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opencc-by-4.0Dec 2019View details →

Supplementary material for the manuscript: Genetic structure of the European hedgehog (Erinaceus europaeus) in Denmark

This database contains supplementary material for our manuscript "Genetic structure of the European hedgehog (Erinaceus europaeus) in Denmark": S1 Fig/Figure 1a. Box plot of the individual heterozygosity (iHO) estimated for the six populations S2 Fig/Figure 1b. Plot of the iHO values ranked from the lowest to the highest values within each population S3 Fig/Figure 2. Likelihood plot of STRUCTURE results S4 Fig/Figure 3. Likelihood plot of STRUCTURE results (for separate populations) S5 Fig/Figure 4. Principal Component Analysis S1 Table/Table 2. Overview of individuals for genetic sampling S2 Table/Table 3. Dataset from GENEPOP S3 Table/ Table 4. Data for fragmentation analyses S4 Table/Table 1. Tukey’s test matrix for testing pairwise significant differences of the mean iHO between the six populations

opennotspecifiedMay 2019View details →

Figure 3 in Preliminary report on the genetic structure of Glyphoglossus molossus (Anura: Microhylidae) from the Khorat Plateauı north-eastern Thailand

Figure 3. Median-joining haplotype network (MJN) illustrating hierarchical relationships among haplotypes represented by sampled populations of Glyphoglossus molossus. Each circle showed a haplotype and the size of each circle is scaled to the number of individuals sharing that haplotype. Branch numbers is proportional to number of mutational steps.

opennotspecifiedMay 2019View details →

Figure 1 in Preliminary report on the genetic structure of Glyphoglossus molossus (Anura: Microhylidae) from the Khorat Plateauı north-eastern Thailand

Figure 1. Map of north-eastern Thailand (a) showing collection localities of Glyphoglossus molossus samples. Names associated with locality numbers are in Table 1. Examples of sampled habitats in this study: secondary forest, Maha Sarakham Province (b); rice field, Sakon Nakhon Province (c); agricultural pond, Nong Khai Province (d). A sample of Glyphoglossus molossus was caught by excavation (e).

opencc-by-4.0Dec 2019View details →

Datasets of "Whole genome sequencing of European autochthonous and commercial pig breeds provides selection signatures of adaptation of genetic resources to different breeding and production systems"

Results of the FST and HP analyses.

opennotspecifiedNov 2018View details →

FIGURE 2 in Genetic variability among Paralaudakia microlepis (Blanford, 1874) (Sauria: Agamidae) populations in the Iranian Plateau

FIGURE 2. Phylogenetic relationships (BI) among Paralaudakia microlepis populations based on the 707 bp ND4 gene fragment. The numbers next to the nodes refer to the bootstrap support and posterior probability (ML/PP).

opennotspecifiedMar 2020View details →

FIGURE 3. Dentitheca dendritica A in Genetic and morphologic identities of hydrozoans (Cnidaria, Hydrozoa) from reef patches of Santa Marta, Colombian Caribbean

FIGURE 3. Dentitheca dendritica A. Basal part of polysiphonic hydrocaulus. Arrow indicates one of the channels. B. Apical part of the hydrocaulus. Oblique node that divides the hydrocaulus in sections. C. Lateral apophyses that support the hydrocladium. D. Hydrothecae in a hydrocladium with mobile lateral nematotheca. E. Mid-lower nematotheca. F. Cone- shaped nematotheca from the apophyses. G. Male gonotheca with gonophore.

opennotspecifiedOct 2019View details →

Subspecies and Distribution. R.f. frantisi Soisook et al, 2015 - known only from a few localities in N, SW & S Borneo. R.f. thailandicus Soisook & Bates, 2015 — known only from type locality in SW Thailand. Genetic data suggest that the species may also occur in Vietnam, but this requires more research. in Rhinolophidae

Subspecies and Distribution. R.f. frantisi Soisook et al, 2015 - known only from a few localities in N, SW & S Borneo. R.f. thailandicus Soisook & Bates, 2015 — known only from type locality in SW Thailand. Genetic data suggest that the species may also occur in Vietnam, but this requires more research.

opencc-by-4.0Apr 2020View details →

In the intimacy of the darkness: genetic polyandry in deep-sea luminescent lanternsharks Etmopterus spinax and Etmopterus molleri (Squaliformes, Etmopteridae)

Multiple paternity seems common within elasmobranchs. Focusing on two deep-sea shark species: the velvet belly lanternshark, Etmopterus spinax, and the slendertail lanternshark, Etmopterus molleri, we inferred the paternity in 31 E. spinax litters from Norway (3-18 embryos per litter) and 6 E. molleri litters from Japan (3-6 embryos), using 21 and 10 specific microsatellites, respectively. At least two E. spinax litters were sired from multiple fathers each, with highly variable paternal skew (1:1 to 9:1). Conversely, no clear signal of genetic polyandry was found in E. molleri. This dataset contains the microsatellite genotypes analysed (281 E. spinax × 29 loci; 42 E. molleri × 19 loci).

