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Srisuka W, Takaoka H, Taai K, Maleewong W, Aupalee K, Saeung A. Morphological description and genetic analysis of a new black fly species (Diptera: Simuliidae) in the subgenus Asiosimulium from central Thailand. Parasit Vectors 2024; 17:379. [PMID: 39238034 DOI: 10.1186/s13071-024-06441-z] [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: 06/07/2024] [Accepted: 08/07/2024] [Indexed: 09/07/2024] Open
Abstract
BACKGROUND Black flies are among the most medically and veterinary important insects, as adult females of certain species are the sole vector of Onchocerca volvulus. Here, a new black fly species belonging to the subgenus Asiosimulium Takaoka & Choochote, 2005, is described and formally named as Simulium (Asiosimulium) kittipati sp. nov. METHODS Pupae and larvae of black flies were collected from available substrates in the stream from central Thailand. Pupae were individually separated in plastic tubes and maintained until adult flies emerged. The emerged adult flies associated with their pupal exuviae and cocoon as well as mature larvae preserved in 85% ethanol were used to describe the new species based on an integrated approach of morphological examination and molecular analysis of the COI gene. RESULTS The new species is characterized in the female by the medium-long sensory vesicle with a medium-sized opening apically, scutum with three faint longitudinal vittae, and the ellipsoidal spermatheca; in the male by the number of upper-eye (large) facets in 20 vertical columns and 21 horizontal rows, hind basitarsus slender, nearly parallel-sided, and median sclerite much wider and upturned apically; in the pupa by the head and thoracic integument densely covered with tiny tubercles, and the pupal gill of arborescent type with 28-30 filaments; and in the larva by the postgenal cleft deep, nearly reaching the posterior margin of the hypostoma, and dark pigmented sheath of the subesophageal ganglion. The DNA barcode successfully differentiated the new species from its congeners with an interspecific genetic divergence of 1.74-18.72%, confirming the morphological identification that the species is a new member of the subgenus Asiosimulium. Phylogenetic analyses also indicated that the new species is genetically closely related to Simulium phurueaense Tangkawanit, Wongpakam & Pramual, 2018, further supporting its morphological classification. CONCLUSIONS This is the ninth species assigned to the subgenus Asiosimulium within the genus Simulium Latreille, 1802. Taxonomic notes and identification keys are given to distinguish this new species from the eight known species members in its same subgenus. Additionally, a distribution map of all species members in this subgenus occurring in Thailand and other countries is provided.
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Affiliation(s)
- Wichai Srisuka
- Entomology Section, Queen Sirikit Botanic Garden, Chiang Mai, 50180, Thailand
| | - Hiroyuki Takaoka
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Higher Institution Centre of Excellence (HICoE), Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Kritsana Taai
- Faculty of Veterinary Medicine, Western University, Kanchanaburi, 71170, Thailand
| | - Wanchai Maleewong
- Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Kittipat Aupalee
- Parasitology and Entomology Research Cluster (PERC), Department of Parasitology, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Atiporn Saeung
- Parasitology and Entomology Research Cluster (PERC), Department of Parasitology, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand.
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Miller ML, Rota C, Welsh A. Transforming gastrointestinal helminth parasite identification in vertebrate hosts with metabarcoding: a systematic review. Parasit Vectors 2024; 17:311. [PMID: 39030625 PMCID: PMC11265005 DOI: 10.1186/s13071-024-06388-1] [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: 02/24/2024] [Accepted: 07/03/2024] [Indexed: 07/21/2024] Open
Abstract
BACKGROUND Gastrointestinal helminths are a very widespread group of intestinal parasites that can cause major health issues in their hosts, including severe illness or death. Traditional methods of helminth parasite identification using microscopy are time-consuming and poor in terms of taxonomic resolution, and require skilled observers. DNA metabarcoding has emerged as a powerful alternative for assessing community composition in a variety of sample types over the last few decades. While metabarcoding approaches have been reviewed for use in other research areas, the use of metabarcoding for parasites has only recently become widespread. As such, there is a need to synthesize parasite metabarcoding methodology and highlight the considerations to be taken into account when developing a protocol. METHODS We reviewed published literature that utilized DNA metabarcoding to identify gastrointestinal helminth parasites in vertebrate hosts. We extracted information from 62 peer-reviewed papers published between 2014 and 2023 and created a stepwise guide to the metabarcoding process. RESULTS We found that studies in our review varied in technique and methodology, such as the sample type utilized, genetic marker regions targeted and bioinformatic databases used. The main limitations of metabarcoding are that parasite abundance data may not be reliably attained from sequence read numbers, metabarcoding data may not be representative of the species present in the host and the cost and bioinformatic expertise required to utilize this method may be prohibitive to some groups. CONCLUSIONS Overall, using metabarcoding to assess gastrointestinal parasite communities is preferable to traditional methods, yielding higher taxonomic resolution, higher throughput and increased versatility due to its utility in any geographical location, with a variety of sample types, and with virtually any vertebrate host species. Additionally, metabarcoding has the potential for exciting new discoveries regarding host and parasite evolution.
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Affiliation(s)
- Madison L Miller
- Division of Forestry and Natural Resources, West Virginia University, Morgantown, WV, USA.
| | - Christopher Rota
- Division of Forestry and Natural Resources, West Virginia University, Morgantown, WV, USA
| | - Amy Welsh
- Division of Forestry and Natural Resources, West Virginia University, Morgantown, WV, USA
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Golden CD, Hartmann AC, Gibbons E, Todinanahary G, Troell MF, Ampalaza G, Behivoke F, David JM, Durand JD, Falinirina AM, Frånberg C, Declèrque F, Hook K, Kelahan H, Kirby M, Koenen K, Lamy T, Lavitra T, Moridy F, Léopold M, Little MJ, Mahefa JC, Mbony J, Nicholas K, Nomenisoa ALD, Ponton D, Rabarijaona RR, Rabearison M, Rabemanantsoa SA, Ralijaona M, Ranaivomanana HS, Randriamady HJ, Randrianandrasana J, Randriatsara HO, Randriatsara RM, Rasoanirina M, Ratsizafy MR, Razafiely KF, Razafindrasoa N, Romario, Solofoarimanana MY, Stroud RE, Tsiresimiary M, Volanandiana AJ, Volasoa NV, Vowell B, Zamborain-Mason J. HIARA study protocol: impacts of artificial coral reef development on fisheries, human livelihoods and health in southwestern Madagascar. Front Public Health 2024; 12:1366110. [PMID: 39076417 PMCID: PMC11284108 DOI: 10.3389/fpubh.2024.1366110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 06/24/2024] [Indexed: 07/31/2024] Open
Abstract
The Health Impacts of Artificial Reef Advancement (HIARA; in the Malagasy language, "together") study cohort was set up in December 2022 to assess the economic and nutritional importance of seafood for the coastal Malagasy population living along the Bay of Ranobe in southwestern Madagascar. Over the course of the research, which will continue until at least 2026, the primary question we seek to answer is whether the creation of artificial coral reefs can rehabilitate fish biomass, increase fish catch, and positively influence fisher livelihoods, community nutrition, and mental health. Through prospective, longitudinal monitoring of the ecological and social systems of Bay of Ranobe, we aim to understand the influence of seasonal and long-term shifts in marine ecological resources and their benefits to human livelihoods and health. Fourteen communities (12 coastal and two inland) were enrolled into the study including 450 households across both the coastal (n = 360 households) and inland (n = 90 households) ecosystems. In the ecological component, we quantify the extent and health of coral reef ecosystems and collect data on the diversity and abundance of fisheries resources. In the social component, we collect data on the diets, resource acquisition strategies, fisheries and agricultural practices, and other social, demographic and economic indicators, repeated every 3 months. At these visits, clinical measures are collected including anthropometric measures, blood pressure, and mental health diagnostic screening. By analyzing changes in fish catch and consumption arising from varying distances to artificial reef construction and associated impacts on fish biomass, our cohort study could provide valuable insights into the public health impacts of artificial coral reef construction on local populations. Specifically, we aim to assess the impact of changes in fish catch (caused by artificial reefs) on various health outcomes, such as stunting, underweight, wasting, nutrient intake, hypertension, anxiety, and depression.
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Affiliation(s)
- Christopher D. Golden
- Department of Nutrition, School of Public Health, Harvard University, Boston, MA, United States
- Department of Environmental Health, School of Public Health, Harvard University, Boston, MA, United States
- Madagascar Health and Environmental Research (MAHERY), Maroantsetra, Madagascar
| | - Aaron C. Hartmann
- Department of Organismic and Evolutionary Biology, Faculty of Arts and Sciences, Harvard University, Cambridge, MA, United States
| | | | - Gildas Todinanahary
- Institute of Fisheries and Marine Sciences, University of Toliara, Toliara, Madagascar
| | - Max F. Troell
- Beijer Institute of Ecological Economics, Stockholm, Sweden
- Stockholm Resilience Centre, Stockholm University, Stockholm, Sweden
| | - Gaelle Ampalaza
- Institute of Fisheries and Marine Sciences, University of Toliara, Toliara, Madagascar
| | - Faustinato Behivoke
- Institute of Fisheries and Marine Sciences, University of Toliara, Toliara, Madagascar
| | - Jean Marie David
- Institute of Fisheries and Marine Sciences, University of Toliara, Toliara, Madagascar
| | - Jean-Dominique Durand
- UMR9190 Centre Pour la Biodiversité Marine, l’exploitation et la Conservation (MARBEC), Sète, France
| | | | - Christopher Frånberg
- Department of Ecology, Environment and Plant Sciences, Faculty of Science, Stockholm University, Stockholm, Sweden
| | - Frédéric Declèrque
- Institute of Fisheries and Marine Sciences, University of Toliara, Toliara, Madagascar
| | - Kimberly Hook
- Department of Epidemiology, School of Public Health, Harvard University, Boston, MA, United States
| | - Heather Kelahan
- Department of Nutrition, School of Public Health, Harvard University, Boston, MA, United States
| | - Megumi Kirby
- Department of Organismic and Evolutionary Biology, Faculty of Arts and Sciences, Harvard University, Cambridge, MA, United States
| | - Karestan Koenen
- Department of Nutrition, School of Public Health, Harvard University, Boston, MA, United States
| | - Thomas Lamy
- UMR9190 Centre Pour la Biodiversité Marine, l’exploitation et la Conservation (MARBEC), Sète, France
| | - Thierry Lavitra
- Institute of Fisheries and Marine Sciences, University of Toliara, Toliara, Madagascar
| | - Franciana Moridy
- Institute of Fisheries and Marine Sciences, University of Toliara, Toliara, Madagascar
| | | | - Mark J. Little
- Department of Organismic and Evolutionary Biology, Faculty of Arts and Sciences, Harvard University, Cambridge, MA, United States
| | - Jean C. Mahefa
- Institute of Fisheries and Marine Sciences, University of Toliara, Toliara, Madagascar
| | - Jovial Mbony
- Institute of Fisheries and Marine Sciences, University of Toliara, Toliara, Madagascar
| | - Khristopher Nicholas
- Department of Nutrition, School of Public Health, Harvard University, Boston, MA, United States
| | - Aina Le Don Nomenisoa
- Institute of Fisheries and Marine Sciences, University of Toliara, Toliara, Madagascar
| | | | - Roddy R. Rabarijaona
- Institute of Fisheries and Marine Sciences, University of Toliara, Toliara, Madagascar
- National School of Computer Science, University of Fianarantsoa, Fianarantsoa, Madagascar
| | - Mihary Rabearison
- Institute of Fisheries and Marine Sciences, University of Toliara, Toliara, Madagascar
| | | | - Mbolahasina Ralijaona
- Institute of Fisheries and Marine Sciences, University of Toliara, Toliara, Madagascar
| | | | - Hervet J. Randriamady
- Department of Nutrition, School of Public Health, Harvard University, Boston, MA, United States
| | | | - Hanitra O. Randriatsara
- Service de la Santé Mentale, Direction de Lutte contre les Maladies Non Transmissibles, Ministère de la Santé Publique, Antananarivo, Madagascar
| | - Roddy M. Randriatsara
- Institute of Fisheries and Marine Sciences, University of Toliara, Toliara, Madagascar
| | - Madeleine Rasoanirina
- Institute of Fisheries and Marine Sciences, University of Toliara, Toliara, Madagascar
| | - Michel R. Ratsizafy
- Institute of Fisheries and Marine Sciences, University of Toliara, Toliara, Madagascar
| | - Kinasa F. Razafiely
- Institute of Fisheries and Marine Sciences, University of Toliara, Toliara, Madagascar
| | - Nivohanitra Razafindrasoa
- Centre Hospitalier Universitaire de Soins et de Santé PubliqueAnalakely (CHUSSPA), Antananarivo, Madagascar
| | - Romario
- Institute of Fisheries and Marine Sciences, University of Toliara, Toliara, Madagascar
| | | | - Rocky E. Stroud
- Department of Epidemiology, School of Public Health, Harvard University, Boston, MA, United States
| | | | | | | | | | - Jessica Zamborain-Mason
- Department of Nutrition, School of Public Health, Harvard University, Boston, MA, United States
- Department of Environmental Health, School of Public Health, Harvard University, Boston, MA, United States
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Rios-Willars E, Chirinos-Arias MC. Mfind: a tool for DNA barcode analysis in angiosperms and its relationship with microsatellites using a sliding window algorithm. PLANTA 2024; 259:134. [PMID: 38671234 DOI: 10.1007/s00425-024-04420-3] [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: 10/12/2023] [Accepted: 04/17/2024] [Indexed: 04/28/2024]
Abstract
MAIN CONCLUSION Mfind is a tool to analyze the impact of microsatellite presence on DNA barcode specificity. We found a significant correlation between barcode entropy and microsatellite count in angiosperm. Genetic barcodes and microsatellites are some of the identification methods in taxonomy and biodiversity research. It is important to establish a relationship between microsatellite quantification and genetic information in barcodes. In order to clarify the association between the genetic information in barcodes (expressed as Shannon's Measure of Information, SMI) and microsatellites count, a total of 330,809 DNA barcodes from the BOLD database (Barcode of Life Data System) were analyzed. A parallel sliding-window algorithm was developed to compute the Shannon entropy of the barcodes, and this was compared with the quantification of microsatellites like (AT)n, (AC)n, and (AG)n. The microsatellite search method utilized an algorithm developed in the Java programming language, which systematically examined the genetic barcodes from an angiosperm database. For this purpose, a computational tool named Mfind was developed, and its search methodology is detailed. This comprehensive study revealed a broad overview of microsatellites within barcodes, unveiling an inverse correlation between the sumz of microsatellites count and barcodes information. The utilization of the Mfind tool demonstrated that the presence of microsatellites impacts the barcode information when considering entropy as a metric. This effect might be attributed to the concise length of DNA barcodes and the repetitive nature of microsatellites, resulting in a direct influence on the entropy of the barcodes.
