Journal of Heredity最新文献_第7页

Beyond population size: Whole-genome data reveal bottleneck legacies in the peninsular Italian wolf. 超越种群规模：全基因组数据揭示了意大利半岛狼的瓶颈遗留问题。

IF 3 2区生物学

Journal of Heredity Pub Date : 2025-01-03 DOI: 10.1093/jhered/esae041

Daniele Battilani, Roberta Gargiulo, Romolo Caniglia, Elena Fabbri, Jazmín Ramos- Madrigal, Claudia Fontsere, Marta Maria Ciucani, Shyam Gopalakrishnan, Matteo Girardi, Ilaria Fracasso, Matteo Mastroiaco, Paolo Ciucci, Cristiano Vernesi

{"title":"Beyond population size: Whole-genome data reveal bottleneck legacies in the peninsular Italian wolf.","authors":"Daniele Battilani, Roberta Gargiulo, Romolo Caniglia, Elena Fabbri, Jazmín Ramos- Madrigal, Claudia Fontsere, Marta Maria Ciucani, Shyam Gopalakrishnan, Matteo Girardi, Ilaria Fracasso, Matteo Mastroiaco, Paolo Ciucci, Cristiano Vernesi","doi":"10.1093/jhered/esae041","DOIUrl":"10.1093/jhered/esae041","url":null,"abstract":"Preserving genetic diversity and adaptive potential while avoiding inbreeding depression is crucial for the long-term conservation of natural populations. Despite demographic increases, traces of past bottleneck events at the genomic level should be carefully considered for population management. From this perspective, the peninsular Italian wolf is a paradigmatic case. After being on the brink of extinction in the late 1960s, peninsular Italian wolves rebounded and recolonized most of the peninsula aided by conservation measures, including habitat and legal protection. Notwithstanding their demographic recovery, a comprehensive understanding of the genomic consequences of the historical bottleneck in Italian wolves is still lacking. To fill this gap, we sequenced whole genomes of 13 individuals sampled in the core historical range of the species in Central Italy to conduct population genomic analyses, including a comparison with wolves from two highly-inbred wolf populations (i.e. Scandinavia and Isle Royale). We found that peninsular Italian wolves, despite their recent recovery, still exhibit relatively low genetic diversity, a small effective population size, signatures of inbreeding, and a non-negligible genetic load. Our findings indicate that the peninsular Italian wolf population is still susceptible to bottleneck legacies, which could lead to local inbreeding depression in case of population reduction or fragmentations. This study emphasizes the importance of considering key genetic parameters to design appropriate long-term conservation management plans.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"10-23"},"PeriodicalIF":3.0,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142074569","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

Neutral genetic structuring of pathogen populations during rapid adaptation. 病原体种群在快速适应过程中的中性基因结构。

IF 3 2区生物学

Journal of Heredity Pub Date : 2025-01-03 DOI: 10.1093/jhered/esae036

Méline Saubin, Solenn Stoeckel, Aurélien Tellier, Fabien Halkett

{"title":"Neutral genetic structuring of pathogen populations during rapid adaptation.","authors":"Méline Saubin, Solenn Stoeckel, Aurélien Tellier, Fabien Halkett","doi":"10.1093/jhered/esae036","DOIUrl":"10.1093/jhered/esae036","url":null,"abstract":"Pathogen species are experiencing strong joint demographic and selective events, especially when they adapt to a new host, for example through overcoming plant resistance. Stochasticity in the founding event and the associated demographic variations hinder our understanding of the expected evolutionary trajectories and the genetic structure emerging at both neutral and selected loci. What would be the typical genetic signatures of such a rapid adaptation event is not elucidated. Here, we build a demogenetic model to monitor pathogen population dynamics and genetic evolution on two host compartments (susceptible and resistant). We design our model to fit two plant pathogen life cycles, \"with\" and \"without\" host alternation. Our aim is to draw a typology of eco-evolutionary dynamics. Using time-series clustering, we identify three main scenarios: 1) small variations in the pathogen population size and small changes in genetic structure, 2) a strong founder event on the resistant host that in turn leads to the emergence of genetic structure on the susceptible host, and 3) evolutionary rescue that results in a strong founder event on the resistant host, preceded by a bottleneck on the susceptible host. We pinpoint differences between life cycles with notably more evolutionary rescue \"with\" host alternation. Beyond the selective event itself, the demographic trajectory imposes specific changes in the genetic structure of the pathogen population. Most of these genetic changes are transient, with a signature of resistance overcoming that vanishes within a few years only. Considering time-series is therefore of utmost importance to accurately decipher pathogen evolution.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"62-77"},"PeriodicalIF":3.0,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141903621","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

