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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.)

   Abstract 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. 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. (January 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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4. A Genomic Perspective on Species Delimitation

   https://doi.org/10.1146/annurev-ecolsys-102723-055311  

   Singhal, Sonal; Leaché, Adam D; Fujita, Matthew K; Cadena, Carlos Daniel; Zapata, Felipe (November 2025, Annual Review of Ecology, Evolution, and Systematics)

   Genomic species delimitation is transforming how we understand and define species by enabling a process-oriented and efficient approach to identifying species boundaries. This review outlines the two key steps in genomic species delimitation: (a) discovering species-level units and (b) assessing their validity. Validity can be evaluated by a diversity of approaches, including applying the multispecies coalescent to delineate the population–species boundary and using estimated gene flow as a proxy for reproductive isolation. We illustrate the utility of these methods across the tree of life through a comprehensive review of published articles and case studies on birds, siphonophores, and bacteria. Despite the many benefits of genomic species delimitation, challenges remain. In particular, genomic divergence does not always accurately reflect ecological divergence and reproductive barriers, and genome heterogeneity can complicate the overall understanding of genetic divergence. We discuss these challenges and potential solutions. 

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5. Diverse Evolution in 111 Plant Genomes Reveals Purifying and Dosage Balancing Selection Models for F-Box Genes

   https://doi.org/10.3390/ijms22020871  

   Hua, Zhihua (January 2021, International Journal of Molecular Sciences)

   The F-box proteins function as substrate receptors to determine the specificity of Skp1-Cul1-F-box ubiquitin ligases. Genomic studies revealed large and diverse sizes of the F-box gene superfamily across plant species. Our previous studies suggested that the plant F-box gene superfamily is under genomic drift evolution promoted by epigenomic programming. However, how the size of the superfamily drifts across plant genomes is currently unknown. Through a large-scale genomic and phylogenetic comparison of the F-box gene superfamily covering 110 green plants and one red algal species, I discovered four distinct groups of plant F-box genes with diverse evolutionary processes. While the members in Clusters 1 and 2 are species/lineage-specific, those in Clusters 3 and 4 are present in over 46 plant genomes. Statistical modeling suggests that F-box genes from the former two groups are skewed toward fewer species and more paralogs compared to those of the latter two groups whose presence frequency and sizes in plant genomes follow a random statistical model. The enrichment of known Arabidopsis F-box genes in Clusters 3 and 4, along with comprehensive biochemical evidence showing that Arabidopsis members in Cluster 4 interact with the Arabidopsis Skp1-like 1 (ASK1), demonstrates over-representation of active F-box genes in these two groups. Collectively, I propose purifying and dosage balancing selection models to explain the lineage/species-specific duplications and expansions of F-box genes in plant genomes. The purifying selection model suggests that most, if not all, lineage/species-specific F-box genes are detrimental and are thus kept at low frequencies in plant genomes. 

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