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1. Population Genetics of Reproductive Genes in Haplodiploid Species

   https://doi.org/10.1093/gbe/evac070  

   Dapper, Amy L. ; Slater, Garett P. ; Shores, Katherynne ; Harpur, Brock A. ( May 2022 , Genome Biology and Evolution)

   Mank, Judith (Ed.)

   Abstract Many animal species are haplodiploid: their fertilized eggs develop into diploid females and their unfertilized eggs develop into haploid males. The unique genetic features of haplodiploidy raise the prospect that these systems can be used to disentangle the population genetic consequences of haploid and diploid selection. To this end, sex-specific reproductive genes are of particular interest because, while they are shared within the same genome, they consistently experience selection in different ploidal environments. However, other features of these genes, including sex-specific expression and putative involvement in postcopulatory sexual selection, are potentially confounding factors because they may also impact the efficacy of selection asymmetrically between the sexes. Thus, to properly interpret evolutionary genomic patterns, it is necessary to generate a null expectation for the relative amount of polymorphism and divergence we expect to observe among sex-specific genes in haplodiploid species, given differences in ploidal environment, sex-limited expression, and their potential role in sexual selection. Here, we derive the theoretical expectation for the rate of evolution of sex-specific genes in haplodiploid species, under the assumption that they experience the same selective environment as genes expressed in both sexes. We find that the null expectation is that reproductive genes evolve more rapidly than constitutively expressed genes in haplodiploid genomes. However, despite the aforementioned differences, the null expectation does not differ between male- and female-specific reproductive genes, when assuming additivity. Our theoretical results provide an important baseline expectation that should be used in molecular evolution studies comparing rates of evolution among classes of genes in haplodiploid species. 

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2. High-Quality Reference Genome for an Arid-Adapted Mammal, the Banner-Tailed Kangaroo Rat ( Dipodomys spectabilis )

   https://doi.org/10.1093/gbe/evac005  

   Harder, Avril M ; Walden, Kimberly K ; Marra, Nicholas J ; Willoughby, Janna R ( January 2022 , Genome Biology and Evolution)

   Fraser, Bonnie (Ed.)

   Kangaroo rats in the genus Dipodomys are found in a variety of habitat types in western North America, including deserts, arid and semiarid grasslands, and scrublands. Many Dipodomys species are experiencing strong population declines due to increasing habitat fragmentation, with two species listed as federally endangered in the United States. The precarious state of many Dipodomys populations, including those occupying extreme environments, make species of this genus valuable subjects for studying the impacts of habitat degradation and fragmentation on population genomic patterns and for characterizing the genomic bases of adaptation to harsh conditions. To facilitate exploration of such questions, we assembled and annotated a reference genome for the banner-tailed kangaroo rat (Dipodomys spectabilis) using PacBio HiFi sequencing reads, providing a more contiguous genomic resource than two previously assembled Dipodomys genomes. Using the HiFi data for D. spectabilis and publicly available sequencing data for two other Dipodomys species (Dipodomys ordii and Dipodomys stephensi), we demonstrate the utility of this new assembly for studies of congeners by conducting inference of historic effective population sizes (Ne) and linking these patterns to the species’ current extinction risk statuses. The genome assembly presented here will serve as a valuable resource for population and conservation genomic studies of Dipodomys species, comparative genomic research within mammals and rodents, and investigations into genomic adaptation to extreme environments and changing landscapes.

    

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3. Are Genomic Updates of Well-Studied Species Worth the Investment for Conservation? A Case Study of the Critically Endangered Magdalena River Turtle

   https://doi.org/10.1093/jhered/esab063  

   Gallego-García, Natalia ; Caballero, Susana ; Shaffer, H. Bradley ; Ruane, ed., Sara ( October 2021 , Journal of Heredity)

   As genomic-scale data sets become economically feasible for most organisms, a key question for conservation biology is whether the increased resolution offered by new genomic approaches justifies repeating earlier studies based on traditional markers, rather than investing those same time and monetary resources in less-known species. Genomic studies offer clear advantages when the objective is to identify adaptive loci that may be critical to conservation policy-makers. However, the answer is far less certain for the population and landscape studies based on neutral loci that dominate the conservation genetics research agenda. We used Restriction-site Associated DNA sequencing (RADseq) to revisit earlier molecular studies of the IUCN Critically Endangered Magdalena River turtle (Podocnemis lewyana), documenting the conservation insights gained by increasing the number of neutral markers by several orders of magnitude. Earlier research indicated that P. lewyana has the lowest genetic diversity known for any chelonian, and little or no population differentiation among independent rivers. In contrast, the RADseq data revealed discrete population structure with isolation-by-distance within river segments and identified precise population breaks clearly delineating management units. It also confirmed that the species does not have extremely low heterozygosity and that effective population sizes are probably sufficient to maintain long-term evolutionary potential. Contrary to earlier inferences from more limited population genetic markers, our genomic data suggest that management strategies should shift from active genetic rescue to more passive protection without extreme interventions. We conclude with a list of examples of conservation studies in other vertebrates indicating that for many systems a genomic update is worth the investment.

