Genomic architecture of ecologically divergent body shape in a pair of sympatric crater lake cichlid fishes

Franchini, Paolo, Fruciano, Carmelo, Spreitzer, Maria L., Jones, Julia C., Elmer, Kathryn R., Henning, Frederico, & Meyer, Axel (2014) Genomic architecture of ecologically divergent body shape in a pair of sympatric crater lake cichlid fishes. Molecular Ecology, 23(7), pp. 1828-1845.

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Abstract

Determining the genetic bases of adaptations and their roles in speciation is a prominent issue in evolutionary biology. Cichlid fish species flocks are a prime example of recent rapid radiations, often associated with adaptive phenotypic divergence from a common ancestor within a short period of time. In several radiations of freshwater fishes, divergence in ecomorphological traits - including body shape, colour, lips and jaws - is thought to underlie their ecological differentiation, specialization and, ultimately, speciation. The Midas cichlid species complex (Amphilophus spp.) of Nicaragua provides one of the few known examples of sympatric speciation where species have rapidly evolved different but parallel morphologies in young crater lakes. This study identified significant QTL for body shape using SNPs generated via ddRAD sequencing and geometric morphometric analyses of a cross between two ecologically and morphologically divergent, sympatric cichlid species endemic to crater Lake Apoyo: an elongated limnetic species (Amphilophus zaliosus) and a high-bodied benthic species (Amphilophus astorquii). A total of 453 genome-wide informative SNPs were identified in 240 F-2 hybrids. These markers were used to construct a genetic map in which 25 linkage groups were resolved. Seventy-two segregating SNPs were linked to 11 QTL. By annotating the two most highly supported QTL-linked genomic regions, genes that might contribute to divergence in body shape along the benthic-limnetic axis in Midas cichlid sympatric adaptive radiations were identified. These results suggest that few genomic regions of large effect contribute to early stage divergence in Midas cichlids.

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ID Code: 87580
Item Type: Journal Article
Refereed: Yes
Additional Information:

We thank T. Lehtonen for collecting fry and help setting up initial breeding crosses, J. Sieling and her team for caring for the fish, L. Beck for laboratory assistance, S. Fan, T. Frickey and H. Recknagel for bionformatic support. We thank three anonymous referees for their helpful suggestions on the manuscript. MARENA granted permits for our field work in Nicaragua, and we thank them kindly for their continued support over the years. CF was funded by DAAD (B1 scholarship A/11/78461) and Marie Curie (IEF fellowship PlasticitySpeciation). KRE was funded by Alexander von Humboldt and NSERC postdoctoral fellowships. MLS was funded by the International Max Planck Research School (IMPRS). JCJ was funded by the Zukunftskolleg at the University of Konstanz and the DFG. The University of Konstanz is thanked for its support of the Meyer laboratory and the GeCKo (Genomic Center Konstanz). Funding for this project came from the European Research Council through ERC-advanced grant 293700-GenAdap (AM).

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Funders: DAAD, Marie Curie (IEF fellowship PlasticitySpeciation), Alexander von Humboldt fellowship, NSERC, International Max Planck Research School (IMPRS), Zukunftskolleg at the University of Konstanz, DFG, University of Konstanz, European Research Council
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Keywords: geometric morphometrics, qtl mapping, sympatric speciation, genomics
DOI: 10.1111/mec.12590
ISSN: 1365-294X
Subjects: Australian and New Zealand Standard Research Classification > BIOLOGICAL SCIENCES (060000) > EVOLUTIONARY BIOLOGY (060300)
Australian and New Zealand Standard Research Classification > BIOLOGICAL SCIENCES (060000) > EVOLUTIONARY BIOLOGY (060300) > Biological Adaptation (060303)
Australian and New Zealand Standard Research Classification > BIOLOGICAL SCIENCES (060000) > EVOLUTIONARY BIOLOGY (060300) > Speciation and Extinction (060311)
Australian and New Zealand Standard Research Classification > BIOLOGICAL SCIENCES (060000) > GENETICS (060400) > Genomics (060408)
Australian and New Zealand Standard Research Classification > BIOLOGICAL SCIENCES (060000) > GENETICS (060400) > Quantitative Genetics (incl. Disease and Trait Mapping Genetics (060412)
Australian and New Zealand Standard Research Classification > BIOLOGICAL SCIENCES (060000) > ZOOLOGY (060800) > Vertebrate Biology (060809)
Divisions: Current > Schools > School of Earth, Environmental & Biological Sciences
Past > QUT Faculties & Divisions > Faculty of Science and Technology
Deposited On: 22 Sep 2015 01:25
Last Modified: 23 Sep 2015 02:11

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