搜索结果：The Journal of heredity

The northern elephant seal (Mirounga angustirostris) is the largest pinniped species in the northern hemisphere. The species is classified as being of least conservation concern by the IUCN-a triumph of conservation efforts despite hunting pressure that nearly led to its extinction more than a century ago. The historical range of the northern elephant seal extended from Baja California to Alaska, but overexploitation caused a severe demographic collapse and genetic bottleneck, with only an estimated 10 to 30 survivors left on Isla Guadalupe, Mexico. As part of the California Conservation Genomics Project, we generated a de novo reference genome and annotation for M. angustirostris, combining PacBio HiFi long-read sequencing data with Dovetail Omni-C chromatin conformation data. Our assembly has a primary haplotype genome length of 2,430,321,998 base pairs (2.4 Gb), with the longest contig of 144 Mb, contig N50 of 58 Mb, largest scaffold of 215 Mb, and scaffold N50 of 154 Mb. The secondary assembly haplotype consists of 422 scaffolds, spanning 2.45 Gb, with contig N50 of 61.24 Mb, scaffold N50 of 152.94 Mb, the largest contig of 204.14 Mb, and the largest scaffold of 216.16 Mb. We used the primary assembly and annotation for a preliminary investigation of repeat element content, historical demography, genome-wide heterozygosity, and loss-of-function variants. We found that M. angustirostris has one of the lowest estimates of genetic diversity of any marine mammal and a complex demographic history that may have reduced genetic diversity several times. This newly constructed genome will facilitate future in-depth explorations into the mechanisms behind resilience and recovery after a severe population bottleneck.

We present genome assemblies for two cyprinoid fishes, the tui chub (Siphateles bicolor) and the arroyo chub (Gila orcuttii). These fishes are ecologically important representatives of native fish assemblages in the western United States and are both species of conservation concern. The two species hybridize where introductions bring them into contact, with potentially important ecological and evolutionary implications that have not yet been thoroughly examined from a genomic perspective. We present de novo assemblies for both species, representing the first scaffold-level genomes within their respective genera, which were developed as part of the California Conservation Genomics Project (CCGP) using Pacific Biosciences HiFi and Omni-C data. Our tui chub assembly consists of 258 scaffolds spanning 1 148 084 093 base pairs, has a scaffold N50 of 45.9 Mb, a contig N50 of 23.7 Mb, and a BUSCO completeness score of 98.1%. Our arroyo chub assembly consists of 179 scaffolds spanning 1 263 410 250 base pairs, has a scaffold N50 of 50.5 Mb, a contig N50 of 13.1 Mb, and a BUSCO completeness score of 97.8%. A comparative analysis of the two species revealed relatively conserved genomes, with the exception of two inversions at chromosome 20. We annotated a total of 34 090 genes with a BUSCO completeness score of 98.1% for the tui chub, and 28 193 genes with a score of 97.4% for the arroyo chub. These assemblies will be valuable resources for characterizing the species' phylogeographic histories and delineating the role of hybridization in their evolution.

Aardwolf (Proteles cristatus) is one of the four extant hyenas. Up to now, chromosome analysis of the aardwolf is limited to the knowledge that this insectivorous hyena shares the same 2n=40 diploid chromosome number with the three bone-crushing hyena species. Here we present a detailed conventional banding and molecular cytogenetic characterization of the aardwolf karyotype. A chromosome-by-chromosome comparison with the spotted hyena (Crocuta crocuta) shows extensive conservation of chromosome size, morphology and banding patters between the two hyenas. Karyotype conservation in hyenas is further supported by cat-aardwolf Zoo-FISH revealing almost identical patterns with previously available cat-spotted hyena Zoo-FISH, as well as extensive conserved synteny between cats and hyenas. Notably, hyena Chr12 and cat E1 share conserved synteny and carry the single nucleolus organizer region in both groups of species. Telomere-FISH in aardwolf and cat revealed only canonical telomeres and no interstitial sites, thus consistent with the overall karyotype conservation. However, there are also differences between aardwolf and spotted hyena Chr15, Chr16, and Chr19 due to heterochromatic additions in the aardwolf. Of these, the metacentric aardwolf Chr16 serves as a genomic feature that distinguishes this species from the spotted hyena in which the homeologous chromosome is acrocentric. In conclusion, improved cytogenetic and molecular characterization of the aardwolf karyotype expands the comparative knowledge about mammalian karyotypes and chromosome evolution, supports karyotypic conservation in feliform carnivores, and facilitates the construction of a high-quality chromosome-level annotated genome assemblies for the aardwolf and other hyenas.

