Samuel A. Speak, Thomas Birley, Chiara Bortoluzzi, Matthew D. Clark, Lawrence Percival-Alwyn, Hernán E. Morales, Cock van Oosterhout
Zoo populations of threatened species are a valuable resource for the restoration of wild populations. However, their small effective population size poses a risk to long-term viability, especially in species with high genetic load. Recent bioinformatic developments can identify harmful genetic variants in genome data. Here, we advance this approach, analysing the genetic load in the threatened pink pigeon (Nesoenas mayeri). We lifted the mutation-impact scores that had been calculated for the chicken (Gallus gallus) to estimate the genetic load in six pink pigeons. Additionally, we perform in silico crossings to predict the genetic load and realized load of potential offspring. We thus identify the optimal mate pairs that are theoretically expected to produce offspring with the least inbreeding depression. We use computer simulations to show how genomics-informed conservation can reduce the genetic load whilst reducing the loss of genome-wide diversity. Genomics-informed management is likely to become instrumental in maintaining the long-term viability of zoo populations.
{"title":"Genomics-informed captive breeding can reduce inbreeding depression and the genetic load in zoo populations","authors":"Samuel A. Speak, Thomas Birley, Chiara Bortoluzzi, Matthew D. Clark, Lawrence Percival-Alwyn, Hernán E. Morales, Cock van Oosterhout","doi":"10.1111/1755-0998.13967","DOIUrl":"10.1111/1755-0998.13967","url":null,"abstract":"<p>Zoo populations of threatened species are a valuable resource for the restoration of wild populations. However, their small effective population size poses a risk to long-term viability, especially in species with high genetic load. Recent bioinformatic developments can identify harmful genetic variants in genome data. Here, we advance this approach, analysing the genetic load in the threatened pink pigeon (<i>Nesoenas mayeri</i>). We lifted the mutation-impact scores that had been calculated for the chicken (<i>Gallus gallus</i>) to estimate the genetic load in six pink pigeons. Additionally, we perform in silico crossings to predict the genetic load and realized load of potential offspring. We thus identify the optimal mate pairs that are theoretically expected to produce offspring with the least inbreeding depression. We use computer simulations to show how genomics-informed conservation can reduce the genetic load whilst reducing the loss of genome-wide diversity. Genomics-informed management is likely to become instrumental in maintaining the long-term viability of zoo populations.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":null,"pages":null},"PeriodicalIF":5.5,"publicationDate":"2024-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.13967","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140896312","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}
Parasitic plants have a heterotrophic lifestyle, in which they withdraw all or part of their nutrients from their host through the haustorium. Despite the release of many draft genomes of parasitic plants, the genome evolution related to the parasitism feature of facultative parasites remains largely unknown. In this study, we present a high-quality chromosomal-level genome assembly for the facultative parasite Pedicularis kansuensis (Orobanchaceae), which invades both legume and grass host species in degraded grasslands on the Qinghai-Tibet Plateau. This species has the largest genome size compared with other parasitic species, and expansions of long terminal repeat retrotransposons accounting for 62.37% of the assembly greatly contributed to the genome size expansion of this species. A total of 42,782 genes were annotated, and the patterns of gene loss in P. kansuensis differed from other parasitic species. We also found many mobile mRNAs between P. kansuensis and one of its host species, but these mobile mRNAs could not compensate for the functional losses of missing genes in P. kansuensis. In addition, we identified nine horizontal gene transfer (HGT) events from rosids and monocots, as well as one single-gene duplication events from HGT genes, which differ distinctly from that of other parasitic species. Furthermore, we found evidence for HGT through transferring genomic fragments from phylogenetically remote host species. Taken together, these findings provide genomic insights into the evolution of facultative parasites and broaden our understanding of the diversified genome evolution in parasitic plants and the molecular mechanisms of plant parasitism.
