DOI: 10.5061/dryad.0rxwdbs3h
title: Demographic modelling helps tracking the rapid and recent divergence of a conifer species pair from central Mexico

description: Secondary contact of recently diverged species may have several outcomes,
 ranging from rampant hybridization to reinforced reproductive isolation.
 In plants, selfing tolerance and disjunct reproductive phenology may lead
 to reproductive isolation at contact zones. However, they can evolve under
 both allopatric or parapatric frameworks and originate from adaptive
 and/or neutral forces. Inferring the historical demography of diverging
 taxa is thus a crucial step to identify those factors that may lead to
 putative reproductive isolation. We explored various competing hypotheses
 to account for the rapid divergence of a fir species complex (Abies
 flinckii - A. religiosa) distributed in ‘sky-islands’ across central
 Mexico (i.e., along the Trans-Mexican Volcanic Belt; TMVB). Despite
 co-occurring in two independent sympatric regions (west and center), these
 taxa rarely interbreed because of disjunct reproductive phenologies. We
 genotyped 1,147 SNPs, generated by GBS, across 23 populations, and
 compared multiple demographic scenarios based on the geological history of
 the TMVB. The best-fitting model revealed one of the most rapid and
 complete speciation cases for a conifer species-pair, dating back to ~1.2
 Ma. Coupled with the lack of support for stepwise colonization, our
 coalescent inferences point to an early cessation of interspecific gene
 flow under parapatric speciation; ancestral gene flow during divergence
 was asymmetrical (mostly from western firs into A. religiosa) and
 exclusive to the most ancient (i.e., central) contact zone. Factors
 promoting rapid reproductive isolation should be explored in other
 slowly-evolving species complexes as they may account for the large
 tropical and subtropical diversity.
description: Please, see Materials and Methods.
description: GBS_Abies contains 11
 subdirectories:<br><br>-ipyrad_Abies/: This directory has
 scrips/command lines and vcf files used to identify the optimal parameter
 values to perform a denovo SNP assembly using ipyrad 0.9.33 and VCFtools
 0.1.16.<br><br>-out/: This directory contains a vcf file
 assembled with ipyrad after parameter optimization. This file is further
 filtered with scripts saved in bin/<br><br>-bin/: This
 directory holds most of the scripts used to perform population genomics
 computations, and genetic structure inferences.<br><br>-meta/:
 This directory has a metadata file and tables with the geographic/genetic
 information for each analized sample.<br><br>-out_TMVB/: This
 directory contains three vcf files (each with different level of missing
 data), which were used to asses the genetic diversity, structure and the
 past demography of fir populations from central Mexico. Outputs are also
 stored in this directory. <br><br>-out_religiosa/: This
 directory holds a vcf file with SNPs discovered only for A. religiosa.
 This files was used to perform a DAPC
 analysis.<br><br>-out_religiosa_NoMan/: This directory
 contains a vcf file with SNPs discovered only for A. religiosa, except the
 W genetic pool. We infered the genetic structure for these samples using
 ADMIXTURE v. 1.3.0.<br><br>-out_Megas/: It holds a filtered
 .vcf file with SNPs discovered from a pair of Megagametophyte samples
 (i.e., haploid tissue).<br><br>-fastsimcoal/: This directory
 contain scripts and input files (.tpl, .est, .obs) to perform demographic
 inferences using fastsimcoal2 v.
 2.6.0.3-14.10.17<br><br>-DnaSP_results/: This directory holds
 input files to perform population genetic computations using DNA v.
 6.12.03. Outputs are also saved.<br><br>-data_raw/: This
 directory was used to store non-demultiplexed samples (i.e., raw
 reads).