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Overcast I, Noguerales V, Meramveliotakis E, Andújar C, Arribas P, Creedy TJ, Emerson BC, Vogler AP, Papadopoulou A, Morlon H. Inferring the ecological and evolutionary determinants of community genetic diversity. Mol Ecol 2023; 32:6093-6109. [PMID: 37221561 DOI: 10.1111/mec.16958] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 04/06/2023] [Accepted: 04/12/2023] [Indexed: 05/25/2023]
Abstract
Understanding the relative contributions of ecological and evolutionary processes to the structuring of ecological communities is needed to improve our ability to predict how communities may respond to future changes in an increasingly human-modified world. Metabarcoding methods make it possible to gather population genetic data for all species within a community, unlocking a new axis of data to potentially unveil the origins and maintenance of biodiversity at local scales. Here, we present a new eco-evolutionary simulation model for investigating community assembly dynamics using metabarcoding data. The model makes joint predictions of species abundance, genetic variation, trait distributions and phylogenetic relationships under a wide range of parameter settings (e.g. high speciation/low dispersal or vice versa) and across a range of community states, from pristine and unmodified to heavily disturbed. We first demonstrate that parameters governing metacommunity and local community processes leave detectable signatures in simulated biodiversity data axes. Next, using a simulation-based machine learning approach we show that neutral and non-neutral models are distinguishable and that reasonable estimates of several model parameters within the local community can be obtained using only community-scale genetic data, while phylogenetic information is required to estimate those describing metacommunity dynamics. Finally, we apply the model to soil microarthropod metabarcoding data from the Troodos mountains of Cyprus, where we find that communities in widespread forest habitats are structured by neutral processes, while high-elevation and isolated habitats act as an abiotic filter generating non-neutral community structure. We implement our model within the ibiogen R package, a package dedicated to the investigation of island, and more generally community-scale, biodiversity using community-scale genetic data.
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Affiliation(s)
- Isaac Overcast
- Institut de Biologie de l'ENS (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- Department of Vertebrate Zoology, American Museum of Natural History, New York, New York, USA
| | - Víctor Noguerales
- Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de La Laguna, Spain
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | | | - Carmelo Andújar
- Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de La Laguna, Spain
| | - Paula Arribas
- Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de La Laguna, Spain
| | - Thomas J Creedy
- Department of Life Sciences, Natural History Museum, London, UK
| | - Brent C Emerson
- Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de La Laguna, Spain
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London, UK
- Department of Life Sciences, Imperial College London, Ascot, UK
| | - Anna Papadopoulou
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Hélène Morlon
- Institut de Biologie de l'ENS (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
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Dos Santos AT, Souza JPA, Jorge IR, Andrade SMM, Rosa BB, Moura MO, Zarbin PHG. Can Pheromones Contribute to Phylogenetic Hypotheses? A Case Study of Chrysomelidae. J Chem Ecol 2023; 49:611-641. [PMID: 37856061 DOI: 10.1007/s10886-023-01450-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 08/15/2023] [Accepted: 08/21/2023] [Indexed: 10/20/2023]
Abstract
Pheromones mediate species-level communication in the search for mates, nesting, and feeding sites. Although the role of pheromones has long been discussed by various authors, their existence was not proven until the mid-twentieth century when the first sex pheromone was identified. From this finding, much has been speculated about whether this communication mechanism has acted as a regulatory agent in the process of speciation, competition, and sexual selection since it acts as an intraspecific barrier. Chrysomelidae is one of the major Phytophaga lineages, with approximately 40,000 species. Due to this immense diversity the internal relationships remain unstable when analyzed only with morphological data, consequently recent efforts have been directed to molecular analyses to establish clarity for the relationships and found their respective monophyly. Therefore, our goals are twofold 1) to synthesize the current literature on Chrysomelidae sex pheromones and 2) to test whether Chrysomelidae sex pheromones and their chemical structures could be used in phylogenetic analysis for the group. The results show that, although this is the first analysis in Chrysomelidae to use pheromones as a phylogenetic character, much can be observed in agreement with previous analyses, thus confirming that pheromones, when known in their entirety within lineages, can be used as characters in phylogenetic analyses, bringing elucidation to the relationships and evolution of organisms.
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Affiliation(s)
- Aluska T Dos Santos
- Setor de Ciências Exatas, Departamento de Química, Universidade Federal do Paraná, Curitiba, Paraná, CEP 81531-980, Brazil
- Setor de Ciências Biológicas, Departamento de Zoologia, Universidade Federal do Paraná, Curitiba, Paraná, CEP 81531-980, Brazil
| | - João P A Souza
- Setor de Ciências Exatas, Departamento de Química, Universidade Federal do Paraná, Curitiba, Paraná, CEP 81531-980, Brazil
| | - Isaac R Jorge
- Setor de Ciências Biológicas, Departamento de Zoologia, Universidade Federal do Paraná, Curitiba, Paraná, CEP 81531-980, Brazil
| | - Samara M M Andrade
- Natural Resources Canada - Great Lakes Forestry Centre, Sault Ste Marie, Ontario, P6A 2E5, Canada
- Graduate Department of Forestry, John H. Daniels Faculty of Architecture, Landscape and Design, University of Toronto, Toronto, Ontario, M5S 3B3, Canada
| | - Brunno B Rosa
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, 14040-901, Brazil
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Center for Integrative Biodiversity Discovery, Invalidenstraße 43, 10115, Berlin, Germany
| | - Maurício O Moura
- Setor de Ciências Biológicas, Departamento de Zoologia, Universidade Federal do Paraná, Curitiba, Paraná, CEP 81531-980, Brazil
| | - Paulo H G Zarbin
- Setor de Ciências Exatas, Departamento de Química, Universidade Federal do Paraná, Curitiba, Paraná, CEP 81531-980, Brazil.
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Paula DP, Andow DA. DNA High-Throughput Sequencing for Arthropod Gut Content Analysis to Evaluate Effectiveness and Safety of Biological Control Agents. NEOTROPICAL ENTOMOLOGY 2023; 52:302-332. [PMID: 36478343 DOI: 10.1007/s13744-022-01011-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 11/20/2022] [Indexed: 06/17/2023]
Abstract
The search for effective biological control agents without harmful non-target effects has been constrained by the use of impractical (field direct observation) or imprecise (cage experiments) methods. While advances in the DNA sequencing methods, more specifically the development of high-throughput sequencing (HTS), have been quickly incorporated in biodiversity surveys, they have been slow to be adopted to determine arthropod prey range, predation rate and food web structure, and critical information to evaluate the effectiveness and safety of a biological control agent candidate. The lack of knowledge on how HTS methods could be applied by ecological entomologists constitutes part of the problem, although the lack of expertise and the high cost of the analysis also are important limiting factors. In this review, we describe how the latest HTS methods of metabarcoding and Lazaro, a method to identify prey by mapping unassembled shotgun reads, can serve biological control research, showing both their power and limitations. We explain how they work to determine prey range and also how their data can be used to estimate predation rates and subsequently be translated into food webs of natural enemy and prey populations helping to elucidate their role in the community. We present a brief history of prey detection through molecular gut content analysis and also the attempts to develop a more precise formula to estimate predation rates, a problem that still remains. We focused on arthropods in agricultural ecosystems, but most of what is covered here can be applied to natural systems and non-arthropod biological control candidates as well.
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Wu X, Lin Y, Zhou B, Sun Y, Luo M, Wu S. The complete mitochondrial genome of Priotyrannus closteroides Thomson, 1877 (Coleoptera: Cerambycidae). Mitochondrial DNA B Resour 2022; 7:1746-1748. [PMID: 36213868 PMCID: PMC9542708 DOI: 10.1080/23802359.2022.2126286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Priotyrannus closteroides Thomson, 1877 (Coleoptera: Cerambycidae) is the trunk borer of orange trees. In this study, we sequenced and annotated the whole mitochondrial genome of P. closteroides. The results showed that the length of the complete mitochondrial genome is 15,854 bp with an overall GC content of 32.11%. The genome encodes 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and two ribosomal RNA genes (rRNAs). The relevant phylogenetic tree distinctly showed that P. closteroides is clustered with Dorysthenes paradoxus and Dorysthenes granulosus. This study provides a piece of valuable genomic information for the population genetics, evolution, and classification of P. closteroides.
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Affiliation(s)
- Xuanxuan Wu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou City, China
- Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Province University, Fujian Agriculture and Forestry University, Fuzhou City, China
| | - Yiqi Lin
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou City, China
- Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Province University, Fujian Agriculture and Forestry University, Fuzhou City, China
| | - Bowei Zhou
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou City, China
- Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Province University, Fujian Agriculture and Forestry University, Fuzhou City, China
| | - Yunzhu Sun
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou City, China
- Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Province University, Fujian Agriculture and Forestry University, Fuzhou City, China
| | | | - Songqing Wu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou City, China
- Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Province University, Fujian Agriculture and Forestry University, Fuzhou City, China
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Paula DP, Timbó RV, Togawa RC, Vogler AP, Andow DA. Quantitative prey species detection in predator guts across multiple trophic levels by mapping unassembled shotgun reads. Mol Ecol Resour 2022; 23:64-80. [DOI: 10.1111/1755-0998.13690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 06/11/2022] [Accepted: 07/05/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Débora P. Paula
- Embrapa Recursos Genéticos e Biotecnologia Brasília DF Brazil
| | - Renata V. Timbó
- Embrapa Recursos Genéticos e Biotecnologia Brasília DF Brazil
- Universidade de Brasília, Campus Universitário Darcy Ribeiro Brasília DF Brazil
| | | | - Alfried P. Vogler
- Imperial College London Ascot UK
- Department of Life Sciences Natural History Museum London UK
| | - David A. Andow
- Department of Entomology University of Minnesota St. Paul USA
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Chua PYS, Carøe C, Crampton-Platt A, Reyes-Avila CS, Jones G, Streicker DG, Bohmann K. A two-step metagenomics approach for the identification and mitochondrial DNA contig assembly of vertebrate prey from the blood meals of common vampire bats (Desmodus rotundus). METABARCODING AND METAGENOMICS 2022. [DOI: 10.3897/mbmg.6.78756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The feeding behaviour of the sanguivorous common vampire bat (Desmodus rotundus) facilitates the transmission of pathogens that can impact both human and animal health. To formulate effective strategies in controlling the spread of diseases, there is a need to obtain information on which animals they feed on. One DNA-based approach, shotgun sequencing, can be used to obtain such information. Even though it is costly, shotgun sequencing can be used to simultaneously retrieve prey and vampire bat mitochondrial DNA for population studies within one round of sequencing. However, due to the challenges of analysing shotgun sequenced metagenomic data such as false negatives/positives and typically low proportion of reads mapped to diet items, shotgun sequencing has not been used for the identification of prey from common vampire bat blood meals. To overcome these challenges and generate longer mitochondrial contigs which could be useful for prey population studies, we shotgun sequenced common vampire bat blood meal samples (n = 8) and utilised a two-step metagenomic approach based on combining existing bioinformatic workflows (alignment and mtDNA contig assembly) to identify prey. After validating our results from detections made through metabarcoding, we accurately identified the common vampire bats’ prey in six out of eight samples without any false positives. We also generated prey mitochondrial contig lengths between 138 bp to 3231 bp (median = 770 bp, Q1 = 262 bp, Q3 = 1766 bp). This opens the potential to conduct phylogenetic and phylogeographic monitoring of elusive prey species in future studies, through the analyses of blood meal metagenomic data.