寄生植物具有异养的生活方式,它们通过寄生体从宿主那里获取全部或部分养分。尽管已经发布了许多寄生植物的基因组草案,但与面寄生植物的寄生特征有关的基因组进化在很大程度上仍然是未知的。在本研究中,我们展示了青藏高原退化草地上同时入侵豆科和禾本科寄主物种的面寄生植物Pedicularis kansuensis(大戟科)的高质量染色体级基因组组装。与其他寄生物种相比,该物种的基因组规模最大,占基因组总数62.37%的长末端重复反转座子的扩增极大地促进了该物种基因组规模的扩大。我们共注释了 42 782 个基因,发现 P. kansuensis 的基因丢失模式与其他寄生物种不同。我们还发现了 P. kansuensis 与其宿主物种之一之间的许多移动 mRNA,但这些移动 mRNA 无法弥补 P. kansuensis 中缺失基因的功能损失。此外,我们还发现了 9 个来自rosids 和单子叶植物的水平基因转移(HGT)事件,以及 1 个来自 HGT 基因的单基因重复事件,它们与其他寄生物种的水平基因转移事件截然不同。此外,我们还发现了从系统发育上较远的宿主物种转移基因组片段进行 HGT 的证据。总之,这些发现提供了对兼性寄生虫进化的基因组学见解,拓宽了我们对寄生植物多样化基因组进化和植物寄生的分子机制的认识。
{"title":"Chromosome-level genome assembly of Pedicularis kansuensis illuminates genome evolution of facultative parasitic plant","authors":"Longfa Fang, Mingyu Li, Jia Zhang, Chenglin Jia, Yuqing Qiang, Xiaojuan He, Tao Liu, Qiang Zhou, Dong Luo, Yuling Han, Zhen Li, Wenxian Liu, Yongzhi Yang, Jianquan Liu, Zhipeng Liu","doi":"10.1111/1755-0998.13966","DOIUrl":"10.1111/1755-0998.13966","url":null,"abstract":"<p>Parasitic plants have a heterotrophic lifestyle, in which they withdraw all or part of their nutrients from their host through the haustorium. Despite the release of many draft genomes of parasitic plants, the genome evolution related to the parasitism feature of facultative parasites remains largely unknown. In this study, we present a high-quality chromosomal-level genome assembly for the facultative parasite <i>Pedicularis kansuensis</i> (Orobanchaceae), which invades both legume and grass host species in degraded grasslands on the Qinghai-Tibet Plateau. This species has the largest genome size compared with other parasitic species, and expansions of long terminal repeat retrotransposons accounting for 62.37% of the assembly greatly contributed to the genome size expansion of this species. A total of 42,782 genes were annotated, and the patterns of gene loss in <i>P. kansuensis</i> differed from other parasitic species. We also found many mobile mRNAs between <i>P. kansuensis</i> and one of its host species, but these mobile mRNAs could not compensate for the functional losses of missing genes in <i>P. kansuensis</i>. In addition, we identified nine horizontal gene transfer (HGT) events from rosids and monocots, as well as one single-gene duplication events from HGT genes, which differ distinctly from that of other parasitic species. Furthermore, we found evidence for HGT through transferring genomic fragments from phylogenetically remote host species. Taken together, these findings provide genomic insights into the evolution of facultative parasites and broaden our understanding of the diversified genome evolution in parasitic plants and the molecular mechanisms of plant parasitism.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":null,"pages":null},"PeriodicalIF":7.7,"publicationDate":"2024-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140833116","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}
Partnerships between Tribes and researchers in wildlife monitoring and application of Traditional Ecological Knowledge (TEK) have taken a variety of forms, and some scholars have noted a need for culturally sensitive approaches. Guided by Indigenous Research Methodologies, this research is coupled with Yurok TEK, or hlkelonah 'ue‐megetohl (‘to take care of the earth’), enabling an applied, culturally sensitive approach in partnership with the Yurok Tribe. We present results from a molecular scatology study of wildlife within the ancestral territory of the Yurok Tribe. Scats were collected opportunistically on road transects. All samples (N = 132) were analysed via DNA barcoding and results matched to documented 'Oohl 'we‐toh (Yurok language) names to determine the depositor species (N = 8). Though there were four focal mesocarnivore species in our study, only bobcat (Chmuuek; Lynx rufus) and gray fox (Wergers; Urocyon cinereoargenteus) were detected as depositor species. Post hoc analyses were conducted to explore distribution, habitat use and selection in a use‐availability context, and food habits of these two species. We found almost complete separation of bobcat and gray fox use of transects, as well as indication of partitioning of vegetation cover types and food. We demonstrate an integrated framework of Western and Indigenous sciences that allows the Indigenous researcher to transcend structured academic disciplinary boundaries. Our approach can be modified for partnerships between Tribes, agencies, academics and students for wildlife monitoring in broader geographic regions in various research applications.
