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Wu D, Lee P, Chen H, Yan F, Huang J, He Y, Wu R, Yuan Z. Validation and development of eDNA metabarcoding primers for comprehensive assessment of Chinese amphibians. Integr Zool 2024. [PMID: 38730493 DOI: 10.1111/1749-4877.12832] [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] [Indexed: 05/13/2024]
Abstract
Environmental DNA (eDNA) metabarcoding has emerged as a powerful, non-invasive tool for biodiversity assessments. However, the accuracy and limitations of these assessment techniques are highly dependent on the choice of primer pairs being used. Although several primer sets have been used in eDNA metabarcoding studies of amphibians, there are few comparisons of their reliability and efficiency. Here, we employed lab- and field-tested sets of publicly available and de novo-designed primers in amplifying 83 species of amphibian from all three orders (Anura, Caudata, and Gymnophiona) and 13 families present in China to evaluate the versatility and specificity of these primers sets in amphibian eDNA metabarcoding studies. Three pairs of primers were highly effective, as they could successfully amplify all the major clades of Chinese amphibians in our study. A few non-amphibian taxa were also amplified by these primers, which implies that further optimization of amphibian-specific primers is still needed. The simultaneous use of three primer sets can completely cover all the species obtained by conventional survey methods and has even effectively distinguished quite a number of species (n = 20) in the Wenshan National Nature Reserve. No single primer set could individually detect all of the species from the studied region, indicating that multiple primers might be necessary for a comprehensive survey of Chinese amphibians. Besides, seasonal variations in amphibian species composition were also revealed by eDNA metabarcoding, which was consistent with traditional survey methods. These results indicate that eDNA metabarcoding has the potential to be a powerful tool for studying spatial and temporal community changes in amphibian species richness.
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Affiliation(s)
- Dongyi Wu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing, China
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Southwest University, Chongqing, China
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Southwest Forestry University, Kunming, Yunnan, China
| | - Pingshin Lee
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Hongman Chen
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Fang Yan
- School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Jiayue Huang
- Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Yanhong He
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Southwest University, Chongqing, China
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Southwest Forestry University, Kunming, Yunnan, China
| | - Ruiyao Wu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing, China
| | - Zhiyong Yuan
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing, China
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Southwest University, Chongqing, China
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Southwest Forestry University, Kunming, Yunnan, China
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Mu Y, Zhang J, Yang J, Wu J, Zhang Y, Yu H, Zhang X. Enhancing amphibian biomonitoring through eDNA metabarcoding. Mol Ecol Resour 2024; 24:e13931. [PMID: 38345249 DOI: 10.1111/1755-0998.13931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 01/03/2024] [Accepted: 01/10/2024] [Indexed: 02/17/2024]
Abstract
Surveying biodiversity has taken a quantum leap with environmental DNA (eDNA) metabarcoding, an immensely powerful approach lauded for its efficiency, sensitivity, and non-invasiveness. This approach emerges as a game-changer for the elusive realm of endangered and rare species-think nocturnal, environmentally elusive amphibians. Here, we have established a framework for constructing a reliable metabarcoding pipeline for amphibians, covering primer design, performance evaluation, laboratory validation, and field validation processes. The Am250 primer, located on the mitochondrial 16S gene, was optimal for the eDNA monitoring of amphibians, which demonstrated higher taxonomic resolution, smaller species amplification bias, and more extraordinary detection ability compared to the other primers tested. Am250 primer exhibit an 83.8% species amplification rate and 75.4% accurate species identification rate for Chinese amphibians in the in silico PCR and successfully amplified all tested species of the standard samples in the in vitro assay. Furthermore, the field-based mesocosm experiment showed that DNA can still be detected by metabarcoding even days to weeks after organisms have been removed from the mesocosm. Moreover, field mesocosm findings indicate that eDNA metabarcoding primers exhibit different read abundances, which can affect the relative biomass of species. Thus, appropriate primers should be screened and evaluated by three experimental approaches: in silico PCR simulation, target DNA amplification, and mesocosm eDNA validation. The selection of a single primer set or multiple primers' combination should be based on the monitoring groups to improve the species detection rate and the credibility of results.
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Affiliation(s)
- Yawen Mu
- State Key Laboratory of Pollution Control & Resource, School of the Environment, Nanjing University, Nanjing, China
- Jiangsu Provincial Environmental Monitoring Center, Nanjing, China
| | - Jingwen Zhang
- State Key Laboratory of Pollution Control & Resource, School of the Environment, Nanjing University, Nanjing, China
| | - Jianghua Yang
- State Key Laboratory of Pollution Control & Resource, School of the Environment, Nanjing University, Nanjing, China
- School of Marine Science and Engineering, Nanjing Normal University, Nanjing, China
| | - Jun Wu
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment of China, Nanjing, China
| | - Yong Zhang
- Jiangsu Provincial Environmental Monitoring Center, Nanjing, China
| | - Hongxia Yu
- State Key Laboratory of Pollution Control & Resource, School of the Environment, Nanjing University, Nanjing, China
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control & Resource, School of the Environment, Nanjing University, Nanjing, China
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Medeiros LADE, Gentil E, Kaefer IL, Cohn-Haft M. Distribution and diversification of Adelphobates, emblematic poison frogs from Brazilian Amazonia. AN ACAD BRAS CIENC 2024; 96:e20230659. [PMID: 38655924 DOI: 10.1590/0001-3765202320230659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 11/16/2023] [Indexed: 04/26/2024] Open
Abstract
Adelphobates contains three species, and the inaccurate identification of A. quinquevittatus and the scarcity of records of A. castaneoticus complicate inference of their distributions; the latter species occurs in sympatry with A. galactonotus. Our objective was to revise the distributions of Adelphobates by compiling data and modeling habitat suitability, as range limits may be shaped by landscape features and biotic interactions. We initially analyzed the existence of operational taxonomic units within the nominal species and subsequently inferred the observed and potential distributions, taking into account the possible independent lineages for the three species, and we also generated a molecular timetree to understand the chronology of interspecific diversification events. Adelphobates quinquevittatus was found to have a more easterly distribution than previously described, and specimens with phenotypic variation were found to occur in areas inconsistent with the modeling, and A. castaneoticus was concentrated in the Tapajós-Xingu interfluve, surrounded by A. galactonotus. Models indicated that the right bank of the Xingu River is suitable for both species, indeed, both were found there. Despite Adelphobates species having their distributions delimited by major Amazonian rivers, estimated divergence times predate the formation of the modern river network, suggesting that other mechanisms were involved in their diversification.
