Journal of Heredity最新文献

Introgressive hybridization is widespread in nature, often between native and introduced species. Closely related species also share ancestral genetic variation that mimics introgressive hybridization. In this study, we employed reduced-representation genome sequencing to test whether elevated levels of genetic variation in a protected fish species were best explained by hybridization or shared ancestry with an introduced nonnative fish. Gila Trout Oncorhynchus gilae is endemic to remote headwaters of the Gila River in the southwestern US. Its close relative, Rainbow Trout O. mykiss, was stocked into the Gila River from the late 1890s to the late 1960s. Shortly thereafter, Gila Trout was protected under the US Endangered Species Act. An isozyme study conducted in the late 1990s identified introgressed individuals in Iron Creek, a genetically distinct Gila Trout lineage. This finding was important for conservation because Iron Creek harbors unique genetic variants and is the 'wildest' Gila Trout lineage with no hatchery influence. We reassessed genetic variation in the Iron Creek lineage using nextRAD and contemporary samples and found little evidence of recent introgression with Rainbow Trout. We simulated Wright-Fisher evolution under different scenarios assuming that Iron Creek was previously hybridized to explore potential mechanisms responsible for loss of nonnative alleles. Though not fully conclusive, the preponderance of evidence indicates genetic variation shared with Rainbow Trout arises from retention of ancestral polymorphism in Iron Creek Gila Trout. Recent common ancestry of potentially hybridizing species poses an important challenge to wholesale application of structured decision frameworks to manage putatively introgressed populations.

The Ural owl (Strix uralensis) is a large member of the Strigidae family and inhabits Eurasian forests from Germany to Japan. However, it faces increased range reduction, particularly at its southwestern distribution edges. Despite being considered "Least Concern" by the IUCN, local populations have become threatened in Central Europe due to severe habitat loss. Reintroduction programs aim to restore these populations by closing distribution gaps and facilitating natural recolonization of suitable habitats. To support these efforts, genomic resources have become an established tool to assess genetic diversity, geographic structure, and potential inbreeding, crucial for maintaining the genetic health and adaptability of newly established populations. Here, we present a de novo genome assembly and transcriptome of the Ural owl based on ONT long-reads, Omni-C Illumina short-reads, and RNASeq data. The final assembly has a total length of 1.26 Gb, of which 96.42% is anchored into the 42 largest scaffolds. The scaffold and contig N50 values of 88.65 Mb and 21.74 Mb, respectively, a BUSCO/compleasm completeness of 97.5%/99.65% and k-mer completeness of 95.18%, emphasize the high quality of this assembly. Furthermore, annotation of the assembly identified 17,650 genes and a repeat content of 12.48%. This new highly contiguous and chromosome-level assembly will greatly benefit Ural owl conservation management by informing reintroduction programs about the species' genetic health and contributing a valuable resource to study genetic function in greater detail across the whole Strigidae family.

Cutthroat trout (Oncorhynchus clarkii) are diverse Pacific salmonids widely distributed throughout western North America. Distinct lineages of cutthroat trout have been defined based on morphology, geography, and genetic differences. Several of these, including Lahontan cutthroat trout (Oncorhynchus clarkii henshawi), are classified as threatened or in danger of extinction. Despite their precarious conservation status, few genomic resources have been developed for these lineages. In an effort to promote the development and application of genomic approaches for research and conservation of this group, we present the first high-quality reference genome for Lahontan cutthroat trout. We use this genome assembly to describe genomic synteny and structural rearrangements with their sister species, rainbow trout (O. mykiss), as well as with the diverged westslope cutthroat trout (O. clarkii lewisi) lineage.