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Affiliation(s)
- Ernesto Rios-Willars
- Faculty of Systems, Autonomous University of Coahuila (UAdeC), 25350, Saltillo, Coahuila, México.
| | - Michelle C Chirinos-Arias
- Molecular Biology and Bioinformatics Area, Instituto de Genetica Barbara McClintock (IGBM), Lima, 15022, Peru
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Moraes Zenker M, Portella TP, Pessoa FAC, Bengtsson-Palme J, Galetti PM. Low coverage of species constrains the use of DNA barcoding to assess mosquito biodiversity. Sci Rep 2024; 14:7432. [PMID: 38548880 PMCID: PMC10978826 DOI: 10.1038/s41598-024-58071-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 03/25/2024] [Indexed: 04/01/2024] Open
Abstract
Mosquitoes (Culicidae) represent the main vector insects globally, and they also inhabit many of the terrestrial and aquatic habitats of the world. DNA barcoding and metabarcoding are now widely used in both research and routine practices involving mosquitoes. However, these methodologies rely on information available in databases consisting of barcode sequences representing taxonomically identified voucher specimens. In this study, we assess the availability of public data for mosquitoes in the main online databases, focusing specifically on the two most widely used DNA barcoding markers in Culicidae: COI and ITS2. In addition, we test hypotheses on possible factors affecting species coverage (i.e., the percentage of species covered in the online databases) for COI in different countries and the occurrence of the DNA barcode gap for COI. Our findings showed differences in the data publicly available in the repositories, with a taxonomic or species coverage of 28.4-30.11% for COI in BOLD + GenBank, and 12.32% for ITS2 in GenBank. Afrotropical, Australian and Oriental biogeographic regions had the lowest coverages, while Nearctic, Palearctic and Oceanian had the highest. The Neotropical region had an intermediate coverage. In general, countries with a higher diversity of mosquitoes and higher numbers of medically important species had lower coverage. Moreover, countries with a higher number of endemic species tended to have a higher coverage. Although our DNA barcode gap analyses suggested that the species boundaries need to be revised in half of the mosquito species available in the databases, additional data must be gathered to confirm these results and to allow explaining the occurrence of the DNA barcode gap. We hope this study can help guide regional species inventories of mosquitoes and the completion of a publicly available reference library of DNA barcodes for all mosquito species.
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Affiliation(s)
- Maurício Moraes Zenker
- Laboratório de Biodiversidade Molecular e Conservação, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, 13565-905, Brazil.
| | - Tatiana Pineda Portella
- Departamento de Ecologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Felipe Arley Costa Pessoa
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz Amazônia, Manaus, Brazil
| | - Johan Bengtsson-Palme
- Division of Systems and Synthetic Biology, Department of Life Sciences, SciLifeLab, Chalmers University of Technology, 412 96, Gothenburg, Sweden
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10A, 413 46, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), Gothenburg, Sweden
| | - Pedro Manoel Galetti
- Laboratório de Biodiversidade Molecular e Conservação, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, 13565-905, Brazil
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Jiang Y, Yang J, Folk RA, Zhao J, Liu J, He Z, Peng H, Yang S, Xiang C, Yu X. Species delimitation of tea plants (Camellia sect. Thea) based on super-barcodes. BMC PLANT BIOLOGY 2024; 24:181. [PMID: 38468197 PMCID: PMC10926627 DOI: 10.1186/s12870-024-04882-3] [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: 10/24/2023] [Accepted: 03/04/2024] [Indexed: 03/13/2024]
Abstract
BACKGROUND The era of high throughput sequencing offers new paths to identifying species boundaries that are complementary to traditional morphology-based delimitations. De novo species delimitation using traditional or DNA super-barcodes serve as efficient approaches to recognizing putative species (molecular operational taxonomic units, MOTUs). Tea plants (Camellia sect. Thea) form a group of morphologically similar species with significant economic value, providing the raw material for tea, which is the most popular nonalcoholic caffeine-containing beverage in the world. Taxonomic challenges have arisen from vague species boundaries in this group. RESULTS Based on the most comprehensive sampling of C. sect. Thea by far (165 individuals of 39 morphospecies), we applied three de novo species delimitation methods (ASAP, PTP, and mPTP) using plastome data to provide an independent evaluation of morphology-based species boundaries in tea plants. Comparing MOTU partitions with morphospecies, we particularly tested the congruence of MOTUs resulting from different methods. We recognized 28 consensus MOTUs within C. sect. Thea, while tentatively suggesting that 11 morphospecies be discarded. Ten of the 28 consensus MOTUs were uncovered as morphospecies complexes in need of further study integrating other evidence. Our results also showed a strong imbalance among the analyzed MOTUs in terms of the number of molecular diagnostic characters. CONCLUSION This study serves as a solid step forward for recognizing the underlying species boundaries of tea plants, providing a needed evidence-based framework for the utilization and conservation of this economically important plant group.
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Affiliation(s)
- Yinzi Jiang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Junbo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Ryan A Folk
- Department of Biological Sciences, Mississippi State University, Starkville, 39762, MS, USA
| | - Jianli Zhao
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Laboratory of Ecology and Evolutionary Biology, School of Ecology and Environmental Sciences, Yunnan University, Kunming, 650500, Yunnan, China
| | - Jie Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Zhengshan He
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Hua Peng
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Shixiong Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
| | - Chunlei Xiang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
| | - Xiangqin Yu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
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Phillips JD, Griswold CK, Young RG, Hubert N, Hanner RH. A Measure of the DNA Barcode Gap for Applied and Basic Research. Methods Mol Biol 2024; 2744:375-390. [PMID: 38683332 DOI: 10.1007/978-1-0716-3581-0_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
DNA barcoding has largely established itself as a mainstay for rapid molecular taxonomic identification in both academic and applied research. The use of DNA barcoding as a molecular identification method depends on a "DNA barcode gap"-the separation between the maximum within-species difference and the minimum between-species difference. Previous work indicates the presence of a gap hinges on sampling effort for focal taxa and their close relatives. Furthermore, both theory and empirical work indicate a gap may not occur for related pairs of biological species. Here, we present a novel evaluation approach in the form of an easily calculated set of nonparametric metrics to quantify the extent of proportional overlap in inter- and intraspecific distributions of pairwise differences among target species and their conspecifics. The metrics are based on a simple count of the number of overlapping records for a species falling within the bounds of maximum intraspecific distance and minimum interspecific distance. Our approach takes advantage of the asymmetric directionality inherent in pairwise genetic distance distributions, which has not been previously done in the DNA barcoding literature. We apply the metrics to the predatory diving beetle genus Agabus as a case study because this group poses significant identification challenges due to its morphological uniformity despite both relative sampling ease and well-established taxonomy. Results herein show that target species and their nearest neighbor species were found to be tightly clustered and therefore difficult to distinguish. Such findings demonstrate that DNA barcoding can fail to fully resolve species in certain cases. Moving forward, we suggest the implementation of the proposed metrics be integrated into a common framework to be reported in any study that uses DNA barcoding for identification. In so doing, the importance of the DNA barcode gap and its components for the success of DNA-based identification using DNA barcodes can be better appreciated.
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Affiliation(s)
- Jarrett D Phillips
- School of Computer Science, University of Guelph, Guelph, ON, Canada.
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada.
| | - Cortland K Griswold
- School of Computer Science, University of Guelph, Guelph, ON, Canada
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Robert G Young
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Nicolas Hubert
- UMR ISEM (IRD, UM, CNRS), Université de Montpellier, Montpellier, France
| | - Robert H Hanner
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
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Hubert N, Phillips JD, Hanner RH. Delimiting Species with Single-Locus DNA Sequences. Methods Mol Biol 2024; 2744:53-76. [PMID: 38683311 DOI: 10.1007/978-1-0716-3581-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
DNA sequences are increasingly used for large-scale biodiversity inventories. Because these genetic data avoid the time-consuming initial sorting of specimens based on their phenotypic attributes, they have been recently incorporated into taxonomic workflows for overlooked and diverse taxa. Major statistical developments have accompanied this new practice, and several models have been proposed to delimit species with single-locus DNA sequences. However, proposed approaches to date make different assumptions regarding taxon lineage history, leading to strong discordance whenever comparisons are made among methods. Distance-based methods, such as Automatic Barcode Gap Discovery (ABGD) and Assemble Species by Automatic Partitioning (ASAP), rely on the detection of a barcode gap (i.e., the lack of overlap in the distributions of intraspecific and interspecific genetic distances) and the associated threshold in genetic distances. Network-based methods, as exemplified by the REfined Single Linkage (RESL) algorithm for the generation of Barcode Index Numbers (BINs), use connectivity statistics to hierarchically cluster-related haplotypes into molecular operational taxonomic units (MOTUs) which serve as species proxies. Tree-based methods, including Poisson Tree Processes (PTP) and the General Mixed Yule Coalescent (GMYC), fit statistical models to phylogenetic trees by maximum likelihood or Bayesian frameworks.Multiple webservers and stand-alone versions of these methods are now available, complicating decision-making regarding the most appropriate approach to use for a given taxon of interest. For instance, tree-based methods require an initial phylogenetic reconstruction, and multiple options are now available for this purpose such as RAxML and BEAST. Across all examined species delimitation methods, judicious parameter setting is paramount, as different model parameterizations can lead to differing conclusions. The objective of this chapter is to guide users step-by-step through all the procedures involved for each of these methods, while aggregating all necessary information required to conduct these analyses. The "Materials" section details how to prepare and format input files, including options to align sequences and conduct tree reconstruction with Maximum Likelihood and Bayesian inference. The Methods section presents the procedure and options available to conduct species delimitation analyses, including distance-, network-, and tree-based models. Finally, limits and future developments are discussed in the Notes section. Most importantly, species delimitation methods discussed herein are categorized based on five indicators: reliability, availability, scalability, understandability, and usability, all of which are fundamental properties needed for any approach to gain unanimous adoption within the DNA barcoding community moving forward.
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Affiliation(s)
- Nicolas Hubert
- UMR ISEM (IRD, UM, CNRS), Université de Montpellier, Montpellier, France.
| | - Jarrett D Phillips
- School of Computer Science, University of Guelph, Guelph, ON, Canada
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Robert H Hanner
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
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Lukhtanov VA, Zakharov EV. Taxonomic Structure and Wing Pattern Evolution in the Parnassius mnemosyne Species Complex (Lepidoptera, Papilionidae). INSECTS 2023; 14:942. [PMID: 38132615 PMCID: PMC10744292 DOI: 10.3390/insects14120942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/06/2023] [Accepted: 12/10/2023] [Indexed: 12/23/2023]
Abstract
In our study, using the analysis of DNA barcodes and morphology (wing color, male genitalia, and female sphragis shape), we show that the group of species close to P. mnemosyne comprises the western and eastern phylogenetic lineages. The eastern lineage includes P. stubbendorfii, P. glacialis, and P. hoenei. The western lineage includes three morphologically similar species: P. mnemosyne (Western Eurasia), P. turatii (southwestern Europe), and P. nubilosusstat. nov. (Turkmenistan and NE Iran), as well as the morphologically differentiated P. ariadne (Altai). The latter species differs from the rest of the group in the presence of red spots on the wings. Parnassius mnemosyne s.s. is represented by four differentiated mitochondrial clusters that show clear association with specific geographic regions. We propose to interpret them as subspecies: P. mnemosyne mnemosyne (Central and Eastern Europe, N Caucasus, N Turkey), P. mnemosyne adolphi (the Middle East), P. mnemosyne falsa (Tian Shan), and P. mnemosyne gigantea (Gissar-Alai in Central Asia). We demonstrate that in P. ariadne, the red spots on the wing evolved as a reversion to the ancestral wing pattern. This reversion is observed in Altai, where the distribution areas of the western lineage, represented by P. ariadne, and the eastern lineage, represented by P. stubbendorfii, overlap. These two species hybridize in Altai, and we hypothesize that the color change in P. ariadne is the result of reinforcement of prezygotic isolation in the contact zone. The lectotype of Parnassius mnemosyne var. nubilosus Christoph, 1873, is designated.
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Affiliation(s)
- Vladimir A. Lukhtanov
- Department of Karyosystematics, Zoological Institute, Russian Academy of Sciences, Universitetskaya Nab. 1, 199034 Saint-Petersburg, Russia
| | - Evgeny V. Zakharov
- Centre for Biodiversity Genomics, Department of Integrative Biology, College of Biological Sciences, University of Guelph, Guelph, ON N1G 2W1, Canada;
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10
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Bemis KE, Girard MG, Santos MD, Carpenter KE, Deeds JR, Pitassy DE, Flores NAL, Hunter ES, Driskell AC, Macdonald KS, Weigt LA, Williams JT. Biodiversity of Philippine marine fishes: A DNA barcode reference library based on voucher specimens. Sci Data 2023; 10:411. [PMID: 37355644 PMCID: PMC10290705 DOI: 10.1038/s41597-023-02306-9] [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: 02/08/2023] [Accepted: 06/12/2023] [Indexed: 06/26/2023] Open
Abstract
Accurate identification of fishes is essential for understanding their biology and to ensure food safety for consumers. DNA barcoding is an important tool because it can verify identifications of both whole and processed fishes that have had key morphological characters removed (e.g., filets, fish meal); however, DNA reference libraries are incomplete, and public repositories for sequence data contain incorrectly identified sequences. During a nine-year sampling program in the Philippines, a global biodiversity hotspot for marine fishes, we developed a verified reference library of cytochrome c oxidase subunit I (COI) sequences for 2,525 specimens representing 984 species. Specimens were primarily purchased from markets, with additional diversity collected using rotenone or fishing gear. Species identifications were verified based on taxonomic, phenotypic, and genotypic data, and sequences are associated with voucher specimens, live-color photographs, and genetic samples catalogued at Smithsonian Institution, National Museum of Natural History. The Biodiversity of Philippine Marine Fishes dataset is released herein to increase knowledge of species diversity and distributions and to facilitate accurate identification of market fishes.
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Affiliation(s)
- Katherine E Bemis
- National Systematics Laboratory, Office of Science and Technology, NOAA Fisheries, Washington, D.C., 20560, USA.
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., 20560, USA.
| | - Matthew G Girard
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., 20560, USA.
- Biodiversity Institute, University of Kansas, Lawrence, Kansas, 66045, USA.
| | - Mudjekeewis D Santos
- Genetic Fingerprinting Laboratory, National Fisheries Research and Development Institute, Quezon City, 1103, Philippines
| | - Kent E Carpenter
- Department of Biological Sciences, Old Dominion University, Norfolk, Virginia, 23529, USA
| | - Jonathan R Deeds
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, College Park, Maryland, 20740, USA
| | - Diane E Pitassy
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., 20560, USA
| | - Nicko Amor L Flores
- Genetic Fingerprinting Laboratory, National Fisheries Research and Development Institute, Quezon City, 1103, Philippines
| | - Elizabeth S Hunter
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, College Park, Maryland, 20740, USA
| | - Amy C Driskell
- Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., 20560, USA
| | - Kenneth S Macdonald
- Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., 20560, USA
| | - Lee A Weigt
- Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., 20560, USA
| | - Jeffrey T Williams
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., 20560, USA.
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11
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Shimbori EM, Querino RB, Costa VA, Zucchi RA. Taxonomy and Biological Control: New Challenges in an Old Relationship. NEOTROPICAL ENTOMOLOGY 2023; 52:351-372. [PMID: 36656493 PMCID: PMC9851596 DOI: 10.1007/s13744-023-01025-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 01/03/2023] [Indexed: 05/13/2023]
Abstract
Biological control and taxonomy are continuously developing fields with remarkable impacts on society. At least 80 years of literature have documented this relationship, which remains essentially the same in its mutualistic nature, as well as in its major challenges. From the perspective of Brazilian taxonomists, we discuss the impacts of important scientific and social developments that directly affect research in these areas, posing new challenges for this lasting relationship. The increasing restrictions and concerns regarding the international transit of organisms require improvements in research related to risk assessment for exotic biological control agents and also stimulate prospecting within the native biota. In our view, this is a positive situation that can foster a closer relationship between taxonomists and applied entomologists, as well as local surveys and taxonomic studies that are necessary before new programs and agents can be implemented. We discuss the essential role of molecular biology in this context, as an iconic example of the synergy between applied sciences and natural history. As our society comes to need safer and more sustainable solutions for food security and the biodiversity crisis, scientific progress will build upon this integration, where biological control and taxonomy play an essential role.
