Abstract
Low coverage survey sequencing shows that although Lake Malawi cichlids are phenotypically and behaviorally diverse, they appear genetically like a subdivided population.
Highlights
Cichlid fish from East Africa are remarkable for phenotypic and behavioral diversity on a backdrop of genomic similarity
Given the theoretical expectation that individual bases should only be sequenced a maximum of four to five times, we examined whether contigs were built from five or more trace sequences contributing overlapping bases
Individual sequences contributing to these 'high trace number' contigs were not identified by RepeatMasker but did sometimes have Basic Local Alignment Search Tool (BLAST) matches to putative repetitive elements
Summary
Cichlid fish from East Africa are remarkable for phenotypic and behavioral diversity on a backdrop of genomic similarity. Cichlid fishes from the East African Rift lakes Victoria, Tanganyika, and Malawi represent a preeminent example of replicated and rapid evolutionary radiation [1] This group of fishes is a significant model of the evolutionary process and the coding of genotype to phenotype, largely because tremendous diversity has evolved in a short period of time among lineages with similar genomes [2,3,4]. Numerous genomic resources have been developed for East African cichlids (many of which are summarized by the Cichlid Genome Consortium [9]) These include the following: genetic linkage maps for tilapia [10,11,12] and Lake Malawi species [10,13]; fingerprinted bacterial artificial chromosome libraries [14]; expressed sequence tag sequences for Lake Tanganyika and Lake Victoria cichlids [15]; and first-generation microarrays [16,17]. Recent reports have capitalized on the diversity among East African cichlids to study the evolution and genetic basis of many traits, including behavior [20], olfaction [21], pigmentation [22,23,24], vision [25,26], sex determination [24,27], the brain [28], and craniofacial development [10,13,29]
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