Journal of Heredity最新文献_第7页

Correction to: Implications of methodologies for integrating empirical kinships into ex situ population management using PMx: A case study of Baer's Pochard (Aythya baeri) in North America. 更正：使用 PMx 将经验亲缘关系纳入异地种群管理的方法学意义：北美巴尔雉（Aythya baeri）案例研究。

IF 3.1 2区生物学

Journal of Heredity Pub Date : 2024-05-09 DOI: 10.1093/jhered/esae014

引用次数: 0

A reference genome for the Andean cavefish Trichomycterus rosablanca (Siluriformes, Trichomycteridae): Building genomic resources to study evolution in cave environments. 安第斯洞穴鱼Trichomycterus rosablanca（丝形目，Trichomycteridae）的参考基因组：为研究洞穴环境中的进化建立基因组资源。

IF 3.1 2区生物学

Journal of Heredity Pub Date : 2024-05-09 DOI: 10.1093/jhered/esae019

Carlos Daniel Cadena, Laura Pabón, Carlos DoNascimiento, Linelle Abueg, Tatiana Tilley, Brian O-Toole, Dominic Absolon, Ying Sims, Giulio Formenti, Olivier Fedrigo, Erich D Jarvis, Mauricio Torres

{"title":"A reference genome for the Andean cavefish Trichomycterus rosablanca (Siluriformes, Trichomycteridae): Building genomic resources to study evolution in cave environments.","authors":"Carlos Daniel Cadena, Laura Pabón, Carlos DoNascimiento, Linelle Abueg, Tatiana Tilley, Brian O-Toole, Dominic Absolon, Ying Sims, Giulio Formenti, Olivier Fedrigo, Erich D Jarvis, Mauricio Torres","doi":"10.1093/jhered/esae019","DOIUrl":"10.1093/jhered/esae019","url":null,"abstract":"Animals living in caves are of broad relevance to evolutionary biologists interested in understanding the mechanisms underpinning convergent evolution. In the Eastern Andes of Colombia, populations from at least two distinct clades of Trichomycterus catfishes (Siluriformes) independently colonized cave environments and converged in phenotype by losing their eyes and pigmentation. We are pursuing several research questions using genomics to understand the evolutionary forces and molecular mechanisms responsible for repeated morphological changes in this system. As a foundation for such studies, here we describe a diploid, chromosome-scale, long-read reference genome for Trichomycterus rosablanca, a blind, depigmented species endemic to the karstic system of the department of Santander. The nuclear genome comprises 1 Gb in 27 chromosomes, with a 40.0× HiFi long-read genome coverage having an N50 scaffold of 40.4 Mb and N50 contig of 13.1 Mb, with 96.9% (Eukaryota) and 95.4% (Actinopterygii) universal single-copy orthologs (BUSCO). This assembly provides the first reference genome for the speciose genus Trichomycterus, serving as a key resource for research on the genomics of phenotypic evolution.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140186331","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}

引用次数: 0

Differentiated sex chromosomes, karyotype evolution, and spontaneous triploidy in carphodactylid geckos. 腕足动物的性染色体分化、核型进化和自发三倍体。

