Journal of Heredity最新文献_第4页

Drift drives the evolution of chromosome number II: The impact of range size on genome evolution in Carnivora. 漂移驱动染色体数目的进化 II：食肉目动物的活动范围大小对基因组进化的影响。

IF 3 2区生物学

Journal of Heredity Pub Date : 2024-08-20 DOI: 10.1093/jhered/esae025

Michelle M Jonika, Kayla T Wilhoit, Maximos Chin, Abhimanyu Arekere, Heath Blackmon

{"title":"Drift drives the evolution of chromosome number II: The impact of range size on genome evolution in Carnivora.","authors":"Michelle M Jonika, Kayla T Wilhoit, Maximos Chin, Abhimanyu Arekere, Heath Blackmon","doi":"10.1093/jhered/esae025","DOIUrl":"10.1093/jhered/esae025","url":null,"abstract":"Chromosome number is a fundamental genomic trait that is often the first recorded characteristic of a genome. Across large clades, a common pattern emerges: many or even most lineages exhibit relative stasis, while a handful of lineages or species exhibit striking variation. Despite recent developments in comparative methods, most of this heterogeneity is still poorly understood. It is essential to understand why some lineages have rapid rates of chromosome number evolution, as it can impact a variety of other traits. Previous research suggests that biased female meiotic drive may shape rates of karyotype evolution in some mammals. However, Carnivora exhibits variation that this female meiotic drive model cannot explain. We hypothesize that variation in effective population size may underlie rate variation in Carnivora. To test this hypothesis, we estimated rates of fusions and fissions while accounting for range size, which we use as a proxy for effective population size. We reason fusions and fissions are deleterious or underdominant and that only in lineages with small range sizes will these changes be able to fix due to genetic drift. In this study, we find that the rates of fusions and fissions are elevated in taxa with small range sizes relative to those with large range sizes. Based on these findings, we conclude that 1) naturally occurring structural mutations that change chromosome number are underdominant or mildly deleterious, and 2) when population sizes are small, structural rearrangements may play an important role in speciation and reduction in gene flow among populations.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11334210/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140868755","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

Divergent ecological selection maintains species boundaries despite gene flow in a rare endemic tree, Quercus acerifolia (maple-leaf oak). 尽管枫叶栎（Quercus acerifolia）是一种罕见的特有树种，但在其基因流动过程中，不同的生态选择仍能维持物种边界。

IF 3 2区生物学

Journal of Heredity Pub Date : 2024-08-20 DOI: 10.1093/jhered/esae033

Yingtong Wu, Alexander G Linan, Sean Hoban, Andrew L Hipp, Robert E Ricklefs

{"title":"Divergent ecological selection maintains species boundaries despite gene flow in a rare endemic tree, Quercus acerifolia (maple-leaf oak).","authors":"Yingtong Wu, Alexander G Linan, Sean Hoban, Andrew L Hipp, Robert E Ricklefs","doi":"10.1093/jhered/esae033","DOIUrl":"10.1093/jhered/esae033","url":null,"abstract":"Strong gene flow from outcrossing relatives tends to blur species boundaries, while divergent ecological selection can counteract gene flow. To better understand how these two forces affect the maintenance of species boundaries, we focused on a species complex including a rare species, maple-leaf oak (Quercus acerifolia), which is found in only four disjunct ridges in Arkansas. Its limited range and geographic proximity to co-occurring close relatives create the possibility for genetic swamping. In this study, we gathered genome-wide single nucleotide polymorphisms (SNPs) using restriction-site-associated DNA sequencing (RADseq) from 190 samples of Q. acerifolia and three of its close relatives, Q. shumardii, Q. buckleyi, and Q. rubra. We found that Q. shumardii and Q. acerifolia are reciprocally monophyletic with low support, suggesting incomplete lineage sorting, introgression between Q. shumardii and Q. acerifolia, or both. Analyses that model allele distributions demonstrate that admixture contributes strongly to this pattern. Populations of Q. acerifolia experience gene flow from Q. shumardii and Q. rubra, but we found evidence that divergent selection is likely maintaining species boundaries: 1) ex situ collections of Q. acerifolia have a higher proportion of hybrids compared to the mature trees of the wild populations, suggesting ecological selection against hybrids at the seed/seedling stage; 2) ecological traits co-vary with genomic composition; and 3) Q. acerifolia shows genetic differentiation at loci hypothesized to influence tolerance of radiation, drought, and high temperature. Our findings strongly suggest that in maple-leaf oak, selection results in higher divergence at regions of the genome despite gene flow from close relatives.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141332532","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

