Journal of Heredity最新文献_第3页

The role of conflict in the formation and maintenance of variant sex chromosome systems in mammals. 冲突在哺乳动物变异性染色体系统的形成和维持中的作用。

IF 3 2区生物学

Journal of Heredity Pub Date : 2024-10-23 DOI: 10.1093/jhered/esae031

Jonathan J Hughes, German Lagunas-Robles, Polly Campbell

{"title":"The role of conflict in the formation and maintenance of variant sex chromosome systems in mammals.","authors":"Jonathan J Hughes, German Lagunas-Robles, Polly Campbell","doi":"10.1093/jhered/esae031","DOIUrl":"10.1093/jhered/esae031","url":null,"abstract":"The XX/XY sex chromosome system is deeply conserved in therian mammals, as is the role of Sry in testis determination, giving the impression of stasis relative to other taxa. However, the long tradition of cytogenetic studies in mammals documents sex chromosome karyotypes that break this norm in myriad ways, ranging from fusions between sex chromosomes and autosomes to Y chromosome loss. Evolutionary conflict, in the form of sexual antagonism or meiotic drive, is the primary predicted driver of sex chromosome transformation and turnover. Yet conflict-based hypotheses are less considered in mammals, perhaps because of the perceived stability of the sex chromosome system. To address this gap, we catalog and characterize all described sex chromosome variants in mammals, test for family-specific rates of accumulation, and consider the role of conflict between the sexes or within the genome in the evolution of these systems. We identify 152 species with sex chromosomes that differ from the ancestral state and find evidence for different rates of ancestral to derived transitions among families. Sex chromosome-autosome fusions account for 79% of all variants whereas documented sex chromosome fissions are limited to three species. We propose that meiotic drive and drive suppression provide viable explanations for the evolution of many of these variant systems, particularly those involving autosomal fusions. We highlight taxa particularly worthy of further study and provide experimental predictions for testing the role of conflict and its alternatives in generating observed sex chromosome diversity.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"601-624"},"PeriodicalIF":3.0,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141249078","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

United by conflict: Convergent signatures of parental conflict in angiosperms and placental mammals. 因冲突而团结：被子植物和胎生哺乳动物亲子冲突的趋同特征。

IF 3 2区生物学

Journal of Heredity Pub Date : 2024-10-23 DOI: 10.1093/jhered/esae009

Hagar K Soliman, Jenn M Coughlan

{"title":"United by conflict: Convergent signatures of parental conflict in angiosperms and placental mammals.","authors":"Hagar K Soliman, Jenn M Coughlan","doi":"10.1093/jhered/esae009","DOIUrl":"10.1093/jhered/esae009","url":null,"abstract":"Endosperm in angiosperms and placenta in eutherians are convergent innovations for efficient embryonic nutrient transfer. Despite advantages, this reproductive strategy incurs metabolic costs that maternal parents disproportionately shoulder, leading to potential inter-parental conflict over optimal offspring investment. Genomic imprinting-parent-of-origin-biased gene expression-is fundamental for endosperm and placenta development and has convergently evolved in angiosperms and mammals, in part, to resolve parental conflict. Here, we review the mechanisms of genomic imprinting in these taxa. Despite differences in the timing and spatial extent of imprinting, these taxa exhibit remarkable convergence in the molecular machinery and genes governing imprinting. We then assess the role of parental conflict in shaping evolution within angiosperms and eutherians using four criteria: 1) Do differences in the extent of sibling relatedness cause differences in the inferred strength of parental conflict? 2) Do reciprocal crosses between taxa with different inferred histories of parental conflict exhibit parent-of-origin growth effects? 3) Are these parent-of-origin growth effects caused by dosage-sensitive mechanisms and do these loci exhibit signals of positive selection? 4) Can normal development be restored by genomic perturbations that restore stoichiometric balance in the endosperm/placenta? Although we find evidence for all criteria in angiosperms and eutherians, suggesting that parental conflict may help shape their evolution, many questions remain. Additionally, myriad differences between the two taxa suggest that their respective biologies may shape how/when/where/to what extent parental conflict manifests. Lastly, we discuss outstanding questions, highlighting the power of comparative work in quantifying the role of parental conflict in evolution.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"625-642"},"PeriodicalIF":3.0,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11498613/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139747779","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

ParthenoGenius: A User-Friendly Heuristic for Inferring Presence and Mechanism of Facultative Parthenogenesis from Genetic and Genomic Data Sets. 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 : 2024-10-22 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 Data Sets.","authors":"Brenna A Levine, Warren Booth","doi":"10.1093/jhered/esae060","DOIUrl":"https://doi.org/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 data sets 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 data sets 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 data sets (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 presence and mechanism of FP from even large genomic data sets 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 data sets, 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 data sets 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":""},"PeriodicalIF":3.0,"publicationDate":"2024-10-22","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

