Journal of Heredity最新文献

{"title":"Life history and chromosome organization determine chemoreceptor gene expression in rattlesnakes.","authors":"Michael P Hogan, Matthew L Holding, Gunnar S Nystrom, Kylie C Lawrence, Emilie M Broussard, Schyler A Ellsworth, Andrew J Mason, Mark J Margres, H Lisle Gibbs, Christopher L Parkinson, Darin R Rokyta","doi":"10.1093/jhered/esae078","DOIUrl":"10.1093/jhered/esae078","url":null,"abstract":"<p><p>Predatory species who hunt for their prey rely on a suite of integrated characters, including sensory traits that are also used for nonpredatory behaviors. Linking the evolution of sensory traits to specific selection pressures therefore requires a deep understanding of the underlying genetics and molecular mechanisms producing these complex phenotypes. However, this relationship remains poorly understood for complex sensory systems that consist of proteins encoded by large gene families. The chemosensory repertoire of rattlesnakes includes hundreds of type-2 vomeronasal receptors and olfactory receptors, representing the two largest gene families found in the genome. To investigate the biological importance of this chemoreceptor diversity, we assessed gene expression in the eastern diamondback rattlesnake (Crotalus adamanteus) and identified sex- and age-biased genes. We found type-2 vomeronasal receptor expression in the vomeronasal epithelium was limited to juvenile snakes, suggesting the sensory programming of this tissue may be correlated with early life development. In the olfactory epithelium, we found subtle expression biases that were more indicative of life history rather than development. We also found transcriptional evidence for dosage compensation of sex-linked genes and trait integration in the expression of transcription factors. We overlay our molecular characterizations in Crotalus adamanteus onto updated olfactory receptor and type-2 vomeronasal receptor phylogenies, providing a genetic road map for future research on these receptors. Finally, we investigated the deeper macroevolutionary context of the most highly expressed type-2 vomeronasal receptor gene spanning the rise of tetrapods and estimated the strength of positive selection for individual amino acid residues in the predicted protein structure. We hypothesize that this gene may have evolved as a conserved signaling subunit to ensure consistent G-protein coupled receptor functionality, potentially relaxing signaling constraints on other type-2 vomeronasal receptor paralogs and promoting ligand binding specificity.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"617-631"},"PeriodicalIF":2.5,"publicationDate":"2025-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12400810/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144057397","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phylogenetic relationships and species delimitation of bunchgrass lizards of the genus Sceloporus from Mexico with the description of a new species.","authors":"Tristan Charran, Jesús A Loc-Barragan, Rafael Alejandro Calzada-Arciniega, Liz A Alfaro-Juantorena, Raúl Cueva Del Castillo, Christopher Blair, Víctor H Jiménez-Arcos","doi":"10.1093/jhered/esaf020","DOIUrl":"10.1093/jhered/esaf020","url":null,"abstract":"<p><p>Molecular data continue to serve as an invaluable tool to assess species limits and patterns of cryptic diversity, particularly in areas harboring high levels of biodiversity. The Sceloporus scalaris group, known as bunchgrass lizards, contains 13 described and one undescribed species distributed throughout high elevation biotas of Mexico. However, recent studies suggest that diversity in the group may be substantially underestimated. We collect new sequence data from four independent loci to determine the evolutionary distinctiveness and phylogenetic relationships of an isolated population of bunchgrass lizard in the Sierra San Juan (SSJ) in the Mexican state of Nayarit. Concatenation and coalescent-based phylogenetic and species delimitation analyses suggest that this population represents a distinct evolutionary lineage allied to the S. scalaris group. We describe the new SSJ population as a new species to better account for its morphological and evolutionary distinctiveness. Divergence within the species group occurred during the Neogene and Quaternary, most likely due to range shifts associated with mountain uplift and glacial-interglacial cycles. Our results provide additional evidence that supports the importance of the Mexican highlands as a biodiversity hotspot which maintains cryptic lineages awaiting discovery.