Dataset Ruggeri et al. (archived anchovies DNA)

Dataset in spreadsheet format reporting basic information about (microsatellite) genotypes and collection data from an archived DNA study of European anchovy (Engraulis ancrasicolus) in the Adriatic basin

BOTTLENECK 1.2 results.

<p>IAM = Infinite Allele Model; TPM = Two Phase Mutation Model; SMM = Stepwise Mutation Model. <i>H</i>_def = One-tailed heterozygosity deficiency test; <i>H</i>_exc = One-tailed heterozygosity excess test; <i>H</i>_exc<i>–H</i>_def = Two-tailed heterozygosity deficiency or excess test. Values in bold are significant P-values (<i>P</i> < 0.05).</p

BOTTLESIM simulation.

<p>(<b>a</b>) Trend (solid line) of <i>H</i>_e and (<b>b</b>) <i>N</i>_A simulated values for a population (represented by CH78) experiencing a bottleneck for over 32 generations (years). Red squares represent the observed (<b>a</b>) <i>H</i>_e and (<b>b</b>) <i>N</i>_A values in CH78, CH87, CH94, CH00, and CH10. (<b>c</b>) Trend (solid line) of <i>H</i>_e and (<b>d</b>) <i>N</i>_A simulated values for a population (represented by VI85) that went through a bottleneck for over 25 generations (years). Red squares represent the observed (<b>c</b>) <i>H</i>_e and (<b>d</b>) <i>N</i>_A values in VI85, VI87, VI89, and VI10. Light grey bars are standard errors for simulated values.</p

Pairwise multilocus estimates of θ_ST.

<p>Bold values are significant after a sequential Bonferroni correction [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0151507#pone.0151507.ref042" target="_blank">42</a>] for 36 multiple tests (<i>P</i> < 0.0014).</p

Sampling area.

<p>The solid circle indicates the location of the Chioggia time series between 1978 and 2010. The solid triangle indicates the locations of the Vieste time series between 1985 and 2010.</p

Temporal changes in estimates of expected (<i>H</i>_e) and observed (<i>H</i>_o) heterozygosities, and mean number of alleles (<i>N</i>_A).

<p>Panels (<b>a</b>) (<i>H</i>_e), (<b>b</b>) (<i>H</i>_O) and (<b>c</b>) (<i>N</i>_A) depict temporal trends at Chioggia, and panels (<b>d</b>) (<i>H</i>_e), (<b>e</b>) (<i>H</i>_o) and (<b>f</b>) (<i>N</i>_A) depict temporal trends at Vieste. Standard deviation intervals are provided for each sample, estimated from 1000 resampled samples per year and standardized at 24 individuals. Statistical significances of <i>b</i> (slope) and <i>r</i> (Pearson’s regression coefficient) indicate global trends (into the box to the left of each panel) and trends from consecutive temporal samples (above or below each timeframe considered). Level of significance: * <i>P</i> < 0.05; ** <i>P</i> < 0.01; *** <i>P</i> < 0.001.</p

Temporal TM3 coalescent-based effective population size estimates.

<p><i>N</i>_G = number of generations between a pair of samples. <i>N</i>_e = effective population size estimate. Lower and Upper 95% CI = represents a 95% Confidence Interval (CI) for <i>N</i>_e estimated for a pair of samples. Ne MAX = maximum prior effective population size defined in coalescent-based simulations. Values in bold represent the most likely coalescent estimates based on higher 95% CI limit per simulation.</p