1
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Peres PA, Mantelatto FL. Demographic changes and life-history strategies predict the genetic diversity in crabs. J Evol Biol 2023; 36:432-443. [PMID: 36537369 DOI: 10.1111/jeb.14138] [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: 06/22/2022] [Revised: 10/15/2022] [Accepted: 10/24/2022] [Indexed: 12/24/2022]
Abstract
Uncovering what predicts genetic diversity (GD) within species can help us access the status of populations and their evolutionary potential. Traits related to effective population size show a proportional association to GD, but evidence supports life-history strategies and habitat as the drivers of GD variation. Instead of investigating highly divergent taxa, focusing on one group could help to elucidate the factors influencing the GD. Additionally, most empirical data is based on vertebrate taxa; therefore, we might be missing novel patterns of GD found in neglected invertebrate groups. Here, we investigated the predictors of the GD in crabs (Brachyura) by compiling the most comprehensive cytochrome c oxidase subunit I (COI) available. Eight predictor variables were analysed across 150 species (16 992 sequences) using linear models (multiple linear regression) and comparative methods (PGLS). Our results indicate that population size fluctuation represents the most critical trait predicting GD, with species that have undergone bottlenecks followed by population expansion showing lower GD. Egg size, pelagic larval duration and habitat might play a role probably because of their association with how species respond to disturbances. Ultimately, K-strategists that have undergone bottlenecks are the species showing lower GD. Some variables do not show an association with GD as expected, most likely due to the taxon-specific role of some predictors, which should be considered in further investigations and generalizations. This work highlights the complexity underlying the predictors of GD and adds results from a marine invertebrate group to the current understanding of this topic.
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Affiliation(s)
- Pedro A Peres
- Faculty of Philosophy, Sciences and Letters at Ribeirão Preto (FFCLRP), Laboratory of Bioecology and Crustacean Systematics (LBSC), Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Fernando L Mantelatto
- Faculty of Philosophy, Sciences and Letters at Ribeirão Preto (FFCLRP), Laboratory of Bioecology and Crustacean Systematics (LBSC), Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
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2
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Han W, Tang H, Wei L, Zhang E. The first DNA barcode library of Chironomidae from the Tibetan Plateau with an evaluation of the status of the public databases. Ecol Evol 2023; 13:e9849. [PMID: 36861023 PMCID: PMC9969238 DOI: 10.1002/ece3.9849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 01/26/2023] [Accepted: 02/02/2023] [Indexed: 03/03/2023] Open
Abstract
The main aim of this study was to curate a COI barcode library of Chironomidae from the Tibetan Plateau (TP) as an essential supplement to the public database. Another aim is to evaluate the current status of the public database of Chironomidae in aspects of taxonomic coverage, geographic representation, barcode quality, and efficiency for molecular identification, the Tibetan Plateau, China. In this study, 512 individuals of Chironomidae from the TP were identified based on morphological taxonomy and barcode analysis. The metadata of public records of Chironomidae were downloaded from the BOLD, and the quality of the public barcodes was ranked using the BAGS program. The reliability of the public library for molecular identification was evaluated with the newly curated library using the BLAST method. The newly curated library comprised 159 barcode species of 54 genera, of which 58.4% of species were likely new to science. There were great gaps in the taxonomic coverage and geographic representation in the public database, and only 29.18% of barcodes were identified at the species level. The quality of the public database was of concern, with only 20% of species being determined as concordant between BINs and morphological species. The accuracy of molecular identification using the public database was poor, and about 50% of matched barcodes could be correctly identified at the species level at the identity threshold of 97%. Based on these data, some recommendations are included here for improving barcoding studies on Chironomidae. The species richness of Chironomidae from the TP is much higher than ever recorded. Barcodes from more taxonomic groups and geographic regions are urgently needed to fill the great gap in the current public database of Chironomidae. Users should take caution when public databases are adopted as reference libraries for the taxonomic assignment.
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Affiliation(s)
- Wu Han
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and LimnologyChinese Academy of ScienceNanjingChina
- University of Chinese Academy of SciencesBeijing100039China
| | - Hongqu Tang
- Life Science and Technology CollegeJinan UniversityGuangzhouChina
| | - Lili Wei
- Life Science and Technology CollegeJinan UniversityGuangzhouChina
| | - Enlou Zhang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and LimnologyChinese Academy of ScienceNanjingChina
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3
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Siregar IZ, Majiidu M, Dwiyanti FG, Harnelly E, Damayanti R, Karlinasari L, Rafi M, Septaningsih DA, Parker-Forney M. Collecting Wood Core Samples from Macassar Ebony (Diospyros celebica Bakh.) for Multi-Purpose Analysis using Pickering Punch. MethodsX 2022; 9:101728. [PMID: 35677845 PMCID: PMC9168166 DOI: 10.1016/j.mex.2022.101728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 05/08/2022] [Indexed: 11/02/2022] Open
Abstract
Sample collection activities for a study of population genetics across the natural distribution of targeted tree species require a lot of resources, mainly if repeated field visits are necessary. Conventionally, population genetic studies use good sample material like leaves. In addition, cambium or small pieces of fresh wood can be used to replace leaf samples. Currently, restrictions from the permit regulation have caused only a limited number of samples that can be collected. Therefore, efficient use of samples must be designed to maximize their uses for research. Due to the small amount of successfully sampled materials, hence there are limitations to extend their uses for other analyses and are often sufficient only for genetic analysis. Therefore, innovation in sampling methods using pickering punch (https://www.agroisolab.com/pickering-punch) to collect ebony wood cores in this study is required to cover multi-analyses not only limited to genetics but also for other analyses such as isotopes, near-infrared spectroscopy (NIRs), anatomy, and chemical compounds.Pickering punch is recommended for efficient wood core sample collection from ebony standing trees. 323 wood core samples were successfully collected from 16 natural populations across Celebes (Sulawesi). Multi-analyses studies on sampled wood cores are possible for ebony wood identification (e.g., species and origin/provenance).