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"603-616"},"PeriodicalIF":2.5,"publicationDate":"2025-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143774983","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome assembly of the endangered Santa Marta Harlequin Toad, Atelopus laetissimus, endemic to the Sierra Nevada de Santa Marta of Colombia.","authors":"Victor L N Araújo, José H Grau, Luis Alberto Rueda-Solano, José D Barros-Castañeda, Sandra V Flechas, Andrew J Crawford","doi":"10.1093/jhered/esaf029","DOIUrl":"10.1093/jhered/esaf029","url":null,"abstract":"<p><p>Despite the critical conservation status of many harlequin toads (Anura: Bufonidae: Atelopus) and their significance in elucidating the impacts of emerging diseases on amphibians, genomic data for this genus are scarce. Here, we present a de novo genome assembly of the Santa Marta Harlequin Toad, Atelopus laetissimus, using PacBio HiFi sequencing data, representing the first published Atelopus genome assembly and only the second amphibian genome assembly from Colombia. The assembly consists of 1,487 contigs at 35× coverage with an N50 of 31 Mb and a total length of 3.5 Gb. A Tetrapoda BUSCO score of 92% suggests our assembly is very nearly complete. Analysis revealed a high repeat content, with 70% of the genome consisting of interspersed repeats. This high-contiguity draft assembly will drive the search for a possible genetic basis of pathogen resistance in these endangered toads of the Sierra Nevada de Santa Marta, as well as facilitate ongoing evolutionary studies.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"673-679"},"PeriodicalIF":2.5,"publicationDate":"2025-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144082166","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction to: Forensic assessment of kinship, genomic ancestry, and natural history of an iconic tiger of Harlem, New York City.","authors":"","doi":"10.1093/jhered/esaf043","DOIUrl":"10.1093/jhered/esaf043","url":null,"abstract":"","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"713"},"PeriodicalIF":2.5,"publicationDate":"2025-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144546230","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Insights from the timber rattlesnake (Crotalus horridus) genome for MHC gene architecture and evolution in threatened rattlesnakes.","authors":"Marissa A Roseman, Andrew J Mason, Emily R Bode, Peri E Bolton, Pedro G Nachtigall, William E Peterman, H Lisle Gibbs","doi":"10.1093/jhered/esae075","DOIUrl":"10.1093/jhered/esae075","url":null,"abstract":"<p><p>Conservation of threatened species can benefit from an evaluation of genes in the major histocompatibility complex (MHC), whose loci encode proteins that bind pathogens and are often under strong selection to maintain diversity in immune response to diseases. Despite this gene family's importance to disease resistance, little is known about these genes in reptiles including snakes. To address this issue, we assembled and annotated a highly contiguous genome assembly for the timber rattlesnake (Crotalus horridus), a pit viper which is threatened or endangered in parts of its range, and analyzed this new genome along with three other rattlesnake genomes to characterize snake MHC loci. We identified highly duplicated MHC Class I and Class IIβ genes in all species typified by a genomic architecture of discrete gene clusters localized on chromosome 2. The number of loci varied between species from 14 to 23 for MHC I and from 8 to 32 for MHC IIβ and was greater than previously identified in the few non-genome-based studies of reptile MHC to date. We present evidence of the gene family's complex evolutionary history, with extensive duplication and loss concurrent with speciation resulting in incomplete lineage sorting. The differences in gene number between species combined with a dynamic evolutionary history suggest that gene family expansion/contraction via rapid duplication/gene loss may represent an important mechanism for generating genetic diversity in rattlesnake MHC. Our work demonstrates the utility of whole-genome sequences for identifying functional genetic variation in the form of MHC genes relevant for conservation genomic studies in threatened snakes.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"591-602"},"PeriodicalIF":2.5,"publicationDate":"2025-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142866480","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The first de novo genome assembly and annotation of a green-blooded skink (Prasinohaema aff. flavipes) from a historic museum sample.","authors":"Taylor S Probst, Daniel D Davis, Alison S Whiting, Paul B Frandsen","doi":"10.1093/jhered/esaf014","DOIUrl":"10.1093/jhered/esaf014","url":null,"abstract":"<p><p>The scincid genus Prasinohaema represents the only group of amniotes to possess green blood, resulting from the accumulation of the bile pigment biliverdin. Recent phylogenetic analyses have shown Prasinohaema to be polyphyletic with four independent origins for green blood. It is