Biology subjects

Yusuf, L. H.

Publications and source records attributed to Yusuf, L. H..

4 recordsLinked to original sources

bioRxiv2025

Cis-regulatory divergence and mate recognition in behaviourally isolated cricket species.

Cis-regulatory evolution has been implicated in morphological and physiological reproductive isolation, but its role in divergence of mate recognition behaviours is unknown. The latter are often the first, most powerful mating barriers to evolve during speciation, but understanding their genetics is hampered by the context-dependence of mate choice. We circumvented this challenge by using allele-specific expression analyses in F1 hybrids of sexually isolated cricket species, Teleogryllus oceanicus and T. commodus. Female crickets choose mating partners based on species-specific male advertisement songs, and we found extensive cis-regulatory divergence in neural tissues exposed to conspecific, heterospecific, or mixed-species songs. Genes with divergent expression were implicated in learning, memory and transcriptional regulation, and they showed elevated population genetic differentiation in allopatry but not sympatry. This implies that genes recruited during evolutionary divergence of mate recognition systems may be homogenised by gene flow. Regulatory divergence was asymmetrical between the two species; divergent selection on genes associated with female perception of male song was more prominent in T. oceanicus than in T. commodus. Evolved differences in gene regulation are strongly associated with sexual signal perception in closely related species, supporting the idea that rapid cis-regulatory evolution of mate recognition can accelerate speciation.

evolutionary biology↗

bioRxiv2022

Speciation on a complex landscape; phylogeny and demography of Mexican Goodeid fish.

Understanding the phylogeographic history of a group and identifying the factors contributing to speciation is an important challenge in evolutionary biology. Vicariance has clearly played a major role in diversification across diverse groups of organisms, but how this interacts with intrinsic biological features such as changes in reproductive system or sexual selection is less well understood. The Goodeinae are a Mexican endemic group of live-bearing fish. Here, we develop genomic resources for species within the Goodeinae and use phylogenomic approaches to characterise their evolutionary history. We sequenced, assembled and annotated the genomes of four new Goodeinae genomes, including A. toweri, the only matrotrophic live-bearing fish without a trophotaenia in the group. We produced a phylogeny of the Goodeinae and estimate timings of species divergence. We determined the extent and timing of introgression between the species to assess if this may have occurred during an early radiation, or in more recent episodes of secondary contact. We also analyse patterns in the changes of effective population size for the species and examine the time course of expansion and decline. We used branch-site models to detect genome-wide positive selection across Goodeinae, and we specifically ask if this differs in A. toweri, where reversal of placental viviparity has recently occurred. We find that Goodeinae diverged rapidly, with reductions in effective population size after each split. Contrary to expectations, we find evidence of gene flow between geographically isolated species, suggesting vicariant speciation was supplemented by limited post-speciation gene flow, potentially as a result of river piracy. Genes under positive selection in the group are likely to be associated with the switch to live-bearing. Overall, our studies suggest that both volcanism driven vicariance and changes in reproductive mode influenced radiation in the Goodeinae.

evolutionary biology↗

bioRxiv2022

Genomic signatures associated with transitions to viviparity in Cyprinodontiformes

The transition from oviparity to viviparity has occurred independently over a hundred times across vertebrates, presenting a compelling case of phenotypic convergence. However, whether repeated, independent evolution of viviparity is driven by redeployment of similar genetic mechanisms and whether these leave a common genetic signature in genomic divergence remains unknown. Whilst investigations into the evolution of viviparity have demonstrated striking similarity among the genes and pathways involved across vertebrate groups, quantitative tests for genome-wide convergence provide ambivalent answers. Here, we investigate molecular convergence during independent transitions to viviparity across an order of ray-finned freshwater fish (Cyprinodontiformes). We assembled de novo and publicly-available genomes of viviparous and oviparous species to quantify molecular convergence across coding and non-coding regions. We found no evidence for an excess of molecular convergence in amino acid substitutions and rates of sequence divergence, implying independent genetic changes are associated with these transitions. However, statistical power and biological confounds (hemiplasy and introgression) could constrain our ability to detect correlated evolution. We therefore also identified candidate genes with potential signatures of molecular convergence in viviparous Cyprinodontiformes lineages. While we detected no evidence of positive or relaxed selection for these genes in branches associated with the evolution of viviparity in Cyprinodontiformes, motif-enrichment and gene ontology analyses suggest transcriptional changes associated with early morphogenesis, brain development and immunity occurred alongside the evolution of viviparity. Overall, our findings indicate that an excess of molecular convergence, at any level, is not strongly associated with independent transitions to viviparity in these fish.

evolutionary biology↗

bioRxiv2020

Within-population sperm competition intensity does not predict asymmetry in conpopulation sperm precedence

Postcopulatory sexual selection can generate coevolutionary arms races between the sexes resulting in the rapid coevolution of reproductive phenotypes. As traits affecting fertilisation success diverge between populations postmating prezygotic barriers to gene flow may evolve. Conspecific sperm precedence is a form of such isolation thought to evolve early during speciation yet has mostly been studied between species. Here we show conpopulation sperm precedence between Drosophila montana populations. Using genomic data to estimate divergence times and patterns of gene flow between populations, we show gene flow has played a considerable role during divergence. We find conpopulation sperm precedence is asymmetric and is concordant with asymmetry in non-competitive postmating prezygotic reproductive isolation. These results suggest these phenomena have a shared mechanism, but we show that this asymmetry is unrelated to the strength of postcopulatory sexual selection acting within populations. We tested whether overlapping foreign and coevolved ejaculates within the female reproductive tract altered fertilisation success but found no effect. Our results show that neither time since divergence nor sperm competitiveness predicts the strength of postmating prezygotic reproductive isolation. We suggest that divergence of postcopulatory phenotypes resulting in postmating prezygotic isolation is potentially driven by cryptic female choice, or mutation order divergence.

evolutionary biology↗