Molecular Ecology Resources最新文献_第5页

Quantifying Bone Collagen Fingerprint Variation Between Species 物种间骨胶原指纹图谱的定量分析。

IF 5.5 1区生物学

Molecular Ecology Resources Pub Date : 2025-01-29 DOI: 10.1111/1755-0998.14072

Andrew Baker, Michael Buckley

{"title":"Quantifying Bone Collagen Fingerprint Variation Between Species","authors":"Andrew Baker, Michael Buckley","doi":"10.1111/1755-0998.14072","DOIUrl":"10.1111/1755-0998.14072","url":null,"abstract":"Collagen is the most ubiquitous protein in the animal kingdom and one of the most abundant proteins on Earth. Despite having a relatively repetitive amino acid sequence motif that enables its triple helical structure, in type 1 collagen, that dominates skin and bone, there is enough variation for its increasing use for the biomolecular species identification of animal tissues processed or degraded beyond the amenability of DNA-based analyses. In recent years, this has been most commonly achieved through the technique of collagen peptide mass fingerprinting (PMF) known as ZooMS (Zooarchaeology by Mass Spectrometry), applied to the analysis of tens of thousands of samples across over one hundred studies in the past decade alone. However, a robust means to quantify variation between these fingerprints remains elusive, despite being increasingly required due to the shift towards a wider range of wild fauna and those that are more distantly related from currently known sequences. This is particularly problematic in fish due to their greater sequence variation. Here we evaluate the quantification of the relative closeness of collagen fingerprints between families using ANOSIM and a modified SIMPER analysis, incorporating relative peak intensity. Our results show a clear correlation between sequence differentiation and statistical distance of PMFs, indicating that the additional complexity of type 1 collagen in fish could directly affect the efficacy of biomolecular techniques such as ZooMS. Furthermore, this multivariate statistical analysis demonstrates that PMFs in fish are substantively more distinct than those of mammalian or amphibian taxa.","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 4","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.14072","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143057608","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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

Pangenomics Links Boll Weevil Divergence With Ancient Mesoamerican Cotton Cultivation 泛基因组学：棉铃象鼻虫分化与古代中美洲棉花种植

IF 5.5 1区生物学

Molecular Ecology Resources Pub Date : 2025-01-22 DOI: 10.1111/1755-0998.14054

Zachary P. Cohen, Lindsey C. Perkin, Tyler J. Raszick, Sheina B. Sim, Scott M. Geib, Anna K. Childers, Gregory A. Sword, Charles P.-C. Suh

{"title":"Pangenomics Links Boll Weevil Divergence With Ancient Mesoamerican Cotton Cultivation","authors":"Zachary P. Cohen, Lindsey C. Perkin, Tyler J. Raszick, Sheina B. Sim, Scott M. Geib, Anna K. Childers, Gregory A. Sword, Charles P.-C. Suh","doi":"10.1111/1755-0998.14054","DOIUrl":"10.1111/1755-0998.14054","url":null,"abstract":"<div>\u0000 \u0000 The boll weevil, Anthonomus grandis grandis Boheman, and thurberia weevil, Anthonomus grandis thurberiae Pierce, together comprise a species complex that ranges throughout Mexico, the southwestern regions of the United States and parts of South America. The boll weevil is a historically damaging and contemporaneously threatening pest to commercial upland cotton, Gossypium hirsutum L. (Malvales: Malvaceae), whereas the thurberia weevil is regarded as an innocuous non-pest subspecies that is mostly found on non-cultivated Thurber's or Arizona cotton, Gossypium thurberi L., throughout its native range in western Mexico and the southwestern United States. Recent independent analyses, using mitochondrial and whole-genome markers, have suggested the independent evolution of these lineages is more attributable to geographic isolation than biotic factors. We suggest a combination of drivers after employing comparative genomic, population genetic and pangenome methodologies to identify large and small polymorphisms. By leveraging genetic differences, we determined 39,310 diagnostic loci between the subspecies, find genes under selection, and model the subspecies' shared and unique evolutionary history. Interestingly, structural variations capture a large proportion of genes at the population level and demographic reconstruction suggests a split between approximately 3,320–16,300 before present (YBP), which coincides with cotton cultivation in Mesoamerica, approximately 3,000-5,000 YBP. Observed polymorphisms are enriched for reproductive, regulatory, and metabolic genes, which may be attributed to the subspecies split and coevolution with cultivated cotton. Our results demonstrate the utility of a holistic, comparative framework utilising small and large polymorphisms to reconstruct demography and identify genetic novelty via pangenomics.\u0000 </div>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 3","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142997006","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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