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4
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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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5
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Lin X, Jiang K, Liu W, Liu W, Bu W, Wang X, Mo L. Toward a global DNA barcode reference library of the intolerant nonbiting midge genus Rheocricotopus Brundin, 1956. Ecol Evol 2021; 11:12161-12172. [PMID: 34522368 PMCID: PMC8427567 DOI: 10.1002/ece3.7979] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/16/2021] [Accepted: 07/19/2021] [Indexed: 01/01/2023] Open
Abstract
Environmental DNA metabarcoding is becoming a predominant tool in biodiversity assessment, as this time- and cost-efficient tactics have the ability to increase monitoring accuracy. As a worldwide distributed genus, Rheocricotopus Brundin, 1956 still does not possess a complete and comprehensive global DNA barcode reference library for biodiversity monitoring. In the present study, we compiled a cytochrome c oxidase subunit 1 (COI) DNA barcode library of Rheocricotopus with 434 barcodes around the world, including 121 newly generated DNA barcodes of 32 morphospecies and 313 public barcodes. Automatic Barcode Gap Discovery (ABGD) was applied on the 434 COI barcodes to provide a comparison between the operational taxonomic units (OTU) number calculated from the Barcode Index Number (BIN) with the "Barcode Gap Analysis" and neighbor-joining (NJ) tree analysis. Consequently, these 434 COI barcodes were clustered into 78 BINs, including 42 new BINs. ABGD yielded 51 OTUs with a prior intraspecific divergence of Pmax = 7.17%, while NJ tree revealed 52 well-separated clades. Conservatively, 14 unknown species and one potential synonym were uncovered with reference to COI DNA barcodes. Besides, based on our ecological analysis, we discovered that annual mean temperature and annual precipitation could be considered as key factors associated with distribution of certain members from this genus. Our global DNA barcode reference library of Rheocricotopus provides one fundamental database for accurate species delimitation in Chironomidae taxonomy and facilitates the biodiversity monitoring of aquatic biota.
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Affiliation(s)
- Xiao‐Long Lin
- College of Life SciencesNankai UniversityTianjinChina
| | - Kun Jiang
- College of Life SciencesNankai UniversityTianjinChina
| | - Wen‐Bin Liu
- Tianjin Key Laboratory of Conservation and Utilization of Animal DiversityTianjin Normal UniversityTianjinChina
| | - Wei Liu
- College of Life SciencesNankai UniversityTianjinChina
| | - Wen‐Jun Bu
- College of Life SciencesNankai UniversityTianjinChina
| | - Xin‐Hua Wang
- College of Life SciencesNankai UniversityTianjinChina
| | - Lidong Mo
- Crowther LabInstitute of Integrative BiologyETH Zurich (Swiss Federal Institute of Technology)ZurichSwitzerland
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Heylen OCG, Debortoli N, Marescaux J, Olofsson JK. A Revised Phylogeny of the Mentha spicata Clade Reveals Cryptic Species. PLANTS (BASEL, SWITZERLAND) 2021; 10:819. [PMID: 33924227 PMCID: PMC8074783 DOI: 10.3390/plants10040819] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/30/2021] [Accepted: 04/18/2021] [Indexed: 05/29/2023]
Abstract
The genus Mentha is taxonomically and phylogenetically challenging due to complex genomes, polyploidization and an extensive historical nomenclature, potentially hiding cryptic taxa. A straightforward interpretation of phylogenetic relationships within the section Mentha is further hindered by dominant but outdated concepts on historically identified hybrid taxa. Mentha spicata is traditionally considered to be of hybrid origin, but the evidence for this is weak. Here, we aim to understand the phylogenetic relationships within the section Mentha using large sample sizes and to revisit the hybrid status and identity of M. spicata. We show that two of three traditional species in the subsection Spicatae are polyphyletic, as is the subsection as a whole, while the real number of cryptic species was underestimated. Compared to previous studies we present a fundamentally different phylogeny, with a basal split between M. spicata s.s. and M. longifolia s.s. Cluster analyses of morphological and genotypic data demonstrate that there is a dissociation between morphologically and genotypically defined groups of samples. We did not find any evidence that M. spicata is of hybrid origin, and we conclude its taxonomic status should be revised. The combination of genetic and phenotypic information is essential when evaluating hyperdiverse taxonomic groups.
