Article series: Study designs

Making sense of genomic islands of differentiation in light of speciation

Journal name:
Nature Reviews Genetics
Year published:
Published online


As populations diverge, genetic differences accumulate across the genome. Spurred by rapid developments in sequencing technology, genome-wide population surveys of natural populations promise insights into the evolutionary processes and the genetic basis underlying speciation. Although genomic regions of elevated differentiation are the focus of searches for 'speciation genes', there is an increasing realization that such genomic signatures can also arise by alternative processes that are not related to population divergence, such as linked selection. In this Review, we explore methodological trends in speciation genomic studies, highlight the difficulty in separating processes related to speciation from those emerging from genome-wide properties that are not related to reproductive isolation, and provide a set of suggestions for future work in this area.

At a glance


  1. A schematic of alternative processes that generate regional genomic islands of elevated differentiation.
    Figure 1: A schematic of alternative processes that generate regional genomic islands of elevated differentiation.

    Red and white circles represent different alleles in a population at the depicted genomic region. The branching schematic indicates the segregation of these alleles between populations that are diverging. a | In regions of gene flow (indicated by the double-headed arrows), differentiation becomes reduced relative to loci where there is selection against gene flow because of reproductive incompatibility, for example. b | In regions where the effective population size (Ne) is reduced by processes that are independent from gene flow (middle panel) the rate of lineage sorting is enhanced relative to background levels, leading to elevated differentiation.

  2. A summary of central aspects of our literature survey on speciation genomic studies.
    Figure 2: A summary of central aspects of our literature survey on speciation genomic studies.

    The figure shows the percentage of studies in our data set that included central aspects of speciation genomic analyses.


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Author information


  1. Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden.

    • Jochen B. W. Wolf &
    • Hans Ellegren
  2. Section of Evolutionary Biology, Department of Biology II, Ludwig Maximilian University of Munich, Grosshaderner Strasse 2, Planegg-Martinsried 82152, Germany.

    • Jochen B. W. Wolf

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The authors declare no competing interests.

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  • Jochen B. W. Wolf

    Jochen B. W. Wolf is a professor in evolutionary biology at the Faculty of Biology, Ludwig-Maximilians University Munich, Germany. He is also guest professor at the Evolutionary Biology Centre, Uppsala University, Sweden. His research group takes an integrative approach to the study of evolutionary processes in a variety of natural and experimental systems, often using large-scale genomic approaches. Jochen B. W. Wolf's homepage

  • Hans Ellegren

    Hans Ellegren is a professor in evolutionary biology at the Evolutionary Biology Centre, Uppsala University, Sweden. His laboratory studies evolutionary genetic questions relating to molecular ecology, molecular evolution, sex chromosome evolution and speciation genetics using bioinformatic and genomic approaches. Hans Ellegren's homepage

Supplementary information

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  1. Supplementary information S1 (table) (29 KB)

    A Compilation of a literature survey including 67 studies drawn from searching the ISI Web of Knowledge database for terms 'speciation genomics', 'islands of differentiation', 'islands of speciation' and 'speciation with gene flow', and complemented with other references.

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