Moss, Stephen P., Domino A. Joyce, Stuart Humphries, Katherine J. Tindall and David H. Lunt (2011) Comparative analysis of teleost genome sequences reveals an ancient intron size expansion in the zebrafish lineage. Genome Biology and Evolution doi: 10.1093/gbe/evr090, (PDF)
We have developed a bioinformatics pipeline for the comparative evolutionary analysis of Ensembl genomes, and have used it to analyse the introns of the five available teleost fish genomes. We show our pipeline to be a powerful tool for revealing variation between genomes that may otherwise be overlooked with simple summary statistics. We identify that the zebrafish, Danio rerio, has an unusual distribution of intron sizes, with a greater number of larger introns in general and a notable peak in the frequency of introns of ∼500 bp to 2,000 bp compared to the monotonically decreasing frequency distributions of the other fish. We determine that 47% of Danio rerio introns are composed of repetitive sequences, although the remainder, over 331 Mb, is not. Since repetitive elements may be the origin of the majority of all non-coding DNA, it is likely that the remaining Danio rerio intronic sequence has an ancient repetitive origin and has since accumulated so many mutations that it can no longer be recognised as such. To study such an ancient expansion of repeats in the Danio lineage will require further comparative analysis of fish genomes incorporating a broader distribution of teleost lineages.
Through adaptive radiation, ancestral species rapidly diversify into multiple species with different ecological adaptations. The haplochromine cichlid fishes of the East African Great Lakes are considered classic examples of adaptive radiation, but our understanding of the evolutionary origins of these radiations has been limited by inadequate taxonomic and genomic sampling [1,2]. Perhaps the largest of these radiations is from Lake Malawi, estimated to contain between 500 and 800 endemic species. Surprisingly, its monophyly – the origin from a single ancestral species – has never been critically tested. This is because river populations which could have seeded the radiation, with one very limited exception [3], have never been included in phylogenetic reconstructions. Moreover, phylogenies have relied heavily on mitochondrial DNA (mtDNA), which can be a misleading phylogenetic marker for species capable of hybridization [4,5] because its non-recombining nature means that transfer to other species can occur via asymmetric introgression and ‘allele surfing’[6]. Here, we used broad taxonomic sampling and nuclear DNA markers with wide genomic coverage and find that the Lake Malawi radiation is not monophyletic, but instead contains genetic material from divergent riverine ancestors indicating multiple invasions and hybridization.
