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Data for: Perishing rich, expanding poor: Demography and population genetic patterns in two congeneric butterflies

In human-altered landscapes, specialist butterflies typically form spatially restricted populations, genetically differentiated due to dispersal restrictions. Generalists, in contrast, display minimum differentiation but high genetic diversity. While local-level actions suffice to conserve specialists and landscape-level actions are necessary for generalists, minimum information exists regarding conservation of species with intermediate features. We targeted two congeneric butterflies, the recently re-expanding Argynnis adippe and the strongly declining A. niobe, co-occurring in the pastoral landscape of the Carpathian Mountains, Czech Republic. We integrated species distribution models, mark-recapture, and microsatellite analysis to compare their habitat requirements, adult demography, dispersal, and genetic patterns, and expanded the genetic analysis across the Carpathian Arc and beyond to delimit spatial conservation units. In two mountain valleys, both species formed interconnected populations numbering thousands of individuals. Mobility patterns suggested the populations' interconnection across the Czech Carpathians. Genetic diversity was extremely poor in the non-threatened A. adippe and moderate in the declining A. niobe. No population differentiation was detected within the Czech Carpathians (ca 1500 km2). Low genetic diversity and no differentiation was preserved in A. adippe across East Central Europe, whereas in A. niobe, populations from Serbia were differentiated from the Carpathian Arc + Alps. The high adult mobility linked to low differentiation probably reflect the distribution of larval resources, historically widespread but sparse and currently declining for A. niobe (grazing-disturbed grounds), while currently increasing for A. adippe (abandonment scrub, disturbed woodlands). Units as large as entire mountain systems define population boundaries, and hence conservation management units, for both species.

opencc-by-4.0Feb 2023View details →

Data for "Brain cell-type shifts in Alzheimer's disease, autism and schizophrenia interrogated using methylomics and genetics"