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Paula DP, Barros SKA, Pitta RM, Barreto MR, Togawa RC, Andow DA. Metabarcoding versus mapping unassembled shotgun reads for identification of prey consumed by arthropod epigeal predators. Gigascience 2022; 11:giac020. [PMID: 35333301 PMCID: PMC8952265 DOI: 10.1093/gigascience/giac020] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 12/07/2021] [Accepted: 02/09/2022] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND A central challenge of DNA gut content analysis is to identify prey in a highly degraded DNA community. In this study, we evaluated prey detection using metabarcoding and a method of mapping unassembled shotgun reads (Lazaro). RESULTS In a mock prey community, metabarcoding did not detect any prey, probably owing to primer choice and/or preferential predator DNA amplification, while Lazaro detected prey with accuracy 43-71%. Gut content analysis of field-collected arthropod epigeal predators (3 ants, 1 dermapteran, and 1 carabid) from agricultural habitats in Brazil (27 samples, 46-273 individuals per sample) revealed that 64% of the prey species detections by either method were not confirmed by melting curve analysis and 87% of the true prey were detected in common. We hypothesized that Lazaro would detect fewer true- and false-positive and more false-negative prey with greater taxonomic resolution than metabarcoding but found that the methods were similar in sensitivity, specificity, false discovery rate, false omission rate, and accuracy. There was a positive correlation between the relative prey DNA concentration in the samples and the number of prey reads detected by Lazaro, while this was inconsistent for metabarcoding. CONCLUSIONS Metabarcoding and Lazaro had similar, but partially complementary, detection of prey in arthropod predator guts. However, while Lazaro was almost 2× more expensive, the number of reads was related to the amount of prey DNA, suggesting that Lazaro may provide quantitative prey information while metabarcoding did not.
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Affiliation(s)
- Débora Pires Paula
- Embrapa Genetic Resources and Biotechnology, Brasília-DF, 70770-917, Brazil
| | | | | | | | | | - David A Andow
- Department of Entomology, University of Minnesota, MN, 55108, St. Paul, USA
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Dai TM, Tian H, Liu X, Zhang GF, Wang YS. The complete mitochondrial genome of invasive insect Leptinotarsa decemlineata Say 1824 (Coleoptera: Chrysomelidae). Mitochondrial DNA B Resour 2022; 7:358-360. [PMID: 35174290 PMCID: PMC8843170 DOI: 10.1080/23802359.2022.2035280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Leptinotarsa decemlineata Say 1824, an invasive and globally devastating beetle, inflicts great damage to potato crops worldwide. The complete mitogenome of L. decemlineata is described in this study. It is a 16,741 bp long circular DNA molecule with a high A + T content of 76.9%, containing a typical 37 gene pattern. All PCGs (protein-coding genes) initiate with typical ATN codons. Most PCGs use TAN as a stop codon, whereas ND4 and COX3 use the incomplete codon TA as the stop codon. The lengths of rrnL and rrnS genes are 1,337 bp and 811 bp, respectively. All 22 tRNAs ranged from 62 to 77 bp. Phylogenetic analysis of Chrysomelidae indicated that L. decemlineata clusteres with three other Chrysomelinae species, which is consistent with previous analyses.
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Affiliation(s)
- Tian-Mei Dai
- Hunan Provincial Key Laboratory for Control of Forest Diseases and Pests, College of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Hu Tian
- Caofeidian Customs District P. R. China, Tangshan, China
| | - Xu Liu
- Caofeidian Customs District P. R. China, Tangshan, China
| | - Gui-Fen Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yu-Sheng Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests and College of Plant Protection, Hunan Agricultural University, Changsha, China
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Jiang M, Xu SF, Tang TS, Miao L, Luo BZ, Ni Y, Kong FD, Liu C. Development and evaluation of a meat mitochondrial metagenomic (3MG) method for composition determination of meat from fifteen mammalian and avian species. BMC Genomics 2022; 23:36. [PMID: 34996352 PMCID: PMC8742424 DOI: 10.1186/s12864-021-08263-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 12/17/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Bioassessment and biomonitoring of meat products are aimed at identifying and quantifying adulterants and contaminants, such as meat from unexpected sources and microbes. Several methods for determining the biological composition of mixed samples have been used, including metabarcoding, metagenomics and mitochondrial metagenomics. In this study, we aimed to develop a method based on next-generation DNA sequencing to estimate samples that might contain meat from 15 mammalian and avian species that are commonly related to meat bioassessment and biomonitoring. RESULTS In this project, we found the meat composition from 15 species could not be identified with the metabarcoding approach because of the lack of universal primers or insufficient discrimination power. Consequently, we developed and evaluated a meat mitochondrial metagenomics (3MG) method. The 3MG method has four steps: (1) extraction of sequencing reads from mitochondrial genomes (mitogenomes); (2) assembly of mitogenomes; (3) mapping of mitochondrial reads to the assembled mitogenomes; and (4) biomass estimation based on the number of uniquely mapped reads. The method was implemented in a python script called 3MG. The analysis of simulated datasets showed that the method can determine contaminant composition at a proportion of 2% and the relative error was < 5%. To evaluate the performance of 3MG, we constructed and analysed mixed samples derived from 15 animal species in equal mass. Then, we constructed and analysed mixed samples derived from two animal species (pork and chicken) in different ratios. DNAs were extracted and used in constructing 21 libraries for next-generation sequencing. The analysis of the 15 species mix with the method showed the successful identification of 12 of the 15 (80%) animal species tested. The analysis of the mixed samples of the two species revealed correlation coefficients of 0.98 for pork and 0.98 for chicken between the number of uniquely mapped reads and the mass proportion. CONCLUSION To the best of our knowledge, this study is the first to demonstrate the potential of the non-targeted 3MG method as a tool for accurately estimating biomass in meat mix samples. The method has potential broad applications in meat product safety.
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Affiliation(s)
- Mei Jiang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, 100193 Beijing, PR China
| | - Shu-Fei Xu
- Technology Center of Xiamen Entry-exit Inspection and Quarantine Bureau, Xiamen, Fujian 361026 PR China
| | - Tai-Shan Tang
- Technology Center of Jiangsu Entry-exit Inspection and Quarantine Bureau, Nanjing, Jiangsu 210009 PR China
| | - Li Miao
- Technology Center of Henan Entry-exit Inspection and Quarantine Bureau, Zhengzhou, Henan 450003 PR China
| | - Bao-Zheng Luo
- Technology Center of Zhuhai Entry-exit Inspection and Quarantine Bureau, Zhuhai, Guangdong 519000 PR China
| | - Yang Ni
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province 350002 PR China
| | - Fan-De Kong
- Technology Center of Xiamen Entry-exit Inspection and Quarantine Bureau, Xiamen, Fujian 361026 PR China
| | - Chang Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, 100193 Beijing, PR China
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Bell KL, Petit RA, Cutler A, Dobbs EK, Macpherson JM, Read TD, Burgess KS, Brosi BJ. Comparing whole-genome shotgun sequencing and DNA metabarcoding approaches for species identification and quantification of pollen species mixtures. Ecol Evol 2021; 11:16082-16098. [PMID: 34824813 PMCID: PMC8601920 DOI: 10.1002/ece3.8281] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 10/04/2021] [Accepted: 10/08/2021] [Indexed: 12/12/2022] Open
Abstract
Molecular identification of mixed-species pollen samples has a range of applications in various fields of research. To date, such molecular identification has primarily been carried out via amplicon sequencing, but whole-genome shotgun (WGS) sequencing of pollen DNA has potential advantages, including (1) more genetic information per sample and (2) the potential for better quantitative matching. In this study, we tested the performance of WGS sequencing methodology and publicly available reference sequences in identifying species and quantifying their relative abundance in pollen mock communities. Using mock communities previously analyzed with DNA metabarcoding, we sequenced approximately 200Mbp for each sample using Illumina HiSeq and MiSeq. Taxonomic identifications were based on the Kraken k-mer identification method with reference libraries constructed from full-genome and short read archive data from the NCBI database. We found WGS to be a reliable method for taxonomic identification of pollen with near 100% identification of species in mixtures but generating higher rates of false positives (reads not identified to the correct taxon at the required taxonomic level) relative to rbcL and ITS2 amplicon sequencing. For quantification of relative species abundance, WGS data provided a stronger correlation between pollen grain proportion and sequence read proportion, but diverged more from a 1:1 relationship, likely due to the higher rate of false positives. Currently, a limitation of WGS-based pollen identification is the lack of representation of plant diversity in publicly available genome databases. As databases improve and costs drop, we expect that eventually genomics methods will become the methods of choice for species identification and quantification of mixed-species pollen samples.
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Affiliation(s)
- Karen L Bell
- Department of Environmental Sciences Emory University Atlanta Georgia USA
- Present address: School of Biological Sciences University of Western Australia Perth Australia
- Present address: CSIRO Land & Water and CSIRO Health & Biosecurity Floreat WA Australia
| | - Robert A Petit
- Division of Infectious Diseases Department of Medicine Emory University Atlanta Georgia USA
| | - Anya Cutler
- Department of Environmental Sciences Emory University Atlanta Georgia USA
| | - Emily K Dobbs
- Department of Environmental Sciences Emory University Atlanta Georgia USA
- Present address: Department of Biology Northern Kentucky University Highland Heights Kentucky USA
| | - J Michael Macpherson
- Department of Biology Chapman University Orange California USA
- Present address: 23andMe Mountain View California USA
| | - Timothy D Read
- Division of Infectious Diseases Department of Medicine Emory University Atlanta Georgia USA
| | - Kevin S Burgess
- Department of Biology Columbus State University Columbus Georgia USA
| | - Berry J Brosi
- Department of Environmental Sciences Emory University Atlanta Georgia USA
- Present address: Department of Biology University of Washington Seattle Washington USA
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Paula DP. Next-Generation Sequencing and Its Impacts on Entomological Research in Ecology and Evolution. NEOTROPICAL ENTOMOLOGY 2021; 50:679-696. [PMID: 34374956 DOI: 10.1007/s13744-021-00895-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 07/06/2021] [Indexed: 06/13/2023]
Abstract
The advent of NGS-based methods has been profoundly transforming entomological research. Through continual development and improvement of different methods and sequencing platforms, NGS has promoted mass elucidation of partial or whole genetic materials associated with beneficial insects, pests (of agriculture, forestry and animal, and human health), and species of conservation concern, helping to unravel ecological and evolutionary mechanisms and characterizing survival, trophic interactions, and dispersal. It is shifting the scale of biodiversity and environmental analyses from individuals and biodiversity indicator species to the large-scale study of communities and ecosystems using bulk samples of species or a mixed "soup" of environmental DNA. As the NGS-based methods have become more affordable, complexity demystified, and specificity and sensitivity proven, their use in entomological research has spread widely. This article presents several examples on how NGS-based methods have been used in entomology to provide incentives to apply them when appropriate and to open our minds to the expected advances in entomology that are yet to come.
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Xu SL, Han BP, Martínez A, Schwentner M, Fontaneto D, Dumont HJ, Kotov AA. Mitogenomics of Cladocera (Branchiopoda): Marked gene order rearrangements and independent predation roots. Mol Phylogenet Evol 2021; 164:107275. [PMID: 34339827 DOI: 10.1016/j.ympev.2021.107275] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 07/14/2021] [Accepted: 07/28/2021] [Indexed: 11/18/2022]
Abstract
Cladocera (Crustacea: Branchiopoda) is a key group of invertebrates. Despite a long history of phylogenetic research, relationships within this group remain disputed. We here provide new insights based on 15 new mitochondrial genomes obtained from high-throughput sequencing (HTS) and 40 mitogenomes extracted from published HTS datasets. Together with 25 mitogenomes from GenBank, we generated a matrix of 80 mitogenomes, 44 of them belonging to Cladocera. We also obtained a matrix with 168 nuclear orthologous genes to further assess the phylogenetic result from mitogenomes based on published data and one new HTS data ofLeptodora. Maximum likelihood and Bayesian phylogenetic analyses recovered all Branchiopoda orders as monophyletic and supported a sister-group relationship between Anomopoda and Onychopoda, making the taxon Gymnomera paraphyletic and supporting an independent origin of predatory Haplopoda and Onychopoda. The nuclear phylogeny and topological tests also support Gymnomera as paraphyletic, and the nuclear phylogeny strongly supports a sister-group relationship between Ctenopoda and Haplopoda. We provide a fossil-calibrated time tree, congruent with a Carboniferous origin for Cladocera and a subsequent diversification of the crown group of Anomopoda, Onychopoda, and Ctenopoda, at least in the Triassic. Despite their long evolutionary history, non-Cladoceran Branchiopoda exhibited high mitogenome structural stability. On the other hand, 21 out of 24 gene rearrangements occurred within the relatively younger Cladocera. We found the differential base compositional skewness patterns between Daphnia s.s. and Ctenodaphnia, which might be related to the divergence between these taxa. We also provide evidence to support the recent finding that Spinicaudata possesses mitogenomes with inversed compositional skewness without gene rearrangement. Such a pattern has only been reported in Spinicaudata.