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Affiliation(s)
- Larissa A DE Medeiros
- Instituto Nacional de Pesquisas da Amazônia, Programa de Pós-Graduação em Ecologia, Av. André Araújo, 2936, Petrópolis, 69067-375 Manaus, AM, Brazil
| | - Eduardo Gentil
- Instituto Nacional de Pesquisas da Amazônia, Programa de Pós-Graduação em Ecologia, Av. André Araújo, 2936, Petrópolis, 69067-375 Manaus, AM, Brazil
| | - Igor L Kaefer
- Instituto Nacional de Pesquisas da Amazônia, Programa de Pós-Graduação em Ecologia, Av. André Araújo, 2936, Petrópolis, 69067-375 Manaus, AM, Brazil
- Universidade Federal do Amazonas, Instituto de Ciências Biológicas, Av. Rodrigo Otávio, 6200, Coroado I, 69077-000 Manaus, AM, Brazil
| | - Mario Cohn-Haft
- Instituto Nacional de Pesquisas da Amazônia, Programa de Pós-Graduação em Ecologia, Av. André Araújo, 2936, Petrópolis, 69067-375 Manaus, AM, Brazil
- Instituto Nacional de Pesquisas da Amazônia, Coleção de Aves, Coordenação de Pesquisas em Biodiversidade, Av. André Araújo, 2936, Petrópolis, 69067-375 Manaus, AM, Brazil
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Chen WC, Mo YM, Lin L, Qin K. A new species of Odorrana Fei, Ye & Huang, 1990 (Amphibia, Anura, Ranidae) from central Guangxi, China with a discussion of the taxonomy of Odorrana (Bamburana). Zookeys 2024; 1190:131-152. [PMID: 38313454 PMCID: PMC10835719 DOI: 10.3897/zookeys.1190.109886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 12/29/2023] [Indexed: 02/06/2024] Open
Abstract
A new species of odorous frog, Odorranadamingshanensissp. nov., was found at the Damingshan National Nature Reserve in Guangxi, China. This species can be distinguished from its congeners by a combination of the following characters: medium body size (SVL 52.3-54.8 mm in males and 74.8-81.2 mm in females), sawtooth spinules on the upper lip, obtusely rounded snout that extends beyond the lower margin, distinct dorsolateral folds, horny tubercles on the rear of the back, presence of outer metatarsal tubercles, dilated nuptial pad with velvety spinules, distinct maxillary gland with tiny spines, and external lateral vocal sac. Through analysis of the 16S mitochondria gene, the new species is closely related to O.nasica and O.yentuensis, but the genetic divergence between the new species and the latter exceeds 7% (uncorrected p-distance). Currently, the new species is only known from its original discovery site. Furthermore, a discussion on the taxonomy of Odorrana (Bamburana) was conducted, identifying seven species within the subgenus Odorrana (Bamburana).
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Affiliation(s)
- Wei-Cai Chen
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf Ministry of Education, Nanning Normal University, Nanning 530001, China
| | - Yun-Ming Mo
- Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, Nanning 530001, China
| | - Li Lin
- Natural History Museum of Guangxi, Nanning 530012, China
| | - Kun Qin
- Damingshan National Nature Reserve of Guangxi, Wuming 530114, China
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Li H, Zhu LQ, Xiao B, Huang J, Wu SW, Yang LX, Zhang ZQ, Mo XY. A new species of the genus Achalinus (Squamata, Xenodermatidae) from southwest Hunan Province, China. Zookeys 2024; 1189:257-273. [PMID: 38282714 PMCID: PMC10809267 DOI: 10.3897/zookeys.1189.112784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/25/2023] [Indexed: 01/30/2024] Open
Abstract
A new species of xenodermid snake, Achalinusnanshanensis H. Li, L.-Q. Zhu, Z.-Q. Zhang & X.-Y. Mo, sp. nov., is described based on three specimens collected from Nanshan National Park and Tongdao County of southwest Hunan Province. This new species is genetically distinct amongst its congeners with the mitochondrial COI uncorrected p-distance ranging from 4.4% (in A.yangdatongi) to 17.7% (in A.meiguensis). In addition, this new species can be distinguished from its congeners by a combination of the following morphological characters: (1) dorsal scales with 23 or 25 rows throughout and strongly keeled; (2) tail relatively longer so that TaL/ToL = 0.215-0.248; (3) length of suture between internasals significantly longer than that between prefrontals, LSBI/LSBP = 1.66-1.84; (4) single loreal scale present; (5) SPL 6 in number, with the fourth and fifth contacting eye; (6) IFL 6 in number, with the first three touching the first pair of chin shields; (7) TMP is 2-2-4/2-2(3)-4, with the anterior pair elongated and in contact with the eye; (8) ventrals 2 + 147-158; (9) subcaudals 64-77, unpaired; (10) dorsal body brownish black, with a bright yellow neck collar extending to the head and abdomen in the occipital region. The recognition of the new species increases the number of described Achalinus species to 28, of which 21 are found in China.