Data for "Genetic and methylomic interrogation of brain cell-type shifts in autism, schizophrenia, and Alzheimer’s disease" (Yap et al. 2023). Source data from ROSMAP, LIBD and UCLA_ASD post-mortem brain datasets. This data repository contains 3 files: 220819_Supplementary_Tables.xlsx Supplementary Tables for the manuscript: <ol> <li>Supplementary Table 1: Comparison of CTP deconvolution methods in the ROSMAP dataset. mcc* denotes methylCC deconvolution; sSV* denotes smartSVA; h* indicates Houseman using array reference data; hseq* indicates Houseman with sequencing reference data; celfie* indicates CelFIE (and includes an output titled "unknown1"); VAEe* indicates variational autoencoder embeddings.</li> <li>Supplementary Table 2: Comparison of CTP deconvolution methods in the LIBD dataset. mcc* denotes methylCC deconvolution; sSV* denotes smartSVA; h* indicates Houseman using array reference data; hseq* indicates Houseman with sequencing reference data; celfie* indicates CelFIE (and includes an output titled "unknown1"); VAEe* indicates variational autoencoder embeddings.</li> <li>Supplementary Table 3: Comparison of CTP deconvolution methods in the UCLA_ASD dataset. mcc* denotes methylCC deconvolution; sSV* denotes smartSVA; h* indicates Houseman using array reference data; hseq* indicates Houseman with sequencing reference data; celfie* indicates CelFIE (and includes an output titled "unknown1"); VAEe* indicates variational autoencoder embeddings.</li> <li>Supplementary Table 4: Deconvolved brain CTPs (raw), with covariates.</li> <li>Supplementary Table 5: Deconvolved brain CTPs (clr-transform, offset 1e-3), with covariates and raw PGS for all ancestries. Comp* indicates compositionally-aware principal components of the CTP data; *pgs_raw indicates PGS calculated for using genotyping across all ancestries. This table has a total of n=1,098 across all ancestries, including n=885 EUR. After applying a rel<0.05 threshold on the n=885 EUR, there were n=878 EUR which were used in the PGS analysis so that population stratification PCs did not simply capture family structure.</li> <li>Supplementary Table 6: Deconvolved brain CTPs (clr-transform, offset 1e-3), with covariates and standardised PGS for n=878 Europeans. *pgs_raw indicates unstandardised PGS, PC* indicates genotyping PCs within the European dataset, *_PGS indicates standardised PGS within the European subset.</li> <li>Supplementary Table 7: Deconvolved brain CTPs (clr-transform, offset 1e-3), adjusted for oligodendrocyte proportions, with covariates.</li> <li>Supplementary Table 8: Deconvolved brain CTPs (raw), adjusted for oligodendrocyte proportions, with covariates.</li> </ol> 20220108_maf05_gwas_ctp.tar.gz GWAS summary statistics for the 7 brainCTPs (clr-transformed): Exc, Inh, Astro, Endo, Micro, Oligo, OPC METAL output format: MarkerName: SNP Allele1 Allele2 Freq1: Allele1 frequency FreqSE: frequency standard error MinFreq: minimum Allele1 frequency in meta-analysis MaxFreq: maximum Allele1 frequency in meta-analysis Effect: effect size StdErr: standard error of effect size P-value: calculated in inverse variance weighted meta-analysis Direction: directions of effects across the 3 datasets HetISq: heterozygosity I-squared HetChiSq: heterozygosity chi-squared HetDf: heterozygosity degress of freedom HetPVal: heterozygosity test p-value 20220108_maf05_gwas_ctp_pc.tar.gz GWAS summary statistics for the 5 CTP_PCs METAL output format (see above)   Source data: ROSMAP: Raw methylation .idat files were obtained from Synapse accession syn7357283. Whole genome sequencing .vcf files (variants jointly called with MSBB and Mayo studies) were obtained from Synapse accession syn11707420. LIBD: Raw methylation .idat files were obtained from GEO accession GSE74193. SNP genotypes were downloaded from dbGaP accession phs000417.v2.p1. UCLA-ASD: The processed methylation beta matrix was downloaded from Synapse accession syn8263588. SNP genotypes were downloaded from Synapse accession syn10537134. GWAS summary statistics are available at: 10.5281/zenodo.7604231 Code is available on GitHub: gandallab/brain_CTP_deconv

Genomic evidence for contrasting patterns of host‐associated genetic differentiation across shared host‐plant species in leaf‐ and bud‐galling sawflies

Resource specialization and host-associated genetic differentiation (HAD) are frequently invoked as an explanation for the high diversity of plant-feeding insects and other organisms with a parasitic lifestyle. While genetic studies have demonstrated numerous examples of HAD in insect herbivores, the general rarity of comparative studies means that we still lack an understanding of how deterministic HAD is, and whether patterns of host shifts can be predicted over evolutionary time scales. We applied genome-wide SNP data obtained through low-coverage genome resequencing to define species limits and to compare host-plant use in population samples of leaf- and bud-galling sawflies collected from seven shared willow (Salix) host species. To infer the repeatability of long-term cophylogenetic patterns, we also contrasted the phylogenies of the two galler groups with each other as well as with the phylogeny of their Salix hosts estimated based on RADseq data. We found clear evidence for host specialization and HAD in both of the focal galler groups, but also that leaf gallers are more specialized to single host species than are most bud gallers. In contrast to bud gallers, leaf gallers also exhibit statistically significant cophylogenetic signal with their Salix hosts. The observed discordant patterns of resource specialization and long-term host use in two related galler groups that have radiated in parallel across a shared resource base indicate a general lack of evolutionary repeatability and suggest that short- and long-term host use and ecological diversification in plant-feeding insects are dominated by stochasticity and/or lineage-specific effects.

