1
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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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2
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Arteaga A, Batista A. A consolidated phylogeny of snail-eating snakes (Serpentes, Dipsadini), with the description of five new species from Colombia, Ecuador, and Panama. Zookeys 2023; 1143:1-49. [DOI: 10.3897/zookeys.1143.93601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 01/03/2023] [Indexed: 01/26/2023] Open
Abstract
A molecular phylogeny of the Neotropical snail-eating snakes (tribe Dipsadini Bonaparte, 1838) is presented that includes 60 of the 133 species currently recognized. There is morphological and phylogenetic support for four new species of Sibon Fitzinger, 1826 and one of Dipsas Laurenti, 1768, which are described here based on their unique combination of molecular, meristic, and color pattern characteristics. PlesiodipsasHarvey et al., 2008 is designated as a junior synonym of Dipsas and additional evidence is presented to support the transfer of the genus Geophis Wagler, 1830 to the tribe Dipsadini. Two of the subspecies of S. nebulatus (Linnaeus, 1758) are elevated to full species status. Insight into additional undescribed cryptic diversity within the S. nebulatus species complex is provided. Evidence that supports the existence of an undescribed species previously confused with D. temporalis is provided, as well as the first country record of S. ayerbeorum Vera-Pérez, 2019 in Ecuador with a comment on the ontogenetic variation of the latter. Finally, photographs of Colombian, Ecuadorian, and Panamanian snail-eating snakes are provided.
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Koroiva R, Santana DJ. Evaluation of partial 12S rRNA, 16S rRNA, COI and Cytb gene sequence datasets for potential single DNA barcode for hylids (Anura: Hylidae). AN ACAD BRAS CIENC 2022; 94:e20200825. [PMID: 36477987 DOI: 10.1590/0001-3765202220200825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 05/19/2021] [Indexed: 12/09/2022] Open
Abstract
We evaluated the extent of intraspecific and interspecific genetic distances and the effectiveness of predefined threshold values using the main genes for estimates of biodiversity and specimens' identification in anurans. Partial sequences of the mitochondrial genes for small (12S) and large (16S) ribosomal subunits, cytochrome c oxidase subunit I (COI) and Cytochrome b (Cytb) of the family Hylidae were downloaded from GenBank and curated for length, coverage, and potential contaminations. We performed analyses for all sequences of each gene and the same species present in these datasets by distance and tree (monophyly)-based evaluations. We also evaluated the ability to identify specimens using these datasets applying "nearest neighbor" (NN), "best close match" (BCM) and "BOLD ID" tests. Genetic distance thresholds were generated by the function 'threshVal' and "localMinima" from SPIDER package and traditional threshold values (1%, 3%, 6% and 10%) were also evaluated. Coding genes, especially COI, had a better identification capacity than non-coding genes on barcoding gap and monophyly analysis and NN, BCM, BOLD ID tests. Considering the multiple factors involved in global DNA barcoding evaluations, we present a critical assessment of the use of these genes for biodiversity estimation and specimens' identification in anurans (e.g. hylids).
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Affiliation(s)
- Ricardo Koroiva
- Universidade Federal da Paraíba, Departamento de Sistemática e Tecnologia, Centro de Ciências Exatas e da Natureza, Laboratório Multiusuário do Programa de Pós-Graduação em Ciências Biológicas/Zoologia, Castelo Branco, Campus Universitário, s/n, 58051900 João Pessoa, PB, Brazil.,Universidade Federal de Mato Grosso do Sul, Instituto de Biociências, Laboratório Mapinguari, Cidade Universitária, Avenida Costa e Silva, s/n, 79070900 Campo Grande, MS, Brazil
| | - Diego José Santana
- Universidade Federal de Mato Grosso do Sul, Instituto de Biociências, Laboratório Mapinguari, Cidade Universitária, Avenida Costa e Silva, s/n, 79070900 Campo Grande, MS, Brazil
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4
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Velo-Antón G, Henrique M, Liz AV, Martínez-Freiría F, Pleguezuelos JM, Geniez P, Crochet PA, Brito JC. DNA barcode reference library for the West Sahara-Sahel reptiles. Sci Data 2022; 9:459. [PMID: 35915106 PMCID: PMC9343634 DOI: 10.1038/s41597-022-01582-1] [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: 05/06/2022] [Accepted: 07/19/2022] [Indexed: 11/09/2022] Open
Abstract
DNA barcode reference libraries are now continuously produced for the tree of life, which are essential pillars for the study of biological diversity. Yet, our knowledge about global diversity is largely limited in undersampled regions such as the largest warm desert, the Sahara-Sahel. This dataset provides a DNA barcode reference library for the reptiles of the Western Sahara-Sahel (WSS) and neighbouring countries across this region. It includes 760 barcodes from 133 reptile taxa, distributed in 23 families, and covering the intraspecific diversity of some species. A total of 84 species were collected in the WSS (83% of the total reptile species richness) over 18 overland field expeditions conducted since 2003. DNA barcodes resulted in a high success rate (95%) of species identification and barcoding gap analysis highlighted the effectiveness of the COI fragment as a barcode marker for the WSS reptiles. This dataset represents a comprehensive and reliable DNA reference library for the WSS, filling an important biodiversity gap across a remote and hard-to-sample region. Measurement(s) | reptile diversity | Technology Type(s) | DNA barcoding | Factor Type(s) | DNA barcode sequencing | Sample Characteristic - Organism | reptiles | Sample Characteristic - Environment | terrestrial | Sample Characteristic - Location | Western Sahara-Sahel |
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Affiliation(s)
- Guillermo Velo-Antón
- Universidade de Vigo, Departamento de Ecoloxía e Bioloxía Animal, Grupo GEA, Vigo, E-36310, Spain. .,CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal. .,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal.
| | - Margarida Henrique
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal
| | - André Vicente Liz
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002, Porto, Portugal
| | - Fernando Martínez-Freiría
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | | | - Philippe Geniez
- CEFE, EPHE-PSL, CNRS, Univ Montpellier, Biogéographie et Ecologie des Vertébrés, Montpellier, France
| | | | - José Carlos Brito
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal. .,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal. .,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002, Porto, Portugal.
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5
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Chan KO, Hertwig ST, Neokleous DN, Flury JM, Brown RM. Widely used, short 16S rRNA mitochondrial gene fragments yield poor and erratic results in phylogenetic estimation and species delimitation of amphibians. BMC Ecol Evol 2022; 22:37. [PMID: 35346025 PMCID: PMC8959075 DOI: 10.1186/s12862-022-01994-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 03/10/2022] [Indexed: 11/24/2022] Open
Abstract
Background The 16S mitochondrial rRNA gene is the most widely sequenced molecular marker in amphibian systematic studies, making it comparable to the universal CO1 barcode that is more commonly used in other animal groups. However, studies employ different primer combinations that target different lengths/regions of the 16S gene ranging from complete gene sequences (~ 1500 bp) to short fragments (~ 500 bp), the latter of which is the most ubiquitously used. Sequences of different lengths are often concatenated, compared, and/or jointly analyzed to infer phylogenetic relationships, estimate genetic divergence (p-distances), and justify the recognition of new species (species delimitation), making the 16S gene region, by far, the most influential molecular marker in amphibian systematics. Despite their ubiquitous and multifarious use, no studies have ever been conducted to evaluate the congruence and performance among the different fragment lengths. Results Using empirical data derived from both Sanger-based and genomic approaches, we show that full-length 16S sequences recover the most accurate phylogenetic relationships, highest branch support, lowest variation in genetic distances (pairwise p-distances), and best-scoring species delimitation partitions. In contrast, widely used short fragments produce inaccurate phylogenetic reconstructions, lower and more variable branch support, erratic genetic distances, and low-scoring species delimitation partitions, the numbers of which are vastly overestimated. The relatively poor performance of short 16S fragments is likely due to insufficient phylogenetic information content. Conclusions Taken together, our results demonstrate that short 16S fragments are unable to match the efficacy achieved by full-length sequences in terms of topological accuracy, heuristic branch support, genetic divergences, and species delimitation partitions, and thus, phylogenetic and taxonomic inferences that are predicated on short 16S fragments should be interpreted with caution. However, short 16S fragments can still be useful for species identification, rapid assessments, or definitively coupling complex life stages in natural history studies and faunal inventories. While the full 16S sequence performs best, it requires the use of several primer pairs that increases cost, time, and effort. As a compromise, our results demonstrate that practitioners should utilize medium-length primers in favor of the short-fragment primers because they have the potential to markedly improve phylogenetic inference and species delimitation without additional cost. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-022-01994-y.
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Affiliation(s)
- Kin Onn Chan
- Lee Kong Chian Natural History Museum, Faculty of Science, National University of Singapore, 2 Conservatory Drive, Singapore, 117377, Singapore.
