Data from: Gene duplication in an African cichlid adaptive radiation

Background: Gene duplication is a source of evolutionary innovation and
can contribute to the divergence of lineages; however, the relative
importance of this process remains to be determined. The explosive
divergence of the African cichlid adaptive radiations provides both a
model for studying the general role of gene duplication in the divergence
of lineages and also an exciting foray into the identification of genomic
features that underlie the dramatic phenotypic and ecological
diversification in this particular lineage. We present the first
genome-wide study of gene duplication in African cichlid fishes,
identifying gene duplicates in three species belonging to the Lake Malawi
adaptive radiation (Metriaclima estherae, Protomelas similis,
Rhamphochromis “chilingali”) and one closely related species from a
non-radiated riverine lineage (Astatotilapia tweddlei). Results: Using
Astatotilapia burtoni as reference, microarray comparative genomic
hybridization analysis of 5689 genes reveals 134 duplicated genes among
the four cichlid species tested. Between 51 and 55 genes were identified
as duplicated in each of the three species from the Lake Malawi radiation,
representing a 38% – 49% increase in number of duplicated genes relative
to the non-radiated lineage (37 genes). Duplicated genes include several
that are involved in immune response, ATP metabolism and detoxification.
Conclusions: These results contribute to our understanding of the
abundance and type of gene duplicates present in cichlid fish lineages.
The duplicated genes identified in this study provide candidates for the
analysis of functional relevance with regard to phenotype and divergence.
Comparative sequence analysis of gene duplicates can address the role of
positive selection and adaptive evolution by gene duplication, while
further study across the phylogenetic range of cichlid radiations (and
more generally in other adaptive radiations) will determine whether the
patterns of gene duplication seen in this study consistently accompany
rapid radiation.