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Affiliation(s)
- Shao-Lin Xu
- Jinan University, Department of Ecology, Guangzhou 510632, China
| | - Bo-Ping Han
- Jinan University, Department of Ecology, Guangzhou 510632, China.
| | - Alejandro Martínez
- National Research Council of Italy (CNR), Water Research Institute (IRSA), Molecular Ecology Group (MEG), Largo Tonolli 50, I-28922 Verbania Pallanza, Italy
| | | | - Diego Fontaneto
- National Research Council of Italy (CNR), Water Research Institute (IRSA), Molecular Ecology Group (MEG), Largo Tonolli 50, I-28922 Verbania Pallanza, Italy
| | - Henri J Dumont
- Jinan University, Department of Ecology, Guangzhou 510632, China; Ghent University, Department of Biology, Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Alexey A Kotov
- Laboratory of Aquatic Ecology and Invasions, A.N. Severtsov Institute of Ecology and Evolution of Russian Academy of Sciences, Moscow, Russia
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13
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Garrido-Sanz L, Senar MÀ, Piñol J. Relative species abundance estimation in artificial mixtures of insects using mito-metagenomics and a correction factor for the mitochondrial DNA copy number. Mol Ecol Resour 2021; 22:153-167. [PMID: 34251746 DOI: 10.1111/1755-0998.13464] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 06/21/2021] [Accepted: 07/07/2021] [Indexed: 11/27/2022]
Abstract
Mito-metagenomics (MMG) is becoming an alternative to amplicon metabarcoding for the assessment of biodiversity in complex biological samples using high-throughput sequencing. Whereas MMG overcomes the biases introduced by the PCR step in the generation of amplicons, it is not yet a technique free of shortcomings. First, as the reads are obtained from shotgun sequencing, a very low proportion of reads map into the mitogenomes, so a high sequencing effort is needed. Second, as the number of mitogenomes per cell can vary among species, the relative species abundance (RSA) in a mixture could be wrongly estimated. Here, we challenge the MMG method to estimate the RSA using artificial libraries of 17 insect species whose complete genomes are available on public repositories. With fresh specimens of these species, we created single-species libraries to calibrate the bioinformatic pipeline and mixed-species libraries to estimate the RSA. Our results showed that the MMG approach confidently recovers the species list of the mixtures, even when they contain congeneric species. The method was also able to estimate the abundance of a species across different samples (within-species estimation) but failed to estimate the RSA within a single sample (across-species estimation) unless a correction factor accounting for the variable number of mitogenomes per cell was used. To estimate this correction factor, we used the proportion of reads mapping into mitogenomes in the single-species libraries and the lengths of the whole genomes and mitogenomes.
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Affiliation(s)
| | | | - Josep Piñol
- Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain.,CREAF, Cerdanyola del Vallès, Spain
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14
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Magoga G, Fontaneto D, Montagna M. Factors affecting the efficiency of molecular species delimitation in a species-rich insect family. Mol Ecol Resour 2021; 21:1475-1489. [PMID: 33565247 DOI: 10.1111/1755-0998.13352] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 01/19/2021] [Accepted: 02/03/2021] [Indexed: 11/28/2022]
Abstract
In the context of global biodiversity loss, molecular species delimitation approaches can be very useful for accelerating species discovery through DNA taxonomy and inventory through DNA metabarcoding. In this study, the effect of some intrinsic factors on the efficiency of various single-marker species delimitation methods (fixed and variable nucleotide distance thresholds, ABGD, ASAP, GMYC, mPTP) was tested on more than 90 empirical data sets, derived from a set of 7,237 COI sequences attributed to 542 leaf beetles species (Coleoptera: Chrysomelidae). The considered factors were: (i) the number of haplotypes per species (as a proxy for genetic diversity), (ii) the geographic distance among conspecific collection localities (as a proxy of sampling width), (iii) the difficulty related to morphological identification of species, and (iv) the taxonomic rank. Distance-based methods, with on average more than 70% of match with morphological identification, outperformed those relying on phylogenetic trees, with less than 59%. A high number of haplotypes per species was found to have a negative effect on delimitation efficiency, whereas large geographic distances within species had a positive effect. All methods delimitations (except for GMYC) were significantly affected by the presence of species that are difficult to be identified, decreasing their efficiency. Finally, the only method influenced by the taxonomic rank of the data set was GMYC, showing lower efficiency in data sets at the genus than at higher levels. The observed biases we highlighted affecting efficiency could be accounted for when developing input data sets for species delimitation analyses to obtain a more reliable representation of biological diversity.
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Affiliation(s)
- Giulia Magoga
- Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Milano, Milano, Italy
| | - Diego Fontaneto
- Consiglio Nazionale delle Ricerche (CNR), Istituto di Ricerca Sulle Acque (IRSA), Molecular Ecology Group (MEG), Verbania, Italy
| | - Matteo Montagna
- Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Milano, Milano, Italy.,BAT Center - Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology, University of Napoli "Federico II", Portici, Italy
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15
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Piñol J. Genotype by sequencing: An alternative new method to amplicon metabarcoding and shotgun metagenomics for the assessment of eukaryote biodiversity. Mol Ecol Resour 2021; 21:1001-1004. [PMID: 33423396 DOI: 10.1111/1755-0998.13320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 12/07/2020] [Accepted: 01/05/2021] [Indexed: 11/28/2022]
Abstract
The use of high-throughput DNA sequencing (HTS) has revolutionized the assessment of biodiversity in plant and animal communities. There are two main approaches to estimate the identity and the relative species abundance (RSA) in complex mixtures using HTS: amplicon metabarcoding and shotgun metagenomics. While amplicon metabarcoding targets one or a few genomic regions, shotgun metagenomics randomly explores the genome of the species. In this issue of Molecular Ecology Resources, Wagemaker et al. (2021) present a new method, multi-species Genotyping by Sequencing (msGBS), as an alternative middle ground between metabarcoding and metagenomics. They apply the technique to mixtures of plant roots and report the remarkable capacity of msGBS to estimate the RSA. If validated in other laboratories and biological communities, msGBS might become a third method to explore the biodiversity of biological communities, especially of plants, where current techniques are struggling to get sufficient taxonomic resolution.
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Affiliation(s)
- Josep Piñol
- Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain.,CREAF, Cerdanyola del Vallès, Spain
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16
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Compson ZG, McClenaghan B, Singer GAC, Fahner NA, Hajibabaei M. Metabarcoding From Microbes to Mammals: Comprehensive Bioassessment on a Global Scale. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.581835] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Global biodiversity loss is unprecedented, and threats to existing biodiversity are growing. Given pervasive global change, a major challenge facing resource managers is a lack of scalable tools to rapidly and consistently measure Earth's biodiversity. Environmental genomic tools provide some hope in the face of this crisis, and DNA metabarcoding, in particular, is a powerful approach for biodiversity assessment at large spatial scales. However, metabarcoding studies are variable in their taxonomic, temporal, or spatial scope, investigating individual species, specific taxonomic groups, or targeted communities at local or regional scales. With the advent of modern, ultra-high throughput sequencing platforms, conducting deep sequencing metabarcoding surveys with multiple DNA markers will enhance the breadth of biodiversity coverage, enabling comprehensive, rapid bioassessment of all the organisms in a sample. Here, we report on a systematic literature review of 1,563 articles published about DNA metabarcoding and summarize how this approach is rapidly revolutionizing global bioassessment efforts. Specifically, we quantify the stakeholders using DNA metabarcoding, the dominant applications of this technology, and the taxonomic groups assessed in these studies. We show that while DNA metabarcoding has reached global coverage, few studies deliver on its promise of near-comprehensive biodiversity assessment. We then outline how DNA metabarcoding can help us move toward real-time, global bioassessment, illustrating how different stakeholders could benefit from DNA metabarcoding. Next, we address barriers to widespread adoption of DNA metabarcoding, highlighting the need for standardized sampling protocols, experts and computational resources to handle the deluge of genomic data, and standardized, open-source bioinformatic pipelines. Finally, we explore how technological and scientific advances will realize the promise of total biodiversity assessment in a sample—from microbes to mammals—and unlock the rich information genomics exposes, opening new possibilities for merging whole-system DNA metabarcoding with (1) abundance and biomass quantification, (2) advanced modeling, such as species occupancy models, to improve species detection, (3) population genetics, (4) phylogenetics, and (5) food web and functional gene analysis. While many challenges need to be addressed to facilitate widespread adoption of environmental genomic approaches, concurrent scientific and technological advances will usher in methods to supplement existing bioassessment tools reliant on morphological and abiotic data. This expanded toolbox will help ensure that the best tool is used for the job and enable exciting integrative techniques that capitalize on multiple tools. Collectively, these new approaches will aid in addressing the global biodiversity crisis we now face.
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17
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Arribas P, Andújar C, Moraza ML, Linard B, Emerson BC, Vogler AP. Mitochondrial Metagenomics Reveals the Ancient Origin and Phylodiversity of Soil Mites and Provides a Phylogeny of the Acari. Mol Biol Evol 2020; 37:683-694. [PMID: 31670799 DOI: 10.1093/molbev/msz255] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
High-throughput DNA methods hold great promise for phylogenetic analysis of lineages that are difficult to study with conventional molecular and morphological approaches. The mites (Acari), and in particular the highly diverse soil-dwelling lineages, are among the least known branches of the metazoan Tree-of-Life. We extracted numerous minute mites from soils in an area of mixed forest and grassland in southern Iberia. Selected specimens representing the full morphological diversity were shotgun sequenced in bulk, followed by genome assembly of short reads from the mixture, which produced >100 mitochondrial genomes representing diverse acarine lineages. Phylogenetic analyses in combination with taxonomically limited mitogenomes available publicly resulted in plausible trees defining basal relationships of the Acari. Several critical nodes were supported by ancestral-state reconstructions of mitochondrial gene rearrangements. Molecular calibration placed the minimum age for the common ancestor of the superorder Acariformes, which includes most soil-dwelling mites, to the Cambrian-Ordovician (likely within 455-552 Ma), whereas the origin of the superorder Parasitiformes was placed later in the Carboniferous-Permian. Most family-level taxa within the Acariformes were dated to the Jurassic and Triassic. The ancient origin of Acariformes and the early diversification of major extant lineages linked to the soil are consistent with a pioneering role for mites in building the earliest terrestrial ecosystems.