unknown why this trait has evolved in multiple instances and how Prasinohaema species are able to tolerate such high concentrations of a cytotoxic bile pigment. Here, we report the first de novo genome assembly and annotation for a green-blooded skink, Prasinohaema aff. flavipes, which was sequenced from an ethanol-preserved specimen that was collected more than 20 years ago. Our assembly comprises 907 contigs spanning 1.52 Gbp with contig N50 of 3.2 Mbp. The genome is highly complete, with a BUSCO completeness score of 97.76%. Phylogenetic analysis confirmed that our specimen is sister to P. flavipes with high support; however, the two specimens exhibit deep genetic divergence, perhaps supporting their distinctiveness. Searches for the gene encoding serum albumin, a common blood transport protein known to bind biliverdin, suggested it is absent from our P. aff. flavipes genome. Yet, we found a tandem duplication of the serum albumin paralog alpha-fetoprotein, which may play a role in biliverdin retention. BUSTED analysis of alpha-fetoprotein sequences across reptiles revealed that both copies of alpha-fetoprotein from our Prasinohaema genome are under diversifying selection. We envision this new genome assembly as a valuable source in examining the key genes, regulatory mechanisms, and functional mutations involved in the elevated biliverdin levels.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"653-662"},"PeriodicalIF":2.5,"publicationDate":"2025-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12400806/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143676731","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ex situ reared black-footed ferrets exhibit altered sperm DNA methylation.","authors":"Alexandra L DeCandia, Stavi R Tennenbaum, Rachel Santymire, Travis Livieri, Robyn Bortner, Della Garelle, Adrienne Crosier, Paul Marinari, Budhan S Pukazhenthi, Pierre Comizzoli, Jesús E Maldonado, Klaus-Peter Koepfli, Bridgett M vonHoldt","doi":"10.1093/jhered/esaf056","DOIUrl":"https://doi.org/10.1093/jhered/esaf056","url":null,"abstract":"<p><p>Many endangered species rely on ex situ management for survival when external threats exist on the landscape. Yet ex situ settings pose challenges through space limitation, altered environment, and diet. This can lead to environmentally-determined inbreeding depression, where ex situ animals exhibit reduced reproductive fitness compared to their in situ counterparts, despite originating from the same genetic stock. We investigated epigenetic differences as a potential mechanism underlying environmentally-determined inbreeding depression in black-footed ferrets (Mustela nigripes), an North American endemic species reliant on ex situ conservation. More specifically, we explored how environmental context may influence sperm DNA methylation in samples collected from 12 ex situ and 5 in situ males. Average sperm DNA methylation was significantly higher in ex situ individuals. We additionally identified >500 differentially methylated regions between ex situ and in situ sperm samples that were enriched for gene ontology terms pertaining to reproduction and development. Putative genes of interest included NPR2, WEE2, SLC15A1, PDE10A, PIP5K1B, CACNA1E, and CACNA1A, all of which have previously been linked to spermatogenesis, sperm motility, or fertilization in mammals. Results suggest that environmental conditions may alter sperm DNA methylation in black-footed ferrets, with possible links to decreased reproductive success in ex situ settings. These findings provide valuable insights to the molecular mechanisms underlying environmentally-determined inbreeding depression in black-footed ferrets and other conservation-reliant species, and can serve as a foundation for future research on improving reproductive health in endangered wildlife.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144979329","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Chromosome-Level Genome Assembly and Annotation for the Beauty Snake Elaphe taeniura.","authors":"Jiahao Chen, Qin Liu, Songwen Tan, Peng Guo, Lianming Du","doi":"10.1093/jhered/esaf055","DOIUrl":"https://doi.org/10.1093/jhered/esaf055","url":null,"abstract":"<p><p>The genus Elaphe Fitzinger, a large species clade within Colubridae, comprises 18 non-venomous snake species. Among them, Elaphe taeniura serves as a representative species due to its wide distribution and strong adaptability. However, genomic studies on this group remain limited. Here, we present a chromosome-level, high-quality reference genome for this species. The genome is assembled by integrating high-accuracy PacBio HiFi long-read sequencing and Hi-C chromatin conformation capture technologies and comprehensively annotated with the aid of transcriptomic data. The genome of E. taeniura spans 1.62 Gb, with a scaffold N50 of 206.4 Mb and the longest scaffold reaching 344.4 Mb. The genome exhibits a BUSCO completeness score of 98.2% and contains 22,246 protein-coding genes. Comparative analysis between the assembled genome and three other colubrid species revealed high synteny. In addition, several chromosomal fusion and fission events were observed. This reference genome provides a valuable resource for studying the taxonomy, conservation, and evolutionary history of the widely distributed Elaphe species.