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Affiliation(s)
| | | | | | - Jill K. Olofsson
- Section for GeoGenetics, GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5, bygning 7, DK-1353 Copenhagen, Denmark;
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Lin X, Mo L, Bu W, Wang X. The first comprehensive DNA barcode reference library of Chinese
Tanytarsus
(Diptera: Chironomidae) for environmental DNA metabarcoding. DIVERS DISTRIB 2020. [DOI: 10.1111/ddi.13209] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Affiliation(s)
- Xiao‐Long Lin
- College of Life Sciences Nankai University Tianjin China
- Department of Natural History NTNU University Museum Norwegian University of Science and Technology Trondheim Norway
| | - Lidong Mo
- Institute of Integrative Biology ETH Zurich (Swiss Federal Institute of Technology) Zurich Switzerland
| | - Wen‐Jun Bu
- College of Life Sciences Nankai University Tianjin China
| | - Xin‐Hua Wang
- College of Life Sciences Nankai University Tianjin China
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8
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Jiang HH, Li B, Ma Y, Bai SY, Dahmer TD, Linacre A, Xu YC. Forensic validation of a panel of 12 SNPs for identification of Mongolian wolf and dog. Sci Rep 2020; 10:13249. [PMID: 32764603 PMCID: PMC7413520 DOI: 10.1038/s41598-020-70225-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 07/24/2020] [Indexed: 11/26/2022] Open
Abstract
Wolf (Canis lupus) is a species included in appendices of CITES and is often encountered in cases of alleged poaching and trafficking of their products. When such crimes are suspected, those involved may attempt to evade legal action by claiming that the animals involved are domestic dogs (C. l. familiaris). To respond effectively to such claims, law enforcement agencies require reliable and robust methods to distinguish wolves from dogs. Reported molecular genetic methods are either unreliable (mitogenome sequence based), or operationally cumbersome and require much DNA (un-multiplexed microsatellites), or financially expensive (genome wide SNP genotyping). We report on the validation of a panel of 12 ancestral informative single nucleotide polymorphism (SNP) markers for discriminating wolves from dogs. A SNaPshot multiplex genotyping system was developed for the panel, and 97 Mongolian wolves (C. l. chanco) and 108 domestic dogs were used for validation. Results showed this panel had high genotyping success (0.991), reproducibility (1.00) and origin assignment accuracy (0.97 ± 0.05 for dogs and 1.00 ± 0.03 for wolves). Species-specificity testing suggested strong tolerance to DNA contamination across species, except for Canidae. The minimum DNA required for reliable genotyping was 6.25 pg/μl. The method and established gene frequency database are available to support identification of wolves and dogs by law enforcement agencies.
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Affiliation(s)
- Hong Hui Jiang
- College of Wildlife and Protected Areas, Northeast Forestry University, No. 26, Hexing Road, Xiangfang District, Harbin, 150040, China
| | - Bo Li
- College of Wildlife and Protected Areas, Northeast Forestry University, No. 26, Hexing Road, Xiangfang District, Harbin, 150040, China.
- National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization, No. 26, Hexing Road, Xiangfang District, Harbin, 150040, China.
- National Forestry and Grassland Administration Detecting Center of Wildlife, No. 26, Hexing Road, Xiangfang District, Harbin, 150040, China.
| | - Yue Ma
- College of Wildlife and Protected Areas, Northeast Forestry University, No. 26, Hexing Road, Xiangfang District, Harbin, 150040, China
- National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization, No. 26, Hexing Road, Xiangfang District, Harbin, 150040, China
| | - Su Ying Bai
- College of Wildlife and Protected Areas, Northeast Forestry University, No. 26, Hexing Road, Xiangfang District, Harbin, 150040, China
- National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization, No. 26, Hexing Road, Xiangfang District, Harbin, 150040, China
| | | | - Adrian Linacre
- College of Science and Engineering, Flinders University, Adelaide, SA, 5042, Australia
| | - Yan Chun Xu
- College of Wildlife and Protected Areas, Northeast Forestry University, No. 26, Hexing Road, Xiangfang District, Harbin, 150040, China.
- National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization, No. 26, Hexing Road, Xiangfang District, Harbin, 150040, China.
- National Forestry and Grassland Administration Detecting Center of Wildlife, No. 26, Hexing Road, Xiangfang District, Harbin, 150040, China.
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9
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Kolter A, Gemeinholzer B. Plant DNA barcoding necessitates marker-specific efforts to establish more comprehensive reference databases. Genome 2020; 64:265-298. [PMID: 32649839 DOI: 10.1139/gen-2019-0198] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The problem of low species-level identification rates in plants by DNA barcoding is exacerbated by the fact that reference databases are far from being comprehensive. We investigate the impact of increased sampling depth on identification success by analyzing the efficacy of established plant barcode marker sequences (rbcL, matK, trnL-trnF, psbA-trnH, ITS). Adding sequences of the same species to the reference database led to an increase in correct species assignment of +10.9% for rbcL and +19.0% for ITS. Simultaneously, erroneous identification dropped from ∼40% to ∼12.5%. Despite its evolutionary constraints, ITS showed the highest identification rate and identification gain by increased sampling effort, which makes it a very suitable marker in the planning phase of a barcode study. The limited sequence availability of trnL-trnF is problematic for an otherwise very promising plastid plant barcoding marker. Future developments in machine learning algorithms have the potential to give new impetus to plant barcoding, but are dependent on extensive reference databases. We expect that our results will be incorporated into future plans for the development of DNA barcoding reference databases and will lead to these being developed with greater depth and taxonomic coverage.
