Journal of Heredity最新文献

Castilleja lassenensis, a species of root-parasitic plants endemic to the Mt. Lassen region in northern California, has been subject to taxonomic debate since its first description in 1940. While morphological and ecological distinctions from its close relative C. lemmonii have been documented, many regional floras do not list C. lassenensis or treat it as a synonym of C. lemmonii. We sequenced the nuclear genomes of C. lassenensis and C. lemmonii and performed comparative genomic analyses including gene content, functional enrichment, and phylogenetic placement. The genome of C. lassenensis, although slightly smaller than that of C. lemmonii, shows higher gene content, with different patterns of gene duplication. Functional genomic analysis revealed distinct enrichment patterns in the two species, with metabolic and transport functions enriched in C. lassenensis versus cellular organization in C. lemmonii. The taxa also show divergence in peptidase and CAZyme distributions, as well as in KAI2d proteins involved in strigolactone perception. Population-level validation using diagnostic PCR markers across multiple individuals from geographically separate populations confirmed stable genomic differences. Our results support the recognition of C. lassenensis as a distinct species underscore the need for measures to ensure its conservation.

Appropriate identification of evolutionary significant units (ESUs) is essential for effective conservation planning. Genomic data has emerged as a key tool to inform ESU decisions, yet it remains unclear how genomic data are being used in practice to identify the number of ESUs. To address this, we conducted a systematic literature review and found that genomic data are increasingly being used to suggest numbers of ESUs globally across plant and animal taxa. However, our review revealed inconsistencies in how ESUs are defined, with many studies not providing a definition. We also found inconsistencies in the methods used to analyze genomic data, highlighting the need for greater standardization to ensure studies adequately address both the discreteness and evolutionary significant components of an ESUs. For example, separation on a PCA or a high Fst cannot ensure evolutionary significance as they may be due to recent processes such as habitat fragmentation. Adaptive loci, a key advantage of genomic data, need to be interpreted with caution and simply identifying these loci may lead to inflated ESU estimates. Overall, we found that 68% of studies suggested an increase in the number of ESUs, and that the amount of gene flow detected did not appear to influence this conclusion. We provide clear definitions of the two key components of ESUs and specify which analyses can be used to assess each, as well as provide recommendations for future studies aiming to identify ESUs with genomic data.

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.

We generated the first chromosome-level genome assembly for California grunion, Leuresthes tenuis, using PacBio HiFi long reads and Omni-C chromatin-proximity sequencing, yielding a 0.917 Gb genome with a scaffold N50 of 35 Mb and a BUSCO completeness score of 99.37. This beach-spawning marine silverside is the target of a unique recreational hand-grab fishery during its nocturnal spawning runs. Regulation of this fishery, initiated in 1927, remained unchanged from 1949 to 2022, when recent data suggesting a stock decrease led California Department of Fish and Wildlife to reduce the fishing season length. California grunion are endemic to the coast of California and northern Baja California, but within the last two decades the northern limit of spawning has expanded roughly 470 kilometers from Point Conception to north of San Francisco Bay. This genome will facilitate studies addressing the temporal and spatial genetic stock structure, and recent range expansion, of this unique charismatic native species and will also allow assessment of genetic responses to present and future environmental challenges such as changing temperature, and pollution as well as the impacts of harvest and effects of management.

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.

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.

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.

Tropical mountains are hotspots of biodiversity and they can harbor species with sky-island distributions on mountaintops. The summit rat, Rattus baluensis, is a Bornean endemic previously known from two populations in the Kinabalu range. Here, we report the discovery of a third, genetically distinct population on Mt. Trusmadi, Sabah, Borneo. Using 27 nuclear introns genotyped in 44 individuals, we show that this population is genetically isolated and more differentiated than those in the Kinabalu range. ABC analyses reveal the three populations likely became isolated in mountain tops during the Holocene. Genetic diversity and effective population size across the three populations correlate with the area of high-elevation habitat on each mountain. Despite relatively large population sizes and well-preserved habitats, the species' strict association with montane forest and confinement to three mountaintops make it particularly vulnerable to climate change, stochastic events, and localized anthropogenic impacts.

Ancestry variation in hybrid zones can reflect the causes and genetic basis of reproductive isolation and result in novel phenotypic variation with the potential for extended ecological effects. Junipers (Juniperus) are foundational tree species in many semi-arid landscapes of western North America and often hybridize in zones of secondary contact. Such hybridization can be ecologically significant in foundational tree species, due to the strong genetic control and ecological consequences of plant chemistry. We generated genetic and phytochemical data to analyze hybridization among Juniperus grandis, J. occidentalis, and J. osteosperma in western Nevada and the impact of hybridization on plant chemistry. We used population genomic data (9,125 SNPs, 326 individuals, 25 populations) to quantify patterns of genetic variation across populations and species and to characterize ancestry variation in hybrids. While populations within species showed little genetic differentiation, the parental species formed distinct, monophyletic lineages with clear phenotypic and ecological differences. Hybrids occupied intermediate environments, contained ancestry from all three parents, and were mainly F1 or backcross hybrids. Phytochemical data (GC-MS; 163 terpenoid compounds) were likewise analyzed to understand the consequences of hybridization for plant chemistry. The parental species and hybrids displayed distinct phytochemical profiles; hybrids had higher chemical diversity overall, and hybrid terpenoid concentrations were often intermediate or exceeded the range of all parental species. Our results illustrate that geography and environment shape hybrid ancestry for a syngameon involving three Juniperus species, and that admixture generates novel phytochemical variation likely to have ecological consequences.

Estimators for the numbers of polymorphic loci or alleles, such as private allele counts or allelic richness, are not as commonly used or well developed for single nucleotide polymorphism (SNP) data as are genetic estimators which rely on direct measurements of allele frequencies (such as expected heterozygosity, nucleotide diversity, and Tajima's θ). The number of segregating sites (S), the number of nucleotide sites that have more than one allele across the genome (e.g., SNPs), is one such estimator which does not rely on estimates of allele frequencies. S can provide informative estimates of genetic diversity across multiple scales, from genes to chromosomes to entire genomes, and is particularly informative when used in conjunction with allele frequency dependent estimators such as expected heterozygosity. However, segregating site counts are rarely adjusted to correct for unequal sample sizes or differences in missing data among populations or sample groups, and when they are, they typically fail to account for deviations from Hardy-Weinberg Proportions (HWP). Here, we introduce an unbiased estimator for the number of segregating sites expected in a sample group following rarefaction (S') and we use simulated data sets to illustrate that S' allows for accurate comparisons of the number of segregating sites among multiple sample groups with varied sample sizes and deviations from HWP. Lastly, by re-analyzing two existing empirical datasets which calculated S we show that S' produces different and less variable rank-order genetic diversity estimates than either S or Watterson's θ, which may have potential impacts on downstream biological inference.