A chromosome-level genome assembly for the desert scorpion Mesobuthus przewalskii from Asian drylands. 亚洲旱地沙漠蝎 Mesobuthus przewalskii 染色体级基因组组装。

IF 3 2区生物学

Journal of Heredity Pub Date : 2024-10-21 DOI: 10.1093/jhered/esae059

Yan-Kai Su, Ming-Hua Xiu, Hao-Yan Yang, Cheng-Min Shi

引用次数: 0

Frequencies of house fly proto-Y chromosomes across populations are predicted by temperature heterogeneity within populations. 家蝇原 Y 染色体在不同种群中的频率是由种群内的温度异质性预测的。

IF 3 2区生物学

Journal of Heredity Pub Date : 2024-10-15 DOI: 10.1093/jhered/esae056

Patrick D Foy, Sara R Loetzerich, David Boxler, Edwin R Burgess, R T Trout Fryxell, Alec C Gerry, Nancy C Hinkle, Erika T Machtinger, Cassandra Olds, Aaron M Tarone, Wes Watson, Jeffrey G Scott, Richard P Meisel

{"title":"Frequencies of house fly proto-Y chromosomes across populations are predicted by temperature heterogeneity within populations.","authors":"Patrick D Foy, Sara R Loetzerich, David Boxler, Edwin R Burgess, R T Trout Fryxell, Alec C Gerry, Nancy C Hinkle, Erika T Machtinger, Cassandra Olds, Aaron M Tarone, Wes Watson, Jeffrey G Scott, Richard P Meisel","doi":"10.1093/jhered/esae056","DOIUrl":"https://doi.org/10.1093/jhered/esae056","url":null,"abstract":"Sex chromosomes often differ between closely related species and can even be polymorphic within populations. Species with multifactorial sex determination segregate for multiple different sex determining loci within populations, making them uniquely informative of the selection pressures that drive the evolution of sex chromosomes. The house fly (Musca domestica) is a model species for studying multifactorial sex determination because male determining genes have been identified on all six of the chromosomes, which means that any chromosome can be a \"proto-Y\". Natural populations of house fly also segregate for a recently derived female-determining locus, meaning house flies also have a proto-W chromosome. The different proto-Y chromosomes are distributed along latitudinal clines on multiple continents, their distributions can be explained by seasonality in temperature, and they have temperature-dependent effects on physiological and behavioral traits. It is not clear, however, how the clinal distributions interact with the effect of seasonality on the frequencies of house fly proto-Y and proto-W chromosomes across populations. To address this question, we measured the frequencies of house fly proto-Y and proto-W chromosomes across nine populations in the United States of America. We confirmed the clinal distribution along the eastern coast of North America, but it is limited to the eastern coast. In contrast, annual mean daily temperature range predicts proto-Y chromosome frequencies across the entire continent. Our results therefore suggest that temperature heterogeneity can explain the distributions of house fly proto-Y chromosomes in a way that does not depend on the cline.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2024-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142481271","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

Maintaining Breed Integrity: Successful Introgression of the SLICK1 Allele into the Holstein Breed. 保持品种完整性：将 SLICK1 等位基因成功引入荷斯坦品种。

IF 3 2区生物学

Journal of Heredity Pub Date : 2024-10-14 DOI: 10.1093/jhered/esae057

Gabriel A Zayas, Serdal Dikmen, Raluca G Mateescu, Peter J Hansen

{"title":"Maintaining Breed Integrity: Successful Introgression of the SLICK1 Allele into the Holstein Breed.","authors":"Gabriel A Zayas, Serdal Dikmen, Raluca G Mateescu, Peter J Hansen","doi":"10.1093/jhered/esae057","DOIUrl":"https://doi.org/10.1093/jhered/esae057","url":null,"abstract":"This study evaluated the effectiveness of genetic introgression of the SLICK1 allele derived from Senepol cattle into the Holstein breed to enhance thermotolerance. The SLICK1 allele, located in PRLR gene, confers a short and sleek coat that is inherited as a simple dominant phenotype. Approximately 40 years ago, the University of Florida initiated efforts to introgress this allele into the Holstein population. Here we tracked the introgression of the SLICK1 allele using a medium-density genotyping array and a reference population of both breeds (50 Holstein, 46 Senepol). Among the 31 SLICK1+ Holsteins, there was 15.25% ± 11.11% (mean ± SD) Senepol ancestry on BTA20. Holsteins at the University of Florida descended from slick matings that did not inherit the SLICK1 allele (n=9) exhibited no Senepol ancestry. A secondary introgression of Senepol genetics in SLICK1+ animals was found on BTA4, spanning 54 markers and 15 genes, with 26.67% Senepol ancestry. This region, previously linked to heat stress adaptation, suggests that the introgression extends beyond the SLICK1 allele to incorporate additional beneficial genetics for thermal stress adaptation. These findings indicate that deliberate introgression of the SLICK1 allele enhances specific traits and potentially introduces other adaptive genetic variations. The study demonstrates the successful use of genetic interventions to improve livestock resilience against environmental challenges without significantly disrupting the recipient breed's genetic structure. The introgression of the SLICK1 allele serves as a model for breeding programs aimed at optimizing animal welfare and productivity in the face of global climate change while maintaining breed integrity.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142481272","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 : 2024-10-07 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":"https://doi.org/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 interpopulation crossing alleviates fitness loss. Because fitness depends on 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 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 6400-hectare area. We then assessed cumulative offspring fitness after 14 years of growth in a natural experimental plot (N = 1136). 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":""},"PeriodicalIF":3.0,"publicationDate":"2024-10-07","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