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Affiliation(s)
- Andreas Kolter
- Justus Liebig University Giessen, Systematic Botany, Heinrich-Buff-Ring 38, Giessen, Hessen, DE 35390, Germany.,Justus Liebig University Giessen, Systematic Botany, Heinrich-Buff-Ring 38, Giessen, Hessen, DE 35390, Germany
| | - Birgit Gemeinholzer
- Justus Liebig University Giessen, Systematic Botany, Heinrich-Buff-Ring 38, Giessen, Hessen, DE 35390, Germany.,Justus Liebig University Giessen, Systematic Botany, Heinrich-Buff-Ring 38, Giessen, Hessen, DE 35390, Germany
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10
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Phillips JD, French SH, Hanner RH, Gillis DJ. HACSim: an R package to estimate intraspecific sample sizes for genetic diversity assessment using haplotype accumulation curves. PeerJ Comput Sci 2020; 6:e243. [PMID: 33816897 PMCID: PMC7924493 DOI: 10.7717/peerj-cs.243] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 11/07/2019] [Indexed: 05/25/2023]
Abstract
Assessing levels of standing genetic variation within species requires a robust sampling for the purpose of accurate specimen identification using molecular techniques such as DNA barcoding; however, statistical estimators for what constitutes a robust sample are currently lacking. Moreover, such estimates are needed because most species are currently represented by only one or a few sequences in existing databases, which can safely be assumed to be undersampled. Unfortunately, sample sizes of 5-10 specimens per species typically seen in DNA barcoding studies are often insufficient to adequately capture within-species genetic diversity. Here, we introduce a novel iterative extrapolation simulation algorithm of haplotype accumulation curves, called HACSim (Haplotype Accumulation Curve Simulator) that can be employed to calculate likely sample sizes needed to observe the full range of DNA barcode haplotype variation that exists for a species. Using uniform haplotype and non-uniform haplotype frequency distributions, the notion of sampling sufficiency (the sample size at which sampling accuracy is maximized and above which no new sampling information is likely to be gained) can be gleaned. HACSim can be employed in two primary ways to estimate specimen sample sizes: (1) to simulate haplotype sampling in hypothetical species, and (2) to simulate haplotype sampling in real species mined from public reference sequence databases like the Barcode of Life Data Systems (BOLD) or GenBank for any genomic marker of interest. While our algorithm is globally convergent, runtime is heavily dependent on initial sample sizes and skewness of the corresponding haplotype frequency distribution.
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Affiliation(s)
| | - Steven H. French
- School of Computer Science, University of Guelph, Guelph, Ontario, Canada
| | - Robert H. Hanner
- Department of Integrative Biology, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Daniel J. Gillis
- School of Computer Science, University of Guelph, Guelph, Ontario, Canada
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11
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Zhang Z, Wang X, Zhang Z, Yao H, Zhang X, Zhang Y, Zhang B. The impact of genetic diversity on the accuracy of DNA barcoding to identify species: A study on the genus Phellodendron. Ecol Evol 2019; 9:10723-10733. [PMID: 31624576 PMCID: PMC6787823 DOI: 10.1002/ece3.5590] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 07/28/2019] [Accepted: 07/30/2019] [Indexed: 11/30/2022] Open
Abstract
DNA barcoding is widely used in species identification, but there is considerable controversy regarding the extent of sampling in research methods. Some scholars have proposed that this small sample size underestimates the intraspecific genetic diversity, which would impact on the accuracy of DNA barcoding to identify species. In study, we selected all Phellodendron species (including P. amurense Rupr., P. chinense Schneid., and P. chinense var. glabriusculum Schneid.) as the materials, collected 59 P. amurense samples from 35 populations greatly to represent the genetic diversity, and analyzed the haplotype, genetic distance, barcoding gap, and Neighbor-Joining (NJ) trees based on psbA-trnH and internal transcribed spacer gene sequences. Additionally, a sampling simulation was conducted to assess the correlation between genetic diversity and the number of populations. Finally, analysis of critical geographical populations was performed. Based on analysis of haplotype, genetic distance, barcoding gap, and NJ trees, we found that eight P. amurense samples impacted on the effectiveness of DNA barcoding, which genetic information were very important to identify Phellodendron species. Moreover, the result of the NJ tree analysis performed the small-scale P. amurense sample size did not completely match the objective phylogenetic relationship in Phellodendron. In simulation sampling analysis, the data showed the genetic diversity indexes at the same population level gradually decreased and stabilized as the number of simulation sampling populations increased. We found that 1-2 samples from over 24 populations based on uniform geographical distribution could represent 80% of the genetic diversity of P. amurense and ensure authenticity and reliability of DNA barcoding. Thus, we proposed it is particularly important adequately samples to cover infraspecific genetic diversity in order to ensure identification accuracy of DNA barcoding.