Data from: Multiple introductions, polyploidy and mixed reproductive strategies are linked to genetic diversity and structure in the most widespread invasive plant across Southern Ocean archipelagos

Biological invasions in remote areas that experience low human activity provide unique opportunities to elucidate processes responsible for invasion success. Here we study the most widespread invasive plant species across the isolated islands of the Southern Ocean, the annual bluegrass, Poa annua. To analyze geographic variation in genome size, genetic diversity, and reproductive strategies, we sampled all major sub-Antarctic archipelagos in this region and generated microsatellite data for 470 individual plants representing 31 populations. We also estimated genome sizes for a subset of individuals using flow cytometry. Occasional events of island colonization are expected to result in high genetic structure among islands, overall low genetic diversity, and increased self-fertilization, but we show that this is not the case for Poa annua. Microsatellite data indicated low population genetic structure and lack of isolation-by-distance among the sub-Antarctic archipelagos we sampled, but high population structure within each archipelago. We identified high levels of genetic diversity, low clonality, and low selfing rates in sub-Antarctic P. annua populations (contrary to rates typical of continental populations). In turn, estimates of autogamy declined in populations as genetic diversity increased. Additionally, we found that most P. annua individuals are likely tetraploid and that only slight variation exists in genome size across the Southern Ocean. Our findings suggest multiple independent introductions of P. annua into the sub-Antarctic, which promoted the establishment of genetically diverse populations. Despite multiple introductions, the adoption of convergent reproductive strategies (outcrossing) happened independently in each major archipelago. The combination of polyploidy and a mixed reproductive strategy likely benefited P. annua in the Southern Ocean by increasing genetic diversity and its ability to cope with the novel environmental conditions.

Code for the population genetic models of the evolution of preference strength

Sexual selection has a rich history of mathematical models that consider why preferences favor one trait phenotype over another (for population genetic models) or what specific trait value is preferred (for quantitative genetic models). Less common is exploration of the evolution of choosiness or preference strength: that is, by how much a trait is preferred. We examine both population and quantitative genetic models of the evolution of preferences, specifically developing "baseline models" of the evolution of preference strength during the Fisher process. Using a population genetic approach based on the classic model of Kirkpatrick (1982), we find selection for stronger and stronger preferences when trait variation is maintained by mutation. However, this force is quite weak and likely to be swamped by drift in moderately-sized populations. In a quantitative genetic model based on Lande (1981), unimodal preferences will generally not evolve to be increasingly strong without bounds when male traits are under stabilizing viability selection, but evolve to extreme values when viability selection is directional. Our results highlight that different shapes of fitness and preference functions lead to qualitatively different trajectories for preference strength evolution ranging from no evolution to extreme evolution of preference strength.

Data from: Effective population size in a partially clonal plant is not predicted by the number of genetic individuals

Estimating effective population size (Ne) is important for theoretical and practical applications in evolutionary biology and conservation. Nevertheless, estimates of Ne in organisms with complex life-history traits remain scarce because of the challenges associated with estimation methods. Partially clonal plants capable of both vegetative (clonal) growth and sexual reproduction are a common group of organisms for which the discrepancy between the apparent number of individuals (ramets) and the number of genetic individuals (genets) can be striking, and it is unclear how this discrepancy relates to Ne. In this study, we analysed two populations of the orchid Cypripedium calceolus to understand how the rate of clonal vs. sexual reproduction affected Ne. We genotyped >1,000 ramets at microsatellite and SNP loci, and estimated contemporary Ne with the linkage disequilibrium method, starting from the theoretical expectation that variance in reproductive success among individuals caused by clonal reproduction and by constraints on sexual reproduction would lower Ne. We considered factors potentially affecting our estimates, including different marker types and sampling strategies, and the influence of pseudoreplication in genomic datasets on Ne confidence intervals. The magnitude of Ne/Nramets and Ne/Ngenets ratios we provide may be used as reference points for other species with similar life-history traits. Our findings demonstrate that Ne in partially clonal plants cannot be predicted based on the number of genets generated by sexual reproduction, because demographic changes over time can strongly influence Ne. This is especially relevant in species of conservation concern, in which population declines may not be detected by only ascertaining the number of genets.

opencc-by-4.0Dec 2022View details →

Long-distance dispersal drives the genetic variation and historical demography of Quercus magnoliifolia and Quercus resinosa (Fagaceae) in the Mexican highlands