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Affiliation(s)
- Hui Li
- Vertebrate Zoology Laboratory, College of Life Science, Hunan Normal University, Changsha 410081, ChinaHunan Normal UniversityChangshaChina
| | - Le-Qiang Zhu
- Vertebrate Zoology Laboratory, College of Life Science, Hunan Normal University, Changsha 410081, ChinaHunan Normal UniversityChangshaChina
| | - Bei Xiao
- Vertebrate Zoology Laboratory, College of Life Science, Hunan Normal University, Changsha 410081, ChinaHunan Normal UniversityChangshaChina
| | - Jie Huang
- College of Biology Resources and Environmental Sciences, Jishou University, Jishou 416000, ChinaJishou UniversityJishouChina
| | - Shao-Wu Wu
- Forestry Bureau of Tongdao Dong Autonomous County, Huaihua 418500, ChinaForestry Bureau of Tongdao Dong Autonomous CountyHuaihuaChina
| | - Li-Xun Yang
- Forestry Bureau of Tongdao Dong Autonomous County, Huaihua 418500, ChinaForestry Bureau of Tongdao Dong Autonomous CountyHuaihuaChina
| | - Zhi-Qiang Zhang
- Institute of Wildlife Conservation, Central South University of Forestry and Technology, Changsha 410004, ChinaCentral South University of Forestry and TechnologyChangshaChina
| | - Xiao-Yang Mo
- Vertebrate Zoology Laboratory, College of Life Science, Hunan Normal University, Changsha 410081, ChinaHunan Normal UniversityChangshaChina
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Li SZ, Liu J, Ke XC, Cheng G, Wang B. A new species of Amolops (Amphibia, Anura, Ranidae) from Guizhou Province, China. Zookeys 2024; 1189:33-54. [PMID: 38314114 PMCID: PMC10836220 DOI: 10.3897/zookeys.1189.115621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 12/13/2023] [Indexed: 02/06/2024] Open
Abstract
The Torrent frogs of the genus Amolops are widely distributed in Nepal and northern India eastwards to southern China and southwards to Malaysia. The genus currently contains 84 species. Previous studies indicated underestimated species diversity in the genus. In the context, a new species occurring from the mountains in the northwestern Guizhou Province, China is found and described based on morphological comparisons and molecular phylogenetic analyses, Amolopsdafangensissp. nov. Phylogenetic analyses based on DNA sequences of the mitochondrial 16S rRNA and COI genes supported the new species as an independent lineage. The uncorrected genetic distances between the 16S rRNA and COI genes in the new species and its closest congener were 0.7% and 2.6%, respectively, which are higher than or at the same level as those among many pairs of congeners. Morphologically, the new species can be distinguished from its congeners by a combination of the following characters: body size moderate (SVL 43.2-46.8 mm in males); head length larger than head width slightly; tympanum distinct, oval; vocal sacs absent; vomerine teeth present; dorsolateral folds weak formed by series of glands; nuptial pads present on the base of finger I; heels overlapping when thighs are positioned at right angles to the body; tibiotarsal articulation reaching the level far beyond the tip of the snout when leg stretched forward.
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Affiliation(s)
- Shi-Ze Li
- Department of Food Science and Engineering, Moutai Institute, Renhuai 564500, China Chinese Academy of Sciences Chengdu China
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China Moutai Institute Renhuai China
| | - Jing Liu
- Department of Food Science and Engineering, Moutai Institute, Renhuai 564500, China Chinese Academy of Sciences Chengdu China
| | - Xiao-Cong Ke
- Guizhou Yahua Forestry Engineering Design Consulting Co., Ltd., Guiyang, 550002, China Guizhou Yahua Forestry Engineering Design Consulting Co., Ltd. Guiyang China
| | - Gang Cheng
- College of Materials Science and Engineering, Guiyang College, Guiyang, 550002, China College of Materials Science and Engineering, Guiyang College Guiyang China
| | - Bin Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China Moutai Institute Renhuai China
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Li S, Li W, Cheng Y, Liu J, Wei G, Wang B. Description of a new Asian Leaf Litter Toad of the genus Leptobrachella Smith, 1925 (Anura, Megophryidae) from southern Guizhou Province, China. Biodivers Data J 2024; 12:e113427. [PMID: 38235166 PMCID: PMC10793113 DOI: 10.3897/bdj.12.e113427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 12/29/2023] [Indexed: 01/19/2024] Open
Abstract
Background The Asian leaf litter toads of the genus Leptobrachella Smith, 1925 (Anura, Megophryidae) inhabit the forest floor and rocky streams in hilly evergreen forests and are widely distributed from southern China, west to north-eastern India and Myanmar, through mainland Indochina to Peninsular Malaysia and the Island of Borneo. New information A new species of the Asian leaf litter toad genus Leptobrachella from Guizhou Province, China is described. Molecular phylogenetic analyses, based on mitochondrial 16S rRNA and COI genes and nuclear RAG1 gene sequences indicated that the new species is genetically divergent from its congeners. The new species could be distinguished from its congeners by a combination of the following characters: (1) body of medium size in males (SVL 31.9 - 32.9 mm); (2) distinct black spots present on flanks; (3) toes rudimentarily webbed, with wide lateral fringes; (4) skin on dorsum shagreened with fine tiny granules and short ridges; (5) heels overlapped when thighs are positioned at right angles to the body; (6) tibia-tarsal articulation reaching interior corner of the eye.A new species of the Asian leaf litter toad genus Leptobrachella from Guizhou Province, China is described. Molecular phylogenetic analyses, based on mitochondrial 16S rRNA and COI genes and nuclear RAG1 gene sequences indicated that the new species is genetically divergent from its congeners. The new species could be distinguished from its congeners by a combination of the following characters: (1) body of medium size in males (SVL 31.9 - 32.9 mm); (2) distinct black spots present on flanks; (3) toes rudimentarily webbed, with wide lateral fringes; (4) skin on dorsum shagreened with fine tiny granules and short ridges; (5) heels overlapped when thighs are positioned at right angles to the body; (6) tibia-tarsal articulation reaching interior corner of the eye.
