Natalie Czajka, Joseph M. Northrup, Meaghan J. Jones, Aaron B. A. Shafer
The development of epigenetic clocks, or the DNA methylation-based inference of age, is an emerging tool for ageing in free ranging populations. In this study, we developed epigenetic clocks for three species of large mammals that are the focus of extensive management throughout their range in North America: white-tailed deer, black bear and mountain goat. We quantified differential DNA methylation patterns at over 30,000 cytosine-guanine sites (CpGs) from tissue samples of all three species (black bear n = 49; white-tailed deer n = 47; mountain goat n = 45). We used a penalized regression model (elastic net) to build explanatory (black bear r = .95; white-tailed deer r = .99; mountain goat r = .97) and robust (black bear Median Absolute Error or MAE = 1.33; white-tailed deer MAE = 0.29; mountain goat MAE = 0.61) models of age or clocks. We also characterized individual CpG sites within each species that demonstrated clear differences in methylation levels between age classes and sex, which can be used to develop a suite of accessible diagnostic markers. This tool has the potential to contribute to wildlife monitoring by providing easily obtainable representations of age structure in managed populations.
表观遗传时钟的开发或基于 DNA 甲基化的年龄推断是一种新兴的工具,可用于自由活动种群的年龄测定。在这项研究中,我们为白尾鹿、黑熊和山羊这三种大型哺乳动物开发了表观遗传时钟。我们对所有三个物种(黑熊 n = 49;白尾鹿 n = 47;山羊 n = 45)组织样本中超过 30,000 个胞嘧啶-鸟嘌呤位点(CpGs)的不同 DNA 甲基化模式进行了量化。我们使用惩罚回归模型(弹性网)建立了年龄或时钟的解释性(黑熊 r = .95;白尾鹿 r = .99;山羊 r = .97)和稳健性(黑熊中位绝对误差或 MAE = 1.33;白尾鹿 MAE = 0.29;山羊 MAE = 0.61)模型。我们还表征了每个物种中的单个 CpG 位点,这些位点在不同年龄段和性别之间的甲基化水平存在明显差异,可用于开发一套可访问的诊断标记。该工具可提供易于获取的受管理种群年龄结构表征,从而有可能为野生动物监测做出贡献。
{"title":"Epigenetic clocks, sex markers and age-class diagnostics in three harvested large mammals","authors":"Natalie Czajka, Joseph M. Northrup, Meaghan J. Jones, Aaron B. A. Shafer","doi":"10.1111/1755-0998.13956","DOIUrl":"10.1111/1755-0998.13956","url":null,"abstract":"<p>The development of epigenetic clocks, or the DNA methylation-based inference of age, is an emerging tool for ageing in free ranging populations. In this study, we developed epigenetic clocks for three species of large mammals that are the focus of extensive management throughout their range in North America: white-tailed deer, black bear and mountain goat. We quantified differential DNA methylation patterns at over 30,000 cytosine-guanine sites (CpGs) from tissue samples of all three species (black bear <i>n</i> = 49; white-tailed deer <i>n</i> = 47; mountain goat <i>n</i> = 45). We used a penalized regression model (elastic net) to build explanatory (black bear <i>r</i> = .95; white-tailed deer <i>r</i> = .99; mountain goat <i>r</i> = .97) and robust (black bear Median Absolute Error or MAE = 1.33; white-tailed deer MAE = 0.29; mountain goat MAE = 0.61) models of age or clocks. We also characterized individual CpG sites within each species that demonstrated clear differences in methylation levels between age classes and sex, which can be used to develop a suite of accessible diagnostic markers. This tool has the potential to contribute to wildlife monitoring by providing easily obtainable representations of age structure in managed populations.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":null,"pages":null},"PeriodicalIF":7.7,"publicationDate":"2024-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.13956","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140326110","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}
Recent declines in insect abundances, especially populations of wild pollinators, pose a threat to many natural and agricultural ecosystems. Traditional species monitoring relies on morphological character identification and is inadequate for efficient and standardized surveys. DNA barcoding has become a standard approach for molecular identification of organisms, aiming to overcome the shortcomings of traditional biodiversity monitoring. However, its efficacy depends on the completeness of reference databases. Large DNA barcoding efforts are (almost entirely) lacking in many European countries and such patchy data limit Europe-wide analyses of precisely how to apply DNA barcoding in wild bee identification. Here, we advance towards an effective molecular identification of European wild bees. We conducted a high-effort survey of wild bees at the junction of central and southern Europe and DNA barcoded all collected morphospecies. For global analyses, we complemented our DNA barcode dataset with all relevant European species and conducted global analyses of species delimitation, general and genus-specific barcoding gaps and examined the error rate in DNA data repositories. We found that (i) a sixth of all specimens from Slovenia could not be reliably identified, (ii) species delimitation methods show numerous systematic discrepancies, (iii) there is no general barcoding gap across all bees and (iv) the barcoding gap is genus specific, but only after curating for errors in DNA data repositories. Intense sampling and barcoding efforts in underrepresented regions and strict curation of DNA barcode repositories are needed to enhance the use of DNA barcoding for the identification of wild bees.
