Journal of Heredity最新文献

The genus Martes consists of medium-sized carnivores within the family Mustelidae that are commonly known as martens, many of which exhibit extensive geographic variation and taxonomic uncertainty. Here, we report chromosome-length genome assemblies for three subspecies, each representing a different marten species: the Tobol sable (Martes zibellina zibellina), the Ural pine marten (Martes martes uralensis), and the Far East yellow-throated marten (Martes flavigula aterrima). Using linked-read sequencing and Hi-C scaffolding, we generated assemblies with total lengths of 2.39-2.45 Gbp, N50 values of 137-145 Mbp, and high BUSCO scores (93.6-96.4%). We identified 19 chromosomal scaffolds for sable and pine marten, and 20 for yellow-throated marten, which agrees with the known karyotypes of these species (2n = 38 and 2n = 40, respectively). Annotation predicted ~ 20 000 protein-coding genes per genome, of which > 90% were assigned functional names. Repeats encompass 36.9-40.4% of the assemblies, with a prevalence of LINEs and SINEs, and is conservative across the genus. Synteny analysis of our generated and available marten genome assemblies revealed assembly artifacts in previously published assemblies, which we confirmed through investigation of Hi-C contact maps. Among other rearrangements, we verified a sable-specific inversion on chromosome 11 using the published cytogenetic data. Our assemblies broaden the genomic resources available for Martes, extending coverage to geographically distant and taxonomically significant subspecies. Together, they provide a robust framework for assessing intraspecific genetic diversity, identifying signatures of hybridization, and refining the complex taxonomy of the genus. Beyond conservation and evolutionary applications, these references will facilitate comparative genomics across Mustelidae and other carnivorans.

Rhesus (Macaca mulatta) and long-tailed (M. fascicularis) macaques, important for biomedical research, are distributed across Thailand, and hybridization and introgression between species influence genetic diversity, potentially leading to variability in traits and pathogen susceptibility. Elucidation of the genetic components directly related to pathogen susceptibility, such as major histocompatibility complex genes (MHC) across different environmental conditions, is crucial. Thus, this study examined the MHC class II DQB diversity in 18 populations of wild rhesus and long-tailed macaques in Thailand. Next-generation sequencing was used to screen 298 bp partial exon 2 of DQB. Habitat suitability was analyzed using Maximum Entropy Modeling to identify the main factors affecting macaque distribution, which may relate to allelic diversity. Six alleles (Mamu-Mafa-DQB1*TH01-Mamu-Mafa-DQB1*TH06) were observed in both species, with no evidence of species-specific alleles. Two alleles (Mamu-Mafa-DQB1*TH05 and Mamu-Mafa-DQB1*TH06) were restricted to two Northeastern populations. Selection analysis indicated that purifying selection acted on the MHC gene pool. Northeastern Thailand was identified as a suitable habitat for rhesus macaques, with the distance to roads as a primary predictor. Central to southern Thailand, with its elevation and distance to rivers, was predicted to be suitable for long-tailed macaques. The homozygous genotype of Mamu-Mafa-DQB1*TH02 allele was found in all individuals of one long-tailed macaque population, resulting in an increased risk of poor population health and pathogen infection. This study provides insights into the evolution of Thai macaques with potential implications for their use in biomedical research, such as disease susceptibility and resistance, as well as in vaccine development.

Fall webworm (Hyphantria cunea) is a widespread, highly polyphagous moth in the family Erebidae, whose native range spans much of North America and invasive range includes Asia and Europe. The species uses over 600 plant species as a larval host, making it among the most generalized insect herbivores described. Its variable host use, wide range, and genetic diversity make fall webworm an attractive emerging model system for the study of diet breadth, but studies have been limited by the lack of a high-quality annotated reference genome. Here we report an annotated, chromosome-scale genome of much improved continuity and completeness over the previously available unannotated fall webworm reference genome. We used PacBioHiFi long reads and Omni-C proximity ligation sequencing technology to produce a de novo assembled genome. Our genome assembly, the first for any species in the genus and third in the family, contains 321 scaffolds spanning 0.572 gigabases with a N50 of 14.6 Mb and BUSCO complete score of 99.1%. This genome will represent a valuable resource for research into the ecology, evolution, and genetics of dietary generalism and diet breadth in insect herbivores.

