DOI: 10.5061/dryad.qj5cr
title: Data from: Interpreting the genomic landscape of speciation: a road map for finding barriers to gene flow

description: Speciation, the evolution of reproductive isolation amongst populations,
 is continuous, complex, and involves multiple, interacting barriers. Until
 it is complete, the effects of this process vary along the genome and can
 lead to a heterogeneous genomic landscape with peaks and troughs of
 differentiation and divergence. When gene flow occurs during speciation,
 barriers restricting migration locally in the genome lead to patterns of
 heterogeneity. However, genomic heterogeneity can also be produced or
 modified by variation in factors such as background selection and
 selective sweeps, recombination- and mutation-rate variation, and
 heterogeneous gene density. Extracting the effects of gene flow, divergent
 selection and reproductive isolation from such modifying factors presents
 a major challenge to speciation genomics. We argue one of the principal
 aims of the field is to identify the barrier loci involved in limiting
 gene flow. We first summarise the expected signatures of selection at
 barrier loci, at the genomic regions linked to them and across the entire
 genome. We then discuss the modifying factors that complicate the
 interpretation of the observed genomic landscape. Finally, we end with a
 roadmap for future speciation research; a proposal for how to account for
 these modifying factors and to progress towards understanding the nature
 of barrier loci. Despite the difficulties of interpreting empirical data,
 we argue that the availability of promising technical and analytical
 methods will shed further light on the important roles that gene flow and
 divergent selection have in shaping the genomic landscape of speciation.
description: ReadMeFirstThis file lists and explains the computer codes and data files used in Ravinet et al. (2017).data_Fig3AData used to generate Fig. 3A in Ravinet et al. (2017). For more explanations, please refer to the separate file "ReadMeFirst".data_Fig3BData used to generate Fig. 3B in Ravinet et al. (2017). For further details, please refer to the separate file "ReadMeFirst".data_Fig3CData used to generate Fig. 3C in Ravinet et al. (2017). For further details, please refer to the separate file "ReadMeFirst".data_Fig4AData used to generate Fig. 4A in Ravinet et al. (2017). For further details, please refer to the separate file "ReadMeFirst".data_Fig4BData used to generate Fig. 4B in Ravinet et al. (2017). For further details, please refer to the separate file "ReadMeFirst".data_Fig5Data used to generate Fig. 5 in Ravinet et al. (2017). For further details, please refer to the separate file "ReadMeFirst".Initial ConditionsInitial conditions used as the input for the main simulations performed by Ravinet et al. (2017). For further details, please refer to the separate file "ReadMeFirst".InConds.matRavinet_et_al_Neutral_Evolution_PhaseComputer code for the neutral-evolution phase (explained in detail in Ravinet et al. 2017). For further details, please refer to the separate file "ReadMeFirst".Ravinet_et_al_Prim_Cont_Soft_SweepComputer code for a soft sweep occurring in the face of gene flow between a pair of populations under divergent selection (explained in detail in Ravinet et al. 2017). For further details, please refer to the separate file "ReadMeFirst".Ravinet_et_al_Prim_Cont_Hard_SweepComputer code for a hard sweep occurring in the face of gene flow between a pair of populations under divergent selection (explained in detail in Ravinet et al. 2017). For further details, please refer to the separate file "ReadMeFirst".Ravinet_et_al_Sec_Cont_Hard_SweepComputer code for a hard sweep occurring during a period of isolation of a pair of populations under divergent selection; the sweep is followed by gene flow (the model is explained in detail in Ravinet et al. 2017). For further details, please refer to the separate file "ReadMeFirst".Ravinet_et_al_Fig5Computer code used to generate results shown in Fig. 5 in Ravinet et al. (2017). For further details, please see Ravinet et al. (2017), and the separate file "ReadMeFirst".