最近昆虫数量的减少,尤其是野生传粉昆虫种群的减少,对许多自然和农业生态系统构成了威胁。传统的物种监测依赖于形态特征鉴定,不足以进行高效和标准化的调查。DNA 条形码已成为生物分子鉴定的标准方法,旨在克服传统生物多样性监测的不足。然而,其有效性取决于参考数据库的完整性。许多欧洲国家(几乎完全)缺乏大规模的DNA条形码工作,这种零散的数据限制了对如何在野生蜜蜂鉴定中精确应用DNA条形码的全欧洲范围的分析。在此,我们将推进对欧洲野生蜜蜂的有效分子鉴定。我们在中欧和南欧交界处对野生蜜蜂进行了一次艰苦的调查,并对收集到的所有形态物种进行了DNA条形码编码。为了进行全球分析,我们用所有相关的欧洲物种对 DNA 条形码数据集进行了补充,并对物种划界、一般和属特异性条形码差距进行了全球分析,还检查了 DNA 数据库中的错误率。我们发现:(i) 斯洛文尼亚有六分之一的标本无法得到可靠的鉴定;(ii) 物种划分方法存在大量系统性差异;(iii) 所有蜜蜂不存在普遍的条形码缺口;(iv) 条形码缺口是针对具体属的,但仅限于在对 DNA 数据库中的错误进行整理之后。需要在代表性不足的地区加强采样和条形码工作,并严格管理 DNA 条形码库,以加强 DNA 条形码在野生蜜蜂鉴定中的应用。
{"title":"DNA barcoding insufficiently identifies European wild bees (Hymenoptera, Anthophila) due to undefined species diversity, genus-specific barcoding gaps and database errors","authors":"Šet Janko, Šturm Rok, Koderman Blaž, Bevk Danilo, Gogala Andrej, Kutnjak Denis, Čandek Klemen, Gregorič Matjaž","doi":"10.1111/1755-0998.13953","DOIUrl":"10.1111/1755-0998.13953","url":null,"abstract":"<p>Recent declines in insect abundances, especially populations of wild pollinators, pose a threat to many natural and agricultural ecosystems. Traditional species monitoring relies on morphological character identification and is inadequate for efficient and standardized surveys. DNA barcoding has become a standard approach for molecular identification of organisms, aiming to overcome the shortcomings of traditional biodiversity monitoring. However, its efficacy depends on the completeness of reference databases. Large DNA barcoding efforts are (almost entirely) lacking in many European countries and such patchy data limit Europe-wide analyses of precisely how to apply DNA barcoding in wild bee identification. Here, we advance towards an effective molecular identification of European wild bees. We conducted a high-effort survey of wild bees at the junction of central and southern Europe and DNA barcoded all collected morphospecies. For global analyses, we complemented our DNA barcode dataset with all relevant European species and conducted global analyses of species delimitation, general and genus-specific barcoding gaps and examined the error rate in DNA data repositories. We found that (i) a sixth of all specimens from Slovenia could not be reliably identified, (ii) species delimitation methods show numerous systematic discrepancies, (iii) there is no general barcoding gap across all bees and (iv) the barcoding gap is genus specific, but only after curating for errors in DNA data repositories. Intense sampling and barcoding efforts in underrepresented regions and strict curation of DNA barcode repositories are needed to enhance the use of DNA barcoding for the identification of wild bees.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":null,"pages":null},"PeriodicalIF":7.7,"publicationDate":"2024-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.13953","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140206014","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}
Xinyi Zhang, Haimei Chen, Yang Ni, Bin Wu, Jingling Li, Artur Burzyński, Chang Liu
Tools for visualizing genomes are essential for investigating genomic features and their interactions. Currently, tools designed originally for animal mitogenomes and plant plastomes are used to visualize the mitogens of plants but cannot accurately display features specific to plant mitogenomes, such as nonlinear exon arrangement for genes, the prevalence of functional noncoding features and complex chromosomal architecture. To address these problems, a software package, plant mitochondrial genome map (PMGmap), was developed using the Python programming language. PMGmap can draw genes at exon levels; draw cis- and trans-splicing gene maps, noncoding features and repetitive sequences; and scale genic regions by using the scaling of the genic regions on the mitogenome (SAGM) algorithm. It can also draw multiple chromosomes simultaneously. Compared with other state-of-the-art tools, PMGmap showed better performance in visualizing 405 plant mitogenomes, showing potential as an invaluable tool for plant mitogenome research. The web and container versions and the source code of PMGmap can be accessed through the following link: http://www.1kmpg.cn/pmgmap.
