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1. Temporal genomics reveal a century of genomic diversity shifts across a biodiversity hotspot avian assemblage

   https://doi.org/10.1093/gbe/evaf163  

   Manthey, Joseph D; Settlecowski, Amie E; Meheretu, Yonas; Behrends, Garrett J; Bourgeois, Yann; Campillo, Luke C; Boissinot, Stéphane; Marks, Ben D (August 2025, Genome Biology and Evolution)

   Gossmann, Toni (Ed.)

   Abstract Biodiversity has experienced tremendous shifts in community, species, and genetic diversity during the Anthropocene. Understanding temporal diversity shifts is especially critical in biodiversity hotspots, i.e., regions that are exceptionally biodiverse and threatened. Here, we use museomics and temporal genomics approaches to quantify temporal shifts in genomic diversity in an assemblage of eight generalist highland bird species from the Ethiopian Highlands (part of the Eastern Afromontane Biodiversity Hotspot). With genomic data from contemporary and historical samples, we demonstrate an assemblage-wide trend of increased genomic diversity through time, potentially due to improved habitat connectivity within highland regions. Genomic diversity shifts in these generalist species contrast with general trends of genomic diversity declines in specialist or imperiled species. In addition to genetic diversity shifts, we found an assemblage-wide trend of decreased realized mutational load, indicative of overall trends for potentially deleterious variation to be masked or selectively purged. Across this avian assemblage, we also show that shifts in population genomic structure are idiosyncratic, with species-specific trends. These results are in contrast with other charismatic and imperiled African taxa that have largely shown strong increases in population genetic structure over the recent past. This study highlights that not all taxa respond the same to environmental change, and generalists, in some cases, may even respond positively. Future comparative conservation genomics assessments on species groups or assemblages with varied natural history characteristics would help us better understand how diverse taxa respond to anthropogenic landscape changes. 

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2. Resurrection genomics provides molecular and phenotypic evidence of rapid adaptation to salinization in a keystone aquatic species

   https://doi.org/10.1073/pnas.2217276120  

   Wersebe, Matthew J.; Weider, Lawrence J. (February 2023, Proceedings of the National Academy of Sciences)

   Ecologists and evolutionary biologists are increasingly cognizant of rapid adaptation in wild populations. Rapid adaptation to anthropogenic environmental change is critical for maintaining biodiversity and ecosystems services into the future. Anthropogenic salinization of freshwater ecosystems is quickly emerging as a primary threat, which is well documented in the northern temperate ecoregion. Specifically, many northern temperate lakes have undergone extensive salinization because of urbanization and the associated increase in impervious surfaces causing runoff, and the extensive use of road deicing salts (e.g., NaCl). It remains unclear whether increasing salinization will lead to extirpation of species from these systems. Using a “resurrection genomics” approach, we investigated whether the keystone aquatic herbivore,Daphnia pulicaria,has evolved increased salinity tolerance in a severely salinized lake located in Minnesota, USA. Whole-genome resequencing of 54Daphniaclones from the lake and hatched from resting eggs that represent a 25-y temporal contrast demonstrates that many regions of the genome containing genes related to osmoregulation are under selection in the study population. Tolerance assays of clones revealed that the most recent clones are more tolerant to salinity than older clones; this pattern is concomitant with the temporal pattern of stabilizing salinity in this lake. Together, our results demonstrate that keystone species such asDaphniacan rapidly adapt to increasing freshwater salinization. Further, our results indicate that rapid adaptation to salinity may allow lakeDaphniapopulations to persist in the face of anthropogenic salinization maintaining the food webs and ecosystem services they support despite global environmental change. 

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3. 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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4. Ion Transporter Gene Families as Physiological Targets of Natural Selection During Salinity Transitions in a Copepod

   https://doi.org/10.1152/physiol.00009.2021  

   Lee, Carol Eunmi (November 2021, Physiology)

   Salinity is a key factor that structures biodiversity on the planet. With anthropogenic change, such as climate change and species invasions, many populations are facing rapid and dramatic changes in salinity throughout the globe. Studies on the copepod Eurytemora affinis species complex have implicated ion transporter gene families as major loci contributing to salinity adaptation during freshwater invasions. Laboratory experiments and population genomic surveys of wild populations have revealed evolutionary shifts in genome-wide gene expression and parallel genomic signatures of natural selection during independent salinity transitions. Our results suggest that balancing selection in the native range and epistatic interactions among specific ion transporter paralogs could contribute to parallel freshwater adaptation. Overall, these studies provide unprecedented insights into evolutionary mechanisms underlying physiological adaptation during rapid salinity change. 

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5. A lizard is never late: Squamate genomics as a recent catalyst for understanding sex chromosome and microchromosome evolution

   https://doi.org/10.1093/jhered/esad023  

   Pinto, Brendan J; Gamble, Tony; Smith, Chase H; Wilson, Melissa A (April 2023, Journal of Heredity)

   Blackmon, Heath (Ed.)

   Abstract In 2011, the first high-quality genome assembly of a squamate reptile (lizard or snake) was published for the green anole. Dozens of genome assemblies were subsequently published over the next decade, yet these assemblies were largely inadequate for answering fundamental questions regarding genome evolution in squamates due to their lack of contiguity or annotation. As the “genomics age” was beginning to hit its stride in many organismal study systems, progress in squamates was largely stagnant following the publication of the green anole genome. In fact, zero high-quality (chromosome-level) squamate genomes were published between the years 2012 and 2017. However, since 2018, an exponential increase in high-quality genome assemblies has materialized with 24 additional high-quality genomes published for species across the squamate tree of life. As the field of squamate genomics is rapidly evolving, we provide a systematic review from an evolutionary genomics perspective. We collated a near-complete list of publicly available squamate genome assemblies from more than half-a-dozen international and third-party repositories and systematically evaluated them with regard to their overall quality, phylogenetic breadth, and usefulness for continuing to provide accurate and efficient insights into genome evolution across squamate reptiles. This review both highlights and catalogs the currently available genomic resources in squamates and their ability to address broader questions in vertebrates, specifically sex chromosome and microchromosome evolution, while addressing why squamates may have received less historical focus and has caused their progress in genomics to lag behind peer taxa. 

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