IF 3.1 2区生物学

Journal of Heredity Pub Date : 2024-05-09 DOI: 10.1093/jhered/esae010

Eleonora Pensabene, Barbora Augstenová, Lukáš Kratochvíl, Michail Rovatsos

{"title":"Differentiated sex chromosomes, karyotype evolution, and spontaneous triploidy in carphodactylid geckos.","authors":"Eleonora Pensabene, Barbora Augstenová, Lukáš Kratochvíl, Michail Rovatsos","doi":"10.1093/jhered/esae010","DOIUrl":"10.1093/jhered/esae010","url":null,"abstract":"Geckos exhibit derived karyotypes without a clear distinction between macrochromosomes and microchromosomes and intriguing diversity in sex determination mechanisms. We conducted cytogenetic analyses in six species from the genera Nephrurus, Phyllurus, and Saltuarius of the gecko family Carphodactylidae. We confirmed the presence of a female heterogametic system with markedly differentiated and heteromorphic sex chromosomes in all examined species, typically with the W chromosome notably larger than the Z chromosome. One species, Nephrurus cinctus, possesses unusual multiple Z1Z1Z2Z2/Z1Z2W sex chromosomes. The morphology of the sex chromosomes, along with repetitive DNA content, suggests that the differentiation or emergence of sex chromosomes occurred independently in the genus Phyllurus. Furthermore, our study unveils a case of spontaneous triploidy in a fully grown individual of Saltuarius cornutus (3n = 57) and explores its implications for reproduction in carphodactylid geckos. We revealed that most carphodactylids retain the putative ancestral gekkotan karyotype of 2n = 38, characterized by predominantly acrocentric chromosomes that gradually decrease in size. If present, biarmed chromosomes emerge through pericentric inversions, maintaining the chromosome (and centromere) numbers. However, Phyllurus platurus is a notable exception, with a karyotype of 2n = 22 chromosomes. Its eight pairs of biarmed chromosomes were probably formed by Robertsonian fusions of acrocentric chromosomes. The family underscores a remarkable instance of evolutionary stability in chromosome numbers, followed by a profound transformation through parallel interchromosomal rearrangements. Our study highlights the need to continue generating cytogenetic data in order to test long-standing ideas about reproductive biology and the evolution of genome and sex determination.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139747777","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}

引用次数: 0

Phylogeography of the freshwater crab Potamon persicum (Decapoda: Potamidae): an ancestral ring species? 淡水蟹Potamon persicum（十足目：Potamidae）的系统地理学：一个祖先环物种？

IF 3.1 2区生物学

Journal of Heredity Pub Date : 2024-05-09 DOI: 10.1093/jhered/esae016

Yaser Amir Afzali, Reza Naderloo, Alireza Keikhosravi, Sebastian Klaus

{"title":"Phylogeography of the freshwater crab Potamon persicum (Decapoda: Potamidae): an ancestral ring species?","authors":"Yaser Amir Afzali, Reza Naderloo, Alireza Keikhosravi, Sebastian Klaus","doi":"10.1093/jhered/esae016","DOIUrl":"10.1093/jhered/esae016","url":null,"abstract":"The Zagros Mountains, characterized by complex topography and three large drainage systems, harbor the endemic freshwater crab Potamon persicum in Iran. Our study delves into the evolutionary history of P. persicum, utilizing two mitochondrial and one nuclear marker. We collected 214 specimens from 24 localities, identifying 21 haplotypes grouped into two major evolutionary lineages. Substantial differentiation exists between drainage systems and lineages. Historical demographic analysis revealed a significant decrease in population size during the late Holocene, accompanied by a recent population bottleneck. Species distribution modeling has revealed eastward shifts in suitable habitats between the last glacial maximum and the present day. Following the last glacial maximum, habitat fragmentation occurred, resulting in the establishment of small populations. These smaller populations are more vulnerable to climatic and geological events, thereby limiting gene flow and accelerating genetic differentiation within species. Historical biogeographic analysis traced the origin of P. persicum to the western Zagros Mountains, with major genetic divergence occurring during the Pleistocene. Our genetic analyses suggest that P. persicum may have shown a genetic pattern similar to a classical ring species before the Pleistocene. The Namak Lake sub-basin could have served as a contact zone where populations did not interbreed but were connected through gene flow in a geographic ring. Currently, genetic separation is evident between basins, indicating that P. persicum in the Zagros Mountains is not a contemporary ring species. Also, our biogeographical analysis estimated that range evolution may have been driven initially by dispersal, and only during the late Pleistocene by vicariance.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140159542","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}