Structural variants (SVs) comprise an axis of genetic diversity with strong consequences for phenotype and fitness, making them a potentially important target for conservation genomics. Here we review how and why SVs can play a role in in conservation genomics; the different types of SVs and how they can affect phenotype; and how pangenomes and long-read sequencing are illuminating their evolution in populations, including small populations and those of conservation concern. SVs comprise multinucleotide mutations including insertions, deletions, transpositions, inversions, and other multinucleotide mutations, often overlapping genes and other functional genome regions. As a result, SVs often play important roles in phenotypic evolution and local adaptation and can contribute substantially to genetic load in inbred populations. However, our understanding of the factors influencing SV diversity in populations is still in its infancy and is complicated by the vast range of sizes, effects, and mechanisms of formation of these mutations. We argue that SVs are an important axis of genetic diversity that should be characterized alongside more traditional metrics of genetic diversity in conservation contexts. There are a number of analytical challenges to detecting and studying SVs, but analyses aimed at understanding the role of SVs in inbreeding load and population health are rapidly becoming realizable goals, accelerated by new technologies and analytical approaches. New tools, including population-scale long-read sequencing and pangenome approaches, are beginning to make SVs accessible in ways that can be readily applied in conservation settings.

Phyllospadix spp. (surfgrass) are flowering plants and keystone species in the rocky intertidal and subtidal environments of the North Pacific Ocean. Here we report a chromosome level assembly for P. torreyi, which occurs along the coast of California, sometimes in sympatry with P. scouleri. Both of these species and their putative hybrids are being studied as part of the California Conservation Genomics Project (CCGP). Phyllospadix are dioecious, and males are exceptionally rare compared to females. Using high throughput, long reads (PacBio) and chromatin capture (Omni-C), we assembled a chromosome level genome for a male individual and a contig level assembly for a female individual. Comparison between the male and female assembly confirmed that the male is the heterogametic sex and has a massive Y chromosome at 124.8 megabases (Mb), which encompasses over 27% of the male genome. We also compared the male P. torreyi assembly to a genome from its sister genus, the monoecious Zostera marina, and found relatively high levels of synteny, that syntenic gene blocks on the P. torreyi sex chromosomes align to a single chromosome of Z. marina, and an estimated divergence time of ca. 25 million years ago (Mya). The Phyllospadix genome will be a powerful tool for studying marine dispersal, sex ratios, genetic diversity, sex chromosome evolution, and other dynamics in a keystone marine species.

Chronic wasting disease (CWD) is a fatal disease in cervids caused by abnormally folded proteins known as prions. Since its identification in 1967, CWD has spread to wild cervid populations in 36 U.S. states. Some variants in the prion protein gene (PRNP) are known to confer advantages against prion diseases in many species including cervids. In elk (Cervus canadensis), a non-synonymous mutation in PRNP is associated with CWD susceptibility and/or progression. PRNP codon 132L, which encodes leucine rather than methionine (132M), is relatively less frequent among CWD positive elk than among CWD negative elk. In 2021, CWD was detected in Idaho near the Oregon border, heightening concerns about potential spread into Oregon's cervid populations. We therefore sequenced the complete coding region of PRNP in 183 elk collected across their range in Oregon, to assess PRNP variation. PRNP sequences have not previously been examined in the Roosevelt elk (C. c. roosevelti) subspecies. We assessed 101 Roosevelt elk in western Oregon, finding that 42% carried at least one copy of 132L. Among Rocky Mountain elk (n = 82; C. c. nelsoni) in Oregon, 49% carried at least one copy of the advantageous allele 132L. Oregon elk carry a relatively high proportion of 132L compared to previously examined elk populations nationwide. Despite this high frequency, Oregon elk populations remain at substantial risk from CWD. These findings can inform management strategies aimed at mitigating CWD risk in Oregon's cervid populations.

The ocelot, Leopardus pardalis, is a medium-size member of the cat family Felidae found throughout the Neotropics. This solitary, nocturnal species is of increasing conservation concern in the United States due to habitat loss and fragmentation. Historically, the northern extent of the species range extended throughout the American Southwest. Today this subspecies, Leopardus pardalis albescens, is restricted to just two small, isolated populations in South Texas. Conservation genomics can provide invaluable insights into the genetic status and management of declining populations, however, there is currently no reference genome available for this species. To address this deficit, here we report a high-quality chromosome-level reference genome for the Texas ocelot, with a total length of 2.47Gb placed on 211 scaffolds. The assembly is highly contiguous, with a contig N50 of 84Mb and 99.2% gene completeness. This assembly provides a key genomic resource that will enhance ongoing conservation and management strategies for this endangered subspecies.