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Affiliation(s)
- Shize Li
- Moutai Institute, Guizhou, ChinaMoutai InstituteGuizhouChina
| | - Wei Li
- Chengdu Institute of Biology, the Chinese Academy of Sciences, Chengdu, ChinaChengdu Institute of Biology, the Chinese Academy of SciencesChengduChina
| | - Yanlin Cheng
- Moutai Institute, Guizhou, ChinaMoutai InstituteGuizhouChina
| | - Jing Liu
- Moutai Institute, Guizhou, ChinaMoutai InstituteGuizhouChina
| | - Gang Wei
- Guiyang College, Guizhou, ChinaGuiyang CollegeGuizhouChina
| | - Bin Wang
- Chengdu Institute of Biology, the Chinese Academy of Sciences, Chengdu, ChinaChengdu Institute of Biology, the Chinese Academy of SciencesChengduChina
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Shi SC, Sui LL, Ma S, Ji FR, Bu-Dian AY, Jiang JP. A new Asian lazy toad of the genus Scutiger Theobald, 1868 (Anura, Megophryidae) from southern Tibet, China. Zookeys 2023; 1187:31-62. [PMID: 38312231 PMCID: PMC10838179 DOI: 10.3897/zookeys.1187.107958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 11/01/2023] [Indexed: 02/06/2024] Open
Abstract
In this study, a new species named Scutigerluozhaensissp. nov. is described from Luozha, southern Tibet, China. Genetic analysis based on two mitochondrial genes 16S rRNA and COI and the nuclear gene RAG1 revealed that the new species belongs to an independent phylogenetic clade close to S.gongshanensis and S.nyingchiensis and shares no RAG1 haplotype with other species. Morphological comparisons based on examined specimens and literatures indicated that it can be diagnosed from congeners by the following combination of characters: (1) body moderate, male body length 47.0-67.2 mm (n = 13), female body length 49.8-66.2 mm (n = 8); (2) maxillary teeth and budding absent; (3) numerous tiny dense nuptial spines present on dorsal surface of fingers I, II and inner surface of finger III of males in breeding condition with similar size; (4) spine patches on belly of males in breeding condition absent; (5) spines on inner surface of forearm and upper arm of males in breeding condition absent; (6) small patches of black spines present near armpit of males in breeding condition absent; (7) adult males without vocal sac; (8) some large warts and tubercles on dorsum gathered into short skin ridges with several spines present on top; (9) space between upper eyelids wider than upper eyelids; (10) spots or irregular cross bands on limbs absent; (11) webbing between toes rudimentary; (12) coloration of dorsal body olive brown to bronze.
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Affiliation(s)
- Sheng-Chao Shi
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, ChinaChengdu Institute of Biology, Chinese Academy of SciencesChengduChina
- University of Chinese Academy of Sciences, Beijing 100049, ChinaUniversity of Chinese Academy of SciencesBeijingChina
| | - Lu-Lu Sui
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, ChinaChengdu Institute of Biology, Chinese Academy of SciencesChengduChina
- University of Chinese Academy of Sciences, Beijing 100049, ChinaUniversity of Chinese Academy of SciencesBeijingChina
| | - Shun Ma
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, ChinaChengdu Institute of Biology, Chinese Academy of SciencesChengduChina
- University of Chinese Academy of Sciences, Beijing 100049, ChinaUniversity of Chinese Academy of SciencesBeijingChina
| | - Fei-Rong Ji
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, ChinaChengdu Institute of Biology, Chinese Academy of SciencesChengduChina
- University of Chinese Academy of Sciences, Beijing 100049, ChinaUniversity of Chinese Academy of SciencesBeijingChina
| | - A-Yi Bu-Dian
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, ChinaChengdu Institute of Biology, Chinese Academy of SciencesChengduChina
- University of Chinese Academy of Sciences, Beijing 100049, ChinaUniversity of Chinese Academy of SciencesBeijingChina
| | - Jian-Ping Jiang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, ChinaChengdu Institute of Biology, Chinese Academy of SciencesChengduChina
- University of Chinese Academy of Sciences, Beijing 100049, ChinaUniversity of Chinese Academy of SciencesBeijingChina
- Mangkang Biodiversity and Ecological Station, Tibet Ecological Safety Monitor Network, Chengdu 854500, ChinaMangkang Biodiversity and Ecological Station, Tibet Ecological Safety Monitor NetworkChengduChina
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Karuno AP, Mi X, Chen Y, Zou DH, Gao W, Zhang BL, Xu W, Jin JQ, Shen WJ, Huang S, Zhou WW, Che J. Impacts of climate change on herpetofauna diversity in the Qinghai-Tibetan Plateau. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2023; 37:e14155. [PMID: 37551770 DOI: 10.1111/cobi.14155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 06/07/2023] [Accepted: 06/12/2023] [Indexed: 08/09/2023]
Abstract
Although numerous studies on the impacts of climate change on biodiversity have been published, only a handful are focused on the intraspecific level or consider population-level models (separate models per population). We endeavored to fill this knowledge gap relative to the Qinghai-Tibetan plateau (QTP) by combining species distribution modeling (SDMs) with population genetics (i.e., population-level models) and phylogenetic methods (i.e., phylogenetic tree reconstruction and phylogenetic diversity analyses). We applied our models to 11 endemic and widely distributed herpetofauna species inhabiting high elevations in the QTP. We aimed to determine the influence of environmental heterogeneity on species' responses to climate change, the magnitude of climate-change impacts on intraspecific diversity, and the relationship between species range loss and intraspecific diversity losses under 2 shared socioeconomic pathways (SSP245 and SSP585) and 3 future periods (2050s, 2070s, and 2090s). The effects of global climatic change were more pronounced at the intraspecific level (22% of haplotypes lost and 36% of populations lost) than the morphospecies level in the SSP585 climate change scenario. Maintenance of genetic diversity was in general determined by a combination of factors including range changes, species genetic structure, and the part of the range predicted to be lost. This is owing to the fact that the loss and survival of populations were observed in species irrespective of the predicted range changes (contraction or expansion). In the southeast (mountainous regions), climate change had less of an effect on range size (>100% in 3 species) than in central and northern QTP plateau regions (range size <100% in all species). This may be attributed to environmental heterogeneity, which provided pockets of suitable climate in the southeast, whereas ecosystems in the north and central regions were homogeneous. Generally, our results imply that mountainous regions with high environmental heterogeneity and high genetic diversity may buffer the adverse impacts of climate change on species distribution and intraspecific diversity. Therefore, genetic structure and characteristics of the ecosystem may be crucial for conservation under climate change.
