-limited predators: body size and relative jaw size. As proxies of habitat quality, we used protection status, fishing pressure and lagoon characteristics (lagoon width and distance of islands to the barrier reef). In both sexes, spatial variation in body sizes and relative jaw sizes was linked to habitat quality; albeit in different ways, consistent with sex-based divergences in foraging ecology. Strong spatial divergence in morphology among snake colonies, despite genetic homogeneity, supports the idea that phenotypic plasticity can facilitate speciation by creating multiple phenotypically distinct sub-populations shaped by their environment.

Low genetic variability in Bemisia tabaci MEAM1 populations within farmscapes of Georgia, USA

Sweetpotato whitefly, Bemisia tabaci Gennadius, is a serious pest of many agricultural crops worldwide. Numerous studies have examined the genetic structure of whitefly populations separated by geographical barriers; however, very few have assessed the population structure of B. tabaci at a farmscape level. A farmscape in this study is defined as heterogenous habitat with crop and non-crop areas spanning about 8 square kilometers. To assess the roles of farmscapes as drivers of B. tabaci genetic variations, thirty-five populations of the sweetpotato whitefly were collected from crop and non-crop plant species from fifteen farmscapes. Using mitochondrial COI gene sequences (mtCOI) and six nuclear microsatellite markers, the genetic diversity and genetic differentiation among collected B. tabaci MEAM1 populations were examined. Haplotype analysis using mtCOI sequences revealed the presence of a single B. tabaci MEAM1 haplotype across farmscapes of Georgia. Results from microsatellite markers further showed no significant genetic structuring among populations that corresponded to plant species or farmscapes from which they were collected. Annual whitefly population explosions and subsequent dispersal might have facilitated the presence of a single panmictic B. tabaci population over all sampled farmscapes in this region.

Data from: Conserving the genetic diversity of condemned populations: optimizing collections and translocation

We generated SNP genotype data from two endangered plant species, Pimelea spicata and Eucalyptus sp. Cattai. For each, we genotyped plants from a population that was 'condemned,' or that would soon be destoyed. We used the genotype data to design ex situ germplasm collections that preserved the diversity in the condemned populations, in ways that were optimized. Here, we provide an archive of these SNP genotype data, and the code that was used to analyse these data, including the optimizations.

Datasets for: Genome wide analysis reveals genetic divergence between Goldsinny wrasse populations

Background: Marine fish populations are often characterized by high levels of gene flow and correspondingly low genetic divergence. This presents a challenge to define management units. Goldsinny wrasse (Ctenolabrus rupestris) is a heavily exploited species due to its importance as a cleaner-fish in commercial salmonid aquaculture. However, at the present, the population genetic structure of this species is still largely unresolved. Here, full-genome sequencing was used to produce the first genomic reference for this species, to study population-genomic divergence among four geographically distinct populations, and, to identify informative SNP markers for future studies. Results: After construction of a de novo assembly, the genome was estimated to be highly polymorphic and of ~600Mbp in size. 33 235 genome wide SNPs were thereafter selected to assess genomic diversity and differentiation among four populations collected from Scandinavia, Scotland, and Spain. Global FST among these populations was 0.015–0.092. Approximately 4% of the investigated loci were identified as putative global outliers, and ~1% within Scandinavia. SNPs showing large divergence (FST>0.15) were picked as candidate diagnostic markers for population assignment. 173 of the most diagnostic SNPs between the two Scandinavian populations were validated by genotyping 47 individuals from each end of the species' Scandinavian distribution range. 69 of these SNPs were significantly (p<0.05) differentiated (mean FST_173_loci=0.065, FST_69_loci=0.140). Using these validated SNPs, individuals were assigned with high probability (≥ 94%) to their populations of origin. Conclusions: Goldsinny wrasse displays a highly polymorphic genome, and substantial population genomic structure. Diversifying selection likely affects population structuring globally and within Scandinavia. The diagnostic loci identified now provide a promising and cost-efficient tool to investigate goldsinny wrasse populations further.

