Journal of Heredity最新文献

Forensic Assessment of Kinship, Genomic Ancestry, and Natural History of an Iconic Tiger of Harlem-New York City.

IF 3 2区生物学

Journal of Heredity Pub Date : 2025-01-27 DOI: 10.1093/jhered/esaf003

Zhen-Bo Wu, Zheng-Yan Sui, Lan-Hui Peng, Mirna Ghemrawi, George Duncan, Henry Jones, Stephen J O'Brien, Shu-Jin Luo

{"title":"Forensic Assessment of Kinship, Genomic Ancestry, and Natural History of an Iconic Tiger of Harlem-New York City.","authors":"Zhen-Bo Wu, Zheng-Yan Sui, Lan-Hui Peng, Mirna Ghemrawi, George Duncan, Henry Jones, Stephen J O'Brien, Shu-Jin Luo","doi":"10.1093/jhered/esaf003","DOIUrl":"https://doi.org/10.1093/jhered/esaf003","url":null,"abstract":"In the fall of 2003, a two-year-old tiger named Ming, weighing some four hundred pounds, was discovered living in an apartment in Harlem, New York. Ming's rescue by NYPD was witnessed, recalled, and venerated by scores of neighbors. The tiger's history and ancestry stimulated considerable media interest, investigative sleuthing, and forensic genomic analyses. The Harlem tiger's subspecies makeup, his relationship to his putative sibling named Cheeky living in Homestead, Florida, and his genetic distinctiveness from wild tigers was assessed by Whole Genome Sequence (WGS) analyses of trace materials from plucked whiskers. Verified Subspecies Ancestry (VSA) of Ming and Cheeky was determined by comparing their WGS to SNP annotation from WGS of 35 voucher (pure subspecies) tiger specimens from six living subspecies. Genome-wide structure analyses based on 3,422,109 SNPs and a subset of 6,724 Ancestry-Informative Markers (AIMS) showed that Ming has an admixed genetic background from five subspecies: Indochinese tiger (Panthera tigris corbetti 35 ~ 40%), Bengal tiger (P. t. tigris 17 ~ 23%), Sumatran tiger (P. t. sumatrae 12 ~ 14%), Amur tiger (P. t. altaica ~ 10%), and Malayan tiger (P. t. jacksoni 1 ~ 10%). Cheeky is confirmed to be a full sibling to Ming and displayed an admixed genetic background with similar subspecies proportions as Ming's. The forensic assessment of the tigers' subspecies composition, kinship, and recent history of animal transaction provides an analytical pipeline and promises to assist in tiger conservation effort worldwide through standardized genomic analysis of tigers or tiger products with unknown origin.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143048770","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

Secrets of the Goo: the Genome assembly of the Pacific Banana Slug, Ariolimax columbianus.

IF 3 2区生物学

Journal of Heredity Pub Date : 2025-01-24 DOI: 10.1093/jhered/esaf002

Maximilian Genetti, Merly Escalona, Cade Mirchandani, Jonas Oppenheimer, Eric Beraut, Samuel Sacco, William Seligmann, Colin W Fairbairn, Ruta Sahasrabudhe, Mohan P A Marimuthu, Oanh Nguyen, Noravit Chumchim, Russell Corbett-Detig