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144859947","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome assembly of the Antipodean and Gibson's albatrosses (Diomedea antipodensis antipodensis and D. a. gibsoni).","authors":"Imogen Foote, Tom Oosting, Kath Walker, Graeme Elliott, Kalinka Rexer-Huber, Graham C Parker, Geoffrey K Chambers, Peter A Ritchie","doi":"10.1093/jhered/esaf054","DOIUrl":"https://doi.org/10.1093/jhered/esaf054","url":null,"abstract":"<p><p>Albatrosses are a highly threatened family of seabirds that are facing widespread declines, largely attributed to incidental fisheries bycatch mortality. Protection relies upon sound knowledge of distinct breeding units, but population structure has been difficult to detect due to low levels of genetic differentiation between closely related taxa. Whole-genome data have not yet been used to investigate this issue, and genomic resources for albatrosses are currently limited to a few fragmented genome assemblies. Here, we present high-quality reference genomes for both the Antipodean and Gibson's albatrosses (Diomedea antipodensis antipodensis and D. a. gibsoni), sequenced using Oxford Nanopore Technology and assembled with the Flye assembly algorithm. Both assemblies were around 1.25 Gb in length and comprised 255 and 313 scaffolds for the Antipodean and Gibson's assemblies, respectively. Although not chromosome-resolution assemblies the largest 60 scaffolds of each genome showed BUSCO completeness of ~ 97%. As well, most chromosomes are likely represented by only a few large scaffolds, as suggested by alignment of the two genomes, and alignment of each genome to an available chromosome-level assembly of Cory's shearwater (Calonectris borealis). These two high-quality reference genomes for albatross will allow population-level analysis of genomic diversity, gene flow and adaptive diversity to inform taxonomy and conservation management in a changing world.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144838590","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome Resources-A chromosome-Level genome assembly for the long-nosed leopard lizard, Gambelia wislizenii, the first reference genome for the lizard family crotaphytidae.","authors":"Jimmy A McGuire, Jonathan Q Richmond, Merly Escalona, Mohan P A Marimuthu, Oanh Nguyen, Samuel Sacco, Eric Beraut, Erin Toffelmier, Robert D Cooper, Michael Westphal, Robert N Fisher, Ian J Wang, H Bradley Shaffer","doi":"10.1093/jhered/esaf053","DOIUrl":"https://doi.org/10.1093/jhered/esaf053","url":null,"abstract":"<p><p>We report on an annotated chromosome-level genome assembly for the long-nosed leopard lizard, Gambelia wislizenii, as part of the California Conservation Genomics Project (CCGP). All seventeen species of reptiles, including two turtles, seven lizards, and seven snakes targeted for reference genome sequencing by the CCGP are now complete and posted on NCBI, and this paper is the third of seven CCGP lizard release papers to be published. It is also the first species of the family Crotaphytidae to have a released reference genome. Following the CCGP pipeline, the G. wislizenii genome was produced using Pacific Biosciences HiFi long reads and Omni-C proximity ligation data. The de novo assembly includes 69 scaffolds and has a total length of ~ 2.47 Gb, a scaffold N50 length of 380.1 Mb, and a BUSCO completeness score of 97.4% based on the tetrapod gene set. We improved the annotation of the genome using transcriptome sequencing (seven tissue types), identifying 23 279 genes, with BUSCO completeness of 98.9%. This reference genome, when combined with CCGP's on-going state-wide resequencing efforts for the three species of Gambelia in California, including the federally endangered blunt-nosed leopard lizard (Gambelia sila), and Cope's leopard lizard (G. copei), will be a powerful tool enabling researchers to characterize hybridization dynamics between Gambelia species, document the remaining diversity within G. sila, and explore the genetic underpinnings of key traits that vary between the three Gambelia species, such as territoriality, sexual size dimorphism, presence versus absence of male breeding coloration, and skull morphologies.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144755162","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}