Catalpa huangxin, a distinctive taxon within the genus Catalpa in China, is valued for its ornamental beauty and durable yellow heartwood. However, its wild populations are declining due to climate change and human activities, posing urgent conservation challenges. The unclear genetic diversity and population structure further complicate its protection and breeding efforts. To address these issues, this study employed RAD-seq to analyze 198 samples, including 169 C. huangxin, 24 Catalpa duclouxii, and 5 Catalpa ovata (outgroup), focusing on phylogeny, genetic diversity, gene flow, and dispersal routes. The results show that C. huangxin and C. duclouxii are distinct but closely related taxa. C. huangxin was divided into five subgroups with moderate genetic diversity (He = 0.2935, Ho = 0.4401). Subgroup 5 exhibited the highest diversity, but significant genetic differentiation (FST = 0.1983) was observed between subgroups, limiting gene flow and adaptation. Human activities, reproductive traits, and habitat fragmentation contribute to this differentiation. The study recommends in-situ conservation of genetically diverse subgroups, particularly Subgroup 5, artificial population restoration, germplasm banks, and expansion of its current distribution range. These strategies are essential for C. huangxin's protection and genetic improvement, offering valuable insights for the conservation of other species with similarly restricted distributions.

New mutations are the source of all genetic variation, including variation affecting quantitative phenotypes. Here, in order to evaluate the impact of mutations on the integrated function of entire tissues, we estimated the mutational variation (Vm) introduced by new mutations each generation for gene expression. Using deep transcriptome sequencing, we estimated Vm for brain and liver gene expression in individuals from a mutation accumulation experiment (MA) with the C3H inbred mouse strain. Expression was measured in 200 mice from 40 MA lines maintained for 15-19 generations and in 100 mice from 20 control lines. The control lines allow us to account for environmental variation in gene expression. Based on the difference in the between-line variance component for expression between the MA lines and controls, the median Vm in the brain was 2.22 × 10-3, while in the liver it was markedly lower (Vm = 0.35 × 10-3). A greater proportion of genes also showed Vm values statistically higher than zero in the brain (29%) than in the liver (7%). These differences could be due to a higher rate of mutation-driven transcriptome evolution in the brain compared to the liver, which we discuss in the context of differences in the mutational target, distribution of mutation effects, cellular complexity, and estimation biases. A differential expression analysis revealed minimal contributions to Vm from the subset of genes that have significant variation in expression. This indicates that most new mutations exert small effects on gene expression and go undetected in differential expression analyses.

Duplications and concerted evolution of control regions (CRs) in animal mitogenomes have been reported across diverse taxa, yet the tempo and mechanism of gene conversion remain poorly understood. Here, we assembled the complete mitochondrial genome of the western Indian ricefish Oryzias setnai and found that the CR is duplicated. Comparative analysis of CR1 and CR2 sequences across individuals sampled throughout the species' range revealed that they are identical in most individuals, and differ by only one or two mutations in the rest-indicating recent and ongoing concerted evolution. We estimated that gene conversion events occur at a rapid pace, on the order of once every 1000 years or less. Using both short- and long-read amplicon sequencing, we directly detected a substantial number of recombinant mitogenome molecules resulting from homologous recombination between CR paralogues. This provides the first clear evidence that homologous recombination is the mechanism driving mitochondrial gene conversion. Our findings challenge the prevailing view that recombination in animal mitochondria is exceedingly rare, and demonstrate that mitogenome recombination can occur routinely in natural populations.