ParthenoGenius: A user-friendly heuristic for inferring presence and mechanism of facultative parthenogenesis from genetic and genomic datasets. ParthenoGenius：从遗传学和基因组数据集推断兼性孤雌生殖的存在和机制的用户友好启发式。

IF 3 2区生物学

Journal of Heredity Pub Date : 2025-01-03 DOI: 10.1093/jhered/esae060

Brenna A Levine, Warren Booth

{"title":"ParthenoGenius: A user-friendly heuristic for inferring presence and mechanism of facultative parthenogenesis from genetic and genomic datasets.","authors":"Brenna A Levine, Warren Booth","doi":"10.1093/jhered/esae060","DOIUrl":"10.1093/jhered/esae060","url":null,"abstract":"Facultative parthenogenesis (FP), or asexual reproduction by sexually reproducing female animals, has been reported across several clades of vertebrates and is increasingly being recognized as a reproductive mechanism with significant implications for the genetic variation of captive and wild populations. The definitive identification of parthenogens requires molecular confirmation, with large genomic datasets necessary to accurately parse the parthenogenetic mechanism (i.e. endoduplication, gametic duplication, terminal fusion automixis, or central fusion automixis). Current methods for inferring FP from large genomic datasets are statistically intensive, require competency in R scripting for their execution, and are not designed for detection of facultative parthenogenesis or screening of large numbers of mother/offspring pairs, whereas small datasets (i.e. microsatellites) that can be evaluated visually lack the power to discriminate among FP mechanisms. Here, we present the user-friendly software program, ParthenoGenius, that uses intuitive logic to infer the presence and mechanism of FP from even large genomic datasets comprising many mothers and offspring. ParthenoGenius runs relatively quickly and does not require the researcher to have knowledge of R scripting or statistics. ParthenoGenius was tested on eight empirical datasets and in each case identified parthenogens (and parthenogenic mechanism when present) consistent with results of previous studies or corroborating evidence. ParthenoGenius will facilitate the rapid screening of large genomic datasets comprising many mothers and offspring for the presence and mechanism of parthenogenesis, improving our understanding of the frequency and phylogenetic distribution of FP across the animal kingdom.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"34-42"},"PeriodicalIF":3.0,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142513204","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

Individual and social heterosis act independently in honey bee (Apis mellifera) colonies. 蜜蜂（Apis mellifera）蜂群中的个体异质性和社会异质性是独立作用的。

IF 3 2区生物学

Journal of Heredity Pub Date : 2025-01-03 DOI: 10.1093/jhered/esae043

Dylan K Ryals, Amos C Buschkoetter, J Krispn Given, Brock A Harpur

{"title":"Individual and social heterosis act independently in honey bee (Apis mellifera) colonies.","authors":"Dylan K Ryals, Amos C Buschkoetter, J Krispn Given, Brock A Harpur","doi":"10.1093/jhered/esae043","DOIUrl":"10.1093/jhered/esae043","url":null,"abstract":"Heterosis occurs in individuals when genetic diversity, e.g., heterozygosity, increases fitness. Many advanced eusocial insects evolved mating behaviors, including polyandry and polygyny, which increase inter-individual genetic diversity within colonies. The possibility of this structure of diversity to improve group fitness has been termed social heterosis. Neither the independence of individual and social heterosis nor their relative effect sizes have been explicitly measured. Through controlled breeding between pairs of Western honey bee queens (Apis mellifera L.; n = 3 pairs) from two distinct populations, we created inbred colonies with low genetic diversity, hybrid colonies with high heterozygosity, and mixed colonies (combining inbred workers from each population) with low heterozygosity and high social diversity. We then quantified two independent traits in colonies: survival against bacterial challenge and maintenance of brood nest temperature. For both traits, we found hybrid and mixed colonies outperformed inbred colonies but did not perform differently from each other. During immune challenge assays, hybrid and mixed colonies experienced hazard ratios of 0.49 (95% CI [0.37, 0.65]) and 0.69 (95% CI [0.50, 0.96]) compared to inbred colonies. For nest temperatures, hybrid and mixed colonies experienced 1.94 ± 0.97 °C and 2.82 ± 2.46 °C less thermal error and 0.14 ± 0.11 °C2 and 0.16 ± 0.06 °C2 less thermal variance per hour than inbred lines. This suggests social and individual heterosis operate independently and may have similar effect sizes. These results highlight the importance of both inter- and intra-individual diversity to fitness, which may help explain the emergence of polyandry/polygyny in eusocial insects and inform breeding efforts in these systems.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"54-61"},"PeriodicalIF":3.0,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141989583","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