opennotspecifiedDec 2019View details →

Figure 3 in DNA Barcodes Reveal High Genetic Diversity in Philippine Fruit Bats

Figure 3. COI ML tree for Pteropodidae dataset using GTR+G+I model of substitution. Bootstrap supports 50% or greater are shown in the nodes. Clades with more than one sequence have been compressed. Labels indicate scientific name and number of sequences for that taxon in the clade. Scientific names in bold text indicate known Philippine endemic species. Colored shapes indicate the geographic origin of the sequences from Genbank and BOLD: purple – Southeast Asia, red – East Asia, blue – South Asia, white – Middle East, yellow – Africa, and black – Oceania. Red lines indicate sequences generated by this study. Scale indicates five nucleotide substitutions per 100 nucleotides.

opennotspecifiedDec 2019View details →

Figure 2 in DNA Barcodes Reveal High Genetic Diversity in Philippine Fruit Bats

Figure 2. COI NJ tree for Pteropodidae dataset using K2P model of substitution. Bootstrap supports 50% or greater are shown in the nodes. Clades with more than one sequence have been compressed. Labels indicate scientific name and number of sequences for that taxon in the clade. Red lines indicate Philippine pteropodid sequences generated in this study. Scientific names in bold text indicate known Philippine endemic species. Colored shapes indicate the geographic origin of the sequences from Genbank and BOLD: purple – Southeast Asia, red – East Asia, blue – South Asia, white – Middle East, yellow – Africa, and black – Oceania. Scale indicates two nucleotide substitutions per 100 nucleotides.

opencc-zeroApr 2020View details →

Supplementary material 3 from: Patterson BD, Webala PW, Lavery TH, Agwanda BR, Goodman SM, Kerbis Peterhans JC, Demos TC (2020) Evolutionary relationships and population genetics of the Afrotropical leaf-nosed bats (Chiroptera, Hipposideridae). ZooKeys 929: 117-161. https://doi.org/10.3897/zookeys.929.50240

Figure S3. Phylogeny of Hipposideridae based on Bayesian inference analysis of cyt-b based on 452 individuals

opencc-zeroApr 2020View details →

Supplementary material 2 from: Patterson BD, Webala PW, Lavery TH, Agwanda BR, Goodman SM, Kerbis Peterhans JC, Demos TC (2020) Evolutionary relationships and population genetics of the Afrotropical leaf-nosed bats (Chiroptera, Hipposideridae). ZooKeys 929: 117-161. https://doi.org/10.3897/zookeys.929.50240

Figure S2. Phylogeny of Hipposideridae based on maximum likelihood analysis of cyt-b based on 452 individuals

opencc-zeroApr 2021View details →

Historical translocations and stocking alter the genetic structure of a Mediterranean lobster fishery

Stocking is often used to supplement wild populations that are overexploited or have collapsed, yet it is unclear how this affects the genetic diversity of marine invertebrate populations. During the 1970s, a lobster stock enhancement programme was carried out around the island of Corsica in the Mediterranean using individuals translocated from the Atlantic coast of France. This included the release of thousands of hatchery-reared post-larval lobsters and several adult individuals, but no monitoring plan was established to assess whether these animals survived and recruited to the population. In this study, we sampled European lobster (Homarus gammarus) individuals caught around Corsica and tested whether they showed Atlantic ancestry. Due to a natural marked phylogeographic break between Atlantic and Mediterranean lobsters, we hypothesised that lobsters with dominant (>0.50) Atlantic ancestry were descended from historical stocking releases. Twenty Corsican lobsters were genotyped at 79 single nucleotide polymorphisms and assignment analysis showed that the majority (13) had dominant Atlantic ancestry. This suggests that the hatchery stocking programme carried out in Corsica during the 1970s, using individuals translocated from the Atlantic coast of France, has likely augmented local recruitment but at a cost of altering the genetic structure of the Corsican lobster population.

opencc-zeroMay 2020View details →

Data from: Disease swamps molecular signatures of genetic-environmental associations to abiotic factors in Tasmanian devil (Sarcophilus harrisii) populations

Landscape genomics studies focus on identifying candidate genes under selection via spatial variation in abiotic environmental variables, but rarely by biotic factors such as disease. The Tasmanian devil (Sarcophilus harrisii) is found only on the environmentally heterogeneous island of Tasmania and is threatened with extinction by a nearly 100% fatal, transmissible cancer, devil facial tumor disease (DFTD). Devils persist in regions of long-term infection despite epidemiological model predictions of species' extinction, suggesting possible adaptation to DFTD. Here, we test the extent to which spatial variation and genetic diversity are associated with the abiotic environment and/or DFTD. We employ genetic-environment association analyses using a RAD-capture panel including 6,886 SNPs from 3,286 individuals sampled pre- and post-disease arrival. Pre-disease, we find significant correlations of allele frequencies with environmental variables, including 365 unique loci linked to 71 genes, suggesting local adaptation to abiotic environment. The majority of candidate loci detected pre-DFTD were not detected post disease arrival. Several post-DFTD candidate loci were associated with disease prevalence and were in linkage disequilibrium with genes involved in tumor suppression and immune response. Loss of apparent signal of abiotic local adaptation post-disease suggests swamping by the strong selection resulting from the rapid onset of DFTD.

