High-resolution mapping reveals hundreds of genetic incompatibilities in hybridizing fish species

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Abstract

Hybridization is increasingly being recognized as a common process in both animal and plant species. Negative epistatic interactions between genes from different parental genomes decrease the fitness of hybrids and can limit gene flow between species. However, little is known about the number and genome-wide distribution of genetic incompatibilities separating species. To detect interacting genes, we perform a high-resolution genome scan for linkage disequilibrium between unlinked genomic regions in naturally occurring hybrid populations of swordtail fish. We estimate that hundreds of pairs of genomic regions contribute to reproductive isolation between these species, despite them being recently diverged. Many of these incompatibilities are likely the result of natural or sexual selection on hybrids, since intrinsic isolation is known to be weak. Patterns of genomic divergence at these regions imply that genetic incompatibilities play a significant role in limiting gene flow even in young species.

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Molly Schumer

Princeton University, Princeton, United States

For correspondence
schumer@princeton.edu

Competing interests
The authors declare that no competing interests exist.
Rongfeng Cui

Texas A&M University, College Station, United States

Competing interests
The authors declare that no competing interests exist.
Daniel Powell

Texas A&M University, College Station, United States

Competing interests
The authors declare that no competing interests exist.
Rebecca Dresner

Princeton University, Princeton, United States

Competing interests
The authors declare that no competing interests exist.
Gil G Rosenthal

Texas A&M University, College Station, United States

Competing interests
The authors declare that no competing interests exist.
Peter Andolfatto

Princeton University, Princeton, United States

Competing interests
The authors declare that no competing interests exist.

Ethics

Animal experimentation: The procedures used in this study were approved by the Institutional Animal Care and Use Committee at Texas A&M University (Protocols # 2010-111 and 2012-164). Procedures were designed to minimize animal stress and suffering by using anesthesia during fin clipping and minimal handling of the fish. Samples were collected from the wild under Mexican federal collector's license FAUT-217 to W. Scott Monks.

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This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.