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Affiliation(s)
- Paula Arribas
- Island Ecology and Evolution Research Group, IPNA-CSIC, La Laguna, Tenerife, Spain.,Department of Life Sciences, Natural History Museum, London, United Kingdom.,Department of Life Sciences, Imperial College London, Ascot, United Kingdom
| | - Carmelo Andújar
- Island Ecology and Evolution Research Group, IPNA-CSIC, La Laguna, Tenerife, Spain.,Department of Life Sciences, Natural History Museum, London, United Kingdom.,Department of Life Sciences, Imperial College London, Ascot, United Kingdom
| | - María Lourdes Moraza
- Departamento de Biología Ambiental, Universidad de Navarra, Facultad de Ciencias, Pamplona, Spain
| | - Benjamin Linard
- Department of Life Sciences, Natural History Museum, London, United Kingdom.,LIRMM, Université de Montpellier, CNRS, Montpellier, France.,ISEM, Université de Montpellier, CNRS, IRD, EPHE, CIRAD, INRAP, Montpellier, France
| | - Brent C Emerson
- Island Ecology and Evolution Research Group, IPNA-CSIC, La Laguna, Tenerife, Spain
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London, United Kingdom.,Department of Life Sciences, Imperial College London, Ascot, United Kingdom
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18
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Sweet AD, Johnson KP, Cameron SL. Mitochondrial genomes of Columbicola feather lice are highly fragmented, indicating repeated evolution of minicircle-type genomes in parasitic lice. PeerJ 2020; 8:e8759. [PMID: 32231878 PMCID: PMC7098387 DOI: 10.7717/peerj.8759] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 02/16/2020] [Indexed: 01/21/2023] Open
Abstract
Most animals have a conserved mitochondrial genome structure composed of a single chromosome. However, some organisms have their mitochondrial genes separated on several smaller circular or linear chromosomes. Highly fragmented circular chromosomes (“minicircles”) are especially prevalent in parasitic lice (Insecta: Phthiraptera), with 16 species known to have between nine and 20 mitochondrial minicircles per genome. All of these species belong to the same clade (mammalian lice), suggesting a single origin of drastic fragmentation. Nevertheless, other work indicates a lesser degree of fragmentation (2–3 chromosomes/genome) is present in some avian feather lice (Ischnocera: Philopteridae). In this study, we tested for minicircles in four species of the feather louse genus Columbicola (Philopteridae). Using whole genome shotgun sequence data, we applied three different bioinformatic approaches for assembling the Columbicola mitochondrial genome. We further confirmed these approaches by assembling the mitochondrial genome of Pediculus humanus from shotgun sequencing reads, a species known to have minicircles. Columbicola spp. genomes are highly fragmented into 15–17 minicircles between ∼1,100 and ∼3,100 bp in length, with 1–4 genes per minicircle. Subsequent annotation of the minicircles indicated that tRNA arrangements of minicircles varied substantially between species. These mitochondrial minicircles for species of Columbicola represent the first feather lice (Philopteridae) for which minicircles have been found in a full mitochondrial genome assembly. Combined with recent phylogenetic studies of parasitic lice, our results provide strong evidence that highly fragmented mitochondrial genomes, which are otherwise rare across the Tree of Life, evolved multiple times within parasitic lice.
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Affiliation(s)
- Andrew D Sweet
- Department of Entomology, Purdue University, West Lafayette, IN, United States of America
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL, United States of America
| | - Stephen L Cameron
- Department of Entomology, Purdue University, West Lafayette, IN, United States of America
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19
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Garrido-Sanz L, Senar MÀ, Piñol J. Estimation of the relative abundance of species in artificial mixtures of insects using low-coverage shotgun metagenomics. METABARCODING AND METAGENOMICS 2020. [DOI: 10.3897/mbmg.4.48281] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Amplicon metabarcoding is an established technique to analyse the taxonomic composition of communities of organisms using high-throughput DNA sequencing, but there are doubts about its ability to quantify the relative proportions of the species, as opposed to the species list. Here, we bypass the enrichment step and avoid the PCR-bias, by directly sequencing the extracted DNA using shotgun metagenomics. This approach is common practice in prokaryotes, but not in eukaryotes, because of the low number of sequenced genomes of eukaryotic species. We tested the metagenomics approach using insect species whose genome is already sequenced and assembled to an advanced degree. We shotgun-sequenced, at low-coverage, 18 species of insects in 22 single-species and 6 mixed-species libraries and mapped the reads against 110 reference genomes of insects. We used the single-species libraries to calibrate the process of assignation of reads to species and the libraries created from species mixtures to evaluate the ability of the method to quantify the relative species abundance. Our results showed that the shotgun metagenomic method is easily able to set apart closely-related insect species, like four species of Drosophila included in the artificial libraries. However, to avoid the counting of rare misclassified reads in samples, it was necessary to use a rather stringent detection limit of 0.001, so species with a lower relative abundance are ignored. We also identified that approximately half the raw reads were informative for taxonomic purposes. Finally, using the mixed-species libraries, we showed that it was feasible to quantify with confidence the relative abundance of individual species in the mixtures.
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20
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Bell KL, Batchelor KL, Bradford M, McKeown A, Macdonald SL, Westcott D. Optimisation of a pollen DNA metabarcoding method for diet analysis of flying-foxes (Pteropus spp.). AUST J ZOOL 2020. [DOI: 10.1071/zo20085] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Determining the diet of flying-foxes can increase understanding of how they function as pollinators and seed dispersers, as well as managing any negative impacts of large roosts. Traditional methods for diet analysis are time consuming, and not feasible to conduct for hundreds of animals. In this study, we optimised a method for diet analysis, based on DNA metabarcoding of environmental DNA (eDNA) from pollen and other plant parts in the faeces. We found that existing eDNA metabarcoding protocols are suitable, with the most useful results being obtained using a commercial food DNA extraction kit, and sequencing 350–450 base pairs of a DNA barcode from the internally transcribed spacer region (ITS2), with ~550 base pairs of the chloroplast rubisco large subunit (rbcL) as a secondary DNA barcode. A list of forage plants was generated for the little red flying-fox (Pteropus scapulatus), the black flying-fox (Pteropus alecto) and the spectacled flying-fox (Pteropus conspicillatus) from our collection sites across Queensland. The diets were determined to comprise predominantly Myrtaceae species, particularly those in the genera Eucalyptus, Melaleuca and Corymbia. With more plant genomes becoming publicly available in the future, there are likely to be further applications of eDNA methods in understanding the role of flying-foxes as pollinators and seed dispersers.
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21
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Meng G, Li Y, Yang C, Liu S. MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization. Nucleic Acids Res 2019; 47:e63. [PMID: 30864657 PMCID: PMC6582343 DOI: 10.1093/nar/gkz173] [Citation(s) in RCA: 508] [Impact Index Per Article: 101.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 01/25/2019] [Accepted: 03/08/2019] [Indexed: 12/27/2022] Open
Abstract
Mitochondrial genome (mitogenome) plays important roles in evolutionary and ecological studies. It becomes routine to utilize multiple genes on mitogenome or the entire mitogenomes to investigate phylogeny and biodiversity of focal groups with the onset of High Throughput Sequencing (HTS) technologies. We developed a mitogenome toolkit MitoZ, consisting of independent modules of de novo assembly, findMitoScaf (find Mitochondrial Scaffolds), annotation and visualization, that can generate mitogenome assembly together with annotation and visualization results from HTS raw reads. We evaluated its performance using a total of 50 samples of which mitogenomes are publicly available. The results showed that MitoZ can recover more full-length mitogenomes with higher accuracy compared to the other available mitogenome assemblers. Overall, MitoZ provides a one-click solution to construct the annotated mitogenome from HTS raw data and will facilitate large scale ecological and evolutionary studies. MitoZ is free open source software distributed under GPLv3 license and available at https://github.com/linzhi2013/MitoZ.
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Affiliation(s)
- Guanliang Meng
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Yiyuan Li
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Chentao Yang
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Shanlin Liu
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Plant Protection, China Agricultural University, Beijing 100193, China
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22
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Song N, Li X, Yin X, Li X, Xi Y. The mitochondrial genomes of ladybird beetles and implications for evolution and phylogeny. Int J Biol Macromol 2019; 147:1193-1203. [PMID: 31751694 DOI: 10.1016/j.ijbiomac.2019.10.089] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 10/08/2019] [Accepted: 10/08/2019] [Indexed: 12/15/2022]
Abstract
Ladybirds formed the most familiar beetle group, namely the family Coccinellidae, whose internal relationships remain unclear. In particular, the subfamily relationships could not be well resolved in previous studies based on the conventional nuclear and/or mitochondrial gene fragments. In this study, we used next-generation sequencing to obtain new mitochondrial genomes (mitogenomes) from 13 species representing four coccinellid subfamilies (i.e., Coccinellinae, Epilachninae, Coccidulinae and Chilocorinae). Together with 24 existing mitogenome sequences of Cucujoidea, we conducted phylogenetic analyses to investigate the deep phylogenetic relationships in Coccinellidae, under maximum likelihood and Bayesian inference criteria. The analyses from nucleotide datasets resulted in a largely identical tree topology, where Epilachninae and Coccinellinae were monophyletic groups. The Scymninae and Coccidulinae were recovered as non-monophyletic. Amino acids differed from nucleotides in that the Epilachninae was retrieved as paraphyletic, with respect to Epilachna admirabilis. Ancestral state reconstruction suggested that the plant eating ladybird beetles arose within an aphidophagous/coccidophagous clade. In addition, three independent shifts toward coccidophagy and one shift toward mycophagy occurred in Coccinellidae.
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Affiliation(s)
- Nan Song
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China.
| | - Xinxin Li
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Xinming Yin
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Xinghao Li
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Yuqiang Xi
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
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23
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Gauthier M, Konecny‐Dupré L, Nguyen A, Elbrecht V, Datry T, Douady C, Lefébure T. Enhancing DNA metabarcoding performance and applicability with bait capture enrichment and DNA from conservative ethanol. Mol Ecol Resour 2019; 20:79-96. [DOI: 10.1111/1755-0998.13088] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 08/15/2019] [Accepted: 08/19/2019] [Indexed: 12/27/2022]
Affiliation(s)
- Mailys Gauthier
- CNRS UMR 5023 ENTPE Laboratoire d’Ecologie des Hydrosystèmes Naturels et Anthropisés Univ Lyon Université Claude Bernard Lyon 1 Villeurbanne France
- IRSTEA UR‐RiverLy Centre de Lyon‐Villeurbanne Villeurbanne Cedex France
| | - Lara Konecny‐Dupré
- CNRS UMR 5023 ENTPE Laboratoire d’Ecologie des Hydrosystèmes Naturels et Anthropisés Univ Lyon Université Claude Bernard Lyon 1 Villeurbanne France
| | | | - Vasco Elbrecht
- Centre for Biodiversity Genomics University of Guelph Guelph Ontario Canada
| | - Thibault Datry
- IRSTEA UR‐RiverLy Centre de Lyon‐Villeurbanne Villeurbanne Cedex France
| | - Christophe Douady
- CNRS UMR 5023 ENTPE Laboratoire d’Ecologie des Hydrosystèmes Naturels et Anthropisés Univ Lyon Université Claude Bernard Lyon 1 Villeurbanne France
| | - Tristan Lefébure
- CNRS UMR 5023 ENTPE Laboratoire d’Ecologie des Hydrosystèmes Naturels et Anthropisés Univ Lyon Université Claude Bernard Lyon 1 Villeurbanne France
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24
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Nie R, Wei J, Zhang S, Vogler AP, Wu L, Konstantinov AS, Li W, Yang X, Xue H. Diversification of mitogenomes in three sympatric
Altica
flea beetles (Insecta, Chrysomelidae). ZOOL SCR 2019. [DOI: 10.1111/zsc.12371] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rui‐E Nie
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Jing Wei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
| | - Shou‐Ke Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences Beijing China
- Research Institute of Subtropical Forestry Chinese Academy of Forestry Fuyang China
| | - Alfried P. Vogler
- Department of Life Sciences Natural History Museum London UK
- Department of Life Sciences, Silwood Park Campus Imperial College London Ascot UK
| | - Ling Wu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences Beijing China
- College of Life Sciences Hebei University Baoding China
| | | | - Wen‐Zhu Li
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Xing‐Ke Yang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Huai‐Jun Xue
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences Beijing China
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25
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Ji Y, Huotari T, Roslin T, Schmidt NM, Wang J, Yu DW, Ovaskainen O. SPIKEPIPE: A metagenomic pipeline for the accurate quantification of eukaryotic species occurrences and intraspecific abundance change using DNA barcodes or mitogenomes. Mol Ecol Resour 2019; 20:256-267. [PMID: 31293086 DOI: 10.1111/1755-0998.13057] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 06/15/2019] [Accepted: 07/03/2019] [Indexed: 11/24/2022]
Abstract
The accurate quantification of eukaryotic species abundances from bulk samples remains a key challenge for community ecology and environmental biomonitoring. We resolve this challenge by combining shotgun sequencing, mapping to reference DNA barcodes or to mitogenomes, and three correction factors: (a) a percent-coverage threshold to filter out false positives, (b) an internal-standard DNA spike-in to correct for stochasticity during sequencing, and (c) technical replicates to correct for stochasticity across sequencing runs. The SPIKEPIPE pipeline achieves a strikingly high accuracy of intraspecific abundance estimates (in terms of DNA mass) from samples of known composition (mapping to barcodes R2 = .93, mitogenomes R2 = .95) and a high repeatability across environmental-sample replicates (barcodes R2 = .94, mitogenomes R2 = .93). As proof of concept, we sequence arthropod samples from the High Arctic, systematically collected over 17 years, detecting changes in species richness, species-specific abundances, and phenology. SPIKEPIPE provides cost-efficient and reliable quantification of eukaryotic communities.