Genotypes of chloroplast microsatellites used in Albarrán-Lara et al. Data comprises six loci from 61 localities sampling in Mexico

opencc-by-4.0Feb 2023View details →

Supplementary data for "Testing the efficacy of different molecular tools for parasite conservation genetics: a case study using horsehair worms (Phylum Nematomorpha)"

Supplementary data for "Testing the efficacy of different molecular tools for parasite conservation genetics: a case study using horsehair worms (Phylum Nematomorpha)" alignments: alignments used for BEAST ("bayes") and PopArt ("popart"). The "popart" folder also has a traits file per each species. bayesian_plots: TSVs ("tsv") and PDF files ("ogs") generated by BEAST. The "tsv" folder also has the scripts for plotting the results in R. easysfs: scripts, population file and results from the VCF to SFS conversione done by easySFS. fineRADstructure: fineRADstructure input files and output PDF plots ("plots") for C. formosanus ipyrad and Stacks ("stacks") data.  logs: logs for ipyrad, ModelTest, PGDspider, PopArt ("popart") and Stacks ("stacks"). The "popart" folder also have the generated networks in a TXT file. The "stacks" folder also has ODS files for calculating the amount of loci per each M/n fixed value. snapclust: STR files used with R for snapclust. Scripts included. stairway_plot: input (blueprint files) and outputs for Stairway Plot 2 analyses. The C. formosanus folder ("chordodes") also has scripts for R plotting. vcfs: VCF and HDF5 files used in this study. Also scripts for filtering/converting data and plotting the PCA with ipyrad (activate python first!) for C. formosanus. "acutogordius" = A. taiwanensis "chordodes" = C. formosanus "gordius" = G. chiashanus

Phylogeography and genetic variation in Western Jacob's ladder (Polemonium occidentale) provide insights into the origin and conservation of rare species in the Great Lakes region

The perennial herb Western Jacob's Ladder (Polemonium occidentale, Polemoniaceae) is widespread in the mountains of western North America but reappears as a disjunct in the Great Lakes Region in Minnesota and Wisconsin, USA as the narrow endemic P. occidentale subsp. lacustre. This distribution is shown by a diverse assemblage of angiosperms. It has been hypothesized that these species became isolated just after the Last Glacial Maximum, but this has not been tested. Additionally, the genetic diversity and population connectivity of the endemic Great Lakes flora has been understudied, with important conservation implications. Using Genotyping-by-sequencing, we examined the relationship of P. occidentale subsp. lacustre to its closest relatives, relationships among all known populations, and genetic diversity within these populations. Polemonium occidentale subsp. lacustre represents an isolated, unique lineage that diverged from its closest relatives 1.3 ma and arrived in the Great Lakes Region by at least 38 ka. Nearly all extant populations diverged prior to the Last Glacial Maximum, are largely genetically distinct, and show relatively little within-population genetic diversity. Clonality may mitigate reduction in diversity due to drift. Mixed population signal between Wisconsin and some Minnesota populations may be due to gene flow during the Late Pleistocene. While populations of Polemonium occidentale subsp. lacustre may be relictual from a now-extinct western relative, it is best treated as a distinct species. Conservation efforts should focus more on ensuring that current populations remain rather than maintaining large population sizes across a few populations. However, encouraging habitat heterogeneity may accomplish both simultaneously.

Using inbreeding to test the contribution of non-additive genetic effects to additive genetic variance: A case study in Drosophila serrata

Additive genetic variance, VA, is the key parameter for predicting adaptive and neutral phenotypic evolution. Changes in demography (e.g., increased close-relative inbreeding) can alter VA, but how depends on the, typically unknown, gene action and allele frequencies across many loci. For example, VA increases proportionally with the inbreeding coefficient when allelic effects are additive, but larger (or smaller) increases can occur when allele frequencies are unequal at causal loci with dominance effects. Here, we describe an experimental approach to assess the potential for rare, recessive alleles to inflate VA under inbreeding. Applying a powerful paired pedigree design in Drosophila serrata, we measured 11 wing traits on half-sibling families bred via either random or sibling mating, differing only in homozygosity (not allele frequency). Despite close inbreeding and substantial power to detect small VA, we detected no deviation from the expected additive effect of inbreeding on genetic (co)variances. Our results suggest the average dominance coefficient is very small relative to the additive effect, or that allele frequencies are relatively equal at loci affecting wing traits. We outline the further opportunities for this paired pedigree approach to reveal the characteristics of VA, providing insight into historical selection and future evolutionary potential.