{"title":"Integration of Indigenous Research Methodologies, Traditional Ecological Knowledge and molecular scatology in an assessment of mesocarnivore presence, diet and habitat use on Yurok Ancestral Lands","authors":"Seafha C. Ramos, Melanie Culver","doi":"10.1111/1755-0998.13963","DOIUrl":"https://doi.org/10.1111/1755-0998.13963","url":null,"abstract":"Partnerships between Tribes and researchers in wildlife monitoring and application of Traditional Ecological Knowledge (TEK) have taken a variety of forms, and some scholars have noted a need for culturally sensitive approaches. Guided by Indigenous Research Methodologies, this research is coupled with Yurok TEK, or <jats:italic>hlkelonah 'ue‐megetohl</jats:italic> (‘to take care of the earth’), enabling an applied, culturally sensitive approach in partnership with the Yurok Tribe. We present results from a molecular scatology study of wildlife within the ancestral territory of the Yurok Tribe. Scats were collected opportunistically on road transects. All samples (<jats:italic>N</jats:italic> = 132) were analysed via DNA barcoding and results matched to documented 'Oohl 'we‐toh (Yurok language) names to determine the depositor species (<jats:italic>N</jats:italic> = 8). Though there were four focal mesocarnivore species in our study, only bobcat (<jats:italic>Chmuuek</jats:italic>; <jats:italic>Lynx rufus</jats:italic>) and gray fox (<jats:italic>Wergers</jats:italic>; <jats:italic>Urocyon cinereoargenteus</jats:italic>) were detected as depositor species. Post hoc analyses were conducted to explore distribution, habitat use and selection in a use‐availability context, and food habits of these two species. We found almost complete separation of bobcat and gray fox use of transects, as well as indication of partitioning of vegetation cover types and food. We demonstrate an integrated framework of Western and Indigenous sciences that allows the Indigenous researcher to transcend structured academic disciplinary boundaries. Our approach can be modified for partnerships between Tribes, agencies, academics and students for wildlife monitoring in broader geographic regions in various research applications.","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":null,"pages":null},"PeriodicalIF":7.7,"publicationDate":"2024-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140833115","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}
Şevval Aktürk, Igor Mapelli, Merve N. Güler, Kanat Gürün, Büşra Katırcıoğlu, Kıvılcım Başak Vural, Ekin Sağlıcan, Mehmet Çetin, Reyhan Yaka, Elif Sürer, Gözde Atağ, Sevim Seda Çokoğlu, Arda Sevkar, N. Ezgi Altınışık, Dilek Koptekin, Mehmet Somel
There is growing interest in uncovering genetic kinship patterns in past societies using low-coverage palaeogenomes. Here, we benchmark four tools for kinship estimation with such data: lcMLkin, NgsRelate, KIN, and READ, which differ in their input, IBD estimation methods, and statistical approaches. We used pedigree and ancient genome sequence simulations to evaluate these tools when only a limited number (1 to 50 K, with minor allele frequency ≥0.01) of shared SNPs are available. The performance of all four tools was comparable using ≥20 K SNPs. We found that first-degree related pairs can be accurately classified even with 1 K SNPs, with 85% F1 scores using READ and 96% using NgsRelate or lcMLkin. Distinguishing third-degree relatives from unrelated pairs or second-degree relatives was also possible with high accuracy (F1 > 90%) with 5 K SNPs using NgsRelate and lcMLkin, while READ and KIN showed lower success (69 and 79% respectively). Meanwhile, noise in population allele frequencies and inbreeding (first-cousin mating) led to deviations in kinship coefficients, with different sensitivities across tools. We conclude that using multiple tools in parallel might be an effective approach to achieve robust estimates on ultra-low-coverage genomes.
