Journal of Heredity最新文献_第6页

Sensitivity of transcriptomics: Different samples and methodology alter conclusions in Gulf pipefish (Syngnathus scovelli). 转录组学的敏感性：不同样本和方法改变了海湾琵琶鱼（Syngnathus scovelli）的结论。

IF 3 2区生物学

Journal of Heredity Pub Date : 2025-03-01 DOI: 10.1093/jhered/esae067

Bernadette D Johnson, Emily Rose, Adam G Jones

{"title":"Sensitivity of transcriptomics: Different samples and methodology alter conclusions in Gulf pipefish (Syngnathus scovelli).","authors":"Bernadette D Johnson, Emily Rose, Adam G Jones","doi":"10.1093/jhered/esae067","DOIUrl":"10.1093/jhered/esae067","url":null,"abstract":"Transcriptome analysis has become a central tool in evolutionary and functional genomics. However, variation among biological samples and analysis techniques can greatly influence results, potentially compromising insights into the phenomenon under study. Here, we evaluate differences in the brain transcriptome between female and male Gulf pipefish (Syngnathus scovelli). We perform comparisons between results from entire pipelines for brain transcriptome assembly, quantification, and analysis. We also offer a unique biological comparison between two sampling instances (Redfish Bay: n = 15, Port Lavaca: n = 7). Our results demonstrate crucial shortcomings with current experimental approaches. We found high variation within our results that was driven by both technical differences between pipelines and biological differences between pipefish samples. In our analysis of highly expressed genes, we found that the choice of methods influenced the degree of contamination or noise included in the identified genes. Notably, genes identified within the same pipeline were more similar than any other comparison. Our differential expression analysis revealed that both methodology and sampling location influenced the quantity and consistency of statistically significant transcripts. In the context of these results, we offer modifications to current practices that may increase the robustness of transcriptome-based conclusions. In particular, the use of a reference-guided assembly and an increase in sample sizes are likely to improve resistance to noise or error.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"139-148"},"PeriodicalIF":3.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11879219/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142640233","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

Mutation of mpv17 results in loss of iridophores due to mitochondrial dysfunction in tilapia. mpv17 基因突变会导致罗非鱼线粒体功能障碍而失去虹膜。

IF 3 2区生物学

Journal of Heredity Pub Date : 2025-03-01 DOI: 10.1093/jhered/esae034

Jia Xu, Peng Li, Mengmeng Xu, Chenxu Wang, Thomas D Kocher, Deshou Wang

{"title":"Mutation of mpv17 results in loss of iridophores due to mitochondrial dysfunction in tilapia.","authors":"Jia Xu, Peng Li, Mengmeng Xu, Chenxu Wang, Thomas D Kocher, Deshou Wang","doi":"10.1093/jhered/esae034","DOIUrl":"10.1093/jhered/esae034","url":null,"abstract":"Mpv17 (mitochondrial inner membrane protein MPV17) deficiency causes severe mitochondrial DNA depletion syndrome in mammals and loss of pigmentation of iridophores and a significant decrease of melanophores in zebrafish. The reasons for this are still unclear. In this study, we established an mpv17 homozygous mutant line in Nile tilapia. The developing mutants are transparent due to the loss of iridophores and aggregation of pigment granules in the melanophores and disappearance of the vertical pigment bars on the side of the fish. Transcriptome analysis using the skin of fish at 30 dpf (days post fertilization) revealed that the genes related to purine (especially pnp4a) and melanin synthesis were significantly downregulated. However, administration of guanine diets failed to rescue the phenotype of the mutants. In addition, no obvious apoptosis signals were observed in the iris of the mutants by TUNEL staining. Significant downregulation of genes related to iridophore differentiation was detected by qPCR. Insufficient ATP, as revealed by ATP assay, α-MSH treatment, and adcy5 mutational analysis, might account for the defects of melanophores in mpv17 mutants. Several tissues displayed less mtDNA and decreased ATP levels. Taken together, these results indicated that mutation of mpv17 led to mitochondrial dTMP deficiency, followed by impaired mtDNA content and mitochondrial function, which in turn, led to loss of iridophores and a transparent body color in tilapia.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"101-112"},"PeriodicalIF":3.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141472787","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 : 2025-03-01 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 clusters 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 A. 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":" ","pages":"89-100"},"PeriodicalIF":3.0,"publicationDate":"2025-03-01","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