Phylogenetic assessment within a species complex of a subterranean rodent (Geomys bursarius) with conservation implications for isolated subspecies. 地下啮齿动物（Geomys bursarius）物种群内部的系统发育评估，以及对孤立亚种的保护意义。

IF 3 2区生物学

Journal of Heredity Pub Date : 2024-08-20 DOI: 10.1093/jhered/esae035

Nathan Alexander, Alida de Flamingh, Bradley J Cosentino, Robert L Schooley

{"title":"Phylogenetic assessment within a species complex of a subterranean rodent (Geomys bursarius) with conservation implications for isolated subspecies.","authors":"Nathan Alexander, Alida de Flamingh, Bradley J Cosentino, Robert L Schooley","doi":"10.1093/jhered/esae035","DOIUrl":"10.1093/jhered/esae035","url":null,"abstract":"Range contraction and expansion from glaciation have led to genetic divergence that may be particularly pronounced in fossorial species with low dispersal. The plains pocket gopher (Geomys bursarius) is a fossorial species that ranges widely across North America but has a poorly understood phylogeny. We used mitogenomes (14,996 base pairs) from 56 individuals across seven subspecies, plus two outgroup species, to assess genetic divergence from minimum spanning trees, measure genetic distances, and infer phylogenetic trees using BEAST. We found G. b. wisconsinensis was monophyletic with recent divergence. Further assessment is needed for G. b. major because it was paraphyletic and exhibited inconsistent groupings with other clades. Importantly, we identified G. b. illinoensis as being genetically distinct and monophyletic likely due to a unique colonization event eastward across the Mississippi River. Because G. b. illinoensis faces continued pressures from niche reduction and habitat loss, we recommend that G. b. illinoensis be considered an evolutionary significant unit warranting conservation actions to promote connectivity and restore suitable habitat. Such conservation efforts should benefit other grassland species including those originating from clades west of the Mississippi River that may also be evolutionary significant units.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11334213/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141565044","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

A genome assembly of the American black bear, Ursus americanus, from California. 加利福尼亚州美洲黑熊的基因组组装。

IF 3 2区生物学

Journal of Heredity Pub Date : 2024-08-20 DOI: 10.1093/jhered/esae037

Megan A Supple, Merly Escalona, Jillian Adkins, Michael R Buchalski, Nicolas Alexandre, Ruta M Sahasrabudhe, Oanh Nguyen, Samuel Sacco, Colin Fairbairn, Eric Beraut, William Seligmann, Richard E Green, Erin Meredith, Beth Shapiro

{"title":"A genome assembly of the American black bear, Ursus americanus, from California.","authors":"Megan A Supple, Merly Escalona, Jillian Adkins, Michael R Buchalski, Nicolas Alexandre, Ruta M Sahasrabudhe, Oanh Nguyen, Samuel Sacco, Colin Fairbairn, Eric Beraut, William Seligmann, Richard E Green, Erin Meredith, Beth Shapiro","doi":"10.1093/jhered/esae037","DOIUrl":"10.1093/jhered/esae037","url":null,"abstract":"The American black bear, Ursus americanus, is a widespread and ecologically important species in North America. In California, the black bear plays an important role in a variety of ecosystems and serves as an important species for recreational hunting. While research suggests that the populations in California are currently healthy, continued monitoring is critical, with genomic analyses providing an important surveillance tool. Here we report a high-quality, near chromosome-level genome assembly from a U. americanus sample from California. The primary assembly has a total length of 2.5 Gb contained in 316 scaffolds, a contig N50 of 58.9 Mb, a scaffold N50 of 67.6 Mb, and a BUSCO completeness score of 96%. This U. americanus genome assembly will provide an important resource for the targeted management of black bear populations in California, with the goal of achieving an appropriate balance between the recreational value of black bears and the maintenance of viable populations. The high quality of this genome assembly will also make it a valuable resource for comparative genomic analyses among black bear populations and among bear species.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11334205/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141617668","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 insights into the critically endangered King Island scrubtit. 从基因组学角度了解极度濒危的国王岛恙虫病。