Data from: Examination of the efficacy of small genetic panels in genomic conservation of companion animal populations

In many ways dogs are an ideal model for the study of genetic erosion and population recovery, problems of major concern in the field of conservation genetics. Genetic diversity in many dog breeds has been declining systematically since the beginning of the 1800's, when modern breeding practices came into fashion. As such, inbreeding in domestic dog breeds is substantial and widespread and has led to an increase in recessive deleterious mutations of high effect as well as general inbreeding depression. Pedigrees can in theory be used to guide breeding decisions, though are often incomplete and do not reflect the full history of inbreeding. Small microsatellite panels are also used in some cases to choose mating pairs to produce litters with low levels of inbreeding. However, the long-term impact of such practices have not been thoroughly evaluated. Here, we use forward simulation on a model of the dog genome to examine the impact of using limited markers panels to guide pairwise mating decisions on genome-wide population level genetic diversity. Our results suggest that in unmanaged populations, where breeding decisions are made at the pairwise- rather than population-level, such panels can lead to accelerated loss of genetic diversity at genome regions unlinked to panel markers, compared to random mating. These results demonstrate the importance of genome-wide genetic panels for managing and conserving genetic diversity in dogs and other companion animals.

Data from: Different genetic basis for ADH activity and plasticity in a novel alcohol environment for Drosophila melanogaster

Phenotypic plasticity is known to enhance population persistence (Wang and Althoff, 2019), facilitate adaptive evolution (Levis et al., 2018), and initiate novel phenotypes in novel environments (Levis and Pfennig, 2016). How plasticity can contribute or hinder adaptation to different environments hinges on its genetic architecture. Even though plasticity in many traits is genetically controlled, whether and how plasticity's genetic architecture might change in novel environments is still unclear. Because much of gene expression can be environmentally influenced, each environment may trigger different sets of genes that influence a trait. Using a quantitative trait loci (QTL) approach, we investigated the genetic basis of plasticity in a classic functional trait, alcohol dehydrogenase (ADH) activity in D. melanogaster, across both historical and novel alcohol environments. Previous research in D. melanogaster has also demonstrated that ADH activity is plastic in response to alcohol concentration in substrates used by both adult flies and larvae. We found that across all environments tested, ADH activity was largely influenced by a single QTL encompassing the Adh coding gene and its known regulatory locus, delta-1. After controlling for the allelic variation of the Adh and delta-1 loci, we found additional but different minor QTLs in the 0% and 14% alcohol environments. In contrast, we discovered no major QTL for plasticity itself, including the Adh locus, regardless of the environmental gradients. This suggests that plasticity in ADH activity is likely influenced by many loci with small effects and that the Adh locus is not environmentally sensitive to dietary alcohol.

Population genetic structure and demographic history of the lone star tick, Amblyomma americanum (Ixodida: Ixodidae): new evidence supporting old records

Range expansions are a potential outcome of climate change. Population genetic structure and demography can be used as tools to evaluate hypotheses on changes in geographic distribution. In this study we explored the genetic variability, population genetic structure, demographic history, and habitat suitability of Amblyomma americanum, a North American tick species that is a known vector of several pathogenic microorganisms. We used a novel double digestion restriction site-associated DNA sequencing (dd-RAD seq), and we discovered 8181 independent single nucleotide polymorphisms (SNPs) from 189 ticks from across the geographic range of the species. Overall, genetic diversity was lower than expected. Further, the edge populations did not have a statistically significant lower diversity than core populations, and hypotheses of range expansion are not supported by a test based on genetic data. Nonetheless, moderate levels of population structure were detected among geographic regions, with the northeast cluster the least variable. Demographic and species distribution models support a scenario where A. americanum was present in more northern locations in the past, underwent a bottleneck, and is now recovering. These findings highlight the importance of demographic modeling and genomic data in assessing the recent history and genetic structure of pathogen vectors.

Conservation genetics of Armeria belgenciencis

This the data set of the paper "Population genetic structure and management perspectives for Armeria belgenciencis, a narrow endemic plant from Provence (France)" published in Plant Ecology and Evolution: ###############. The genetic structure of Armeria belgenciensis and geographically close populations of Armeria arenaria was analyzed on the basis of 328 AFLP markers using model-based and model-free clustering methods. In addition, flowering phenology was estimated to address the possibility of pre-zygotic isolation between A. belgenciensis and A. arenaria subsp. peirescii. Key results are available in the companion paper.