| | - Stefan T Hertwig
- Naturhistorisches Museum der Burgergemeinde Bern, Bernastrasse 15, 3005, Bern, Switzerland.,Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012, Bern, Switzerland
| | - Dario N Neokleous
- Naturhistorisches Museum der Burgergemeinde Bern, Bernastrasse 15, 3005, Bern, Switzerland.,Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012, Bern, Switzerland
| | - Jana M Flury
- Leibniz-Institute for the Analysis of Biodiversity Change, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 53113, Bonn, Germany
| | - Rafe M Brown
- Department of Ecology and Evolutionary Biology, Biodiversity Institute, University of Kansas, 1345 Jayhawk Blvd, Dyche Hall, Lawrence, KS, 66045, USA
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6
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Poyarkov NA, Nguyen TV, Pawangkhanant P, Yushchenko PV, Brakels P, Nguyen LH, Nguyen HN, Suwannapoom C, Orlov N, Vogel G. An integrative taxonomic revision of slug-eating snakes (Squamata: Pareidae: Pareineae) reveals unprecedented diversity in Indochina. PeerJ 2022; 10:e12713. [PMID: 35047234 PMCID: PMC8757378 DOI: 10.7717/peerj.12713] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 12/09/2021] [Indexed: 01/07/2023] Open
Abstract
Slug-eating snakes of the subfamily Pareinae are an insufficiently studied group of snakes specialized in feeding on terrestrial mollusks. Currently Pareinae encompass three genera with 34 species distributed across the Oriental biogeographic region. Despite the recent significant progress in understanding of Pareinae diversity, the subfamily remains taxonomically challenging. Here we present an updated phylogeny of the subfamily with a comprehensive taxon sampling including 30 currently recognized Pareinae species and several previously unknown candidate species and lineages. Phylogenetic analyses of mtDNA and nuDNA data supported the monophyly of the three genera Asthenodipsas, Aplopeltura, and Pareas. Within both Asthenodipsas and Pareas our analyses recovered deep differentiation with each genus being represented by two morphologically diagnosable clades, which we treat as subgenera. We further apply an integrative taxonomic approach, including analyses of molecular and morphological data, along with examination of available type materials, to address the longstanding taxonomic questions of the subgenus Pareas, and reveal the high level of hidden diversity of these snakes in Indochina. We restrict the distribution of P. carinatus to southern Southeast Asia, and recognize two subspecies within it, including one new subspecies proposed for the populations from Thailand and Myanmar. We further revalidate P. berdmorei, synonymize P. menglaensis with P. berdmorei, and recognize three subspecies within this taxon, including the new subspecies erected for the populations from Laos and Vietnam. Furthermore, we describe two new species of Pareas from Vietnam: one belonging to the P. carinatus group from southern Vietnam, and a new member of the P. nuchalis group from the central Vietnam. We provide new data on P. temporalis, and report on a significant range extension for P. nuchalis. Our phylogeny, along with molecular clock and ancestral area analyses, reveal a complex diversification pattern of Pareinae involving a high degree of sympatry of widespread and endemic species. Our analyses support the "upstream" colonization hypothesis and, thus, the Pareinae appears to have originated in Sundaland during the middle Eocene and then colonized mainland Asia in early Oligocene. Sundaland and Eastern Indochina appear to have played the key roles as the centers of Pareinae diversification. Our results reveal that both vicariance and dispersal are responsible for current distribution patterns of Pareinae, with tectonic movements, orogeny and paleoclimatic shifts being the probable drivers of diversification. Our study brings the total number of Pareidae species to 41 and further highlights the importance of comprehensive taxonomic revisions not only for the better understanding of biodiversity and its evolution, but also for the elaboration of adequate conservation actions.
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Affiliation(s)
- Nikolay A. Poyarkov
- Laboratory of Tropical Ecology, Joint Russian-Vietnamese Tropical Research and Technological Center, Hanoi, Vietnam,Faculty of Biology, Department of Vertebrate Zoology, Moscow State University, Moscow, Russia
| | - Tan Van Nguyen
- Department of Species Conservation, Save Vietnam’s Wildlife, Ninh Binh, Vietnam
| | - Parinya Pawangkhanant
- Division of Fishery, School of Agriculture and Natural Resources, University of Phayao, Phayao, Thailand
| | - Platon V. Yushchenko
- Faculty of Biology, Department of Vertebrate Zoology, Moscow State University, Moscow, Russia
| | | | - Linh Hoang Nguyen
- Department of Zoology, Southern Institute of Ecology, Vietnam Academy of Science and Technology, Ho Chi Minh City, Vietnam
| | - Hung Ngoc Nguyen
- Department of Zoology, Southern Institute of Ecology, Vietnam Academy of Science and Technology, Ho Chi Minh City, Vietnam
| | - Chatmongkon Suwannapoom
- Division of Fishery, School of Agriculture and Natural Resources, University of Phayao, Phayao, Thailand
| | - Nikolai Orlov
- Department of Herpetology, Zoological Institute, Russian Academy of Sciences, St. Petersburg, Russia
| | - Gernot Vogel
- Society for Southeast Asian Herpetology, Heidelberg, Germany
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7
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Esquerré D, Keogh JS, Demangel D, Morando M, Avila LJ, Sites JW, Ferri-Yáñez F, Leaché AD. Rapid radiation and rampant reticulation: Phylogenomics of South American Liolaemus lizards. Syst Biol 2021; 71:286-300. [PMID: 34259868 DOI: 10.1093/sysbio/syab058] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 06/25/2021] [Accepted: 06/30/2021] [Indexed: 01/09/2023] Open
Abstract
Understanding the factors that cause heterogeneity among gene trees can increase the accuracy of species trees. Discordant signals across the genome are commonly produced by incomplete lineage sorting (ILS) and introgression, which in turn can result in reticulate evolution. Species tree inference using the multispecies coalescent is designed to deal with ILS and is robust to low levels of introgression, but extensive introgression violates the fundamental assumption that relationships are strictly bifurcating. In this study, we explore the phylogenomics of the iconic Liolaemus subgenus of South American lizards, a group of over 100 species mostly distributed in and around the Andes mountains. Using mitochondrial DNA (mtDNA) and genome-wide restriction-site associated DNA sequencing (RADseq; nDNA hereafter), we inferred a time-calibrated mtDNA gene tree, nDNA species trees, and phylogenetic networks. We found high levels of discordance between mtDNA and nDNA, which we attribute in part to extensive ILS resulting from rapid diversification. These data also reveal extensive and deep introgression, which combined with rapid diversification, explain the high level of phylogenetic discordance. We discuss these findings in the context of Andean orogeny and glacial cycles that fragmented, expanded, and contracted species distributions. Finally, we use the new phylogeny to resolve long-standing taxonomic issues in one of the most studied lizard groups in the New World.
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Affiliation(s)
- Damien Esquerré
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - J Scott Keogh
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | | | - Mariana Morando
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales (IPEEC- CONICET), Puerto Madryn, Chubut, Argentina
| | - Luciano J Avila
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales (IPEEC- CONICET), Puerto Madryn, Chubut, Argentina
| | - Jack W Sites
- Department of Biology and M.L. Bean Life Science Museum, Brigham Young University, Provo, Utah, USA
| | - Francisco Ferri-Yáñez
- Departamento de Biogeografía y Cambio Global, Museo Nacional de Ciencias Naturales, CSIC & Laboratorio Internacional en Cambio Global CSIC-PUC (LINCGlobal), Calle José Gutiérrez Abascal, 2, 28006, Madrid, Spain
| | - Adam D Leaché
- Department of Biology & Burke Museum of Natural History and Culture, University of Washington, Seattle, Washington, USA
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8
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Beyond the comfort zone: amphibian diversity and distribution in the West Sahara-Sahel using mtDNA and nuDNA barcoding and spatial modelling. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01331-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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9
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'Barcode fishing' for archival DNA from historical type material overcomes taxonomic hurdles, enabling the description of a new frog species. Sci Rep 2020; 10:19109. [PMID: 33154397 PMCID: PMC7644772 DOI: 10.1038/s41598-020-75431-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 09/28/2020] [Indexed: 11/08/2022] Open
Abstract
Taxonomic progress is often hindered by intrinsic factors, such as morphologically cryptic species that require a broad suite of methods to distinguish, and extrinsic factors, such as uncertainties in the allocation of scientific names to species. These uncertainties can be due to a wide variety of factors, including old and poorly preserved type specimens (which contain only heavily degraded DNA or have lost important diagnostic characters), inappropriately chosen type specimens (e.g. juveniles without diagnostic characters) or poorly documented type specimens (with unprecise, incorrect, or missing locality data). Thanks to modern sequencing technologies it is now possible to overcome many such extrinsic factors by sequencing DNA from name-bearing type specimens of uncertain assignment and assigning these to known genetic lineages. Here, we apply this approach to frogs of the Mantidactylus ambreensis complex, which was recently shown to consist of two genetic lineages supported by concordant differentiation in mitochondrial and nuclear genes. These lineages co-occur on the Montagne d'Ambre Massif in northern Madagascar but appear to have diverged in allopatry. We use a recently published bait set based on three mitochondrial markers from all known Malagasy frog lineages to capture DNA sequences from the 127-year-old holotype of Mantidactylus ambreensis Mocquard, 1895. With the obtained sequences we are able to assign the name M. ambreensis to the lowland lineage, which is rather widespread in the rainforests of northern Madagascar, leaving the microendemic high-elevation lineage on Montagne d'Ambre in north Madagascar in need of description. We describe this species as Mantidactylus ambony sp. nov., differing from M. ambreensis in call parameters and a smaller body size. Thus, using target enrichment to obtain DNA sequence data from this old specimen, we were able to resolve the extrinsic (nomenclatural) hindrances to taxonomic resolution of this complex. We discuss the broad-scale versatility of this 'barcode fishing' approach, which can draw on the enormous success of global DNA barcoding initiatives to quickly and efficiently assign type specimens to lineages.
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Zangl L, Daill D, Schweiger S, Gassner G, Koblmüller S. A reference DNA barcode library for Austrian amphibians and reptiles. PLoS One 2020; 15:e0229353. [PMID: 32163447 PMCID: PMC7067431 DOI: 10.1371/journal.pone.0229353] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 02/04/2020] [Indexed: 11/19/2022] Open
Abstract
In the last few years, DNA barcoding became an established method for species identification in biodiversity inventories and monitoring studies. Such studies depend on the access to a comprehensive reference data base, covering all relevant taxa. Here we present a comprehensive DNA barcode inventory of all amphibian and reptile species native to Austria, except for the putatively extinct Vipera ursinii rakosiensis and Lissotriton helveticus, which has been only recently reported for the very western edge of Austria. A total of 194 DNA barcodes were generated in the framework of the Austrian Barcode of Life (ABOL) initiative. Species identification via DNA barcodes was successful for most species, except for the hybridogenetic species complex of water frogs (Pelophylax spp.) and the crested newts (Triturus spp.), in areas of sympatry. However, DNA barcoding also proved powerful in detecting deep conspecific lineages, e.g. within Natrix natrix or the wall lizard (Podarcis muralis), resulting in more than one Barcode Index Number (BIN) per species. Moreover, DNA barcodes revealed the presence of Natrix helvetica, which has been elevated to species level only recently, and genetic signatures of the Italian water frog Pelophylax bergeri in Western Austria for the first time. Comparison to previously published DNA barcoding data of European amphibians and reptiles corroborated the results of the Austrian data but also revealed certain peculiarities, underlining the particular strengths and in the case of the genus Pelophylax also the limitations of DNA barcoding. Consequently, DNA barcoding is not only powerful for species identification of all life stages of most Austrian amphibian and reptile species, but also for the detection of new species, the monitoring of gene flow or the presence of alien populations and/or species. Thus, DNA barcoding and the data generated in this study may serve both scientific and national or even transnational conservation purposes.