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Affiliation(s)
- Eduardo Mitio Shimbori
- Departamento de Entomologia e Acarologia, Escola Superior de Agricultura “Luiz de Queiroz” (ESALQ), Universidade de São Paulo (USP), São Paulo Piracicaba, Brazil
| | - Ranyse Barbosa Querino
- Empresa Brasileira de Pesquisa Agropecuária, Embrapa Cerrados, Planaltina, Distrito Federal Brazil
| | - Valmir Antonio Costa
- Centro Avançado de Pesquisa e Desenvolvimento em Sanidade Agropecuária, Instituto Biológico, São Paulo Campinas, Brazil
| | - Roberto Antonio Zucchi
- Departamento de Entomologia e Acarologia, Escola Superior de Agricultura “Luiz de Queiroz” (ESALQ), Universidade de São Paulo (USP), São Paulo Piracicaba, Brazil
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12
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Song F, Deng YF, Yan HF, Lin ZL, Delgado A, Trinidad H, Gonzales-Arce P, Riva S, Cano-Echevarría A, Ramos E, Aroni YP, Rivera S, Arakaki M, Ge XJ. Flora diversity survey and establishment of a plant DNA barcode database of Lomas ecosystems in Peru. Sci Data 2023; 10:294. [PMID: 37208352 DOI: 10.1038/s41597-023-02206-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 05/03/2023] [Indexed: 05/21/2023] Open
Abstract
Lomas formations or "fog oases" are islands of vegetation in the desert belt of the west coast of South America, with a unique vegetation composition among the world's deserts. However, plant diversity and conservation studies have long been neglected, and there exists a severe gap in plant DNA sequence information. To address the lack of DNA information, we conducted field collections and laboratory DNA sequencing to establish a DNA barcode reference library of Lomas plants from Peru. This database provides 1,207 plant specimens and 3,129 DNA barcodes data corresponding with collections from 16 Lomas locations in Peru, during 2017 and 2018. This database will facilitate both rapid species identification and basic studies on plant diversity, thereby enhancing our understanding of Lomas flora's composition and temporal variation, and providing valuable resources for conserving plant diversity and maintaining the stability of the fragile Lomas ecosystems.
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Affiliation(s)
- Feng Song
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Yun-Fei Deng
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Hai-Fei Yan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Zhe-Li Lin
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- Henry Fok College of Biology and Agriculture, Shaoguan University, Shaoguan, 512005, China
| | - Amalia Delgado
- División Botánica, Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Av. Arenales 1256, Lima, 11, Perú
| | - Huber Trinidad
- División Botánica, Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Av. Arenales 1256, Lima, 11, Perú
| | - Paúl Gonzales-Arce
- División Botánica, Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Av. Arenales 1256, Lima, 11, Perú
| | - Sebastián Riva
- División Botánica, Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Av. Arenales 1256, Lima, 11, Perú
| | - Asunción Cano-Echevarría
- División Botánica, Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Av. Arenales 1256, Lima, 11, Perú
| | - Elmer Ramos
- División Botánica, Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Av. Arenales 1256, Lima, 11, Perú
| | - Yaquelin Pamela Aroni
- División Botánica, Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Av. Arenales 1256, Lima, 11, Perú
| | - Soledad Rivera
- División Botánica, Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Av. Arenales 1256, Lima, 11, Perú
| | - Mónica Arakaki
- División Botánica, Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Av. Arenales 1256, Lima, 11, Perú
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
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13
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Santos BF, Miller ME, Miklasevskaja M, McKeown JTA, Redmond NE, Coddington JA, Bird J, Miller SE, Smith A, Brady SG, Buffington ML, Chamorro ML, Dikow T, Gates MW, Goldstein P, Konstantinov A, Kula R, Silverson ND, Solis MA, deWaard SL, Naik S, Nikolova N, Pentinsaari M, Prosser SWJ, Sones JE, Zakharov EV, deWaard JR. Enhancing DNA barcode reference libraries by harvesting terrestrial arthropods at the Smithsonian's National Museum of Natural History. Biodivers Data J 2023; 11:e100904. [PMID: 38327288 PMCID: PMC10848724 DOI: 10.3897/bdj.11.e100904] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 03/30/2023] [Indexed: 02/09/2024] Open
Abstract
The use of DNA barcoding has revolutionised biodiversity science, but its application depends on the existence of comprehensive and reliable reference libraries. For many poorly known taxa, such reference sequences are missing even at higher-level taxonomic scales. We harvested the collections of the Smithsonian's National Museum of Natural History (USNM) to generate DNA barcoding sequences for genera of terrestrial arthropods previously not recorded in one or more major public sequence databases. Our workflow used a mix of Sanger and Next-Generation Sequencing (NGS) approaches to maximise sequence recovery while ensuring affordable cost. In total, COI sequences were obtained for 5,686 specimens belonging to 3,737 determined species in 3,886 genera and 205 families distributed in 137 countries. Success rates varied widely according to collection data and focal taxon. NGS helped recover sequences of specimens that failed a previous run of Sanger sequencing. Success rates and the optimal balance between Sanger and NGS are the most important drivers to maximise output and minimise cost in future projects. The corresponding sequence and taxonomic data can be accessed through the Barcode of Life Data System, GenBank, the Global Biodiversity Information Facility, the Global Genome Biodiversity Network Data Portal and the NMNH data portal.
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Affiliation(s)
- Bernardo F. Santos
- National Museum of Natural History, Smithsonian Institution, Washington, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashingtonUnited States of America
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire naturelle, CNRS, SU, EPHE, UA, Paris, FranceInstitut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire naturelle, CNRS, SU, EPHE, UAParisFrance
| | - Meredith E. Miller
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
| | - Margarita Miklasevskaja
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
| | - Jaclyn T. A. McKeown
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
| | - Niamh E. Redmond
- National Museum of Natural History, Smithsonian Institution, Washington, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashingtonUnited States of America
| | - Jonathan A. Coddington
- National Museum of Natural History, Smithsonian Institution, Washington, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashingtonUnited States of America
| | - Jessica Bird
- National Museum of Natural History, Smithsonian Institution, Washington, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashingtonUnited States of America
| | - Scott E. Miller
- National Museum of Natural History, Smithsonian Institution, Washington, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashingtonUnited States of America
| | - Ashton Smith
- National Museum of Natural History, Smithsonian Institution, Washington, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashingtonUnited States of America
| | - Seán G. Brady
- National Museum of Natural History, Smithsonian Institution, Washington, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashingtonUnited States of America
| | - Matthew L. Buffington
- Systematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Washington, United States of AmericaSystematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of AgricultureWashingtonUnited States of America
| | - M. Lourdes Chamorro
- Systematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Washington, United States of AmericaSystematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of AgricultureWashingtonUnited States of America
| | - Torsten Dikow
- National Museum of Natural History, Smithsonian Institution, Washington, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashingtonUnited States of America
| | - Michael W. Gates
- Systematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Washington, United States of AmericaSystematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of AgricultureWashingtonUnited States of America
| | - Paul Goldstein
- Systematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Washington, United States of AmericaSystematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of AgricultureWashingtonUnited States of America
| | - Alexander Konstantinov
- Systematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Washington, United States of AmericaSystematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of AgricultureWashingtonUnited States of America
| | - Robert Kula
- Systematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Washington, United States of AmericaSystematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of AgricultureWashingtonUnited States of America
| | - Nicholas D. Silverson
- National Museum of Natural History, Smithsonian Institution, Washington, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashingtonUnited States of America
| | - M. Alma Solis
- Systematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Washington, United States of AmericaSystematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of AgricultureWashingtonUnited States of America
| | - Stephanie L. deWaard
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
| | - Suresh Naik
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
- Department of Integrative Biology, University of Guelph, Guelph, CanadaDepartment of Integrative Biology, University of GuelphGuelphCanada
| | - Nadya Nikolova
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
| | - Mikko Pentinsaari
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
| | - Sean W. J. Prosser
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
| | - Jayme E. Sones
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
| | - Evgeny V. Zakharov
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
- Department of Integrative Biology, University of Guelph, Guelph, CanadaDepartment of Integrative Biology, University of GuelphGuelphCanada
| | - Jeremy R. deWaard
- National Museum of Natural History, Smithsonian Institution, Washington, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashingtonUnited States of America
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
- School of Environmental Sciences, University of Guelph, Guelph, CanadaSchool of Environmental Sciences, University of GuelphGuelphCanada
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14
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Wu YH, Hou SB, Yuan ZY, Jiang K, Huang RY, Wang K, Liu Q, Yu ZB, Zhao HP, Zhang BL, Chen JM, Wang LJ, Stuart BL, Chambers EA, Wang YF, Gao W, Zou DH, Yan F, Zhao GG, Fu ZX, Wang SN, Jiang M, Zhang L, Ren JL, Wu YY, Zhang LY, Yang DC, Jin JQ, Yin TT, Li JT, Zhao WG, Murphy RW, Huang S, Guo P, Zhang YP, Che J. DNA barcoding of Chinese snakes reveals hidden diversity and conservation needs. Mol Ecol Resour 2023. [PMID: 36924341 DOI: 10.1111/1755-0998.13784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 02/25/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023]
Abstract
DNA barcoding has greatly facilitated studies of taxonomy, biodiversity, biological conservation, and ecology. Here, we establish a reliable DNA barcoding library for Chinese snakes, unveiling hidden diversity with implications for taxonomy, and provide a standardized tool for conservation management. Our comprehensive study includes 1638 cytochrome c oxidase subunit I (COI) sequences from Chinese snakes that correspond to 17 families, 65 genera, 228 named species (80.6% of named species) and 36 candidate species. A barcode gap analysis reveals gaps, where all nearest neighbour distances exceed maximum intraspecific distances, in 217 named species and all candidate species. Three species-delimitation methods (ABGD, sGMYC, and sPTP) recover 320 operational taxonomic units (OTUs), of which 192 OTUs correspond to named and candidate species. Twenty-eight other named species share OTUs, such as Azemiops feae and A. kharini, Gloydius halys, G. shedaoensis, and G. intermedius, and Bungarus multicinctus and B. candidus, representing inconsistencies most probably caused by imperfect taxonomy, recent and rapid speciation, weak taxonomic signal, introgressive hybridization, and/or inadequate phylogenetic signal. In contrast, 43 species and candidate species assign to two or more OTUs due to having large intraspecific distances. If most OTUs detected in this study reflect valid species, including the 36 candidate species, then 30% more species would exist than are currently recognized. Several OTU divergences associate with known biogeographic barriers, such as the Taiwan Strait. In addition to facilitating future studies, this reliable and relatively comprehensive reference database will play an important role in the future monitoring, conservation, and management of Chinese snakes.
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Affiliation(s)
- Yun-He Wu
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Shao-Bing Hou
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, Yunnan, 650204, China
| | - Zhi-Yong Yuan
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Ke Jiang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Ru-Yi Huang
- Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Kai Wang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Qin Liu
- Faculty of Agriculture, Forest and Food Engineering, Yibin University, Yibin, Sichuan, 644007, China
| | - Zhong-Bin Yu
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Hai-Peng Zhao
- School of Life Science, Henan University, Kaifeng, Henan, 475001, China
| | - Bao-Lin Zhang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Jin-Min Chen
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Li-Jun Wang
- School of Life Sciences, Hainan Normal University, Haikou, Hainan, 571158, China
| | - Bryan L Stuart
- Section of Research & Collections, North Carolina Museum of Natural Sciences, Raleigh, North Carolina, 27601, USA
| | - E Anne Chambers
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, California, 94720, USA
| | - Yu-Fan Wang
- Zhejiang Forest Resource Monitoring Center, Hangzhou, Zhejiang, 310020, China
| | - Wei Gao
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Da-Hu Zou
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- College of Science, Tibet University, Lhasa, Tibet, 850000, China
| | - Fang Yan
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Gui-Gang Zhao
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Zhong-Xiong Fu
- Yunnan Senye Biotechnology Co., Ltd, Xishuangbanna, Yunnan, 666100, China
| | - Shao-Neng Wang
- Bureau of Guangxi Mao'er Mountain Nature Reserve, Guilin, Guangxi, 541316, China
| | - Ming Jiang
- Gongshan Bureau of Gaoligongshan National Nature Reserve, Gongshan, Yunnan, 650224, China
| | - Liang Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, Guangdong, 510260, China
| | - Jin-Long Ren
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, 610041, China
| | - Ya-Yong Wu
- Faculty of Agriculture, Forest and Food Engineering, Yibin University, Yibin, Sichuan, 644007, China
| | - Lu-Yang Zhang
- Beijing Mountains & Seas Eco Technology Co. Ltd, Beijing, 101100, China
| | - Dian-Cheng Yang
- Anhui Province Key Laboratory of the Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, 241000, China
| | - Jie-Qiong Jin
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Ting-Ting Yin
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Jia-Tang Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, 610041, China
| | - Wen-Ge Zhao
- College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang, 150025, China
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- Reptilia Zoo and Education Centre, Vaughn, Ontario, L4K 2N6, Canada
| | - Song Huang
- Anhui Province Key Laboratory of the Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, 241000, China
| | - Peng Guo
- Faculty of Agriculture, Forest and Food Engineering, Yibin University, Yibin, Sichuan, 644007, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
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15
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Rongier G, Sagne A, Etienne S, Petitclerc F, Jaouen G, Murienne J, Orivel J. Ants of French Guiana: 16S rRNA sequence dataset. Biodivers Data J 2023; 11:e91577. [PMID: 38327367 PMCID: PMC10848834 DOI: 10.3897/bdj.11.e91577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 11/30/2022] [Indexed: 02/10/2023] Open
Abstract
This dataset represents a reference library of DNA sequences for ants from French Guiana. A total of 3931 new sequences from the 16S rRNA gene has been generated. The reference library covers 344 species distributed in 57 genera. Overall, 3920 sequences have been assigned at the species level and 11 at the genus level. All these sequences were submitted to DDBJ/EMBL/GenBank databases in the Bioproject: PRJNA779056: 16S French Guiana Ants (Hymenoptera: Formicidae), sequence identifier KFFS00000000.