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Affiliation(s)
- Zhi‐peng Zhang
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal MedicineMinistry of Education/Institute of Medicinal Plant DevelopmentChinese Academy of Medical SciencesPeking Union Medical CollegeBeijingChina
| | - Xiao‐yue Wang
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal MedicineMinistry of Education/Institute of Medicinal Plant DevelopmentChinese Academy of Medical SciencesPeking Union Medical CollegeBeijingChina
| | - Zhao Zhang
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal MedicineMinistry of Education/Institute of Medicinal Plant DevelopmentChinese Academy of Medical SciencesPeking Union Medical CollegeBeijingChina
| | - Hui Yao
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal MedicineMinistry of Education/Institute of Medicinal Plant DevelopmentChinese Academy of Medical SciencesPeking Union Medical CollegeBeijingChina
| | - Xiao‐mei Zhang
- China‐ASEAN Traditional Medicine Cooperation and Exchange CenterGuangxi Botanical Garden of Medicinal PlantsNanningChina
| | - Yang Zhang
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal MedicineMinistry of Education/Institute of Medicinal Plant DevelopmentChinese Academy of Medical SciencesPeking Union Medical CollegeBeijingChina
| | - Ben‐gang Zhang
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal MedicineMinistry of Education/Institute of Medicinal Plant DevelopmentChinese Academy of Medical SciencesPeking Union Medical CollegeBeijingChina
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12
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The Prevalence of Single-Specimen/Locality Species in Insect Taxonomy: An Empirical Analysis. DIVERSITY-BASEL 2019. [DOI: 10.3390/d11070106] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Although about two million species have been named, our knowledge about the biodiversity of many taxonomic groups remains inadequate and incomplete. There has been increased taxonomic effort for the discovery of more species and their geographical distribution information. During this process, species collected only from a single specimen/locality often appear. However, there are very few empirical data available to understand the current situation of single specimen/locality species in insect taxonomy. In this paper, we collected 1261 articles containing 4811 insect species from ZooKeys between 2009 and 2017, and we extracted data, including the publication date, number of specimens/locality, and DNA usage. Our analyses demonstrated that 21.53% and 21.74% of new species were described from only one specimen and one locality, respectively, and approximately half of all new species were published based on fewer than five specimens. Meanwhile, the rate of single-specimen species in papers with or without DNA data was 15.06% and 23.43%, respectively, which indicates that incorporating DNA data in species descriptions might effectively decrease the occurrence of single-specimen species. We suggest that taxonomists should adopt more beneficial practices, such as increasing specimen diversity, incorporating DNA data, and improving international collaboration, in the description of new species.
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13
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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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Dinh TD, Ngatia JN, Cui LY, Ma Y, Dhamer TD, Xu YC. Influence of pairwise genetic distance computation and reference sample size on the reliability of species identification using Cyt b and COI gene fragments in a group of native passerines. Forensic Sci Int Genet 2019; 40:85-95. [PMID: 30780122 DOI: 10.1016/j.fsigen.2019.02.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 01/23/2019] [Accepted: 02/12/2019] [Indexed: 01/09/2023]
Abstract
Species identification is fundamental to wildlife forensic practice. The desirability of molecular genetic methods is increasing rapidly. The sequence of a marker, rather than its particular diagnostic nucleotides, provides greater safety through comparisons between intra- and inter-specific pairwise genetic distances. However, it has not been well described how reliability of species assignment is influenced by distance computing methods and reference sample sizes. In this study, the influences were tested using 12 species from 4 genera of passerine birds and the sequences of partial Cytochrome b (Cyt b) and Cytochrome Oxidase subunit I (COI) genes. Results showed that different substitution types have different outcomes of pairwise genetic distance estimation and this influences the risk of false inclusion and exclusion. Transition (Ts) is the most effective substitution type to reveal optimal species resolution for both Cyt b and COI gene fragments no matter whether K2P and p-distance are used. Sample size required to accurately estimate pairwise distance is essentially determined by the genetic diversity of a species in reference to a given strictness of predefined acceptable accuracy. These findings suggest that for future forensic work on birds by use of Cyt b and COI gene fragments, transition should be used exclusively for marker validation and identification practice when targeting closely related species. Meanwhile, the reference database should sufficiently represent overall genetic diversity of the species. The minimum sample size should be estimated based on existing knowledge of genetic diversity. Special caution should be used for species assignment when only several reference data are available for animals that are considered likely to have high genetic diversity.
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Affiliation(s)
- Thi Dao Dinh
- College of Wildlife Resources, Northeast Forestry University, China
| | | | - Liang Yu Cui
- College of Wildlife Resources, Northeast Forestry University, China
| | - Yue Ma
- College of Wildlife Resources, Northeast Forestry University, China; State Forestry and Grassland Administration Detecting Center of Wildlife of China, China
| | | | - Yan Chun Xu
- College of Wildlife Resources, Northeast Forestry University, China; State Forestry and Grassland Administration Detecting Center of Wildlife of China, China; State Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization of China, China.