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Affiliation(s)
- Lukas Zangl
- Institute of Biology, University of Graz, Graz, Austria
- Studienzentrum Naturkunde, Universalmuseum Joanneum, Graz, Austria
- * E-mail: (LZ); (SK)
| | - Daniel Daill
- Institute of Biology, University of Graz, Graz, Austria
- Consultants in Aquatic Ecology and Engineering—blattfisch e.U., Wels, Austria
| | - Silke Schweiger
- First Zoological Department, Herpetological Collection, Museum of Natural History Vienna, Vienna, Austria
| | - Georg Gassner
- First Zoological Department, Herpetological Collection, Museum of Natural History Vienna, Vienna, Austria
| | - Stephan Koblmüller
- Institute of Biology, University of Graz, Graz, Austria
- * E-mail: (LZ); (SK)
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Vilela DS, Koroiva R, Cordero-Rivera A, Guillermo-Ferreira R. A further study on Franciscobasis Machado & Bedê, 2016 (Odonata: Coenagrionidae), a newly described genus from Minas Gerais, Brazil. PLoS One 2019; 14:e0223241. [PMID: 31593578 PMCID: PMC6782088 DOI: 10.1371/journal.pone.0223241] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 09/17/2019] [Indexed: 11/21/2022] Open
Abstract
The genus Franciscobasis Machado & Bedê, 2016 is endemic to the Serra da Canastra National Park in Minas Gerais state, Brazil. Two species of Franciscobasis were described simultaneously with the genus description: F. franciscoi and F. sonia, the latter described only from females. Through morphological and molecular analysis, we investigated if F. sonia may represent the young female of F. franciscoi. Resulting data did not present adequate differences between females to characterize them as different species. Therefore, we suggest that F. sonia is a junior synonym of F. franciscoi, and the female of F. franciscoi goes through a complex ontogenetic color change.
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Affiliation(s)
- Diogo Silva Vilela
- Graduate Program in Entomology, Department of Biology, University of São Paulo (USP), Ribeirão Preto, Brazil
- Laboratory of Ecological Studies on Ethology and Evolution (LESTES), Department of Hydrobiology, Federal University of São Carlos, São Carlos, Brazil
| | - Ricardo Koroiva
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
| | - Adolfo Cordero-Rivera
- ECOEVO Lab, Departamento de Ecoloxía e Bioloxía Animal, Universidade de Vigo, Pontevedra, Spain
| | - Rhainer Guillermo-Ferreira
- Laboratory of Ecological Studies on Ethology and Evolution (LESTES), Department of Hydrobiology, Federal University of São Carlos, São Carlos, Brazil
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Esquerré D, Ramírez-Álvarez D, Pavón-Vázquez CJ, Troncoso-Palacios J, Garín CF, Keogh JS, Leaché AD. Speciation across mountains: Phylogenomics, species delimitation and taxonomy of the Liolaemus leopardinus clade (Squamata, Liolaemidae). Mol Phylogenet Evol 2019; 139:106524. [DOI: 10.1016/j.ympev.2019.106524] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 02/14/2019] [Accepted: 05/29/2019] [Indexed: 11/30/2022]
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13
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Kundu S, Kumar V, Tyagi K, Chakraborty R, Chandra K. The first complete mitochondrial genome of the Indian Tent Turtle, Pangshura tentoria (Testudines: Geoemydidae): Characterization and comparative analysis. Ecol Evol 2019; 9:10854-10868. [PMID: 31624586 PMCID: PMC6787814 DOI: 10.1002/ece3.5606] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 06/24/2019] [Accepted: 08/07/2019] [Indexed: 11/09/2022] Open
Abstract
The characterization of a complete mitogenome is widely used in genomics studies for systematics and evolutionary research. However, the sequences and structural motifs contained within the mitogenome of Testudines taxa have rarely been examined. The present study decodes the first complete mitochondrial genome of the Indian Tent Turtle, Pangshura tentoria (16,657 bp) by using next-generation sequencing. This denovo assembly encodes 37 genes: 13 protein-coding genes (PCGs), 22 transfer RNA (tRNAs), two ribosomal RNA, and one control region (CR). Most of the genes were encoded on majority strand, except for one PCG (NADH dehydrogenase subunit 6) and eight tRNAs. Most of the PCGs were started with an ATG initiation codon, except for Cytochrome oxidase subunit 1 with "GTG" and NADH dehydrogenase subunit 5 with "ATA." The termination codons, "TAA" and "AGA" were observed in two subunits of NADH dehydrogenase gene. The relative synonymous codon usage analysis revealed the maximum abundance of alanine, isoleucine, leucine, and threonine. The nonsynonymous/synonymous ratios were <1 in all PCGs, which indicates strong negative selection among all Geoemydid species. The study also found the typical cloverleaf secondary structure in most of the tRNA genes, except for serine with the lack of the conventional DHU arm. The comparative study of Geoemydid mitogenomes revealed the occurrence of tandem repeats was frequent in the 3' end of CR. Further, two copies of a unique tandem repeat "TTCTCTTT" were identified in P. tentoria. The Bayesian and maximum-likelihood phylogenetic trees using concatenation of 13 PCGs revealed the close relationships of P. tentoria with Batagur trivittata in the studied dataset. All the Geoemydid species showed distinct clustering with high bootstrap support congruent with previous evolutionary hypotheses. We suggest that the generations of more mitogenomes of Geoemydid species are required, to improve our understanding of their in-depth phylogenetic and evolutionary relationships.
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Affiliation(s)
- Shantanu Kundu
- Centre for DNA TaxonomyMolecular Systematics DivisionZoological Survey of IndiaKolkataIndia
| | - Vikas Kumar
- Centre for DNA TaxonomyMolecular Systematics DivisionZoological Survey of IndiaKolkataIndia
| | - Kaomud Tyagi
- Centre for DNA TaxonomyMolecular Systematics DivisionZoological Survey of IndiaKolkataIndia
| | - Rajasree Chakraborty
- Centre for DNA TaxonomyMolecular Systematics DivisionZoological Survey of IndiaKolkataIndia
| | - Kailash Chandra
- Centre for DNA TaxonomyMolecular Systematics DivisionZoological Survey of IndiaKolkataIndia
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Abstract
Paraguay is a key spot in the central region of South America where several ecoregions converge. Its fauna (and specifically its herpetofauna) is getting better studied than years before, but still there is a lack of information regarding molecular genetics, and barcoding analyses have proven to be an excellent tool in this matter. Here, we present results of a barcoding analysis based on 16S rRNA gene sequences, providing valuable data for the scientific community in the region. We based our fieldwork in several areas of Paraguay. We analyzed 249 samples (142 sequenced by us) with a final alignment of 615 bp length. We identified some taxonomic incongruences that can be addressed based on our results. Furthermore, we identify groups, where collecting efforts and research activities should be reinforced. Even though we have some blanks in the geographical coverage of our analysis—and there is still a lot to do towards a better understanding of the taxonomy of the Paraguayan herpetofauna—here, we present the largest genetic dataset for the mitochondrial DNA gene 16S of reptiles (particularly, Squamata) from Paraguay, which can be used to solve taxonomic problems in the region.
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Hofmann EP, Nicholson KE, Luque-Montes IR, Köhler G, Cerrato-Mendoza CA, Medina-Flores M, Wilson LD, Townsend JH. Cryptic Diversity, but to What Extent? Discordance Between Single-Locus Species Delimitation Methods Within Mainland Anoles (Squamata: Dactyloidae) of Northern Central America. Front Genet 2019; 10:11. [PMID: 30804976 PMCID: PMC6378269 DOI: 10.3389/fgene.2019.00011] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 01/11/2019] [Indexed: 01/10/2023] Open
Abstract
Single-locus molecular barcoding is a useful method for identifying overlooked and undescribed biodiversity, providing the groundwork for further systematic study and taxonomic investigation. A variety of methods for delimiting species from barcoding libraries have been developed and applied, allowing for rapid estimates of species diversity in a broad range of taxa. However, tree-based and distance-based analyses can infer different group assignments, potentially over- or underestimating the number of putative species groups. Here, we explore diversity of mainland species of anole lizards from the Chortís Block biogeographical province of northern Central America using a DNA barcoding approach, generating and analyzing cytochrome oxidase subunit I (COI) sequences for over 400 samples assignable to 33 of 38 (86.8%) native and one introduced mainland species. We subsequently tested the effects different models of nucleotide substitution, different species-delimitation algorithms, and reducing our dataset had on species delimitation estimates. We performed of two distance-based (ABGD, RESL) and three tree-based (bPTP, mPTP, GMYC) analyses on both the full dataset and a dataset consisting only of unique halotypes. From 34 nominal taxa, analyses of the full dataset recovered between 34 and 64 operational taxonomic units (OTUs), while analyses of the reduced dataset inferred between 36 and 59. Reassigning individuals to either mPTP-inferred or ABGD clustered (7.2% threshold) groups improved the detection of a barcoding gap across three different models of nucleotide substitution, removing overlap between intra- and interspecific distances. Our results highlight the underestimated diversity of mainland Chortís Block anoles, but the lack of congruence between analyses demonstrates the importance of considering multiple analytical methods when dealing with single-locus datasets. We recommend future studies consider the effects of different models of nucleotide substitution on proposed barcoding gaps, as well as the effect reducing a dataset to unique haplotypes may have on proposed diversity estimates.