人们对利用低覆盖率古基因组揭示过去社会的遗传亲缘关系模式越来越感兴趣。在此,我们对使用此类数据进行亲缘关系估计的四种工具进行了基准测试:lcMLkin、NgsRelate、KIN 和 READ,它们在输入、IBD 估计方法和统计方法上各不相同。我们使用血统和古基因组序列模拟来评估这些工具,当只有有限数量(1 到 50 K,小等位基因频率≥0.01)的共享 SNP 可用时。使用≥20 K SNPs时,所有四种工具的性能相当。我们发现,即使只有 1 K 个 SNPs,也能对一级亲属配对进行准确分类,使用 READ 的 F1 得分率为 85%,使用 NgsRelate 或 lcMLkin 的 F1 得分率为 96%。利用 5 K SNPs,使用 NgsRelate 和 lcMLkin 也能以较高的准确率(F1 > 90%)将三代亲属与无亲属关系的配对或二代亲属区分开来,而 READ 和 KIN 的成功率较低(分别为 69% 和 79%)。同时,种群等位基因频率和近亲繁殖(嫡亲交配)的噪声导致亲缘关系系数出现偏差,不同工具的敏感度也不同。我们的结论是,并行使用多种工具可能是在超低覆盖率基因组上实现稳健估计的有效方法。
{"title":"Benchmarking kinship estimation tools for ancient genomes using pedigree simulations","authors":"Şevval Aktürk, Igor Mapelli, Merve N. Güler, Kanat Gürün, Büşra Katırcıoğlu, Kıvılcım Başak Vural, Ekin Sağlıcan, Mehmet Çetin, Reyhan Yaka, Elif Sürer, Gözde Atağ, Sevim Seda Çokoğlu, Arda Sevkar, N. Ezgi Altınışık, Dilek Koptekin, Mehmet Somel","doi":"10.1111/1755-0998.13960","DOIUrl":"10.1111/1755-0998.13960","url":null,"abstract":"<p>There is growing interest in uncovering genetic kinship patterns in past societies using low-coverage palaeogenomes. Here, we benchmark four tools for kinship estimation with such data: lcMLkin, NgsRelate, KIN, and READ, which differ in their input, IBD estimation methods, and statistical approaches. We used pedigree and ancient genome sequence simulations to evaluate these tools when only a limited number (1 to 50 K, with minor allele frequency ≥0.01) of shared SNPs are available. The performance of all four tools was comparable using ≥20 K SNPs. We found that first-degree related pairs can be accurately classified even with 1 K SNPs, with 85% <i>F</i><sub>1</sub> scores using READ and 96% using NgsRelate or lcMLkin. Distinguishing third-degree relatives from unrelated pairs or second-degree relatives was also possible with high accuracy (<i>F</i><sub>1</sub> > 90%) with 5 K SNPs using NgsRelate and lcMLkin, while READ and KIN showed lower success (69 and 79% respectively). Meanwhile, noise in population allele frequencies and inbreeding (first-cousin mating) led to deviations in kinship coefficients, with different sensitivities across tools. We conclude that using multiple tools in parallel might be an effective approach to achieve robust estimates on ultra-low-coverage genomes.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":null,"pages":null},"PeriodicalIF":7.7,"publicationDate":"2024-04-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.13960","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140805597","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}
Phylogenetic studies now routinely require manipulating and summarizing thousands of data files. For most of these tasks, currently available software requires considerable computing resources and substantial knowledge of command-line applications. We develop an ultrafast and memory-efficient software, SEGUL, that performs common phylogenomic dataset manipulations and calculates statistics summarizing essential data features. Our software is available as standalone command-line interface (CLI) and graphical user interface (GUI) applications, and as a library for Rust, R and Python, with possible support of other languages. The CLI and library versions run native on Windows, Linux and macOS, including Apple ARM Macs. The GUI version extends support to include mobile iOS, iPadOS and Android operating systems. SEGUL leverages the high performance of the Rust programming language to offer fast execution times and low memory footprints regardless of dataset size and platform choice. The inclusion of a GUI minimizes bioinformatics barriers to phylogenomics while SEGUL's efficiency reduces economic barriers by allowing analysis on inexpensive hardware. Our support for mobile operating systems further enables teaching phylogenomics where access to computing power is limited.
{"title":"SEGUL: Ultrafast, memory-efficient and mobile-friendly software for manipulating and summarizing phylogenomic datasets","authors":"Heru Handika, Jacob A. Esselstyn","doi":"10.1111/1755-0998.13964","DOIUrl":"10.1111/1755-0998.13964","url":null,"abstract":"<p>Phylogenetic studies now routinely require manipulating and summarizing thousands of data files. For most of these tasks, currently available software requires considerable computing resources and substantial knowledge of command-line applications. We develop an ultrafast and memory-efficient software, SEGUL, that performs common phylogenomic dataset manipulations and calculates statistics summarizing essential data features. Our software is available as standalone command-line interface (CLI) and graphical user interface (GUI) applications, and as a library for Rust, R and Python, with possible support of other languages. The CLI and library versions run native on Windows, Linux and macOS, including Apple ARM Macs. The GUI version extends support to include mobile iOS, iPadOS and Android operating systems. SEGUL leverages the high performance of the Rust programming language to offer fast execution times and low memory footprints regardless of dataset size and platform choice. The inclusion of a GUI minimizes bioinformatics barriers to phylogenomics while SEGUL's efficiency reduces economic barriers by allowing analysis on inexpensive hardware. Our support for mobile operating systems further enables teaching phylogenomics where access to computing power is limited.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":null,"pages":null},"PeriodicalIF":5.5,"publicationDate":"2024-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140652800","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}
Preparation of DNA polymorphism datasets for analysis is an important step in evolutionary genetic and molecular ecology studies. Ever-growing dataset sizes make this step time consuming, but few convenient software tools are available to facilitate processing of large-scale datasets including thousands of sequence alignments. Here I report “processor of sequences v4” (proSeq4)—a user-friendly multiplatform software for preparation and evolutionary genetic analyses of genome- or transcriptome-scale sequence polymorphism datasets. The program has an easy-to-use graphic user interface and is designed to process and analyse many thousands of datasets. It supports over two dozen file formats, includes a flexible sequence editor and various tools for data visualization, quality control and most commonly used evolutionary genetic analyses, such as NJ-phylogeny reconstruction, DNA polymorphism analyses and coalescent simulations. Command line tools (e.g. vcf2fasta) are also provided for easier integration into bioinformatic pipelines. Apart of molecular ecology and evolution research, proSeq4 may be useful for teaching, e.g. for visual illustration of different shapes of phylogenies generated with coalescent simulations in different scenarios. ProSeq4 source code and binaries for Windows, MacOS and Ubuntu are available from https://sourceforge.net/projects/proseq/.