We describe a chromosome-level genome assembly from a wild alpine reindeer individual (Rangifer tarandus tarandus) from the Rondane area in Southern Norway. The assembly is resolved into two pseudo-haplotypes: hap 1 spanning 3,081 megabases and hap 2 spanning 2,633 megabases. Contig N50 and scaffold N50 lengths are in the range of 31-41 Mb and 66-69 Mb, respectively. A large part of these two haplotypes (83.8% and 90.4%, respectively) are scaffolded into 34 autosomal chromosomal pseudomolecules, and in sex chromosomes X and Y for hap 1. The BUSCO completeness scores are 98.0% and 95.2%, respectively, and gene annotations of the assemblies identified 37,998 and 36,977 protein-coding genes. We also present an updated and improved genome assembly for Svalbard reindeer (Rangifer tarandus platyrhynchus; contig N50 46-48 Mb, scaffold N50 67-71 Mb, BUSCO 95.4% - 98.0%) and a comparison with previously published genome assemblies of reindeer.

Microsatellites are powerful markers for tracking genetic variation in wildlife populations due to their high polymorphism and genome-wide abundance. While PCR-based fragment size analysis has been the standard for genotyping microsatellites, high-throughput sequencing offers greater resolution and the opportunity to sync historical datasets with modern analyses. We evaluated how genotypes from whole-genome sequencing align with PCR data for 15 microsatellite loci in 11 North American brown bears (Ursus arctos). Brown bear populations in the lower 48 United States have declined from approximately 50,000 to fewer than 2,000 over the past decades. Their endangered status has prompted extensive research and genetic monitoring, yielding large, multi-year microsatellite datasets upon which future conservation efforts can build. We achieved a microsatellite genotype concordance rate of 94.5% with PCR results. All discrepancies occurred at complex loci containing multiple insertions and/or deletions (indels). Physically linked indels or single nucleotide polymorphisms (SNPs) occurring within the loci were misinterpreted as independent insertions, underscoring the need for genotyping tools that incorporate phasing when genotyping. To evaluate coverage effects, we downsampled from 30x to 2x. Concordance remained high at 20-30x but dropped sharply at 10x, with 5x and 2x having discordant genotypes or insufficient coverage for genotyping. Accurate genotyping required both sufficient depth and number of reads spanning the entire repeat regions. Our results show that short-read whole-genome sequencing can recover microsatellite genotypes with high accuracy when paired with careful variant interpretation. By aligning historical PCR datasets with modern sequencing data, we can preserve decades of genetic insight and strengthen long-term monitoring of at-risk populations.

Efforts to recover endangered species often rely on restoring populations to their historical range, yet reestablishing lost genetic variation is challenging when the ancestral genetic landscape is poorly understood. The Pacific pocket mouse (Perognathus longimembris pacificus), a federally endangered heteromyid rodent, has been extirpated from most of its range in coastal southern California. Recovery efforts call for establishing new populations in their historic range through translocation, but the extent to which historical patterns of genetic variation can be recapitulated is unknown. To inform conservation planning, we sequenced whole genomes of historical samples, including individuals from populations that went extinct in the mid-1900's. Phylogenetic analyses revealed that mice from the southernmost extirpated population form a clade with a different subspecies, while populations to the north form a sister clade. These findings support morphological evidence calling for a taxonomic revision, which would modify the definition of the historic range and complicate the interpretation of suitable reintroduction sites. Despite this divergence, D-statistics and demographic models indicate historical gene flow among coastal populations, suggesting that alleles reintroduced to the southern coast may echo ancestral connectivity. Thus, management efforts should consider potential receiver sites that contain suitable habitat within this range as viable for population creation. These results highlight the value of historical genomics in guiding conservation decisions, particularly when taxonomic uncertainty, extirpation, and limited genetic diversity constrain modern management. Although historical baselines often cannot be restored, conservation strategies can leverage genomic insights to enhance future adaptive potential and long-term resilience of threatened species.