Fremontodendron (Malvaceae) is a genus of shrubs native to the California Floristic Province (CFP) with dense, stellate trichomes on their leaves (hence the common name "flannelbush"). The current treatment of the genus includes the widespread and morphologically variable species Fremontodendron californicum, along with the rare F. decumbens and F. mexicanum. While F. californicum is spread across several ecoregions of the CFP, F. decumbens and F. mexicanum are highly restricted. Here, we introduce the first genome-scale resource with which to study this important genus, a de novo, scaffold scale assembly of an individual of F. californicum. Following the overall strategy of the California Conservation Genomics Project (CCGP), we used Pacific Biosciences HiFi long reads and Omni-C chromatin mapping to produce an assembly of the nuclear and plastid (chloroplast) genomes. The nuclear assembly consists of two, phased haplotypes, haplotypes one and two, with similar sizes of around 1.2 Gb, similar scaffold N50s around 26 Mb, and each with a Benchmarking Universal Single-Copy Ortholog (BUSCO) completeness score of 99.4%. This assembly will be a valuable resource for understanding the distribution, genetic variation, and species delimitation of this California genus of conservation value, as well as a tool to further investigate the complex evolutionary history of Malvaceae s.l.

The evolutionary dynamics of sex chromosomes differ from autosomes due to their unique pattern of inheritance and regions of hemizygosity in non-recombining areas. However, the study of sex chromosomes and sex-linked gene evolution has been limited by the rarity of truly novel sex chromosome complements in model systems. Recent advances in next-generation sequencing have enabled the identification of neo-sex chromosomes, created by the fission or fusion of autosomes with sex chromosomes, providing a new avenue to investigate the dynamics of sex chromosome evolution. Squamate reptiles, particularly Anolis lizards, are an excellent system for studying the consequences of sex-linkage due to their frequent sex chromosome-autosome fusions. The Hispaniolan Bark Anole, Anolis distichus, has experienced two sex chromosome and autosome fusions that led to a multiple sex chromosome system (X1X2Y). We present a high-quality whole-genome assembly and annotation of a male A. distichus (X1X2Y), enabling a detailed analysis of all three of its neo-sex chromosomes. We identify AnoDisX1, AnoDisX2, and AnoDisY chromosomes from assembly scaffolds using an integrative approach, and estimate degeneration and selection strength. Our results support long-held theories of differential evolutionary pressures in sex chromosomes, such as the Fast X effect and Y degeneration. Additionally, we observe that chromosome 12 has become sex-linked in two different Anolis species, suggesting that some autosomes may be more likely to become sex-linked. Altogether, our genome adds to the diversity of available taxa sequenced and enables novel comparative analyses in a variety of fields, including speciation, chromosomal synteny, and sex chromosome evolution.

Admixed genomes, particularly those with an evolutionary history of genetic exchange with an endangered or extinct species, are valued for innovative and unconventional conservation actions. Here, we show the substantial conservation value that the admixed canids of the Gulf Coast have as they retain high amounts of contemporary Red Wolf ancestry and unique genetic variation of past Red Wolf lineages (e.g., ghost ancestry). We analyzed 54,439 loci genotyped across the genome of 413 North American canids and investigated the role that assortative mating with respect to ancestry proportions played in the retention of endangered genetic variation. We report high correlations of inter-chromosomal ancestry proportions that varied with geographic location along Texas and Louisiana Gulf Coast populations, with the stronger signatures reported in the latter. We found that models of assortative mating promoted greater ancestry variance compared to random mating leading to increased efficiency of selection for Red Wolf and ghost alleles. Despite the Red Wolf being extinct in the wild, original and ghost genomic variation persists in Gulf Coast admixed canids. We suggest two conservation strategies that value and preserve this unique and endangered genomic variation through designed breeding programs. Ultimately the incorporation of this ghost genetic variation would be valuable to boost the genetic viability of the ex situ Red Wolf breeding program, create in situ redundancy, and avoid extinction for this endemic American wolf species.