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Affiliation(s)
- Alex Plimo Karuno
- 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, P. R. China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, P. R. China
| | - Xue Mi
- 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, P. R. China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, P. R. China
| | - Youhua Chen
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, P. R. 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, P. R. China
- Research Center for Ecology, College of Science, Tibet University, Lhasa, P. R. 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, P. R. 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, P. R. China
| | - Wei Xu
- 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, P. R. 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, P. R. China
| | - Wen-Jing Shen
- 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, P. R. China
| | - Song Huang
- College of Life Sciences, Anhui Normal University, Wuhu, P. R. China
| | - Wei-Wei Zhou
- 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, P. R. China
- State Key Laboratory of Grassland Agro-ecosystems, Institute of Innovation Ecology & College of Life Sciences, Lanzhou University, Lanzhou, P. R. 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, P. R. China
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10
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Boruah B, Deepak V, DAS A. Musicians in the marsh: a new species of music frog (Anura: Ranidae: Nidirana) from Arunachal Pradesh, India. Zootaxa 2023; 5374:51-73. [PMID: 38220873 DOI: 10.11646/zootaxa.5374.1.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Indexed: 01/16/2024]
Abstract
We describe a new species of ranid frog of the genus Nidirana from northeast India based on morphological, molecular and acoustic evidence. The new species is phenotypically distinct from its congeners by a combination of morphological characters: body robust with SVL 46.559.1 mm (n= 3) in adult males and SVL 60.666.0 mm (n= 2) in adult females; a pair of subgular vocal sacs and two patches of nuptial pad on the first finger in adult males; toe tips slightly dilated and oval; circum-marginal grooves present on all toes; dorsal skin with scattered small tubercles. A pale cream-coloured mid-dorsal line from the snout tip to the vent is present. Phylogenetically, the new species differs from its congeners by a genetic divergence of 3.48.0% and 7.712.4% in 16S and COI genes respectively. Furthermore, the new species can be differentiated from its congeners by its advertisement call, which consists of two different types of notes, call duration (0.580.92 s) and dominant frequency of the call (473.7 Hz). The discovery of a new species validates the presence of the genus Nidirana from India and emphasizes the importance of exploring specialized habitats such as marshlands, which are often overlooked.
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Affiliation(s)
- Bitupan Boruah
- Wildlife Institute of India; Chandrabani; Dehradun; Uttarakhand 248001; India.
| | - V Deepak
- Senckenberg Dresden; Knigsbrcker Landstrae 159; 01109 Dresden; Germany; Department of Life Sciences; The Natural History Museum; London SW7 5BD; UK; University of Wolverhampton; Wulfruna St; Wolverhampton WV1 1LY; UK.
| | - Abhijit DAS
- Wildlife Institute of India; Chandrabani; Dehradun; Uttarakhand 248001; India.
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11
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Bastin S, Percy DM, Siverio F. Establishing reliable DNA barcoding primers for jumping plant lice (Psylloidea, Hemiptera). BMC Res Notes 2023; 16:322. [PMID: 37941051 PMCID: PMC10634070 DOI: 10.1186/s13104-023-06585-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 10/20/2023] [Indexed: 11/10/2023] Open
Abstract
OBJECTIVES DNA Barcoding has proven to be a reliable method for rapid insect identification. The success of this method is based on the amplification of a specific region, the 'Folmer' barcode region at the 5´ start of the cytochrome c oxidase 1 gene (cox1), with universal primers. Previous studies showed failures of standard "universal" primers to amplify this region in psyllids. The aim of the study was the design of a new alternative more reliable primer combination for taxa of the superfamily Psylloidea and its comparison with the performance of the standard "universal" Folmer-primers. RESULTS A newly designed degenerate forward primer LCOP-F was developed following comparison of the sequence alignment of the priming site of "universal" primer LCO1490 and the standard insect forward primer LepF1. When combined with the "universal" reverse primer, HCO2198, this new primer pairing was able to generate barcode sequence for all 36 species in 20 genera across the five families of psyllids tested in this study, and these primers were found to be more universally reliable across psyllid taxa than other primer pairs tested.
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Affiliation(s)
- Saskia Bastin
- Instituto Canario de Investigaciones Agrarias, Unidad de Protección Vegetal, C/ El Boquerón s/n, 38270, La Laguna, Tenerife, Spain
- Universidad de La Laguna, Avda. Astrofísico Francisco Sánchez, SN. Edificio Calabaza-AN.2D Apdo. 456., 38200, La Laguna, Tenerife, Spain
| | - Diana M Percy
- Botany Department and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Felipe Siverio
- Instituto Canario de Investigaciones Agrarias, Unidad de Protección Vegetal, C/ El Boquerón s/n, 38270, La Laguna, Tenerife, Spain.
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12
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Tang S, Liu S, Yu G. A New Species of Nanorana (Anura: Dicroglossidae) from Northwestern Yunnan, China, with Comments on the Taxonomy of Nanorana arunachalensis and Allopaa. Animals (Basel) 2023; 13:3427. [PMID: 37958182 PMCID: PMC10649098 DOI: 10.3390/ani13213427] [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: 08/15/2023] [Revised: 10/28/2023] [Accepted: 11/04/2023] [Indexed: 11/15/2023] Open
Abstract
The genus Nanorana contains three subgenera, namely Nanorana, Paa, and Chaparana, and currently, there are four species known to science in Nanorana (Nanorana). In this study, we describe a new species belonging to the subgenus Nanorana from northwestern Yunnan, China. Phylogenetically, the new species, Nanorana laojunshanensissp. nov., is the sister to the clade of N. pleskei and N. ventripunctata. Morphologically, the new species can be distinguished from known congeners by the combination of following characters: present tympanum, equal fingers I and II, small body size, yellow ventral surface of limbs, distinct vomerine teeth, indistinct subarticular tubercles, head width greater than head length, slender supratympanic fold, absent dorsolateral fold, nuptial spines present on fingers I and II in adult males, absent vocal sac, and paired brown spines on the chest. Moreover, we suggest moving the genus Allopaa into Nanorana (Chaparana) and consider that N. arunachalensis is neither an Odorrana species nor a member of the subfamily Dicroglossinae (therefore Nanorana), but probably represents a distinct genus closely related to Ingerana or belongs to Ingerana, pending more data. Additionally, we consider that Nanorana minica deserves the rank of an independent subgenus, and we suggest assigning N. arnoldi, N. blanfordii, N. ercepeae, N. polunini, N. rarica, N. rostandi, N. vicina, N. xuelinensis, and N. zhaoermii into the subgenus Paa and placing N. kangxianensis, N. phrynoides, and N. sichuanensis in the subgenus Chaparana.