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Affiliation(s)
- Gaëtan Rongier
- UMR Écologie des Forêts de Guyane (AgroParisTech, CIRAD, CNRS, INRAE, Université de Guyane, Université des Antilles), Kourou, French GuianaUMR Écologie des Forêts de Guyane (AgroParisTech, CIRAD, CNRS, INRAE, Université de Guyane, Université des Antilles)KourouFrench Guiana
| | - Audrey Sagne
- UMR Écologie des Forêts de Guyane (AgroParisTech, CIRAD, CNRS, INRAE, Université de Guyane, Université des Antilles), Kourou, French GuianaUMR Écologie des Forêts de Guyane (AgroParisTech, CIRAD, CNRS, INRAE, Université de Guyane, Université des Antilles)KourouFrench Guiana
| | - Sandrine Etienne
- UMR Écologie des Forêts de Guyane (AgroParisTech, CIRAD, CNRS, INRAE, Université de Guyane, Université des Antilles), Kourou, French GuianaUMR Écologie des Forêts de Guyane (AgroParisTech, CIRAD, CNRS, INRAE, Université de Guyane, Université des Antilles)KourouFrench Guiana
| | - Frederic Petitclerc
- UMR Écologie des Forêts de Guyane (AgroParisTech, CIRAD, CNRS, INRAE, Université de Guyane, Université des Antilles), Kourou, French GuianaUMR Écologie des Forêts de Guyane (AgroParisTech, CIRAD, CNRS, INRAE, Université de Guyane, Université des Antilles)KourouFrench Guiana
| | - Gaelle Jaouen
- UMR Écologie des Forêts de Guyane (AgroParisTech, CIRAD, CNRS, INRAE, Université de Guyane, Université des Antilles), Kourou, French GuianaUMR Écologie des Forêts de Guyane (AgroParisTech, CIRAD, CNRS, INRAE, Université de Guyane, Université des Antilles)KourouFrench Guiana
| | - Jerome Murienne
- Laboratoire Evolution et Diversité Biologique (EDB UMR5174) CNRS, Université Paul Sabatier Toulouse 3, IRD, Toulouse, FranceLaboratoire Evolution et Diversité Biologique (EDB UMR5174) CNRS, Université Paul Sabatier Toulouse 3, IRDToulouseFrance
| | - Jerome Orivel
- UMR Écologie des Forêts de Guyane (AgroParisTech, CIRAD, CNRS, INRAE, Université de Guyane, Université des Antilles), Kourou, French GuianaUMR Écologie des Forêts de Guyane (AgroParisTech, CIRAD, CNRS, INRAE, Université de Guyane, Université des Antilles)KourouFrench Guiana
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Tessler M, Galen SC, DeSalle R, Schierwater B. Let’s end taxonomic blank slates with molecular morphology. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1016412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Many known evolutionary lineages have yet to be described formally due to a lack of traditional morphological characters. This is true for genetically distinctive groups within the amoeboid Placozoa animals, the protists in ponds, and the bacteria that cover nearly everything. These taxonomic tabula rasae, or blank slates, are problematic; without names, communication is hampered and other scientific progress is slowed. We suggest that the morphology of molecules be used to help alleviate this issue. Molecules, such as proteins, have structure. Proteins are even visualizable with X-ray crystallography, albeit more easily detected by and easier to work with using genomic sequencing. Given their structured nature, we believe they should not be considered as anything less than traditional morphology. Protein-coding gene content (presence/absence) can also be used easily with genomic sequences, and is a convenient binary character set. With molecular morphology, we believe that each taxonomic tabula rasa can be solved.
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17
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Mandal FB. Interaction between marine protists and bacteria results in magnetotaxis and iron recycling. Isr J Ecol Evol 2022. [DOI: 10.1163/22244662-bja10042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Abstract
Marine protists are eukaryotic trophic linkers that play a crucial role in iron recycling. Some marine protists have the ability of magnetotaxis, which they gain by consuming their ectosymbiotic bacteria. They graze and internalize the magnetotactic bacteria along with their magnetosome chains. Through egestion, marine protists avoid iron toxicity. Colloidal iron digestion by protists produces bioavailable iron for other marine organisms, passing to phytoplankton and mesozooplankton through the mesotrophic system. Indeed, ectosymbiotic bacteria and their protistan host form a microbial holobiont acting as an ecological unit. Some of the genetic mechanisms influencing the biosynthesis of magnetite in both prokaryotes and eukaryotes appear to be common. The recorded history of the magnetoreception ability of some marine protists goes back to the study by F.F. Torres de Araujo in 1986. After research over 35 years or more, it is safe to record that magnetotaxis in marine protists is yet to be fully understood, and might be similar to that of free-living magnetotactic bacteria. However, the attainment of magnetotaxis by protistan grazers through bacterivory and its role in iron recycling in the marine ecosystem is very interesting. The present article aims to provide an account of such interesting facts.
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Affiliation(s)
- Fatik Baran Mandal
- Department of Zoology, Bankura Christian College, College Road, Bankura, West Bengal, 722101, India
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18
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Cruz MM, Hoffmann LS, de Freitas TRO. Saint Peter and Saint Paul Archipelago barcoded: Fish diversity in the remoteness and DNA barcodes reference library for metabarcoding monitoring. Genet Mol Biol 2022; 45:e20210349. [PMID: 36205729 PMCID: PMC9540803 DOI: 10.1590/1678-4685-gmb-2021-0349] [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: 10/28/2021] [Accepted: 08/04/2022] [Indexed: 11/04/2022] Open
Abstract
In order to monitor the effects of anthropogenic pressures in ecosystems,
molecular techniques can be used to characterize species composition. Among
molecular markers capable of identifying species, the cytochrome c oxidase I
(COI) is the most used. However, new possibilities of
biodiversity profiling have become possible, in which molecular fragments of
medium and short-length can now be analyzed in metabarcoding studies. Here, a
survey of fishes from the Saint Peter and Saint Paul Archipelago was barcoded
using the COI marker, which allowed the identification of 21
species. This paved the way to further investigate the fish biodiversity of the
archipelago, transitioning from barcoding to metabarcoding analysis. As
preparatory steps for future metabarcoding studies, the first extensive
COI library of fishes listed for these islands was
constructed and includes new data generated in this survey as well as previously
available data, resulting in a final database with 9,183 sequences from 169
species and 63 families of fish. A new primer specifically designed for those
fishes was tested in silico to amplify a region of 262 bp. The
new approach should guarantee a reliable surveillance of the archipelago and can
be used to generate policies that will enhance the archipelago’s protection.
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Affiliation(s)
- Marcelo Merten Cruz
- Universidade Federal do Rio Grande do Sul, Programa de
Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Porto
Alegre, RS, Brazil
| | - Lilian Sander Hoffmann
- Universidade Federal do Rio Grande do Sul, Programa de
Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Porto
Alegre, RS, Brazil
| | - Thales R. O. de Freitas
- Universidade Federal do Rio Grande do Sul, Programa de
Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Porto
Alegre, RS, Brazil
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Molecular tools for resolving Merodon ruficornis group (Diptera, Syrphidae) taxonomy. ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-022-00571-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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20
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Phillips JD, Gillis DJ, Hanner RH. Lack of Statistical Rigor in DNA Barcoding Likely Invalidates the Presence of a True Species' Barcode Gap. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.859099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
DNA barcoding has been largely successful in satisfactorily exposing levels of standing genetic diversity for a wide range of taxonomic groups through the employment of only one or a few universal gene markers. However, sufficient coverage of geographically-broad intra-specific haplotype variation within genomic databases like the Barcode of Life Data Systems (BOLD) and GenBank remains relatively sparse. As reference sequence libraries continue to grow exponentially in size, there is now the need to identify novel ways of meaningfully analyzing vast amounts of available DNA barcode data. This is an important issue to address promptly for the routine tasks of specimen identification and species discovery, which have seen broad adoption in areas as diverse as regulatory forensics and resource conservation. Here, it is demonstrated that the interpretation of DNA barcoding data is lacking in statistical rigor. To highlight this, focus is set specifically on one key concept that has become a household name in the field: the DNA barcode gap. Arguments outlined herein specifically center on DNA barcoding in animal taxa and stem from three angles: (1) the improper allocation of specimen sampling effort necessary to capture adequate levels of within-species genetic variation, (2) failing to properly visualize intra-specific and interspecific genetic distances, and (3) the inconsistent, inappropriate use, or absence of statistical inferential procedures in DNA barcoding gap analyses. Furthermore, simple statistical solutions are outlined which can greatly propel the use of DNA barcoding as a tool to irrefutably match unknowns to knowns on the basis of the barcoding gap with a high degree of confidence. Proposed methods examined herein are illustrated through application to DNA barcode sequence data from Canadian Pacific fish species as a case study.
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21
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Crone MK, Biddinger DJ, Grozinger CM. Wild Bee Nutritional Ecology: Integrative Strategies to Assess Foraging Preferences and Nutritional Requirements. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.847003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Bees depend on flowering plants for their nutrition, and reduced availability of floral resources is a major driver of declines in both managed and wild bee populations. Understanding the nutritional needs of different bee species, and how these needs are met by the varying nutritional resources provided by different flowering plant taxa, can greatly inform land management recommendations to support bee populations and their associated ecosystem services. However, most bee nutrition research has focused on the three most commonly managed and commercially reared bee taxa—honey bees, bumble bees, and mason bees—with fewer studies focused on wild bees and other managed species, such as leafcutting bees, stingless bees, and alkali bees. Thus, we have limited information about the nutritional requirements and foraging preferences of the vast majority of bee species. Here, we discuss the approaches traditionally used to understand bee nutritional ecology: identification of floral visitors of selected focal plant species, evaluation of the foraging preferences of adults in selected focal bee species, evaluation of the nutritional requirements of focal bee species (larvae or adults) in controlled settings, and examine how these methods may be adapted to study a wider range of bee species. We also highlight emerging technologies that have the potential to greatly facilitate studies of the nutritional ecology of wild bee species, as well as evaluate bee nutritional ecology at significantly larger spatio-temporal scales than were previously feasible. While the focus of this review is on bee species, many of these techniques can be applied to other pollinator taxa as well.
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22
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Yuan Z, Wu D, Wen Y, Xu W, Gao W, Dahn HA, Liu X, Jin J, Yu C, Xiao H, Che J. Historical mitochondrial genome introgression confounds species delimitation: Evidence from phylogenetic inference in the odorrana grahami species complex. Curr Zool 2022; 69:82-90. [PMID: 36974146 PMCID: PMC10039181 DOI: 10.1093/cz/zoac010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 02/11/2022] [Indexed: 11/12/2022] Open
Abstract
Abstract
Species delimitation is essential to informing conservation policy and understanding ecological and evolutionary processes. Most of our recent gains in knowledge on animal diversity rely on morphological characteristics and mitochondrial (mt) DNA variation. Concordant results based on both have led to an unprecedented acceleration in the identification of new species and enriched the field of taxonomy. However, discordances are also found commonly between morphological and mtDNA evidence. This confounds species delimitation, especially when gene flow or mitochondrial genome introgression has occurred. Here we illustrate how mitochondrial genome introgression among species of the Odorrana grahami complex confounds species delimitation using the combined evidence of morphological characters, mitochondrial variation, and thousands of nuclear single nucleotide polymorphisms (SNPs) from genotyping-by-sequencing (GBS). Fifty-eight samples across the distribution of the O. grahami complex were included. The mtDNA matrilineal genealogy indicated two clades, with O. grahami and O. junlianensis clustered together. In contrast, all nuclear evidence including gene trees, species trees, and genetic structure analyses based on GBS data support three species with distinct genetic clusters. These three distinct genetic clusters also correspond to distinct morphological characters. They affirm the distinct taxonomic entities of both O. grahami and O. junlianensis, as well as a third clade distinct from either. Which species the third clade belongs to remains unclear and will require further testing. The nuclear genomic loci contradict the COI evidence, with indications of rampant historical mitochondrial genome introgression among the species of the O. grahami complex. These discordant signals previously confused species delimitation efforts in this group. Based on these findings, we recommend the integration of independent data, especially nuclear genomic evidence, in species delimitation so as to be robust against the pitfalls of mitochondrial introgression.
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Affiliation(s)
- Zhiyong Yuan
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Southwest University, Chongqing, 400715, China
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Southwest Forestry University, Kunming, 650224, China
| | - Dongyi Wu
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Southwest Forestry University, Kunming, 650224, China
| | - Yang Wen
- School of Life Sciences, Yunnan University, Kunming, 650091, China
- School of Ecology and Environment Sciences, Yunnan University, Kunming, 650091, China
| | - Wei Xu
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Wei Gao
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Hollis A Dahn
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Xiaolong Liu
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Southwest Forestry University, Kunming, 650224, China
| | - Jieqiong Jin
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Chuanxin Yu
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Heng Xiao
- School of Ecology and Environment Sciences, Yunnan University, Kunming, 650091, China
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
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Delrieu-Trottin E, Hartmann-Salvo H, Saenz-Agudelo P, Landaeta MF, Pérez-Matus A. DNA reconciles morphology and colouration in the drunk blenny genus Scartichthys (Teleostei: Blenniidae) and provides insights into their evolutionary history. JOURNAL OF FISH BIOLOGY 2022; 100:507-518. [PMID: 34821381 DOI: 10.1111/jfb.14960] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/17/2021] [Accepted: 11/22/2021] [Indexed: 06/13/2023]
Abstract
The blenniids of the genus Scartichthys are one of the most common fishes of Central and South American Pacific coastal reefs. This being said, Scartichthys spp. remain difficult to identify in the field, and identification is particularly challenging across the c. 6000 km where three of the four currently accepted species are known to occur in sympatry. A reason for this is that the main taxonomic characters from traditional taxonomy are indeed elusive. In addition, at the same time, species can display multiple colour patterns in the field, depending on their ontogenetic stage, habitat association and reproductive behaviour. Overall, molecular characterization is warranted to help address these issues. In this study, the authors have used a novel approach to revise the genus by combining colouration, morphological and molecular data of representative specimens of the four currently valid species and seven described colour patterns. From this, the authors show that only three of the four species should be considered as valid; Scartichthys gigas (Steindachner, 1876), Scartichthys variolatus (Valenciennes, 1836) and Scartichthys viridis (Valenciennes, 1836), whereas Scartichthys crapulatus (Williams, 1990) should be synonymized with S. viridis. In the same way, the analyses in this study show that one of the colour patterns attributed so far only to S. gigas is characteristic of the juvenile stages of S. viridis. The time-calibrated phylogeny of this study shows that this genus is relatively young and that the estimated time of divergence between S. gigas and S. viridis is c. 1.71 Ma. In comparison, the Desventuradas and Juan Fernandez Islands endemic S. variolatus diverged c. 1.95 Ma. The results of this study help to clarify the taxonomy of Scartichthys.
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Affiliation(s)
- Erwan Delrieu-Trottin
- ISEM, CNRS, EPHE, IRD, Université de Montpellier, Montpellier cedex 5, France
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
- CEFE, Univ Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France
| | - Hans Hartmann-Salvo
- Subtidal Ecology Laboratory, Estación Costera de Investigaciones Marinas, Departamento de Ecología, Facultad de Ciencias Biológicas Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Pablo Saenz-Agudelo
- Instituto de Ciencias Ambientales y Evolutivas (ICAEV), Universidad Austral de Chile, Valdivia, Chile
- Millennium Nucleus for Ecology and Conservation of Temperate Mesophotic Reef Ecosystem (NUTME)
| | - Mauricio F Landaeta
- Millennium Nucleus for Ecology and Conservation of Temperate Mesophotic Reef Ecosystem (NUTME)
- Laboratorio de Ictioplancton (LABITI), Instituto de Biología, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile
- Centro de Observación Marino para Estudios del Ambiente Costero (COSTA-R), Universidad de Valparaíso, Valparaíso, Chile
| | - Alejandro Pérez-Matus
- Subtidal Ecology Laboratory, Estación Costera de Investigaciones Marinas, Departamento de Ecología, Facultad de Ciencias Biológicas Pontificia Universidad Católica de Chile, Santiago, Chile
- Millennium Nucleus for Ecology and Conservation of Temperate Mesophotic Reef Ecosystem (NUTME)
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Majoros SE, Adamowicz SJ. Phylogenetic signal of sub-arctic beetle communities. Ecol Evol 2022; 12:e8520. [PMID: 35222946 PMCID: PMC8848465 DOI: 10.1002/ece3.8520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 11/30/2021] [Accepted: 12/14/2021] [Indexed: 11/07/2022] Open
Abstract
Postglacial dispersal and colonization processes have shaped community patterns in sub-Arctic regions such as Churchill, Manitoba, and Canada. This study investigates evolutionary community structure within the beetle (Coleoptera) families of Churchill and tests whether biological traits have played a role in governing colonization patterns from refugial and southerly geographic regions. This study quantifies sub-Arctic beetle phylogenetic community structure for each family using the net relatedness index (NRI) and nearest taxon index (NTI), calculated using publicly available data from the Barcode of Life Data Systems (BOLD); compares patterns across families with different traits (habitat, diet) using standard statistical analysis (ANOVA) as well as phylogenetic generalized least squares (PGLS) using a family-level beetle phylogeny obtained from the literature; and compares community structure in Churchill with a region in southern Canada (Guelph, Ontario). These analyses were also repeated at a genus level. The dominant pattern detected in our study was that aquatic families were much better represented in Churchill compared to terrestrial families, when compared against richness sampled from across Canada and Alaska. Individually, most families showed significant phylogenetic clustering in Churchill, likely due to the strong environmental filtering present in Arctic environments. There was no significant difference in phylogenetic structure between Churchill and Guelph but with a trend toward stronger clustering in the North. Fungivores were significantly more overdispersed than other feeding modes, predators were significantly more clustered, and aquatic families showed significantly stronger clustering compared to terrestrial. This study contributes to our understanding of the traits and processes structuring insect biodiversity and macroecological trends in the sub-Arctic.