{"title":"ProSeq4: A user-friendly multiplatform program for preparation and analysis of large-scale DNA polymorphism datasets","authors":"Dmitry A. Filatov","doi":"10.1111/1755-0998.13962","DOIUrl":"10.1111/1755-0998.13962","url":null,"abstract":"<p>Preparation of DNA polymorphism datasets for analysis is an important step in evolutionary genetic and molecular ecology studies. Ever-growing dataset sizes make this step time consuming, but few convenient software tools are available to facilitate processing of large-scale datasets including thousands of sequence alignments. Here I report “processor of sequences v4” (proSeq4)—a user-friendly multiplatform software for preparation and evolutionary genetic analyses of genome- or transcriptome-scale sequence polymorphism datasets. The program has an easy-to-use graphic user interface and is designed to process and analyse many thousands of datasets. It supports over two dozen file formats, includes a flexible sequence editor and various tools for data visualization, quality control and most commonly used evolutionary genetic analyses, such as NJ-phylogeny reconstruction, DNA polymorphism analyses and coalescent simulations. Command line tools (e.g. vcf2fasta) are also provided for easier integration into bioinformatic pipelines. Apart of molecular ecology and evolution research, proSeq4 may be useful for teaching, e.g. for visual illustration of different shapes of phylogenies generated with coalescent simulations in different scenarios. ProSeq4 source code and binaries for Windows, MacOS and Ubuntu are available from https://sourceforge.net/projects/proseq/.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":null,"pages":null},"PeriodicalIF":7.7,"publicationDate":"2024-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.13962","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140672187","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}
Bruno H. Saranholi, Filipe M. França, Alfried P. Vogler, Jos Barlow, Fernando Z. Vaz de Mello, Maria E. Maldaner, Edrielly Carvalho, Carla C. Gestich, Benjamin Howes, Cristina Banks-Leite, Pedro M. Galetti Jr
Over the past few years, insects have been used as samplers of vertebrate diversity by assessing the ingested-derived DNA (iDNA), and dung beetles have been shown to be a good mammal sampler given their broad feeding preference, wide distribution and easy sampling. Here, we tested and optimized the use of iDNA from dung beetles to assess the mammal community by evaluating if some biological and methodological aspects affect the use of dung beetles as mammal species samplers. We collected 403 dung beetles from 60 pitfall traps. iDNA from each dung beetle was sequenced by metabarcoding using two mini-barcodes (12SrRNA and 16SrRNA). We assessed whether dung beetles with different traits related to feeding, nesting and body size differed in the number of mammal species found in their iDNA. We also tested differences among four killing solutions in preserving the iDNA and compared the effectiveness of each mini barcode to recover mammals. We identified a total of 50 mammal OTUs (operational taxonomic unit), including terrestrial and arboreal species from 10 different orders. We found that at least one mammal-matching sequence was obtained from 70% of the dung beetle specimens. The number of mammal OTUs obtained did not vary with dung beetle traits as well as between the killing solutions. The 16SrRNA mini-barcode recovered a higher number of mammal OTUs than 12SrRNA, although both sets were partly non-overlapping. Thus, the complete mammal diversity may not be achieved by using only one of them. This study refines the methodology for routine assessment of tropical mammal communities via dung beetle ‘samplers’ and its universal applicability independently of the species traits of local beetle communities.
