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1. Data from: Experimental studies of adaptation in Clarkia xantiana. III. Phenotypic selection across a subspecies border

   https://doi.org/10.5061/dryad.b631d  

   Anderson, Jill Theresa; Eckhart, Vincent M; Geber, Monica Ann (January 2015, Dryad)

   Sister taxa with distinct phenotypes often occupy contrasting environments in parapatric ranges, yet we generally do not know whether trait divergence reflects spatially-varying selection. We conducted a reciprocal transplant experiment to test whether selection favors “native phenotypes” in two subspecies of Clarkia xantiana (Onagraceae), an annual plant in California. For four quantitative traits that differ between subspecies, we estimated phenotypic selection in subspecies’ exclusive ranges and their contact zone in two consecutive years. We predicted that in the arid, pollinator-scarce eastern region, selection favors phenotypes of the native subspecies parviflora: small leaves, slow leaf growth, early flowering, and diminutive flowers. In the wetter, pollinator-rich, western range of subspecies xantiana, we expected selection for opposite phenotypes. We investigated pollinator contributions to selection by comparing naturally-pollinated and pollen-supplemented individuals. For reproductive traits and for subspecies xantiana, selection generally matched expectations. The contact zone sometimes showed distinctive selection, and in ssp. parviflora selection sometimes favored non-native phenotypes. Pollinators influenced selection on flowering time but not on flower size. Little temporal variation in selection occurred, possibly because of plastic trait responses across years. Though there were exceptions and some causes of selection remain obscure, phenotypic differentiation between subspecies appears to reflect spatially variable selection. 

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2. Patterns of Gene Family Evolution and Selection Across Daphnia

   https://doi.org/10.1002/ece3.71453  

   Murray, Connor S; Bergland, Alan O (May 2025, Ecology and Evolution)

   ABSTRACT Gene family expansion underlies a host of biological innovations across the tree of life. Understanding why specific gene families expand or contract requires comparative genomic investigations clarifying further how species adapt in the wild. This study investigates the gene family change dynamics within several species ofDaphnia, a group of freshwater microcrustaceans that are insightful model systems for evolutionary genetics' research. We employ comparative genomics approaches to understand the forces driving gene evolution and draw upon candidate gene families that change gene numbers acrossDaphnia. Our results suggest that genes related to stress responses and glycoproteins generally expand across taxa, and we investigate evolutionary hypotheses of adaptation that may underpin expansions. Through these analyses, we shed light on the interplay between gene expansions and selection within other ecologically relevant stress response gene families. While we show generalities in gene family turnover in genes related to stress response (i.e., DNA repair mechanisms), most gene family evolution is driven in a species‐specific manner. Additionally, while we show general trends toward positive selection within some expanding gene families, many genes are not under selection, highlighting the complexity of diversification and evolution withinDaphnia. Our research enhances the understanding of individual gene family evolution withinDaphniaand provides a case study of ecologically relevant genes prone to change. 

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3. Tissue topography steers migrating Drosophila border cells

   https://doi.org/10.1126/science.aaz4741  

   Dai, Wei; Guo, Xiaoran; Cao, Yuansheng; Mondo, James A.; Campanale, Joseph P.; Montell, Brandon J.; Burrous, Haley; Streichan, Sebastian; Gov, Nir; Rappel, Wouter-Jan; et al (November 2020, Science)

   Moving cells can sense and respond to physical features of the microenvironment; however, in vivo, the significance of tissue topography is mostly unknown. Here, we usedDrosophilaborder cells, an established model for in vivo cell migration, to study how chemical and physical information influences path selection. Although chemical cues were thought to be sufficient, live imaging, genetics, modeling, and simulations show that microtopography is also important. Chemoattractants promote predominantly posterior movement, whereas tissue architecture presents orthogonal information, a path of least resistance concentrated near the center of the egg chamber. E-cadherin supplies a permissive haptotactic cue. Our results provide insight into how cells integrate and prioritize topographical, adhesive, and chemoattractant cues to choose one path among many. 

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4. Positive Selection Drives cis- regulatory Evolution Across the Threespine Stickleback Y Chromosome

   https://doi.org/10.1093/molbev/msae020  

   Shaw, Daniel E; Naftaly, Alice Shanfelter; White, Michael A (February 2024, Molecular Biology and Evolution)

   Wittkopp, Patricia (Ed.)

   Abstract Allele-specific gene expression evolves rapidly on heteromorphic sex chromosomes. Over time, the accumulation of mutations on the Y chromosome leads to widespread loss of gametolog expression, relative to the X chromosome. It remains unclear if expression evolution on degrading Y chromosomes is primarily driven by mutations that accumulate through processes of selective interference, or if positive selection can also favor the down-regulation of coding regions on the Y chromosome that contain deleterious mutations. Identifying the relative rates of cis-regulatory sequence evolution across Y chromosomes has been challenging due to the limited number of reference assemblies. The threespine stickleback (Gasterosteus aculeatus) Y chromosome is an excellent model to identify how regulatory mutations accumulate on Y chromosomes due to its intermediate state of divergence from the X chromosome. A large number of Y-linked gametologs still exist across 3 differently aged evolutionary strata to test these hypotheses. We found that putative enhancer regions on the Y chromosome exhibited elevated substitution rates and decreased polymorphism when compared to nonfunctional sites, like intergenic regions and synonymous sites. This suggests that many cis-regulatory regions are under positive selection on the Y chromosome. This divergence was correlated with X-biased gametolog expression, indicating the loss of expression from the Y chromosome may be favored by selection. Our findings provide evidence that Y-linked cis-regulatory regions exhibit signs of positive selection quickly after the suppression of recombination and allow comparisons with recent theoretical models that suggest the rapid divergence of regulatory regions may be favored to mask deleterious mutations on the Y chromosome. 

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5. Correlated responses to selection across diverse environments during experimental evolution of Tetrahymena thermophila

   https://doi.org/10.1002/ece3.11395  

   Tarkington, Jason; Zufall, Rebecca_A (July 2024, Ecology and Evolution)

   Abstract Correlated responses to selection have long been observed and studied; however, it remains unclear when they will arise, and in what direction. To contribute to a growing understanding of correlated responses to selection, we used experimental evolution of the ciliateTetrahymena thermophilato study direct and correlated responses in a variety of different environmental conditions. One experiment focused on adaptation to two different temperatures and the correlated responses across temperatures. Another experiment used inhibitory concentrations of a variety of compounds to test direct and correlated responses to selection. We found that all populations adapted to the environments in which they evolved. We also found many cases of correlated evolution across environments; few conditions resulted in trade‐offs and many resulted in a positive correlated response. Surprisingly, in many instances, the correlated response was of a larger magnitude than the direct response. We find that ancestral fitness predicts the extent of adaptation, consistent with diminishing returns epistasis. Unexpectedly, we also find that this pattern of diminishing returns holds across environments regardless of the environment in which evolution occurs. We also found that the correlated response is asymmetric across environments, that is, the fitness of a population evolved in one environment and assayed in a second was inversely related to the fitness of a population evolved in the second environment and assayed in the first. These results support the notion that positive correlated responses to selection across environments are frequent, and worth further study. 

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