Reference genome for the endangered, genetically subdivided, northern tidewater goby, Eucyclogobius newberryi. 濒危、基因细分的北部潮水虾虎鱼 Eucyclogobius newberryi 的参考基因组。

IF 3 2区生物学

Journal of Heredity Pub Date : 2024-10-05 DOI: 10.1093/jhered/esae053

David K Jacobs, Andrew Kinziger, Mira Abrecht, W Tyler McCraney, Benjamin A Hà, Brenton T Spies, Elizabeth Heath-Heckman, Mohan P A Marimuhtu, Oanh Nguyen, Colin W Fairbairn, William E Seligmann, Merly Escalona, Courtney Miller, H Bradley Shaffer

{"title":"Reference genome for the endangered, genetically subdivided, northern tidewater goby, Eucyclogobius newberryi.","authors":"David K Jacobs, Andrew Kinziger, Mira Abrecht, W Tyler McCraney, Benjamin A Hà, Brenton T Spies, Elizabeth Heath-Heckman, Mohan P A Marimuhtu, Oanh Nguyen, Colin W Fairbairn, William E Seligmann, Merly Escalona, Courtney Miller, H Bradley Shaffer","doi":"10.1093/jhered/esae053","DOIUrl":"https://doi.org/10.1093/jhered/esae053","url":null,"abstract":"The federally endangered sister species, Eucyclogobius newberryi (northern tidewater goby) and E. kristinae (southern tidewater goby) comprise the California endemic genus Eucyclogobius, which historically occurred in all coastal California counties. Isolated lagoons that only intermittently connect to the sea are their primary habitat. Reproduction occurs during lagoon closure, minimizing marine dispersal and generating the most genetically subdivided vertebrate genus on the California coast. We present a new genome assembly for E. newberryi using HiFi long reads and Hi-C chromatin-proximity sequencing. The 980Mb E. newberryi reference genome has an N50 of 34Mb with 22 well-described scaffolds comprising 88% of the genome and a complete BUSCO score of 96.7%. This genome will facilitate studies addressing selection, drift, and metapopulation genetics in subdivided populations, as well as the persistence of the critically endangered E. kristinae, where reintroduction will be an essential element of conservation actions for recovery. It also provides tools critical to the recovery of the genetically distinct management units in the northern tidewater goby, as well as broader ecological and evolutionary studies of gobies, the most speciose family of fishes in the world.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2024-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142378628","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 genome of the Australian water dragon (Intellagama lesueurii), an agamid model for urban adaptation. 澳大利亚水龙（Intellagama lesueurii）的基因组--城市适应性的蚕食模式。

IF 3 2区生物学

Journal of Heredity Pub Date : 2024-10-04 DOI: 10.1093/jhered/esae054

Daniel Powell, Nicola Jackson, Parwinder Kaur, Olga Dudchenko, Erez Lieberman Aiden, Arthur Georges, Céline H Frère

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 : 2024-09-24 DOI: 10.1093/jhered/esae052

Sergei Kliver, Iva Kovacic, Sarah Mak, Mikkel-Holger S Sinding, Julia Stagegaard, Bent Petersen, Joseph Nesme, M Thomas P 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, M Thomas P Gilbert","doi":"10.1093/jhered/esae052","DOIUrl":"https://doi.org/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 as well as 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 VGP 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, mat consists of only 166 contigs with an N50 of 39 Mbp. BUSCO analysis showed 95.4 % completeness based on Сarnivora conservative genes (carnivora_odb10). When compared to other available genomes from subtribe Canina, the quality of the assembly is excellent, typically between the 1st and 3rd 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":""},"PeriodicalIF":3.0,"publicationDate":"2024-09-24","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