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15
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Labisko J, Griffiths RA, Chong-Seng L, Bunbury N, Maddock ST, Bradfield KS, Taylor ML, Groombridge JJ. Endemic, endangered and evolutionarily significant: cryptic lineages in Seychelles’ frogs (Anura: Sooglossidae). Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/bly183] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Jim Labisko
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Canterbury, UK
- Island Biodiversity and Conservation, Anse Royale, Mahé, Seychelles
| | - Richard A Griffiths
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Canterbury, UK
| | | | - Nancy Bunbury
- Seychelles Islands Foundation, Victoria, Mahé, Seychelles
- Centre for Ecology and Conservation, University of Exeter, UK
| | - Simon T Maddock
- Island Biodiversity and Conservation, Anse Royale, Mahé, Seychelles
- School of Biology, Chemistry and Forensic Science, Faculty of Science and Engineering, University of Wolverhampton, Wolverhampton, UK
- Department of Life Sciences, The Natural History Museum, London, UK
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | | | - Michelle L Taylor
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Canterbury, UK
| | - Jim J Groombridge
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Canterbury, UK
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16
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Luo A, Ling C, Ho SYW, Zhu CD. Comparison of Methods for Molecular Species Delimitation Across a Range of Speciation Scenarios. Syst Biol 2018; 67:830-846. [PMID: 29462495 PMCID: PMC6101526 DOI: 10.1093/sysbio/syy011] [Citation(s) in RCA: 185] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Accepted: 02/10/2018] [Indexed: 11/14/2022] Open
Abstract
Species are fundamental units in biological research and can be defined on the basis of various operational criteria. There has been growing use of molecular approaches for species delimitation. Among the most widely used methods, the generalized mixed Yule-coalescent (GMYC) and Poisson tree processes (PTP) were designed for the analysis of single-locus data but are often applied to concatenations of multilocus data. In contrast, the Bayesian multispecies coalescent approach in the software Bayesian Phylogenetics and Phylogeography (BPP) explicitly models the evolution of multilocus data. In this study, we compare the performance of GMYC, PTP, and BPP using synthetic data generated by simulation under various speciation scenarios. We show that in the absence of gene flow, the main factor influencing the performance of these methods is the ratio of population size to divergence time, while number of loci and sample size per species have smaller effects. Given appropriate priors and correct guide trees, BPP shows lower rates of species overestimation and underestimation, and is generally robust to various potential confounding factors except high levels of gene flow. The single-threshold GMYC and the best strategy that we identified in PTP generally perform well for scenarios involving more than a single putative species when gene flow is absent, but PTP outperforms GMYC when fewer species are involved. Both methods are more sensitive than BPP to the effects of gene flow and potential confounding factors. Case studies of bears and bees further validate some of the findings from our simulation study, and reveal the importance of using an informed starting point for molecular species delimitation. Our results highlight the key factors affecting the performance of molecular species delimitation, with potential benefits for using these methods within an integrative taxonomic framework.
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Affiliation(s)
- Arong Luo
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Cheng Ling
- Department of Computer Science and Technology, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Chao-Dong Zhu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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17
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Manin BO, Drakeley CJ, Chua TH. Mitochondrial variation in subpopulations of Anopheles balabacensis Baisas in Sabah, Malaysia (Diptera: Culicidae). PLoS One 2018; 13:e0202905. [PMID: 30138386 PMCID: PMC6107281 DOI: 10.1371/journal.pone.0202905] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 08/10/2018] [Indexed: 11/19/2022] Open
Abstract
Anopheles balabacensis, the primary vector of Plasmodium knowlesi in Sabah, Malaysia, is both zoophilic and anthropophilic, feeding on macaques as well as humans. It is the dominant Anopheles species found in Kudat Division where it is responsible for all the cases of P. knowlesi. However there is a paucity of basic biological and ecological information on this vector. We investigated the genetic variation of this species using the sequences of cox1 (1,383 bp) and cox2 (685 bp) to gain an insight into the population genetics and inter-population gene flow in Sabah. A total of 71 An. balabacensis were collected from seven districts constituting 14 subpopulations. A total of 17, 10 and 25 haplotypes were detected in the subpopulations respectively using the cox1, cox2 and the combined sequence. Some of the haplotypes were common among the subpopulations due to gene flow occurring between them. AMOVA showed that the genetic variation was high within subpopulations as compared to between subpopulations. Mantel test results showed that the variation between subpopulations was not due to the geographical distance between them. Furthermore, Tajima's D and Fu's Fs tests showed that An. balabacensis in Sabah is experiencing population expansion and growth. High gene flow between the subpopulations was indicated by the low genetic distance and high gene diversity in the cox1, cox2 and the combined sequence. However the population at Lipasu Lama appeared to be isolated possibly due to its higher altitude at 873 m above sea level.
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Affiliation(s)
- Benny Obrain Manin
- Department of Pathobiology and Medical Diagnostics, Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
| | - Chris J. Drakeley
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Tock H. Chua
- Department of Pathobiology and Medical Diagnostics, Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
- * E-mail:
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18
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DNA Barcoding Highlights Cryptic Diversity in the New Zealand Psylloidea (Hemiptera: Sternorrhyncha). DIVERSITY-BASEL 2018. [DOI: 10.3390/d10030050] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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19
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Liu S, Yang C, Zhou C, Zhou X. Filling reference gaps via assembling DNA barcodes using high-throughput sequencing-moving toward barcoding the world. Gigascience 2017; 6:1-8. [PMID: 29077841 PMCID: PMC5726475 DOI: 10.1093/gigascience/gix104] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 09/26/2017] [Accepted: 10/23/2017] [Indexed: 01/17/2023] Open
Abstract
Over the past decade, biodiversity researchers have dedicated tremendous efforts to constructing DNA reference barcodes for rapid species registration and identification. Although analytical cost for standard DNA barcoding has been significantly reduced since early 2000, further dramatic reduction in barcoding costs is unlikely because Sanger sequencing is approaching its limits in throughput and chemistry cost. Constraints in barcoding cost not only led to unbalanced barcoding efforts around the globe, but also prevented high-throughput sequencing (HTS)-based taxonomic identification from applying binomial species names, which provide crucial linkages to biological knowledge. We developed an Illumina-based pipeline, HIFI-Barcode, to produce full-length Cytochrome c oxidase subunit I (COI) barcodes from pooled polymerase chain reaction amplicons generated by individual specimens. The new pipeline generated accurate barcode sequences that were comparable to Sanger standards, even for different haplotypes of the same species that were only a few nucleotides different from each other. Additionally, the new pipeline was much more sensitive in recovering amplicons at low quantity. The HIFI-Barcode pipeline successfully recovered barcodes from more than 78% of the polymerase chain reactions that didn't show clear bands on the electrophoresis gel. Moreover, sequencing results based on the single molecular sequencing platform Pacbio confirmed the accuracy of the HIFI-Barcode results. Altogether, the new pipeline can provide an improved solution to produce full-length reference barcodes at about one-tenth of the current cost, enabling construction of comprehensive barcode libraries for local fauna, leading to a feasible direction for DNA barcoding global biomes.