Literature compilation for: The rise of animal biotelemetry and genetics research data integration

The advancement and availability of innovative animal biotelemetry and genomic technologies are improving our understanding of how the movements of individuals influence gene flow within and between populations and ultimately drive evolutionary and ecological processes. There is a growing body of work that is integrating what were once disparate fields of biology, and here we reviewed the published literature up until January 2023 (139 papers) to better understand the drivers of this research and how it is improving our knowledge of animal biology. The review showed that the predominant drivers for this research were: i) understanding how individual-based movements affect animal populations, ii) analyzing the relationship between genetic relatedness and social structuring, and iii) studying how the landscape affects the flow of genes, and how this is impacted by environmental change. However, there was a divergence between taxa as to the most prevalent research aim, and the methodologies applied. We also found that after 2010 there was an increase in studies that integrated the two data types using innovative statistical techniques instead of analyzing the data independently using traditional statistics from the respective fields. This new approach greatly improved our understanding of the link between the individual, the population, and the environment and is being used to better conserve and manage species. We discuss the challenges and limitations, as well as the potential for growth and diversification of this research approach. The paper provides a guide for researchers who wish to consider applying these disparate disciplines and advancing the field.

opencc-by-4.0Apr 2013View details →

Fig. 9 in A new polymorphic species of Leptochelia (Crustacea: Tanaidacea) from Guinea Bissau, West Africa, with comments on genetic variation within Leptochelia

Fig. 9. Population structure.

A sexually-selected male weapon characterised by strong additive genetic variance and no evidence for sexually antagonistic polyphenic maintenance

Sexual selection and sexual antagonism are important drivers of eco-evolutionary processes. The evolution of traits shaped by these processes depends on their genetic architecture, which remains poorly studied. Here, implementing a quantitative genetics approach using diallel crosses of the bulb mite, Rhizoglyphus robini, we investigated the genetic variance that underlies a sexually-selected weapon that is dimorphic among males and female fecundity. Previous studies indicated that a negative genetic correlation between these two traits likely exists. We found male morph showed considerable additive genetic variance, which is unlikely to be explained solely by mutation-selection balance, indicating the likely presence of large-effect loci. However, a significant magnitude of inbreeding depression also indicates that morph expression is likely to be condition-dependent to some degree and that deleterious recessives can simultaneously contribute to morph expression. Female fecundity also showed a high degree of inbreeding depression, but variance in female fecundity was mostly explained by epistatic effects, with very little contribution from additive effects. We found no significant genetic correlation, nor any evidence for dominance reversal, between male morph and female fecundity. The complex genetic architecture underlying male morph and female fecundity in this system has important implications for our understanding of the evolutionary interplay between purifying selection and sexually antagonistic selection.

Origins of green turtle fishery bycatch in the Central Pacific revealed by mixed genetic markers

