Continental diversification and insular speciation in a widespread passerine (Troglodytes musculus) in southern South America.

Evolutionary history of Ridge-nosed Rattlesnakes (Crotalus willardi): A specialized and diverse montane species.

To characterize the genetic diversity and evolutionary patterns of four Weining chicken strains from Guizhou Province, China, we generated genome-wide single nucleotide polymorphisms (SNPs) using dd-RAD sequencing. We found that Weining chicken exhibited moderate genetic diversity, with observed heterozygosity (Ho = 0.267) lower than expected heterozygosity (He = 0.312) and a positive inbreeding coefficient (FIS ≈ 0.14), indicating some degree of inbreeding across the population. Among strains, HM showed the highest diversity while HT had the lowest. Analyses of population structure, phylogeny, principal component analysis, and admixture consistently revealed weak genetic differentiation (FST < 0.06) and frequent gene flow among strains. Kinship analysis demonstrated mostly low pairwise relatedness, with a minority of individuals exhibiting closer kinship. Selection signature scans identified multiple candidate regions; genes within these regions were significantly enriched for biological processes and pathways related to immune response (e.g., IL-17 signaling) and metabolic regulation (e.g., MAPK signaling), which were consistently highlighted in both GO and KEGG enrichment analyses. These results demonstrate that Weining chicken has moderate genetic diversity, low population differentiation, and evidence of inbreeding and gene flow, with candidate selection signals in immune and metabolic pathways (e.g., IL-17 and MAPK signaling), providing a quantitative basis for conservation and breeding programs.

Livin’ on the edge. A case study on gene flow restoration for the endemic species Primula palinuri Petagna with a fragmented habitat

The Hengduan Mountains (HDM), a biodiversity hotspot in Southwest China, harbour numerous endemic taxa whose diversification has been driven by the complex geological history of this region. This study investigates the diversification of the katydid genus Sichuana, endemic to the HDM, integrating mitochondrial genomics, morphology and biogeography. We sequenced complete mitochondrial genomes of all known geographic populations of Sichuana, revealing four major clades diverging during the Late Miocene (5.06-8.37 Ma). Orogeny-driven vicariance fragmented ancestral populations, while unstable barriers may facilitate mitochondrial introgression, as evidenced by paraphyletic lineages contrasting with distinct morphologies. We describe five new species (S. brevicerca sp. nov., S. fortidens sp. nov., S. qiuzhi sp. nov., S. luqiaoensis sp. nov. and S. pseudomagna sp. nov.) and two subspecies (S. pseudomagna pseudomagna subsp. nov. and S. pseudomagna borealis subsp. nov.), highlighting the taxonomic challenges posed by discordance between mitochondrial DNA-based phylogenies and morphological classifications. This study demonstrates that orogeny-driven vicariance dominates speciation in low-dispersal insects, but transient gene flow complicates species delimitation. Our findings advocate for integrative taxonomy in biodiversity hotspots and highlight the HDM as a model system for studying biogeographic complexity.

Inference of interspecific gene flow using genomic data is important to reliable reconstruction of species phylogenies and to our understanding of the speciation process. Gene flow is harder to detect if it involves sister lineages than nonsisters; for example, most heuristic methods based on data summaries are unable to infer gene flow between sisters. Likelihood-based methods can identify introgression between sisters but the test exhibits several nonstandard features, including boundary problems, indeterminate parameters, and multiple routes from the alternative to the null hypotheses. In the Bayesian test, those irregularities pose challenges to the use of the Savage-Dickey (S-D) density ratio to calculate the Bayes factor. Here we develop a theory for applying the S-D approach under nonstandard conditions. We show that the Bayesian test of introgression between sister lineages has low false-positive rates and high power. We discuss issues surrounding the estimation of the rate of gene flow between sister lineages, especially at very low or very high rates, and suggest that evidence for gene flow between sisters be assessed via a Bayesian test. We find that the species split time has a major impact on the information content in the data, with more information at deeper divergence. We use a genomic dataset from Sceloporus lizards to illustrate the test of gene flow between sister lineages.