引用次数: 0

Patterns of genetic divergence in the Rio Grande cooter (Pseudemys gorzugi), a riverine turtle inhabiting an arid and anthropogenically modified system. 格兰德河乌龟（Pseudemys gorzugi）的遗传分化模式，这是一种栖息在干旱和人为改造系统中的河龟。

IF 3.1 2区生物学

Journal of Heredity Pub Date : 2024-05-09 DOI: 10.1093/jhered/esae011

Michael W Vandewege, Javier Gutierrez, Drew R Davis, Michael R J Forstner, Ivana Mali

{"title":"Patterns of genetic divergence in the Rio Grande cooter (Pseudemys gorzugi), a riverine turtle inhabiting an arid and anthropogenically modified system.","authors":"Michael W Vandewege, Javier Gutierrez, Drew R Davis, Michael R J Forstner, Ivana Mali","doi":"10.1093/jhered/esae011","DOIUrl":"10.1093/jhered/esae011","url":null,"abstract":"The lower Rio Grande and Pecos River of the southwest United States have been heavily modified by human activities, profoundly impacting the integrity of their aquatic wildlife. In this context, we focused our study on the population genomics of the Rio Grande Cooter (Pseudemys gorzugi), a freshwater turtle of increasing conservation concern, residing in these two rivers and their tributaries. The genetic data revealed two distinct populations: one in the Pecos and Black Rivers of New Mexico and another in the Rio Grande and Devils River of Texas, with admixed individuals identified at the confluence of the Rio Grande and Pecos River. In addition to having a smaller geographic range, we found lower observed heterozygosity, reduced nucleotide diversity, and a smaller effective population size (Ne) in New Mexico population. Our results depict a significant isolation-by-distance pattern across their distribution, with migration being notably infrequent at river confluences. These findings are pivotal for future conservation and restoration strategies, emphasizing the need to recognize the unique needs of each population.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11081133/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139906896","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}

引用次数: 0

Genomic Diversity and Demographic History of the Endangered Sichuan hill-partridge (Arborophila rufipectus) 濒危四川山鹧鸪的基因组多样性和种群历史

IF 3.1 2区生物学

Journal of Heredity Pub Date : 2024-04-18 DOI: 10.1093/jhered/esae020

Yi Liu, Weimin Kuang, Bisong Yue, Chuang Zhou

{"title":"Genomic Diversity and Demographic History of the Endangered Sichuan hill-partridge (Arborophila rufipectus)","authors":"Yi Liu, Weimin Kuang, Bisong Yue, Chuang Zhou","doi":"10.1093/jhered/esae020","DOIUrl":"https://doi.org/10.1093/jhered/esae020","url":null,"abstract":"Species conservation can be improved by knowledge of genetic diversity and demographic history. The Sichuan hill-partridge (Arborophila rufipectus, SP) is an endangered species endemic to the mountains in southwestern China. However, little is known about this species’ genomic variation and demographic history. Here, we present a comprehensive whole-genome analysis of six SP individuals from the Laojunshan National Nature Reserve in Sichuan Province, China. We observe a relatively high genetic diversity and low level of recent inbreeding in the studied SP individuals. This suggests that the current population carries genetic variability that may benefit the long-term survival of this species, and that the present population may be larger than currently recognized. Analyses of demographic history showed that fluctuations in the effective population size of SP are inconsistent with changes of the historical climate. Strikingly, evidence from demographic modeling suggests SPs population decreased dramatically 15,100 years ago after the Last Glacial Maximum (LGM), possibly due to refugial isolation and later human interference. These results provide the first detailed and comprehensive genomic insights into genetic diversity, genomic inbreeding levels, and demographic history of the Sichuan hill-partridge, which are crucial for the conservation and management of this endangered species.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140627078","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}

引用次数: 0

Missing History of a Modern Domesticate: Historical Demographics and Genetic Diversity in Farm-bred Red Fox Populations 现代驯养动物的缺失历史：农场饲养的赤狐种群的历史人口统计和遗传多样性

