Brown bear genotypes from Slovenia (Northern Dinaric Mountains) - MS Excel

The dataset contains genotypes of 513 brown bears genotyped on 20 microsatellite loci. They were obtained by genotyping tissue samples of legally killed bears between 2003 and 2008. The genotypes are mostly complete, there are missing data on a single locus in two samples (denoted "NA"). | Columns in the table: | sample - laboratory name of the sample | sex - sex of the animal (recorded by the field crew and rechecked by genotyping the SRY marker) | Genotypes: alleles at each locus are recorded in two columns, e.g. Cxx20_1, Cxx20_2. Missing data are recorded as "NA". | Note: this dataset mostly corresponds to the dataset used in the manuscript: Skrbinšek T, Jelenčič M, Waits L, Kos I, Jerina K, Trontelj P (2012). Monitoring the effective population size of a brown bear (Ursus arctos) population using new single-sample approaches. Molecular Ecology 21(4): 862-875. Data: doi:10.5061/dryad.22rm1728. This present dataset doesn't have age data for the animals, but includes genotypes of three additional individuals for which we had no age data available

Population genetics results

Population genetics analysis: number of alleles, observed and expected heterozygosity, tests of Hardy-Weinberg equilibrium for each locus separately and linkage disequilibrium. Included are also results from Structure analysis of the Romanian samples

Morphometric data ecomorphs Asellus aquaticus

Morphometric data: List of 60 traits used in morphometric analysis of surface and subterranean Asellus aquaticus ecomorphs from Slovenia and Romania. Means, standard deviations (SD) and standard errors (SE) of 60 morphometric traits (listed in Table A) in the surface and subterranean ecomorph pairs of Asellus aquaticus from Slovenia (PP/PR*) and Romania (MD/AW*). Asterisk (*) denotes the subterranean ecomorph relative to its ancestral surface form

Genotypes of Asellus aquaticus on 8 microsatellite loci

Dataset contains genotypes of surface and subterranean ecomorph pairs of Asellus aquaticus from Slovenia and Romania. 324 individuals were genotyped on 8 microsatellite loci. Columns in the table: sampling site – site code on Figure 1 in the article; Voucher ID – sample name from the SubBioDatabase; alleles at each locus are recorded in separate columns. Missing data is recorded as "?"

Difference in body size measured in Euclidean distances for pairs of co-occurring <i>Niphargus</i> species and their inferred ancestors.

<p>Species pair: upper, mean, lower—COMPARE provides estimates of ancestral states with standard errors. We calculated three estimates of ancestral states, as mean, lower (reconstructed value—standard error) and upper (mean + standard error) and repeated the analyses for all three values.</p><p>Ecological process: the putative process leading to either significant similarity or significant difference of coexisting species. The p value indicates the probability that species pair is more similar or different than expected when compared to pairs of species randomly drawn from the corresponding regional species pool.</p><p>Difference in body size measured in Euclidean distances for pairs of co-occurring <i>Niphargus</i> species and their inferred ancestors.</p

Geographic position of the studied sulfidic caves (F = Frasassi cave system, M = Movile Cave).

<p>Shaded dots indicate the distributional range of <i>Niphargus</i> in Europe, after [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0123535#pone.0123535.ref061" target="_blank">61</a>].</p

Phylogenetic relationships among 44 species of <i>Niphargus</i> obtained by Bayesian inference.

<p>The two studied species pairs from sulfidic caves are indicated in bold. Numbers on the nodes indicate Bayesian posterior probabilities; only nodes with support > 0.7 are indicated. Distinct yet undescribed species from the ‘longicaudatus’ group are labeled geographically. The tree was rooted using topological information from a genus-wide molecular phylogeny [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0123535#pone.0123535.ref028" target="_blank">28</a>].</p

Difference in ventral channel measured in Euclidean distances for pairs of co-occurring <i>Niphargus</i> species and their inferred ancestors.

<p>Species pair: upper, mean, lower—COMPARE provides estimates of ancestral states with standard errors. We calculated three estimates of ancestral states, as mean, lower (reconstructed value—standard error) and upper (mean + standard error) and repeated the analyses for all three values.</p><p>Ecological process: the putative process leading to either significant similarity or significant difference of coexisting species. The p value indicates the probability that species pair is more similar or different than expected when compared to pairs of species randomly drawn from the corresponding regional species pool.</p><p>Difference in ventral channel measured in Euclidean distances for pairs of co-occurring <i>Niphargus</i> species and their inferred ancestors.</p

Genotypes of bears from Slovenia

The dataset contains genotypes of 510 brown bears genotyped on 22 microsatellite loci. They were obtained by genotyping tissue samples of legally killed bears between 2003 and 2008. Genotype on locus G10H is unrealiable (genotyping problems), and locus Mu26 has null alleles. Both were excluded from analysis, and have some missing data. All genotypes are complete on all other loci. Additional information is the age data (determined by tooth cross-section), sex and the date of mortality. Columns in the table: sample - laboratory name of the sample; sex - sex of the animal (recorded by the field crew and rechecked by genotyping the SRY marker); date_killed - the date on which the animal was killed; born - year of birth, estimated using the age data; age_months - age of the animal in months, calculated from the age determined by tooth cross-section, Feb 1 as the birthday and the recorded date of death. Genotypes: alleles at each locus are recorded in two columns, e.g. Cxx20_1, Cxx20_2. Missing data at loci G10H and Mu26 are recorded as "NA"