{"title":"Testing and optimizing metabarcoding of iDNA from dung beetles to sample mammals in the hyperdiverse Neotropics","authors":"Bruno H. Saranholi, Filipe M. França, Alfried P. Vogler, Jos Barlow, Fernando Z. Vaz de Mello, Maria E. Maldaner, Edrielly Carvalho, Carla C. Gestich, Benjamin Howes, Cristina Banks-Leite, Pedro M. Galetti Jr","doi":"10.1111/1755-0998.13961","DOIUrl":"10.1111/1755-0998.13961","url":null,"abstract":"<p>Over the past few years, insects have been used as samplers of vertebrate diversity by assessing the ingested-derived DNA (iDNA), and dung beetles have been shown to be a good mammal sampler given their broad feeding preference, wide distribution and easy sampling. Here, we tested and optimized the use of iDNA from dung beetles to assess the mammal community by evaluating if some biological and methodological aspects affect the use of dung beetles as mammal species samplers. We collected 403 dung beetles from 60 pitfall traps. iDNA from each dung beetle was sequenced by metabarcoding using two mini-barcodes (12SrRNA and 16SrRNA). We assessed whether dung beetles with different traits related to feeding, nesting and body size differed in the number of mammal species found in their iDNA. We also tested differences among four killing solutions in preserving the iDNA and compared the effectiveness of each mini barcode to recover mammals. We identified a total of 50 mammal OTUs (operational taxonomic unit), including terrestrial and arboreal species from 10 different orders. We found that at least one mammal-matching sequence was obtained from 70% of the dung beetle specimens. The number of mammal OTUs obtained did not vary with dung beetle traits as well as between the killing solutions. The 16SrRNA mini-barcode recovered a higher number of mammal OTUs than 12SrRNA, although both sets were partly non-overlapping. Thus, the complete mammal diversity may not be achieved by using only one of them. This study refines the methodology for routine assessment of tropical mammal communities via dung beetle ‘samplers’ and its universal applicability independently of the species traits of local beetle communities.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":null,"pages":null},"PeriodicalIF":7.7,"publicationDate":"2024-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140673023","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}
Éadin N. O'Mahony, Angela L. Sremba, Eric M. Keen, Nicole Robinson, Archie Dundas, Debbie Steel, Janie Wray, C. Scott Baker, Oscar E. Gaggiotti
In coastal British Columbia, Canada, marine megafauna such as humpback whales (Megaptera novaeangliae) and fin whales (Balaenoptera physalus velifera) have been subject to a history of exploitation and near extirpation. While their populations have been in recovery, significant threats are posed to these vulnerable species by proposed natural resource ventures in this region, in addition to the compounding effects of anthropogenic climate change. Genetic tools play a vital role in informing conservation efforts, but the associated collection of tissue biopsy samples can be challenging for the investigators and disruptive to the ongoing behaviour of the targeted whales. Here, we evaluate a minimally intrusive approach based on collecting exhaled breath condensate, or respiratory ‘blow’ samples, from baleen whales using an unoccupied aerial system (UAS), within Gitga'at First Nation territory for conservation genetics. Minimal behavioural responses to the sampling technique were observed, with no response detected 87% of the time (of 112 UAS deployments). DNA from whale blow (n = 88 samples) was extracted, and DNA profiles consisting of 10 nuclear microsatellite loci, sex identification and mitochondrial (mt) DNA haplotypes were constructed. An average of 7.5 microsatellite loci per individual were successfully genotyped. The success rates for mtDNA and sex assignment were 80% and 89% respectively. Thus, this minimally intrusive sampling method can be used to describe genetic diversity and generate genetic profiles for individual identification. The results of this research demonstrate the potential of UAS‐collected whale blow for conservation genetics from a remote location.