IF 3.1 2区生物学

Journal of Heredity Pub Date : 2024-04-16 DOI: 10.1093/jhered/esae022

Halie Rando, Emmarie P Alexander, Sophie Preckler-Quisquater, Cate B Quinn, Jeremy T Stutchman, Jennifer L Johnson, Estelle R Bastounes, Beata Horecka, Kristina L Black, Michael P Robson, Darya V Shepeleva, Yury E Herbeck, Anastasiya V Kharlamova, Lyudmila N Trut, Jonathan N Pauli, Benjamin N Sacks, Anna V Kukekova

{"title":"Missing History of a Modern Domesticate: Historical Demographics and Genetic Diversity in Farm-bred Red Fox Populations","authors":"Halie Rando, Emmarie P Alexander, Sophie Preckler-Quisquater, Cate B Quinn, Jeremy T Stutchman, Jennifer L Johnson, Estelle R Bastounes, Beata Horecka, Kristina L Black, Michael P Robson, Darya V Shepeleva, Yury E Herbeck, Anastasiya V Kharlamova, Lyudmila N Trut, Jonathan N Pauli, Benjamin N Sacks, Anna V Kukekova","doi":"10.1093/jhered/esae022","DOIUrl":"https://doi.org/10.1093/jhered/esae022","url":null,"abstract":"The first record of captive bred red foxes (Vulpes vulpes) dates to 1896, when a breeding enterprise emerged in the provinces of Atlantic Canada. Because its domestication happened during recent history, the red fox offers a unique opportunity to examine the genetic diversity of an emerging domesticated species in the context of documented historical and economic influences. In particular, the historical record suggests that North American and Eurasian farm-bred populations likely experienced different demographic trajectories. Here, we focus on the likely impacts of founder effects and genetic drift given historical trends in fox farming on North American and Eurasian farms. A total of 15 mitochondrial haplotypes were identified in 369 foxes from 10 farm populations that we genotyped (n=161) or that were previously published. All haplotypes are endemic to North America. Although most haplotypes were consistent with eastern Canadian ancestry, a small number of foxes carried haplotypes typically found in Alaska and other regions of western North America. The presence of these haplotypes supports historical reports of wild foxes outside of Atlantic Canada being introduced into the breeding stock. These putative Alaskan and Western haplotypes were more frequently identified in Eurasian farms compared to North American farms, consistent with historical documentation suggesting that Eurasian economic and breeding practices were likely to maintain low-frequency haplotypes more effectively than in North America. Contextualizing inter- versus intra-farm genetic diversity alongside the historical record is critical to understanding of the origins of this emerging domesticate and the relationships between wild and farm-bred fox populations.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140608838","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}

引用次数: 0

A draft reference genome assembly of California Pipevine, Aristolochia californica Torr 加利福尼亚琵琶藤（Aristolochia californica Torr）参考基因组组装草案

IF 3.1 2区生物学

Journal of Heredity Pub Date : 2024-04-15 DOI: 10.1093/jhered/esae023

Samridhi Chaturvedi, Merly Escalona, Mohan P A Marimuthu, Oanh Nguyen, Noravit Chumchim, Colin W Fairbairn, William Seligmann, Courtney Miller, H Bradley Shaffer, Noah K Whiteman