{"title":"Plant mitochondrial genome map (PMGmap): A software tool for the comprehensive visualization of coding, noncoding and genome features of plant mitochondrial genomes","authors":"Xinyi Zhang, Haimei Chen, Yang Ni, Bin Wu, Jingling Li, Artur Burzyński, Chang Liu","doi":"10.1111/1755-0998.13952","DOIUrl":"10.1111/1755-0998.13952","url":null,"abstract":"<p>Tools for visualizing genomes are essential for investigating genomic features and their interactions. Currently, tools designed originally for animal mitogenomes and plant plastomes are used to visualize the mitogens of plants but cannot accurately display features specific to plant mitogenomes, such as nonlinear exon arrangement for genes, the prevalence of functional noncoding features and complex chromosomal architecture. To address these problems, a software package, plant mitochondrial genome map (PMGmap), was developed using the Python programming language. PMGmap can draw genes at exon levels; draw cis- and trans-splicing gene maps, noncoding features and repetitive sequences; and scale genic regions by using the scaling of the genic regions on the mitogenome (SAGM) algorithm. It can also draw multiple chromosomes simultaneously. Compared with other state-of-the-art tools, PMGmap showed better performance in visualizing 405 plant mitogenomes, showing potential as an invaluable tool for plant mitogenome research. The web and container versions and the source code of PMGmap can be accessed through the following link: http://www.1kmpg.cn/pmgmap.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":null,"pages":null},"PeriodicalIF":7.7,"publicationDate":"2024-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140206015","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}
Dorothea Heimeier, Ellen C. Garland, Franca Eichenberger, Claire Garrigue, Adriana Vella, C. Scott Baker, Emma L. Carroll
The major histocompatibility complex (MHC) is a highly polymorphic gene family that is crucial in immunity, and its diversity can be effectively used as a fitness marker for populations. Despite this, MHC remains poorly characterised in non-model species (e.g., cetaceans: whales, dolphins and porpoises) as high gene copy number variation, especially in the fast-evolving class I region, makes analyses of genomic sequences difficult. To date, only small sections of class I and IIa genes have been used to assess functional diversity in cetacean populations. Here, we undertook a systematic characterisation of the MHC class I and IIa regions in available cetacean genomes. We extracted full-length gene sequences to design pan-cetacean primers that amplified the complete exon 2 from MHC class I and IIa genes in one combined sequencing panel. We validated this panel in 19 cetacean species and described 354 alleles for both classes. Furthermore, we identified likely assembly artefacts for many MHC class I assemblies based on the presence of class I genes in the amplicon data compared to missing genes from genomes. Finally, we investigated MHC diversity using the panel in 25 humpback and 30 southern right whales, including four paternity trios for humpback whales. This revealed copy-number variable class I haplotypes in humpback whales, which is likely a common phenomenon across cetaceans. These MHC alleles will form the basis for a cetacean branch of the Immuno-Polymorphism Database (IPD-MHC), a curated resource intended to aid in the systematic compilation of MHC alleles across several species, to support conservation initiatives.
