Biology subjects

Mwaiko, S.

Publications and source records attributed to Mwaiko, S..

5 recordsLinked to original sources

bioRxiv2025

Highly modular genomic architecture underlies combinatorial mechanism of speciation and adaptive radiation

Hybridisation can fuel rapid adaptive radiation, but how it enables the formation of phenotypically highly dimensional species-rich radiations remains unclear. We investigated this by analysing genotype-phenotype associations for 14 ecological (trophic, body patterns) and mating traits (nuptial colour) across 107 species of Lake Victoria cichlid fishes. We find weak trait covariance across the radiation, with many different trait combinations constituting different species. Across the radiation, polygenic, redundant, and lowly pleiotropic genomic architectures of hybrid origin underlie the repeated evolution of key traits. Such independent genomic modules can be reshuffled and recombined like Lego bricks, generating diverse trait combinations from a finite number of elements. During speciation, dispersed oligogenic trait modules become coupled through long-range linkage disequilibrium. We propose that this genomic and phenotypic modularity emerged from repeated cycles of past hybridisation, enabling superfast adaptive radiation through combinatorial speciation.

evolutionary biology↗

bioRxiv2025

Genomes reveal age and demographic consequence of ultrafast adaptive radiation

New species typically evolve over several million years1. However, rates of speciation and ecological diversification vary by orders of magnitude across the tree of life1-3, with the fastest shown by some adaptive radiations. Eight hundred endemic species of cichlid fishes emerged and formed entire food webs in Lake Victoria and nearby lakes in East Africa. According to Victorias paleolimnological history4, five hundred may have arisen within the past 16,700 years, but molecular phylogenies estimated a much older origin5-8. We reconstruct the age and demography of all Lake Victoria region radiations from whole genomes. We show that indeed, in Lake Victoria all trophic guilds diverged <16,700 years ago, corresponding to between 537 and nearly 30000 speciation events per species per million years, the fastest speciation rate in metazoans1,2. Cichlid radiations in lakes Edward, Albert and Kivu too began <20,000 years ago, an order of magnitude faster than previously thought. Evolutionary transitions between trophic levels led to divergence in effective population sizes as predicted by the trophic pyramid of numbers concept9 and replicated across three parallel food web radiations. Our results demonstrate that classical theory of trophic interactions in ecologically assembled food webs applies equally to food webs that assembled through rapid adaptive radiation.

evolutionary biology↗

bioRxiv2021

The genetic population structure of Lake Tanganyika's Lates species flock, an endemic radiation of pelagic top predators

Understanding genetic connectivity plays a crucial role in species conservation decisions, and genetic connectivity is an important component of modern fisheries management. In this study, we investigated the population genetics of four endemic Lates species of Lake Tanganyika (Lates stappersii, L. microlepis, L. mariae and L. angustifrons) using reduced-representation genomic sequencing methods. We find the four species to be strongly differentiated from one another (mean interspecific FST = 0.665), with no evidence for contemporary admixture. We also find evidence for strong genetic structure within L. mariae, with the majority of individuals from the most southern sampling site forming a genetic group that is distinct from the individuals at other sampling sites. We find evidence for much weaker structure within the other three species (L. stappersii, L. microlepis, and L. angustifrons). Our ability to detect this weak structure despite small and unbalanced sample sizes and imprecise geographic sampling locations suggests the possibility for further structure undetected in our study. We call for further research into the origins of the genetic differentiation in these four species--particularly that of L. mariae--which may be important for conservation and management of this culturally and economically important clade of fish.

evolutionary biology↗

bioRxiv2020

Movement of transposable elements contributes to cichlid diversity

African cichlid fishes are a prime model for studying the mechanisms of speciation. Despite the development of extensive genomic resources, it has been difficult to determine which sources of genetic variation are responsible for variation in cichlid phenotypes. Cichlids have some of the largest known shifts in vertebrate visual sensitivity. These shifts arise mainly from the differential expression of seven cone opsin genes. By mapping expression quantitative trait loci (eQTL) in intergeneric crosses of Lake Malawi (LM) cichlids, we have thus far identified four causative genetic variants that correspond to indels in the promoters of either key transcription factors or of the opsin gene itself. Here we show that these indels are caused by the movement of transposable elements (TEs). These precise indels are not found outside of LM, suggesting that these TEs are recently active and are segregating within the Malawi cichlid lineage. A similar indel has arisen independently outside of LM at one locus, suggesting that some locations are primed for TE insertion and the resulting indels. Increased TE mobility may be associated with interspecific hybridization, which disrupt mechanisms of TE suppression. Overall, our study suggests that TEs may contribute to key regulatory changes, and may facilitate rapid phenotypic change and possibly speciation in African cichlids.

evolutionary biology↗

bioRxiv2019

Sex differentiation and a chromosomal inversion lead to cryptic diversity in Lake Tanganyika sardines

Identifying patterns in genetic structure and the genetic basis of ecological adaptation is a core goal of evolutionary biology and can inform the management and conservation of species that are vulnerable to population declines exacerbated by climate change. We used reduced representation genomic sequencing methods to gain a better understanding of genetic structure among and within populations of Lake Tanganyikas two sardine species, Limnothrissa miodon and Stolothrissa tanganicae. Samples of these ecologically and economically important species were collected across the length of Lake Tanganyika, as well as from nearby Lake Kivu, where L. miodon was introduced in 1959. Our results reveal unexpected differentiation within both S. tanganicae and L. miodon that is not explained by geography. Instead, this genetic differentiation is due to the presence of large sex-specific regions in the genomes of both species, but involving different polymorphic sites in each species. Our results therefore indicate rapidly evolving XY sex determination in the two species. Additionally, we found evidence of a large segregating inversion in L. miodon. We found all inversion karyotypes throughout Lake Tanganyika, but the frequencies vary along a north-south gradient, and differ substantially in the introduced Lake Kivu population. We do not find evidence for significant isolation-by-distance, even over the hundreds of kilometers covered by our sampling, but we do find shallow population structure.

evolutionary biology↗