A chromosome-length genome assembly for the Pismo clam, Tivela stultorum, a long-lived bivalve species severely impacted by overfishing. 受过度捕捞严重影响的长寿命双壳类物种皮斯莫蛤的染色体长度基因组组装。

IF 3 2区生物学

Journal of Heredity Pub Date : 2025-02-19 DOI: 10.1093/jhered/esaf008

Kyle A Emery, Melissa B DeBiasse, Merly Escalona, Mohan P A Marimuthu, Oanh H Nguyen, Colin W Fairbairn, William Seligmann, Courtney Miller, Nicholas K Schooler, David M Hubbard, Jenifer E Dugan, Michael N Dawson

{"title":"A chromosome-length genome assembly for the Pismo clam, Tivela stultorum, a long-lived bivalve species severely impacted by overfishing.","authors":"Kyle A Emery, Melissa B DeBiasse, Merly Escalona, Mohan P A Marimuthu, Oanh H Nguyen, Colin W Fairbairn, William Seligmann, Courtney Miller, Nicholas K Schooler, David M Hubbard, Jenifer E Dugan, Michael N Dawson","doi":"10.1093/jhered/esaf008","DOIUrl":"https://doi.org/10.1093/jhered/esaf008","url":null,"abstract":"The Pismo clam, Tivela stultorum, is an ecologically and economically important species that inhabiting sandy beaches and subtidal zones in central and southern California, USA, and northern Baja California, Mexico. This long lived venerid clam species is of great management, cultural and conservation interest in California where it was harvested for centuries by indigenous people and then nearly extirpated by intense commercial and recreational overfishing in the mid 1900's. A recreational fishery continues today in California, however T. stultorum faces pressure from poaching, overharvest, and the loss of sandy beaches from rising sea levels and beach erosion. Understanding the susceptibility and resilience of Pismo clams to these pressures is essential for their conservation. We used Pacific Biosciences HiFi long sequencing reads and Dovetail Omni-C proximity reads to assemble a highly contiguous genome of 763 Mb. The genome had a contig N50 of 13 Mb and a scaffold N50 of 38 Mb with a BUSCO completeness score of 95%. Most of the genome sequences (96%) were contained in 19 scaffolds at least 10MB long, consistent with prior evidence that venerid clam genomes are composed of 19 autosomes. This reference genome will enable a more complete understanding of the ecology and evolutionary dynamics of T. stultorum via population genomic analyses, which will help assess risks from climate, fishing, environmental change, and susceptibilities due to life history. Our goal is to better support the continued recovery, informed management and conservation, and future persistence of T. stultorum, a long lived and highly valued clam species.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143451004","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

Decoding Cattle (Bos taurus) Diacylglycerol Acyltransferase (DGAT) Gene Families: A Pathway to Functional Understanding. 解码牛（Bos taurus）二酰基甘油酰基转移酶（DGAT）基因家族：了解功能的途径。

IF 3 2区生物学

Journal of Heredity Pub Date : 2025-02-11 DOI: 10.1093/jhered/esae079

Effat Nasre Esfahani, Saeid Ansari Mahyari, Peymaneh Davoodi, Mostafa Ghaderi-Zefrehei, Bluma J Lesch

{"title":"Decoding Cattle (Bos taurus) Diacylglycerol Acyltransferase (DGAT) Gene Families: A Pathway to Functional Understanding.","authors":"Effat Nasre Esfahani, Saeid Ansari Mahyari, Peymaneh Davoodi, Mostafa Ghaderi-Zefrehei, Bluma J Lesch","doi":"10.1093/jhered/esae079","DOIUrl":"https://doi.org/10.1093/jhered/esae079","url":null,"abstract":"Diacylglycerol acyltransferases (DGAT) are key enzymes in fat storage, converting diacylglycerol and fatty acyl CoA into triacylglycerol. In cattle (Bos taurus), the DGAT1 and DGAT2 genes are well-known for their significant influence on milk production traits, particularly milk fat yield and percentage. However, the cattle genome contains twelve other DGAT gene family members that remain largely uncharacterized. The research examined the genetic makeup of these DGAT proteins, revealing differences in exon count, isoforms, amino acid composition, molecular weight, isoelectric points, and predicted SNP locations. The genes are distributed across five chromosomes (2, 14, 15, 25, and X), and the expansion of this gene family in cattle is likely the result of gene duplication events, driven by specific motifs that favor such duplication. By identifying these distinctions, the study provides foundational insights into the lesser-known DGAT genes, which could be involved in regulating important traits like milk fat production. This comprehensive in silico analysis of the DGAT gene family offers valuable insights into the genetic and structural diversity of these enzymes in cattle. It also establishes a platform for future research into functional SNPs and their potential role in improving milk fat production traits, contributing to the advancement of cattle genetics and dairy production optimization. To this end, the identification of previously uncharacterized DGAT genes and their possible involvement in milk fat synthesis could pave the way for innovative breeding strategies focused on improving both milk yield and fat content in dairy cattle.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143392483","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 length genome assembly of the stone marten (Martes foina, Mustelidae): a new view on one of the cornerstones in carnivore cytogenetics. 石貂（Martes foina, Mustelidae）染色体长度基因组组装：食肉动物细胞遗传学基石之一的新观点。