Patterns of genetic divergence and demographic history shed light on island-mainland population dynamics and melanic plumage evolution in the white-winged fairywren

The existence of distinct traits in island versus mainland populations offers opportunities to gain insights into how eco-evolutionary processes operate under natural conditions. We used two island colonization events in the white-winged fairywren (Malurus leucopterus) to investigate the genomic and demographic origin of melanic plumage. This avian species is distributed across most of Australia, and males of the mainland subspecies (M. l. leuconotus) exhibit a blue nuptial plumage in contrast to males of two island subspecies – M. l. leucopterus on Dirk Hartog Island and M. l. edouardion Barrow Island – that exhibit a black nuptial plumage. We used reduced-representation sequencing to explore differentiation and demographic history in this species and found clear patterns of divergence between mainland and island populations, with additional substructuring on the mainland. Divergence between the mainland and Dirk Hartog was approximately 10 times more recent than the split between the mainland and Barrow Island, supporting two independent colonizations. In both cases, estimated gene flow between the mainland and the islands was low, contributing to signals of divergence among subspecies. Our results present demographic reconstructions of mainland-island dynamics and associated plumage variation in white-winged fairywrens, with broader implications regarding our understanding of convergent evolution in insular populations.

opencc-zeroFeb 2021View details →

Standing genetic variation in laboratory populations of insecticide-susceptible Phlebotomus papatasi and Lutzomyia longipalpis (Diptera: Psychodidae: Phlebotominae) for the evolution of resistance

Insecticides can exert strong selection on insect pest species, including those that vector diseases, and have led to rapid evolution of resistance. Despite such rapid evolution, relatively little is known about standing genetic variation for resistance in insecticide-susceptible populations of many species. To help fill this knowledge gap, we generated genotyping-by-sequencing data from insecticide-susceptible Phlebotomus papatasi and Lutzomyia longipalpis sand flies that survived or died from a sub-diagnostic exposure to either permethrin or malathion using a modified version of the Centers for Disease Control and Prevention bottle bioassay. Multi-locus genome-wide association mapping methods were used to quantify standing genetic variation for insecticide resistance in these populations and to identify specific alleles associated with insecticide survival. For each insecticide treatment, we estimated the proportion of the variation in survival explained by the genetic data (i.e. 'chip' heritability) and the number and contribution of individual loci with measurable effects. For all treatments, survival to an insecticide exposure was heritable with a polygenic architecture. Both P. papatasi and L. longipalpis had alleles for survival that resided within many genes throughout their genomes. The implications for resistance conferred by many alleles, as well as inferences made about the utility of laboratory insecticide resistance association studies compared to field observations, are discussed in the manuscript that accompanies this data.

opencc-zeroDec 2013View details →

Data from: Dispersal capacity predicts both population genetic structure and species richness in reef fishes

Dispersal is a fundamental species characteristic that should directly affect both rates of gene flow among spatially distributed populations and opportunities for speciation. Yet no single trait associated with dispersal has been demonstrated to affect both micro- and macroevolutionary patterns of diversity across a diverse biological assemblage. Here, we examine patterns of genetic differentiation and species richness in reef fishes, an assemblage of over 7,000 species comprising approximately one-third of the extant bony fishes and over one-tenth of living vertebrates. In reef fishes, dispersal occurs primarily during a planktonic larval stage. There are two major reproductive and parental investment syndromes among reef fishes, and the differences between them have implications for dispersal: (1) benthic guarding fishes lay negatively buoyant eggs, typically guarded by the male parent, and from these eggs hatch large, strongly swimming larvae; in contrast, (2) pelagic spawning fishes release small floating eggs directly into the water column, which drift unprotected before small weakly swimming larvae hatch. Using phylogenetic comparative methods, we show that benthic guarders have significantly greater population structure than pelagic spawners and additionally that taxonomic families of benthic guarders are more species rich than families of pelagic spawners. Our findings provide a compelling case for the continuity between micro- and macroevolutionary processes of biological diversification and underscore the importance of dispersal-related traits in influencing the mode and tempo of evolution.