Insights from the timber rattlesnake (Crotalus horridus) genome for MHC gene architecture and evolution in threatened rattlesnakes. 来自木响尾蛇（Crotalus horridus）基因组对濒危响尾蛇MHC基因结构和进化的见解。

IF 3 2区生物学

Journal of Heredity Pub Date : 2024-12-20 DOI: 10.1093/jhered/esae075

Marissa A Roseman, Andrew J Mason, Emily R Bode, Peri E Bolton, Pedro G Nachtigall, William E Peterman, H Lisle Gibbs

{"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":"https://doi.org/10.1093/jhered/esae075","url":null,"abstract":"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. 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 suggests 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.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2024-12-20","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}

引用次数: 0

Chromosome-level genome assembly of the king horseshoe bat (Rhinolophus rex) provides insights into its conservation status and chromosomal evolution of Rhinolophus. 马蹄蝠王（Rhinolophus rex）染色体水平的基因组组装有助于深入了解其保护状况和 Rhinolophus 的染色体进化。

IF 3 2区生物学

Journal of Heredity Pub Date : 2024-12-16 DOI: 10.1093/jhered/esae077

Linjing Lan, Xin Zhang, Shanxiu Yang, Xiuguang Mao, Ji Dong

{"title":"Chromosome-level genome assembly of the king horseshoe bat (Rhinolophus rex) provides insights into its conservation status and chromosomal evolution of Rhinolophus.","authors":"Linjing Lan, Xin Zhang, Shanxiu Yang, Xiuguang Mao, Ji Dong","doi":"10.1093/jhered/esae077","DOIUrl":"https://doi.org/10.1093/jhered/esae077","url":null,"abstract":"A high-quality reference genome is quite valuable in assessing the conservation status of a rare species when adequate data from other sources are unavailable. Bats comprise almost a fifth of all mammals and contribute greatly to ecosystem. However, due to the nocturnal and elusive habits, it is difficult to obtain the accurate census population size of a rare bat species and assess its conservation status. Here, we generate a chromosome-level genome assembly for the king horseshoe bat (Rhinolophus rex) and assess its conservation status by comparing the genome-wide summary statistics to other related species. The genome assembly size was 2.1 Gb (contig N50: 75.26 Mb) and 99.9% of the total sequences were anchored onto 30 autosomes, X and Y chromosomes. Despite lower genome-wide heterozygosity and recent inbreeding, R. rex did not exhibit higher genetic load comparing to the other two Rhinolophus species. Historical demography analysis revealed that R. rex maintained a long term (~2 million years) stable population size (~150,000). In the future whole-genome sequencing data from more individuals will be needed to comprehensively assess the conservation status at recent timescales. We also reconstructed the ancestral karyotype of Rhinolophus as 2n=54 and found that Robertsonian fissions and fusions were the main mechanism of chromosomal rearrangements in this genus. Overall, our study shows important implications of reference-quality genomes in both conservation genomics and comparative genomics.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142830839","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

Evidence of Extensive Home Range Sharing Among Mother-Daughter Bobcat Pairs in the Wildland-Urban Interface of the Tucson Mountains. 图森山脉野地-城市交界地区山猫母女广泛共享活动范围的证据。

IF 3 2区生物学

Journal of Heredity Pub Date : 2024-12-05 DOI: 10.1093/jhered/esae072

Natalie Payne, Desiree Andersen, Robert Davis, Cheryl Mollohan, Kerry Baldwin, Albert L LeCount, Melanie Culver