IF 3 2区生物学

Journal of Heredity Pub Date : 2025-01-29 DOI: 10.1093/jhered/esaf001

Andrey Tomarovsky, Ruqayya Khan, Olga Dudchenko, Azamat Totikov, Natalia A Serdyukova, David Weisz, Nadejda V Vorobieva, Tatiana Bulyonkova, Alexei V Abramov, Wenhui Nie, Jinhuan Wang, Svetlana A Romanenko, Anastasiya A Proskuryakova, Nikolay Cherkasov, Malcolm A Ferguson-Smith, Fengtang Yang, Elena Balanovskaya, M Thomas P Gilbert, Alexander S Graphodatsky, Erez Lieberman Aiden, Roger Powell, Klaus-Peter Koepfli, Polina L Perelman, Sergei Kliver

{"title":"Chromosome length genome assembly of the stone marten (Martes foina, Mustelidae): a new view on one of the cornerstones in carnivore cytogenetics.","authors":"Andrey Tomarovsky, Ruqayya Khan, Olga Dudchenko, Azamat Totikov, Natalia A Serdyukova, David Weisz, Nadejda V Vorobieva, Tatiana Bulyonkova, Alexei V Abramov, Wenhui Nie, Jinhuan Wang, Svetlana A Romanenko, Anastasiya A Proskuryakova, Nikolay Cherkasov, Malcolm A Ferguson-Smith, Fengtang Yang, Elena Balanovskaya, M Thomas P Gilbert, Alexander S Graphodatsky, Erez Lieberman Aiden, Roger Powell, Klaus-Peter Koepfli, Polina L Perelman, Sergei Kliver","doi":"10.1093/jhered/esaf001","DOIUrl":"https://doi.org/10.1093/jhered/esaf001","url":null,"abstract":"The stone marten (Martes foina) is an important species for cytogenetic studies in the order Carnivora. ZooFISH probes created from its chromosomes provided a strong and clean signal in chromosome painting experiments and were valuable for studying the evolution of carnivoran genome architecture. The research revealed that the stone marten chromosome set is similar to the presumed ancestral karyotype of the Carnivora, which added an additional value for the species. Using linked-read and Hi-C sequencing, we generated a chromosome-length genome assembly of a male stone marten (Gansu province, China) from a primary cell line. The stone marten assembly had a length of 2.42 Gbp, scaffold N50 of 144 Mbp, and a 96.2% BUSCO completeness score. We identified 19 chromosomal scaffolds (2n=38) and assigned them chromosome ids based on chromosome painting data. Annotation identified 20,087 protein-coding gene models, of which 18,283 were assigned common names. Comparison of the stone marten assembly with the cat, dog, and human genomes revealed several small syntenic blocks absent on the published painting maps. Finally, we assessed the heterozygosity and its distribution over the chromosomes. The detected low heterozygosity level (0.4 hetSNPs/kbp) and the presence of long RoHs require further research and a new evaluation of the conservation status of the stone marten in China. Combined with available carnivoran genomes in large scale synteny analysis, the stone marten genome will highlight new features and events in carnivoran evolution, hidden from cytogenetic approaches.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143069192","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

Forensic Assessment of Kinship, Genomic Ancestry, and Natural History of an Iconic Tiger of Harlem-New York City. 哈莱姆-纽约标志性老虎的亲属关系、基因组祖先和自然史的法医评估。

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

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