Exploring Environmental Microfungal Diversity Through Serial Single Cell Screening 通过连续单细胞筛选探索环境微真菌多样性。

IF 5.5 1区生物学

Molecular Ecology Resources Pub Date : 2025-01-20 DOI: 10.1111/1755-0998.14055

Joana Mariz, Ali Nawaz, Yvonne Bösch, Christian Wurzbacher

{"title":"Exploring Environmental Microfungal Diversity Through Serial Single Cell Screening","authors":"Joana Mariz, Ali Nawaz, Yvonne Bösch, Christian Wurzbacher","doi":"10.1111/1755-0998.14055","DOIUrl":"10.1111/1755-0998.14055","url":null,"abstract":"Known for its remarkable diversity and ecological importance, the fungal kingdom remains largely unexplored. In fact, the number of unknown and undescribed fungi is predicted to exceed the number of known fungal species by far. Despite efforts to uncover these dark fungal taxa, we still face inherent sampling biases and methodological limitations. Here, we present a framework that combines taxonomic knowledge, molecular biology and data processing to explore the fungal biodiversity of enigmatic aquatic fungal lineages. Our work is based on serial screening of environmental fungal cells to approach unknown fungal taxa. Microscopic documentation is followed by DNA analysis of laser micro-dissected cells, coupled with a ribosomal operon barcoding step realised by long-read sequencing, followed by an optional whole genome sequencing step. We tested this approach on a range of aquatic fungal cells mostly belonging to the ecological group of aquatic hyphomycetes derived from environmental samples. From this initial screening, we were able to identify 60 potentially new fungal taxa in the target dataset. By extending this methodology to other fungal lineages associated with different habitats, we expect to increasingly characterise the molecular barcodes of dark fungal taxa in diverse environmental samples. This work offers a promising solution to the challenges posed by unknown and unculturable fungi and holds the potential to be applied to the diverse lineages of undescribed microeukaryotes.","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 3","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.14055","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142996936","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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 and Methylomic Signatures Associated With the Maintenance of Genome Stability and Adaptive Evolution in Two Closely Allied Wolf Spiders 两种亲缘关系密切的狼蛛基因组稳定性维持和适应性进化相关的基因组和甲基组特征。

IF 5.5 1区生物学

Molecular Ecology Resources Pub Date : 2025-01-20 DOI: 10.1111/1755-0998.14071

Qing Zuo, Run-Biao Wu, Li-Na Sun, Tian-Yu Ren, Zheng Fan, Lu-Yu Wang, Bing Tan, Bin Luo, Muhammad Irfan, Qian Huang, Yan-Jun Shen, Zhi-Sheng Zhang

{"title":"Genomic and Methylomic Signatures Associated With the Maintenance of Genome Stability and Adaptive Evolution in Two Closely Allied Wolf Spiders","authors":"Qing Zuo, Run-Biao Wu, Li-Na Sun, Tian-Yu Ren, Zheng Fan, Lu-Yu Wang, Bing Tan, Bin Luo, Muhammad Irfan, Qian Huang, Yan-Jun Shen, Zhi-Sheng Zhang","doi":"10.1111/1755-0998.14071","DOIUrl":"10.1111/1755-0998.14071","url":null,"abstract":"<div>\u0000 \u0000 Pardosa spiders, belonging to the wolf spider family Lycosidae, play a vital role in maintaining the health of forest and agricultural ecosystems due to their function in pest control. This study presents chromosome-level genome assemblies for two allied Pardosa species, P. laura and P. agraria. Both species' genomes show a notable expansion of helitron transposable elements, which contributes to their large genome sizes. Methylome analysis indicates that P. laura has higher overall DNA methylation levels compared to P. agraria. DNA methylation may not only aids in transposable element-driven genome expansion but also positively affects the three-dimensional organisation of P. laura after transposon amplification, thereby potentially enhancing genome stability. Genes associated with hyper-differentially methylated regions in P. laura (compared to P. agraria) are enriched in functions related to mRNA processing and energy production. Furthermore, combined transcriptome and methylome profiling has uncovered a complex regulatory interplay between DNA methylation and gene expression, emphasising the important role of gene body methylation in the regulation of gene expression. Comparative genomic analysis shows a significant expansion of cuticle protein and detoxification-related gene families in P. laura, which may improve its adaptability to various habitats. This study provides essential genomic and methylomic insights, offering a deeper understanding of the relationship between transposable elements and genome stability, and illuminating the adaptive evolution and species differentiation among allied spiders.\u0000 </div>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 4","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142996949","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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

gscramble: Simulation of Admixed Individuals Without Reuse of Genetic Material 不重复使用遗传物质的混合个体的模拟。