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Affiliation(s)
- Erich P. Hofmann
- Department of Biology, Indiana University of Pennsylvania, Indiana, PA, United States
- Department of Biological Sciences, Clemson University, Clemson, SC, United States
| | - Kirsten E. Nicholson
- Department of Biology, Central Michigan University, Mount Pleasant, MI, United States
| | | | - Gunther Köhler
- Senckenberg Forschungsinstitut und Naturmuseum, Frankfurt, Germany
| | - César A. Cerrato-Mendoza
- Federación Hondureña de Deportes de Montaña Y Escalada, Departamento de Francisco Morazán, Tegucigalpa, Honduras
| | - Melissa Medina-Flores
- Federación Hondureña de Deportes de Montaña Y Escalada, Departamento de Francisco Morazán, Tegucigalpa, Honduras
| | - Larry David Wilson
- Centro Zamorano de Biodiversidad, Escuela Agrícola Panamericana Zamorano, Departamento de Francisco Morazán, Tegucigalpa, Honduras
| | - Josiah H. Townsend
- Department of Biology, Indiana University of Pennsylvania, Indiana, PA, United States
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Jennings WB, Ruschi PA, Ferraro G, Quijada CC, Silva-Malanski ACG, Prosdocimi F, Buckup PA. Barcoding the Neotropical freshwater fish fauna using a new pair of universal COI primers with a discussion of primer dimers and M13 primer tails. Genome 2019; 62:77-83. [PMID: 30730769 DOI: 10.1139/gen-2018-0145] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Designing primers for DNA barcoding is a significant challenge for the rich Neotropical fish fauna, which is comprised of ∼6000 species. Previously, researchers required multiple pairs of PCR primers or primer cocktails to obtain standard COI (i.e., mitochondrial cytochrome c oxidase subunit I) barcode sequences from assemblages of freshwater fish in this region. To simplify DNA barcoding and metabarcoding studies of Neotropical freshwater fish, we present a new pair of COI primers, which have yielded high quality barcodes across six teleost orders-Characiformes, Cichliformes, Cyprinodontiformes, Gymnotiformes, Siluriformes, and Synbranchiformes-native to South America. Following previous fish barcoding studies, we also tailed our primers with M13 forward and reverse primers to facilitate the DNA sequencing process. Although this practice generates primer dimers, we obtained complete and high quality COI barcode sequences for all samples. We discuss the problem of primer dimers and suggest strategies for neutralizing their influence on data quality.
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Affiliation(s)
- W Bryan Jennings
- a Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista, 20940-040 Rio de Janeiro, RJ, Brazil
| | - Piero A Ruschi
- a Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista, 20940-040 Rio de Janeiro, RJ, Brazil
| | - Gustavo Ferraro
- a Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista, 20940-040 Rio de Janeiro, RJ, Brazil
| | - Carla Christie Quijada
- a Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista, 20940-040 Rio de Janeiro, RJ, Brazil
| | - Ana Cecilia Gomes Silva-Malanski
- a Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista, 20940-040 Rio de Janeiro, RJ, Brazil
| | - Francisco Prosdocimi
- b Laboratório de Genômica e Biodiversidade, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, RJ, Brazil
| | - Paulo A Buckup
- a Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista, 20940-040 Rio de Janeiro, RJ, Brazil
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DNA Barcoding Analysis and Phylogenetic Relation of Mangroves in Guangdong Province, China. FORESTS 2019. [DOI: 10.3390/f10010056] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Mangroves are distributed in the transition zone between sea and land, mostly in tropical and subtropical areas. They provide important ecosystem services and are therefore economically valuable. DNA barcoding is a useful tool for species identification and phylogenetic reconstruction. To evaluate the effectiveness of DNA barcoding in identifying mangrove species, we sampled 135 individuals representing 23 species, 22 genera, and 17 families from Zhanjiang, Shenzhen, Huizhou, and Shantou in the Guangdong province, China. We tested the universality of four DNA barcodes, namely rbcL, matK, trnH-psbA, and the internal transcribed spacer of nuclear ribosomal DNA (ITS), and examined their efficacy for species identification and the phylogenetic reconstruction of mangroves. The success rates for PCR amplification of rbcL, matK, trnH-psbA, and ITS were 100%, 80.29% ± 8.48%, 99.38% ± 1.25%, and 97.18% ± 3.25%, respectively, and the rates of DNA sequencing were 100%, 75.04% ± 6.26%, 94.57% ± 5.06%, and 83.35% ± 4.05%, respectively. These results suggest that both rbcL and trnH–psbA are universal in mangrove species from the Guangdong province. The highest success rate for species identification was 84.48% ± 12.09% with trnH-psbA, followed by rbcL (82.16% ± 9.68%), ITS (66.48% ± 5.97%), and matK (65.09% ± 6.00%), which increased to 91.25% ± 9.78% with the addition of rbcL. Additionally, the identification rate of mangroves was not significantly different between rbcL + trnH-psbA and other random fragment combinations. In conclusion, rbcL and trnH-psbA were the most suitable DNA barcode fragments for species identification in mangrove plants. When the phylogenetic relationships were constructed with random fragment combinations, the optimal evolutionary tree with high supporting values (86.33% ± 4.16%) was established using the combination of matK + rbcL + trnH-psbA + ITS in mangroves. In total, the 476 newly acquired sequences in this study lay the foundation for a DNA barcode database of mangroves.
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DNA barcodes from snake venom: a broadly applicable method for extraction of DNA from snake venoms. Biotechniques 2018; 65:339-345. [PMID: 30477329 DOI: 10.2144/btn-2018-0096] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
DNA barcoding is a simple technique used to develop a large-scale system of classification that is broadly applicable across a wide variety of taxa. DNA-based analysis of snake venoms can provide a system of classification independent of currently accepted taxonomic relationships by generating DNA barcodes specific to each venom sample. DNA purification from dried snake venoms has previously required large amounts of starting material, has resulted in low yields and inconsistent amplification, and was possible with front-fanged snakes only. Here, we present a modified DNA extraction protocol applied to venoms of both front- and rear-fanged snakes that requires significantly less starting material (1 mg) and yields sufficient amounts of DNA for successful PCR amplification of regions commonly used for DNA barcoding. [Formula: see text].
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Adeoba MI, Kabongo R, der Bank HV, Yessoufou K. Re-evaluation of the discriminatory power of DNA barcoding on some specimens of African Cyprinidae (subfamilies Cyprininae and Danioninae). Zookeys 2018:105-121. [PMID: 29674898 PMCID: PMC5906743 DOI: 10.3897/zookeys.746.13502] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 12/14/2017] [Indexed: 12/02/2022] Open
Abstract
Specimen identification in the absence of diagnostic morphological characters (e.g., larvae) can be problematic even for experts. The goal of the present study was to assess the performance of COI in discriminating specimens of the fish family Cyprinidae in Africa, and to explore whether COI-phylogeny can be reliably used for phylogenetic comparative analysis. The main objective was to analyse a matrix of COI sequences for 315 specimens from 15 genera of African Cyprinidae using various distance-based identification methods alongside multiple tests of DNA barcode efficacy (barcode gap, species monophyly on NJ tree). Some morphological and biological characters were also mapped on a COI-phylogeny reconstructed using Maximum Parsimony. First, the results indicated the existence of barcode gaps, a discriminatory power of COI ranging from 79 % to 92 %, and that most nodes form well-supported monophyletic clades on an NJ tree. Second, it was found that some morphological and biological characters are clustered on the COI-phylogeny, and this indicates the reliability of these characters for taxonomic discrimination within the family. Put together, our results provide not only an additional support for the COI as a good barcode marker for the African Cyprinidae but it also indicate the utility of COI-based phylogenies for a wide spectrum of ecological questions related to African Cyprinidae.
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Affiliation(s)
- Mariam I Adeoba
- Department of Zoology, University of Johannesburg, Kingsway Campus PO Box 524, Auckland Park 2006, South Africa
| | - Ronny Kabongo
- African Centre for DNA Barcoding, University of Johannesburg, Kingsway Campus, PO Box 524, Auckland Park 2006, South Africa
| | - Herman Van der Bank
- Department of Zoology, University of Johannesburg, Kingsway Campus PO Box 524, Auckland Park 2006, South Africa
| | - Kowiyou Yessoufou
- Department of Geography, Environmental management and Energy studies, University of Johannesburg, Kingsway Campus PO Box 524, Auckland Park 2006, South Africa
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Adeoba MI, Kabongo R, Van der Bank H, Yessoufou K. Re-evaluation of the discriminatory power of DNA barcoding on some specimens of African Cyprinidae (subfamilies Cyprininae and Danioninae). Zookeys 2018. [DOI: 10.3897/zookeys.744.13502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Specimen identification in the absence of diagnostic morphological characters (e.g., larvae) can be problematic even for experts. The goal of the present study was to assess the performance of COI in discriminating specimens of the fish family Cyprinidae in Africa, and to explore whether COI-phylogeny can be reliably used for comparative phylogenetic analysis. The main objective was to analyse a matrix of COI sequences for 315 specimens from 15 genera of African Cyprinidae using various distance-based identification methods alongside multiple tests of DNA barcode efficacy (barcode gap, species monophyly on NJ tree). Some morphological and biological characters were also mapped on a COI-phylogeny reconstructed using Maximum Parsimony. First, the results indicated the existence of barcode gaps, a discriminatory power of COI ranging from 79 % to 92 %, and that most nodes form well-supported monophyletic clades on an NJ tree. Second, it was found that some morphological and biological characters are clustered on the COI-phylogeny, and this indicates the reliability of these characters for taxonomic discrimination within the family. Put together, our results provide not only an additional support for the COI as a good barcode marker for the African Cyprinidae but it also indicate the utility of COI-based phylogenies for a wide spectrum of ecological questions related to African Cyprinidae.
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21
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Adeoba MI, Kabongo R, Van der Bank H, Yessoufou K. Re-evaluation of the discriminatory power of DNA barcoding on some specimens of African Cyprinidae (subfamilies Cyprininae and Danioninae). Zookeys 2018. [DOI: 10.3897/zookeys.740.13502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Specimen identification in the absence of diagnostic morphological characters (e.g., larvae) can be problematic even for experts. The goal of the present study was to assess the performance of COI in discriminating specimens of the fish family Cyprinidae in Africa, and to explore whether COI-phylogeny can be reliably used for phylogenetic comparative analysis. The main objective was to analyse a matrix of COI sequences for 315 specimens from 15 genera of African Cyprinidae using various distance-based identification methods alongside multiple tests of DNA barcode efficacy (barcode gap, species monophyly on NJ tree). Some morphological and biological characters were also mapped on a COI-phylogeny reconstructed using Maximum Parsimony. First, the results indicated the existence of barcode gaps, a discriminatory power of COI ranging from 79 % to 92 %, and that most nodes form well-supported monophyletic clades on an NJ tree. Second, it was found that some morphological and biological characters are clustered on the COI-phylogeny, and this indicates the reliability of these characters for taxonomic discrimination within the family. Put together, our results provide not only an additional support for the COI as a good barcode marker for the African Cyprinidae but it also indicate the utility of COI-based phylogenies for a wide spectrum of ecological questions related to African Cyprinidae.
