Details of sample locations, population code and the number of individuals (N) analysed by the two methods (mtCR, AFLP).

<p>Haplotypes first described in this study are highlighted with bold. S.D.: South Transdanubian Region; (N): number of individuals, P.loci%: percentage of polymorphic loci; UHe: mean unbiased heterozygosity of a certain population; F_is: Inbreeding coefficient of a certain population; F_st: measure of population differentiation; *: mean±SD.</p

Median-Joining network of mtCR sequence data relating <i>Gobio spp.</i> with previously published data.

<p>Circle size is relative to the number of individuals carrying the same haplotype. Line length refers to the genetic distances of haplotypes. Small open circles represent median vectors (missing or theoretical haplotypes). CR01–17: Haplotypes of the 168 specimens analysed in this study. Letter code of haplogroups/“boxes” and numbers (N ) of previously published haplotypes in each box correspond with the numbers and codes displayed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0097278#pone-0097278-t002" target="_blank">Table 2</a>.</p

Location of the Carpathian Basin in Europe (A), location of the sampling sites (1–27) in the Carpathian Basin (B) and PCoA representation of hydrologic distances between the sampling sites (C).

<p>Hungarian country border is marked with the dotted line. Different symbols refer to sites belonging to different catchment areas: ○ - North Danubian; □ - Middle Danubian; ⋄ - South Danubian and ▵ - the Tisza River catchment. For detailed information see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0097278#pone-0097278-t001" target="_blank">Table 1</a>.</p

Recent river network of the Danubian region (Hungary).

<p>The four subcatchment areas are indicated by different colours. Flow direction of Zala River during the Middle and Late Pleistocene is indicated by blackframed green and red arrows respectively. The thick broken line indicates the Pleistocene watershed between the North and Middle Danubian regions. Intra-valley drainage divides (Síkhegyi, 2002) are shown by black bidirectional arrows. Numbered circles: sampling sites displayed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0097278#pone-0097278-t001" target="_blank">Table 1</a>. Dotted arrows: recent flow direction.</p

GenBank haplotypes used for the network computation. Numbers (N) of haplotypes correspond with the numbers displayed in Figure 2.

<p>(#: taxon name described in Mendel <i>et al.,</i> 2008).</p

Estimates of evolutionary divergence over sequence pairs within and between haplogroups (see Fig. 4) based on 652b long mtCR sequence data.

<p>N: the number of haplotypes in each box. Diagonal (bold): within haplogroup percentage genetic differences (mean±SD); above: Φpt values of pairwise AMOVA (* and ** indicate p<0.05 and p<0.01, respectively); below: between haplogroups percentage differences (mean±SD); (#: taxon name described in Mendel <i>et al.,</i> 2008).</p

Population level differences of the studied <i>Gobio</i> populations based on the AFLP. Data are only displayed for those 21 populations where N≥8.

<p>Diagonal: within population genetic distances (GD); above: pairwise Φpt calculated by AMOVA (* and ** indicate p<0.05 and p<0.01 respectively); below: pairwise Unbiased Nei Genetic Distances.</p

Determination of the number of clusters best fitting the AFLP data: STRUCTURE-based mean±SD likelihood values of ten runs for each K from K = 1 to 10 (A), similarity coefficient (min., mean and max values) of ten runs for each K from K = 1 to 10 (mean±SD) (B), Delta K statistic (C), and Triangle plot with allocation of individuals to clusters mapped according to K = 3 (D).

<p>Where ○: specimens from the North Danubian region (the two emphasized individuals are identified as <i>Gobio gobio</i> in the CR analysis), □: Middle Danubian sites, ⋄: South Danubian sites, ▵: specimens from the Tisza region (the two emphasized individuals are identified as <i>Gobio carpathicus</i> in the CR analysis).</p

Bayesian consensus tree derived from the analysis of the mtCR sequence data.

<p>Haplotypes revealed in this study are marked with their CR codes (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0097278#pone-0097278-t003" target="_blank">Table 3</a>). Bayesian posterior probabilities are assigned on nodes. For GenBank accession numbers see the text and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0097278#pone-0097278-t002" target="_blank">Table 2</a>. #: taxon name described in Mendel et al. (2008).</p

Plots of cross-validation tables for AFLP data based on DAPC.

<p>Correctly classified individuals are placed on the diagonal. The square size equals the number of individuals of posterior group assignment based on posterior probabilities. Rows correspond to actual sites (a priori), while columns correspond to inferred sites (posteriori). Squares with broken lines show regional detachments of populations.</p