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Affiliation(s)
- Shanlin Liu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Plant Protection, China Agricultural University, Beijing 100193, People's Republic of China
- BGI-Shenzhen, Shenzhen, 518083, China
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350, Copenhagen, Denmark
| | | | - Chengran Zhou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Plant Protection, China Agricultural University, Beijing 100193, People's Republic of China
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Xin Zhou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Plant Protection, China Agricultural University, Beijing 100193, People's Republic of China
- National Engineering Research Center for Fruit and Vegetable Processing, China Agricultural University, Beijing 100193, People's Republic of China
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20
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Ye Z, Vollhardt IMG, Tomanovic Z, Traugott M. Evaluation of three molecular markers for identification of European primary parasitoids of cereal aphids and their hyperparasitoids. PLoS One 2017; 12:e0177376. [PMID: 28562603 PMCID: PMC5451020 DOI: 10.1371/journal.pone.0177376] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 04/26/2017] [Indexed: 12/02/2022] Open
Abstract
Aphids are major pests of cereal crops and a suite of hymenopteran primary parasitoids play an important role in regulating their populations. However, hyperparasitoids may disrupt the biocontrol services provided by primary parasitoids. As such, understanding cereal aphid-primary parasitoid-hyperparasitoid interactions is vital for a reliable parasitoid-based control of cereal aphids. For this, the ability to identify the different primary and hyperparasitoid species is necessary. Unfortunately, this is often difficult due to a lack of morphologically diagnostic features. DNA sequence-based species identification of parasitoids can overcome these hurdles. However, comprehensive DNA sequence information is lacking for many of these groups, particularly for hyperparasitoids. Here we evaluate three genes [cytochrome c oxidase subunit I (COI), 16S ribosomal RNA (16S) and 18S ribosomal RNA (18S)] for their suitability to identify 24 species of primary parasitoids and 16 species of hyperparasitoids associated with European cereal aphids. To identify aphelinid primary parasitoid species and hyperparasitoids, we found 16S to be more suitable compared to COI sequences. In contrast, the Aphidiinae are best identified using COI due to better species-level resolution and a more comprehensive DNA sequence database compared to 16S. The 18S gene was better suited for group-specific identification of parasitoids, but did not provide resolution at the species level. Our results provide a DNA sequence database for cereal aphid primary parasitoids and their associated hyperparasitoids in Central Europe, which will allow further improvement of our understanding of cereal aphid-primary parasitoid-hyperparasitoid interactions in relation to aphid biological control.
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Affiliation(s)
- Zhengpei Ye
- Mountain Agriculture Research Unit, Institute of Ecology, University of Innsbruck, Innsbruck, Austria
- * E-mail: ,
| | - Ines M. G. Vollhardt
- Agroecology, Department of Crop Sciences, Georg-August-University Göttingen, Göttingen, Germany
| | - Zeljko Tomanovic
- Institute of Zoology, Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Michael Traugott
- Mountain Agriculture Research Unit, Institute of Ecology, University of Innsbruck, Innsbruck, Austria
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21
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Gallo-Franco JJ, Velasco-Cuervo SM, Aguirre-Ramirez E, González Obando R, Carrejo NS, Toro-Perea N. Genetic diversity and population structure of Anastrepha striata (Diptera: Tephritidae) in three natural regions of southwestern Colombia using mitochondrial sequences. Genetica 2017; 145:79-89. [PMID: 28093669 DOI: 10.1007/s10709-016-9947-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 12/22/2016] [Indexed: 10/20/2022]
Abstract
Anastrepha striata is widely distributed across the Americas and is a pest of economically important crops, especially crops of the Myrtaceae family. Insect population structures can be influenced by the presence of physical barriers or characteristics associated with habitat differences. This study evaluated the effect of the Western Andes on the population structure of A. striata. Individuals were collected from Psidium guajava fruits from three natural regions of southwestern Colombia (Pacific Coast, mountainous region and the inter-Andean valley of the Cauca River). Based on a 1318 bp concatenated of the genes Cytochrome Oxidase subunit I (COI) and NADH dehydrogenase subunit 6 (ND6), 14 haplotypes with few changes among them (between 1 and 3) were found. There was only one dominant haplotype in all three regions. No genetic structure associated with the three eco-geographical regions of the study was found. Moreover, the Western Andes are not an effective barrier for the genetic isolation of the populations from the Pacific Coast compared with the inter-Andean valley populations. This genetic homogeneity could be partially due to anthropogenic intervention, which acts as a dispersal agent of infested fruits. Another hypothesis to explain the lack of structure would be the relatively recent arrival of A. striata to the region, as indicated by an analysis of the demographic history, which reveals a process of population expansion. This study represents the first attempt to understand the population genetics of A. striata in Colombia and could contribute to the integral management of this pest.
