DOI: 10.5061/dryad.nd1hg
title: Data from: Genetic diversity and distribution patterns of diploid and polyploid hybrid water frog populations (Pelophylax esculentus complex) across Europe

description: Polyploidization is a rare yet sometimes successful way for animals to
 rapidly create geno- and phenotypes that may colonize new habitats and
 quickly adapt to environmental changes. In this study, we use water frogs
 of the Pelophylax esculentus complex, comprising two species (Pelophylax
 lessonae, genotype LL; Pelophylax ridibundus, RR) and various diploid (LR)
 and triploid (LLR, LRR) hybrid forms, summarized as P. esculentus, as a
 model for studying recent hybridization and polyploidization in the
 context of speciation. Specifically, we compared the geographic
 distribution and genetic diversity of diploid and triploid hybrids across
 Europe to understand their origin, maintenance and potential role in
 hybrid speciation. We found that different hybrid and parental genotypes
 are not evenly distributed across Europe. Rather, their genetic diversity
 is structured by latitude and longitude and the presence/absence of
 parental species but not of triploids. Highest genetic diversity was
 observed in central and eastern Europe, the lowest in the northwestern
 parts of Europe. This gradient can be explained by the decrease in genetic
 diversity during postglacial expansion from southeastern glacial refuge
 areas. Genealogical relationships calculated on the basis of
 microsatellite data clearly indicate that hybrids are of multiple origin
 and include a huge variety of parental genomes. Water frogs in
 mixed-ploidy populations without any parental species (i.e. all-hybrid
 populations) can be viewed as evolutionary units that may be on their way
 towards hybrid speciation. Maintenance of such all-hybrid populations
 requires a continuous exchange of genomes between diploids and triploids,
 but scenarios for alternative evolutionary trajectories are discussed.
description: Study sites, sample
 sizes and population compositionGeographic coordinates,
 sample sizes and genotypic composition of water frog populations sampled
 for microsatellite analysis. Classification was based on microsatellite
 results and was complemented by additional information on the population
 through personal observation (e.g. on presence of parental genotypes even
 though none were captured for sampling). nL represents the number of
 individuals used for the L genome data set, nR stands for the number of
 individuals used for the R genome data set. N represents the number of
 individuals used in total from the respective population. Percentages
 account for the proportion of genotypes within N. Please note that the
 population marked with * is a subsample from a larger sample. Individuals
 from this population used in this study were selected to represent the
 proportion of genotypes in the larger original sample, which partly
 resulted in a deviation in sample size between nL and
 nR.Hoffmann
 et al S1 (new).docxOrigin and number of
 frogs used for mtDNA analysisPopulations, geographic
 coordinates and sample sizes of samples used for mtDNA analysis. The
 column “Microsat No.*” refers to the numbering of populations in Table S1
 (new), where only populations used in microsatellite analyses are listed.
 Types of mtDNA are abbreviated as follows: les = lessonae-type, rid =
 ridibundus-type, ber = bergeri-type, cf. bed = cf.
 bedriagae-type.Hoffmann et al S2
 (new).xlsxSamples for
 microsatellite and mt DNA analysisThe Table summarizes
 which samples have been analyzed with microsatellites and/or mtDNA
 sequencing. Given are ID numbers, names and coordinates of samples sites
 an genotypes of frogsHoffmann et al S3
 (new).xlsxMicrosatellite
 markersThis Table lists the
 alleles found in each sampled individual (specified by ID numbers) on the
 Basis of six microsatellite markersHoffmann et al S4
 (new).xlsxGenetic structure within
 the R and L genomeGenetic differentiation
 within the R and L genome of water frogs of the Pelophylax esculentus
 complex, according to Bayesian analyses implemented in the program
 STRUCTURE. The proportion of membership (parameter q according to
 Pritchard et al. 2000) of each individual in each of the two (R genome)
 and four (L genome) inferred clusters is shown.Hoffmann et al S5
 (new).xlsxR-genome phylogeny
 (input)Data input for R-Genome
 phylogeny in Fig. 6Hoffmann et al S6a
 (new).txtR-phylogeny
 (output)Data Output for RgGenome
 phylogeny in Fig. 6Hoffman et al S6b
 (new).nwkL-genome phylogeny
 (input)Data input for L-genome
 phylogeny in Fig. 7Hoffmann et al S7a
 (new).txtL-phylogeny
 (output)Data output for L-Genome
 phylogeny in Fig. 7Hoffman et al S7b
 (new).nwkmtDNA
 sequencesShown are mtDNAsequences
 for all individuals (characterized by ID numbers) that were anaylzed
 according to Table S3 (new).Hoffmann et al S8
 (new).nexusmt DNA haplotypes across
 genotypes and populationsSupplement to Figure 8,
 showing the distribution of mtDNA haplotypes across genotypes and
 population types. Asterisks (*, **) indicate novel findings of the
 respective type of mtDNA in mixed-ploidy populations [24]* (Untermassfeld,
 Germany) and [52]** (Gaidary Iskov, Ukraine).Hoffmann et al S9
 (new).docx