{"title":"Collecting baleen whale blow samples by drone: A minimally intrusive tool for conservation genetics","authors":"Éadin N. O'Mahony, Angela L. Sremba, Eric M. Keen, Nicole Robinson, Archie Dundas, Debbie Steel, Janie Wray, C. Scott Baker, Oscar E. Gaggiotti","doi":"10.1111/1755-0998.13957","DOIUrl":"https://doi.org/10.1111/1755-0998.13957","url":null,"abstract":"In coastal British Columbia, Canada, marine megafauna such as humpback whales (<jats:italic>Megaptera novaeangliae</jats:italic>) and fin whales (<jats:italic>Balaenoptera physalus velifera</jats:italic>) have been subject to a history of exploitation and near extirpation. While their populations have been in recovery, significant threats are posed to these vulnerable species by proposed natural resource ventures in this region, in addition to the compounding effects of anthropogenic climate change. Genetic tools play a vital role in informing conservation efforts, but the associated collection of tissue biopsy samples can be challenging for the investigators and disruptive to the ongoing behaviour of the targeted whales. Here, we evaluate a minimally intrusive approach based on collecting exhaled breath condensate, or respiratory ‘blow’ samples, from baleen whales using an unoccupied aerial system (UAS), within Gitga'at First Nation territory for conservation genetics. Minimal behavioural responses to the sampling technique were observed, with no response detected 87% of the time (of 112 UAS deployments). DNA from whale blow (<jats:italic>n</jats:italic> = 88 samples) was extracted, and DNA profiles consisting of 10 nuclear microsatellite loci, sex identification and mitochondrial (mt) DNA haplotypes were constructed. An average of 7.5 microsatellite loci per individual were successfully genotyped. The success rates for mtDNA and sex assignment were 80% and 89% respectively. Thus, this minimally intrusive sampling method can be used to describe genetic diversity and generate genetic profiles for individual identification. The results of this research demonstrate the potential of UAS‐collected whale blow for conservation genetics from a remote location.","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":null,"pages":null},"PeriodicalIF":7.7,"publicationDate":"2024-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140569086","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}
Lignin, as an abundant organic carbon, plays a vital role in the global carbon cycle. However, our understanding of the global lignin-degrading microbiome remains elusive. The greatest barrier has been absence of a comprehensive and accurate functional gene database. Here, we first developed a curated functional gene database (LCdb) for metagenomic profiling of lignin degrading microbial consortia. Via the LCdb, we draw a clear picture describing the global biogeography of communities with lignin-degrading potential. They exhibit clear niche differentiation at the levels of taxonomy and functional traits. The terrestrial microbiomes showed the highest diversity, yet the lowest correlations. In particular, there were few correlations between genes involved in aerobic and anaerobic degradation pathways, showing a clear functional redundancy property. In contrast, enhanced correlations, especially closer inter-connections between anaerobic and aerobic groups, were observed in aquatic consortia in response to the lower diversity. Specifically, dypB and dypA, are widespread on Earth, indicating their essential roles in lignin depolymerization. Estuarine and marine consortia featured the laccase and mnsod genes, respectively. Notably, the roles of archaea in lignin degradation were revealed in marine ecosystems. Environmental factors strongly influenced functional traits, but weakly shaped taxonomic groups. Null mode analysis further verified that composition of functional traits was deterministic, while taxonomic composition was highly stochastic, demonstrating that the environment selects functional genes rather than taxonomic groups. Our study not only develops a useful tool to study lignin degrading microbial communities via metagenome sequencing but also advances our understanding of ecological traits of these global microbiomes.
{"title":"Metagenomic-based discovery and comparison of the lignin degrading potential of microbiomes in aquatic and terrestrial ecosystems via the LCdb database","authors":"Jiyu Chen, Lu Lin, Qichao Tu, Qiannan Peng, Xiaopeng Wang, Congying Liang, Jiayin Zhou, Xiaoli Yu","doi":"10.1111/1755-0998.13950","DOIUrl":"10.1111/1755-0998.13950","url":null,"abstract":"<p>Lignin, as an abundant organic carbon, plays a vital role in the global carbon cycle. However, our understanding of the global lignin-degrading microbiome remains elusive. The greatest barrier has been absence of a comprehensive and accurate functional gene database. Here, we first developed a curated functional gene database (LCdb) for metagenomic profiling of lignin degrading microbial consortia. Via the LCdb, we draw a clear picture describing the global biogeography of communities with lignin-degrading potential. They exhibit clear niche differentiation at the levels of taxonomy and functional traits. The terrestrial microbiomes showed the highest diversity, yet the lowest correlations. In particular, there were few correlations between genes involved in aerobic and anaerobic degradation pathways, showing a clear functional redundancy property. In contrast, enhanced correlations, especially