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Affiliation(s)
- Shangjing Tang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin 541004, China;
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, College of Life Science, Guangxi Normal University, Guilin 541004, China
| | - Shuo Liu
- Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Guohua Yu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin 541004, China;
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, College of Life Science, Guangxi Normal University, Guilin 541004, China
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13
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Shu G, Li K, Wu Y, Liu Q, He Z, Li L, Zhang H, Guo P. A new species of Xenophrys (Amphibia, Anura, Megophryidae) from southern Tibet, China. Zookeys 2023; 1182:307-329. [PMID: 37900706 PMCID: PMC10612118 DOI: 10.3897/zookeys.1182.106828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 09/13/2023] [Indexed: 10/31/2023] Open
Abstract
A new species of Xenophrys is described from Yadong County, Tibet Autonomous Region, China based on morphological and molecular evidence. Phylogenetic analyses based on the mitochondrial genes 16S rRNA and COI indicated that this new species represents an independent lineage and the minimum p-distance based on 16S rRNA between this species and its congeners is 4.4%. Additionally, the new species is distinguished from its congeners by a combination of the following morphological characters: (1) small body size, SVL 17.9-22.2 mm in adult males and SVL 23.4 mm in the single adult female; (2) tympanum indistinct, supratympanic fold distinct; (3) canthus rostralis well-developed, snout tip far beyond the margin of the lower lip; (5) pupil vertical; (6) vomerine teeth present, maxillary teeth present; (7) tongue notched posteriorly; (8) supernumerary tubercles absent, subarticular, metacarpal and metatarsal tubercles indistinct; (9) relative finger lengths I < II < IV < III, finger tips rounded, slightly expanded relative to digit widths; (10) toes with narrow lateral fringes and tarsal folds; (11) a dark triangular marking with light edge between eyes, a dark ")("-shaped marking, with light edge, present on center of dorsum, pectoral glands on sides of the breast.
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Affiliation(s)
- Guocheng Shu
- Faculty of Agriculture, Forest and Food Engineering, Yibin University, Yibin 644007, ChinaYibin UniversityYibinChina
- Key Lab of Aromatic Plant Resources Exploitation and Utilization in Sichuan Higher Education, Yibin 644007, ChinaKey Lab of Aromatic Plant Resources Exploitation and Utilization in Sichuan Higher EducationYibinChina
| | - Ke Li
- Faculty of Agriculture, Forest and Food Engineering, Yibin University, Yibin 644007, ChinaYibin UniversityYibinChina
| | - Yayong Wu
- Faculty of Agriculture, Forest and Food Engineering, Yibin University, Yibin 644007, ChinaYibin UniversityYibinChina
| | - Qin Liu
- Faculty of Agriculture, Forest and Food Engineering, Yibin University, Yibin 644007, ChinaYibin UniversityYibinChina
| | - Zhongping He
- Faculty of Agriculture, Forest and Food Engineering, Yibin University, Yibin 644007, ChinaYibin UniversityYibinChina
| | - Ling Li
- Faculty of Agriculture, Forest and Food Engineering, Yibin University, Yibin 644007, ChinaYibin UniversityYibinChina
- College of Life Sciences, Shenyang Normal University, Shenyang 110034, ChinaShenyang Normal UniversityShenyangChina
| | - He Zhang
- Faculty of Agriculture, Forest and Food Engineering, Yibin University, Yibin 644007, ChinaYibin UniversityYibinChina
- College of Life Sciences, Shenyang Normal University, Shenyang 110034, ChinaShenyang Normal UniversityShenyangChina
| | - Peng Guo
- Faculty of Agriculture, Forest and Food Engineering, Yibin University, Yibin 644007, ChinaYibin UniversityYibinChina
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14
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Yang DC, Xu YH, Wu JX, Gong YA, Huang RY, Xiang J, Feng ZL, Huang TQ, Huang S. A new species of the genus Achalinus (Squamata: Xenodermidae) from Nanning, Guangxi, China. Zootaxa 2023; 5319:389-402. [PMID: 37518224 DOI: 10.11646/zootaxa.5319.3.5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Indexed: 08/01/2023]
Abstract
We describe a new species of the genus Achalinus Peters, 1869 from Daming Mountain, Shanglin County, Nanning City, Guangxi Zhuang Autonomous Region, China, based on a single adult male specimen. It can be distinguished from all the other species in Achalinus by a combination of the following morphological characters: (1) a bright yellow collar around the neck, extending forward to the ventral of the head; (2) tail length comparatively long, TaL/Tol ratio 0.25; (3) DSR 23-23-23, moderately keeled; (4) VS 3+162; (5) SC 74, unpaired; (6) cloacal plate entire; (7) SPL 6, the fourth and fifth in contact with the eye; (8) IFL 6, the first three touching the first pair of chin shields; (9) a single loreal; (10) length of suture between internasal significantly longer than that between prefrontal, LSBI/LSBP ratio 1.34; (11) two pairs of chin shields; (12) longitudinal vertebral line absent. In addition, the uncorrected p-distances between the new species and other known congeners ranged from 6.3% to 25.4% for the cytochrome c oxidase subunit 1 (CO1). With the addition of the new species the total number of described Achalinus species is increased to 23 of which 17 are found in China.