IF 3 2区生物学

Journal of Heredity Pub Date : 2024-08-20 DOI: 10.1093/jhered/esae029

Ross Crates, Brenton von Takach, Catherine M Young, Dejan Stojanovic, Linda E Neaves, Liam Murphy, Daniel Gautschi, Carolyn J Hogg, Robert Heinsohn, Phil Bell, Katherine A Farquharson

{"title":"Genomic insights into the critically endangered King Island scrubtit.","authors":"Ross Crates, Brenton von Takach, Catherine M Young, Dejan Stojanovic, Linda E Neaves, Liam Murphy, Daniel Gautschi, Carolyn J Hogg, Robert Heinsohn, Phil Bell, Katherine A Farquharson","doi":"10.1093/jhered/esae029","DOIUrl":"10.1093/jhered/esae029","url":null,"abstract":"Small, fragmented, or isolated populations are at risk of population decline due to fitness costs associated with inbreeding and genetic drift. The King Island scrubtit Acanthornis magna greeniana is a critically endangered subspecies of the nominate Tasmanian scrubtit A. m. magna, with an estimated population of <100 individuals persisting in three patches of swamp forest. The Tasmanian scrubtit is widespread in wet forests on mainland Tasmania. We sequenced the scrubtit genome using PacBio HiFi and undertook a population genomic study of the King Island and Tasmanian scrubtits using a double-digest restriction site-associated DNA (ddRAD) dataset of 5,239 SNP loci. The genome was 1.48 Gb long, comprising 1,518 contigs with an N50 of 7.715 Mb. King Island scrubtits formed one of four overall genetic clusters, but separated into three distinct subpopulations when analyzed independently of the Tasmanian scrubtit. Pairwise FST values were greater among the King Island scrubtit subpopulations than among most Tasmanian scrubtit subpopulations. Genetic diversity was lower and inbreeding coefficients were higher in the King Island scrubtit than all except one of the Tasmanian scrubtit subpopulations. We observed crown baldness in 8/15 King Island scrubtits, but 0/55 Tasmanian scrubtits. Six loci were significantly associated with baldness, including one within the DOCK11 gene which is linked to early feather development. Contemporary gene flow between King Island scrubtit subpopulations is unlikely, with further field monitoring required to quantify the fitness consequences of its small population size, low genetic diversity, and high inbreeding. Evidence-based conservation actions can then be implemented before the taxon goes extinct.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11334212/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141181523","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

Comparative analyses of the banded alder borer (Rosalia funebris) and Asian longhorned beetle (Anoplophora glabripennis) genomes reveal significant differences in genome architecture and gene content among these and other Cerambycidae. 对带状桤木螟（Rosalia funebris）和亚洲长角甲虫（Anoplophora glabripennis）基因组的比较分析表明，这些甲虫和其他角虫的基因组结构和基因含量存在显著差异。

IF 3 2区生物学

Journal of Heredity Pub Date : 2024-08-20 DOI: 10.1093/jhered/esae021

Terrence Sylvester, Richard Adams, Robert F Mitchell, Ann M Ray, Rongrong Shen, Na Ra Shin, Duane D McKenna

{"title":"Comparative analyses of the banded alder borer (Rosalia funebris) and Asian longhorned beetle (Anoplophora glabripennis) genomes reveal significant differences in genome architecture and gene content among these and other Cerambycidae.","authors":"Terrence Sylvester, Richard Adams, Robert F Mitchell, Ann M Ray, Rongrong Shen, Na Ra Shin, Duane D McKenna","doi":"10.1093/jhered/esae021","DOIUrl":"10.1093/jhered/esae021","url":null,"abstract":"Rosalia funebris (RFUNE; Cerambycidae), the banded alder borer, is a longhorn beetle whose larvae feed on the wood of various economically and ecologically significant trees in western North America. Adults are short-lived and not known to consume plant material substantially. We sequenced, assembled, and annotated the RFUNE genome using HiFi and RNASeq data. We documented genome architecture and gene content, focusing on genes putatively involved in plant feeding (phytophagy). Comparisons were made to the well-studied genome of the Asian longhorned beetle (AGLAB; Anoplophora glabripennis) and other Cerambycidae. The 814 Mb RFUNE genome assembly was distributed across 42 contigs, with an N50 of 30.18 Mb. Repetitive sequences comprised 60.27% of the genome, and 99.0% of expected single-copy orthologous genes were fully assembled. We identified 12,657 genes, fewer than in the four other species studied, and 46.4% fewer than for Aromia moschata (same subfamily as RFUNE). Of the 7,258 orthogroups shared between RFUNE and AGLAB, 1,461 had more copies in AGLAB and 1,023 had more copies in RFUNE. We identified 240 genes in RFUNE that putatively arose via horizontal transfer events. The RFUNE genome encoded substantially fewer putative plant cell wall degrading enzymes than AGLAB, which may relate to the longer-lived plant-feeding adults of the latter species. The RFUNE genome provides new insights into cerambycid genome architecture and gene content and provides a new vantage point from which to study the evolution and genomic basis of phytophagy in beetles.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140319882","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