IF 5.5 1区生物学

Molecular Ecology Resources Pub Date : 2025-01-12 DOI: 10.1111/1755-0998.14069

Eric C. Anderson, Rachael M. Giglio, Matthew G. DeSaix, Timothy J. Smyser

{"title":"gscramble: Simulation of Admixed Individuals Without Reuse of Genetic Material","authors":"Eric C. Anderson, Rachael M. Giglio, Matthew G. DeSaix, Timothy J. Smyser","doi":"10.1111/1755-0998.14069","DOIUrl":"10.1111/1755-0998.14069","url":null,"abstract":"While a best practice for evaluating the behaviour of genetic clustering algorithms on empirical data is to conduct parallel analyses on simulated data, these types of simulation techniques often involve sampling genetic data with replacement. In this paper we demonstrate that sampling with replacement, especially with large marker sets, inflates the perceived statistical power to correctly assign individuals (or the alleles that they carry) back to source populations—a phenomenon we refer to as resampling-induced, spurious power inflation (RISPI). To address this issue, we present gscramble, a simulation approach in R for creating biologically informed individual genotypes from empirical data that: (1) samples alleles from populations without replacement and (2) segregates alleles based on species-specific recombination rates. This framework makes it possible to simulate admixed individuals in a way that respects the physical linkage between markers on the same chromosome and which does not suffer from RISPI. This is achieved in gscramble by allowing users to specify pedigrees of varying complexity in order to simulate admixed genotypes, segregating and tracking haplotype blocks from different source populations through those pedigrees, and then sampling—using a variety of permutation schemes—alleles from empirical data into those haplotype blocks. We demonstrate the functionality of gscramble with both simulated and empirical data sets and highlight additional uses of the package that users may find valuable.","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 4","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.14069","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142968815","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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

FOGS: A SNPSTR Marker Database to Combat Wildlife Trafficking and a Cell Culture Bank for Ex-Situ Conservation FOGS：打击野生动物走私的SNPSTR标记数据库和移地保护的细胞培养库。

IF 5.5 1区生物学

Molecular Ecology Resources Pub Date : 2025-01-10 DOI: 10.1111/1755-0998.14062

Annika Mozer, Camilla Bruno Di-Nizo, Albia Consul, Bruno Huettel, Richard Jäger, Ayodélé Akintayo, Christoph Erhardt, Lena Fenner, Dominik Fischer, Sophia Forat, France Gimnich, Peter Grobe, Sebastian Martin, Vikram Nathan, Ammar Saeed, Laura von der Mark, Christian Woehle, Klaus Olek, Bernhard Misof, Jonas J. Astrin

{"title":"FOGS: A SNPSTR Marker Database to Combat Wildlife Trafficking and a Cell Culture Bank for Ex-Situ Conservation","authors":"Annika Mozer, Camilla Bruno Di-Nizo, Albia Consul, Bruno Huettel, Richard Jäger, Ayodélé Akintayo, Christoph Erhardt, Lena Fenner, Dominik Fischer, Sophia Forat, France Gimnich, Peter Grobe, Sebastian Martin, Vikram Nathan, Ammar Saeed, Laura von der Mark, Christian Woehle, Klaus Olek, Bernhard Misof, Jonas J. Astrin","doi":"10.1111/1755-0998.14062","DOIUrl":"10.1111/1755-0998.14062","url":null,"abstract":"Illegal wildlife trade is a growing problem internationally. Poaching of animals not only leads to the extinction of populations and species but also has serious consequences for ecosystems and economies. This study introduces a molecular marker system that authorities can use to detect and substantiate wildlife trafficking. SNPSTR markers combine short tandem repeats with single nucleotide polymorphisms within an amplicon to increase discriminatory power. Within the FOGS (Forensic Genetics for Species Protection) project, we have established SNPSTR marker sets for 74 vertebrate species. On average, each set consists of 19 SNPSTR markers with 82 SNPs per set. More than 1300 SNPSTR markers and over 300 STR markers were identified. Also, through its biobanking pipeline, the FOGS project enabled the cryopreservation of somatic cells from 91 vertebrate species as well as viable tissues for later cell initiation from a further 109 species, providing future strategies for ex situ conservation. In addition, many more fixed tissues and DNA samples of endangered species were biobanked. Therefore, FOGS was an interdisciplinary study, combining molecular wildlife forensics and conservation tools. The SNPSTR sets and cell culture information are accessible through the FOGS database (https://fogs-portal.de/data) that is open to scientists, researchers, breeders and authorities worldwide to protect wildlife from illegal trade.","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 4","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.14062","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142963247","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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

