Biology subjects

Donny, A.

Publications and source records attributed to Donny, A..

3 recordsLinked to original sources

bioRxiv2023

Genome evolution is surprisingly predictable after initial hybridization

Over the past two decades, evolutionary biologists have come to appreciate that hybridization, or genetic exchange between distinct lineages, is remarkably common - not just in particular lineages but in taxonomic groups across the tree of life. As a result, the genomes of many modern species harbor regions inherited from related species. This observation has raised fundamental questions about the degree to which the genomic outcomes of hybridization are repeatable and the degree to which natural selection drives such repeatability. However, a lack of appropriate systems to answer these questions has limited empirical progress in this area. Here, we leverage independently formed hybrid populations between the swordtail fish Xiphophorus birchmanni and X. cortezi to address this fundamental question. We find that local ancestry in one hybrid population is remarkably predictive of local ancestry in another, demographically independent hybrid population. Applying newly developed methods, we can attribute much of this repeatability to strong selection in the earliest generations after initial hybridization. We complement these analyses with time-series data that demonstrates that ancestry at regions under selection has remained stable over the past [~]40 generations of evolution. Finally, we compare our results to the well-studied X. birchmannixX. malinche hybrid populations and conclude that deeper evolutionary divergence has resulted in stronger selection and higher repeatability in patterns of local ancestry in hybrids between X. birchmanni and X. cortezi.

evolutionary biology↗

bioRxiv2022

Selection-driven trait loss in independently evolved cavefish populations

Predicting the outcome of evolution is a central goal of modern biology, yet, determining the relative contributions of deterministic events (i.e., selection) and stochastic events (i.e., drift and mutation) to the evolutionary process remains a major challenge. Systems where the same traits have evolved repeatedly provide natural replication that can be leveraged to study the predictability of molecular evolution and the genetic basis of adaptation. Although mutational screens in the laboratory have demonstrated that a diversity of genetic mutations can produce phenocopies of one another, in natural systems, similar genetic changes frequently underly the evolution of phenotypes across independent lineages. This suggests a substantial role for constraint and determinism in evolution and supports the notion that there may be characteristics which make certain mutations more likely to contribute to phenotypic evolution. Here we use large-scale whole genome resequencing in the Mexican tetra, Astyanax mexicanus, to demonstrate that selection has played a primary role in repeated evolution of both trait loss and trait enhancement across independent cave lineages. We identify candidate genes underlying repeated adaptation to caves and infer the mode of repeated evolution, revealing that selection on standing genetic variation and de novo mutations both contribute substantially to repeated adaptation. Finally, we show that genes with evidence of repeated evolution have significantly longer coding regions compared to the rest of the genome, and this effect is most pronounced in genes evolving convergently via independent mutations. Importantly, our findings provide the first empirical support for the hypothesis that genes with larger mutational targets are more likely to be the substrate of repeated evolution and indicate that features of the novel cave environment may impact the rate at which mutations occur.

evolutionary biology↗

bioRxiv2019

Evidence for rapid phenotypic and behavioral change in a recently established cavefish population

Substantial morphological and behavioral shifts often accompany rapid environmental change, yet, little is known about the early stages of cave colonization. Relative to surface streams, caves are extreme environments with perpetual darkness and low nutrient availability. The Mexican tetra (Astyanax mexicanus), has repeatedly colonized caves throughout Mexico, suggesting an ability to adapt to these conditions. Here, we survey for phenotypic and behavioral differences between a surface population and a cave population of A. mexicanus that has recently colonized Honey Creek Cave, Comal County, Texas, likely within the last century. We found that fish from Honey Creek Cave and fish from Honey Creek surface populations differ significantly in morphological traits including length, coloration, body condition, eye size, and dorsal fin placement. Cavefish also exhibit an increased number of superficial neuromasts relative to surface fish. Behaviorally, cavefish consume fewer worms when trials are performed in both lighted and darkened conditions. Cavefish are more aggressive than surface fish and exhibit fewer behaviors associated with stress. Further in contrast to surface fish, cavefish prefer the edges to the center of an arena and are qualitatively more likely to investigate a novel object placed in the tank. While cavefish and surface fish were wild-caught and developmental environment likely play a role in shaping these differences, our work demonstrates morphological and behavioral shifts for Texas cavefish and offers an exciting opportunity for future work to explore the genetic and environmental contributions to early cave colonization.

animal behavior and cognition↗