Correction to: Limited evidence for extensive genetic differentiation between X and Y chromosomes in Hybognathus amarus (Cypriniformes: Leuciscidae). 更正：鲤形目：鯈鱼X和Y染色体广泛遗传分化的有限证据。

IF 3 2区生物学

Journal of Heredity Pub Date : 2024-08-20 DOI: 10.1093/jhered/esae038

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 : 2024-08-16 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":"https://doi.org/10.1093/jhered/esae043","url":null,"abstract":"Heterosis occurs in individuals when genetic diversity, i.e., 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":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2024-08-16","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

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 : 2024-08-08 DOI: 10.1093/jhered/esae036

M Eline Saubin, Solenn Stoeckel, Aur Elien Tellier, Fabien Halkett

{"title":"Neutral genetic structuring of pathogen populations during rapid adaptation.","authors":"M Eline Saubin, Solenn Stoeckel, Aur Elien Tellier, Fabien Halkett","doi":"10.1093/jhered/esae036","DOIUrl":"https://doi.org/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 bot- tleneck 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":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2024-08-08","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

Quantitative trait loci concentrate in specific regions of the Mexican cavefish genome and reveal key candidate genes for cave-associated evolution. 定量性状位点集中在墨西哥洞穴鱼基因组的特定区域，揭示了洞穴相关进化的关键候选基因。

IF 3 2区生物学

Journal of Heredity Pub Date : 2024-07-30 DOI: 10.1093/jhered/esae040

Jonathan Wiese, Emilie Richards, Johanna E Kowalko, Suzanne E McGaugh

{"title":"Quantitative trait loci concentrate in specific regions of the Mexican cavefish genome and reveal key candidate genes for cave-associated evolution.","authors":"Jonathan Wiese, Emilie Richards, Johanna E Kowalko, Suzanne E McGaugh","doi":"10.1093/jhered/esae040","DOIUrl":"10.1093/jhered/esae040","url":null,"abstract":"A major goal of modern biology is connecting phenotype with its underlying genetic basis. The Mexican cavefish (Astyanax mexicanus), a characin fish species comprised of a surface ecotype and a cave-derived ecotype, is well suited as a model to study the genetic mechanisms underlying adaptation to extreme environments. Here we map 206 previously published quantitative trait loci (QTL) for cave-derived traits in A. mexicanus to the newest version of the surface fish genome assembly, AstMex3. These analyses revealed that QTL cluster in the genome more than expected by chance, and this clustering is not explained by the distribution of genes in the genome. To investigate whether certain characteristics of the genome facilitate phenotypic evolution, we tested whether genomic characteristics associated with increased opportunities for mutation, such as highly mutagenic CpG sites, are reliable predictors of the sites of trait evolution but did not find any significant trends. Finally, we combined the QTL map with previously collected expression and selection data to identify 36 candidate genes that may underlie the repeated evolution of cave phenotypes, including rgrb, which is predicted to be involved in phototransduction. We found this gene has disrupted exons in all non-hybrid cave populations but intact reading frames in surface fish. Overall, our results suggest specific regions of the genome may play significant roles in driving adaptation to the cave environment in Astyanax mexicanus and demonstrate how this compiled dataset can facilitate our understanding of the genetic basis of repeated evolution in the Mexican cavefish.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2024-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141857224","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