Too Far From Relatives? Impact of the Genetic Distance on the Success of Exon Capture in Phylogenomics 离亲戚太远？遗传距离对系统基因组中外显子捕获成功的影响。

IF 5.5 1区生物学

Molecular Ecology Resources Pub Date : 2025-01-09 DOI: 10.1111/1755-0998.14064

Thomas Lemarcis, Amandine Blin, Marie Cariou, Alessandro Derzelle, Sarah Farhat, Alexander Fedosov, Paul Zaharias, Dario Zuccon, Nicolas Puillandre

{"title":"Too Far From Relatives? Impact of the Genetic Distance on the Success of Exon Capture in Phylogenomics","authors":"Thomas Lemarcis, Amandine Blin, Marie Cariou, Alessandro Derzelle, Sarah Farhat, Alexander Fedosov, Paul Zaharias, Dario Zuccon, Nicolas Puillandre","doi":"10.1111/1755-0998.14064","DOIUrl":"10.1111/1755-0998.14064","url":null,"abstract":"<div>\u0000 \u0000 The exon capture approach allows for sequencing a large number of loci to reconstruct phylogenetic relationships at varying taxonomic levels. In order to efficiently recover the targeted loci, the probes designed to capture the exons need to be genetically sufficiently similar to bind to the DNA, with a proposed limit of 10% of divergence. However, this threshold has never been tested with a specific protocol. We have designed a set of probes to capture 1125 exons in the Neogastropoda (Mollusca, Gastropoda), processed with the same protocol from the field to the DNA sequencing to control for potential bias in DNA quantity and quality. We sequenced 30 different species, including 14 species of Neogastropoda and 16 species of Caenogastropoda non-Neogastropoda. Each species includes five specimens, for a total of 150 specimens, and for four specimens among the 150, DNA extracts were aliquoted in four samples, sequenced separately, to estimate the intraspecific and intraspecimen variability in capture success. Our results confirm the impact of genetic distance on the success of exon capture with a negative linear correlation between the genetic distance and the number of exons captured for each sample. Consequently, designing new capture probes would allow for capturing exons in genetically more distant groups without the need to redesign a new set of exons.\u0000 </div>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 4","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142941880","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Chromosome-Level Genome Assembly of Five Emberiza Species Reveals the Genomic Characteristics and Intrinsic Drivers of Adaptive Radiation. 五种Emberiza物种的染色体水平基因组组装揭示了适应性辐射的基因组特征和内在驱动因素。

IF 5.5 1区生物学

Molecular Ecology Resources Pub Date : 2025-01-08 DOI: 10.1111/1755-0998.14063

Tingli Hu, Haohao Ma, Yongxuan Xiao, Ruolei Sun, Chunlin Li, Lei Shan, Baowei Zhang

{"title":"Chromosome-Level Genome Assembly of Five Emberiza Species Reveals the Genomic Characteristics and Intrinsic Drivers of Adaptive Radiation.","authors":"Tingli Hu, Haohao Ma, Yongxuan Xiao, Ruolei Sun, Chunlin Li, Lei Shan, Baowei Zhang","doi":"10.1111/1755-0998.14063","DOIUrl":"https://doi.org/10.1111/1755-0998.14063","url":null,"abstract":"Emberiza buntings (Aves: Emberizidae) exhibit extensive diversity and rapid diversification within the Old World, particularly in the eastern Palearctic, making them valuable models for studying rapid radiation among sympatric species. Despite their ecological and morphological diversity, there remains a significant gap in understanding the genomic underpinnings driving their rapid speciation. To fill this gap, we assembled high-quality chromosome-level genomes of five representative Emberiza species (E. aureola, E. pusilla, E. rustica, E. rutila and E. spodocephala). Comparative genomic analysis revealed distinct migration-related evolutionary adaptations in their genomes, including variations in lipid metabolism, oxidative stress response, locomotor ability and circadian regulation. These changes may facilitate the rapid occupation of emerging ecological niches and provide opportunities for species diversification. Additionally, these five species exhibited abnormal abundances of long terminal repeat retrotransposons (LTRs), comprising over 20% of their genomes, with insertion times corresponding to their divergence (~2.5 million years ago). The presence of LTRs influenced genome size, chromosomal structure and single-gene expression, suggesting their role in promoting the rapid diversification of Emberiza species. These findings offer valuable insights into the adaptive radiation of Emberiza and establish a robust theoretical foundation for further exploration of the patterns and mechanisms underlying their diversification.","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14063"},"PeriodicalIF":5.5,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142941634","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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 Post-Mortem Molecular Damage Profile in the Ancient Human Mitochondrial DNA 远古人类线粒体DNA的死后分子损伤图谱。