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ITS DNA Barcoding Reveals That Halophila stipulacea Still Remains the Only Non-Indigenous Seagrass of the Mediterranean Sea. DIVERSITY 2022. [DOI: 10.3390/d14020076] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Non-indigenous species (NIS) are one of the major threats to the native marine ecosystems of the Mediterranean Sea. Halophila stipulacea was the only exotic seagrass of the Mediterranean until 2018, when small patches of a species morphologically identified as Halophila decipiens were reported in Salamina Island, Greece. Given the absence of reproductive structures during the identification and the taxonomic ambiguities known to lead to misidentifications on this genus, we reassessed the identity of this new exotic record using DNA barcoding (rbcL, matK and ITS) and the recently published taxonomic key. Despite their morphologic similarity to H. decipiens based on the new taxonomic key, the specimens showed no nucleotide differences with H. stipulacea specimens (Crete) for the three barcodes and clustered together on the ITS phylogenetic tree. Considering the high species resolution of the ITS region and the common morphological variability within the genus, the unequivocal genetic result suggests that the Halophila population found in Salamina Island most likely corresponds to a morphologically variant H. stipulacea. Our results highlight the importance of applying an integrated taxonomic approach (morphological and molecular) to taxonomically complex genera such as Halophila, in order to avoid overlooking or misreporting species range shifts, which is essential for monitoring NIS introductions.
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Young RG, Gill R, Gillis D, Hanner RH. Molecular Acquisition, Cleaning and Evaluation in R (MACER) - A tool to assemble molecular marker datasets from BOLD and GenBank. Biodivers Data J 2021; 9:e71378. [PMID: 34594153 PMCID: PMC8443542 DOI: 10.3897/bdj.9.e71378] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 08/25/2021] [Indexed: 11/20/2022] Open
Abstract
Molecular sequence data is an essential component for many biological fields of study. The strength of these data is in their ability to be centralised and compared across research studies. There are many online repositories for molecular sequence data, some of which are very large accumulations of varying data types like NCBI’s GenBank. Due to the size and the complexity of the data in these repositories, challenges arise in searching for data of interest. While data repositories exist for molecular markers, taxa and other specific research interests, repositories may not contain, or be suitable for, more specific applications. Manually accessing, searching, downloading, accumulating, dereplicating and cleaning data to construct project-specific datasets is time-consuming. In addition, the manual assembly of datasets presents challenges with reproducibility. Here, we present the MACER package to assist researchers in assembling molecular datasets and provide reproducibility in the process.
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Affiliation(s)
- Robert G Young
- University of Guelph, Guelph, Canada University of Guelph Guelph Canada
| | - Rekkab Gill
- University of Guelph, Guelph, Canada University of Guelph Guelph Canada
| | - Daniel Gillis
- University of Guelph, Guelph, Canada University of Guelph Guelph Canada
| | - Robert H Hanner
- University of Guelph, Guelph, Canada University of Guelph Guelph Canada
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27
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Ng CKC, Tan J. Cryptic species and grey zone speciation of the Barbodes binotatus complex (Teleostei, Cyprinidae) in Sundaland. JOURNAL OF FISH BIOLOGY 2021; 99:1256-1273. [PMID: 34159593 DOI: 10.1111/jfb.14829] [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: 03/04/2021] [Revised: 06/03/2021] [Accepted: 06/12/2021] [Indexed: 06/13/2023]
Abstract
Morphology-based taxonomy of freshwater fish is effective when there are representative specimens covering large regions. However, in Sundaland, where the presence of cryptic species is high, the technique has its limitations. This is compounded by uncritical descriptions of holotypes in old literature. We demonstrate the problem using Barbodes binotatus first described from an ink drawing. Several species in the Barbodes genus of Sundaland exhibit morphological similarity to B. binotatus. We applied new DNA sequences of 16S, cytochrome c oxidase subunit I (COI), cytochrome b (Cytb) and recombination-activating gene 1 (RAG1), and pigmentation markers to clarify species complex boundaries in the Malay Peninsula, namely B. aff. binotatus "Malay Peninsula", Barbodes cf. banksi and Barbodes rhombeus. Results suggest B. binotatus-like specimens in the Malay Peninsula are B. rhombeus based on a threshold of 3% COI genetic divergence. B. aff. binotatus recorded in Sumatra, Borneo and the Philippines are likely valid but undescribed species. However, if the 2% COI threshold is applied, some populations in the northern Malay Peninsula would qualify as new and undescribed species. The implications of the 2% threshold and the likelihood of "grey zone" incipient populations are discussed. We further found a rapid visual method, not reported previously, to delineate B. aff. binotatus and B. cf. banksi, but it requires further validation. Additionally, we offer fresh perspectives by discussing the roles of biological species concept, morphological species concept, genetic species concept and mate recognition concept in the B. binotatus complex. Our findings reinforce the standpoint that species delineation is not entirely a binary process, but there is a spectrum to consider, especially in biogeography intersection regions.
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Affiliation(s)
- Casey Keat-Chuan Ng
- School of Biological Sciences, Universiti Sains Malaysia, Pulau Pinang, Malaysia
| | - Ji Tan
- Department of Agricultural and Food Sciences, Faculty of Science, Universiti Tunku Abdul Rahman, Kampar, Malaysia
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Carugati L, Melis R, Cariani A, Cau A, Crobe V, Ferrari A, Follesa MC, Geraci ML, Iglésias SP, Pesci P, Tinti F, Cannas R. Combined COI barcode‐based methods to avoid mislabelling of threatened species of deep‐sea skates. Anim Conserv 2021. [DOI: 10.1111/acv.12716] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- L. Carugati
- Department of Life and Environmental Sciences University of Cagliari Cagliari Italy
| | - R. Melis
- Department of Life and Environmental Sciences University of Cagliari Cagliari Italy
| | - A. Cariani
- Department of Biological, Geological and Environmental Sciences (BiGeA) University of Bologna Bologna Italy
| | - A. Cau
- Department of Life and Environmental Sciences University of Cagliari Cagliari Italy
| | - V. Crobe
- Department of Biological, Geological and Environmental Sciences (BiGeA) University of Bologna Bologna Italy
| | - A. Ferrari
- Department of Biological, Geological and Environmental Sciences (BiGeA) University of Bologna Bologna Italy
| | - M. C. Follesa
- Department of Life and Environmental Sciences University of Cagliari Cagliari Italy
| | - M. L. Geraci
- Department of Biological Geological and Environmental Sciences (BiGeA) – Marine biology and fisheries laboratory University of Bologna Fano (PU) Italy
- Institute for Biological Resources and Marine Biotechnologies (IRBIM) National Research Council (CNR) Mazara del Vallo (TP) Italy
| | - S. P. Iglésias
- Institut de Systématique, Evolution, Biodiversité (ISYEB) Muséum national d’Histoire naturelleCNRSSorbonne UniversitéEPHEUniversité des AntillesStation Marine de Concarneau Concarneau France
| | - P. Pesci
- Department of Life and Environmental Sciences University of Cagliari Cagliari Italy
| | - F. Tinti
- Department of Biological, Geological and Environmental Sciences (BiGeA) University of Bologna Bologna Italy
| | - R. Cannas
- Department of Life and Environmental Sciences University of Cagliari Cagliari Italy
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Talavera G, Lukhtanov V, Pierce NE, Vila R. DNA barcodes combined with multi-locus data of representative taxa can generate reliable higher-level phylogenies. Syst Biol 2021; 71:382-395. [PMID: 34022059 PMCID: PMC8830075 DOI: 10.1093/sysbio/syab038] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 05/13/2021] [Accepted: 05/25/2021] [Indexed: 12/04/2022] Open
Abstract
Taxa are frequently labeled incertae sedis when their placement is debated at ranks above the species level, such as their subgeneric, generic, or subtribal placement. This is a pervasive problem in groups with complex systematics due to difficulties in identifying suitable synapomorphies. In this study, we propose combining DNA barcodes with a multilocus backbone phylogeny in order to assign taxa to genus or other higher-level categories. This sampling strategy generates molecular matrices containing large amounts of missing data that are not distributed randomly: barcodes are sampled for all representatives, and additional markers are sampled only for a small percentage. We investigate the effects of the degree and randomness of missing data on phylogenetic accuracy using simulations for up to 100 markers in 1000-tips trees, as well as a real case: the subtribe Polyommatina (Lepidoptera: Lycaenidae), a large group including numerous species with unresolved taxonomy. Our simulation tests show that when a strategic and representative selection of species for higher-level categories has been made for multigene sequencing (approximately one per simulated genus), the addition of this multigene backbone DNA data for as few as 5–10% of the specimens in the total data set can produce high-quality phylogenies, comparable to those resulting from 100% multigene sampling. In contrast, trees based exclusively on barcodes performed poorly. This approach was applied to a 1365-specimen data set of Polyommatina (including ca. 80% of described species), with nearly 8% of representative species included in the multigene backbone and the remaining 92% included only by mitochondrial COI barcodes, a phylogeny was generated that highlighted potential misplacements, unrecognized major clades, and placement for incertae sedis taxa. We use this information to make systematic rearrangements within Polyommatina, and to describe two new genera. Finally, we propose a systematic workflow to assess higher-level taxonomy in hyperdiverse groups. This research identifies an additional, enhanced value of DNA barcodes for improvements in higher-level systematics using large data sets. [Birabiro; DNA barcoding; incertae sedis; Kipepeo; Lycaenidae; missing data; phylogenomic; phylogeny; Polyommatina; supermatrix; systematics; taxonomy]
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Affiliation(s)
- Gerard Talavera
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia s/n, 08038 Barcelona, Catalonia, Spain.,Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, United States
| | - Vladimir Lukhtanov
- Department of Karyosystematics, Zoological Institute of Russian Academy of Sciences, Universitetskaya nab. 1, 199034 St. Petersburg, Russia
| | - Naomi E Pierce
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, United States
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-UPF), Passeig Marítim de la Barceloneta, 08003 Barcelona, Catalonia, Spain
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30
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Papa Y, Le Bail PY, Covain R. Genetic landscape clustering of a large DNA barcoding data set reveals shared patterns of genetic divergence among freshwater fishes of the Maroni Basin. Mol Ecol Resour 2021; 21:2109-2124. [PMID: 33892518 DOI: 10.1111/1755-0998.13402] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 03/27/2021] [Accepted: 04/13/2021] [Indexed: 11/27/2022]
Abstract
The Maroni is one of the most speciose basins of the Guianas and hosts a megadiverse freshwater fish community. Although taxonomic references based on morphological identification exist for both the Surinamese and Guianese parts of the basin, there are still taxonomic uncertainties concerning the status of several species. We used COI sequences of 1284 fish in conjunction with morphological and biogeographical evidence to assist with species delineation and discovery in order to validate and standardize the current taxonomy. This resulted in a final DNA barcode data set of 199 fish species (125 genera, 36 families and eight orders; 68.86% of strictly freshwater fishes from the basin), among which 25 are new putative candidate species flagged as requiring taxonomic update. DNA barcoding delineation through Barcode Index Numbers (BINs) revealed further cryptic diversity (230 BINs in total). To explore global genetic patterns across the basin, genetic divergence landscapes were computed for 128 species, showing a global trend of high genetic divergence between the Surinamese southwest (Tapanahony and Paloemeu), the Guianese southeast (Marouini, Litany, Tampok, etc.), and the river outlet in the north. This could be explained by lower levels of connectivity between these three main areas and/or the exchange of individuals between these areas and the neighbouring basins. A new method of ordination of genetic landscapes successfully assigned species into cluster groups based on their respective pattern of genetic divergence across the Maroni Basin: genetically homogeneous species were effectively discriminated from species showing high spatial genetic fragmentation and possible lower capacity for dispersal.
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Affiliation(s)
- Yvan Papa
- Herpetology and Ichthyology, Museum of Natural History of Geneva, Geneva, Switzerland.,School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | | | - Raphaël Covain
- Herpetology and Ichthyology, Museum of Natural History of Geneva, Geneva, Switzerland
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31
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Arida E, Ashari H, Dahruddin H, Fitriana YS, Hamidy A, Irham M, Kadarusman, Riyanto A, Wiantoro S, Zein MSA, Hadiaty RK, Apandi, Krey F, Kurnianingsih, Melmambessy EHP, Mulyadi, Ohee HL, Saidin, Salamuk A, Sauri S, Suparno, Supriatna N, Suruwaky AM, Laksono WT, Warikar EL, Wikanta H, Yohanita AM, Slembrouck J, Legendre M, Gaucher P, Cochet C, Delrieu-Trottin E, Thébaud C, Mila B, Fouquet A, Borisenko A, Steinke D, Hocdé R, Semiadi G, Pouyaud L, Hubert N. Exploring the vertebrate fauna of the Bird's Head Peninsula (Indonesia, West Papua) through DNA barcodes. Mol Ecol Resour 2021; 21:2369-2387. [PMID: 33942522 DOI: 10.1111/1755-0998.13411] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 04/06/2021] [Accepted: 04/13/2021] [Indexed: 11/27/2022]
Abstract
Biodiversity knowledge is widely heterogeneous across the Earth's biomes. Some areas, due to their remoteness and difficult access, present large taxonomic knowledge gaps. Mostly located in the tropics, these areas have frequently experienced a fast development of anthropogenic activities during the last decades and are therefore of high conservation concerns. The biodiversity hotspots of Southeast Asia exemplify the stakes faced by tropical countries. While the hotspots of Sundaland (Java, Sumatra, Borneo) and Wallacea (Sulawesi, Moluccas) have long attracted the attention of biologists and conservationists alike, extensive parts of the Sahul area, in particular the island of New Guinea, have been much less explored biologically. Here, we describe the results of a DNA-based inventory of aquatic and terrestrial vertebrate communities, which was the objective of a multidisciplinary expedition to the Bird's Head Peninsula (West Papua, Indonesia) conducted between 17 October and 20 November 2014. This expedition resulted in the assembly of 1005 vertebrate DNA barcodes. Based on the use of multiple species-delimitation methods (GMYC, PTP, RESL, ABGD), 264 molecular operational taxonomic units (MOTUs) were delineated, among which 75 were unidentified and an additional 48 were considered cryptic. This study suggests that the diversity of vertebrates of the Bird's Head is severely underestimated and considerations on the evolutionary origin and taxonomic knowledge of these biotas are discussed.
