Structural Variation in Adaptive Radiation: Determining the Potential Role of Large Genomic Inversions in Lake Malawi Cichlids
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Kumar, Nikesh Manish
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Abstract
Large chromosomal inversions restructure the genome, linking together small genetic variants by suppressing recombination between inverted and non-inverted segments. Large inversions have been shown to play an important evolutionary role in local adaptation, resolution of sexual conflict, and in speciation. This thesis investigates whether large inversions could be involved in the recent adaptive radiation in Lake Malawi cichlids, where ~800 species, characterized by large amounts of sexual dimorphism and adaptation to local niches, have evolved in the past 1.2 million years. Using optical genome mapping on a discovery cohort of 12 species from Lake Malawi, we identified six large inversions that span over 12% of the genome and then validated them using new long-read genome assemblies. We genotyped these inversions in 118 species, encompassing all seven major ecogroups distributed throughout the lake. We found that the inversions are correlated with ecogroup, consistent with a role for these structural variants to facilitate the separation of the major lake lineages into specific lake habitats. Furthermore, to investigate the functional impact of inversion heterozygosity, we found that at least one of these inversions functions as an XY sex-determination system in the deep benthic species Aulonocara sp. ‘chitande type north’ Nkhata Bay, where males are heterozygous for the inversion while females are homozygous. To map the causal locus within this non-recombining region, we utilized backcrossed hybrids generated between this deep benthic species and a species lacking the chromosome 10 inversion, successfully restoring meiotic recombination across the non-inverted, male-specific Y (MSY) sex-determining region. Leveraging this mapping population, we employed quantitative trait locus (QTL) mapping to narrow the sex-determining locus within the Aulonocara MSY to a 2Mbp region. Subsequent fine-mapping using highly informative recombinant offspring further isolated the locus to a 200kbp window containing three key candidate genes, including a long non-coding RNA and a histone variant that collectively implicate a novel epigenetic regulatory network. The findings presented in this dissertation conclusively demonstrate that chromosomal inversions can play significant roles in driving both local adaptation and sex chromosome evolution within adaptive radiations.
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2026-05
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Dissertation (PhD)