DOI: 10.5061/dryad.j6q573ngd
title: Whole-genome analysis of multiple wood ant population pairs supports similar speciation histories, but different degrees of gene flow, across their European ranges

description: The application of demographic history modelling and inference to the
 study of divergence between species has become a cornerstone of speciation
 genomics. Speciation histories are usually reconstructed by analysing
 single populations from each species, assuming that the inferred
 population history represents the actual speciation history. However, this
 assumption may not be met when species diverge with gene flow, e.g., when
 secondary contact may be confined to specific geographic regions. Here, we
 tested whether divergence histories inferred from
 heterospecific populations may vary depending on their geographic
 locations, using the two wood ant species Formica polyctena and F.
 aquilonia. We performed whole-genome resequencing of 20
 individuals sampled in multiple locations across the
 European ranges of both species. Then, we reconstructed the
 histories of distinct heterospecific population pairs using a
 coalescent-based approach. Our analyses always supported a
 scenario of divergence with gene flow, suggesting that divergence started
 in the Pleistocene (ca. 500 kya) and occurred with continuous
 asymmetrical gene flow from F. aquilonia to F. polyctena until a recent
 time, when migration became negligible (2-19 kya). However, we found
 support for contemporary gene flow in a sympatric pair from
 Finland, where the species hybridise, but no signature of recent
 bidirectional gene flow elsewhere. Overall, our results suggest
 that divergence histories reconstructed from a few individuals
 may be applicable at the species level. Nonetheless,
 the geographical context of populations chosen to represent their
 species should be taken into account, as it may affect estimates
 of migration rates between species when gene flow is spatially
 heterogeneous.
description: Whole-genome data of 10 <em>Formica polyctena</em>
 and 10 <em>F. aquilonia</em> wood ants.
description: Questions should be directed to the corresponding authors,
 Beatriz Portinha (bcportinha@gmail.com) and Dr. Pierre Nouhaud
 (pierr3.nouhaud@gmail.com) This Dryad directory
 contains Variant Call Format (VCF) files, Site Frequency Spectra (SFS) and
 model input files (.tpl and .est) used for fastsimcoal2 analyses in the
 Portinha et al. manuscript to be published in Molecular Ecology.
 In this directory, you will find the following folders:
 -
 VCF_files: this folder contains two compressed VCF files, one of which
 includes all of the called sites (whole_genome.vcf.gz) and the other,
 which had SNPs in genic regions and within 10kbs of genes removed
 (non_genic.vcf.gz); this folder also includes a README.txt file with
 further details. - VCF_script: this
 folder contains a bash script used to produce the VCF files present in the
 "VCF_files" folder; this folder also includes a README.txt file
 with further details. - SFS_files: this
 folder contains the SFSs used for the demographic modelling analyses
 performed with fastsimcoal2, built from the VCF files provided in this
 directory; in this folder, you will find the datasets built for each
 population comparison, as well as a README.txt file with instructions on
 how to compute these SFSs. -
 fastsimcoal2_input_files: this folder contains the input files (.tpl and
 .est) of all models tested with fastsimcoal2; you will also find a
 README.txt file in this folder with detailed explanations of the model
 name tags. -
 fastsimcoal2_scripts: this folder contains the bash scripts we used to run
 each demographic model 100 times; you will also find a README.txt file in
 this folder with further details.