A pangenome framework uncovers the role of deletions in repeated evolution of cave-derived traits.

A pangenome framework uncovers the role of deletions in repeated evolution of cave-derived traits

The results reveal that recurrent deletion events have repeatedly contributed to the evolution of cave-adapted phenotypes and highlight deletions as underexplored contributors of adaptive evolution in a system characterized by trait loss.

Cave evolution on repeat: reuse of the same genomic regions across lineages of Astyanax mexicanus.

Similar traits repeatedly evolve across independent populations in response to similar environmental conditions. For many repeatedly evolved traits, it is unknown if populations evolve similar traits through the same or different genetic mechanisms. To address this question, we leveraged the Mexican tetra fish, Astyanax mexicanus, which has repeatedly evolved many traits including reduced sleep duration, eye degeneration, and metabolic shifts to accommodate limited nutrient availability. We defined whether shared or independent genetic architecture governs the repeated evolution of sleep loss, increased food consumption, early onset adipose deposition, and eye loss in different evolutionary origins of the cavefish phenotype by using Quantitative Trait Locus (QTL) mapping across three cave x surface F2 mapping populations. We found that, among the traits evaluated, eye loss exhibits the most genetic repeatability, with ∼43% of QTL shared across lineages. Sleep loss and metabolic traits (i.e., feeding, adiposity) were genetically less repeatable, with only ∼25-33% of QTL shared across lineages. Next, we explored whether QTL for metabolism, eye loss, and sleep traits in cavefish co-localize in the cavefish genome and are inherited together to facilitate potential cavefish adaptation. Although these traits have repeatedly co-evolved in cave populations, we did not find evidence for extensive genetic linkage among them. Overall, we found that genetic repeatability is a common feature in the repeated evolution of cave traits, the extent of genetic repeatability varies across cave traits, and there is little evidence for widespread colocalization of sleep, eye loss, and metabolic traits within the genome.

Ecotype-associated structural variants across multiple locally adapted Poeciliid fishes

Extreme environments provide powerful natural laboratories for studying evolutionary convergence across taxa. While convergent phenotypes frequently evolve in response to similar selective pressures, consistent molecular signatures at the nucleotide level are often elusive, potentially due to overlooked genetic variants such as structural variants. Here, we leverage recent advances in long-read sequencing and pangenome approaches to investigate the role of structural variants in repeated adaptation to toxic springs rich in hydrogen sulfide (H 2 S) across multiple independently evolved populations within the Poecilia mexicana species complex. We identified more than 99,000 structural variants over 50 base pairs in length, including insertions, deletions, duplications and inversions, using complementary graph- and read-based methods. We then integrated these with population genomic data and RNA-sequencing data to detect variants in highly differentiated regions between ecotypes and assess their functional impacts. Structural variants in both coding and regulatory regions were enriched in genes involved in sulfide metabolism and ion transport, including ethe1 , slc13a1 , and sqor . We found ecotype-specific structural variants in promoter and intronic regions of key detoxification genes that exhibited elevated expression in H 2 S-adapted populations. Our findings suggest that structural variation may contribute to adaptive phenotypes and should be considered in studies of genomic convergence.

Transposable element activity and polymorphisms drive structural variability within and between individuals in bivalves

Structural variants (SVs) represent one of the most abundant sources of genetic variation across eukaryotes, with transposable elements (TEs) standing out as primary contributors in their emergence. While sequencing advances have highlighted the central role of SVs in generating genomic diversity, their contribution to adaptive evolution remains critically understudied, particularly in non-model invertebrates. Bivalves represent an ideal study system in this context due to their highly dynamic genomes and adaptation to diverse environmental conditions. Here, we use oysters as a model system to characterize how SVs and TEs reshape their genome and promote local adaptation. To achieve this, we leverage four publicly available assemblies, and we re-analyzed a large-scale dataset of the Estuarine oyster ( Crassostrea ariakensis ) collected across a wide range of different temperature and salinity conditions. We explicitly account for strengths and limitations of SV-calling software and benchmark our results through simulations. We uncover pervasive within-individual structural variability, with up to 14% of the oyster genome being affected by heterozygous INDELs. The strong enrichment of TEs within these SVs is driven by a prevalence of insertions over deletions, reflecting population-level TE activity. Strikingly, both SVs and de novo TE insertions — driven by the concurrent mobilization of diverse TE families — segregate among C. ariakensis populations and contribute to genomic differentiation potentially associated with local adaptations. Our study establishes oysters as a powerful framework for SV research and provides empirical evidence that SVs are an active evolutionary force generating potentially adaptive genetic variation in a key lineage of ecologically and economically important bivalves.

From few to many: How non-model organisms’ genomics broadened our understanding of molecular evolution

Abstract For much of the 20th century, our understanding of genetics and evolution was predominantly shaped by intensive studies of a few model organisms such as Drosophila melanogaster, Caenorhabditis elegans, and Mus musculus. While these species provided fundamental insights, their laboratory-adapted characteristics potentially made them evolutionary outliers. The advent of next-generation sequencing technologies and sophisticated bioinformatic tools has increased accessibility of genomic research, enabling comprehensive studies of diverse non-model organisms across the tree of life. This expansion has substantially transformed our understanding of molecular evolution, revealing, for example, that convergent evolution operates through multiple mechanisms across different organizational levels, that speciation is a genomically heterogeneous process involving structural variants and adaptive introgression, and that genome architecture exhibits extensive variation in size, content, and organization. Using aquatic mammals as exemplars, we illustrate how comparative genomics of non-model species illuminates the molecular basis of convergent and divergent adaptations. This paradigm shift demonstrates that understanding evolution’s general principles and creative solutions requires embracing life’s full diversity.

Cross-species discovery of large structural variants reveals distinct evolutionary dynamics in primates