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Affiliation(s)
- Evy Arida
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Hidayat Ashari
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Hadi Dahruddin
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Yuli Sulistya Fitriana
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Amir Hamidy
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Mohammad Irham
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Kadarusman
- Politeknik Kelautan dan Perikanan Sorong, Jl. Kapitan Pattimura, Suprau, Indonesia
| | - Awal Riyanto
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Sigit Wiantoro
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Moch Syamsul Arifin Zein
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Renny K Hadiaty
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Apandi
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Frengky Krey
- Jurusan Perikanan, Fakultas Perikanan dan Ilmu Kelautan, Universitas Papua, Jl. Gunung Salju Amban, Manokwari, Indonesia
| | - Kurnianingsih
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Edy H P Melmambessy
- Program Studi Manajemen Sumberdaya Perairan, Fakultas Pertanian, Universitas Musamus, Jl. Kamizaun Mopah Lama, Rimba Jaya, Merauke, Indonesia
| | - Mulyadi
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Henderite L Ohee
- Jurusan Biologi, Fakultas MIPA, Universitas Cendrawasih, Jl. Kamp Wolker Waena Jayapura, Jayapura, Indonesia
| | - Saidin
- Politeknik Kelautan dan Perikanan Sorong, Jl. Kapitan Pattimura, Suprau, Indonesia
| | - Ayub Salamuk
- Dinas Kelautan dan Perikanan Kabupaten Kaimana, Jl.Utarum Kampung Coa, Kaimana, Indonesia
| | - Sopian Sauri
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Suparno
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Nanang Supriatna
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Amir M Suruwaky
- Politeknik Kelautan dan Perikanan Sorong, Jl. Kapitan Pattimura, Suprau, Indonesia
| | - Wahyudi Tri Laksono
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Evie L Warikar
- Jurusan Biologi, Fakultas MIPA, Universitas Cendrawasih, Jl. Kamp Wolker Waena Jayapura, Jayapura, Indonesia
| | - Hadi Wikanta
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Aksamina M Yohanita
- Jurusan Biologi, Fakultas MIPA, Universitas Papua Jl. Gunung Salju - Amban, Manokwari, Indonesia
| | - Jacques Slembrouck
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Montpellier, France
| | - Marc Legendre
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Montpellier, France
| | - Philippe Gaucher
- USR LEEISA- Laboratoire Ecologie, Evolution, Interactions des Systèmes amazoniens, Centre de Recherche de Montabo, cayenne, French Guiana
| | - Christophe Cochet
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Montpellier, France
| | | | | | - Borja Mila
- Department of Biodiversity and Evolutionary Biology, National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
| | - Antoine Fouquet
- UMR 5174 EDB CNRS, Université Paul Sabatier, IRD, Toulouse, France
| | - Alex Borisenko
- Department of Integrative Biology, Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Dirk Steinke
- Department of Integrative Biology, Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Régis Hocdé
- UMR 9190 MARBEC (IRD, UM, CNRS, IFREMER), Université de Montpellier, Montpellier, France
| | - Gono Semiadi
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Laurent Pouyaud
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Montpellier, France
| | - Nicolas Hubert
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Montpellier, France
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32
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Turanov SV, Kartavtsev YP. A complement to DNA barcoding reference library for identification of fish from the Northeast Pacific. Genome 2021; 64:927-936. [PMID: 33852820 DOI: 10.1139/gen-2020-0192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The seas of the North Pacific Ocean are characterized by a large variety of fish fauna, including endemic species. Molecular genetic methods, often based on DNA barcoding approaches, have been recently used to determine species boundaries and identify cryptic diversity within these species. This study complements the DNA barcode library of fish from the Northeast Pacific area. A library based on 154 sequences of the mitochondrial COI gene from 44 species was assembled and analyzed. It was found that 39 species (89%) can be unambiguously identified by the clear thresholds forming a barcoding gap. Deviations from the standard 2% threshold value resulted in detection of the species Enophrys lucasi in the sample, which is not typical for the eastern part of the Bering Sea. This barcoding gap also made it possible to identify naturally occurring low values of interspecific divergence of eulittoral taxa Aspidophoroides and the deep-sea genus Coryphaenoides. Synonymy of the genus Albatrossia in favor of the genus Coryphaenoides is suggested based on both the original and previously published data.
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Affiliation(s)
- Sergei V Turanov
- Laboratory of Molecular Systematic, A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, 690041 Vladivostok, Russia.,Chair of Water Biological Resources and Aquaculture, Far Eastern State Technical Fisheries University, 690087 Vladivostok, Russia
| | - Yuri Ph Kartavtsev
- Laboratory of Molecular Systematic, A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, 690041 Vladivostok, Russia
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33
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Nugent CM, Elliott TA, Ratnasingham S, Hebert PDN, Adamowicz SJ. Debar: A sequence-by-sequence denoiser for COI-5P DNA barcode data. Mol Ecol Resour 2021; 21:2832-2846. [PMID: 33749132 DOI: 10.1111/1755-0998.13384] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 03/05/2021] [Indexed: 12/14/2022]
Abstract
DNA barcoding and metabarcoding are now widely used to advance species discovery and biodiversity assessments. High-throughput sequencing (HTS) has expanded the volume and scope of these analyses, but elevated error rates introduce noise into sequence records that can inflate estimates of biodiversity. Denoising -the separation of biological signal from instrument (technical) noise-of barcode and metabarcode data currently employs abundance-based methods which do not capitalize on the highly conserved structure of the cytochrome c oxidase subunit I (COI) region employed as the animal barcode. This manuscript introduces debar, an R package that utilizes a profile hidden Markov model to denoise indel errors in COI sequences introduced by instrument error. In silico studies demonstrated that debar recognized 95% of artificially introduced indels in COI sequences. When applied to real-world data, debar reduced indel errors in circular consensus sequences obtained with the Sequel platform by 75%, and those generated on the Ion Torrent S5 by 94%. The false correction rate was less than 0.1%, indicating that debar is receptive to the majority of true COI variation in the animal kingdom. In conclusion, the debar package improves DNA barcode and metabarcode workflows by aiding the generation of more accurate sequences aiding the characterization of species diversity.
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Affiliation(s)
- Cameron M Nugent
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada.,Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Tyler A Elliott
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Sarah J Adamowicz
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
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Aghayeva P, Cozzolino S, Cafasso D, Ali-Zade V, Fineschi S, Aghayeva D. DNA barcoding of native Caucasus herbal plants: potentials and limitations in complex groups and implications for phylogeographic patterns. Biodivers Data J 2021; 9:e61333. [PMID: 33551655 PMCID: PMC7858560 DOI: 10.3897/bdj.9.e61333] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 01/07/2021] [Indexed: 11/12/2022] Open
Abstract
DNA barcoding has rapidly become a useful complementary tool in floristic investigations particularly for identifying specimens that lack diagnostic characters. Here, we assess the capability of three DNA barcode markers (chloroplast rpoB, accD and nuclear ITS) for correct species assignment in a floristic survey on the Caucasus. We focused on two herbal groups with potential for ornamental applications, namely orchids and asterids. On these two plant groups, we tested whether our selection of barcode markers allows identification of the “barcoding gap” in sequence identity and to distinguish between monophyletic species when employing distance-based methods. All markers successfully amplified most specimens, but we found that the rate of species-level resolution amongst selected markers largely varied in the two plant groups. Overall, for both lineages, plastid markers had a species-level assignment success rate lower than the nuclear ITS marker. The latter confirmed, in orchids, both the existence of a barcoding gap and that all accessions of the same species clustered together in monophyletic groups. Further, it also allowed the detection of a phylogeographic signal.The ITS marker resulted in its being the best performing barcode for asterids; however, none of the three tested markers showed high discriminatory ability. Even if ITS were revealed as the most promising plant barcode marker, we argue that the ability of this barcode for species assignment is strongly dependent on the evolutionary history of the investigated plant lineage.
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Affiliation(s)
- Parvin Aghayeva
- Institute of Botany, Azerbaijan National Academy of Sciences, Baku, Azerbaijan Institute of Botany, Azerbaijan National Academy of Sciences Baku Azerbaijan
| | - Salvatore Cozzolino
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Napoli, Italy Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo Napoli Italy
| | - Donata Cafasso
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Napoli, Italy Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo Napoli Italy
| | - Valida Ali-Zade
- Institute of Botany, Azerbaijan National Academy of Sciences, Baku, Azerbaijan Institute of Botany, Azerbaijan National Academy of Sciences Baku Azerbaijan
| | - Silvia Fineschi
- CNR - Istituto di Scienze del Patrimonio Culturale, Sesto Fiorentino, Italy CNR - Istituto di Scienze del Patrimonio Culturale Sesto Fiorentino Italy
| | - Dilzara Aghayeva
- Institute of Botany, Azerbaijan National Academy of Sciences, Baku, Azerbaijan Institute of Botany, Azerbaijan National Academy of Sciences Baku Azerbaijan
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35
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Collins JE, Rabone M, Vanagt T, Amon DJ, Gobin J, Huys I. Strengthening the global network for sharing of marine biological collections: recommendations for a new agreement for biodiversity beyond national jurisdiction. ICES JOURNAL OF MARINE SCIENCE : JOURNAL DU CONSEIL 2021; 78:305-314. [PMID: 33814897 PMCID: PMC7988798 DOI: 10.1093/icesjms/fsaa227] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 09/28/2020] [Accepted: 11/04/2020] [Indexed: 11/13/2022]
Abstract
Biological collections are fundamental to marine scientific research and understanding of biodiversity at various scales. Despite their key importance, sample collections and the institutes that house them are often underfunded and receive comparatively little attention in the discussions associated with global biodiversity agreements. Furthermore, access to collections can be limited by inadequate systems, infrastructure, and networks. With negotiations underway for a new implementing agreement on biodiversity beyond national jurisdiction, marine genetic resources (MGR), including questions on the sharing of benefits, remains the most debated and contentious element. Disparities remain between States regarding access to and utilization of marine biological samples (including MGR) from areas beyond national jurisdiction. Addressing capacity gaps related to collections could provide a point of agreement during negotiations and enhance global inclusivity in access to and utilization of MGR. Here, we examine both existing capacity and regional gaps in marine collections. We propose the strengthening of a distributed network of marine biological collections, building on existing initiatives and emphasizing best practices to bridge regional gaps. Our recommendations include: promoting scientific best practice for the curation of collections; alignment with ocean observing, and sampling initiatives; a potential pairing scheme for collections in developing and developed States; raising awareness of collections and benefits to marine science including through a global registry/directory; and promoting sustainable funding mechanisms to support collections and sustain global generation of contributors and users.
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Affiliation(s)
- Jane Eva Collins
- ABSint, Bruges, Belgium
- Faculty of Pharmaceutical Sciences, Clinical Pharmacology and Pharmacotherapy, KU Leuven, Leuven, Belgium
| | - Muriel Rabone
- Life Sciences Department, Natural History Museum, London, UK
| | | | - Diva J Amon
- Life Sciences Department, Natural History Museum, London, UK
| | - Judith Gobin
- Department of Life Sciences, University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Isabelle Huys
- Faculty of Pharmaceutical Sciences, Clinical Pharmacology and Pharmacotherapy, KU Leuven, Leuven, Belgium
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36
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Nugent CM, Adamowicz SJ. Alignment-free classification of COI DNA barcode data with the Python package Alfie. METABARCODING AND METAGENOMICS 2020. [DOI: 10.3897/mbmg.4.55815] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Characterization of biodiversity from environmental DNA samples and bulk metabarcoding data is hampered by off-target sequences that can confound conclusions about a taxonomic group of interest. Existing methods for isolation of target sequences rely on alignment to existing reference barcodes, but this can bias results against novel genetic variants. Effectively parsing targeted DNA barcode data from off-target noise improves the quality of biodiversity estimates and biological conclusions by limiting subsequent analyses to a relevant subset of available data. Here, we present Alfie, a Python package for the alignment-free classification of cytochrome c oxidase subunit I (COI) DNA barcode sequences to taxonomic kingdoms. The package determines k-mer frequencies of DNA sequences, and the frequencies serve as input for a neural network classifier that was trained and tested using ~58,000 publicly available COI sequences. The classifier was designed and optimized through a series of tests that allowed for the optimal set of DNA k-mer features and optimal machine learning algorithm to be selected. The neural network classifier rapidly assigns COI sequences of varying lengths to kingdoms with greater than 99% accuracy and is shown to generalize effectively and make accurate predictions about data from previously unseen taxonomic classes. The package contains an application programming interface that allows the Alfie package’s functionality to be extended to different DNA sequence classification tasks to suit a user’s need, including classification of different genes and barcodes, and classification to different taxonomic levels. Alfie is free and publicly available through GitHub (https://github.com/CNuge/alfie) and the Python package index (https://pypi.org/project/alfie/).
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37
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Delrieu‐Trottin E, Durand J, Limmon G, Sukmono T, Kadarusman, Sugeha HY, Chen W, Busson F, Borsa P, Dahruddin H, Sauri S, Fitriana Y, Zein MSA, Hocdé R, Pouyaud L, Keith P, Wowor D, Steinke D, Hanner R, Hubert N. Biodiversity inventory of the grey mullets (Actinopterygii: Mugilidae) of the Indo-Australian Archipelago through the iterative use of DNA-based species delimitation and specimen assignment methods. Evol Appl 2020; 13:1451-1467. [PMID: 32684969 PMCID: PMC7359824 DOI: 10.1111/eva.12926] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 01/16/2020] [Accepted: 01/20/2020] [Indexed: 12/25/2022] Open
Abstract
DNA barcoding opens new perspectives on the way we document biodiversity. Initially proposed to circumvent the limits of morphological characters to assign unknown individuals to known species, DNA barcoding has been used in a wide array of studies where collecting species identity constitutes a crucial step. The assignment of unknowns to knowns assumes that species are already well identified and delineated, making the assignment performed reliable. Here, we used DNA-based species delimitation and specimen assignment methods iteratively to tackle the inventory of the Indo-Australian Archipelago grey mullets, a notorious case of taxonomic complexity that requires DNA-based identification methods considering that traditional morphological identifications are usually not repeatable and sequence mislabeling is common in international sequence repositories. We first revisited a DNA barcode reference library available at the global scale for Mugilidae through different DNA-based species delimitation methods to produce a robust consensus scheme of species delineation. We then used this curated library to assign unknown specimens collected throughout the Indo-Australian Archipelago to known species. A second iteration of OTU delimitation and specimen assignment was then performed. We show the benefits of using species delimitation and specimen assignment methods iteratively to improve the accuracy of specimen identification and propose a workflow to do so.
