Species Delimitation in East African Cichlid Fish Adaptive Radiations

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Taxonomy is necessary for documenting and understanding changes in biodiversity through time. To better discover, name, and quantify organismal diversity, we need better models and criteria for how to effectively and reproducibly integrate taxonomy with huge phylogenomic data sets. Only very recently have genomic and computational tools became available that permit taxonomists and systematists to establish robust taxonomic hypotheses also for extremely young species. Whole-genome de novo sequencing and re-sequencing (WGS) is becoming technically and financially feasible for more laboratories. This applies also to research on hyper-diverse and often extremely young East African adaptive radiations of cichlid fishes (genome sizes =< 1Gb). The species flocks in Lake Victoria are particularly young (500 species arose in probably less than 12,000 years) whereas those of Lake Malawi (800-1000 species that are 2-4 MYA) are of intermediate age compared to the much older lineages of Lake Tanganyika (250 species that are up to 8-10MYA). Hybridization, incomplete lineage sorting, and the retention of ancient polymorphisms all contribute to gene/allele trees not agreeing with species trees. These phenomena are believed to be particularly onerous among the younger species, but less problematic for the older species of Lake Tanganyika. We plan to re-sequence (reference genomes are available) about 200 cichlid genomes of systematically chosen species pairs from each of the three radiations (25 individuals per species to be able to discover alleles at 5% frequency). These vast amounts of sequence data also cause novel challenges on how to elucidate the relationships between evolutionary processes and how genetic variation is distributed among lineages and species. The diagnoses of new taxa in the genomic age will demand phylogenomic analyses that account for the interplay between processes that affect genome architecture, interspecific gene flow, and the time-scales for speciation. Using entire genomes we plan to explore, partition, and analyze these data in an effort to develop more objective and reproducible taxonomic criteria based on particular molecular marker sets. The WGS data will be analyzed in full and also in several partitioned data sets whose congruence between gene and species trees will be evaluate through analyses including Structure, PCA, and Bayesian statistical methods, with the aim to devise rules for taxon diagnosis that, of course, are expected to apply not only for cichlids.