{"title":"Secrets of the Goo: the Genome assembly of the Pacific Banana Slug, Ariolimax columbianus.","authors":"Maximilian Genetti, Merly Escalona, Cade Mirchandani, Jonas Oppenheimer, Eric Beraut, Samuel Sacco, William Seligmann, Colin W Fairbairn, Ruta Sahasrabudhe, Mohan P A Marimuthu, Oanh Nguyen, Noravit Chumchim, Russell Corbett-Detig","doi":"10.1093/jhered/esaf002","DOIUrl":"https://doi.org/10.1093/jhered/esaf002","url":null,"abstract":"The Pacific banana slug, Ariolimax columbianus, is endemic to the forests of the Pacific Northern West. Found throughout coastal foothills and mountains of California, the hermaphroditic molluscs Ariolimax spp. are niche-constrained, hyper-localized, and phenotypically diverse. The evolutionary history and more recent population history and environmental conditions leading to their phenotypic and genetic variation are not understood. To facilitate such research, we present the first high-quality de novo genome assembly of A. columbianus as part of the California Conservation Genomics Project (CCGP). Pacific Biosciences HiFi long reads and Omni-C chromatin-proximity sequencing technologies were used to produce a de novo genome assembly, consistent with the standard CCGP genome assembly protocol. This assembly comprises 401 scaffolds spanning 2.29 Gb, represented by a scaffold N50 of 94.9 Mb, a contig N50 of 3.7 Mb, and a benchmarking universal single-copy ortholog (BUSCO) completeness score of 93.9%. Future work will use the A. columbianus genome to study the population structure of Ariolimax spp. across California to understand patterns of population structure, genetic diversity and the broader ecological connections with their habitat. This data will contribute to the CCGP, expanding the knowledge about the partitioning of genomic variation across the different ecoregions of California.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143030353","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

Genomic implications of the repeated shift to self-fertilization across a species' geographic distribution. 在一个物种的地理分布范围内反复转向自交的基因组影响。

IF 3 2区生物学

Journal of Heredity Pub Date : 2025-01-03 DOI: 10.1093/jhered/esae046

Kay Lucek, Jana M Flury, Yvonne Willi

{"title":"Genomic implications of the repeated shift to self-fertilization across a species' geographic distribution.","authors":"Kay Lucek, Jana M Flury, Yvonne Willi","doi":"10.1093/jhered/esae046","DOIUrl":"10.1093/jhered/esae046","url":null,"abstract":"The ability to self-fertilize often varies among closely related hermaphroditic plant species, though, variation can also exist within species. In the North American Arabidopsis lyrata, the shift from self-incompatibility (SI) to selfing established in multiple regions independently, mostly since recent postglacial range expansion. This has made the species an ideal model for the investigation of the genomic basis of the breakdown of SI and its population genetic consequences. By comparing nearby selfing and outcrossing populations across the entire species' geographic distribution, we investigated variation at the self-incompatibility (S-)locus and across the genome. Furthermore, a diallel crossing experiment on one mixed-mating population was performed to gain insight into the inheritance of mating system variation. We confirmed that the breakdown of SI had evolved in several S-locus backgrounds. The diallel suggested the involvement of biparental contributions with dominance relations. Though, the population-level genome-wide association study did not single out clear-cut candidate genes but several regions with one near the S-locus. On the implication side, selfing as compared to outcrossing populations had less than half of the genomic diversity, while the number and length of runs of homozygosity (ROHs) scaled with the degree of inbreeding. Selfing populations with a history of long expansion had the longest ROHs. The results highlight that mating system shift to selfing, its genetic underpinning and the likely negative genomic consequences for evolutionary potential can be strongly interlinked with past range dynamics.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"43-53"},"PeriodicalIF":3.0,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142019604","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

The conservation value of small population remnants: Variability in inbreeding depression and heterosis of a perennial herb, the narrow-leaved purple coneflower (Echinacea angustifolia). 小种群残余的保护价值：多年生草本植物狭叶紫锥花（Echinacea angustifolia）近交抑郁和异花授粉的变异性。