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Affiliation(s)
- Dian-Cheng Yang
- Anhui Province Key Laboratory of the Conservation and Exploitation of Biological Resource; College of Life Sciences; Anhui Normal University; Wuhu 241000; Huangshan Noah Biodiversity Institute; Huangshan 245000; China.
| | - Yu-Hao Xu
- Anhui Province Key Laboratory of the Conservation and Exploitation of Biological Resource; College of Life Sciences; Anhui Normal University; Wuhu 241000; China; School of Life Sciences; Anhui Agricultural University; Hefei 230036; China; Huangshan Noah Biodiversity Institute; Huangshan 245000; China.
| | - Jia-Xiang Wu
- Guangxi Nanning Photography Player Culture Communication Co.; Ltd; Nanning 530021; China.
| | - Yan-An Gong
- Anhui Province Key Laboratory of the Conservation and Exploitation of Biological Resource; College of Life Sciences; Anhui Normal University; Wuhu 241000; Huangshan Noah Biodiversity Institute; Huangshan 245000; China.
| | - Ru-Yi Huang
- Anhui Province Key Laboratory of the Conservation and Exploitation of Biological Resource; College of Life Sciences; Anhui Normal University; Wuhu 241000; Huangshan Noah Biodiversity Institute; Huangshan 245000; China; Engineering Research Center of Environmental DNA and Ecological Water Health Assessment; Shanghai Ocean University; Shanghai 201306; China.
| | - Jun Xiang
- Guangxi Nanning Photography Player Culture Communication Co.; Ltd; Nanning 530021; China.
| | - Zheng-Lian Feng
- Nanning Qingxiu Shan Tourist Attraction; Nanning 530000; China.
| | - Tian-Qi Huang
- Graduate Program in Ecology and Evolution; Department of Ecology; Evolution; and Natural Resources; Rutgers; the State University of New Jersey; New Brunswick; NJ 08901; USA.
| | - Song Huang
- Anhui Province Key Laboratory of the Conservation and Exploitation of Biological Resource; College of Life Sciences; Anhui Normal University; Wuhu 241000; Huangshan Noah Biodiversity Institute; Huangshan 245000; China.
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15
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Tang S, Sun T, Liu S, Luo S, Yu G, Du L. A new species of cascade frog (Anura: Ranidae: Amolops) from central Yunnan, China. ZOOLOGICAL LETTERS 2023; 9:15. [PMID: 37461094 PMCID: PMC10351143 DOI: 10.1186/s40851-023-00214-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 06/27/2023] [Indexed: 07/20/2023]
Abstract
A new species of the genus Amolops, Amolops ailao sp. nov., is described from central Yunnan, China. The new species belongs to the A. mantzorum species group. Phylogenetic analyses based on the combination of mitochondrial 16S rRNA, COI, and cytb genes revealed that the new species is the sister taxon to Amolops ottorum with strong support. Genetically, the new species differs from A. ottorum by 5.0% in cytb sequences. Morphologically, the new species can be distinguished from known congeners by the combination of the following characters: true dorsolateral folds absent, but dorsolateral folds formed by series of glands present; circummarginal groove on tip of first finger absent; body size small (males SVL 33.0-35.1 mm and female SVL 41.3 mm); HW/SVL 0.32‒0.35; UEW/SVL 0.08‒0.10; THL/SVL 0.52‒0.56; vomerine teeth absent; interorbital distance narrower than internarial distance; tympanum distinct, less than half eye diameter; supratympanic fold present, indistinct; a pair of large tubercles on sides of cloaca; tibiotarsal articulation reaching beyond anterior corner of eye; and vocal sac absent. The cladogenesis events within the A. mantzorum group rapidly occurred from Pliocene 4.23 Mya to Pleistocene 1.2 Mya, coinciding with the recent intensive uplift of the Qinghai-Tibetan Plateau since the Pliocene. Combining findings in this study with the most recent taxonomic progress, we consider that there are 20 known Amolops species in Yunnan, China, accounting for the highest proportion of amphibian diversity of Yunnan, and five of them belong to the A. mantzorum group. Among different subfauna and water systems in Yunnan, the species diversity of Amolops in northwestern Yunnan and Nu River Basin is highest.
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Affiliation(s)
- Shangjing Tang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, Guilin, 541004, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, College of Life Science, Guangxi Normal University, Guilin, 541004, China
| | - Tao Sun
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, Guilin, 541004, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, College of Life Science, Guangxi Normal University, Guilin, 541004, China
| | - Shuo Liu
- Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Sangdi Luo
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, Guilin, 541004, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, College of Life Science, Guangxi Normal University, Guilin, 541004, China
| | - Guohua Yu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, Guilin, 541004, China.
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, College of Life Science, Guangxi Normal University, Guilin, 541004, China.
| | - Lina Du
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, Guilin, 541004, China.
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, College of Life Science, Guangxi Normal University, Guilin, 541004, China.
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16
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Mônico AT, Ferrão M, Moravec J, Fouquet A, Lima AP. A new species of Pristimantis (Anura: Strabomantidae) from white-sand forests of central Amazonia, Brazil. PeerJ 2023; 11:e15399. [PMID: 37304878 PMCID: PMC10252896 DOI: 10.7717/peerj.15399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 04/20/2023] [Indexed: 06/13/2023] Open
Abstract
The white-sand ecosystems in the Solimões-Negro Interfluve are among the less studied in Amazonia. Recent herpetological surveys conducted west of Manaus, Brazil (central Amazonia) indicate that white-sand forests host a unique anuran fauna comprising habitat specialized and endemic species. In the present study we describe a new species of rain frog belonging to the Pristimantis unistrigatus species group from the white-sand forest locally called "campinarana" (thin-trunked forests with canopy height below 20 m). The new species is phylogenetically close to rain frogs from western Amazonian lowlands (P. delius, P. librarius, P. matidiktyo and P. ockendeni). It differs from its closest relatives mainly by its size (male SVL of 17.3-20.1 mm, n = 16; female SVL of 23.2-26.5 mm, n = 6), presence of tympanum, tarsal tubercles and dentigerous processes of vomers, its translucent groin without bright colored blotches or marks, and by its advertisement call (composed of 5-10 notes, call duration of 550-1,061 ms, dominant frequency of 3,295-3,919 Hz). Like other anuran species recently discovered in the white-sand forests west of Manaus, the new species seems to be restricted to this peculiar ecosystem.
