Data from: Genomics of speciation and introgression in Princess cichlid fishes from Lake Tanganyika

How variation in the genome translates into biological diversity and new
species originate has endured as the mystery of mysteries in evolutionary
biology. African cichlid fishes are prime model systems to address
speciation-related questions for their remarkable taxonomic and phenotypic
diversity, and the possible role of gene flow in this process. Here, we
capitalize on genome sequencing and phylogenomic analyses to address the
relative impacts of incomplete lineage sorting, introgression and hybrid
speciation in the Neolamprologus savoryi-complex (the ‘Princess cichlids’)
from Lake Tanganyika. We present a time-calibrated species tree based on
whole-genome sequences and provide strong evidence for incomplete lineage
sorting in the early phases of diversification and multiple introgression
events affecting different stages. Importantly, we find that the
Neolamprologus chromosomes show centre-to-periphery biases in nucleotide
diversity, sequence divergence, GC content, incomplete lineage sorting and
rates of introgression, which are likely modulated by recombination
density and linked selection. The detection of heterogeneous genomic
landscapes has strong implications on the genomic mechanisms involved in
speciation. Collinear chromosomal regions can be protected from gene flow
and harbour incompatibility genes if they reside in lowly recombining
regions, and coupling can evolve between nonphysically linked genomic
regions (chromosome centres in particular). Simultaneously, higher
recombination towards chromosome peripheries makes these more dynamic,
evolvable regions where adaptation polymorphisms have a fertile ground.
Hence, differences in genome architecture could explain the levels of
taxonomic and phenotypic diversity seen in taxa with collinear genomes and
might have contributed to the spectacular cichlid diversity observed
today.