{"title":"A draft reference genome assembly of California Pipevine, Aristolochia californica Torr","authors":"Samridhi Chaturvedi, Merly Escalona, Mohan P A Marimuthu, Oanh Nguyen, Noravit Chumchim, Colin W Fairbairn, William Seligmann, Courtney Miller, H Bradley Shaffer, Noah K Whiteman","doi":"10.1093/jhered/esae023","DOIUrl":"https://doi.org/10.1093/jhered/esae023","url":null,"abstract":"The California Pipevine, Aristolochia californica Torr., is the only endemic California species within the cosmopolitan birthwort family Aristolochiaceae. It occurs as an understory vine in riparian and chaparral areas and in forest edges and windrows. The geographic range of this plant species almost entirely overlaps with that of its major specialized herbivore, the California Pipevine Swallowtail Butterfly Battus philenor hirsuta. While this species pair is a useful, ecologically well-understood system to study co-evolution, until recently, genomic resources for both have been lacking. Here, we report a new, chromosome-level assembly of A. californica as part of the California Conservation Genomics Project (CCGP). Following the sequencing and assembly strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin proximity sequencing technology to produce a de novo assembled genome. Our genome assembly, the first for any species in the genus, contains 531 scaffolds spanning 661 megabase (Mb) pairs, with a contig N50 of 6.53 Mb, a scaffold N50 of 42.2 Mb, and BUSCO complete score of 98%. In combination with the recently published B. philenor hirsuta reference genome assembly, the A. californica reference genome assembly will be a powerful tool for studying co-evolution in a rapidly changing California landscape.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140575604","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}

引用次数: 0

Insight into the adaptive role of arachnid genome-wide duplication through chromosome-level genome assembly of the Western black widow spider 通过西部黑寡妇蜘蛛染色体级基因组组装深入了解蛛形纲动物全基因组复制的适应性作用

IF 3.1 2区生物学

Journal of Heredity Pub Date : 2024-04-03 DOI: 10.1093/jhered/esae018

Lindsay S Miles, Hannah Waterman, Nadia A Ayoub, Jessica E Garb, Robert A Haney, Michael S Rosenberg, Trevor J Krabbenhoft, Brian C Verrelli

{"title":"Insight into the adaptive role of arachnid genome-wide duplication through chromosome-level genome assembly of the Western black widow spider","authors":"Lindsay S Miles, Hannah Waterman, Nadia A Ayoub, Jessica E Garb, Robert A Haney, Michael S Rosenberg, Trevor J Krabbenhoft, Brian C Verrelli","doi":"10.1093/jhered/esae018","DOIUrl":"https://doi.org/10.1093/jhered/esae018","url":null,"abstract":"Although spiders are one of the most diverse groups of arthropods, the genetic architecture of their evolutionary adaptations is largely unknown. Specifically, ancient genome-wide duplication occurring during arachnid evolution ~450 mya resulted in a vast assembly of gene families, yet the extent to which selection has shaped this variation is understudied. To aid in comparative genome sequence analyses, we provide a chromosome-level genome of the Western black widow spider (Latrodectus hesperus)—a focus due to its silk properties, venom applications, and as a model for urban adaptation. We used long-read and Hi-C sequencing data, combined with transcriptomes, to assemble 14 chromosomes in a 1.46 Gb genome, with 38,393 genes annotated, and a BUSCO score of 95.3%. Our analyses identified high repetitive gene content and heterozygosity, consistent with other spider genomes, which has led to challenges in genome characterization. Our comparative evolutionary analyses of eight genomes available for species within the Araneoidea group (orb weavers and their descendants) identified 1,827 single-copy orthologs. Of these, 155 exhibit significant positive selection primarily associated with developmental genes, and with traits linked to sensory perception. These results support the hypothesis that several traits unique to spiders emerged from the adaptive evolution of ohnologs—or retained ancestrally duplicated genes—from ancient genome-wide duplication. These comparative spider genome analyses can serve as a model to understand how positive selection continually shapes ancestral duplications in generating novel traits today within and between diverse taxonomic groups.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140575320","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}

引用次数: 0

NewickTreeModifier: A simple web tool to prune and modify Newick trees. NewickTreeModifier: 用于修剪和修改 Newick 树的简单网页。

IF 3.1 2区生物学

Journal of Heredity Pub Date : 2024-03-13 DOI: 10.1093/jhered/esae005

Lynn Ogoniak, Raphael Steffen, Norbert Grundmann, Ben Stöver, Kai Müller, Jürgen Schmitz

引用次数: 0