The genus Linum comprises over 230 species, with L. usitatissimum valued for linen and oil, yet crop wild relatives (CWRs) remain underutilized due to limited availability and poor molecular characterization. In this study, 96 accessions representing 16 wild and one cultivated species were evaluated using 49 SSR markers to assess genetic diversity and cross-species transferability (CST). A total of 473 alleles were detected, with allelic richness ranging from 1 to 22 alleles per locus and polymorphic information content (PIC) values reaching up to 0.91, underscoring the discriminatory power of the markers. High genetic diversity parameters, including Shannon's index (up to 1.296), revealed substantial allelic variation in species such as L. bienne and L. lewisii. Population structure analysis indicated moderate differentiation (global Fst = 0.186) and the presence of admixed individuals, reflecting complex evolutionary histories shaped by multiple gene flow events and introgression. Cluster analysis proved effective for uncovering pedigree relationships among genotypes and offered advantages over PCoA, while CST rates ranged from 45.45 to 100% across species. The high CST observed within sections (Linum, Dasylinum) highlights conserved genomic regions, whereas variable amplification in Linastrum points to divergent evolutionary trajectories. Together, these findings demonstrate that SSR markers not only capture allelic richness and population structure but also illuminate evolutionary processes such as speciation, introgression, and lineage divergence. The study establishes a valuable foundation for integrating Linum CWRs into breeding programs, thereby broadening the genetic base in cultivated linseed. These findings can enhance the scope and effectiveness of future breeding initiatives, particularly where such markers are lacking.

North Africa has experienced significant gene flow throughout history, with Morocco occupying a strategic location at the crossroads of Africa and Europe. In this study, we compiled 869 complete mitogenome sequences from six North African populations to explore genetic diversity, haplogroup distributions, and phylogenetic relationships, with a specific emphasis on the Moroccan population. We obtained a high haplotype diversity across all populations, and neutrality tests yielded significant negative values, consistent with demographic expansion. We identified 56 haplogroups, dominated by U6, H, and L. Genetic differentiation between populations was low (FST = 0.001-0.014), and analysis of molecular variance indicated that most genetic variation occurs within populations, and reinforces the presence of a genetically cohesive Maghreb core. Phylogenetic and NeighborNet analyses showed that Moroccan sequences are widely distributed across haplogroups, with deep branching of macro-haplogroup L subclades, indicating early human migration patterns, including out-of-Africa dispersal and subsequent back-migrations. Bayesian demographic analysis of the prevalent haplogroups in Morocco revealed distinct evolutionary trajectories: an expansion of haplogroup L, a decline of U6, and an expansion of H. To complement the maternal perspective, we analyzed published Y-chromosome STR data from 2114 North African males. Haplotypic diversity remains high (> 0.97), and the haplogroup E-M81 predominates in Moroccan, Algerian, and Tunisian populations. Low pairwise Rst values further confirm the genetic homogeneity of North Africa and reinforce the strong cohesion of the Maghreb core. This study highlights a rich genetic heritage shaped by ancient and ongoing gene flow in North Africa.

Hybridization and introgression play crucial roles in evolution and adaptation. Although the influence of ploidy differences on interspecific hybridization has been documented, most studies have focused on single pairs of hybridizing species, thereby limiting our understanding of broader patterns of interspecific gene flow. Here, we investigate hybridization among six partially sympatric Betula species to examine patterns of genetic admixture involving diploid, tetraploid and octoploid species occupying diverse microhabitats. We sampled 148 populations across China, representing three diploid species (B. ashburneri and B. costata from section Costatae, and B. platyphylla from section Betula), two tetraploid species (B. ermanii and B. utilis from section Costatae), and one octoploid species (B. dahurica from section Dahuricae), and genotyped 2,610 individuals at 15 microsatellite loci. We assessed population structure and compared levels of genetic admixture among the six Betula species using pairwise analyses. Genetic diversity increased with ploidy level and was positively correlated with latitude. Analyses of population genetic structure revealed genetic admixture among Betula species with different ploidy levels. The proportion of hybrids among species within section Costatae was significantly higher than that among sections, although it was not significantly associated with phylogenetic distances between species. Higher genetic diversity in northern populations of the six Betula species suggests the existence of glacial refugia at higher latitude. The comprehensive dataset for six Betula species not only enables investigation of patterns of genetic admixture across ploidy levels but also fosters novel hypotheses regarding the origins of polyploid lineages and the factors influencing the dynamics of interspecific hybridization.

