1
|
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.
Collapse
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
| |
Collapse
|
2
|
Mulcahy DG, Ibáñez R, Jaramillo CA, Crawford AJ, Ray JM, Gotte SW, Jacobs JF, Wynn AH, Gonzalez-Porter GP, McDiarmid RW, Crombie RI, Zug GR, de Queiroz K. DNA barcoding of the National Museum of Natural History reptile tissue holdings raises concerns about the use of natural history collections and the responsibilities of scientists in the molecular age. PLoS One 2022; 17:e0264930. [PMID: 35245325 PMCID: PMC8896674 DOI: 10.1371/journal.pone.0264930] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 02/22/2022] [Indexed: 01/09/2023] Open
Abstract
Natural history collections are essential to a wide variety of studies in biology because they maintain large collections of specimens and associated data, including genetic material (e.g., tissues) for DNA sequence data, yet they are currently under-funded and collection staff have high workloads. With the advent of aggregate databases and advances in sequencing technologies, there is an increased demand on collection staff for access to tissue samples and associated data. Scientists are rapidly developing large DNA barcode libraries, DNA sequences of specific genes for species across the tree of life, in order to document and conserve biodiversity. In doing so, mistakes are made. For instance, inconsistent taxonomic information is commonly taken from different lending institutions and deposited in data repositories, such as the Barcode of Life Database (BOLD) and GenBank, despite explicit disclaimers regarding the need for taxonomic verification by the lending institutions. Such errors can have profound effects on subsequent research based on these mis-labelled sequences in data repositories. Here, we present the production of a large DNA barcode library of reptiles from the National Museum of Natural History tissue holdings. The library contains 2,758 sequences (2,205 COI and 553 16S) from 2260 specimens (four crocodilians, 37 turtles, and 2,219 lizards, including snakes), representing 583 named species, from 52 countries. In generating this library, we noticed several common mistakes made by scientists depositing DNA barcode data in public repositories (e.g., BOLD and GenBank). Our goal is to raise awareness of these concerns and offer advice to avoid such mistakes in the future to maintain accurate DNA barcode libraries to properly document Earth’s biodiversity.
Collapse
Affiliation(s)
- Daniel G. Mulcahy
- Division of Amphibians and Reptiles, Department of Vertebrate Zoology, National Museum of Natural History, Washington, DC, United States of America
- * E-mail:
| | - Roberto Ibáñez
- Smithsonian Tropical Research Institute, Panama City, Republic of Panama
- Sistema Nacional de Investigación, SENACYT, Panamá City, República de Panamá
- Departamento de Zoología, Universidad de Panamá, Panamá City, República de Panamá
| | - Cesar A. Jaramillo
- Smithsonian Tropical Research Institute, Panama City, Republic of Panama
- Departamento de Histología y Neuroanatomía, Facultad de Medicina, Universidad de Panamá, Panamá City, República de Panamá
| | - Andrew J. Crawford
- Smithsonian Tropical Research Institute, Panama City, Republic of Panama
- Department of Biological Sciences, Museo de Historia Natural C.J. Marinkelle, Universidad de los Andes, Bogotá, Colombia
| | - Julie M. Ray
- Department of Biology, University of Nevada, Reno, Nevada, United States of America
| | - Steve W. Gotte
- Division of Amphibians and Reptiles, Department of Vertebrate Zoology, National Museum of Natural History, Washington, DC, United States of America
| | - Jeremy F. Jacobs
- Division of Amphibians and Reptiles, Department of Vertebrate Zoology, National Museum of Natural History, Washington, DC, United States of America
| | - Addison H. Wynn
- Division of Amphibians and Reptiles, Department of Vertebrate Zoology, National Museum of Natural History, Washington, DC, United States of America
| | | | - Roy W. McDiarmid
- Division of Amphibians and Reptiles, Department of Vertebrate Zoology, National Museum of Natural History, Washington, DC, United States of America
| | - Ronald I. Crombie
- Department of Herpetology, California Academy of Sciences, San Francisco, California, United States of America
| | - George R. Zug
- Division of Amphibians and Reptiles, Department of Vertebrate Zoology, National Museum of Natural History, Washington, DC, United States of America