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.

Ecological and genetic interactions of species at the far end of the speciation continuum can often be studied in sympatry. Triturus cristatus (C) and T. marmoratus (M) are two deeply differentiated yet hybridizing salamander species that engage in a mosaic distribution over a wide zone of range overlap in the west of France. Interspecies hybrids are easy to distinguish from both parentals and occur at ca. 3% of the total breeding population. Most hybrids are thought to be F1 diploids (CM). We aim to identify triploid F1 hybrids with single nucleotide polymorphism (SNP) data and determine their frequency. Special attention to the genus Triturus is warranted because triploidy might in principle constitute an escape route to the enigmatic chromosome-1 syndrome that constitutes a long-term 50% genetic load. Species-specific signals for a panel of 30 SNPs, analysed with metric multidimensional scaling, suggest that triploid frequency is one out of 26 (3.8%), although a frequence of 18% was found in a larger sampling (N=100) that paid particular attention to aberrant hybrid phenotypes. Triploids with a CMM genetic configuration appear more frequent than the CCM counterpart. The triploid status could be confirmed for two CMM females, either by target capture or cellular morphometric data. One triploid individual relocated in the field showed a hybrid phenotype leaning towards T. marmoratus, an exceptional life span (17+ yrs), length (187 mm) and the frequent skipping of annual breeding opportunities. Future research on the T. cristatus - T. marmoratus system should consider the different classes of interspecies hybrids.

The Adriatic sturgeon, Acipenser naccarii, a tetraploid species endemic to the North Adriatic region, has experienced significant population declines, resulting in its classification as "Critically Endangered" by the IUCN. Historically widespread in the Adriatic Sea's tributaries, the species is now at high risk of extinction with occasional reproductions occurring in the wild. Using long-read sequencing (PacBio HiFi) and chromatin conformation capture sequencing (Hi-C), we generated a phased reference genome for the tetraploid Adriatic sturgeon. The haploid assembly spans 1.94 Gb across 2,083 scaffolds, with a contig N50 of 1.024 Mb, a scaffold N50 of 39.6 Mb, and a scaffold L90 of 276. Approximately 80% of the genome is contained within the first 60 scaffolds, indicating a high degree of contiguity. The BUSCO completeness score of the haploid assembly reached 88.9%, while combined metrics for all four haploid assemblies increased to 94.1%. This comprehensive genomic resource provides valuable insights into the genetic and evolutionary mechanisms of polyploidy and, more specifically, it will improve our understanding of the genetic diversity of the Adriatic sturgeon, thereby informing targeted conservation strategies for this critically endangered species.

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 to 2.45 Gbp, N50 values of 137 to 145 Mbp, and high BUSCO scores (93.6% to 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% to 40.4% of the assemblies, with a prevalence of LINEs and SINEs, and are 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 verify 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.

The phylum Bryozoa is an understudied, yet commonly-occurring, globally distributed bilaterian metazoan organismal group. They have a colonial lifestyle and an evolutionary history that spans at least 480 million years but likely longer. Despite their contentious phylogenetic affinities among metazoans, disproportionately few genomic investigations have been performed thus far. Here, we describe the first chromosome-level genome assembly of an individual Flustra foliacea colony belonging to the order Cheilostomatida, collected in southern Norway. The haplotype-resolved assembly of F. foliacea contains two pseudo-haplotypes spanning 956 megabases and 880 megabases, respectively. Both assemblies are highly complete both in terms of scaffolding (>90% of sequences placed in 8 autosomal chromosomal pseudomolecules), and gene content (BUSCO completeness scores > 90%). We also present gene and repeat annotations of the two assemblies. A comparison of our newly sequenced F. foliacea with five previously published bryozoan genomes supports the hypothesis that the group has undergone extensive genome rearrangements. This includes multiple chromosomal fusions in F. foliacea since their split with other cheilostome bryozoans. These fusions were enriched with long terminal repeat (LTR) retrotransposons, highlighting the complex interplay between genome organization and genomic repeats. Our study contributes to a deeper understanding of bryozoan genome evolution and the role of repeats in metazoan genome organization.

