DOI: 10.5061/dryad.2547d7wnt
title: Contrasting levels of hybridization across the two contact zones between two hedgehog species revealed by genome-wide SNP data

description: Hybridization and introgression have played important roles in the history
 of various species, including lineage diversification and the evolution of
 adaptive traits. Hybridization can accelerate the development of
 reproductive isolation between diverging species, and thus valuable
 insight into the evolution of reproductive barrier formation may be gained
 by studying secondary contact zones. Hedgehogs of the genus Erinaceus,
 which are insectivores sensitive to changes in climate, are a pioneer
 model in Pleistocene phylogeography. The present study provides the first
 genome-wide SNP data regarding the Erinaceus hedgehogs species complex,
 offering a unique comparison of two secondary contact zones between
 Erinaceus europaeus and E. roumanicus. Results confirmed diversification
 of the genus during the Pleistocene period and detected a new refugial
 lineage of E. roumanicus outside the Mediterranean region, most likely in
 the Ponto-Caspian region. In the Central European zone, the level of
 hybridization was low, whereas in the Russian-Baltic zone, both species
 hybridise extensively. Asymmetrical gene flow from E. europaeus to E.
 roumanicus suggests that reproductive isolation varies according to the
 direction of the crosses in the hybrid zones. However, no loci with
 significantly different patterns of introgression were detected. Markedly
 different pre- and post-zygotic barriers, and thus diverse modes of
 species boundary maintenance in the two contact zones, likely exist. This
 pattern is probably a consequence of the different ages and thus of the
 different stages of evolution of reproductive isolating mechanisms in each
 hybrid zone.
description: The sample list includes 33 specimens of
 <em>Erinaceus</em> <em>europaeus</em>, 48 of
 <em>E</em>. <em>roumanicus</em>, five of
 <em>E</em>. <em>concolor</em>, two
 <em>E</em>. <em>amurensis</em> and one
 <em>Hemiechinus</em> <em>auritus</em> and
 <em>Atelerix</em> <em>albiventris</em>. All tissue
 samples were obtained from roadkill animals or from animals that died in
 rescue centres. No animals were sacrificed for the purpose of this study.
 The samples from Russia were imported to the Czech Republic under
 requested veterinary conditions for import with reference numbers
 SVS/2019/061603-G. The remainder of the samples were collected before
 2013. The tissues were fixed in 96% ethanol and stored at -20 °C in the
 laboratory which has approval (No CZ 11712934) for storage and usage of
 animal material according to § 48(1)(i) of Act No 166/1999s concerning
 veterinary care and amending certain related laws, as amended, pursuant to
 Article 17(1) of Regulation of the European Parliament and the Council
 (EC) No 169/2009 and Article 27(1) of Commission Regulation (EU) No
 142/2011. The sample names, their geographic coordinates and species
 determination are listed in the metadat.txt file. DNA was extracted using spin-column protocol (Qiagen DNeasy Blood and Tissue kit, Qiagen). Mitochondrial control region sequences and combinations of microsatellite loci were used for species determination. Restriction‐site associated DNA (RAD) libraries were prepared for 50 samples using the restriction enzyme <em>Sbfl1</em> and performed at the European Molecular Biology Laboratory in Heidelberg. The codewords used in multiplexing are specified in the metadata.txt file. For DNA fragmentation, adapter ligation, purification and fragment size segregation, the protocol of the NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (Illumina Inc.) was used. Two prepared paired-end libraries were sequenced at the European Molecular Biology Laboratory (Heidelberg) using the Illumina HiSeq2000 sequencer, in two lanes separately, according to the manufacturer's protocol (Illumina Inc.). A single-end library was subsequently prepared for 40 samples from the Russian-Baltic contact zone, with the same restriction enzyme. The library was then sequenced using Illumina NextSeq at the European Molecular Biology Laboratory (Heidelberg). The sequencing method applied to each sample is specified in the metadata.txt file. Sequence demultiplexing based on individual specific codewords was performed using Sabre (https://github.com/najoshi/sabre), and read quality assessment was performed in FastQC 0.11.5 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The three sequencing batches were processed independently, producing three complementary sets of fastq files: fastq2016.tar and fastq2018.tar contain the paired-end sequences from the first 50 samples, sequenced twice; and fastq2020.tar contains the single-read sequences from the 40 additional samples sequenced.
description: The data set is composed of several files:
 metadata.txt describes the samples.
 fastq2016_X.tar (with "X" between 1 and 5) extract a
 directory named fastq2016 with the compressed fastq files corresponding to
 the first sequencing batch of the 50 first samples. Note that there are
 two files per sample, for the forward and the reverse reads.
 fastq2018_X.tar (with "X" between 1 and 3) extract a
 directory named fastq2018 with the compressed fastq files corresponding to
 the second sequencing batch of the same 50 first samples. Note that the
 file names in this directory are the same as in fastq2016, because they
 are the same samples. fastq2020_X.tar (with
 "X" between 1 and 6) extract a directory named fastq2020 with
 the compressed fastq files corresponding to the sequencing of 40
 additional samples. Here there is one file per sample, because they were
 sequenced with single reads.