Investigating geological and climatic shifts in the Himalayan-Hengduan Mountains (HHM) and Qinghai-Tibet Plateau (QTP) is vital for unraveling environmental impacts on biogeography and evolution. We analyzed the evolutionary history of 3 Notholirion species across these regions, studying 254 individuals from 31 populations using 5 chloroplast DNA markers (matK, ndhA, ndhG-ndhI, petB-petD, and petL-petG) and nuclear ITS. A total of 1,145 low-copy nuclear genes (LCGs) and 112 chloroplast genes from 11 representative individuals were further utilized for phylogenetic reconstruction. Divergence timing was estimated with 147 plastomes, including 10 Notholirion populations. Fourteen cpDNA and 27 ITS haplotypes revealed species-specific variation. Phylogenetic analyses confirmed a monophyletic origin for all 3 species, with population-level nested relationships and cytonuclear discordance attributed to incomplete lineage sorting (ILS) and hybridization. Dating and ancestral reconstruction traced Notholirion's origin to the southern Himalayas during the Late Oligocene (25.05 Ma), with diversification commencing in the Late Pliocene (7.43 Ma). MaxEnt modeling indicated stable species distributions from the Last Interglacial to future projections. The initial split of Notholirion was triggered by climate changes following the uplift of the QTP. Subsequently, dramatic climatic fluctuations during the Pleistocene and the complex topography of the HHM region jointly promoted species dispersal and diversification, ultimately shaping its current biogeographic distribution and phylogenetic structure. High genetic diversity likely stems from prolonged evolutionary history, sexual reproduction, and habitat fragmentation. The high genetic differentiation observed among Notholirion populations may be attributed to pronounced environmental changes across their distribution range, along with limited seed production and dispersal capacity.

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.

Globally, many bumble bee species are declining in abundance due to diverse factors that include habitat loss, pesticide exposure, disease, and climate change. Some species' populations, however, appear to be relatively stable or even increasing, with reasons for this disparity unclear. Increased genomic resources for different bumble bee species will aid in identifying any genetic causes of these differences. We assembled highly contiguous and complete de novo genomes of two species with different levels of population imperilment: the Sonoran bumble bee (Bombus sonorus Say 1837) and the Vosnesenky or yellow-faced bumble bee (B. vosnesenskii Radoszkowski 1862). Here we present genomes for both species assembled with Pacific Biosciences HiFi long reads and Dovetail Omni-C data. These genomes are at the scaffold level, but contain multiple chromosome-length scaffolds, and have similar or higher levels of contiguity of other published chromosome-level Bombus genomes. These genomic resources support conservation planning for both important pollinator species by facilitating future resequencing efforts to understand genetic variation within the species.

The Sierra Nevada Parnassian (Parnassius behrii W. H. Edwards, 1870) (Lepidoptera: Papilionidae) is a high-elevation specialist butterfly endemic to the Sierra Nevada, California. We present a genome assembly for P. behrii, representing the first major genomic resource for the Parnassius phoebus species complex. The assembly consists of two haplotypes, 1.59 Gb and 1.46 Gb in length, with contig N50 values of 10.93 Mb and 11.84 Mb, scaffold N50 values of 52.56 Mb and 51.90 Mb, scaffold L50 values of 13 and 14, and BUSCO completeness scores of 98.7% and 94.4%, respectively. Both haplotypes are highly contiguous, with 31 chromosome-length scaffolds, including putative Z and W sex chromosomes. We annotated the genome with NCBI's EGAPx pipeline, integrating database and novel transcript alignment with Hidden Markov Model-based gene predictions, yielding 17 191 genes with a BUSCO score of 98.1%. RepeatMasker identified that 26.68% (424.97 Mb) of the genome consists of repetitive elements. We also assembled a mitochondrial genome for P. behrii (15 391 bp) containing 2 rRNAs, 22 unique transfer RNAs, and 13 protein-coding genes. We also reviewed 514 high-quality butterfly genomes available from the National Center for Biotechnology Information (NCBI). Parnassius species were observed to have the largest genomes, with P. behrii being the largest. This assembly provides a foundational resource for whole-genome research on P. behrii and the broader P. phoebus complex, enabling analyses of evolutionary differentiation, local adaptation, inbreeding, gene flow, speciation, and conservation practices.

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.

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 F. 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 26Mb, and each with a 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.