Journal of Heredity最新文献

The ConGen Global course "Recent Advances in Conservation Genetics" was established to educate and empower new generations of researchers and practitioners in genetic and genomic approaches to biodiversity conservation. Since its first offering in 1996, the course has evolved from a focus on sample collection, population diversity assessment, and molecular phylogeography using (polymerase chain reaction (PCR) and Sanger sequencing to a curriculum centered on next-generation sequencing, whole-genome assembly, demographic inference, and bioinformatic analyses. Originally hosted at venues near Washington, D.C., the course expanded internationally in 2011 and has since been held near biodiversity hotspots across the globe, incorporating local researchers, and drawing an increasingly diverse global audience from every part of the world. Each edition integrates region-specific conservation challenges with hands-on tutorials, case studies, and personal narratives from leading conservation geneticists. This combination of rigorous science, practical applications, and international participation has created a uniquely impactful and inclusive program. Here, we review the last decade of ConGen Global (2015 to 2025), highlighting its contributions to conservation genetics education, its role in standardizing and disseminating new genomic methods, and its influence on policy-relevant research agendas. Beyond training, the course has shaped the broader field of conservation genetics by accelerating the adoption of genomic tools, strengthening global research networks, and translating genetic insights into conservation practice. Drawing on nearly three decades of experience, ConGen Global continues to serve as a model for advancing conservation genetics education and for inspiring future training programs worldwide.

The forked fungus beetle Bolitotherus cornutus has long served as a model organism for the study of population ecology, behavior, chemical ecology, and natural selection in the wild. Today, it has become one of the best model systems for the understanding of social evolution and group selection. To understand the mechanistic drivers of group selection and its ultimate evolutionary consequences, it is crucial to begin studying these traits at the molecular level. Here, we take the first necessary step towards these goals by producing a chromosome-level genome assembly for this species. Using a combination of PacBio HiFi and Hi-C sequencing technologies, we produce a 196 Mb genome assembly with ten major chromosomal scaffolds as well as an assembled mitochondrial genome. We also provide a carefully curated annotation of 12,459 protein-coding genes. The quality and completeness of these resources present essential tools for future genetic and genomic studies of B. cornutus.

De-extinction, once the realm of science fiction, has evolved into a tangible scientific endeavor thanks to breakthroughs in genome sequencing, engineering, advanced assisted reproductive technologies, and stem cell biology. Alongside this work are innovations in reintroduction science and artificial intelligence, which are refining strategies for species translocations, rewilding, and long-term ecosystem monitoring of de-extinct species and populations. While the primary motivation for de-extinction is restoring lost ecological functions to eroded ecosystems, each of these technologies can also be applied to conservation biology for de-endangerment, offering new solutions for biodiversity preservation. This review synthesizes the technological advancements emerging from de-extinction science and explores their broad applications in conservation, demonstrating how de-extinction is both about resurrecting lost species and about expanding the conservation toolkit to sustain and rebuild biodiversity in the face of accelerating environmental change.

Salicornia depressa (American pickleweed) is the most widespread member of its salt-loving genus in North America. Pickleweeds typically colonize high marsh areas that tides make highly saline. Most other salt marsh plants cannot withstand the same salt pressure, so these bare patches are free from competitive pressures. Understanding the genetic origin of American Pickleweed's high salinity adaptations has potential application to salt-tolerant agriculture and salt marsh conservation but requires genome resources to study. S. depressa is a tetraploid species, which presents unique challenges to traditional genome assembly pipelines. We present a high-quality, chromosome-scale reference genome of S. depressa and the pipeline we used to assemble it. Our reference is phased to each of the tetraploid's ancestral subgenomes with a scaffold N50 of 69.3 Mb, BUSCO completeness of 96.4%, and k-mer completeness of 98.4%. The subassemblies are evenly split, with subassembly A containing 56.7% and subassembly B containing 59.1% of genomic k-mers. Our gene annotation identifies 80 883 genes and our methylome annotation contains 2.5 million methylated cytosines. We find that gene and methylation density are negatively correlated across the genome. We also assembled and annotated a chloroplast assembly which includes all expected photosystem, tRNA, and rRNA genes. We provide a guide to our successful assembly pipeline involving > 30 programs. Our reference and annotation join resources for three other Salicornia species, allowing global scale ecological-evolutionary studies.

Biodiversity is declining at an alarming rate due to ongoing habitat destruction, climate change, pollution, the spread of invasive species, and unsustainable use of natural resources. In response, the Kunming-Montreal Global Biodiversity Framework (KMGBF), adopted in 2022, outlines a transformative goal to reverse biodiversity loss by 2030. The framework focuses on three main pillars: mitigating biodiversity threats, advancing implementation, and ensuring fair and sustainable use of biological resources. Meeting these objectives requires the adoption of innovative, adaptable, and inclusive monitoring strategies. Among these, environmental DNA (eDNA) has gained recognition as a non-invasive biodiversity assessment method that detects trace genetic material in environmental samples like sediment, soil, water, and air. Compared to conventional survey techniques, eDNA offers improved accuracy, sampling flexibility, and a non-destructive approach to monitoring ecosystems. Herein, we examine eDNA's role in achieving KMGBF goals to enable fulfilment of the Convention on Biological Diversity's vision of living in harmony with nature by 2050. We discuss its use in meeting several KMGBF targets including early detection of invasive species, enhancing biosecurity, monitoring species recovery, assessing pollution impacts, and supporting climate resilience. The standardization of eDNA protocols and alignment with FAIR (Findable, Accessible, Interoperable, Reusable) data principles ensure that results are transparent and interoperable across regions and platforms. Integrating eDNA into existing biodiversity monitoring networks enhances conservation planning, restoration efforts, and the management of protected areas. Additionally, eDNA facilitates inclusive conservation by supporting Indigenous-led and community-based monitoring, promoting stewardship, and enabling equitable access to biodiversity data worldwide.

