Title:
Comparative analysis reveals signatures of differentiation amid genomic polymorphism in Lake Malawi cichlids
Comparative analysis reveals signatures of differentiation amid genomic polymorphism in Lake Malawi cichlids
Author(s)
Loh, Yong-Hwee E.
Katz, Lee S.
Mims, Meryl C.
Kocher, Thomas D.
Yi, Soojin V.
Streelman, J. Todd
Katz, Lee S.
Mims, Meryl C.
Kocher, Thomas D.
Yi, Soojin V.
Streelman, J. Todd
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Abstract
Background: Cichlid fish from East Africa are remarkable for phenotypic and behavioral diversity
on a backdrop of genomic similarity. In 2006, the Joint Genome Institute completed low coverage
survey sequencing of the genomes of five phenotypically and ecologically diverse Lake Malawi
species. We report a computational and comparative analysis of these data that provides insight
into the mechanisms that make closely related species different from one another.
Results: We produced assemblies for the five species ranging in aggregate length from 68 to 79
megabase pairs, identified putative orthologs for more than 12,000 human genes, and predicted
more than 32,000 cross-species single nucleotide polymorphisms (SNPs). Nucleotide diversity was
lower than that found among laboratory strains of the zebrafish. We collected around 36,000
genotypes to validate a subset of SNPs within and among populations and across multiple individuals
of about 75 Lake Malawi species. Notably, there were no fixed differences observed between focal
species nor between major lineages. Roughly 3% to 5% of loci surveyed are statistical outliers for
genetic differentiation (FST) within species, between species, and between major lineages. Outliers
for FST are candidate genes that may have experienced a history of natural selection in the Malawi
lineage.
Conclusion: We present a novel genome sequencing strategy, which is useful when evolutionary
diversity is the question of interest. Lake Malawi cichlids are phenotypically and behaviorally
diverse, but they appear genetically like a subdivided population. The unique structure of Lake
Malawl cichlid genomes should facilitate conceptually new experiments, employing SNPs to identity
genotype-phenotype association, using the entire species flock as a mapping panel.
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Date Issued
2008-07-10
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