Biology subjects

Munby, H.

Publications and source records attributed to Munby, H..

3 recordsLinked to original sources

bioRxiv2025

Revisiting the evidence for long-lived balancing selection in humans.

Balancing selection maintains variation in a population and, when sufficiently long-lived, can lead to polymorphisms shared identical by descent across species. In settings where sharing is extremely unlikely to occur under neutrality, such trans-species polymorphisms provide clear-cut evidence for balancing selection. These considerations have motivated efforts to identify trans-species polymorphisms between humans and close evolutionary relatives, such as chimpanzees, and have led to the discovery of a handful of examples. However, recent demographic modeling suggests that gene flow between humans and chimpanzees may have persisted until much more recently than previously thought, implying that many trans-species polymorphism could potentially have arisen by chance. Here, we reassess the evidence for long-term balancing selection in humans by characterizing shared single base pair polymorphisms in whole genome sequences from 2504 humans and 59 chimpanzees. Using recently-developed methods to reconstruct local gene genealogies, we infer the evolutionary histories surrounding the oldest shared variants and distinguish true trans-species polymorphisms from recurrent mutations, recovering both previously known and novel examples. We then examine multiple lines of independent evidence for the action of natural selection on this set of trans-species polymorphisms. These analyses suggest that the vast majority may have arisen by chance, in regions of neutral, incomplete lineage-sorting. In other words, while a subset of such loci remain compelling candidates for long-term balancing selection, the finding of trans-species polymorphism shared between humans and chimpanzees is not, in itself, strong evidence for long-lived balancing selection.

evolutionary biology↗

bioRxiv2021

Differential use of multiple genetic sex determination systems in divergent ecomorphs of an African crater lake cichlid

African cichlid fishes not only exhibit remarkably high rates of speciation but also have some of the fastest evolving sex determination systems in vertebrates. However, little is known empirically in cichlids about the genetic mechanisms generating new sex-determining variants, what forces dictate their fate, the demographic scales at which they evolve, and whether they are related to speciation. To address these questions, we looked for sex-associated loci in full genome data from 647 individuals of Astatotilapia calliptera from Lake Masoko, a small isolated crater lake in Tanzania, which contains two distinct ecomorphs of the species. We identified three separate XY systems on recombining chromosomes. Two Y alleles derive from mutations that increase expression of the gonadal soma-derived factor gene (gsdf) on chromosome 7; the first is a tandem duplication of the entire gene observed throughout much of the Lake Malawi haplochromine cichlid radiation to which A. calliptera belongs, and the second is a 5 kb insertion directly upstream of gsdf. Both the latter variant and another 700 bp insertion on chromosome 19 responsible for the third Y allele arose from transposable element insertions. Males belonging to the Masoko deep-water benthic ecomorph are determined exclusively by the gsdf duplication, whereas all three Y alleles are used in the Masoko littoral ecomorph, in which they appear to act antagonistically among males with different amounts of benthic admixture. This antagonism in the face of ongoing admixture may be important for sustaining multifactorial sex determination in Lake Masoko. In addition to identifying the molecular basis of three coexisting sex determining alleles, these results demonstrate that genetic interactions between Y alleles and genetic background can potentially affect fitness and adaptive evolution.

evolutionary biology↗

bioRxiv2019

Whole-chromosome hitchhiking driven by a male-killing endosymbiont

Neo-sex chromosomes are found in many taxa, but the forces driving their emergence and spread are poorly understood. The female-specific neo-W chromosome of the African monarch (or queen) butterfly Danaus chrysippus presents an intriguing case study because it is restricted to a single contact zone population, involves a putative colour patterning supergene, and co-occurs with infection by the the male-killing endosymbiont Spiroplasma. We investigated the origin and evolution of this system using whole genome sequencing. We first identify the BC supergene, a broad region of suppressed recombination across nearly half a chromosome, which links two colour patterning loci. Association analysis suggests that the genes yellow and arrow in this region control the forewing colour pattern differences between D. chrysippus subspecies. We then show that the same chromosome has recently formed a neo-W that has spread through the contact zone within [~]2200 years. We also assembled the genome of the male-killing Spiroplasma, and find that it shows perfect genealogical congruence with the neo-W, suggesting that the neo-W has hitchhiked to high frequency as the male killer has spread through the population. The complete absence of female crossing-over in the Lepidoptera causes whole-chromosome hitchhiking of a single neo-W haplotype, carrying a single allele of the BC supergene, and dragging multiple non-synonymous mutations to high frequency. This has created a population of infected females that all carry the same recessive colour patterning allele, making the phenotypes of each successive generation highly dependent on uninfected male immigrants. Our findings show how hitchhiking can occur between the unlinked genomes of host and endosymbiont, with dramatic consequences.

evolutionary biology↗