Longline fishing vessels, such as those that target tuna or billfish, also unintentionally catch endangered marine turtle species on the high seas. The stock composition of this bycatch is often unknown but potentially complex, with individuals coming from many possible origins on an ocean-basin scale. To better understand the stock composition of green turtle (Chelonia mydas) bycatch, we obtained 46 turtles, 27–78 cm in curved carapace length, caught by Hawaii- and American Samoa-based pelagic longline fishing vessels across large areas of the North- and South-central Pacific. We genotyped these at nine microsatellite loci and one mitochondrial DNA marker and used a baseline of 1,043 nesting female green turtles from beaches across the Pacific for population assignment and mixed-stock analysis. By analyzing both marker types jointly we were able to increase power and genetically resolve ten baseline stocks of nesting females with mean self-assignment and simulated accuracies of 75–97%. Above the Equator, green turtle bycatch was composed mostly of individuals from Hawaiian and Eastern Pacific stocks, with a small number from the Western Pacific. Below the Equator, the most common stocks in the bycatch were from Australia and the Coral Sea, American Samoa and French Polynesia, and the Galápagos Islands. Overall, turtles originating from East, West, and Central Pacific breeding populations were major components of the bycatch, suggesting that the geographic ranges of these populations overlap across large tracts of ocean during the pelagic life history stages.

Data from: Aging and memory are altered by genetically manipulating lactate dehydrogenase in the neurons or glia of flies

The astrocyte-neuron lactate shuttle hypothesis posits that glial-generated lactate is transported to neurons to fuel metabolic processes required for long-term memory. Although studies in vertebrates have revealed that lactate shuttling is important for cognitive function, it is uncertain if this form of metabolic coupling is conserved in invertebrates or is influenced by age. Lactate dehydrogenase (Ldh) is a rate-limiting enzyme that interconverts lactate and pyruvate. Here we genetically manipulated expression of Drosophila melanogaster lactate dehydrogenase (dLdh) in neurons or glia to assess the impact of altered lactate metabolism on invertebrate aging and long-term courtship memory at different ages. We also assessed survival, negative geotaxis, brain-neutral lipids (the core component of lipid droplets), and whole head metabolites. Both upregulation and downregulation of dLdh in neurons resulted in decreased survival and memory impairment with age. Glial downregulation of dLdh expression caused age-related memory impairment without altering survival, while upregulated glial dLdh expression lowered survival without disrupting memory. Both neuronal and glial dLdh upregulation increased neutral lipid accumulation. We provide evidence that altered lactate metabolism with age affects the tricarboxylic acid (TCA) cycle, 2-hydroxyglutarate (2HG), and neutral lipid accumulation. Collectively, our findings indicate that the direct alteration of lactate metabolism in either glia or neurons affects memory and survival but only in an age-dependent manner.

Genetic diversity and population structure from a Peruvian nucleus cattle herd using SNP data

New-generation sequencing technologies, among them SNP chips for massive genotyping, have proven to be useful for the effective management of genetic resources. Also, developing nucleus herds is an effective method for genetic improvement work. To date, molecular studies in Peruvian cattle are still in their infancy. To close this gap, we here employed two SNP panels (BovineHD and Bovine100K) to determine for the first time the Peruvian nucleus herd's genetic diversity and population structure that belong to INIA. This nucleus comprises Brahman (N=16), Braunvieh (N=14), Gyr (N=11), and Fleckvieh (N=22) breeds. Additionally, samples from a locally adapted creole cattle, the Arequipa Fighting Bull (AFB, N=12), were incorporated into the study. The genetic diversity indices in all breeds showed a high proportion of polymorphic SNPs, varying from 69.37% in Gyr to 80.81% in Braunvieh. Also, Braunvieh possessed the highest observed heterozygosity (0.53±0.17), while Brahman possessed the lowest (0.44±0.10), indicating that the former is more diverse compared to the other cattle breed groups. According to the molecular variance analysis, 83.92% of the variance occurs within individuals, whereas 16.0% occurs between populations. The pairwise FST estimates between breeds showed values that ranged from 0.054 (Braunvieh vs AFB) to 0.266 (Brahman vs AFB). Pairwise Reynold's distance showed a pattern similar to the one obtained with the FST statistics, with values ranging from 0.058 to 0.309. A dendrogram was constructed using the Neighbor-Joining clustering algorithm, and similar to the principal coordinate analysis, three groups were identified. Results showed a clear separation between Bos indicus (Brahman and Gyr) and B. taurus breeds (Braunvieh and Fleckvieh). For Fleckvieh and Braunvieh, there were two subgroups each one of them grouping with the AFB group. Similar results were obtained with ADMIXTURE analysis with K= 3 as the most optimal number for the inferred genetic structure of the populations. The results from the current study would contribute to the appropriate management avoiding loss of genetic variability in these breeds and to future improvements for this nucleus. Additional work is needed to speed up the breeding process in the Peruvian cattle system.