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Affiliation(s)
- Erwan Delrieu‐Trottin
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE)Université de MontpellierMontpellier CedexFrance
- Museum für NaturkundeLeibniz Institute for Evolution and Biodiversity ScienceBerlinGermany
| | - Jean‐Dominique Durand
- UMR 9190 MARBEC (IRD, UM, CNRS, IFREMER)Université de MontpellierMontpellier CedexFrance
| | - Gino Limmon
- Maritime and Marine Science Center of ExcellenceUniversitas PattimuraAmbonIndonesia
| | - Tedjo Sukmono
- Department of BiologyUniversitas JambiJambiIndonesia
| | - Kadarusman
- Politeknik Kelautan dan Perikanan SorongKota SorongIndonesia
| | - Hagi Yulia Sugeha
- Research Center for OceanographyIndonesian Institute of SciencesJakartaIndonesia
| | - Wei‐Jen Chen
- Institute of OceanographyNational Taiwan UniversityTaipeiTaiwan
| | - Frédéric Busson
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE)Université de MontpellierMontpellier CedexFrance
- UMR 7208 BOREA (MNHN, CNRS, UPMC, IRD, UCBN)Muséum National d’Histoire NaturelleParis CedexFrance
| | - Philippe Borsa
- UMR 250 ENTROPIE (IRD, UR, UNC, CNRS, IFREMER), Centre IRD‐OccitanieMontpellierFrance
| | - Hadi Dahruddin
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE)Université de MontpellierMontpellier CedexFrance
- Division of ZoologyResearch Center for BiologyIndonesian Institute of Sciences (LIPI)CibinongIndonesia
| | - Sopian Sauri
- Division of ZoologyResearch Center for BiologyIndonesian Institute of Sciences (LIPI)CibinongIndonesia
| | - Yuli Fitriana
- Division of ZoologyResearch Center for BiologyIndonesian Institute of Sciences (LIPI)CibinongIndonesia
| | | | - Régis Hocdé
- UMR 9190 MARBEC (IRD, UM, CNRS, IFREMER)Université de MontpellierMontpellier CedexFrance
| | - Laurent Pouyaud
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE)Université de MontpellierMontpellier CedexFrance
| | - Philippe Keith
- UMR 7208 BOREA (MNHN, CNRS, UPMC, IRD, UCBN)Muséum National d’Histoire NaturelleParis CedexFrance
| | - Daisy Wowor
- Division of ZoologyResearch Center for BiologyIndonesian Institute of Sciences (LIPI)CibinongIndonesia
| | - Dirk Steinke
- Centre for Biodiversity GenomicsUniversity of GuelphGuelphONCanada
- Department of Integrative BiologyUniversity of GuelphGuelphONCanada
| | - Robert Hanner
- Centre for Biodiversity GenomicsUniversity of GuelphGuelphONCanada
- Department of Integrative BiologyUniversity of GuelphGuelphONCanada
| | - Nicolas Hubert
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE)Université de MontpellierMontpellier CedexFrance
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Nugent CM, Elliott TA, Ratnasingham S, Adamowicz SJ. coil: an R package for cytochrome c oxidase I (COI) DNA barcode data cleaning, translation, and error evaluation. Genome 2020; 63:291-305. [DOI: 10.1139/gen-2019-0206] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Biological conclusions based on DNA barcoding and metabarcoding analyses can be strongly influenced by the methods utilized for data generation and curation, leading to varying levels of success in the separation of biological variation from experimental error. The 5′ region of cytochrome c oxidase subunit I (COI-5P) is the most common barcode gene for animals, with conserved structure and function that allows for biologically informed error identification. Here, we present coil ( https://CRAN.R-project.org/package=coil ), an R package for the pre-processing and frameshift error assessment of COI-5P animal barcode and metabarcode sequence data. The package contains functions for placement of barcodes into a common reading frame, accurate translation of sequences to amino acids, and highlighting insertion and deletion errors. The analysis of 10 000 barcode sequences of varying quality demonstrated how coil can place barcode sequences in reading frame and distinguish sequences containing indel errors from error-free sequences with greater than 97.5% accuracy. Package limitations were tested through the analysis of COI-5P sequences from the plant and fungal kingdoms as well as the analysis of potential contaminants: nuclear mitochondrial pseudogenes and Wolbachia COI-5P sequences. Results demonstrated that coil is a strong technical error identification method but is not reliable for detecting all biological contaminants.
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Affiliation(s)
- Cameron M. Nugent
- Department of Integrative Biology, University of Guelph. Guelph, Ontario, Canada
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph. Guelph, Ontario, Canada
| | - Tyler A. Elliott
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph. Guelph, Ontario, Canada
| | - Sujeevan Ratnasingham
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph. Guelph, Ontario, Canada
| | - Sarah J. Adamowicz
- Department of Integrative Biology, University of Guelph. Guelph, Ontario, Canada
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Young RG, Yu J, Cote MJ, Hanner RH. The Molecular Data Organization for Publication (MDOP) R package to aid the upload of data to shared databases. Biodivers Data J 2020; 8:e50630. [PMID: 32377152 PMCID: PMC7192956 DOI: 10.3897/bdj.8.e50630] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 04/10/2020] [Indexed: 12/19/2022] Open
Abstract
Molecular identification methods, such as DNA barcoding, rely on centralized databases populated with morphologically identified individuals and their referential nucleotide sequence records. As molecular identification approaches have expanded in use to fields such as food fraud, environmental surveys, and border surveillance, there is a need for diverse international data sets. Although central data repositories, like the Barcode of Life Datasystems (BOLD), provided workarounds for formatting data for upload, these workarounds can be taxing on researchers with few resources and limited funding. To address these concerns, we present the Molecular Data Organization for Publication (MDOP) R package to assist researchers in uploading data to public databases. To illustrate the use of these scripts, we use the BOLD system as an example. The main intent of this writing is to assist in the movement of data, from academic, governmental, and other institutional computer systems, to public locations. The movement of these data can then better contribute to the global DNA barcoding initiative and other global molecular data efforts.
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Affiliation(s)
- Robert G Young
- University of Guelph, Guelph, Canada University of Guelph Guelph Canada
| | - Jiaojia Yu
- University of Guelph, Guelph, Canada University of Guelph Guelph Canada
| | - Marie-José Cote
- Canadian Food Inspection Agency, Ottawa, Canada Canadian Food Inspection Agency Ottawa Canada
| | - Robert H Hanner
- University of Guelph, Guelph, Canada University of Guelph Guelph Canada
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Limmon G, Delrieu-Trottin E, Patikawa J, Rijoly F, Dahruddin H, Busson F, Steinke D, Hubert N. Assessing species diversity of Coral Triangle artisanal fisheries: A DNA barcode reference library for the shore fishes retailed at Ambon harbor (Indonesia). Ecol Evol 2020; 10:3356-3366. [PMID: 32273993 PMCID: PMC7141007 DOI: 10.1002/ece3.6128] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 01/30/2020] [Accepted: 02/03/2020] [Indexed: 01/01/2023] Open
Abstract
The Coral Triangle (CT), a region spanning across Indonesia and Philippines, is home to about 4,350 marine fish species and is among the world's most emblematic regions in terms of conservation. Threatened by overfishing and oceans warming, the CT fisheries have faced drastic declines over the last decades. Usually monitored through a biomass-based approach, fisheries trends have rarely been characterized at the species level due to the high number of taxa involved and the difficulty to accurately and routinely identify individuals to the species level. Biomass, however, is a poor proxy of species richness, and automated methods of species identification are required to move beyond biomass-based approaches. Recent meta-analyses have demonstrated that species richness peaks at intermediary levels of biomass. Consequently, preserving biomass is not equal to preserving biodiversity. We present the results of a survey to estimate the shore fish diversity retailed at the harbor of Ambon Island, an island located at the center of the CT that display exceptionally high biomass despite high levels of threat, while building a DNA barcode reference library of CT shore fishes targeted by artisanal fisheries. We sampled 1,187 specimens and successfully barcoded 696 of the 760 selected specimens that represent 202 species. Our results show that DNA barcodes were effective in capturing species boundaries for 96% of the species examined, which opens new perspectives for the routine monitoring of the CT fisheries.
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Affiliation(s)
- Gino Limmon
- Pusat Kemaritiman dan Kelautan Universitas Pattimura (Maritime and Marine Science Center of Excellence) Ambon Indonesia
| | - Erwan Delrieu-Trottin
- Institut de Recherche pour le Développement UMR 226 ISEM (UM-CNRS-IRD-EPHE) Montpellier France
- Museum für Naturkunde Leibniz-Institut für Evolutions-und Biodiversitätsforschung an der Humboldt-Universität zu Berlin Berlin Germany
| | - Jesaya Patikawa
- Pusat Kemaritiman dan Kelautan Universitas Pattimura (Maritime and Marine Science Center of Excellence) Ambon Indonesia
| | - Frederik Rijoly
- Pusat Kemaritiman dan Kelautan Universitas Pattimura (Maritime and Marine Science Center of Excellence) Ambon Indonesia
| | - Hadi Dahruddin
- Division of Zoology Research Center for Biology Indonesian Institute of Sciences (LIPI) Cibinong Indonesia
| | - Frédéric Busson
- Institut de Recherche pour le Développement UMR 226 ISEM (UM-CNRS-IRD-EPHE) Montpellier France
- UMR 7208 BOREA (MNHN-CNRS-UPMC-IRD-UCBN) Muséum National d'Histoire Naturelle Paris France
| | - Dirk Steinke
- Department of Integrative Biology Centre for Biodiversity Genomics University of Guelph Guelph ON Canada
| | - Nicolas Hubert
- Institut de Recherche pour le Développement UMR 226 ISEM (UM-CNRS-IRD-EPHE) Montpellier France
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Capacity of United States federal government and its partners to rapidly and accurately report the identity (taxonomy) of non-native organisms intercepted in early detection programs. Biol Invasions 2019. [DOI: 10.1007/s10530-019-02147-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AbstractThe early detection of and rapid response to invasive species (EDRR) depends on accurate and rapid identification of non-native species. The 2016–2018 National Invasive Species Council Management Plan called for an assessment of US government (federal) capacity to report on the identity of non-native organisms intercepted through early detection programs. This paper serves as the response to that action item. Here we summarize survey-based findings and make recommendations for improving the federal government’s capacity to identify non-native species authoritatively in a timely manner. We conclude with recommendations to improve accurate identification within the context of EDRR by increasing coordination, maintaining taxonomic expertise, creating an identification tools clearinghouse, developing and using taxonomic standards for naming and identification protocols, expanding the content of DNA and DNA Barcode libraries, ensuring long-term sustainability of biological collections, and engaging and empowering citizens and citizen science groups.
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Bryant PJ, Arehart TE. Diversity and life-cycle analysis of Pacific Ocean zooplankton by videomicroscopy and DNA barcoding: Hydrozoa. PLoS One 2019; 14:e0218848. [PMID: 31652271 PMCID: PMC6814237 DOI: 10.1371/journal.pone.0218848] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 10/11/2019] [Indexed: 11/18/2022] Open
Abstract
Most, but not all cnidarian species in the class Hydrozoa have a life cycle in which a colonial, asexually reproducing hydroid phase alternates with a free-swimming, sexually reproducing medusa phase. They are not well known, in part because many of them are microscopic, at least in the medusa phase. Matching the two phases has previously required rearing of the organism from one phase to another, which has not often been possible. Here we show that DNA barcoding makes it possible to easily link life-cycle phases without the need for laboratory rearing. Hydrozoan medusae were collected by zooplankton tows in Newport Bay and the Pacific Ocean near Newport Beach, California, and hydroid colonies were collected from solid substrates in the same areas. Specimens were documented by videomicroscopy, preserved in ethanol, and sent to the Canadian Centre for DNA Barcoding at the University of Guelph, Ontario, Canada for sequencing of the COI DNA barcode. In the order Anthoathecata (athecate hydroids), DNA barcoding allowed for the discrimination between the medusae of eight putative species of Bougainvillia, and the hydroid stages were documented for two of these. The medusae of three putative species of Amphinema were identified, and the hydroid stages were identified for two of them. DNA barcodes were obtained from medusae of one species of Cladonema, one adult of the by-the wind Sailor, Velella velella, five putative species of Corymorpha with the matching hydroid phase for one; and Coryne eximia, Turritopsis dohrnii and Turritopsis nutricula with the corresponding hydroid phases. The actinula larvae and hydroid for the pink-hearted hydroid Ectopleura crocea were identified and linked by DNA barcoding. In the order Leptothecata (thecate hydroids) medusae were identified for Clytia elsaeoswaldae, Clytia gracilis and Clytia sp. 701 AC and matched with the hydroid phases for the latter two species. Medusae were matched with the hydroid phases for two species of Obelia (including O. dichotoma) and Eucheilota bakeri. Obelia geniculata was collected as a single hydroid. DNA barcodes were obtained for hydroids of Orthopyxis everta and three other species of Orthopyxis. One member of the family Solmarisidae, representing the order Narcomedusae, and one member (Liriope tetraphylla) of the order Trachymedusae were recognized as medusae. The results show the utility of DNA barcoding for matching life-cycle stages as well as for documenting the diversity of this class of organisms.
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Affiliation(s)
- Peter J. Bryant
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, United States of America
- * E-mail:
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Shen Y, Hubert N, Huang Y, Wang X, Gan X, Peng Z, He S. DNA barcoding the ichthyofauna of the Yangtze River: Insights from the molecular inventory of a mega‐diverse temperate fauna. Mol Ecol Resour 2019; 19:1278-1291. [DOI: 10.1111/1755-0998.12961] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 09/07/2018] [Accepted: 09/24/2018] [Indexed: 01/04/2023]
Affiliation(s)
- Yanjun Shen
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology Chinese Academy of Sciences Wuhan China
- University of Chinese Academy of Sciences Beijing China
| | - Nicolas Hubert
- Institut de Recherche pour le Développement UMR 226 ISEM (UM2‐CNRS‐IRD) Montpellier cedex 05 France
| | - Yan Huang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education) Southwest University School of Life Sciences Chongqing China
| | - Xuzheng Wang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology Chinese Academy of Sciences Wuhan China
| | - Xiaoni Gan
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology Chinese Academy of Sciences Wuhan China
| | - Zuogang Peng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education) Southwest University School of Life Sciences Chongqing China
| | - Shunping He
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology Chinese Academy of Sciences Wuhan China
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Morinière J, Balke M, Doczkal D, Geiger MF, Hardulak LA, Haszprunar G, Hausmann A, Hendrich L, Regalado L, Rulik B, Schmidt S, Wägele JW, Hebert PDN. A DNA barcode library for 5,200 German flies and midges (Insecta: Diptera) and its implications for metabarcoding-based biomonitoring. Mol Ecol Resour 2019; 19:900-928. [PMID: 30977972 PMCID: PMC6851627 DOI: 10.1111/1755-0998.13022] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 03/22/2019] [Accepted: 03/25/2019] [Indexed: 11/29/2022]
Abstract
This study summarizes results of a DNA barcoding campaign on German Diptera, involving analysis of 45,040 specimens. The resultant DNA barcode library includes records for 2,453 named species comprising a total of 5,200 barcode index numbers (BINs), including 2,700 COI haplotype clusters without species‐level assignment, so called “dark taxa.” Overall, 88 out of 117 families (75%) recorded from Germany were covered, representing more than 50% of the 9,544 known species of German Diptera. Until now, most of these families, especially the most diverse, have been taxonomically inaccessible. By contrast, within a few years this study provided an intermediate taxonomic system for half of the German Dipteran fauna, which will provide a useful foundation for subsequent detailed, integrative taxonomic studies. Using DNA extracts derived from bulk collections made by Malaise traps, we further demonstrate that species delineation using BINs and operational taxonomic units (OTUs) constitutes an effective method for biodiversity studies using DNA metabarcoding. As the reference libraries continue to grow, and gaps in the species catalogue are filled, BIN lists assembled by metabarcoding will provide greater taxonomic resolution. The present study has three main goals: (a) to provide a DNA barcode library for 5,200 BINs of Diptera; (b) to demonstrate, based on the example of bulk extractions from a Malaise trap experiment, that DNA barcode clusters, labelled with globally unique identifiers (such as OTUs and/or BINs), provide a pragmatic, accurate solution to the “taxonomic impediment”; and (c) to demonstrate that interim names based on BINs and OTUs obtained through metabarcoding provide an effective method for studies on species‐rich groups that are usually neglected in biodiversity research projects because of their unresolved taxonomy.