Gene duplication and loss play an important role in the evolution of the major histocompatibility complex (MHC). Variations in copy number and sequence diversity of MHC genes can have significant fitness consequences. Here, we characterized both MHC class I and class II genes in a group of parrots-lovebirds (Agapornis spp.) using cloning and sequencing, quantitative PCR, and depth-of-coverage (DoC) analysis with whole-genome re-sequencing data. We identified copy number variation in MHC class II genes, with A. roseicollis having a single MHCIIB gene copy, whereas A. canus possesses at least three gene copies. Conversely, the copy number of class I genes is invariable, with only one copy identified in each Agapornis species. Phylogenetic reconstructions revealed both concerted evolution and trans-species polymorphism of MHC genes. In both MHC class I and II genes, sequences from the recently diverged eye-ringed species (e.g., A. fischeri, A. personatus, and A. nigrigenis) and their sister species A. roseicollis showed an intercalating pattern with no species-specific clustering, consistent with trans-species polymorphism. In contrast, sequences from the early-diverged species (e.g., A. canus and A. pullarius) clustered by species, which is typical for avian MHC genes undergoing concerted evolution. The pattern of MHC copy number variation and modes of evolution observed are associated with the timescale of species divergence. We suggest that future studies should include both MHC class I and II genes and multiple species spanning a range of divergence time to enhance our understanding of the evolution of avian MHC diversity.

Somatic mutations in long-lived conifers are rarely characterized yet offer a unique window into the spontaneous genetic forces that shape variation in plants. In Pinus taeda, dwarf phenotypes originate from abnormal branches, colloquially known as "witches' brooms", where progeny derived from the affected branch segregate for dwarfism in an apparent Mendelian 1:1 ratio. In this study, we genotyped six unrelated wind-pollinated families segregating for dwarfism using single-nucleotide polymorphism markers that had been previously positioned on a linkage map. Trait-loci association analyses identified a genomic region on linkage group eight (spanning 98-155 cM) that was strongly associated with dwarfism across unrelated families. This finding suggests that independent, de novo somatic mutations within a common genomic region are the basis for stable dwarf phenotypes in P. taeda. The implicated region is quite large and it remains to be determined if the same growth regulation gene or genes are responsible, but the shared region is evidence for disruption of a common pathway. To more formally describe the witches' broom phenomenon and distinguish mutants from pathogen-induced brooms, we propose the Latin name Ramus nanus mutatus. We discuss the contribution of somatic mutations to variation in forest trees, the potential utility of the dwarfing mutation for rootstocks in forestry seed orchards, and the next steps toward characterizing the pathways underlying dwarfism and their homology in other conifer species.

Pressodonta viridis (Bivalvia: Unionida) is a species of freshwater mussel considered rare and imperiled in 14 U.S. states and Ontario, Canada. Limited population-level genetic information is available for P. viridis despite the species' imperilment status. We used 13,661 single nucleotide polymorphisms (SNPs) derived from double digest restriction site-associated sequencing (ddRAD-seq) to examine patterns in population genetic diversity, structure, and differentiation among P. viridis populations in the Upper Mississippi River, Ohio and Wabash rivers, and Great Lakes watersheds. Structure analyses revealed significant differentiation related to major drainage among groups of P. viridis populations. Evidence of founder effects in Great Lakes populations by colonization routes from Upper Mississippi River and Ohio/Wabash River systems was found in admixture analyses. Limited evidence of isolation-by-distance effects was found, suggesting that multiple colonization routes and glacial refugia are responsible for current P. viridis genetic structure. A combination of ancient river hydrological patterns and more recent headwater stream capture events following the last glacial retreat likely correspond to considerable admixture found among populations of P. viridis in the Upper Mississippi, Wabash, and Ohio Rivers. Population genetic variation, structure, and differentiation described in this study should be used to inform conservation efforts of P. viridis in the future, particularly if recovery actions include population augmentation from translocations or hatchery propagation.

