One of the most striking exceptions to strict maternal inheritance of mitochondrial DNA (mtDNA) in the animal kingdom is a system called doubly uniparental inheritance (DUI), which exists in several bivalve species. DUI is characterized by the presence of two distinct sex-associated mitochondrial lineages: one transmitted through eggs (F-type mtDNA) and the other through sperm (M-type mtDNA). Presently, most known species exhibiting DUI belong to the freshwater bivalve order Unionoida. Other groups with species exhibiting DUI include the orders Mytiloida, Veneroida, and Nuculanoida. In Veneroida, the complete M-type mtDNA is available for two species. We report the presence of DUI in three species belonging to genus Macridiscus (Macridiscus melanaegis, Macridiscus multifarious, and Macridiscus semicancellata), in the order Veneroida, further obtaining their complete M-type mitogenomes. The M-type mitogenome sizes for M. melanaegis, M. multifarious, and M. semicancellata were 19,019 bp, 18,694 bp, and 18,726 bp, respectively, and the mean nucleotide difference between M-type and F-type mitogenomes was 21–23%. We compared the M-type and F-type mitogenomes and found that they show roughly the same genome features, except for gene order. In phylogenetic analyses of Veneroida, a “gender-joining” pattern was revealed within Macridiscus, similar to the pattern of “partial” Mytilus complex (except Unionida). This new insight provides novel evidence supporting the theory that Veneroida and Mytiloida have a more similar DUI pattern than Unionida. A large-scale rearrangement between the sex-linked mitogenomes of the three Macridiscus species was reported. From the observed rearrangement patterns, gene rearrangement between the two sex-linked mitogenomes could be explained by the tandem duplication and random loss (TDRL) model of dimer-mitogenome. This is the first report of heterogeneous genomes with two types of large-scale arrangements in the same organism, and may be contribute significantly to the study of mitochondrial recombination mechanisms.

Rapid and effective methods for tracing the geographic origin of wildlife samples are essential for tackling the illegal wildlife trade. Traditional morphological categorization methods are often inadequate as relying on the mitochondrial COXI barcode is insufficient for determining geographic populations. To address these limitations, we developed a bioinformatics-based pipeline for the rapid identification of traceable nuclear genome loci. This pipeline has been applied to the whole-genome sequence (WGS) data of China’s flagship species, the snub-nosed monkey (Rhinopithecus spp.). These species are known for sex-biased dispersal and hybrid speciation, which complicates genealogy tracing. Using phylogenetic principles, we employed the Robinson and Foulds (RF) distance and scanned over 1,850,726 population-specific loci, identifying five pairs that can trace genealogy origins rapidly and cost-effectively using PCR. Additionally, we found that relying only on mitochondrial genetic information is insufficient for rapid and accurate traceability to subspecies-level geographic populations. Our pipeline efficiently identifies loci and traces the geographic origin of snub-nosed monkey individuals, providing a valuable tool for species preservation and combating the wildlife trade. This approach can be extended to other species, aiding in the conservation of endangered wildlife and tracing criminal evidence.

The Tianshan Mountains, which host two native subspecies of western honeybees, represent the easternmost natural distribution limit of Apis mellifera . The managed Xinjiang black honeybee ( XJ ), introduced a century ago and designated as a Chinese National Animal Genetic Resource, has expanded rapidly under anthropogenic management. However, this expansion simultaneously threatens populations of native subspecies Apis mellifera sinisxinyuan and Apis mellifera pomonella . Herein, we performed the first whole‐genome resequencing of the XJ population and analyzed whole‐genome data from 19 XJ workers and 172 global A. mellifera samples to clarify the evolutionary history of XJ and evaluate its interactions with native bees. Population structure and phylogenomic analyses showed that XJ clustered within C lineage but formed a divergent clade distinct from other C lineage subspecies, with the closest affinity to Apis mellifera carnica (FST = 0.053). Despite higher inbreeding than other C lineage subspecies, XJ displayed comparatively higher genetic diversity (Θπ = 2.15 × 10 ⁻³ ) and heterozygosity (0.0028) than other C lineage populations (0.0015), although XJ 's value falls within the global range of A. mellifera . This genetic pattern can be attributed to substantial introgression (~10%–15%) from the M lineage, specifically from the native A. m. sinisxinyuan . TreeMix and F‐branch analysis identified significant gene flow from A. m. sinisxinyuan into the ancestral population of the XJ . Functional enrichment analysis suggested that genes within introgressed regions are involved in cold adaptation and foraging efficiency, and independent transcriptome validation confirmed differential expression of key candidate genes (e.g., LOC552291/MCM4) within these introgressed regions. Overall, our findings indicate that XJ represents an introduced population that has undergone regional adaptation, facilitated by the introgression of potentially adaptive alleles from native taxa. This case underscores the need for conservation strategies balancing management of economically valuable populations with protection of native lineages from genetic swamping and ecological competition.

Chitons (Mollusca: Polyplacophora) are a relatively primitive group within Aculifera that have retained their past life history and ecological traits. While chitons are recognized for their evolutionary significance and societal value (e.g., food, medicine, biomimetics), key aspects of their phylogeographic patterns and microevolutionary processes remain poorly understood, particularly regarding spatial dispersal and adaptation to the challenging intertidal zone environment. Here we show a population genomic analysis of the Chinese chiton (Liolophura sinensis), a species recently delineated from the Liolophura japonica species complex. Using high-depth resequencing of 68 individuals across nine populations, we identify distinct genetic substructure between the Taizhou and southern groups, with divergence dating back to approximately 19.0 thousand years ago, a timing that overlaps with late Pleistocene sea-level minima. A unidirectional gene flow pattern indicates ocean current-mediated larval dispersal, which is consistent with species-specific life history traits. Moreover, selection scans reveal significant enrichment of genes associated with immune responses, cellular homeostasis, and cytoskeleton dynamics, all traits that are potentially relevant for survival in wave-exposed rocky habitats. Our analyses identify strong population structure, recent divergence, and genomic regions potentially associated with local environmental variation, providing a foundational framework for future research on adaptation in marine intertidal species.

Wildlife trafficking poses a severe threat to global biodiversity and ecosystem stability, necessitating robust forensic tools for tracing the origins of illegally traded taxa. In this study, we developed a method of single-nucleotide polymorphism (SNP)-based molecular markers to enable precise geographical traceability of four animal species native to China: the Tibetan macaque (Macaca thibetana), brown eared pheasant (Crossoptilon mantchuricum), blue eared pheasant (Crossoptilon auritum), and Chinese pangolin (Manis pentadactyla). We studied these four species because their DNA is characterized by distinct population genetic structure, they are subjected to illegal trafficking, and given their diverse evolutionary histories, this allowed us to assess the general applicability of our forensic genetic framework in reducing wildlife crime. Based on whole-genome resequencing data from 26 Tibetan macaques, 51 eared pheasants and 42 Chinese pangolins, we performed population genetic analyses to elucidate their genetic structure and identify population-specific loci. The results indicated that all samples from these four species showed clear genetic differentiation and distinct clustering, allowing us to design primers to facilitate PCR-based traceability. We also assessed the utility of mitochondrial DNA (mtDNA) for tracing Tibetan macaques and both species of eared pheasants. We found that traceability accuracy using mtDNA was lower than when using SNPs. Our research offers a SNP-based traceability framework that accurately determines the geographical origin of wildlife samples to the genetic population level, and this provides a powerful tool for combating illegal trade and aiding conservation efforts.