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Affiliation(s)
| | | | | | - Matthias F Geiger
- Zoological Research Museum Alexander Koenig - Leibniz Institute for Animal Biodiversity, Bonn, Germany
| | | | | | | | | | | | - Björn Rulik
- Zoological Research Museum Alexander Koenig - Leibniz Institute for Animal Biodiversity, Bonn, Germany
| | | | - Johann-Wolfgang Wägele
- Zoological Research Museum Alexander Koenig - Leibniz Institute for Animal Biodiversity, Bonn, Germany
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
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Sonet G, Snoeks J, Nagy ZT, Vreven E, Boden G, Breman FC, Decru E, Hanssens M, Ibala Zamba A, Jordaens K, Mamonekene V, Musschoot T, Van Houdt J, Van Steenberge M, Lunkayilakio Wamuini S, Verheyen E. DNA barcoding fishes from the Congo and the Lower Guinean provinces: Assembling a reference library for poorly inventoried fauna. Mol Ecol Resour 2019; 19:728-743. [DOI: 10.1111/1755-0998.12983] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 11/03/2018] [Accepted: 11/27/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Gontran Sonet
- OD Taxonomy and Phylogeny ‐ JEMU Royal Belgian Institute of Natural Sciences Brussels Belgium
| | - Jos Snoeks
- Department of Biology – Vertebrates, Entomology, JEMU Royal Museum for Central Africa Tervuren Belgium
- Laboratory of Biodiversity and Evolutionary Genomics KU Leuven Leuven Belgium
| | - Zoltán T. Nagy
- OD Taxonomy and Phylogeny ‐ JEMU Royal Belgian Institute of Natural Sciences Brussels Belgium
| | - Emmanuel Vreven
- Department of Biology – Vertebrates, Entomology, JEMU Royal Museum for Central Africa Tervuren Belgium
| | - Gert Boden
- Department of Biology – Vertebrates, Entomology, JEMU Royal Museum for Central Africa Tervuren Belgium
| | - Floris C. Breman
- Department of Biology – Vertebrates, Entomology, JEMU Royal Museum for Central Africa Tervuren Belgium
- Research, Biosystematics Group Wageningen University Wageningen The Netherlands
| | - Eva Decru
- Department of Biology – Vertebrates, Entomology, JEMU Royal Museum for Central Africa Tervuren Belgium
| | - Mark Hanssens
- Department of Biology – Vertebrates, Entomology, JEMU Royal Museum for Central Africa Tervuren Belgium
| | - Armel Ibala Zamba
- Institut de Développement Rural Université Marien Ngouabi Brazzaville Republic of the Congo
| | - Kurt Jordaens
- Department of Biology – Vertebrates, Entomology, JEMU Royal Museum for Central Africa Tervuren Belgium
- Department of Biology ‐ Evolutionary Ecology Group University of Antwerp Antwerp Belgium
| | - Victor Mamonekene
- Institut de Développement Rural Université Marien Ngouabi Brazzaville Republic of the Congo
| | - Tobias Musschoot
- Department of Biology – Vertebrates, Entomology, JEMU Royal Museum for Central Africa Tervuren Belgium
| | | | - Maarten Van Steenberge
- OD Taxonomy and Phylogeny ‐ JEMU Royal Belgian Institute of Natural Sciences Brussels Belgium
- Department of Biology – Vertebrates, Entomology, JEMU Royal Museum for Central Africa Tervuren Belgium
- Laboratory of Biodiversity and Evolutionary Genomics KU Leuven Leuven Belgium
| | - Soleil Lunkayilakio Wamuini
- Département de Biologie I. S. P. Mbanza‐Ngungu Mbanza‐Ngungu Democratic Republic of the Congo
- Functional and Evolutionary Morphology Laboratory University of Liège Liège Belgium
| | - Erik Verheyen
- OD Taxonomy and Phylogeny ‐ JEMU Royal Belgian Institute of Natural Sciences Brussels Belgium
- Department of Biology ‐ Evolutionary Ecology Group University of Antwerp Antwerp Belgium
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Phillips JD, Gillis DJ, Hanner RH. Incomplete estimates of genetic diversity within species: Implications for DNA barcoding. Ecol Evol 2019; 9:2996-3010. [PMID: 30891232 PMCID: PMC6406011 DOI: 10.1002/ece3.4757] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 09/03/2018] [Accepted: 10/12/2018] [Indexed: 02/01/2023] Open
Abstract
DNA barcoding has greatly accelerated the pace of specimen identification to the species level, as well as species delineation. Whereas the application of DNA barcoding to the matching of unknown specimens to known species is straightforward, its use for species delimitation is more controversial, as species discovery hinges critically on present levels of haplotype diversity, as well as patterning of standing genetic variation that exists within and between species. Typical sample sizes for molecular biodiversity assessment using DNA barcodes range from 5 to 10 individuals per species. However, required levels that are necessary to fully gauge haplotype variation at the species level are presumed to be strongly taxon-specific. Importantly, little attention has been paid to determining appropriate specimen sample sizes that are necessary to reveal the majority of intraspecific haplotype variation within any one species. In this paper, we present a brief outline of the current literature and methods on intraspecific sample size estimation for the assessment of COI DNA barcode haplotype sampling completeness. The importance of adequate sample sizes for studies of molecular biodiversity is stressed, with application to a variety of metazoan taxa, through reviewing foundational statistical and population genetic models, with specific application to ray-finned fishes (Chordata: Actinopterygii). Finally, promising avenues for further research in this area are highlighted.
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Affiliation(s)
- Jarrett D. Phillips
- School of Computer ScienceUniversity of GuelphGuelphOntarioCanada
- Centre for Biodiversity GenomicsBiodiversity Institute of OntarioUniversity of GuelphGuelphOntarioCanada
| | - Daniel J. Gillis
- School of Computer ScienceUniversity of GuelphGuelphOntarioCanada
| | - Robert H. Hanner
- Centre for Biodiversity GenomicsBiodiversity Institute of OntarioUniversity of GuelphGuelphOntarioCanada
- Department of Integrative BiologyUniversity of GuelphGuelphOntarioCanada
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Ekrem T, Stur E, Orton MG, Adamowicz SJ. DNA barcode data reveal biogeographic trends in Arctic non-biting midges. Genome 2018; 61:787-796. [DOI: 10.1139/gen-2018-0100] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Chironomid flies (non-biting midges) are among the most abundant and diverse animals in Arctic regions, but detailed analyses of species distributions and biogeographical patterns are hampered by challenging taxonomy and reliance on morphology for species-level identification. Here we take advantage of available DNA barcode data of Arctic Chironomidae in BOLD to analyse similarities in species distributions across a northern Nearctic – West Palearctic gradient. Using more than 260 000 barcodes representing 4666 BINs (Barcode Index Numbers) and 826 named species (some with interim names) from a combination of public and novel data, we show that the Greenland chironomid fauna shows affinities to both the Nearctic and the West Palearctic regions. While raw taxon counts indicate a strong Greenland – North American affinity, comparisons using Chao’s dissimilarity metric support a slightly higher similarity between Greenland and West Palearctic chironomid communities. Results were relatively consistent across different definitions of species taxonomic units, including morphologically determined species, BINs, and superBINs based on a ∼4.5% threshold. While most taxa found in Greenland are shared with at least one other region, reflecting circum-Arctic dispersal, our results also reveal that Greenland harbours a small endemic biodiversity. Our exploratory study showcases how DNA barcoding efforts using standardized gene regions contribute to an understanding of broad-scale patterns in biogeography by enabling joint analysis of public DNA sequence data derived from diverse prior studies.
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Affiliation(s)
- Torbjørn Ekrem
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Elisabeth Stur
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Matthew G. Orton
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, ON N1G 2W1, Canada
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Sarah J. Adamowicz
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, ON N1G 2W1, Canada
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
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Laska A, Majer A, Szydło W, Karpicka-Ignatowska K, Hornyák M, Labrzycka A, Skoracka A. Cryptic diversity within grass-associated Abacarus species complex (Acariformes: Eriophyidae), with the description of a new species, Abacarus plumiger n. sp. EXPERIMENTAL & APPLIED ACAROLOGY 2018; 76:1-28. [PMID: 30171478 DOI: 10.1007/s10493-018-0291-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 08/24/2018] [Indexed: 05/20/2023]
Abstract
Accurate estimation of species richness is often complex as genetic divergence is not always accompanied by appreciable morphological differentiation. In consequence, cryptic lineages or species evolve. Cryptic speciation is common especially in taxa characterized by small and simplified bodies, what makes their proper identification challenging. The cereal rust mite, Abacarus hystrix, was regarded for a long time as a species associated with a wide range of grass hosts, whereas wide host ranges are rather rare in eriophyoid mites. Therefore, the generalist status of A. hystrix was questioned. In this paper we demonstrate that the diversity within Abacarus species associated with grasses is more complex than it was previously thought. The 78 Abacarus mtDNA COI sequences used in this study formed 10 highly supported clades (bootstrap value 99%) and four more distinct genetic lineages were represented by unique sequences. The genetic distances between them ranged from 6.6 to 26.5%. Moreover, morphological study and genetic approach based on the combination of the Poisson Tree Processes model for species delimitation (PTP) and a Bayesian implementation of PTP (bPTP), and Neighbour Joining analyses led to delimitation of a new species within the Abacarus complex: Abacarus plumiger, specialized on smooth brome (Bromus inermis). Furthermore, our analyses demonstrated a pattern of host-associated differentiation within the complex. Overall, our study indicates that cryptic speciation occurs in the grass-associated Abacarus genus, and suggests the need for more extensive sampling using integrative methods.
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Affiliation(s)
- Alicja Laska
- Population Ecology Lab, Faculty of Biology, Adam Mickiewicz University, Poznań, Umultowska 89, 61-614, Poznań, Poland.
| | - Agnieszka Majer
- Population Ecology Lab, Faculty of Biology, Adam Mickiewicz University, Poznań, Umultowska 89, 61-614, Poznań, Poland
| | - Wiktoria Szydło
- Department of Entomology, University of Nebraska-Lincoln, 103 Entomology Hall, Lincoln, NE, 68583-0816, USA
| | - Kamila Karpicka-Ignatowska
- Population Ecology Lab, Faculty of Biology, Adam Mickiewicz University, Poznań, Umultowska 89, 61-614, Poznań, Poland
| | - Marta Hornyák
- Department of Plant Physiology, Faculty of Agriculture and Economics, University of Agriculture in Krakow, Podłużna 3, 30-239, Kraków, Poland
| | - Anna Labrzycka
- Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University, Poznań, Umultowska 89, 61-614, Poznań, Poland
| | - Anna Skoracka
- Population Ecology Lab, Faculty of Biology, Adam Mickiewicz University, Poznań, Umultowska 89, 61-614, Poznań, Poland
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Lörz AN, Jażdżewska AM, Brandt A. A new predator connecting the abyssal with the hadal in the Kuril-Kamchatka Trench, NW Pacific. PeerJ 2018; 6:e4887. [PMID: 29892501 PMCID: PMC5994337 DOI: 10.7717/peerj.4887] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 05/13/2018] [Indexed: 01/25/2023] Open
Abstract
The bathyal to hadal deep sea of north-west Pacific Ocean was recently intensively sampled during four international expeditions (KuramBio I and II, SoJaBio and SokhoBio). A large amphipod, Rhachotropis saskia n. sp., was sampled in the Kuril-Kamchatka Trench and increases the number of described hadal species of that area to eight. A detailed description of the new species is provided, including illustrations, scanning-microscope images and molecular analysis. This predatory species was sampled at both continental and ocean abyssal margins of the Kuril-Kamchatka Trench as well as at hadal depths of the trench. The wide bathymetric distribution of the new species over more than 3,000 m is confirmed by molecular analysis, indicating that the Kuril Kamchatka Trench is not a distribution barrier for this species. However, the molecular analysis indicated the presence of isolation by distance of the populations of the studied taxon.
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Affiliation(s)
- Anne-Nina Lörz
- Centre of Natural History, Zoological Museum, University of Hamburg CeNak, Hamburg, Germany
| | - Anna Maria Jażdżewska
- Laboratory of Polar Biology and Oceanobiology, Department of Invertebrate Zoology and Hydrobiology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Angelika Brandt
- Department of Marine Zoology, Section Crustacea, Senckenberg Research Institute and Natural History Museum, Frankfurt am Main, Germany
- Institute for Ecology, Evolution and Diversity, Goethe-University of Frankfurt, Frankfurt am Main, Germany
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Accumulation and Dissolution of Magnetite Crystals in a Magnetically Responsive Ciliate. Appl Environ Microbiol 2018; 84:AEM.02865-17. [PMID: 29439993 DOI: 10.1128/aem.02865-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 02/05/2018] [Indexed: 11/20/2022] Open
Abstract
Magnetotactic bacteria (MTB) represent a group of microorganisms that are widespread in aquatic habitats and thrive at oxic-anoxic interfaces. They are able to scavenge high concentrations of iron thanks to the biomineralization of magnetic crystals in their unique organelles, the so-called magnetosome chains. Although their biodiversity has been intensively studied, their ecology and impact on iron cycling remain largely unexplored. Predation by protozoa was suggested as one of the ecological processes that could be involved in the release of iron back into the ecosystem. Magnetic protozoa were previously observed in aquatic environments, but their diversity and the fate of particulate iron during grazing are poorly documented. In this study, we report the morphological and molecular characterizations of a magnetically responsive MTB-grazing protozoan able to ingest high quantities of MTB. This protozoan is tentatively identified as Uronema marinum, a ciliate known to be a predator of bacteria. Using light and electron microscopy, we investigated in detail the vacuoles in which the lysis of phagocytized prokaryotes occurs. We carried out high-resolution observations of aligned magnetosome chains and ongoing dissolution of crystals. Particulate iron in the ciliate represented approximately 0.01% of its total volume. We show the ubiquity of this interaction in other types of environments and describe different grazing strategies. These data contribute to the mounting evidence that the interactions between MTB and protozoa might play a significant role in iron turnover in microaerophilic habitats.IMPORTANCE Identifying participants of each biogeochemical cycle is a prerequisite to our understanding of ecosystem functioning. Magnetotactic bacteria (MTB) participate in iron cycling by concentrating large amounts of biomineralized iron minerals in their cells, which impacts their chemical environment at, or below, the oxic-anoxic transition zone in aquatic habitats. It was shown that some protozoa inhabiting this niche could become magnetic by the ingestion of magnetic crystals biomineralized by grazed MTB. In this study, we show that magnetic MTB grazers are commonly observed in marine and freshwater sediments and can sometimes accumulate very large amounts of particulate iron. We describe here different phagocytosis strategies, determined using magnetic particles from MTB as tracers after their ingestion by the protozoa. This study paves the way for potential scientific or medical applications using MTB grazers as magnetosome hyperaccumulators.
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