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22
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Barcoding utility in a mega-diverse, cross-continental genus: keeping pace with Cyrtodactylus geckos. Sci Rep 2017; 7:5592. [PMID: 28717207 PMCID: PMC5514027 DOI: 10.1038/s41598-017-05261-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 05/25/2017] [Indexed: 11/09/2022] Open
Abstract
Over the past decade, DNA barcoding has become a staple of low-cost molecular systematic investigations. The availability of universal primers and subsidized sequencing projects (PolarBOL, SharkBOL, SpongeBOL) have driven this popularity, often without appropriate investigation into the utility of barcoding data for the taxonomic group of interest. Here, our primary aim is to determine the phylogenetic value of DNA barcoding (mitochondrial locus COI) within the gecko genus Cyrtodactylus. With >40 new species described since last systematic investigation, Cyrtodactylus represents one of the most diverse extant squamate genera, and their contemporary distribution spans the Indian subcontinent, eastward through Indochina, and into AustraloPapua. The complex biogeographic history of this group, and morphology-only designation of many species have complicated our phylogenetic understanding of Cyrtodactylus. To highlight the need for continued inclusive molecular assessment, we use Vietnamese Cyrtodactylus as a case study showing the geopolitically paraphyletic nature of their history. We compare COI to the legacy marker ND2, and discuss the value of COI as an interspecific marker, as well as its shortcomings at deeper evolutionary scales. We draw attention back to the Cold Code as a subsidized method for incorporating molecular methods into species descriptions in the effort to maintain accurate phylogenies.
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Lyra ML, Haddad CFB, de Azeredo-Espin AML. Meeting the challenge of DNA barcoding Neotropical amphibians: polymerase chain reaction optimization and new COI primers. Mol Ecol Resour 2017; 17:966-980. [PMID: 28029226 DOI: 10.1111/1755-0998.12648] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 12/09/2016] [Accepted: 12/15/2016] [Indexed: 01/17/2023]
Abstract
Amphibians are one of the most threatened vertebrate classes, yet at the same time new species are being described every year, demonstrating that the number of existing species is grossly underestimated. In groups such as amphibians, with high extinction rates and poorly known species boundaries, DNA barcoding is a tool that can rapidly assess genetic diversity and estimate species richness for prioritizing conservation decisions. However, reliable recovery of the 5' region of the cytochrome c oxidase subunit 1 (COI) gene is critical for the ongoing effort to gather DNA barcodes for all amphibian species. Here, we provide new PCR conditions and tested new primers that increase the efficiency of barcode recovery in amphibians. We found that a low extension temperature for PCR cycles significantly improves the efficiency of amplification for all combinations of primers. Combining low PCR extension temperature and primers AnF1 + AnR1, we were able to recover COI sequences for 100% of the species analysed (N = 161), encompassing ~15% of the species known from Brazil (representing 77 genera and 23 families), which is an important improvement over previous studies. The preliminary assessment of species diversity suggested that number of species might be underestimated by about 25%. We conclude that DNA barcoding is an efficient, simple, and standardized protocol for identifying cryptic diversity in amphibians and advocate for its use in biodiversity inventories and across widespread populations within known species.
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Affiliation(s)
- Mariana L Lyra
- Departamento de Zoologia, Instituto de Biociências, UNESP - Univ Estadual Paulista, Campus Rio Claro, Av. 24 A, No. 1515, Bela Vista, CEP 13506-970, Rio Claro, SP, Brazil
| | - Célio F B Haddad
- Departamento de Zoologia, Instituto de Biociências, UNESP - Univ Estadual Paulista, Campus Rio Claro, Av. 24 A, No. 1515, Bela Vista, CEP 13506-970, Rio Claro, SP, Brazil
| | - Ana Maria L de Azeredo-Espin
- Centro de Biologia Molecular e Engenharia Genética and Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Rua Cândido Rondon No. 400, CEP 13083-875, Campinas, São Paulo, Brazil
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24
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Cariani A, Messinetti S, Ferrari A, Arculeo M, Bonello JJ, Bonnici L, Cannas R, Carbonara P, Cau A, Charilaou C, El Ouamari N, Fiorentino F, Follesa MC, Garofalo G, Golani D, Guarniero I, Hanner R, Hemida F, Kada O, Lo Brutto S, Mancusi C, Morey G, Schembri PJ, Serena F, Sion L, Stagioni M, Tursi A, Vrgoc N, Steinke D, Tinti F. Improving the Conservation of Mediterranean Chondrichthyans: The ELASMOMED DNA Barcode Reference Library. PLoS One 2017; 12:e0170244. [PMID: 28107413 PMCID: PMC5249125 DOI: 10.1371/journal.pone.0170244] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 12/30/2016] [Indexed: 11/18/2022] Open
Abstract
Cartilaginous fish are particularly vulnerable to anthropogenic stressors and environmental change because of their K-selected reproductive strategy. Accurate data from scientific surveys and landings are essential to assess conservation status and to develop robust protection and management plans. Currently available data are often incomplete or incorrect as a result of inaccurate species identifications, due to a high level of morphological stasis, especially among closely related taxa. Moreover, several diagnostic characters clearly visible in adult specimens are less evident in juveniles. Here we present results generated by the ELASMOMED Consortium, a regional network aiming to sample and DNA-barcode the Mediterranean Chondrichthyans with the ultimate goal to provide a comprehensive DNA barcode reference library. This library will support and improve the molecular taxonomy of this group and the effectiveness of management and conservation measures. We successfully barcoded 882 individuals belonging to 42 species (17 sharks, 24 batoids and one chimaera), including four endemic and several threatened ones. Morphological misidentifications were found across most orders, further confirming the need for a comprehensive DNA barcoding library as a valuable tool for the reliable identification of specimens in support of taxonomist who are reviewing current identification keys. Despite low intraspecific variation among their barcode sequences and reduced samples size, five species showed preliminary evidence of phylogeographic structure. Overall, the ELASMOMED initiative further emphasizes the key role accurate DNA barcoding libraries play in establishing reliable diagnostic species specific features in otherwise taxonomically problematic groups for biodiversity management and conservation actions.
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Affiliation(s)
- Alessia Cariani
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy
| | - Silvia Messinetti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy
| | - Alice Ferrari
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy
| | - Marco Arculeo
- Department STEBICEF, University of Palermo, Palermo, Italy
| | | | | | - Rita Cannas
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | | | - Alessandro Cau
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Charis Charilaou
- Department of Fisheries and Marine Research, Ministry of Agriculture, Rural Development and Environment, Nicosia, Republic of Cyprus
| | - Najib El Ouamari
- Centre Régional de Institut National Recherche Halieutique, Nador, Morocco
| | - Fabio Fiorentino
- Institute for Coastal Marine Environment (IAMC) National Research Council (CNR), Mazara del Vallo, Italy
| | | | - Germana Garofalo
- Institute for Coastal Marine Environment (IAMC) National Research Council (CNR), Mazara del Vallo, Italy
| | - Daniel Golani
- Department of Evolution, Systematics and Ecology, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ilaria Guarniero
- Department DIMEVET, University of Bologna, Ozzano dell'Emilia, Italy
| | - Robert Hanner
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Farid Hemida
- Ecole Nationale Superieure des Sciences de la Mer et d'Amenagement du Littoral, Campus Universitaire de Dely Ibrahim, Alger, Algeria
| | - Omar Kada
- Centre Régional de Institut National Recherche Halieutique, Nador, Morocco
| | | | - Cecilia Mancusi
- Regional Agency for Environmental Protection-Toscana (ARPAT), Livorno, Italy
| | | | | | - Fabrizio Serena
- Regional Agency for Environmental Protection-Toscana (ARPAT), Livorno, Italy
| | - Letizia Sion
- Department of Biology, University of Bari Aldo Moro, Bari, Italy
| | - Marco Stagioni
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy
| | - Angelo Tursi
- Department of Biology, University of Bari Aldo Moro, Bari, Italy
| | - Nedo Vrgoc
- Institute of Oceanography and Fisheries, Split, Croatia
| | - Dirk Steinke
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Fausto Tinti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy
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25
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DNA Barcoding ofPhymaturusLizards Reveals Conflicts in Species Delimitation within thepatagonicusClade. J HERPETOL 2016. [DOI: 10.1670/15-104] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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26
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Wilson JJ, Sing KW, Lee PS, Wee AKS. Application of DNA barcodes in wildlife conservation in Tropical East Asia. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2016; 30:982-9. [PMID: 27341687 DOI: 10.1111/cobi.12787] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 02/12/2016] [Indexed: 05/24/2023]
Abstract
Over the past 50 years, Tropical East Asia has lost more biodiversity than any tropical region. Tropical East Asia is a megadiverse region with an acute taxonomic impediment. DNA barcodes are short standardized DNA sequences used for taxonomic purposes and have the potential to lessen the challenges of biodiversity inventory and assessments in regions where they are most needed. We reviewed DNA barcoding efforts in Tropical East Asia relative to other tropical regions. We suggest DNA barcodes (or metabarcodes from next-generation sequencers) may be especially useful for characterizing and connecting species-level biodiversity units in inventories encompassing taxa lacking formal description (particularly arthropods) and in large-scale, minimal-impact approaches to vertebrate monitoring and population assessments through secondary sources of DNA (invertebrate derived DNA and environmental DNA). We suggest interest and capacity for DNA barcoding are slowly growing in Tropical East Asia, particularly among the younger generation of researchers who can connect with the barcoding analogy and understand the need for new approaches to the conservation challenges being faced.
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Affiliation(s)
- John-James Wilson
- Ecology and Biodiversity Program, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.