Hybrid sterility is a critical postzygotic barrier that limits gene flow during speciation, yet the genetic architecture underlying evolution of such barriers in the early stages of speciation remains poorly characterized. In house mice, F1 male sterility observed in crosses between Mus musculus musculus and M. m. domesticus has been attributed to incompatibilities between heterozygous autosomal Prdm9, which controls primarily the position of recombination hotspots, and copy number variation in X-linked Mir465 miRNA genes. This molecular mechanism, identified in laboratory crosses, provided the first genetic evidence of a Dobzhansky-Muller incompatibility causing F1 hybrid sterility in vertebrates and has been considered a general model across strains and laboratories. Here, we use mice from natural populations and find that F1 hybrid sterility is polymorphic and asymmetric, with fertility phenotypes modulated by the direction of the cross. Although sterile males carried incompatible Prdm9 alleles, quantitative trait loci (QTL) mapping in backcross progeny revealed no significant associations with chromosome 17, where Prdm9 resides. Instead, sterility consistently mapped to X-linked loci, and the genomic position of sterility-associated QTL shifted between reciprocal backcrosses. These findings uncover a previously unrecognized mode of hybrid sterility in which X-linked incompatibilities act independently of Prdm9, a mechanism we term Prdm9-independent X-linked sterility (PIXLS). Our results extend the established Prdm9/Mir465 model by demonstrating that hybrid sterility in house mice can arise through alternative genetic routes, highlighting the evolutionary diversity of reproductive barriers in their natural hybrid zone.

A current goal of speciation research is identifying loci underlying reproductive barriers between species. Locating barrier loci in population genomic data is difficult due to the often-complex demographic history of diverged taxa and heterogeneity in evolutionary forces across the genome. We take advantage of natural hybridization between two wood ant species (Formica aquilonia and F. polyctena) to identify regions of reduced long-term gene flow using demographically explicit scans of non-admixed genomes. In addition, we identify candidate Bateson-Dobzhansky-Muller incompatibilities (BDMIs) through an imbalanced recombinant haplotype frequency analysis using a large sample of natural F. aquilonia × F. polyctena hybrid genomes. These approaches find barriers and BDMIs scattered across the genome. Furthermore, BDMIs significantly overlap with long-term barriers, indicating that some BDMIs have persisted despite divergence with gene flow. Intriguingly, the number of pairwise interactions a BDMI has correlates with its long-term barrier strength: hub-like BDMIs with many interactions reduce gene flow more effectively. Finally, we find that long-term barriers are depleted for both coding sequences (CDS) and transposable elements (TEs), while candidate BDMIs are associated with snRNAs and LTR transposons, specifically Ty1-copia. In contrast, regions where long-term barriers and BDMIs co-locate are significantly associated with introns but not CDS or TEs, implying a potential role of alternative splicing or gene regulation in long-term incompatibilities. Our results highlight the underappreciated impact of BDMI connectivity on the persistence of reproductive barriers over time.