IF 3 2区生物学

Journal of Heredity Pub Date : 2025-01-03 DOI: 10.1093/jhered/esae055

Riley D Thoen, Andrea Southgate, Gretel Kiefer, Ruth G Shaw, Stuart Wagenius

{"title":"The conservation value of small population remnants: Variability in inbreeding depression and heterosis of a perennial herb, the narrow-leaved purple coneflower (Echinacea angustifolia).","authors":"Riley D Thoen, Andrea Southgate, Gretel Kiefer, Ruth G Shaw, Stuart Wagenius","doi":"10.1093/jhered/esae055","DOIUrl":"10.1093/jhered/esae055","url":null,"abstract":"Anthropogenically fragmented populations may have reduced fitness due to loss of genetic diversity and inbreeding. The extent of such fitness losses due to fragmentation and potential gains from conservation actions are infrequently assessed together empirically. Controlled crosses within and among populations can identify whether populations are at risk of inbreeding depression and whether inter-population crossing alleviates fitness loss. Because fitness depends on the environment and life stage, studies quantifying cumulative fitness over a large portion of the lifecycle in conditions that mimic natural environments are most informative. To assess the fitness consequences of habitat fragmentation, we leveraged controlled within-family, within-population, and between-population crosses to quantify inbreeding depression and heterosis in seven populations of Echinacea angustifolia within a 6,400-ha area. We then assessed cumulative offspring fitness after 14 yr of growth in a natural experimental plot (N = 1,136). The mean fitness of progeny from within-population crosses varied considerably, indicating genetic differentiation among source populations, even though these sites are all less than 9 km apart. The fitness consequences of within-family and between-population crosses varied in magnitude and direction. Only one of the seven populations showed inbreeding depression of high effect, while four populations showed substantial heterosis. Outbreeding depression was rare and slight. Our findings indicate that local crossings between isolated populations yield unpredictable fitness consequences ranging from slight decreases to substantial increases. Interestingly, inbreeding depression and heterosis did not relate closely to population size, suggesting that all fragmented populations could contribute to conservation goals as either pollen recipients or donors.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"24-33"},"PeriodicalIF":3.0,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142382482","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 phased diploid genome assembly of African hunting dog (Lycaon pictus). 非洲猎犬（Lycaon pictus）染色体分期二倍体基因组组装。

IF 3 2区生物学

Journal of Heredity Pub Date : 2025-01-03 DOI: 10.1093/jhered/esae052

Sergei Kliver, Iva Kovacic, Sarah Mak, Mikkel-Holger S Sinding, Julia Stagegaard, Bent Petersen, Joseph Nesme, Marcus Thomas Pius Gilbert

{"title":"A chromosome phased diploid genome assembly of African hunting dog (Lycaon pictus).","authors":"Sergei Kliver, Iva Kovacic, Sarah Mak, Mikkel-Holger S Sinding, Julia Stagegaard, Bent Petersen, Joseph Nesme, Marcus Thomas Pius Gilbert","doi":"10.1093/jhered/esae052","DOIUrl":"10.1093/jhered/esae052","url":null,"abstract":"The African hunting dog (Lycaon pictus, 2n = 78) once ranged over most sub-Saharan ecosystems except its deserts and rainforests. However, as a result of (still ongoing) population declines, today they remain only as small fragmented populations. Furthermore, the future of the species remains unclear, due to both anthropogenic pressure and interactions with domestic dogs, thus their preservation is a conservation priority. On the tree of life, the hunting dog is basal to Canis and Cuon and forms a crown group with them, making it a useful species for comparative genomic studies. Here, we present a diploid chromosome-level assembly of an African hunting dog. Assembled according to Vertebrate Genomes Project guidelines from a combination of PacBio HiFi reads and HiC data, it is phased at the level of individual chromosomes. The maternal (pseudo)haplotype (mat) of our assembly has a length of 2.38 Gbp, and 99.36% of the sequence is encompassed by 39 chromosomal scaffolds. The rest is included in only 36 unplaced short scaffolds. At the contig level, the mat consists of only 166 contigs with an N50 of 39 Mbp. BUSCO (Benchmarking Universal Single-Copy Orthologue) analysis showed 95.4% completeness based on Carnivora conservative genes (carnivora_odb10). When compared with other available genomes from subtribe Canina, the quality of the assembly is excellent, typically between the first and third depending on the parameter used, and a significant improvement on previously published genomes for the species. We hope this assembly will play an important role in future conservation efforts and comparative studies of canid genomes.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"78-87"},"PeriodicalIF":3.0,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142332622","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

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