- Museum of Zoology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Kong-Wah Sing
- Ecology and Biodiversity Program, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
- Museum of Zoology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Ping-Shin Lee
- Ecology and Biodiversity Program, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
- Museum of Zoology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Alison K S Wee
- Centre for Integrative Conservation, Xisshangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun Township, Mengla County, Yunnan Province, 666303, China
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Lacoursière-Roussel A, Dubois Y, Normandeau E, Bernatchez L. Improving herpetological surveys in eastern North America using the environmental DNA method. Genome 2016; 59:991-1007. [PMID: 27788021 DOI: 10.1139/gen-2015-0218] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Among vertebrates, herpetofauna has the highest proportion of declining species. Detection of environmental DNA (eDNA) is a promising method towards significantly increasing large-scale herpetological conservation efforts. However, the integration of eDNA results within a management framework requires an evaluation of the efficiency of the method in large natural environments and the calibration of eDNA surveys with the quantitative monitoring tools currently used by conservation biologists. Towards this end, we first developed species-specific primers to detect the wood turtle (Glyptemys insculpta) a species at risk in Canada, by quantitative PCR (qPCR). The rate of eDNA detection obtained by qPCR was also compared to the relative abundance of this species in nine rivers obtained by standardized visual surveys in the Province of Québec (Canada). Second, we developed multi-species primers to detect North American amphibian and reptile species using eDNA metabarcoding analysis. An occurrence index based on the distribution range and habitat type was compared with the eDNA metabarcoding dataset from samples collected in seven lakes and five rivers. Our results empirically support the effectiveness of eDNA metabarcoding to characterize herpetological species distributions. Moreover, detection rates provided similar results to standardized visual surveys currently used to develop conservation strategies for the wood turtle. We conclude that eDNA detection rates may provide an effective semiquantitative survey tool, provided that assay calibration and standardization is performed.
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Affiliation(s)
- Anaïs Lacoursière-Roussel
- a Institut de Biologie Intégrative et des Systèmes, Pavillon Charles Eugène Marchand, Université Laval, Québec, QC G1V 0A6, Canada
| | - Yohann Dubois
- b Ministère des Forêts, de la Faune et des Parcs, Direction de l'expertise sur la faune terrestre, l'herpétofaune et l'avifaune, 880 chemin Sainte-Foy, Québec, QC G1S 4X4, Canada
| | - Eric Normandeau
- a Institut de Biologie Intégrative et des Systèmes, Pavillon Charles Eugène Marchand, Université Laval, Québec, QC G1V 0A6, Canada
| | - Louis Bernatchez
- a Institut de Biologie Intégrative et des Systèmes, Pavillon Charles Eugène Marchand, Université Laval, Québec, QC G1V 0A6, Canada
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Chambers EA, Hebert PDN. Assessing DNA Barcodes for Species Identification in North American Reptiles and Amphibians in Natural History Collections. PLoS One 2016; 11:e0154363. [PMID: 27116180 PMCID: PMC4846166 DOI: 10.1371/journal.pone.0154363] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 04/12/2016] [Indexed: 11/19/2022] Open
Abstract
Background High rates of species discovery and loss have led to the urgent need for more rapid assessment of species diversity in the herpetofauna. DNA barcoding allows for the preliminary identification of species based on sequence divergence. Prior DNA barcoding work on reptiles and amphibians has revealed higher biodiversity counts than previously estimated due to cases of cryptic and undiscovered species. Past studies have provided DNA barcodes for just 14% of the North American herpetofauna, revealing the need for expanded coverage. Methodology/Principal Findings This study extends the DNA barcode reference library for North American herpetofauna, assesses the utility of this approach in aiding species delimitation, and examines the correspondence between current species boundaries and sequence clusters designated by the BIN system. Sequences were obtained from 730 specimens, representing 274 species (43%) from the North American herpetofauna. Mean intraspecific divergences were 1% and 3%, while average congeneric sequence divergences were 16% and 14% in amphibians and reptiles, respectively. BIN assignments corresponded with current species boundaries in 79% of amphibians, 100% of turtles, and 60% of squamates. Deep divergences (>2%) were noted in 35% of squamate and 16% of amphibian species, and low divergences (<2%) occurred in 12% of reptiles and 23% of amphibians, patterns reflected in BIN assignments. Sequence recovery declined with specimen age, and variation in recovery success was noted among collections. Within collections, barcodes effectively flagged seven mislabeled tissues, and barcode fragments were recovered from five formalin-fixed specimens. Conclusions/Significance This study demonstrates that DNA barcodes can effectively flag errors in museum collections, while BIN splits and merges reveal taxa belonging to deeply diverged or hybridizing lineages. This study is the first effort to compile a reference library of DNA barcodes for herpetofauna on a continental scale.
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Affiliation(s)
- E. Anne Chambers
- Department of Integrative Biology, University of Texas, Austin, Texas, United States of America
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
- * E-mail:
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
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29
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Vasconcelos R, Montero-Mendieta S, Simó-Riudalbas M, Sindaco R, Santos X, Fasola M, Llorente G, Razzetti E, Carranza S. Unexpectedly High Levels of Cryptic Diversity Uncovered by a Complete DNA Barcoding of Reptiles of the Socotra Archipelago. PLoS One 2016; 11:e0149985. [PMID: 26930572 PMCID: PMC4772999 DOI: 10.1371/journal.pone.0149985] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 01/28/2016] [Indexed: 11/19/2022] Open
Abstract
Few DNA barcoding studies of squamate reptiles have been conducted. Due to the significance of the Socotra Archipelago (a UNESCO Natural World Heritage site and a biodiversity hotspot) and the conservation interest of its reptile fauna (94% endemics), we performed the most comprehensive DNA barcoding study on an island group to date to test its applicability to specimen identification and species discovery. Reptiles constitute Socotra's most important vertebrate fauna, yet their taxonomy remains under-studied. We successfully DNA-barcoded 380 individuals of all 31 presently recognized species. The specimen identification success rate is moderate to high, and almost all species presented local barcoding gaps. The unexpected high levels of intra-specific variability found within some species suggest cryptic diversity. Species richness may be under-estimated by 13.8-54.4%. This has implications in the species' ranges and conservation status that should be considered for conservation planning. Other phylogenetic studies using mitochondrial and nuclear markers are congruent with our results. We conclude that, despite its reduced length (663 base pairs), cytochrome c oxidase 1, COI, is very useful for specimen identification and for detecting intra-specific diversity, and has a good phylogenetic signal. We recommend DNA barcoding to be applied to other biodiversity hotspots for quickly and cost-efficiently flagging species discovery, preferentially incorporated into an integrative taxonomic framework.
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Affiliation(s)
- Raquel Vasconcelos
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- Institute of Evolutionary Biology (CSIC-UPF, Consejo Superior de Investigaciones Científicas- Universitat Pompeu Fabra), Barcelona, Spain
| | - Santiago Montero-Mendieta
- Institute of Evolutionary Biology (CSIC-UPF, Consejo Superior de Investigaciones Científicas- Universitat Pompeu Fabra), Barcelona, Spain
| | - Marc Simó-Riudalbas
- Institute of Evolutionary Biology (CSIC-UPF, Consejo Superior de Investigaciones Científicas- Universitat Pompeu Fabra), Barcelona, Spain
| | | | - Xavier Santos
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
| | - Mauro Fasola
- Dipartimento Scienze della Terra e dell'Ambiente, Università degli studi di Pavia, Pavia, Italy
| | - Gustavo Llorente
- Departament de Biologia Animal, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Edoardo Razzetti
- Museo di Storia Naturale, Università degli studi di Pavia, Pavia, Italy
| | - Salvador Carranza
- Institute of Evolutionary Biology (CSIC-UPF, Consejo Superior de Investigaciones Científicas- Universitat Pompeu Fabra), Barcelona, Spain
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30
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Edwards T, Karl AE, Vaughn M, Rosen PC, Torres CM, Murphy RW. The desert tortoise trichotomy: Mexico hosts a third, new sister-species of tortoise in the Gopherus morafkai-G. agassizii group. Zookeys 2016:131-58. [PMID: 27006625 PMCID: PMC4768471 DOI: 10.3897/zookeys.562.6124] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 01/06/2016] [Indexed: 02/08/2023] Open
Abstract
Desert tortoises (Testudines; Testudinidae; Gopherusagassizii group) have an extensive distribution throughout the Mojave, Colorado, and Sonoran desert regions. Not surprisingly, they exhibit a tremendous amount of ecological, behavioral, morphological and genetic variation. Gopherusagassizii was considered a single species for almost 150 years but recently the species was split into the nominate form and Morafka’s desert tortoise, Gopherusmorafkai, the latter occurring south and east of the Colorado River. Whereas a large body of literature focuses on tortoises in the United States, a dearth of investigations exists for Mexican animals. Notwithstanding, Mexican populations of desert tortoises in the southern part of the range of Gopherusmorafkai are distinct, particularly where the tortoises occur in tropical thornscrub and tropical deciduous forest. Recent studies have shed light on the ecology, morphology and genetics of these southern ‘desert’ tortoises. All evidence warrants recognition of this clade as a distinctive taxon and herein we describe it as Gopherusevgoodeisp. n. The description of the new species significantly reduces and limits the distribution of Gopherusmorafkai to desertscrub habitat only. By contrast, Gopherusevgoodeisp. n. occurs in thornscrub and tropical deciduous forests only and this leaves it with the smallest range of the three sister species. We present conservation implications for the newly described Gopherusevgoodei, which already faces impending threats.