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Affiliation(s)
- Yinqiu Ji
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Tea Huotari
- Department of Agricultural Sciences, Spatial Foodweb Ecology Group, University of Helsinki, Helsinki, Finland
| | - Tomas Roslin
- Department of Agricultural Sciences, Spatial Foodweb Ecology Group, University of Helsinki, Helsinki, Finland.,Department of Ecology, Spatial Foodweb Ecology Group, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Niels Martin Schmidt
- Arctic Research Centre, Aarhus University, Aarhus, Denmark.,Department of Bioscience, Aarhus University, Roskilde, Denmark
| | - Jiaxin Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Douglas W Yu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,School of Biological Sciences, University of East Anglia, Norfolk, UK.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Otso Ovaskainen
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland.,Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
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26
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Piper AM, Batovska J, Cogan NOI, Weiss J, Cunningham JP, Rodoni BC, Blacket MJ. Prospects and challenges of implementing DNA metabarcoding for high-throughput insect surveillance. Gigascience 2019; 8:giz092. [PMID: 31363753 PMCID: PMC6667344 DOI: 10.1093/gigascience/giz092] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 06/25/2019] [Accepted: 07/09/2019] [Indexed: 12/21/2022] Open
Abstract
Trap-based surveillance strategies are widely used for monitoring of invasive insect species, aiming to detect newly arrived exotic taxa as well as track the population levels of established or endemic pests. Where these surveillance traps have low specificity and capture non-target endemic species in excess of the target pests, the need for extensive specimen sorting and identification creates a major diagnostic bottleneck. While the recent development of standardized molecular diagnostics has partly alleviated this requirement, the single specimen per reaction nature of these methods does not readily scale to the sheer number of insects trapped in surveillance programmes. Consequently, target lists are often restricted to a few high-priority pests, allowing unanticipated species to avoid detection and potentially establish populations. DNA metabarcoding has recently emerged as a method for conducting simultaneous, multi-species identification of complex mixed communities and may lend itself ideally to rapid diagnostics of bulk insect trap samples. Moreover, the high-throughput nature of recent sequencing platforms could enable the multiplexing of hundreds of diverse trap samples on a single flow cell, thereby providing the means to dramatically scale up insect surveillance in terms of both the quantity of traps that can be processed concurrently and number of pest species that can be targeted. In this review of the metabarcoding literature, we explore how DNA metabarcoding could be tailored to the detection of invasive insects in a surveillance context and highlight the unique technical and regulatory challenges that must be considered when implementing high-throughput sequencing technologies into sensitive diagnostic applications.
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Affiliation(s)
- Alexander M Piper
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora 3083, VIC, Australia
| | - Jana Batovska
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora 3083, VIC, Australia
| | - Noel O I Cogan
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora 3083, VIC, Australia
| | - John Weiss
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
| | - John Paul Cunningham
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
| | - Brendan C Rodoni
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora 3083, VIC, Australia
| | - Mark J Blacket
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
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Zu Z, Yan C. Identification and analysis of the complete mitochondrial genome of Phyllotreta striolata (Coleoptera, Chrysomelidae). Mitochondrial DNA B Resour 2019; 4:2150-2151. [PMID: 33365449 PMCID: PMC7687497 DOI: 10.1080/23802359.2019.1622469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 05/17/2019] [Indexed: 11/27/2022] Open
Abstract
In this study, the complete mitochondrial genome of Phyllotreta striolata (Coleoptera, Chrysomeloidea, Chrysomelidae) was first determined. The complete genome is 15,689 bp in length. It contains 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a control region (A + T-rich region). The gene organization, nucleotide composition, and codon usage are similar to other Chrysomelidae mitogenomes. The overall nucleotide composition was 39.90% A, 35.94% T, 15.27% C, and 8.89% G, respectively. Phylogenetic analysis both highly supported that P. striolata showed a close relationship with P. undulata. The measure of complete mitogenome sequence of P. striolata will provide fundamental data for the phylogenetic and biogeographic studies of the Chrysomeloidea and Coleoptera.
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Affiliation(s)
- Zhenhua Zu
- Institute of Agriculture and Biotechnology, Wenzhou Vocational College of Science and Technology, Wenzhou, China
| | - Chengjin Yan
- Institute of Agriculture and Biotechnology, Wenzhou Vocational College of Science and Technology, Wenzhou, China
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Salvi D, D’Alessandro P, Biondi M. Host plant associations in Western Palaearctic Longitarsus flea beetles (Chrysomelidae, Galerucinae, Alticini): a preliminary phylogenetic assessment. Zookeys 2019; 856:101-114. [PMID: 31258369 PMCID: PMC6591207 DOI: 10.3897/zookeys.856.32430] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 04/15/2019] [Indexed: 11/25/2022] Open
Abstract
Longitarsus Latreille (Chrysomelidae, Galerucinae, Alticini) is a very large genus of phytophagous insects, with more than 700 species distributed in all zoogeographical regions. Patterns of host use have been a central topic in phytophagous insect research. In this study a first assessment is provided to test the hypothesis that host-plant association is phylogenetically conserved in Western Palaearctic Longitarsus species. Maximum Likelihood and Bayesian Inference methods were used to infer a phylogeny based on DNA sequence data from two mitochondrial genes from 52 Longitarsus species from the Western Palaearctic. In agreement with the host phylogenetic conservatism hypothesis, a strict association between most of the recovered clades and specific plant families was found, except for species associated with Boraginaceae. Low phylogenetic resolution at deep nodes limited the evaluation of whether closely related Longitarsus clades are associated with the same plant family or to closely related plant families.
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Affiliation(s)
- Daniele Salvi
- Department of Health, Life and Environmental Sciences, University of L’Aquila, Via Vetoio, 67100 Coppito, L’Aquila, ItalyUniversity of L’AquilaL’AquilaItaly
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, PortugalUniversidade do PortoVairãoPortugal
| | - Paola D’Alessandro
- Department of Health, Life and Environmental Sciences, University of L’Aquila, Via Vetoio, 67100 Coppito, L’Aquila, ItalyUniversity of L’AquilaL’AquilaItaly
| | - Maurizio Biondi
- Department of Health, Life and Environmental Sciences, University of L’Aquila, Via Vetoio, 67100 Coppito, L’Aquila, ItalyUniversity of L’AquilaL’AquilaItaly
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29
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Ramachandran P, Mammel M, Ottesen A, Pava-Ripoll M. MitochonTrakr: a reference collection of high-quality mitochondrial genomes for detecting insect species in food products. MITOCHONDRIAL DNA PART B 2019. [DOI: 10.1080/23802359.2018.1542986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Padmini Ramachandran
- Division of Microbiology, Office of Regulatory Science Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, USA
| | - Mark Mammel
- Division of Molecular Biology, Office of Applied Research and Safety Assessment Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, USA
| | - Andrea Ottesen
- Division of Microbiology, Office of Regulatory Science Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, USA
| | - Monica Pava-Ripoll
- Division of Dairy Egg and Meat Products, Office of Food Safety, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, USA
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Linard B, Crampton-Platt A, Moriniere J, Timmermans MJ, Andújar C, Arribas P, Miller KE, Lipecki J, Favreau E, Hunter A, Gómez-Rodríguez C, Barton C, Nie R, Gillett CP, Breeschoten T, Bocak L, Vogler AP. The contribution of mitochondrial metagenomics to large-scale data mining and phylogenetic analysis of Coleoptera. Mol Phylogenet Evol 2018; 128:1-11. [DOI: 10.1016/j.ympev.2018.07.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 03/09/2018] [Indexed: 12/16/2022]
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Magoga G, Sahin DC, Fontaneto D, Montagna M. Barcoding of Chrysomelidae of Euro-Mediterranean area: efficiency and problematic species. Sci Rep 2018; 8:13398. [PMID: 30194432 PMCID: PMC6128942 DOI: 10.1038/s41598-018-31545-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 08/03/2018] [Indexed: 11/16/2022] Open
Abstract
Leaf beetles (Coleoptera: Chrysomelidae), with more than 37,000 species worldwide and about 2,300 in the Euro-Mediterranean region, are an ecological and economical relevant family, making their molecular identification of interest also in agriculture. This study, part of the Mediterranean Chrysomelidae Barcoding project (www.c-bar.org), aims to: (i) develop a reference Cytochrome c oxidase I (COI) library for the molecular identification of the Euro-Mediterranean Chrysomelidae; (ii) test the efficiency of DNA barcoding for leaf beetles identification; (iii) develop and compare optimal thresholds for distance-based identifications estimated at family and subfamily level, minimizing false positives and false negatives. Within this study, 889 COI nucleotide sequences of 261 species were provided; after the inclusion of information from other sources, a dataset of 7,237 sequences (542 species) was analysed. The average intra-interspecific distances were in the range of those recorded for Coleoptera: 1.6–24%. The estimated barcoding efficiency (~94%) confirmed the usefulness of this tool for Chrysomelidae identification. The few cases of failure were recorded for closely related species (e.g., Cryptocephalus marginellus superspecies, Cryptocephalus violaceus - Cryptocephalus duplicatus and some Altica species), even with morphologically different species sharing the same COI haplotype. Different optimal thresholds were achieved for the tested taxonomic levels, confirming that group-specific thresholds significantly improve molecular identifications.
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Affiliation(s)
- Giulia Magoga
- Dipartimento di Scienze Agrarie e Ambientali - Università degli Studi di Milano, Via Celoria 2, 20133, Milano, Italy
| | - Didem Coral Sahin
- Directorate of Plant Protection Central Research Institute, Yenimahalle, Ankara, Turkey
| | - Diego Fontaneto
- Consiglio Nazionale delle Ricerche-Istituto per lo Studio degli Ecosistemi, Largo Tonolli 50, 28922, Verbania, Italy
| | - Matteo Montagna
- Dipartimento di Scienze Agrarie e Ambientali - Università degli Studi di Milano, Via Celoria 2, 20133, Milano, Italy.
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32
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Ramirez KS, Geisen S, Morriën E, Snoek BL, van der Putten WH. Network Analyses Can Advance Above-Belowground Ecology. TRENDS IN PLANT SCIENCE 2018; 23:759-768. [PMID: 30072227 DOI: 10.1016/j.tplants.2018.06.009] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 06/05/2018] [Accepted: 06/17/2018] [Indexed: 06/08/2023]
Abstract
An understanding of above-belowground (AG-BG) ecology is important for evaluating how plant interactions with enemies, symbionts, and decomposers affect species diversity and will respond to global changes. However, research questions and experiments often focus on only a limited number of interactions, creating an incomplete picture of how entire communities may be involved in AG-BG community ecology. Therefore, a pressing challenge is to formulate hypotheses of AG-BG interactions when considering communities in their full complexity. Here we discuss how network analyses can be a powerful tool to progress AG-BG research, link across scales from individual to community and ecosystem, visualize community interactions between the two (AG and BG) subsystems, and develop testable hypotheses.