    

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4. Reciprocal transplant gardens as gold standard to detect local adaptation in grassland species: New opportunities moving into the 21st century

   https://doi.org/10.1111/1365-2745.13695  

   Johnson, Loretta C. ; Galliart, Matthew B. ; Alsdurf, Jacob D. ; Maricle, Brian R. ; Baer, Sara G. ; Bello, Nora M. ; Gibson, David J. ; Smith, Adam B. ( July 2021 , Journal of Ecology)

   Local adaptation is a fundamental phenomenon in evolutionary biology, with relevance to formation of ecotypes, and ultimately new species, and application to restoration and species’ response to climate change. Reciprocal transplant gardens, a common garden in which ecotypes are planted among home and away habitats, are the gold standard to detect local adaptation in populations.

   This review focuses on reciprocal transplant gardens to detect local adaptation, especially in grassland species beginning with early seminal studies of grass ecotypes. Fast forward more than half a century, reciprocal gardens have moved into the genomic era, in which the genetic underpinnings of ecotypic variation can now be uncovered. Opportunities to combine genomic and reciprocal garden approaches offer great potential to shed light on genetic and environmental control of phenotypic variation. Our decadal study of adaptation in a dominant grass across the precipitation gradient of the US Great Plains combined genomic approaches and realistic community settings to shed light on controls over phenotype.

   Common gardens are not without limitations and challenges. A survey of recent studies indicated the modal study uses a tree species, three source sites and one growing site, focuses on one species growing in a monoculture, lasts 3 years, and does not use other experimental manipulations and rarely employs population genetic tools. Reciprocal transplant gardens are even more uncommon, accounting for only 39% of the studies in the literature survey with the rest occurring at a single common site. Reciprocal transplant gardens offer powerful windows into local adaptation when (a) placed across wide environmental gradients to encompass the species’ range; (b) conducted across timespans adequate for detecting responses; (c) employing selection studies among competing ecotypes in community settings and (d) combined with measurements of form and function which ultimately determine success in home and away environments.

   Synthesis. Reciprocal transplant gardens have been one of the foundations in evolutionary biology for the study of adaptation for the last century, and even longer in Europe. Moving forward, reciprocal gardens of foundational non‐model species, combined with genomic analyses and incorporation of biotic factors, have the potential to further revolutionize evolutionary biology. These field experiments will help to predict and model response to climate change and inform restoration practices.

    

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5. The practice and promise of temporal genomics for measuring evolutionary responses to global change

   https://doi.org/10.1111/1755-0998.13789  

   Clark, René D. ; Catalano, Katrina A. ; Fitz, Kyra S. ; Garcia, Eric ; Jaynes, Kyle E. ; Reid, Brendan N. ; Sawkins, Allyson ; Snead, Anthony A. ; Whalen, John C. ; Pinsky, Malin L. ( April 2023 , Molecular Ecology Resources)

   Understanding the evolutionary consequences of anthropogenic change is imperative for estimating long‐term species resilience. While contemporary genomic data can provide us with important insights into recent demographic histories, investigating past change using present genomic data alone has limitations. In comparison, temporal genomics studies, defined herein as those that incorporate time series genomic data, utilize museum collections and repeated field sampling to directly examine evolutionary change. As temporal genomics is applied to more systems, species and questions, best practices can be helpful guides to make the most efficient use of limited resources. Here, we conduct a systematic literature review to synthesize the effects of temporal genomics methodology on our ability to detect evolutionary changes. We focus on studies investigating recent change within the past 200 years, highlighting evolutionary processes that have occurred during the past two centuries of accelerated anthropogenic pressure. We first identify the most frequently studied taxa, systems, questions and drivers, before highlighting overlooked areas where further temporal genomic studies may be particularly enlightening. Then, we provide guidelines for future study and sample designs while identifying key considerations that may influence statistical and analytical power. Our aim is to provide recommendations to a broad array of researchers interested in using temporal genomics in their work.

    

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