Many species are undergoing rapid population declines and environmental deterioration, leading to genomic erosion. Here we define genomic erosion as the loss of genetic diversity, accumulation of deleterious mutations, maladaptation, and introgression, all of which can undermine individual fitness and long-term population viability. Critically, this process continues even after demographic recovery due to a time-lagged impact of genetic drift, which is known as drift debt. Current conservation assessments, such as the IUCN Red List, focus on short-term extinction risk and do not capture the long-term consequences of genomic erosion. Likewise, the longer-term assessments of the IUCN Green Status may overestimate population recovery by failing to account for the enduring effects of genomic erosion. As genome sequencing becomes increasingly accessible, there is a growing opportunity to quantify genomic erosion and integrate it into conservation planning. Here, we use genomic simulations to illustrate how different genomic metrics are sensitive to the drift debt. We test how ancestral effective population size (Ne) and bottleneck history influence the tempo and severity of genomic erosion. Furthermore, we demonstrate how these dynamics shape genetic load and additive genetic variation, which are key indicators of long-term evolutionary potential. Finally, we present a proof-of-concept for a Genomic Green Status framework that aligns genomic metrics with conservation impact assessments, laying the foundation for genomics-informed strategies to support species recovery.

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. 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, 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. 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.

The golden jackal (Canis aureus) is rapidly expanding its range in Europe, driven by climate and habitat changes, human influence, and changes in competition with wolves. Its ecological flexibility enables it to thrive in various habitats, including urban areas, raising concerns about its potential role in spreading zoonotic diseases. Jackals may act as reservoirs for pathogens such as Lyme disease and babesiosis, affecting wildlife, humans, and pets. Their close genetic relationship with domestic dogs also increases the risk of hybridization and host-jumping, complicating disease dynamics. To better understand their dispersal ability and host-pathogen dynamics, we present the first pseudochromosomal genome assembly of the golden jackal, generated using PacBio HiFi sequencing and reference-based scaffolding. The final assembly has a total length of 2.53 Gb in 325 scaffolds, with 98.41% of the sequence anchored to the expected 38+XY chromosomes. The assembly shows high contiguity, with scaffold and contig N50 values of 68.03 Mb and 56.64 Mb, respectively. Annotation revealed 20,620 protein-coding genes, and repetitive elements account for 40.58% of the total assembly. This highly contiguous reference genome provides an essential resource for studying the genetic basis of the golden jackal's adaptation, ecological interactions, and potential as a zoonotic reservoir. It also supports efforts to monitor population expansion and its effects on ecosystems. By advancing our understanding of golden jackal genetics, this work enables future research on evolution, host-pathogen dynamics, and the broader consequences of wildlife dispersal in a rapidly changing environment.

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.

Understanding the processes that shape spatial genetic differentiation is essential for understanding how populations adapt to environmental change. By evaluating the influence of these processes, we can gain insights into evolutionary dynamics and the potential for species to respond to shifting landscapes. Three well-accepted processes that create spatial patterns in genetic variation are isolation-by-distance (IBD), where individuals are more genetically similar the closer they are geographically; isolation-by-environment (IBE), where gene flow is reduced due to selection against migrants in unsuitable ecological conditions; and isolation-by-resistance (IBR), where landscape features limit dispersal. We conducted a macrogenetic meta-analysis of single-nucleotide-polymorphism data to identify patterns shaping spatial genetic differentiation in 40 mammalian datasets globally. For each species, we built a species-distribution model and combined it with the global Human Footprint layer to create a composite resistance surface, revealing that habitat suitability and anthropogenic impact contribute roughly equally to resistance. Model selection tests found IBR was the mechanism most frequently retained in the best models and had the highest variable importance. IBD and IBE alone had little effect but were often selected alongside IBR, suggesting they may have secondary, context-dependent effects. However, the probability of finding IBD in the best model of divergence significantly increased as the number of populations sampled increased. Similarly, the probability of finding IBE increased with the spatial scale of the study. Our findings suggest that resistance is pervasive in shaping genetic variation in mammals worldwide, but that study design affects our ability to detect the presence of IBD and IBE.