主要组织相容性复合体(MHC)是一个高度多态的基因家族,在免疫中起着至关重要的作用,其多样性可有效地用作种群的适应性标记。尽管如此,主要组织相容性复合体在非模式物种(如鲸类:鲸鱼、海豚和鼠海豚)中的特性仍然很差,因为高基因拷贝数变异,尤其是在快速进化的 I 类区域,使得基因组序列分析变得困难。迄今为止,只有一小部分 I 类和 IIa 类基因被用于评估鲸目动物种群的功能多样性。在这里,我们对现有鲸目动物基因组中的 MHC I 类和 IIa 区域进行了系统的特征描述。我们提取了全长基因序列来设计泛鲸类引物,在一个组合测序面板中扩增 MHC I 类和 IIa 基因的完整外显子 2。我们在 19 个鲸目动物物种中验证了该测序板,并描述了这两类基因的 354 个等位基因。此外,根据扩增子数据中 I 类基因的存在与基因组中缺失基因的比较,我们确定了许多 MHC I 类基因组合可能存在的组合假象。最后,我们在 25 头座头鲸和 30 头南露脊鲸中使用面板研究了 MHC 多样性,其中包括座头鲸的四个亲子鉴定三组。这揭示了座头鲸中拷贝数可变的 I 类单倍型,这可能是鲸类的一个普遍现象。这些 MHC 等位基因将成为免疫多态性数据库(IPD-MHC)鲸类分支的基础,IPD-MHC 是一个经过整理的资源,旨在帮助系统地汇编多个物种的 MHC 等位基因,以支持保护计划。
{"title":"A pan-cetacean MHC amplicon sequencing panel developed and evaluated in combination with genome assemblies","authors":"Dorothea Heimeier, Ellen C. Garland, Franca Eichenberger, Claire Garrigue, Adriana Vella, C. Scott Baker, Emma L. Carroll","doi":"10.1111/1755-0998.13955","DOIUrl":"10.1111/1755-0998.13955","url":null,"abstract":"<p>The major histocompatibility complex (MHC) is a highly polymorphic gene family that is crucial in immunity, and its diversity can be effectively used as a fitness marker for populations. Despite this, MHC remains poorly characterised in non-model species (e.g., cetaceans: whales, dolphins and porpoises) as high gene copy number variation, especially in the fast-evolving class I region, makes analyses of genomic sequences difficult. To date, only small sections of class I and IIa genes have been used to assess functional diversity in cetacean populations. Here, we undertook a systematic characterisation of the MHC class I and IIa regions in available cetacean genomes. We extracted full-length gene sequences to design pan-cetacean primers that amplified the complete exon 2 from MHC class I and IIa genes in one combined sequencing panel. We validated this panel in 19 cetacean species and described 354 alleles for both classes. Furthermore, we identified likely assembly artefacts for many MHC class I assemblies based on the presence of class I genes in the amplicon data compared to missing genes from genomes. Finally, we investigated MHC diversity using the panel in 25 humpback and 30 southern right whales, including four paternity trios for humpback whales. This revealed copy-number variable class I haplotypes in humpback whales, which is likely a common phenomenon across cetaceans. These MHC alleles will form the basis for a cetacean branch of the Immuno-Polymorphism Database (IPD-MHC), a curated resource intended to aid in the systematic compilation of MHC alleles across several species, to support conservation initiatives.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":null,"pages":null},"PeriodicalIF":7.7,"publicationDate":"2024-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.13955","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140192927","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}
Patrik Macko, Tomáš Derka, Zuzana Čiamporová-Zaťovičová, Michal Grabowski, Fedor Čiampor Jr
Mayflies (Ephemeroptera) are among the crucial water and habitat quality bioindicators. However, despite their intensive long-term use in various studies, more reliable mayfly DNA barcode data have been produced in a negligible number of countries, and only ~40% of European species had been barcoded with less than 50% of families covered. Despite being carried out in a small area, our study presents the second-most species-rich DNA reference library of mayflies from Europe and the first comprehensive view from an important biodiversity hotspot such as the Western Carpathians. Within 1153 sequences, 76 morphologically determined species were recorded and added to the Barcode of Life Data System (BOLD) database. All obtained sequences were assigned to 97 BINs, 11 of which were unique and three represented species never barcoded before. Sequences of 16 species with high intraspecific variability were divided into 40 BINs, confirming the presence of cryptic lineages. Due to the low interspecific divergence and the non-existing barcoding gap, sequences of six species were assigned to three shared BINs. Delimitation analyses resulted in 79 and 107 putative species respectively. Bayesian and maximum-likelihood phylogenies confirmed the monophyly of almost all species and complexes of cryptic taxa and proved that DNA barcoding distinguishes almost all studied mayfly species. We have shown that it is still sufficient to thoroughly investigate the fauna of a small but geographically important area to enrich global databases greatly. In particular, the insights gained here transcend the local context and may have broader implications for advancing barcoding efforts.