Divergence in marine environments is complex, often occurring despite the absence of physical barriers. This study investigates the genomic structure and demographic history of the economically important pink shrimp Farfantepenaeus brasiliensis across its Western Atlantic distribution using genomic data (ddRAD) and mitochondrial sequences. We tested the hypothesis that oceanographic features in the region act as barriers, generating genetically divergent groups despite high connectivity potential. Samples from four regions (Florida-USA, Northeastern-Brazil, Eastern-Brazil, and Southeastern-Brazil) were analyzed, covering the full range of the species' distribution. Results revealed two distinct genetic clusters corresponding to northern and southern populations, with evidence of asymmetrical gene flow. Genetic diversity was higher in the northern population. Demographic analyses indicated population expansions following the Last Glacial Maximum and recent declines, particularly in the southern population. The most likely demographic scenario involved allopatric divergence followed by secondary contact, with an estimated split ~2 million years ago (Mya). Phylogenetic and species delimitation analyses supported the separation of northern and southern populations into distinct taxonomic units. Despite divergence, ongoing gene flow was detected, suggesting a divergence-with-gene-flow scenario and potentially different species. The Amazon-Orinoco Plume appears to act as the main semi-permeable barrier, allowing intermittent connectivity while facilitating divergence through genetic drift. This study provides insights into marine divergence processes, highlighting how ecological factors and oceanographic barriers shape genetic differentiation in high-dispersal marine species. The findings have implications for taxonomy, evolution, fishing and conservation of F. brasiliensis, emphasizing the need for integrated management approaches considering cryptic genetic diversity.

Segregating alleles in natural populations can be driven to fixation or loss by genetic drift or directional selection, or may be maintained in a polymorphic state by balancing selection. Balancing selection in a panmictic population is theoretically well established, but not widely understood at the molecular level. In this study, we focus on the evolutionary processes affecting non-synonymous variants at eight functionally relevant loci (based on candidate SNP genotyping) in a deep-sea fish species (Coryphaenoides rupestris) that lives across habitat zones ranging from ~200 m to ~2000 m depth. At each of these loci, one allele is predominant in the deeper water. Across a shallower depth range, we find that minor allele frequencies show a highly significant increase or decline progressively across five defined age categories. At single depths below a threshold depth, the deep-water allele declines in frequency with age. Together, these data indicate segregation to different depths, either shallow or deep, and balancing selection to retain variants needed for each depth range. This is supported by signals for long-term balancing selection at these loci (based on published genomic data). We discuss alternative interpretations and conclude that balancing selection maintaining ecotype diversity is the best supported mechanism.

The field of population genetics is primarily focused on simple genetic variants such as single nucleotide polymorphisms (SNPs), small insertions or deletions (INDELs), and copy-number variants (CNVs). However, large-scale genomic variants are beginning to undergo increased scrutiny as new sequencing methods facilitate their discovery. Here, we report an unusually large and highly variable structural feature in the Daphnia magna genome that is strongly associated with immune function. Alternative forms of this large structural polymorphism (LSP) encompass 2-5 Mb regions where homology is undetectable and that contain largely non-overlapping sets of genes. One haplotype (LSP-5-1.1) shows a near-perfect correlation with susceptibility to a common strain of the virulent bacterium, Pasteuria ramosa, which is a common and widespread parasite of D. magna. Rapid selection against LSP-5-1.1 was observed during a natural P. ramosa epidemic, coinciding with a strong population-wide increase in resistance. Despite recurrent episodes of strong selection against Pasteuria susceptibility, we observe evidence of balancing selection for this structural polymorphism-suggesting counter selection against the resistant form by a yet unidentified mechanism.

Climate change poses a growing threat to global coffee production, particularly for Coffea arabica, the most widely cultivated species. Coffea canephora (Robusta), with greater tolerance to heat and environmental stress, represents a critical genetic resource for sustaining future supply. Despite its increasing importance, the species is still relatively understudied with respect to population structure and trait architecture-factors that are important for guiding breeding efforts. Here, we combine population genetic analyses with genomic prediction to inform the improvement of C. canephora using a representative breeding collection from West Africa. First, we characterized the genetic structure of the cultivated germplasm and confirmed the presence of three main genetic pools: Robusta, Conilon, and Guinean. Second, we quantified phenotypic variation and genetic parameters for 11 agronomic traits, demonstrating a significant contribution of non-additive effects-particularly for yield. Third, we evaluated the performance of genomic prediction models incorporating additive and dominance effects, and proposed their integration into a reciprocal recurrent selection scheme to exploit heterosis. Altogether, our findings highlight the utility of incorporating structured genetic diversity and non-additive effects into breeding strategies. The framework presented here provides a foundation for improving the predictive accuracy and long-term adaptability of C. canephora, with broader implications for genomic-assisted breeding under climate stress.