closer inter-connections between anaerobic and aerobic groups, were observed in aquatic consortia in response to the lower diversity. Specifically, <i>dypB</i> and <i>dypA</i>, are widespread on Earth, indicating their essential roles in lignin depolymerization. Estuarine and marine consortia featured the <i>laccase</i> and <i>mnsod</i> genes, respectively. Notably, the roles of archaea in lignin degradation were revealed in marine ecosystems. Environmental factors strongly influenced functional traits, but weakly shaped taxonomic groups. Null mode analysis further verified that composition of functional traits was deterministic, while taxonomic composition was highly stochastic, demonstrating that the environment selects functional genes rather than taxonomic groups. Our study not only develops a useful tool to study lignin degrading microbial communities via metagenome sequencing but also advances our understanding of ecological traits of these global microbiomes.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":null,"pages":null},"PeriodicalIF":7.7,"publicationDate":"2024-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140568992","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}
Tianmin Zhang, Haohao Jing, Jinhong Wang, Le Zhao, Yang Liu, Stephen J. Rossiter, Huimeng Lu, Gang Li
The origin of flight and laryngeal echolocation in bats is likely to have been accompanied by evolutionary changes in other aspects of their sensory biology. Of all sensory modalities in bats, olfaction is perhaps the least well understood. Olfactory receptors (ORs) function in recognizing odour molecules, with crucial roles in evaluating food, as well as in processing social information. Here we compare OR repertoire sizes across taxa and apply a new pipeline that integrates comparative genome data with protein structure modelling and then we employ molecular docking techniques with small molecules to analyse OR functionality based on binding energies. Our results suggest a sharp contraction in odorant recognition of the functional OR repertoire during the origin of bats, consistent with a reduced dependence on olfaction. We also compared bat lineages with contrasting different ecological characteristics and found evidence of differences in OR gene expansion and contraction, and in the composition of ORs with different tuning breadths. The strongest binding energies of ORs in non-echolocating fruit-eating bats were seen to correspond to ester odorants, although we did not detect a quantitative advantage of functional OR repertoires in these bats compared with echolocating insectivorous species. Overall, our findings based on molecular modelling and computational docking suggest that bats have undergone olfactory evolution linked to dietary adaptation. Our results from extant and ancestral bats help to lay the groundwork for targeted experimental functional tests in the future.
蝙蝠飞行和喉回声定位的起源很可能伴随着其感官生物学其他方面的进化变化。在蝙蝠的所有感官模式中,嗅觉可能是最不为人所知的。嗅觉受体(OR)具有识别气味分子的功能,在评估食物和处理社会信息方面起着至关重要的作用。在这里,我们比较了不同类群中嗅觉受体的数量,并采用了一种新的方法,将比较基因组数据与蛋白质结构建模结合起来,然后利用小分子的分子对接技术,根据结合能分析嗅觉受体的功能。我们的研究结果表明,在蝙蝠的起源过程中,功能性OR剧目对气味的识别能力急剧收缩,这与蝙蝠对嗅觉的依赖性降低是一致的。我们还比较了具有不同生态特征的蝙蝠种系,发现了OR基因扩张和收缩的差异,以及具有不同调谐广度的OR组成的差异。在非回声定位的食果蝙蝠中,OR 的最强结合能与酯类气味相对应,但与回声定位的食虫蝙蝠相比,我们并未发现这些蝙蝠的功能性 OR 重奏在数量上有优势。总之,我们基于分子建模和计算对接的研究结果表明,蝙蝠的嗅觉进化与饮食适应有关。我们从现生蝙蝠和祖先蝙蝠身上获得的结果有助于为未来有针对性的实验功能测试奠定基础。
{"title":"Evolution of olfactory receptor superfamily in bats based on high throughput molecular modelling","authors":"Tianmin Zhang, Haohao Jing, Jinhong Wang, Le Zhao, Yang Liu, Stephen J. Rossiter, Huimeng Lu, Gang Li","doi":"10.1111/1755-0998.13958","DOIUrl":"10.1111/1755-0998.13958","url":null,"abstract":"<p>The origin of flight and laryngeal echolocation in bats is likely to have been accompanied by evolutionary changes in other aspects of their sensory biology. Of all sensory modalities in bats, olfaction is perhaps the least well understood. Olfactory receptors (ORs) function in recognizing odour molecules, with crucial roles in evaluating food, as well as in processing social information. Here we compare OR repertoire sizes across taxa and apply a new pipeline that integrates comparative genome data with protein structure modelling and then we employ molecular docking techniques with small molecules to analyse OR functionality based on binding energies. Our results suggest a sharp contraction in odorant recognition of the functional OR repertoire during the origin of bats, consistent with a reduced dependence on olfaction. We also compared bat lineages with contrasting different ecological characteristics and found evidence of differences in OR gene expansion and contraction, and in the composition of ORs with different tuning breadths. The strongest binding energies of ORs in non-echolocating fruit-eating bats were seen to correspond to ester odorants, although we did not detect a quantitative advantage of functional OR repertoires in these bats compared with echolocating insectivorous species. Overall, our findings based on molecular modelling and computational docking suggest that bats have undergone olfactory evolution linked to dietary adaptation. Our results from extant and ancestral bats help to lay the groundwork for targeted experimental functional tests in the future.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":null,"pages":null},"PeriodicalIF":7.7,"publicationDate":"2024-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140568995","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}