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1. Balancing Inbreeding and Outbreeding Risks to Inform Translocations Throughout the Range of an Imperiled Darter

   https://doi.org/10.1111/eva.70088  

   Reid, Brendan N; Hofmeier, Jordan; Crockett, Harry; Fitzpatrick, Ryan; Waters, Ryan; Fitzpatrick, Sarah W (March 2025, Evolutionary Applications)

   ABSTRACT Restoring connectivity via assisted migration is a useful but currently underused approach for maintaining genetic diversity and preventing extirpations of threatened species. The use of assisted migration as a conservation strategy may be limited by the difficulty of balancing the benefits of reconnecting populations (including reduced inbreeding depression and increased adaptive capacity) with the perceived risk of outbreeding depression, which requires comprehensive knowledge of the landscape of adaptive, neutral, deleterious, and structural variation across a species' range. Using a combination of reduced‐representation and whole‐genome sequencing, we characterized genomic diversity and differentiation for the Arkansas Darter (Etheostoma cragini) across its range in the Midwestern US. We found strong population structure and large differences in genetic diversity and effective population sizes across drainages. The strength of genetic isolation by river distance differed among drainages, with landscape type surrounding streams and impoundments also contributing to genetic isolation. Despite low effective population sizes in some populations, there was surprisingly little evidence for recent inbreeding (based on the absence of long runs of homozygosity) or for elevated levels of deleterious variation in smaller populations. Considering neutral, adaptive, deleterious, and structural variation allowed us to identify several potential recipient populations that may benefit from translocations and potential donor sites throughout the range. Planning translocation strategies intended for restored connectivity and possible genetic rescue at earlier stages in species decline will likely increase the probability of retaining genetic diversity and population persistence over the long term while minimizing risks associated with translocation. 

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2. Population differentiation and structural variation in the Manduca sexta genome across the United States

   https://doi.org/10.1093/g3journal/jkac047  

   Mongue, Andrew J; Kawahara, Akito Y (February 2022, G3 Genes|Genomes|Genetics)

   Whitehead, A (Ed.)

   Abstract Many species that are extensively studied in the laboratory are less well characterized in their natural habitat, and laboratory strains represent only a small fraction of the variation in a species’ genome. Here we investigate genomic variation in 3 natural North American populations of an agricultural pest and a model insect for many scientific disciplines, the tobacco hornworm (Manduca sexta). We show that hornworms from Arizona, Kansas, and North Carolina are genetically distinct, with Arizona being particularly differentiated from the other 2 populations using Illumina whole-genome resequencing. Peaks of differentiation exist across the genome, but here, we focus in on the most striking regions. In particular, we identify 2 likely segregating inversions found in the Arizona population. One inversion on the Z chromosome may enhance adaptive evolution of the sex chromosome. The larger, 8 Mb inversion on chromosome 12 contains a pseudogene which may be involved in the exploitation of a novel hostplant in Arizona, but functional genetic assays will be required to support this hypothesis. Nevertheless, our results reveal undiscovered natural variation and provide useful genomic data for both pest management and evolutionary genetics of this insect species. 

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3. A genome assembly of the California poppy, Eschscholzia californica

   https://doi.org/10.1093/jhered/esaf058  

   Nguyen, Peter T; Escalona, Merly; Ryan, Elizabeth; Miller, Courtney; Marimuthu, Mohan_P A; Fairbairn, Colin W; Seligmann, William; Chumchim, Noravit; Nguyen, Oanh; Toffelmier, Erin; et al (August 2025, Journal of Heredity)

   Abstract The California poppy (Eschscholzia californica), a native wildflower of western North America and the state wildflower of California, is characterized by extensive ecological variation and adaptation to diverse climatic conditions. Its broad geographic range and adaptability make it a valuable model for studying how plants respond to changing environmental conditions. Here, we present an updated, near-chromosome-level genome assembly for E. californica, developed as part of the California Conservation Genomics Project. This assembly spans 0.401 Gb and represents an advancement over previous versions, with a scaffold N50 of 66.4 Mb, a contig N50 of 11.8 Mb, and BUSCO completeness of 99.2%, providing near-complete genomic coverage. The enhanced genome assembly described here facilitates precise whole-genome resequencing, providing insights into genetic diversity and gene flow between populations—key factors in understanding the adaptive mechanisms that will support the species’ survival in the face of environmental challenges. 

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4. Successful Invasion Into New Environments Without Evidence of Rapid Adaptation by a Predatory Marine Gastropod

   https://doi.org/10.1111/mec.17575  

   Bentley, Blair P; Cheng, Brian S; Brennan, Reid S; Swenson, John D; Adkins, Jamie L; Villeneuve, Andrew R; Komoroske, Lisa M (December 2024, Molecular Ecology)

   ABSTRACT Invasive species with native ranges spanning strong environmental gradients are well suited for examining the roles of selection and population history in rapid adaptation to new habitats, providing insight into potential evolutionary responses to climate change. The Atlantic oyster drill (Urosalpinx cinerea) is a marine snail whose native range spans the strongest coastal latitudinal temperature gradient in the world, with invasive populations established on the US Pacific coast. Here, we leverage this system using genome‐wide SNPs and environmental data to examine invasion history and identify genotype–environment associations indicative of local adaptation across the native range, and then assess evidence for allelic frequency shifts that would signal rapid adaptation within invasive populations. We demonstrate strong genetic structuring among native regions which aligns with life history expectations, identifying southern New England as the source of invasive populations. Then, we identify putatively thermally adaptive loci across the native range but find no evidence of allele frequency shifts in invasive populations that suggest rapid adaptation to new environments. Our results indicate that while these loci may underpin local thermal adaptation in their native range, selection is relaxed in invasive populations, perhaps due to complex polygenic architecture underlying thermal traits and/or standing capacity for phenotypic plasticity. Given the prolific invasion ofUrosalpinx, our study suggests population success in new environments is influenced by factors other than selection on standing genetic variation that underlies local adaptation in the native range and highlights the importance of considering population history and environmental selection pressures when evaluating adaptive capacity. 

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5. Evolutionary Physiology and Genomics in the Highly Adaptable Killifish (Fundulus heteroc

   https://doi.org/10.1002/cphy.c190004  

   Crawford, D. L. Schulte (April 2020, Comprehensive physiology)

   By investigating evolutionary adaptations that change physiological functions, we can enhance our understanding of how organisms work, the importance of physiological traits, and the genes that influence these traits. This approach of investigating the evolution of physiological adaptation has been used with the teleost fish Fundulus heteroclitus and has produced insights into (i) how protein polymorphisms enhance swimming and development; (ii) the role of equilibrium enzymes in modulating metabolic flux; (iii) how variation in DNA sequences and mRNA expression patterns mitigate changes in temperature, pollution, and salinity; and (iv) the importance of nuclear-mitochondrial genome interactions for energy metabolism. Fundulus heteroclitus provides so many examples of adaptive evolution because their local population sizes are large, they have significant standing genetic variation, and they experience large ranges of environmental conditions that enhance the likelihood that adaptive evolution will occur. Thus, F. heteroclitus research takes advantage of evolutionary changes associated with exposure to diverse environments, both across the North American Atlantic coast and within local habitats, to contrast neutral versus adaptive divergence. Based on evolutionary analyses contrasting neutral and adaptive evolution in F. heteroclitus populations, we conclude that adaptive evolution can occur readily and rapidly, at least in part because it depends on large amounts of standing genetic variation among many genes that can alter physiological traits. These observations of polygenic adaptation enhance our understanding of how evolution and physiological adaptation progresses, thus informing both biological and medical scientists about genotype-phenotype relationships 

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