Interestingly, we found strong evidence that at least three inversions are involved in sex determination in some lineages, while the same inversions do not determine sex in other groups.

Focusing on the SNPs from within the inversion regions that were most correlated with inversion state, we identified patterns of positive selection that were enriched for genes related to sensory perception.

... we believe that the most species rich and ecologically diverse subradiation arose from a hybridization event between the ancestors of two ecologically contrasting lineages: the riverine-like 𝐴. 𝑐𝑎𝑙𝑙𝑖𝑝𝑡𝑒𝑟𝑎 and the deepwater specialists 𝐷𝑖𝑝𝑙𝑜𝑡𝑎𝑥𝑜𝑑𝑜𝑛.

Using new chromosome-level assemblies and haplotagged (linked) reads of representatives of the major clades we confirmed that these regions are in fact inversions. Pairwise alignments also showed that the outlier region on chromosome 11 consists of two adjacent but co-segregating inversions.

Using windowed PCA and a new clustering approach we identified five chromosome-scale regions with aberrant phylogenetic patterns – consistent with large and divergent segregating haplotypes.

Check out our new paper about chromosomal inversions in Malawi cichlids! 🐟🧬

Available here without a paywall: hdl.handle.net/10067/214834... (click on the ‘Full text (open access)’ link).