DOI: 10.5061/dryad.c5232
title: Data from: Hybrid origin of European Vipers (Vipera magnifica and Vipera orlovi) from the Caucasus determined using genomic scale DNA markers.

description: Background: Studying patterns of introgression can illuminate the role of
 hybridization in speciation, and help guide decisions relevant to the
 conservation of rare taxa. Vipera magnifica and Vipera orlovi are small
 vipers that have high conservation status due to their rarity and
 restricted distributions in an area of the Caucasus region where two other
 related species are present – V. kaznakovi and V. renardi. Despite
 numerous observations of hybridization between different species of small
 vipers, and the potential of a hybrid origin for V. magnifica and V.
 orlovi based on their distribution with respect to V. kaznakovi and V.
 renardi, hypotheses of a hybrid origin have not been formally tested. Here
 we generate genomic-scale data by performing next generation sequencing of
 double digest restriction-site associated DNA libraries, and use these
 multilocus data to test whether these two species are of hybrid origin.
 Results: We generated over nine hundred loci for 38 specimens of six taxa,
 and analysed the dataset using Bayesian clustering and multivariate
 methods, as well as Patterson D-statistics, which can distinguish between
 incomplete lineage sorting and introgression as explanations for shared
 polymorphism. The results demonstrate a pattern of historical admixture in
 the two purported hybrids that is consistent with past gene flow from V.
 renardi into V. kaznakovi. The average admixture proportion in individuals
 was low (6.39 %) in the case of V. magnifica, but was higher in V. orlovi
 (19.02 %). We also show that the specific individual samples used in
 D-statistic tests can have a significant impact on inferences regarding
 the magnitude of introgression, suggesting the importance of including
 multiple individuals in these analyses. Conclusions: Our results support
 the conclusion that both V. orlovi and V. magnifica had formed through a
 hybridization event between V. kaznakovi and V. renardi. Given a low
 proportion of admixture and absence of clear ecological and morphological
 differences V. magnifica should be treated as a marginal population of V.
 kaznakovi. Further studies that include analyses of ecological segregation
 of V. orlovi from parental taxa and search for evolutionary consequences
 of hybridisation would clarify if V. orlovi is a distinct hybrid species.
 Until this we recommend preserving the current taxonomy and protection
 status of V. orlovi.
description: RAD_14This file contains raw
 single end reads of ddRAD library for the part of specimens used in the
 paper. The file is zipped. Associated barcode information is in ReadMe
 file with the same name and extension (could be viewed in txt
 editor).RAD_40This file contains raw
 single end reads of ddRAD library for the part of specimens used in the
 paper. The file is zipped. Associated barcode information is in ReadMe
 file with the same name and extension (could be viewed in txt
 editor).D_stThis is the script which
 produces all the combinations of sequences from four populations and
 calculates ABBA-BABA D-statisticPop_DStat_Resamp_BinomialThis is the script which calculates population frequency based D statistic and significance of D statistic by resampling from binomial distribution at each locus in each population