Ammopiptanthus nanus (Fabaceae), a nationally protected endangered evergreen shrub endemic to Central Asian deserts, is severely threatened by habitat fragmentation. To conserve its genetic resources, multiple ex situ populations have been established across China. We evaluated conservation efficacy under distinct management strategies across four ex situ populations (n = 114), including a near-site protected area (J), a Forestry and Grassland Administration–managed zone (L), Tazhong Botanical Garden (T), and the Forestry Academy of Sciences (K), using integrated molecular markers: expressed sequence tag–simple sequence repeats (EST-SSRs), chloroplast DNA fragments ( psbA–trnH , trnL–trnF , trnS–trnG ), and nuclear ribosomal ITS (ITS1/ITS4) sequences. The results reveal significant strategy-dependent divergence in genetic conservation efficiency, primarily driven by founder genetic composition and reproductive management protocols. Strategy (J) retained moderate chloroplast diversity but exhibited reduced nuclear diversity and high inbreeding. Strategy (L) maintained moderate nuclear diversity yet limited chloroplast variation. Strategy (T) showed the highest nuclear diversity but minimal maternal lineage preservation. Strategy (K) preserved unique maternal haplotypes and phylogenetic distinctiveness despite constrained nuclear diversity. Critically, all populations displayed high inbreeding coefficients (F &amp;gt; 0.404), indicating genetic bottlenecks and restricted gene flow. To ensure long-term viability, we recommend: (1) diversifying genetic foundations through the introduction of founders from multiple wild sources and expansion of population sizes to mitigate drift; (2) enhancing gene flow via periodic interpopulation transplants and facilitated distant cross-pollination, integrated with long-term monitoring of nuclear and cytoplasmic diversity.

Although the green revolution adapted a handful of crops to homogeneous and high-input industrialized agriculture, much of the global population still relies on the local production of variable crop cultivars by low-input smallholder farms. This diversity of unhomogenized crops1, like that of the grain and bioenergy crop sorghum2-5, offers raw materials for genetic gain and cultivar improvement. However, breeding efforts can be constrained by highly specialized traits and breeding targets6. Here, to bridge this diversity, we constructed a 33-member pangenome reference and a diversity panel across 1,984 cultivars and landraces. We leveraged these resources to explore the complex interplay among historical contingency, ongoing adaptation and previously uncharacterized structural diversity. Specifically, our analyses conclusively demonstrated multiple nested and deeply diverged structural variants in the domestication gene SHATTERING1, which distinguish the previously established multicentric origin of sorghum. We then applied landscape genomics to reveal how gene flow and secondary contact created the complex genetic mosaic in contemporary breeding networks. As proof of concept for pangenome-accelerated trait discovery, we connected biosynthetic gene cluster structural variation to phenotypic leaf concentration of the cyanogenic glucoside dhurrin. Combined, these approaches will accelerate breedingand trait discovery and provide a framework for similar applications in other crops.

ABSTRACTGene flow affects the distribution of genetic variation of a species over time and thus can be crucial for a population's persistence and adaptive capacity. Given the importance of gene flow, it is key to understand the connectivity and genetic differentiation between populations of species with small and segregated breeding populations that are facing population declines, such as many long‐distance migratory birds. In this study, we explored population structure in Hudsonian Godwits (Limosa haemastica) from two geographically distinct breeding areas in the North American sub‐Arctic and two nonbreeding areas in South America using nuclear microsatellites. Despite being spatially and temporally segregated during most of the annual cycle, our results indicate no evidence of population differentiation between breeding populations, nor clustering between individuals from breeding and nonbreeding populations connected by migration. Considering the phenology of the species, godwits from both breeding populations could co‐occur during southward migration and/or throughout the oversummering period, likely in the Las Pampas ecoregion of Argentina. As with many other long‐distance migratory shorebirds, immature godwits stay in their nonbreeding areas until sexual maturity is reached, during which time they can explore, interact, and follow flocks of adults to different nonbreeding areas, thus increasing the chances of mixing between populations. This highlights the importance of recognizing the key role of early life period within the full life cycle of migratory birds for understanding their demography and evolutionary potential.