| | - Kevin de Queiroz
- Division of Amphibians and Reptiles, Department of Vertebrate Zoology, National Museum of Natural History, Washington, DC, United States of America
| |
Collapse
|
3
|
|
4
|
Hawlitschek O, Scherz MD, Webster KC, Ineich I, Glaw F. Morphological, osteological, and genetic data support a new species of Madatyphlops (Serpentes: Typhlopidae) endemic to Mayotte Island, Comoros Archipelago. Anat Rec (Hoboken) 2021; 304:2249-2263. [PMID: 33611842 DOI: 10.1002/ar.24589] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 01/21/2021] [Accepted: 01/25/2021] [Indexed: 11/11/2022]
Abstract
Blind snakes (Typhlopidae) are an enigmatic group of small burrowing snakes whose anatomy, phylogenetics, and biodiversity remain poorly known. Madatyphlops comorensis (Boulenger, 1889), endemic to the Comoros Archipelago in the Western Indian Ocean, is one of many species whose phylogenetic placement and generic assignment is unclear. We used DNA barcoding, external morphological examination, and osteological data from 3D reconstruction with micro-CT to study specimens of Madatyphlops from the Comoros Archipelago. Our results support the placement of M. comorensis in Madatyphlops and the recognition of the specimens from Mayotte Island as a closely related but distinct species, which we describe as Madatyphlops eudelini sp. nov. In this context, we present the first detailed osteological descriptions of any species of Madatyphlops, which we hope will serve as groundwork for further osteological studies in this genus and contribute to our limited but growing understanding of the osteology of typhlopid snakes.
Collapse
Affiliation(s)
| | - Mark D Scherz
- Zoologische Staatssammlung (ZSM-SNSB), Munich, Germany
| | | | - Ivan Ineich
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, Sorbonne Université, École Pratique des Hautes Études, Université des Antilles, CNRS - CP, Paris, France
| | - Frank Glaw
- Zoologische Staatssammlung (ZSM-SNSB), Munich, Germany
| |
Collapse
|
5
|
Bhunjun CS, Dong Y, Jayawardena RS, Jeewon R, Phukhamsakda C, Bundhun D, Hyde KD, Sheng J. A polyphasic approach to delineate species in Bipolaris. FUNGAL DIVERS 2020. [DOI: 10.1007/s13225-020-00446-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
6
|
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.
Collapse
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)
| |
Collapse
|
7
|
Hawlitschek O, Fernández-González A, Balmori-de la Puente A, Castresana J. A pipeline for metabarcoding and diet analysis from fecal samples developed for a small semi-aquatic mammal. PLoS One 2018; 13:e0201763. [PMID: 30106960 PMCID: PMC6091967 DOI: 10.1371/journal.pone.0201763] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 07/20/2018] [Indexed: 12/17/2022] Open
Abstract
Metabarcoding allows the genetic analysis of pooled samples of various sources. It is becoming popular in the study of animal diet, especially because it allows the analysis of the composition of feces without the need of handling animals. In this work, we studied the diet of the Pyrenean desman (Galemys pyrenaicus), a small semi-aquatic mammal endemic to the Iberian Peninsula and the Pyrenees, by sequencing COI minibarcodes from feces using next-generation sequencing techniques. For the identification of assembled sequences, we employed a tree-based identification method that used a reference tree of sequences of freshwater organisms. The comparison of freshly collected fecal samples and older samples showed that fresh samples produced significantly more sequencing reads. They also rendered more operational taxonomical units (OTUs), but not significantly. Our analyses of 41 samples identified 224 OTUs corresponding to species of the reference tree. Ephemeroptera, Diptera excl. Chironomidae, and Chironomidae were the most highly represented groups in terms of reads as well as samples. Other groups of freshwater organisms detected were Plecoptera, Trichoptera, Neuropteroida, Coleoptera, Crustacea, and Annelida. Our results are largely in line with previous morphological and genetic studies on the diet of the Pyrenean desman, but allowed the identification of a higher diversity of OTUs in each sample. Additionally, the bioinformatic pipeline we developed for deep sequencing of fecal samples will enable the quantitative analysis of the diet of this and other species, which can be highly useful to determine their ecological requirements.