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Affiliation(s)
- Taylor Edwards
- School of Natural Resources and the Environment. The University of Arizona, Tucson, AZ 85721 USA; University of Arizona Genetics Core, University of Arizona, Tucson, AZ 85721 USA
| | | | | | - Philip C Rosen
- School of Natural Resources and the Environment. The University of Arizona, Tucson, AZ 85721 USA
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Rockney HJ, Ofori-Boateng C, Porcino N, Leaché AD. A comparison of DNA barcoding markers in West African frogs. AFR J HERPETOL 2015. [DOI: 10.1080/21564574.2015.1114530] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Heidi J. Rockney
- Burke Museum of Natural History and Culture, University of Washington, Seattle, Washington, USA
- Department of Biology, University of Washington, Seattle, Washington, USA
| | - Caleb Ofori-Boateng
- Forestry Research Institute of Ghana, Kumasi, Ghana
- Wildlife and Range Management Department, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Natsuko Porcino
- Burke Museum of Natural History and Culture, University of Washington, Seattle, Washington, USA
- Department of Biology, University of Washington, Seattle, Washington, USA
| | - Adam D. Leaché
- Burke Museum of Natural History and Culture, University of Washington, Seattle, Washington, USA
- Department of Biology, University of Washington, Seattle, Washington, USA
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Muhammad Tahir H, Akhtar S. Services of DNA barcoding in different fields. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4463-4474. [DOI: 10.3109/19401736.2015.1089572] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | - Samreen Akhtar
- Department of Zoology, University of Sargodha, Sargodha, Pakistan
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33
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Female heterogamety in Madagascar chameleons (Squamata: Chamaeleonidae: Furcifer): differentiation of sex and neo-sex chromosomes. Sci Rep 2015; 5:13196. [PMID: 26286647 PMCID: PMC4541320 DOI: 10.1038/srep13196] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 07/14/2015] [Indexed: 12/26/2022] Open
Abstract
Amniotes possess variability in sex determining mechanisms, however, this diversity is still only partially known throughout the clade and sex determining systems still remain unknown even in such a popular and distinctive lineage as chameleons (Squamata: Acrodonta: Chamaeleonidae). Here, we present evidence for female heterogamety in this group. The Malagasy giant chameleon (Furcifer oustaleti) (chromosome number 2n = 22) possesses heteromorphic Z and W sex chromosomes with heterochromatic W. The panther chameleon (Furcifer pardalis) (2n = 22 in males, 21 in females), the second most popular chameleon species in the world pet trade, exhibits a rather rare Z1Z1Z2Z2/Z1Z2W system of multiple sex chromosomes, which most likely evolved from W-autosome fusion. Notably, its neo-W chromosome is partially heterochromatic and its female-specific genetic content has expanded into the previously autosomal region. Showing clear evidence for genotypic sex determination in the panther chameleon, we resolve the long-standing question of whether or not environmental sex determination exists in this species. Together with recent findings in other reptile lineages, our work demonstrates that female heterogamety is widespread among amniotes, adding another important piece to the mosaic of knowledge on sex determination in amniotes needed to understand the evolution of this important trait.
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Klippel AH, Oliveira PV, Britto KB, Freire BF, Moreno MR, dos Santos AR, Banhos A, Paneto GG. Using DNA Barcodes to Identify Road-Killed Animals in Two Atlantic Forest Nature Reserves, Brazil. PLoS One 2015; 10:e0134877. [PMID: 26244644 PMCID: PMC4526655 DOI: 10.1371/journal.pone.0134877] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 07/14/2015] [Indexed: 12/02/2022] Open
Abstract
Road mortality is the leading source of biodiversity loss in the world, especially due to fragmentation of natural habitats and loss of wildlife. The survey of the main species victims of roadkill is of fundamental importance for the better understanding of the problem, being necessary, for this, the correct species identification. The aim of this study was to verify if DNA barcodes can be applied to identify road-killed samples that often cannot be determined morphologically. For this purpose, 222 vertebrate samples were collected in a stretch of the BR-101 highway that crosses two Discovery Coast Atlantic Forest Natural Reserves, the Sooretama Biological Reserve and the Vale Natural Reserve, in Espírito Santo, Brazil. The mitochondrial COI gene was amplified, sequenced and confronted with the BOLD database. It was possible to identify 62.16% of samples, totaling 62 different species, including Pyrrhura cruentata, Chaetomys subspinosus, Puma yagouaroundi and Leopardus wiedii considered Vulnerable in the National Official List of Species of Endangered Wildlife. The most commonly identified animals were a bat (Molossus molossus), an opossum (Didelphis aurita) and a frog (Trachycephalus mesophaeus) species. Only one reptile was identified using the technique, probably due to lack of reference sequences in BOLD. These data may contribute to a better understanding of the impact of roads on species biodiversity loss and to introduce the DNA barcode technique to road ecology scenarios.
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Affiliation(s)
- Angélica H. Klippel
- Federal University of Espirito Santo, Centre of Agricultural Sciences, Alto Universitário, s/n, Guararema, Alegre, Espírito Santo, 29.500–000, Brazil
| | - Pablo V. Oliveira
- Federal University of Espirito Santo, Centre of Agricultural Sciences, Alto Universitário, s/n, Guararema, Alegre, Espírito Santo, 29.500–000, Brazil
| | - Karollini B. Britto
- Federal University of Espirito Santo, Centre of Agricultural Sciences, Alto Universitário, s/n, Guararema, Alegre, Espírito Santo, 29.500–000, Brazil
| | - Bárbara F. Freire
- Federal University of Espirito Santo, Centre of Agricultural Sciences, Alto Universitário, s/n, Guararema, Alegre, Espírito Santo, 29.500–000, Brazil
| | - Marcel R. Moreno
- Chico Mendes Institute of Biodiversity Conservation, Sooretama Biological Reserve, Highway BR-101, km 101, Linhares, Espírito Santo, 29.900–970, Brazil
| | - Alexandre R. dos Santos
- Federal University of Espirito Santo, Centre of Agricultural Sciences, Alto Universitário, s/n, Guararema, Alegre, Espírito Santo, 29.500–000, Brazil
| | - Aureo Banhos
- Federal University of Espirito Santo, Centre of Agricultural Sciences, Alto Universitário, s/n, Guararema, Alegre, Espírito Santo, 29.500–000, Brazil
| | - Greiciane G. Paneto
- Federal University of Espirito Santo, Centre of Agricultural Sciences, Alto Universitário, s/n, Guararema, Alegre, Espírito Santo, 29.500–000, Brazil
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35
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Paz A, Ibáñez R, Lips KR, Crawford AJ. Testing the role of ecology and life history in structuring genetic variation across a landscape: a trait-based phylogeographic approach. Mol Ecol 2015; 24:3723-37. [DOI: 10.1111/mec.13275] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 06/09/2015] [Accepted: 06/12/2015] [Indexed: 11/30/2022]
Affiliation(s)
- Andrea Paz
- Department of Biological Sciences; Universidad de los Andes; A.A. 4976 Bogotá Colombia
| | - Roberto Ibáñez
- Smithsonian Tropical Research Institute; Apartado 0843-03092 Panama City Republic of Panama
- Círculo Herpetológico de Panamá; Apartado 0824-00122 Panama City Republic of Panama
| | - Karen R. Lips
- Smithsonian Tropical Research Institute; Apartado 0843-03092 Panama City Republic of Panama
- Department of Biology; University of Maryland; College Park MD 20742-4415 USA
| | - Andrew J. Crawford
- Department of Biological Sciences; Universidad de los Andes; A.A. 4976 Bogotá Colombia
- Smithsonian Tropical Research Institute; Apartado 0843-03092 Panama City Republic of Panama
- Círculo Herpetológico de Panamá; Apartado 0824-00122 Panama City Republic of Panama
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36
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Jennings WB, Wogel H, Bilate M, Salles RDOL, Buckup PA. DNA barcoding reveals species level divergence between populations of the microhylid frog genus Arcovomer (Anura: Microhylidae) in the Atlantic Rainforest of southeastern Brazil. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3415-22. [PMID: 26016873 DOI: 10.3109/19401736.2015.1022731] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The microhylid frogs belonging to the genus Arcovomer have been reported from lowland Atlantic Rainforest in the Brazilian states of Espírito Santo, Rio de Janeiro, and São Paulo. Here, we use DNA barcoding to assess levels of genetic divergence between apparently isolated populations in Espírito Santo and Rio de Janeiro. Our mtDNA data consisting of cytochrome oxidase subunit I (COI) nucleotide sequences reveals 13.2% uncorrected and 30.4% TIM2 + I + Γ corrected genetic divergences between these two populations. This level of divergence exceeds the suggested 10% uncorrected divergence threshold for elevating amphibian populations to candidate species using this marker, which implies that the Espírito Santo population is a species distinct from Arcovomer passarellii. Calibration of our model-corrected sequence divergence estimates suggests that the time of population divergence falls between 12 and 29 million years ago.
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Affiliation(s)
- W Bryan Jennings
- a Departamento de Vertebrados , Museu Nacional, Universidade Federal do Rio de Janeiro , Rio de Janeiro , RJ , Brazil and
| | - Henrique Wogel
- a Departamento de Vertebrados , Museu Nacional, Universidade Federal do Rio de Janeiro , Rio de Janeiro , RJ , Brazil and.,b Centro Universitário de Volta Redonda - UniFOA, Avenida Paulo Erlei Alves Abrantes , Rio de Janeiro , RJ , Brazil
| | - Marcos Bilate
- a Departamento de Vertebrados , Museu Nacional, Universidade Federal do Rio de Janeiro , Rio de Janeiro , RJ , Brazil and
| | - Rodrigo de O L Salles
- a Departamento de Vertebrados , Museu Nacional, Universidade Federal do Rio de Janeiro , Rio de Janeiro , RJ , Brazil and
| | - Paulo A Buckup
- a Departamento de Vertebrados , Museu Nacional, Universidade Federal do Rio de Janeiro , Rio de Janeiro , RJ , Brazil and
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DNA Barcoding Survey of Anurans across the Eastern Cordillera of Colombia and the Impact of the Andes on Cryptic Diversity. PLoS One 2015; 10:e0127312. [PMID: 26000447 PMCID: PMC4441516 DOI: 10.1371/journal.pone.0127312] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 04/13/2015] [Indexed: 11/23/2022] Open
Abstract
Colombia hosts the second highest amphibian species diversity on Earth, yet its fauna remains poorly studied, especially using molecular genetic techniques. We present the results of the first wide-scale DNA barcoding survey of anurans of Colombia, focusing on a transect across the Eastern Cordillera. We surveyed 10 sites between the Magdalena Valley to the west and the eastern foothills of the Eastern Cordillera, sequencing portions of the mitochondrial 16S ribosomal RNA and cytochrome oxidase subunit 1 (CO1) genes for 235 individuals from 52 nominal species. We applied two barcode algorithms, Automatic Barcode Gap Discovery and Refined Single Linkage Analysis, to estimate the number of clusters or “unconfirmed candidate species” supported by DNA barcode data. Our survey included ~7% of the anuran species known from Colombia. While barcoding algorithms differed slightly in the number of clusters identified, between three and ten nominal species may be obscuring candidate species (in some cases, more than one cryptic species per nominal species). Our data suggest that the high elevations of the Eastern Cordillera and the low elevations of the Chicamocha canyon acted as geographic barriers in at least seven nominal species, promoting strong genetic divergences between populations associated with the Eastern Cordillera.