The genetic structure of bacterial species is most often interpreted in terms of demographic processes such as clonal descent, but can also reflect natural selection and hence give functional and ecological insight. Klebsiella pneumoniae (KP) disperses effectively around the world and has high recombination rates, which should result in the species having a well-mixed gene pool. Nevertheless, phylogenies based on diverse KP strains contain a “backbone.” This structure reflects a component of variation where the first component in Principal Components Analysis (PCA), PC1, explains 16.8% of the total variation. We propose that the component reflects a “bacterial ecocline” generated by diversifying selection on a quantitative genetic trait. We simulated the evolution of a bacterial population with a polygenic quantitative trait, where strains with the most extreme trait values have a small advantage. These simulations can recapitulate our KP PCA results and other features of its genetic diversity. As well as providing an explanation for the phylogenetic backbone, our results provide insight into how species such as KP can speciate, via stronger selection on the trait or a reduction in gene flow. Our hypothesis that there is a bacterial ecocline in KP raises two questions, namely what the trait is underlying it and why is the trait under diversifying selection? The genes that are most strongly associated with PC1 provide some hints, with the top locus encoding Kpa fimbriae. Identification of the trait, if it exists, should facilitate insight into selection on quantitative genetic traits in natural bacterial populations, which have largely been unstudied in microbiology, except in the atypical context of antibiotic resistance.

Pigs are a major source of animal protein and an important model for studying domestication, adaptation, and the genetics of complex traits. Over the past decade, pig genomics has progressed from generating reference assemblies and variant catalogues toward reconstructing population history and interpreting phenotypic divergence with greater resolution. Improvements in reference continuity, breed-matched assemblies, and pangenome/graph representations reduce reference bias in repeat-rich and structural-variant-prone regions, strengthening cross-population comparisons and fine-mapping across cohorts. Time-stratified ancient genomes provide an explicit temporal framework for evaluating lineage turnover and gene flow and support a multi-stage, network-based view of domestication. In parallel, genetic analyses of growth, carcass composition, meat quality, and disease resilience increasingly integrate association signals with regulatory annotation, gene expression, and tissue- or stage-specific context. Across these lines of work, maintaining comparability across reference frameworks remains central, including stable coordinate systems, robust imputation resources, and reproducible approaches for structural-variant genotyping. Together, these developments support more consistent inference and interpretation while providing a clearer basis for translation in breeding and biomedical research with attention to genetic diversity.

How species time reproduction and adapt to environmental conditions are key topics in ecology and evolutionary biology. Here, we conducted a high-resolution population genetic analysis of Baltic herring, a subspecies of Atlantic herring (Clupea harengus). Genotypes at >4,500 SNPs were generated from >4,500 spawning individuals, sampled from 150 locations spanning Swedish's eastern coast. Abiotic factors-week of spawning, latitude, temperature, salinity-were used to assess how genetic variation is shaped by temporal, spatial, and environmental gradients. Our results reaffirm strong genetic differentiation between spring- and autumn-spawning ecotypes, despite hybridization suggesting ongoing gene flow between the two ecotypes. We document significant substructuring within the spring-spawning ecotype, delineating three main, previously unidentified, genetic clusters underpinned by adaptative genetic variation associated with latitude, salinity, temperature, and spawning time. Complementary linkage disequilibrium (LD) partitioning showed that adaptive loci-especially those in inversion regions-exhibit strong elevated among-population LD, consistent with divergence maintained by local selection despite ongoing gene flow. Clinal variation in allele frequencies indicated regionally distinct selection pressures, including shifts in allele frequencies at two major supergenes (inversions) and at a suite of genes correlated with abiotic factors. Importantly, rare genetic outlier populations are identified within each geographic region which further illustrates the unexpected fine-grained population structure of Baltic herring and implies a strong homing behavior in this abundant marine fish. Overall, this study demonstrates the capacity for targeted population genetic studies to detect adaptive variation in natural populations, the outcomes of which have direct implications for sustainable fisheries and biodiversity management.

Summary statement Genomic analyses of Nitraria sibirica reveal that unidirectional gene flow along the Yellow River maintains genetic diversity in fragmented eastern populations. This highlights the river's critical role as a dispersal corridor in counteracting genetic drift and supporting adaptive potential.

Zoonotic risk of transmission of Giardia duodenalis from water resources; Worldwide molecular and network analyses.

The species delimitation challenge resulting from mito-nuclear discordance: A case of Macroscytus burrower bugs from China (Hemiptera: Heteroptera: Cydnidae).