Collapse
Affiliation(s)
- Oliver Hawlitschek
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Maritim de la Barceloneta, Barcelona, Spain
- Zoologische Staatssammlung München (ZSM-SNSB), München, Germany
- * E-mail:
| | | | - Alfonso Balmori-de la Puente
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Maritim de la Barceloneta, Barcelona, Spain
| | - Jose Castresana
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Maritim de la Barceloneta, Barcelona, Spain
| |
Collapse
|
8
|
Kotsakiozi P, Jablonski D, Ilgaz Ç, Kumlutaş Y, Avcı A, Meiri S, Itescu Y, Kukushkin O, Gvoždík V, Scillitani G, Roussos SA, Jandzik D, Kasapidis P, Lymberakis P, Poulakakis N. Multilocus phylogeny and coalescent species delimitation in Kotschy's gecko, Mediodactylus kotschyi: Hidden diversity and cryptic species. Mol Phylogenet Evol 2018; 125:177-187. [DOI: 10.1016/j.ympev.2018.03.022] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 03/12/2018] [Accepted: 03/15/2018] [Indexed: 01/07/2023]
|
9
|
Hawlitschek O, Scherz MD, Ruthensteiner B, Crottini A, Glaw F. Computational molecular species delimitation and taxonomic revision of the gecko genus Ebenavia Boettger, 1878. Naturwissenschaften 2018; 105:49. [PMID: 30030631 DOI: 10.1007/s00114-018-1574-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 06/13/2018] [Accepted: 07/03/2018] [Indexed: 12/27/2022]
Abstract
Cryptic species have been detected in many groups of organisms and must be assumed to make up a significant portion of global biodiversity. We study geckos of the Ebenavia inunguis complex from Madagascar and surrounding islands and use species delimitation algorithms (GMYC, BOLD, BPP), COI barcode divergence, diagnostic codon indels in the nuclear marker PRLR, diagnostic categorical morphological characters, and significant differences in continuous morphological characters for its taxonomic revision. BPP yielded ≥ 10 operational taxonomic units, whereas GMYC (≥ 27) and BOLD (26) suggested substantial oversplitting. In consequnce, we resurrect Ebenavia boettgeri Boulenger 1885 and describe Ebenavia tuelinae sp. nov., Ebenavia safari sp. nov., and Ebenavia robusta sp. nov., increasing the number of recognised species in Ebenavia from two to six. Further lineages of Ebenavia retrieved by BPP may warrant species or subspecies status, but further taxonomic conclusions are postponed until more data become available. Finally, we present an identification key to the genus Ebenavia, provide an updated distribution map, and discuss the diagnostic values of computational species delimitation as well as morphological and molecular diagnostic characters.
Collapse
Affiliation(s)
- Oliver Hawlitschek
- Zoologische Staatssammlung München (ZSM-SNSB), Münchhausenstr. 21, 81247, Munich, Germany.
| | - Mark D Scherz
- Zoologische Staatssammlung München (ZSM-SNSB), Münchhausenstr. 21, 81247, Munich, Germany.,Division of Evolutionary Biology, Zoological Institute, Braunschweig University of Technology, Mendelssohnstr. 4, 38106, Braunschweig, Germany
| | - Bernhard Ruthensteiner
- Zoologische Staatssammlung München (ZSM-SNSB), Münchhausenstr. 21, 81247, Munich, Germany
| | - Angelica Crottini
- CIBIO, Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto, 4485-661, Vairão, Portugal
| | - Frank Glaw
- Zoologische Staatssammlung München (ZSM-SNSB), Münchhausenstr. 21, 81247, Munich, Germany
| |
Collapse
|
10
|
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]
|
11
|
Altmanová M, Rovatsos M, Kratochvíl L, Johnson Pokorná M. Minute Y chromosomes and karyotype evolution in Madagascan iguanas (Squamata: Iguania: Opluridae). Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12751 10.1080/11250000409356641] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Marie Altmanová
- Faculty of Science; Department of Ecology; Charles University in Prague; Viničná 7 Praha 2 Czech Republic
| | - Michail Rovatsos
- Faculty of Science; Department of Ecology; Charles University in Prague; Viničná 7 Praha 2 Czech Republic
| | - Lukáš Kratochvíl
- Faculty of Science; Department of Ecology; Charles University in Prague; Viničná 7 Praha 2 Czech Republic
| | - Martina Johnson Pokorná
- Faculty of Science; Department of Ecology; Charles University in Prague; Viničná 7 Praha 2 Czech Republic