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Affiliation(s)
- Kelly S Ramirez
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6700 AB, Wageningen, The Netherlands.
| | - Stefan Geisen
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6700 AB, Wageningen, The Netherlands; Laboratory of Nematology, Wageningen University, P.O. Box 8123, 6700 ES, Wageningen, The Netherlands
| | - Elly Morriën
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6700 AB, Wageningen, The Netherlands; Institute of Biodiversity and Ecosystem Dynamics, Department of Ecosystem and Landscape Dynamics (IBED-ELD), University of Amsterdam, P.O. Box 94248, 1090 GE Amsterdam, The Netherlands
| | - Basten L Snoek
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6700 AB, Wageningen, The Netherlands; Laboratory of Nematology, Wageningen University, P.O. Box 8123, 6700 ES, Wageningen, The Netherlands; Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Wim H van der Putten
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6700 AB, Wageningen, The Netherlands; Laboratory of Nematology, Wageningen University, P.O. Box 8123, 6700 ES, Wageningen, The Netherlands
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Piñol J, Senar MA, Symondson WOC. The choice of universal primers and the characteristics of the species mixture determine when DNA metabarcoding can be quantitative. Mol Ecol 2018; 28:407-419. [PMID: 29939447 DOI: 10.1111/mec.14776] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 05/24/2018] [Indexed: 12/20/2022]
Abstract
DNA metabarcoding is a technique used to survey biodiversity in many ecological settings, but there are doubts about whether it can provide quantitative results, that is, the proportions of each species in the mixture as opposed to a species list. While there are several experimental studies that report quantitative metabarcoding results, there are a similar number that fail to do so. Here, we provide the rationale to understand under what circumstances the technique can be quantitative. In essence, we simulate a mixture of DNA of S species with a defined initial abundance distribution. In the simulated PCR, each species increases its concentration following a certain amplification efficiency. The final DNA concentration will reflect the initial one when the efficiency is similar for all species; otherwise, the initial and final DNA concentrations would be poorly related. Although there are many known factors that modulate amplification efficiency, we focused on the number of primer-template mismatches, arguably the most important one. We used 15 common primers pairs targeting the mitochondrial COI region and the mitogenomes of ca. 1,200 insect species. The results showed that some primers pairs produced quantitative results under most circumstances, whereas some other primers failed to do so. In conclusion, depending on the primer pair used in the PCR amplification and on the characteristics of the mixture analysed (i.e., high species richness, low evenness), DNA metabarcoding can provide a quantitative estimate of the relative abundances of different species.
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Affiliation(s)
- Josep Piñol
- Universitat Autònoma Barcelona, Cerdanyola del Vallès, Spain.,CREAF, Cerdanyola del Vallès, Spain
| | - Miquel A Senar
- Universitat Autònoma Barcelona, Cerdanyola del Vallès, Spain
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34
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Cilleros K, Valentini A, Allard L, Dejean T, Etienne R, Grenouillet G, Iribar A, Taberlet P, Vigouroux R, Brosse S. Unlocking biodiversity and conservation studies in high‐diversity environments using environmental DNA (eDNA): A test with Guianese freshwater fishes. Mol Ecol Resour 2018; 19:27-46. [DOI: 10.1111/1755-0998.12900] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 03/29/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Kévin Cilleros
- Laboratoire Évolution & Diversité Biologique (EDB UMR5174) Université de Toulouse, CNRS, IRD, UPS Toulouse Cedex France
| | | | - Luc Allard
- Laboratoire Environnement de Petit Saut HYDRECO Kourou Cedex French Guiana
| | - Tony Dejean
- SPYGEN, Savoie Technolac Le Bourget‐du‐Lac France
| | - Roselyne Etienne
- Laboratoire Évolution & Diversité Biologique (EDB UMR5174) Université de Toulouse, CNRS, IRD, UPS Toulouse Cedex France
| | - Gaël Grenouillet
- Laboratoire Évolution & Diversité Biologique (EDB UMR5174) Université de Toulouse, CNRS, IRD, UPS Toulouse Cedex France
| | - Amaia Iribar
- Laboratoire Évolution & Diversité Biologique (EDB UMR5174) Université de Toulouse, CNRS, IRD, UPS Toulouse Cedex France
| | - Pierre Taberlet
- Laboratoire d'Ecologie Alpine (LECA UMR5553) CNRS Université Joseph Fourier Grenoble France
| | - Régis Vigouroux
- Laboratoire Environnement de Petit Saut HYDRECO Kourou Cedex French Guiana
| | - Sébastien Brosse
- Laboratoire Évolution & Diversité Biologique (EDB UMR5174) Université de Toulouse, CNRS, IRD, UPS Toulouse Cedex France
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35
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Zhang LJ, Wu L, Wei CY, Liu XL, Xue HJ, Yang XK, Nie RE. The complete mitochondrial genome of the cowpea weevil, Callosobruchus maculates (Coleoptera: Chrysomelidae: Bruchinae) and a related phylogenetic analysis of Chrysomelidae. Mitochondrial DNA B Resour 2018; 3:645-647. [PMID: 33474270 PMCID: PMC7799975 DOI: 10.1080/23802359.2017.1413308] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 12/01/2017] [Indexed: 12/13/2022] Open
Abstract
In this study, the complete 17,809 bp mitochondrial genome of Callosobruchus maculates (F.) (Coleoptera: Chrysomelidae: Bruchinae) was sequenced using Illumina's HiSeq2000 platform. The mitogenome is a double-stranded circular molecule of 17,809 bp in length with 21 transfer RNA genes, 13 protein-coding genes, and two ribosomal RNA genes as in other insects. Specially, there is a 2008 bp-inserted segment between ND2 and tRNA-Trp from 1180 to 3187, which cannot be aligned to any known gene of mitogenomes. To estimate the taxonomic status of Bruchinae, total 17 species from eight subfamilies of Chrysomelidae were selected as ingroups and three species of Lamiinae as outgroups for phylogenetic analysis based on mitogenome. The results showed that three major lineages were formed, including a basal 'Eumolpine' clade (Cassidinae, Eumolpinae, Cryptocephalinae, Clytrinae), ''Criocerine' clade (Criocerinae, Bruchinae) and 'Chrysomeline' clade (Chrysomelinae, Galerucinae s. l.). Bruchinae showed more closed relationship with Criocerinae than other subfamilies. More thorough taxon sampling will be needed to well understand the relationship in Chrysomelidae.
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Affiliation(s)
- Li-Jie Zhang
- Inspection and Quarantine Technical Center, Beijing Inspection and Quarantine Testing Bureau, Beijing, China
| | - Ling Wu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Chun-Yan Wei
- Jilin Entry-Exit Inspection and Quarantine Bureau, Changchun, China
| | - Xing-Liang Liu
- Inspection and Quarantine Technical Center, Beijing Inspection and Quarantine Testing Bureau, Beijing, China
| | - Huai-Jun Xue
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xing-Ke Yang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Rui-E Nie
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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36
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Bista I, Carvalho GR, Tang M, Walsh K, Zhou X, Hajibabaei M, Shokralla S, Seymour M, Bradley D, Liu S, Christmas M, Creer S. Performance of amplicon and shotgun sequencing for accurate biomass estimation in invertebrate community samples. Mol Ecol Resour 2018; 18:1020-1034. [PMID: 29667329 DOI: 10.1111/1755-0998.12888] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Revised: 03/11/2018] [Accepted: 03/29/2018] [Indexed: 01/10/2023]
Abstract
New applications of DNA and RNA sequencing are expanding the field of biodiversity discovery and ecological monitoring, yet questions remain regarding precision and efficiency. Due to primer bias, the ability of metabarcoding to accurately depict biomass of different taxa from bulk communities remains unclear, while PCR-free whole mitochondrial genome (mitogenome) sequencing may provide a more reliable alternative. Here, we used a set of documented mock communities comprising 13 species of freshwater macroinvertebrates of estimated individual biomass, to compare the detection efficiency of COI metabarcoding (three different amplicons) and shotgun mitogenome sequencing. Additionally, we used individual COI barcoding and de novo mitochondrial genome sequencing, to provide reference sequences for OTU assignment and metagenome mapping (mitogenome skimming), respectively. We found that, even though both methods occasionally failed to recover very low abundance species, metabarcoding was less consistent, by failing to recover some species with higher abundances, probably due to primer bias. Shotgun sequencing results provided highly significant correlations between read number and biomass in all but one species. Conversely, the read-biomass relationships obtained from metabarcoding varied across amplicons. Specifically, we found significant relationships for eight of 13 (amplicons B1FR-450 bp, FF130R-130 bp) or four of 13 (amplicon FFFR, 658 bp) species. Combining the results of all three COI amplicons (multiamplicon approach) improved the read-biomass correlations for some of the species. Overall, mitogenomic sequencing yielded more informative predictions of biomass content from bulk macroinvertebrate communities than metabarcoding. However, for large-scale ecological studies, metabarcoding currently remains the most commonly used approach for diversity assessment.
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Affiliation(s)
- Iliana Bista
- School of Biological Sciences, Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, UK
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Gary R Carvalho
- School of Biological Sciences, Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, UK
| | - Min Tang
- Department of Entomology, China Agricultural University, Beijing, China
| | - Kerry Walsh
- Environment Agency, Horizon House, Bristol, UK
| | - Xin Zhou
- Department of Entomology, China Agricultural University, Beijing, China
| | - Mehrdad Hajibabaei
- Department of Integrative Biology & Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Shadi Shokralla
- Department of Integrative Biology & Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Mathew Seymour
- School of Biological Sciences, Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, UK
| | | | - Shanlin Liu
- Natural History Museum of Denmark, Copenhagen, Denmark
- BGI-Shenzhen, Shenzhen, China
| | | | - Simon Creer
- School of Biological Sciences, Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, UK
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37
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Geisen S, Snoek LB, ten Hooven FC, Duyts H, Kostenko O, Bloem J, Martens H, Quist CW, Helder JA, der Putten WH. Integrating quantitative morphological and qualitative molecular methods to analyse soil nematode community responses to plant range expansion. Methods Ecol Evol 2018. [DOI: 10.1111/2041-210x.12999] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Stefan Geisen
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW) Wageningen The Netherlands
- Laboratory of NematologyWageningen University Wageningen The Netherlands
| | - L. Basten Snoek
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW) Wageningen The Netherlands
- Laboratory of NematologyWageningen University Wageningen The Netherlands
- Theoretical Biology and BioinformaticsUtrecht University Utrecht The Netherlands
| | - Freddy C. ten Hooven
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW) Wageningen The Netherlands
| | - Henk Duyts
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW) Wageningen The Netherlands
| | - Olga Kostenko
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW) Wageningen The Netherlands
| | - Janneke Bloem
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW) Wageningen The Netherlands
| | - Henk Martens
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW) Wageningen The Netherlands
| | - Casper W. Quist
- Laboratory of NematologyWageningen University Wageningen The Netherlands
| | - Johannes A. Helder
- Laboratory of NematologyWageningen University Wageningen The Netherlands
| | - Wim H. der Putten
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW) Wageningen The Netherlands
- Laboratory of NematologyWageningen University Wageningen The Netherlands
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38
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Wang WY, Srivathsan A, Foo M, Yamane SK, Meier R. Sorting specimen-rich invertebrate samples with cost-effective NGS barcodes: Validating a reverse workflow for specimen processing. Mol Ecol Resour 2018; 18:490-501. [PMID: 29314756 DOI: 10.1111/1755-0998.12751] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 12/20/2017] [Accepted: 12/20/2017] [Indexed: 11/28/2022]
Abstract
Biologists frequently sort specimen-rich samples to species. This process is daunting when based on morphology, and disadvantageous if performed using molecular methods that destroy vouchers (e.g., metabarcoding). An alternative is barcoding every specimen in a bulk sample and then presorting the specimens using DNA barcodes, thus mitigating downstream morphological work on presorted units. Such a "reverse workflow" is too expensive using Sanger sequencing, but we here demonstrate that is feasible with an next-generation sequencing (NGS) barcoding pipeline that allows for cost-effective high-throughput generation of short specimen-specific barcodes (313 bp of COI; laboratory cost <$0.50 per specimen) through next-generation sequencing of tagged amplicons. We applied our approach to a large sample of tropical ants, obtaining barcodes for 3,290 of 4,032 specimens (82%). NGS barcodes and their corresponding specimens were then sorted into molecular operational taxonomic units (mOTUs) based on objective clustering and Automated Barcode Gap Discovery (ABGD). High diversity of 88-90 mOTUs (4% clustering) was found and morphologically validated based on preserved vouchers. The mOTUs were overwhelmingly in agreement with morphospecies (match ratio 0.95 at 4% clustering). Because of lack of coverage in existing barcode databases, only 18 could be accurately identified to named species, but our study yielded new barcodes for 48 species, including 28 that are potentially new to science. With its low cost and technical simplicity, the NGS barcoding pipeline can be implemented by a large range of laboratories. It accelerates invertebrate species discovery, facilitates downstream taxonomic work, helps with building comprehensive barcode databases and yields precise abundance information.