Data and R scripts from: Using conservation genetics to prioritise management options for an endangered songbird

Genetic data can be highly informative for answering questions relevant to practical conservation efforts but remain one of the most neglected aspects of species recovery plans. Framing genetic questions with reference to practical and tractable conservation objectives can help bypass this limitation of the application of genetics in conservation. Using a single-nucleotide polymorphism dataset from reduced-representation sequencing (DArTSeq), we conducted a genetic assessment of remnant populations of the endangered forty-spotted pardalote (Pardalotus quadragintus), a songbird endemic to Tasmania, Australia. Our objectives were to inform strategies for conservation of genetic diversity in the species and estimate effective population sizes and patterns of inter-population movement to identify management units relevant to population conservation and habitat restoration. We show population genetic structure and identify two small populations on mainland Tasmania as 'satellites' of larger Bruny Island populations connected by migration. Our data identify management units for conservation objectives relating to genetic diversity and habitat restoration. Although our results do not indicate the immediate need to genetically manage populations, the small effective population sizes we estimated for some populations indicate that they are vulnerable to genetic drift, highlighting the urgent need to implement habitat restoration to increase population size and to conduct genetic monitoring. We discuss how our genetic assessment can be used to inform management interventions for the forty-spotted pardalote, and show that by assessing contemporary genetic aspects, valuable information for conservation planning and decision-making can be produced to guide actions that account for genetic diversity and increase chances of recovery in species of conservation concern.

Historic and contemporary biogeographic perspectives on range-wide spatial genetic structure in a widespread seagrass

This raw data set contains multilocus genotypes for 1,312 individual samples from 44 locations. Aim: Historical and contemporary processes drive spatial patterns of genetic diversity. These include climate-driven range shifts and gene flow mediated by biogeographical influences on dispersal. Assessments that integrate these drivers are uncommon, but critical for testing biogeographic hypotheses. Here, we characterise intraspecific genetic diversity and its spatial structure across the entire distribution of a temperate seagrass to test marine biogeographic concepts for southern Australia. Location: Temperate Australian coastal waters Methods: Predictive modelling was used to contrast the current Posidonia australis distribution to its historical distribution during the Last Glacial Maximum (LGM). Spatial genetic structure was estimated for 44 sampled meadows from across the geographical range of the species using nine microsatellite loci. Results: Historical and contemporary distributions were similar, with the exception of the Bass Strait. Genetic clustering was consistent with the three currently recognised biogeographic provinces and largely consistent with the finer-scale IMCRA bioregions. Discrepancies were found within the Flindersian province and southwest IMCRA bioregion, while two regions of admixture coincided with transitional bioregions. Clonal diversity was highly variable, but positively associated with latitude. Genetic differentiation among meadows was significantly associated with oceanographic distance. Main conclusions: Our approach suggests how shared seascape drivers have influenced the capacity of P. australis to effectively track sea level changes associated with natural climate cycles over millennia, and in particular, the recolonisation of meadows across the Continental Shelf following the LGM. Genetic structure associated with IMCRA bioregions reflects the presence of stable biogeographic barriers, such as oceanic upwellings. This study highlights the importance of biogeography to infer the role of historical drivers in shaping extant diversity and structure.

Sexually antagonistic selection maintains genetic variance when sexual dimorphism evolves

Breeding design data for body size in seed beetles (a sexually antagonistic trait) after 10 generations under different artificial selection conditions to test the effects of selection on the genetic variance of body size. The breeding design and sample size of the study allow us to partition genetic variances into additive autosomal, additive sex-linked, autosomal dominance and X-linked dominance variance. See related dataset for body size data of the ancestral population before selection.