- Institute of Animal Physiology and Genetics; The Czech Academy of Sciences; Rumburská 89 Liběchov Czech Republic
| |
Collapse
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
Altmanová M, Rovatsos M, Kratochvíl L, Johnson Pokorná M. Minute Y chromosomes and karyotype evolution in Madagascan iguanas (Squamata: Iguania: Opluridae). Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12751] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Marie Altmanová
- Faculty of Science; Department of Ecology; Charles University in Prague; Viničná 7 Praha 2 Czech Republic
| | - Michail Rovatsos
- Faculty of Science; Department of Ecology; Charles University in Prague; Viničná 7 Praha 2 Czech Republic
| | - Lukáš Kratochvíl
- Faculty of Science; Department of Ecology; Charles University in Prague; Viničná 7 Praha 2 Czech Republic
| | - Martina Johnson Pokorná
- Faculty of Science; Department of Ecology; Charles University in Prague; Viničná 7 Praha 2 Czech Republic
- Institute of Animal Physiology and Genetics; The Czech Academy of Sciences; Rumburská 89 Liběchov Czech Republic
| |
Collapse
|
15
|
Resurrection of the Comoran fish scale gecko Geckolepis humbloti Vaillant, 1887 reveals a disjunct distribution caused by natural overseas dispersal. ORG DIVERS EVOL 2015. [DOI: 10.1007/s13127-015-0255-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
16
|
Lin X, Stur E, Ekrem T. Exploring Genetic Divergence in a Species-Rich Insect Genus Using 2790 DNA Barcodes. PLoS One 2015; 10:e0138993. [PMID: 26406595 PMCID: PMC4583400 DOI: 10.1371/journal.pone.0138993] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 09/07/2015] [Indexed: 01/08/2023] Open
Abstract
DNA barcoding using a fragment of the mitochondrial cytochrome c oxidase subunit 1 gene (COI) has proven to be successful for species-level identification in many animal groups. However, most studies have been focused on relatively small datasets or on large datasets of taxonomically high-ranked groups. We explore the quality of DNA barcodes to delimit species in the diverse chironomid genus Tanytarsus (Diptera: Chironomidae) by using different analytical tools. The genus Tanytarsus is the most species-rich taxon of tribe Tanytarsini (Diptera: Chironomidae) with more than 400 species worldwide, some of which can be notoriously difficult to identify to species-level using morphology. Our dataset, based on sequences generated from own material and publicly available data in BOLD, consist of 2790 DNA barcodes with a fragment length of at least 500 base pairs. A neighbor joining tree of this dataset comprises 131 well separated clusters representing 121 morphological species of Tanytarsus: 77 named, 16 unnamed and 28 unidentified theoretical species. For our geographically widespread dataset, DNA barcodes unambiguously discriminate 94.6% of the Tanytarsus species recognized through prior morphological study. Deep intraspecific divergences exist in some species complexes, and need further taxonomic studies using appropriate nuclear markers as well as morphological and ecological data to be resolved. The DNA barcodes cluster into 120-242 molecular operational taxonomic units (OTUs) depending on whether Objective Clustering, Automatic Barcode Gap Discovery (ABGD), Generalized Mixed Yule Coalescent model (GMYC), Poisson Tree Process (PTP), subjective evaluation of the neighbor joining tree or Barcode Index Numbers (BINs) are used. We suggest that a 4-5% threshold is appropriate to delineate species of Tanytarsus non-biting midges.
Collapse
Affiliation(s)
- Xiaolong Lin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Elisabeth Stur
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Torbjørn Ekrem
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| |
Collapse
|
17
|
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.
Collapse
|
18
|
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
| |
Collapse
|
19
|
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.
Collapse
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
| |
Collapse
|
20
|
Peterson PM, Romaschenko K, Soreng RJ. A laboratory guide for generating DNA barcodes in grasses: a case study ofLeptochloas.l. (Poaceae: Chloridoideae). ACTA ACUST UNITED AC 2014. [DOI: 10.1080/00837792.2014.927555] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|