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Affiliation(s)
- Jenny Johana Gallo-Franco
- Departamento de Biología, Sección de genética, Universidad del Valle, Calle 13 # 100-00, Cali, Colombia.
| | | | - Elkin Aguirre-Ramirez
- Departamento de Biología, Sección de genética, Universidad del Valle, Calle 13 # 100-00, Cali, Colombia
| | - Ranulfo González Obando
- Departamento de biología, Sección de entomología, Universidad del Valle, Calle 13 # 100-00, Cali, Colombia
| | - Nancy Soraya Carrejo
- Departamento de biología, Sección de entomología, Universidad del Valle, Calle 13 # 100-00, Cali, Colombia
| | - Nelson Toro-Perea
- Departamento de Biología, Sección de genética, Universidad del Valle, Calle 13 # 100-00, Cali, Colombia
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22
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Yang Z, Landry JF, Hebert PDN. A DNA Barcode Library for North American Pyraustinae (Lepidoptera: Pyraloidea: Crambidae). PLoS One 2016; 11:e0161449. [PMID: 27736878 PMCID: PMC5063472 DOI: 10.1371/journal.pone.0161449] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 08/06/2016] [Indexed: 11/24/2022] Open
Abstract
Although members of the crambid subfamily Pyraustinae are frequently important crop pests, their identification is often difficult because many species lack conspicuous diagnostic morphological characters. DNA barcoding employs sequence diversity in a short standardized gene region to facilitate specimen identifications and species discovery. This study provides a DNA barcode reference library for North American pyraustines based upon the analysis of 1589 sequences recovered from 137 nominal species, 87% of the fauna. Data from 125 species were barcode compliant (>500bp, <1% n), and 99 of these taxa formed a distinct cluster that was assigned to a single BIN. The other 26 species were assigned to 56 BINs, reflecting frequent cases of deep intraspecific sequence divergence and a few instances of barcode sharing, creating a total of 155 BINs. Two systems for OTU designation, ABGD and BIN, were examined to check the correspondence between current taxonomy and sequence clusters. The BIN system performed better than ABGD in delimiting closely related species, while OTU counts with ABGD were influenced by the value employed for relative gap width. Different species with low or no interspecific divergence may represent cases of unrecognized synonymy, whereas those with high intraspecific divergence require further taxonomic scrutiny as they may involve cryptic diversity. The barcode library developed in this study will also help to advance understanding of relationships among species of Pyraustinae.
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Affiliation(s)
- Zhaofu Yang
- Key laboratory of Plant Protection Resources and Pest Management, Ministry of Education, Northwest A&F University, Yangling, Shaanxi, China
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
- * E-mail:
| | - Jean-François Landry
- Agriculture and Agri-Food Canada, Ottawa Research & Development Centre, Ottawa, Ontario, Canada
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
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23
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Zhang HG, Lv MH, Yi WB, Zhu WB, Bu WJ. Species diversity can be overestimated by a fixed empirical threshold: insights from DNA barcoding of the genus Cletus (Hemiptera: Coreidae) and the meta-analysis of COI data from previous phylogeographical studies. Mol Ecol Resour 2016; 17:314-323. [PMID: 27437861 DOI: 10.1111/1755-0998.12571] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 05/01/2016] [Accepted: 06/23/2016] [Indexed: 11/28/2022]
Abstract
The use of genetic distances to identify species within the framework of DNA barcoding has to some extent improved the development of biodiversity studies. However, using a fixed empirical threshold to delimit species may lead to overestimating species diversity. In this study, we use a new data set of COI sequences for 366 specimens within the genus of Cletus as well as conduct an analysis on the same genetic data for collected morphologically defined species from previous phylogeographical studies, to test whether high intraspecific genetic divergences are common with the premises of comprehensive sampling. The results indicate C. graminis Hsiao & Cheng , is the same species with C. punctiger (Dallas, 1852) and should be synonymized and that the distributional record of C. pugnator (Fabricius, 1787) in China is correct. High intraspecific genetic differentiations (0%-4.35%) were found in C. punctiger. Furthermore, as to the mined data, the maximum intraspecific K2P distances of 186 species (48.44% of 384) exceed 3%, and 101 species (26.30%) can be divided into two or more clusters with a threshold of 3% in cluster analysis. If genetic distance is used to delimit species boundaries, the minimum interspecific K2P distance of the congeneric species should be considered rather than only using the fixed empirical value; otherwise, the species richness may be overestimated in some cases.
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Affiliation(s)
- Hai-Guang Zhang
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Nankai District, Tianjin, 300071, China.,Shanghai Entomological Museum, Institute of Plant Physiology & Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Xuhui District, Shanghai, 200032, China
| | - Min-Hua Lv
- Center for Experimental Medicine, First Affiliated Hospital of Nanchang University, Nanchang, 330006, China
| | - Wen-Bo Yi
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Nankai District, Tianjin, 300071, China
| | - Wei-Bing Zhu
- Shanghai Entomological Museum, Institute of Plant Physiology & Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Xuhui District, Shanghai, 200032, China
| | - Wen-Jun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Nankai District, Tianjin, 300071, China
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