{"title":"Evidence of Extensive Home Range Sharing Among Mother-Daughter Bobcat Pairs in the Wildland-Urban Interface of the Tucson Mountains.","authors":"Natalie Payne, Desiree Andersen, Robert Davis, Cheryl Mollohan, Kerry Baldwin, Albert L LeCount, Melanie Culver","doi":"10.1093/jhered/esae072","DOIUrl":"https://doi.org/10.1093/jhered/esae072","url":null,"abstract":"Urbanization impacts the structure and viability of wildlife populations. Some habitat generalists, such as bobcats (Lynx rufus), maintain populations at the intersection of wild and urban habitats (wildland urban interface, WUI), but impacts of urbanization on bobcat social structure are not well understood. Although commonly thought to establish exclusive home ranges among females, instances of mother-daughter home range sharing have been documented. We combined GPS localities with genomic relatedness inferences from double-digest restriction site associated DNA sequencing (ddRADseq) to investigate mother-daughter home range sharing in bobcats (n = 38) at the WUI in the Tucson Mountains, Arizona, USA. We found the highest relatedness among females, which showed stronger isolation by distance than males and the population as a whole. Using mother-daughter relationships inferred from pedigree reconstruction, we found extensive mother-daughter home range sharing, compared to other females. Every mother identified as having at least one daughter, shared home ranges with one daughter, while other confirmed daughters established adjacent home ranges. Our results provide substantial support for the mother-daughter home range sharing hypothesis, as well as evidence of spatiotemporal overlap between mothers and daughters, adding to the body of research complicating the solitary felid paradigm. These results additionally challenge the notion of home range partitioning by prior rights land tenure, suggesting a role of matrilineal land tenure in home range establishment of daughters. Habitat fragmentation due to human population growth and urbanization thus has the potential to alter landscape genetic structure and social dynamics in bobcats.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142830841","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

Comparison of dN/dS ratios shows little evidence for faster-Z effect in Furcifer chameleons after controlling for gene-specific evolutionary rates. 对 dN/dS 比率的比较表明，在控制了基因特异性进化速度之后，几乎没有证据表明变色龙中存在快 Z 效应。

IF 3 2区生物学

Journal of Heredity Pub Date : 2024-11-22 DOI: 10.1093/jhered/esae070

Lucija Andjel, Lukáš Kratochvíl, Michail Rovatsos

{"title":"Comparison of dN/dS ratios shows little evidence for faster-Z effect in Furcifer chameleons after controlling for gene-specific evolutionary rates.","authors":"Lucija Andjel, Lukáš Kratochvíl, Michail Rovatsos","doi":"10.1093/jhered/esae070","DOIUrl":"https://doi.org/10.1093/jhered/esae070","url":null,"abstract":"The faster-X/Z effect hypothesis states that genes linked to X/Z chromosomes should accumulate mutations faster than autosomal genes. Although faster evolution of X/Z-linked genes has been reported in several plant and animal lineages, conflicting results have been reported in others. We examined the faster-Z effect in chameleons of the genus Furcifer, a lineage with differentiated ZZ/ZW chromosomes for at least 20 million years. We sequenced the genomes of four species of Furcifer chameleons in the Illumina platform and compared the substitution rates of synonymous and non-synonymous mutations and their ratios among autosomal, Z-specific, and pseudoautosomal protein-coding genes. The inclusion of two chameleon outgroups lacking the differentiated ZZ/ZW sex chromosomes allowed us to control for gene-specific evolutionary rates that might confound the testing of the faster-X/Z effect. Significant differences in evolutionary rates were found between autosomal, Z-specific, and pseudoautosomal genes of Furcifer chameleons. However, the inclusion of the outgroups with different sex chromosomes suggests that these genes had different evolutionary rates prior to their incorporation into the differentiated ZZ/ZW sex chromosomes of the Furcifer genus. The results highlight the need to control for differences in the evolutionary rates of individual genes when testing for the faster X/Z effect.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142689693","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 chromosome-level genome assembly of the mountain lion, Puma concolor. 山狮（Puma concolor）染色体级基因组组装。

IF 3 2区生物学

Journal of Heredity Pub Date : 2024-11-07 DOI: 10.1093/jhered/esae063

Megan A Supple, Merly Escalona, Nicolas Alexandre, Michael R Buchalski, Seth P D Riley, Justin A Dellinger, T Winston Vickers, Ruta Sahasrabudhe, Oanh Nguyen, Colin W Fairbairn, William E Seligmann, Christopher C Wilmers, Beth Shapiro

引用次数: 0

Lopez, J. V. (2023). Assessments and Conservation of Biological Diversity from Coral Reefs to the Deep Sea, Uncovering Buried Treasures and the Value of the Benthos. Academic Press, 253 pages. Lopez, J. V. (2023).从珊瑚礁到深海的生物多样性评估与保护》，《发现埋藏的宝藏和底栖生物的价值》。学术出版社，253 页。

IF 3 2区生物学

Journal of Heredity Pub Date : 2024-11-05 DOI: 10.1093/jhered/esae062

A Schulze

引用次数: 0