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.
ReadMeFirst
This file lists and explains the computer codes and data files used in Ravinet et al. (2017).
data_Fig3A
Data used to generate Fig. 3A in Ravinet et al. (2017). For more explanations, please refer to the separate file "ReadMeFirst".
data_Fig3B
Data used to generate Fig. 3B in Ravinet et al. (2017). For further details, please refer to the separate file "ReadMeFirst".
data_Fig3C
Data used to generate Fig. 3C in Ravinet et al. (2017). For further details, please refer to the separate file "ReadMeFirst".
data_Fig4A
Data used to generate Fig. 4A in Ravinet et al. (2017). For further details, please refer to the separate file "ReadMeFirst".
data_Fig4B
Data used to generate Fig. 4B in Ravinet et al. (2017). For further details, please refer to the separate file "ReadMeFirst".
data_Fig5
Data used to generate Fig. 5 in Ravinet et al. (2017). For further details, please refer to the separate file "ReadMeFirst".
Initial Conditions
Initial 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.mat
Ravinet_et_al_Neutral_Evolution_Phase
Computer 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_Sweep
Computer 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_Sweep
Computer 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_Sweep
Computer 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_Fig5
Computer 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".