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Affiliation(s)
- Wendy Y Wang
- Lee Kong Chian Natural History Museum, Faculty of Science, National University of Singapore, Singapore
| | - Amrita Srivathsan
- Evolutionary Biology Laboratory, Department of Biological Sciences, National University of Singapore, Singapore
| | - Maosheng Foo
- Lee Kong Chian Natural History Museum, Faculty of Science, National University of Singapore, Singapore
| | | | - Rudolf Meier
- Lee Kong Chian Natural History Museum, Faculty of Science, National University of Singapore, Singapore.,Evolutionary Biology Laboratory, Department of Biological Sciences, National University of Singapore, Singapore
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39
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Chesters D. Construction of a Species-Level Tree of Life for the Insects and Utility in Taxonomic Profiling. Syst Biol 2018; 66:426-439. [PMID: 27798407 DOI: 10.1093/sysbio/syw099] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Accepted: 10/18/2016] [Indexed: 12/31/2022] Open
Abstract
Although comprehensive phylogenies have proven an invaluable tool in ecology and evolution, their construction is made increasingly challenging both by the scale and structure of publically available sequences. The distinct partition between gene-rich (genomic) and species-rich (DNA barcode) data is a feature of data that has been largely overlooked, yet presents a key obstacle to scaling supermatrix analysis. I present a phyloinformatics framework for draft construction of a species-level phylogeny of insects (Class Insecta). Matrix-building requires separately optimized pipelines for nuclear transcriptomic, mitochondrial genomic, and species-rich markers, whereas tree-building requires hierarchical inference in order to capture species-breadth while retaining deep-level resolution. The phylogeny of insects contains 49,358 species, 13,865 genera, 760 families. Deep-level splits largely reflected previous findings for sections of the tree that are data rich or unambiguous, such as inter-ordinal Endopterygota and Dictyoptera, the recently evolved and relatively homogeneous Lepidoptera, Hymenoptera, Brachycera (Diptera), and Cucujiformia (Coleoptera). However, analysis of bias, matrix construction and gene-tree variation suggests confidence in some relationships (such as in Polyneoptera) is less than has been indicated by the matrix bootstrap method. To assess the utility of the insect tree as a tool in query profiling several tree-based taxonomic assignment methods are compared. Using test data sets with existing taxonomic annotations, a tendency is observed for greater accuracy of species-level assignments where using a fixed comprehensive tree of life in contrast to methods generating smaller de novo reference trees. Described herein is a solution to the discrepancy in the way data are fit into supermatrices. The resulting tree facilitates wider studies of insect diversification and application of advanced descriptions of diversity in community studies, among other presumed applications. [Data integration; data mining; insects; phylogenomics; phyloinformatics; tree of life.].
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Affiliation(s)
- Douglas Chesters
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
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40
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Krehenwinkel H, Fong M, Kennedy S, Huang EG, Noriyuki S, Cayetano L, Gillespie R. The effect of DNA degradation bias in passive sampling devices on metabarcoding studies of arthropod communities and their associated microbiota. PLoS One 2018; 13:e0189188. [PMID: 29304124 PMCID: PMC5755739 DOI: 10.1371/journal.pone.0189188] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Accepted: 11/21/2017] [Indexed: 11/18/2022] Open
Abstract
PCR amplification bias is a well-known problem in metagenomic analysis of arthropod communities. In contrast, variation of DNA degradation rates is a largely neglected source of bias. Differential degradation of DNA molecules could cause underrepresentation of taxa in a community sequencing sample. Arthropods are often collected by passive sampling devices, like malaise traps. Specimens in such a trap are exposed to varying periods of suboptimal storage and possibly different rates of DNA degradation. Degradation bias could thus be a significant issue, skewing diversity estimates. Here, we estimate the effect of differential DNA degradation on the recovery of community diversity of Hawaiian arthropods and their associated microbiota. We use a simple DNA size selection protocol to test for degradation bias in mock communities, as well as passively collected samples from actual Malaise traps. We compare the effect of DNA degradation to that of varying PCR conditions, including primer choice, annealing temperature and cycle number. Our results show that DNA degradation does indeed bias community analyses. However, the effect of this bias is of minor importance compared to that induced by changes in PCR conditions. Analyses of the macro and microbiome from passively collected arthropod samples are thus well worth pursuing.
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Affiliation(s)
- Henrik Krehenwinkel
- Department of Environmental Sciences, Policy and Management, University of California, Mulford Hall, Berkeley, California, United States of America
- Center for Comparative Genomics, California Academy of Sciences, San Francisco, California, United States of America
| | - Marisa Fong
- Department of Environmental Sciences, Policy and Management, University of California, Mulford Hall, Berkeley, California, United States of America
| | - Susan Kennedy
- Department of Environmental Sciences, Policy and Management, University of California, Mulford Hall, Berkeley, California, United States of America
| | - Edward Greg Huang
- Department of Environmental Sciences, Policy and Management, University of California, Mulford Hall, Berkeley, California, United States of America
| | - Suzuki Noriyuki
- Department of Environmental Sciences, Policy and Management, University of California, Mulford Hall, Berkeley, California, United States of America
- Center for Geo-Environmental Science, Rissho University, Saitama, Japan
| | - Luis Cayetano
- Department of Environmental Sciences, Policy and Management, University of California, Mulford Hall, Berkeley, California, United States of America
| | - Rosemary Gillespie
- Department of Environmental Sciences, Policy and Management, University of California, Mulford Hall, Berkeley, California, United States of America
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41
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Macher J, Zizka VMA, Weigand AM, Leese F. A simple centrifugation protocol for metagenomic studies increases mitochondrial
DNA
yield by two orders of magnitude. Methods Ecol Evol 2017. [DOI: 10.1111/2041-210x.12937] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jan‐Niklas Macher
- Aquatic Ecosystem ResearchFaculty of BiologyUniversity of Duisburg‐Essen Essen Germany
- Centre for Water and Environmental Research (ZWU)University of Duisburg‐Essen Essen Germany
| | - Vera Marie Alida Zizka
- Aquatic Ecosystem ResearchFaculty of BiologyUniversity of Duisburg‐Essen Essen Germany
- Centre for Water and Environmental Research (ZWU)University of Duisburg‐Essen Essen Germany
| | - Alexander Martin Weigand
- Aquatic Ecosystem ResearchFaculty of BiologyUniversity of Duisburg‐Essen Essen Germany
- Centre for Water and Environmental Research (ZWU)University of Duisburg‐Essen Essen Germany
| | - Florian Leese
- Aquatic Ecosystem ResearchFaculty of BiologyUniversity of Duisburg‐Essen Essen Germany
- Centre for Water and Environmental Research (ZWU)University of Duisburg‐Essen Essen Germany
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42
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Krehenwinkel H, Wolf M, Lim JY, Rominger AJ, Simison WB, Gillespie RG. Estimating and mitigating amplification bias in qualitative and quantitative arthropod metabarcoding. Sci Rep 2017; 7:17668. [PMID: 29247210 PMCID: PMC5732254 DOI: 10.1038/s41598-017-17333-x] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 11/16/2017] [Indexed: 11/09/2022] Open
Abstract
Amplicon based metabarcoding promises rapid and cost-efficient analyses of species composition. However, it is disputed whether abundance estimates can be derived from metabarcoding due to taxon specific PCR amplification biases. PCR-free approaches have been suggested to mitigate this problem, but come with considerable increases in workload and cost. Here, we analyze multilocus datasets of diverse arthropod communities, to evaluate whether amplification bias can be countered by (1) targeting loci with highly degenerate primers or conserved priming sites, (2) increasing PCR template concentration, (3) reducing PCR cycle number or (4) avoiding locus specific amplification by directly sequencing genomic DNA. Amplification bias is reduced considerably by degenerate primers or targeting amplicons with conserved priming sites. Surprisingly, a reduction of PCR cycles did not have a strong effect on amplification bias. The association of taxon abundance and read count was actually less predictable with fewer cycles. Even a complete exclusion of locus specific amplification did not exclude bias. Copy number variation of the target loci may be another explanation for read abundance differences between taxa, which would affect amplicon based and PCR free methods alike. As read abundance biases are taxon specific and predictable, the application of correction factors allows abundance estimates.
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Affiliation(s)
- Henrik Krehenwinkel
- Department of Environmental Sciences, Policy and Management University of California Berkeley Mulford Hall, Berkeley, California, USA.
- Center for Comparative Genomics California Academy of Sciences Music Concourse Drive, San Francisco, California, USA.
| | - Madeline Wolf
- Department of Environmental Sciences, Policy and Management University of California Berkeley Mulford Hall, Berkeley, California, USA
| | - Jun Ying Lim
- Department of Environmental Sciences, Policy and Management University of California Berkeley Mulford Hall, Berkeley, California, USA
| | - Andrew J Rominger
- Department of Environmental Sciences, Policy and Management University of California Berkeley Mulford Hall, Berkeley, California, USA
| | - Warren B Simison
- Center for Comparative Genomics California Academy of Sciences Music Concourse Drive, San Francisco, California, USA
| | - Rosemary G Gillespie
- Department of Environmental Sciences, Policy and Management University of California Berkeley Mulford Hall, Berkeley, California, USA
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43
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Song N, Yin X, Zhao X, Chen J, Yin J. Reconstruction of mitogenomes by NGS and phylogenetic implications for leaf beetles. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:1041-1050. [DOI: 10.1080/24701394.2017.1404044] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Nan Song
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Xinming Yin
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
- Xinyang Agriculture and Forestry University, Xinyang, China
| | - Xincheng Zhao
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Junhua Chen
- Xinyang Agriculture and Forestry University, Xinyang, China
| | - Jian Yin
- Xinyang Agriculture and Forestry University, Xinyang, China
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44
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Doña J, Sweet AD, Johnson KP, Serrano D, Mironov S, Jovani R. Cophylogenetic analyses reveal extensive host-shift speciation in a highly specialized and host-specific symbiont system. Mol Phylogenet Evol 2017; 115:190-196. [DOI: 10.1016/j.ympev.2017.08.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 08/10/2017] [Accepted: 08/11/2017] [Indexed: 01/21/2023]
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45
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Choo LQ, Crampton-Platt A, Vogler AP. Shotgun mitogenomics across body size classes in a local assemblage of tropical Diptera: Phylogeny, species diversity and mitochondrial abundance spectrum. Mol Ecol 2017; 26:5086-5098. [PMID: 28742928 DOI: 10.1111/mec.14258] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Accepted: 07/10/2017] [Indexed: 11/29/2022]
Abstract
Mitochondrial genomes can be assembled readily from shotgun-sequenced DNA mixtures of mass-trapped arthropods ("mitochondrial metagenomics"), speeding up the taxonomic characterization. Bulk sequencing was conducted on some 800 individuals of Diptera obtained by canopy fogging of a single tree in Borneo dominated by small (<1.5 mm) individuals. Specimens were split into five body size classes for DNA extraction, to equalize read numbers across specimens and to study how body size, a key ecological trait, interacts with species and phylogenetic diversity. Genome assembly produced 304 orthologous mitochondrial contigs presumed to each represent a different species. The small-bodied fraction was the by far most species-rich (187 contigs). Identification of contigs was through phylogenetic analysis together with 56 reference mitogenomes, which placed most of the Bornean community into seven clades of small-bodied species, indicating phylogenetic conservation of body size. Mapping of shotgun reads against the mitogenomes showed wide ranges of read abundances within each size class. Ranked read abundance plots were largely log-linear, indicating a uniformly filled abundance spectrum, especially for small-bodied species. Small-bodied species differed greatly from other size classes in neutral metacommunity parameters, exhibiting greater levels of immigration, besides greater total community size. We suggest that the established uses of mitochondrial metagenomics for analysis of species and phylogenetic diversity can be extended to parameterize recent theories of community ecology and biodiversity, and by focusing on the number mitochondria, rather than individuals, a new theoretical framework for analysis of mitochondrial abundance spectra can be developed that incorporates metabolic activity approximated by the count of mitochondria.