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Hawlitschek O, Morinière J, Dunz A, Franzen M, Rödder D, Glaw F, Haszprunar G. Comprehensive DNA barcoding of the herpetofauna of Germany. Mol Ecol Resour 2015; 16:242-53. [DOI: 10.1111/1755-0998.12416] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 04/14/2015] [Accepted: 04/15/2015] [Indexed: 01/01/2023]
Affiliation(s)
- O. Hawlitschek
- Zoologische Staatssammlung (ZSM-SNSB); Münchhausenstrasse 21 81247 München Germany
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra); Passeig Maritim de la Barceloneta 37 08003 Barcelona Spain
| | - J. Morinière
- Zoologische Staatssammlung (ZSM-SNSB); Münchhausenstrasse 21 81247 München Germany
| | - A. Dunz
- Zoologische Staatssammlung (ZSM-SNSB); Münchhausenstrasse 21 81247 München Germany
| | - M. Franzen
- Zoologische Staatssammlung (ZSM-SNSB); Münchhausenstrasse 21 81247 München Germany
| | - D. Rödder
- Zoologisches Forschungsmuseum Alexander Koenig; Adenauerallee 160 53113 Bonn Germany
| | - F. Glaw
- Zoologische Staatssammlung (ZSM-SNSB); Münchhausenstrasse 21 81247 München Germany
| | - G. Haszprunar
- Zoologische Staatssammlung (ZSM-SNSB); Münchhausenstrasse 21 81247 München Germany
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Grosjean S, Ohler A, Chuaynkern Y, Cruaud C, Hassanin A. Improving biodiversity assessment of anuran amphibians using DNA barcoding of tadpoles. Case studies from Southeast Asia. C R Biol 2015; 338:351-61. [DOI: 10.1016/j.crvi.2015.03.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 03/19/2015] [Accepted: 03/25/2015] [Indexed: 10/23/2022]
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40
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Liu Q, Zhu F, Zhong G, Wang Y, Fang M, Xiao R, Cai Y, Guo P. COI-based barcoding of Chinese vipers (Reptilia: Squamata: Viperidae). AMPHIBIA-REPTILIA 2015. [DOI: 10.1163/15685381-00003012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
DNA barcoding seeks to assemble a standardized reference library for rapid and unambiguous identification of species, and can be used to screen for potentially cryptic species. The 5′ region of cytochrome oxidase subunit I (COI), which is a mitochondrial DNA (mtDNA) gene fragment, has been proposed as a universal marker for this purpose among animals. However, DNA barcoding of reptiles is still supported only by few datasets compared with other groups. We investigated the utilization of COI to discriminate 34 putative species of vipers, representing almost 92% of the recorded species in China. Based on a total of 241 sequences, our results indicated that the average degree of intraspecific variability (0.0198) tends to be one-sixth the average of interspecific divergence (0.0931), but no barcoding gap was detected between them. The threshold method, BLOG analyses and tree-based methods all can identify species with a high success rate. These results consistently suggested the usefulness and reliability of the DNA barcoding approach in Chinese vipers.
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Affiliation(s)
- Qin Liu
- College of Life Sciences and Food Engineering, Yibin University, Yibin 644007, China
- College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Fei Zhu
- College of Life Sciences and Food Engineering, Yibin University, Yibin 644007, China
- College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Guanghui Zhong
- College of Life Sciences and Food Engineering, Yibin University, Yibin 644007, China
- College of Tourism and Urban-Rural Planning, Chengdu University of Technology, Chengdu 610059, China
| | - Yunyu Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Min Fang
- College of Life Sciences and Food Engineering, Yibin University, Yibin 644007, China
| | - Rong Xiao
- College of Life Sciences and Food Engineering, Yibin University, Yibin 644007, China
| | - Yansen Cai
- Department of Medical Biology and Genetics, Luzhou Medical College, Luzhou, 646000, China
| | - Peng Guo
- College of Life Sciences and Food Engineering, Yibin University, Yibin 644007, China
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New Ichthyophis species from Indochina (Gymnophiona, Ichthyophiidae): 1. The unstriped forms with descriptions of three new species and the redescriptions of I. acuminatus Taylor, 1960, I. youngorum Taylor, 1960 and I. laosensis Taylor, 1969. ORG DIVERS EVOL 2014. [DOI: 10.1007/s13127-014-0190-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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42
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Sex determination in Madagascar geckos of the genus Paroedura (Squamata: Gekkonidae): are differentiated sex chromosomes indeed so evolutionary stable? Chromosome Res 2014; 22:441-52. [PMID: 25056523 DOI: 10.1007/s10577-014-9430-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2014] [Revised: 06/04/2014] [Accepted: 06/12/2014] [Indexed: 01/09/2023]
Abstract
Among amniote vertebrates, geckos represent a clade with exceptional variability in sex determination; however, only a minority of species of this highly diverse group has been studied in this respect. Here, we describe for the first time a female heterogamety in the genus Paroedura, the group radiated in Madagascar and adjacent islands. We identified homomorphic ZZ/ZW sex chromosomes with a highly heterochromatic W chromosome in Paroedura masobe, Paroedura oviceps, Paroedura karstophila, Paroedura stumpffi, and Paroedura lohatsara. Comparative genomic hybridization (CGH) revealed that female-specific sequences are greatly amplified in the W chromosome of P. lohatsara and that P. gracilis seems to possess a derived system of multiple sex chromosomes. Contrastingly, neither CGH nor heterochromatin visualization revealed differentiated sex chromosomes in the members of the Paroedura picta-Paroedura bastardi-Paroedura ibityensis clade, which is phylogenetically nested within lineages with a heterochromatic W chromosome. As a sex ratio consistent with genotypic sex determination has been reported in P. picta, it appears that the members of the P. picta-P. bastardi-P. ibityensis clade possess homomorphic, poorly differentiated sex chromosomes and may represent a rare example of evolutionary loss of highly differentiated sex chromosomes. Fluorescent in situ hybridization (FISH) with a telomeric probe revealed a telomere-typical pattern in all species and an accumulation of telomeric sequences in the centromeric region of autosomes in P. stumpffi and P. bastardi. Our study adds important information for the greater understanding of the variability and evolution of sex determination in geckos and demonstrates how the geckos of the genus Paroedura provide an interesting model for studying the evolution of the sex chromosomes.
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Chapple DG, Ritchie PA. A retrospective approach to testing the DNA barcoding method. PLoS One 2013; 8:e77882. [PMID: 24244283 PMCID: PMC3823873 DOI: 10.1371/journal.pone.0077882] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 09/13/2013] [Indexed: 11/18/2022] Open
Abstract
A decade ago, DNA barcoding was proposed as a standardised method for identifying existing species and speeding the discovery of new species. Yet, despite its numerous successes across a range of taxa, its frequent failures have brought into question its accuracy as a short-cut taxonomic method. We use a retrospective approach, applying the method to the classification of New Zealand skinks as it stood in 1977 (primarily based upon morphological characters), and compare it to the current taxonomy reached using both morphological and molecular approaches. For the 1977 dataset, DNA barcoding had moderate-high success in identifying specimens (78-98%), and correctly flagging specimens that have since been confirmed as distinct taxa (77-100%). But most matching methods failed to detect the species complexes that were present in 1977. For the current dataset, there was moderate-high success in identifying specimens (53-99%). For both datasets, the capacity to discover new species was dependent on the methodological approach used. Species delimitation in New Zealand skinks was hindered by the absence of either a local or global barcoding gap, a result of recent speciation events and hybridisation. Whilst DNA barcoding is potentially useful for specimen identification and species discovery in New Zealand skinks, its error rate could hinder the progress of documenting biodiversity in this group. We suggest that integrated taxonomic approaches are more effective at discovering and describing biodiversity.
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Affiliation(s)
- David G. Chapple
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
- Allan Wilson Centre for Molecular Ecology and Evolution, School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Peter A. Ritchie
- Allan Wilson Centre for Molecular Ecology and Evolution, School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
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Hawlitschek O, Nagy ZT, Berger J, Glaw F. Reliable DNA barcoding performance proved for species and island populations of comoran squamate reptiles. PLoS One 2013; 8:e73368. [PMID: 24069192 PMCID: PMC3772021 DOI: 10.1371/journal.pone.0073368] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 07/23/2013] [Indexed: 12/21/2022] Open
Abstract
In the past decade, DNA barcoding became increasingly common as a method for species identification in biodiversity inventories and related studies. However, mainly due to technical obstacles, squamate reptiles have been the target of few barcoding studies. In this article, we present the results of a DNA barcoding study of squamates of the Comoros archipelago, a poorly studied group of oceanic islands close to and mostly colonized from Madagascar. The barcoding dataset presented here includes 27 of the 29 currently recognized squamate species of the Comoros, including 17 of the 18 endemic species. Some species considered endemic to the Comoros according to current taxonomy were found to cluster with non-Comoran lineages, probably due to poorly resolved taxonomy. All other species for which more than one barcode was obtained corresponded to distinct clusters useful for species identification by barcoding. In most species, even island populations could be distinguished using barcoding. Two cryptic species were identified using the DNA barcoding approach. The obtained barcoding topology, a Bayesian tree based on COI sequences of 5 genera, was compared with available multigene topologies, and in 3 cases, major incongruences between the two topologies became evident. Three of the multigene studies were initiated after initial screening of a preliminary version of the barcoding dataset presented here. We conclude that in the case of the squamates of the Comoros Islands, DNA barcoding has proven a very useful and efficient way of detecting isolated populations and promising starting points for subsequent research.
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Affiliation(s)
| | - Zoltán T. Nagy
- Royal Belgian Institute of Natural Sciences, JEMU, Brussels, Belgium
| | | | - Frank Glaw
- Zoologische Staatssammlung München, Munich, Germany
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