Acmispon is a legume genus that has diversified within the California Floristic Province. Acmispon species live in a variety of habitats including coastal sage scrub, deserts, grasslands, and woodlands, and form symbiotic associations with nitrogen-fixing bacteria. Here, we report the first, chromosome-level assembly of Acmispon strigosus (Strigose bird's-foot trefoil or Strigose lotus) as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genome pipelines of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly is 519 Mb in length, with a contig N50 of 22.97 Mb, scaffolded into seven pseudo-chromosomes. Using the NCBI egapx pipeline, we annotated a total of 21 347 genes resulting in a protein BUSCO completeness score of 91.5%. This is the first genome assembled for Acmispon and among the first genomic resources available for a native California legume. The assembly BUSCO completeness score of 94.8% makes it one of the most complete genomes for the tribe Loteae (Fabaceae). Generating whole genome sequences will contribute to our general understanding of nitrogen-fixing legume's adaptations to diverse soil and environmental conditions, interactions with nitrogen fixing Bradyrhizobium and Mesorhizobium symbionts, and the degrading effects of pollution-induced nitrogen deposition to the legume-rhizobium symbiosis in California. These data will also help to reconstruct phylogenetic relationships among Acmispon spp., which remain unresolved.

Examples of convergent evolution, wherein distantly related organisms evolve similar traits, including behaviors, underscore the adaptive power of natural selection. In birds, obligate brood parasitism, and the associated loss of parental care behaviors, has evolved independently in seven different lineages, though little is known about the genetic basis of the complex suite of traits associated with this rare life history strategy. We generated genome assemblies for ten brood parasitic species plus eight species representatives of their parental/nesting outgroups. This includes nine long-read chromosome-level assemblies, with scaffold N50 sizes ranging from 38.1 to 72.6 MB, and gene representation completeness measures >97%. Leveraging this new catalog of avian genomes, we constructed clade-level alignments that reveal variation in chromosomal synteny, provide first-time or improved annotations of protein-coding and non-coding genes, and define cross-species ortholog reference sets. We also refine estimates for the timing of the seven independent origins of brood parasitism, ranging from recent events such as 1.6-4.5 million years ago in Molothrus cowbirds to much earlier origins over 30 million years ago in two of the three cuckoo lineages. These genomic resources lay the foundation for investigating the genetic and genomic underpinnings of brood parasitism, including the loss of parental care, shifts in mating systems, perhaps resulting in heightened sperm competition, elevated annual fecundity, improved spatial cognition related to nest-finding, and the diverse adaptations shaped by intense coevolution with host species.

The meadowfoams are annual plants in the genus Limnanthes, a group characterized by striking displays of bloom in damp, grassy habitats. The genus is endemic to western North America and, of the seven species and nineteen subspecies currently described, several are listed as rare or endangered due to extensive habitat loss. Species in the genus exhibit diverse reproductive systems and associations with specialist pollinators, both of which influence genetic diversity and gene flow. However, genomic studies across the genus remain limited, particularly for threatened taxa, hindering effective conservation strategies. Morphological variation within Limnanthes subspecies is also poorly understood, and phylogenetic relationships among several taxa remain unresolved. As part of the California Conservation Genomics Project, a reference genome for Limnanthes douglasii R. BR. has been assembled to help address these gaps. This genomic resource will support research into the evolutionary relationships, ecological interactions, and population structure of Limnanthes. Additionally, given that Limnanthes seeds yield a unique, high-stability oil, the genome has agricultural relevance, particularly for enhancing oil production and desirable reproductive traits in cultivated taxa.