蜉蝣(蜉蝣目)是重要的水质和栖息地质量生物指标之一。然而,尽管在各种研究中长期大量使用蜉蝣,但只有极少数国家产生了更可靠的蜉蝣 DNA 条形码数据,只有约 40% 的欧洲物种被进行了条形码编码,覆盖的科还不到 50%。尽管研究是在一个小区域内进行的,但我们的研究提供了欧洲物种第二丰富的蜉蝣 DNA 参考文献库,也是首次对西喀尔巴阡山脉这样一个重要的生物多样性热点地区进行的全面研究。在 1153 条序列中,记录了 76 个形态学上确定的物种,并将其添加到生命条码数据系统(BOLD)数据库中。所有获得的序列被分配到 97 个 BIN 中,其中 11 个是唯一的,3 个代表以前从未进行过条形码编码的物种。种内变异性较高的 16 个物种的序列被划分到 40 个 BIN 中,证实了隐性种系的存在。由于种间差异较小,且不存在条码空白,6 个物种的序列被分配到 3 个共享的 BIN 中。划界分析分别得出了 79 和 107 个推定物种。贝叶斯系统发育和最大似然系统发育证实了几乎所有物种和隐生类群的单系性,并证明了 DNA 条形码几乎可以区分所有研究过的蜉蝣物种。我们的研究结果表明,只需彻底调查一个小规模但地理位置重要的地区的动物群,就能极大地丰富全球数据库。特别是,我们在此获得的见解超越了当地范围,可能对推进条形码工作具有更广泛的意义。
{"title":"Detailed DNA barcoding of mayflies in a small European country proved how far we are from having comprehensive barcode reference libraries","authors":"Patrik Macko, Tomáš Derka, Zuzana Čiamporová-Zaťovičová, Michal Grabowski, Fedor Čiampor Jr","doi":"10.1111/1755-0998.13954","DOIUrl":"10.1111/1755-0998.13954","url":null,"abstract":"<p>Mayflies (Ephemeroptera) are among the crucial water and habitat quality bioindicators. However, despite their intensive long-term use in various studies, more reliable mayfly DNA barcode data have been produced in a negligible number of countries, and only ~40% of European species had been barcoded with less than 50% of families covered. Despite being carried out in a small area, our study presents the second-most species-rich DNA reference library of mayflies from Europe and the first comprehensive view from an important biodiversity hotspot such as the Western Carpathians. Within 1153 sequences, 76 morphologically determined species were recorded and added to the Barcode of Life Data System (BOLD) database. All obtained sequences were assigned to 97 BINs, 11 of which were unique and three represented species never barcoded before. Sequences of 16 species with high intraspecific variability were divided into 40 BINs, confirming the presence of cryptic lineages. Due to the low interspecific divergence and the non-existing barcoding gap, sequences of six species were assigned to three shared BINs. Delimitation analyses resulted in 79 and 107 putative species respectively. Bayesian and maximum-likelihood phylogenies confirmed the monophyly of almost all species and complexes of cryptic taxa and proved that DNA barcoding distinguishes almost all studied mayfly species. We have shown that it is still sufficient to thoroughly investigate the fauna of a small but geographically important area to enrich global databases greatly. In particular, the insights gained here transcend the local context and may have broader implications for advancing barcoding efforts.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":null,"pages":null},"PeriodicalIF":7.7,"publicationDate":"2024-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140192870","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}
Rita Mwima, Tin-Yu J. Hui, Jonathan K. Kayondo, Austin Burt
Diapause, a form of dormancy to delay or halt the reproductive development during unfavourable seasons, has evolved in many insect species. One example is aestivation, an adult-stage diapause enhancing malaria vectors' survival during the dry season (DS) and their re-establishment in the next rainy season (RS). This work develops a novel genetic approach to estimate the number or proportion of individuals undergoing diapause, as well as the breeding sizes of the two seasons, using signals from temporal allele frequency dynamics. Our modelling shows the magnitude of drift is dampened at early RS when previously aestivating individuals reappear. Aestivation severely biases the temporal effective population size (