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Affiliation(s)
- Le Qin Choo
- Department of Life Sciences, Natural History Museum, London, UK.,Department of Life Sciences, Imperial College London, Ascot, UK
| | - Alex Crampton-Platt
- Department of Life Sciences, Natural History Museum, London, UK.,Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London, UK.,Department of Life Sciences, Imperial College London, Ascot, UK
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46
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Elbrecht V, Peinert B, Leese F. Sorting things out: Assessing effects of unequal specimen biomass on DNA metabarcoding. Ecol Evol 2017; 7:6918-6926. [PMID: 28904771 PMCID: PMC5587478 DOI: 10.1002/ece3.3192] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Revised: 05/29/2017] [Accepted: 05/31/2017] [Indexed: 12/05/2022] Open
Abstract
Environmental bulk samples often contain many different taxa that vary several orders of magnitude in biomass. This can be problematic in DNA metabarcoding and metagenomic high‐throughput sequencing approaches, as large specimens contribute disproportionately high amounts of DNA template. Thus, a few specimens of high biomass will dominate the dataset, potentially leading to smaller specimens remaining undetected. Sorting of samples by specimen size (as a proxy for biomass) and balancing the amounts of tissue used per size fraction should improve detection rates, but this approach has not been systematically tested. Here, we explored the effects of size sorting on taxa detection using two freshwater macroinvertebrate bulk samples, collected from a low‐mountain stream in Germany. Specimens were morphologically identified and sorted into three size classes (body size < 2.5 × 5, 5 × 10, and up to 10 × 20 mm). Tissue powder from each size category was extracted individually and pooled based on tissue weight to simulate samples that were not sorted by biomass (“Unsorted”). Additionally, size fractions were pooled so that each specimen contributed approximately equal amounts of biomass (“Sorted”). Mock samples were amplified using four different DNA metabarcoding primer sets targeting the Cytochrome c oxidase I (COI) gene. Sorting taxa by size and pooling them proportionately according to their abundance lead to a more equal amplification of taxa compared to the processing of complete samples without sorting. The sorted samples recovered 30% more taxa than the unsorted samples at the same sequencing depth. Our results imply that sequencing depth can be decreased approximately fivefold when sorting the samples into three size classes and pooling by specimen abundance. Even coarse size sorting can substantially improve taxa detection using DNA metabarcoding. While high‐throughput sequencing will become more accessible and cheaper within the next years, sorting bulk samples by specimen biomass or size is a simple yet efficient method to reduce current sequencing costs.
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Affiliation(s)
- Vasco Elbrecht
- Aquatic Ecosystem Research Faculty of Biology University of Duisburg-Essen Essen Germany
| | - Bianca Peinert
- Aquatic Ecosystem Research Faculty of Biology University of Duisburg-Essen Essen Germany
| | - Florian Leese
- Aquatic Ecosystem Research Faculty of Biology University of Duisburg-Essen Essen Germany.,Centre for Water and Environmental Research (ZWU) Essen University of Duisburg-Essen Essen Germany
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47
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Guo Q, Xu J, Dai X, Liao C, Long C. Complete mitochondrial genome of a leaf-mining beetle, Rhadinosa nigrocyanea (Coleoptera: Chrysomelidae) with phylogenetic consideration. MITOCHONDRIAL DNA PART B-RESOURCES 2017; 2:446-448. [PMID: 33473857 PMCID: PMC7799965 DOI: 10.1080/23802359.2017.1357443] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
The complete circular mitochondrial genome (mitogenome) of Rhadinosa nigrocyanea was 17,965 bp in length, which contained 2 ribosomal RNA genes, 22 transfer RNAs, 13 protein-coding genes (PCGs) and 1 non-coding AT-rich region with the length of 3002 bp. All of the 22 tRNA genes displayed a typical clover-leaf structure, with the exception of tRNASer (TCT). 12 PCGs were initiated by ATN codons, except for ND1 started with TTG. Only six PCGs used the typical stop codon ‘TAA’ and ‘TGA’, while seven PCGs terminated with incomplete stop codons (TA or T). Phylogenetic analysis showed that R. nigrocyanea grouped with Cassidinae species, sister to Clytrinae + Cryptocephalinae.
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Affiliation(s)
- Qingyun Guo
- Leafminer Group, School of Life and Environmental Sciences, Gannan Normal University, Ganzhou, China
| | - Jiasheng Xu
- Leafminer Group, School of Life and Environmental Sciences, Gannan Normal University, Ganzhou, China
| | - Xiaohua Dai
- Leafminer Group, School of Life and Environmental Sciences, Gannan Normal University, Ganzhou, China.,National Navel-Orange Engineering Research Center, Ganzhou, China
| | - Chengqing Liao
- Leafminer Group, School of Life and Environmental Sciences, Gannan Normal University, Ganzhou, China
| | - Chengpeng Long
- Leafminer Group, School of Life and Environmental Sciences, Gannan Normal University, Ganzhou, China
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48
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Deiner K, Renshaw MA, Li Y, Olds BP, Lodge DM, Pfrender ME. Long‐range PCR allows sequencing of mitochondrial genomes from environmental DNA. Methods Ecol Evol 2017. [DOI: 10.1111/2041-210x.12836] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Kristy Deiner
- Department of Biological Sciences Environmental Change Initiative University of Notre Dame Notre Dame IN USA
| | - Mark A. Renshaw
- Department of Biological Sciences Environmental Change Initiative University of Notre Dame Notre Dame IN USA
| | - Yiyuan Li
- Department of Biological Sciences Environmental Change Initiative University of Notre Dame Notre Dame IN USA
| | - Brett P. Olds
- Department of Biological Sciences Environmental Change Initiative University of Notre Dame Notre Dame IN USA
| | - David M. Lodge
- Department of Biological Sciences Environmental Change Initiative University of Notre Dame Notre Dame IN USA
| | - Michael E. Pfrender
- Department of Biological Sciences Environmental Change Initiative University of Notre Dame Notre Dame IN USA
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49
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Nie RE, Breeschoten T, Timmermans MJTN, Nadein K, Xue HJ, Bai M, Huang Y, Yang XK, Vogler AP. The phylogeny of Galerucinae (Coleoptera: Chrysomelidae) and the performance of mitochondrial genomes in phylogenetic inference compared to nuclear rRNA genes. Cladistics 2017; 34:113-130. [DOI: 10.1111/cla.12196] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/20/2017] [Indexed: 11/29/2022] Open
Affiliation(s)
- Rui-E Nie
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
- Department of Life Sciences; Natural History Museum; London SW7 5BD UK
| | | | - Martijn J. T. N. Timmermans
- Department of Life Sciences; Natural History Museum; London SW7 5BD UK
- Department of Life Sciences; Silwood Park Campus; Imperial College London; Ascot SL5 7PY UK
| | - Konstantin Nadein
- Senckenberg German Entomological Institute; Müncheberg 15374 Germany
| | - Huai-Jun Xue
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Ming Bai
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Yuan Huang
- College of Life Sciences; Shaanxi Normal University; Xi'an 710062 China
| | - Xing-Ke Yang
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Alfried P. Vogler
- Department of Life Sciences; Natural History Museum; London SW7 5BD UK
- Department of Life Sciences; Silwood Park Campus; Imperial College London; Ascot SL5 7PY UK
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50
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Cicconardi F, Borges PAV, Strasberg D, Oromí P, López H, Pérez-Delgado AJ, Casquet J, Caujapé-Castells J, Fernández-Palacios JM, Thébaud C, Emerson BC. MtDNA metagenomics reveals large-scale invasion of belowground arthropod communities by introduced species. Mol Ecol 2017; 26:3104-3115. [PMID: 28139037 DOI: 10.1111/mec.14037] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 12/12/2016] [Accepted: 12/24/2016] [Indexed: 11/26/2022]
Abstract
Using a series of standardized sampling plots within forest ecosystems in remote oceanic islands, we reveal fundamental differences between the structuring of aboveground and belowground arthropod biodiversity that are likely due to large-scale species introductions by humans. Species of beetle and spider were sampled almost exclusively from single islands, while soil-dwelling Collembola exhibited more than tenfold higher species sharing among islands. Comparison of Collembola mitochondrial metagenomic data to a database of more than 80 000 Collembola barcode sequences revealed almost 30% of sampled island species are genetically identical, or near identical, to individuals sampled from often very distant geographic regions of the world. Patterns of mtDNA relatedness among Collembola implicate human-mediated species introductions, with minimum estimates for the proportion of introduced species on the sampled islands ranging from 45% to 88%. Our results call for more attention to soil mesofauna to understand the global extent and ecological consequences of species introductions.
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Affiliation(s)
- Francesco Cicconardi
- Institute of Ecology, University of Innsbruck, Technikerstrasse 25, a-6020, Innsbruck, Austria
| | - Paulo A V Borges
- CE3C - Centre for Ecology, Evolution and Environmental Changes/Azorean Biodiversity Group and Departamento de Ciências Agrárias e Ambiente, Universidade dos Açores, Rua Capitão João d'Ávila s/n, 9700-042, Angra do Heroísmo, Açores, Portugal
| | - Dominique Strasberg
- UMR PVBMT, Peuplements Végétaux et Bio-agresseurs en Milieu Tropical, Université de La Réunion, 15 avenue René Cassin, CS 93002, 97 744, Saint Denis Cedex 9, Reunion Island, France
| | - Pedro Oromí
- Departamento de Biología Animal y Edafología y Geología, Universidad de La Laguna, C/Astrofísico Francisco Sánchez, 38206, La Laguna, Tenerife, Canary Islands, Spain
| | - Heriberto López
- Island Ecology and Evolution Research Group, IPNA-CSIC, 38206, La Laguna, Tenerife, Canary Islands, Spain
| | - Antonio J Pérez-Delgado
- Island Ecology and Evolution Research Group, IPNA-CSIC, 38206, La Laguna, Tenerife, Canary Islands, Spain
| | - Juliane Casquet
- Laboratoire Evolution & Diversité Biologique, UMR 5174 CNRS-Université Paul Sabatier-ENFA, 31062, Toulouse Cedex 9, France
| | - Juli Caujapé-Castells
- Departamento de Biodiversidad Molecular y Banco de ADN, Jardín Botánico Canario 'Viera y Clavijo' - Unidad Asociada CSIC, Cabildo de Gran Canaria, Camino del Palmeral 15 de Tafira Alta, 35017, Las Palmas de Gran Canaria, Spain
| | - José María Fernández-Palacios
- Island Ecology and Biogeography Research Group, Instituto de Enfermedades Tropicales y Salud Pública de Canarias (IUETSPC), Universidad de La Laguna, Tenerife, Canary Islands, 38206, Spain
| | - Christophe Thébaud
- Laboratoire Evolution & Diversité Biologique, UMR 5174 CNRS-Université Paul Sabatier-ENFA, 31062, Toulouse Cedex 9, France
| | - Brent C Emerson
- Island Ecology and Evolution Research Group, IPNA-CSIC, 38206, La Laguna, Tenerife, Canary Islands, Spain.,School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
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