IF 5.5 1区生物学

Molecular Ecology Resources Pub Date : 2025-01-07 DOI: 10.1111/1755-0998.14061

Daniel R. Cuesta-Aguirre, Cristina Amor-Jimenez, Assumpció Malgosa, Cristina Santos

{"title":"A Post-Mortem Molecular Damage Profile in the Ancient Human Mitochondrial DNA","authors":"Daniel R. Cuesta-Aguirre, Cristina Amor-Jimenez, Assumpció Malgosa, Cristina Santos","doi":"10.1111/1755-0998.14061","DOIUrl":"10.1111/1755-0998.14061","url":null,"abstract":"Mitochondrial DNA (mtDNA) analysis is crucial for understanding human population structure and genetic diversity. However, post-mortem DNA damage poses challenges, that make analysis difficult. DNA preservation is affected by environmental conditions which, among other factors, complicates the differentiation of endogenous variants from artefacts in ancient mtDNA mix profiles. This study aims to develop a molecular damage profile for ancient mtDNA that can become a useful tool in analysing mtDNA from ancient remains. A dataset of 427 whole genomes or capture of mtDNA sequences from individuals representing different historical periods and climatic regions was compiled from the ENA database. Present-day and UDG-treated ancient samples were also included and used to establish levels of damaged reads. Results indicated that samples from cold regions exhibited the lowest percentage of damaged reads, followed by arid, cold, tropical and temperate regions, with significant differences observed between cold and temperate regions. A global damage profile was generated, identifying 2933 positions (25% of the positions considered) with damage in more than 23.8% of the samples analysed, deemed as damage hotspots. Notably, 2856 of these hotspots had never been reported as damage or mutational hotspots, or heteroplasmic positions. Damage hotspot frequency by position was slightly higher in the non-coding region compared with the coding region. In conclusion, this study provides a molecular damage profile for ancient mtDNA analysis that is expected to be a valuable tool in the interpretation of mtDNA variation in ancient samples.","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 4","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.14061","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142941630","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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 Prediction of Individual Inbreeding Levels for the Management of Genetic Diversity in Populations With Small Effective Size 小有效规模群体遗传多样性管理中个体近交水平的基因组预测

IF 5.5 1区生物学

Molecular Ecology Resources Pub Date : 2025-01-07 DOI: 10.1111/1755-0998.14068

Natalia Soledad Forneris, Mirte Bosse, Mathieu Gautier, Tom Druet

{"title":"Genomic Prediction of Individual Inbreeding Levels for the Management of Genetic Diversity in Populations With Small Effective Size","authors":"Natalia Soledad Forneris, Mirte Bosse, Mathieu Gautier, Tom Druet","doi":"10.1111/1755-0998.14068","DOIUrl":"https://doi.org/10.1111/1755-0998.14068","url":null,"abstract":"<div>\u0000 \u0000 In populations of small effective size (Ne), such as those in conservation programmes, companion animals or livestock species, inbreeding control is essential. Homozygosity-by-descent (HBD) segments provide relevant information in that context, as they allow accurate estimation of the inbreeding coefficient, provide locus-specific information and their length is informative about the “age” of inbreeding. Our objective was to evaluate tools for predicting HBD in future offspring based on parental genotypes, a problem equivalent to identifying segments identical-by-descent (IBD) among the four parental chromosomes. In total, we reviewed and evaluated 16 approaches using simulated and real data from populations with small Ne. The methods included model-based approaches as well as more computationally efficient rule-based approaches. The accuracy of the methods was then evaluated, including with low-density marker panels, genotyping-by-sequencing data and small groups of individuals, typical features of such populations. Two model-based approaches performed consistently well, while some rule-based approaches proved accurate for genome-wide predictions. The model-based approaches were particularly efficient when genomic information was sparse or degraded. Methods using phased data proved to be more accurate, while some approaches relying on unphased genotype data were sensitive to the assumed allele frequencies. In some settings, pedigree-based predictions ranked high for recent inbreeding levels. Finally, we showed that our evaluation is also informative about the accuracy of the methods for estimating relatedness and identifying IBD segments between pairs of present-day individuals. This study shows that future inbreeding can be accurately predicted, including at specific loci, but not all methods perform equally well.\u0000 </div>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 4","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143770300","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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