The California vole (Microtus californicus) is a small cricetid rodent and one of 20 species of Microtus in North America and 60 worldwide. Several subspecies are listed as being of conservation concern in California, and one is federally protected. Here we present the first de novo genome assembly for the California vole, generated as a part of the California Conservation Genomics Project. The M. californicus genome was generated using a combination of PacBio HiFi long reads and Omni-C chromatin-proximity sequencing technology. Our high-quality genome is one of the most complete vole assemblies available, with a contig N50 of 49.8 Mb, scaffold N50 of 83.7 Mb, and BUSCO completeness score of 96.4%. Analysis of this genome together with genomes of closely related species revealed phylogenetic relationships and high levels of synteny among voles. The California vole genome provides an important new resource for comparative work across cricetid and muroid genomes. It will also serve as a reference for the analysis of within-species genetic diversity across widespread subspecies as well as more restricted populations of conservation concern.

The black dwarf honey bee, Apis andreniformis, is indispensable in pollinating tropical cash crops in Southeast Asian countries. It holds considerable ecological and economic importance, while its population is declining due to environmental disturbances and human intervention. Here, we report a high-continuity draft genome of A. andreniformis assembled from a combination of datasets including 30.02 Gb ultra-long Nanopore reads, 1.87 Gb PacBio Circular Consensus sequencing reads and 33.57 Gb short paired reads. The genome assembly is 219.86 Mb long consisting of 20 contigs with a contig N50 value of 14.01 Mb. A total of 10,135 protein-coding genes were predicted, of which 89.76% were functionally annotated. BUSCO evaluation showed high genome completeness with 98.49% of the core Hymenoptera genes being covered. The publication of this genome will facilitate future research on honey bees and also help to provide new insight into adaptive evolution via comparative genomics.

Nuclear mitochondrial DNA segments (NUMTs), which are mitochondrial DNA fragments integrated into the nuclear genome, serve as markers of evolutionary history. This study aims to enhance the detection and analysis of NUMTs by developing a script named NUMTsearcher. Utilizing the latest chromosome-level genome assemblies from various species, including human, rabbit, and six fish species, the study compares NUMTsearcher's performance against traditional methods such as LAST (Local Alignment Search Tool), BLAST (Basic Local Alignment Search Tool), BLAT (BLAST-Like Alignment Tool), and the pan-mitogenome approach, which integrates mitogenomes from diverse sources to identify fixed NUMTs in the nuclear genome. Simulation analyses indicate that false NUMTs affect the detection capabilities of both NUMTsearcher and LAST, with NUMTsearcher mitigating false positives by increasing the hspthresh value (also known as the K value), which sets the score threshold for high-scoring segment pairs (HSPs). In a comparative analysis with LAST on the rabbit genome, following optimization of the hspthresh value, NUMTsearcher reported only ten NUMTs as chromosomal inserts. A comparative analysis with the pan-mitogenome method identified 41 common NUMTs on chromosome 1 of the human genome and 22 previously unreported NUMTs. Our findings confirm the presence of NUMTs in Danio rerio, Takifugu rubripes, Tetraodon nigroviridis, Megalobrama amblycephala, Culter alburnus, and Chanodichthys erythropterus. The study further reveals that NUMT insertion timing varies across the six fish species, suggesting a significant degree of randomness. These results underscore the potential of NUMTs to influence evolutionary interpretations and deepen our understanding of their prevalence across diverse taxa.

The wrentit (Chamaea fasciata) is a chaparral and scrub specialist bird found from coastal Oregon to northern Baja California. We generated a draft reference assembly for the species using PacBio HiFi long read and Omni-C chromatin-proximity sequencing data as part of the California Conservation Genomics Project (CCGP). Sequenced reads were assembled into 1342 scaffolds totaling 1.19 Gb in length. A contig N50 of 4.5 Mb, scaffold N50 of 73.3 Mb, and BUSCO completeness score of 96.8% indicate that the wrentit genome is a highly contiguous assembly in line with other high quality avian assemblies. An annotation of the assembly identified 16 821 protein-coding genes. We detected a translocation between chromosome 4A of the zebra finch to the Z chromosome of the wrentit. This translocation has previously been identified as a neo-sex chromosome shared across the superfamily Sylvioidea. Finally, we found a negative correlation between transposable element richness and gene density across the genome, but a positive relationship between GC content and gene density. This reference will serve as an essential resource for studies on the biogeography, local adaptation, and conservation genetics of this iconic species of California's chaparral.

The California poppy (Eschscholzia californica), a native wildflower of western North America and the state wildflower of California, is characterized by extensive ecological variation and adaptation to diverse climatic conditions. Its broad geographic range and adaptability make it a valuable model for studying how plants respond to changing environmental conditions. Here, we present an updated, near-chromosome-level genome assembly for E. californica, developed as part of the California Conservation Genomics Project (CCGP). This assembly spans 0.401 Gb and represents an advancement over previous versions, with a scaffold N50 of 66.4 Mb, a contig N50 of 11.8 Mb, and BUSCO completeness of 99.2%, providing near-complete genomic coverage. The enhanced genome assembly described here facilitates precise whole-genome resequencing, providing insights into genetic diversity and gene flow between populations - key factors in understanding the adaptive mechanisms that will support the species' survival in the face of environmental challenges.