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Affiliation(s)
- Alexander Tamanini Mônico
- Programa de Pós-Graduação em Biologia (Ecologia), Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
| | - Miquéias Ferrão
- Museum of Comparative Zoology, Harvard University, Cambridge, MA, United States of America
| | - Jiří Moravec
- Department of Zoology, National Museum, Cirkusová, Prague, Czech Republic
| | - Antoine Fouquet
- Laboratoire Evolution et Diversité Biologique, Université Paul Sabatier, Toulouse, France
| | - Albertina P. Lima
- Programa de Pós-Graduação em Biologia (Ecologia), Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
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17
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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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Xu R, Li K, Zhang H, He H, Zhu F, Wu Y, Guo P. Expanded Description of Achalinus yangdatongi (Serpentes: Xenodermidae). CURRENT HERPETOLOGY 2023. [DOI: 10.5358/hsj.42.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Affiliation(s)
- Ruiying Xu
- Faculty of Agriculture, Forest and Food Engineering, Yibin University, Yibin 644007, China
| | - Ke Li
- Faculty of Agriculture, Forest and Food Engineering, Yibin University, Yibin 644007, China
| | - He Zhang
- Faculty of Agriculture, Forest and Food Engineering, Yibin University, Yibin 644007, China
| | - Hao He
- School of Life Sciences, Yunnan Normal University, Yunnan 650500, China
| | - Fei Zhu
- College of Life Science, Guizhou Normal University, Guizhou 550025, China
| | - Yayong Wu
- Faculty of Agriculture, Forest and Food Engineering, Yibin University, Yibin 644007, China
| | - Peng Guo
- Faculty of Agriculture, Forest and Food Engineering, Yibin University, Yibin 644007, China
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A three-gene phylogeny supports taxonomic rearrangements in the family Didymiaceae (Myxomycetes). Mycol Prog 2023. [DOI: 10.1007/s11557-022-01858-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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20
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Description of a New Cobra ( Naja Laurenti, 1768; Squamata, Elapidae) from China with Designation of a Neotype for Naja atra. Animals (Basel) 2022; 12:ani12243481. [PMID: 36552401 PMCID: PMC9774835 DOI: 10.3390/ani12243481] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/05/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
Taxonomic frameworks for medically important species such as cobras (genus Naja Laurenti, 1768; Squamata, Elapidae) are essential for the medical treatment of snake bites and accurate antivenin development. In this paper, we described the former N. kaouthia populations recorded from China as a new species and designated a neotype for N. atra-based morphological and mitochondrial phylogenetic analysis. The new species N. fuxisp. nov. was morphologically diagnosed from N. kaouthia by (1) regular single narrow crossband present on the middle and posterior parts of the dorsum (3-15, 7.9 ± 2.7, n = 32) and the dorsal surface of the tail (1-6, 4.2 ± 1.1, n = 32) of both adults and juveniles, buff-colored with dark fringes on both edges, vs. South Asian populations (n = 39) and Southeast Asian populations (n = 35) without cross bands, with irregular cross bands or multiple light-colored crossbands pairs, or densely woven lines; (2) small scales between the posterior chin shields, usually three (40%) or two (37%), rarely four (13%), or one (10%) (n = 30) vs. mostly one (81%) and rarely two (19%) (n = 28); (3) ventrals 179-205 (195.4 ± 6.7, n = 33) vs. South Asian populations 179-199 (188.7 ± 5.9, n = 12); Southeast Asian populations 168-186 (177.8 ± 4.9, n = 18). Phylogenetically, the new species forms an independent sister clade to the clade including N. atra, N. kaouthia, N. oxiana and N. sagittifera. Furthermore, the subspecies N. naja polyocellata should be resurrected and recognized as a full species, N. polyocellatacomb. nov., and the subspecies N. sumatrana miolepis should be resurrected.
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21
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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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22
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Zhang YP, Liu XL, Stuart BL, Wu DY, Wang YF, Che J, Yuan ZY. Amolops putaoensis Gan, Qin, Lwin, Li, Quan, Liu & Yu, 2020, a newly recorded torrent frog for China. HERPETOZOA 2022. [DOI: 10.3897/herpetozoa.35.e94745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Amolops putaoensis is a recently described torrent frog species from A. monticola group that is known only from its type locality, northern Myanmar. We compared morphology and mitochondrial DNA sequence data from ten recently collected adult male specimens from the upper Dulong River System in Gongshan County, Yunnan Province, China, to the original description of A. putaoensis. Both datasets strongly supported referring the Chinese specimens to A. putaoensis, extending the known range of this species by approximately 133.7 km distance into China. Molecular phylogenetic analyses recovered A. putaoensis to be closely related to A. aniqiaoensis, A. kohimaensis, A. monticola, and A. adicola. We use the newly collected Chinese specimens to expand the morphological description of the species.
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23
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Mônico AT, Ferrão M, Chaparro JC, Fouquet A, Lima AP. A new species of rain frog (Anura: Strabomantidae: Pristimantis) from the Guiana Shield and amended diagnosis of P. ockendeni (Boulenger, 1912). VERTEBRATE ZOOLOGY 2022. [DOI: 10.3897/vz.72.e90435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Pristimantis is already the most speciose genus among vertebrates, yet the current number of species remains largely underestimated. A member of the P. unistrigatus species group from the Guiana Shield has been historically misidentified as P. ockendeni, a species described from southern Peru. We combined mitochondrial (16S and COI) and nuclear (RAG1) loci, external morphology, skull osteology (μ-CT scan), vocalization (advertisement and courtship calls), geographic distribution and natural history data to differentiate the Guiana Shield populations from P. ockendeni, and describe them as a new species. The new species is crepuscular and nocturnal and inhabits the understory of unflooded (terra firme) forests in Brazil, Guyana and Suriname. It is phylogenetically related to P. ardalonychus, P. martiae and undescribed species from Brazilian Amazonia. The new species notably differs from P. ockendeni and its congeners in the P. unistrigatus species group occurring in the Guiana Shield by the combination of the following characters: absence of dentigerous processes of vomers, presence of vocal slits in males, body size (SVL 16.2–20.7 mm in males and 21.4–25.7 mm in females), advertisement call (call with 4–6 notes, call duration of 158–371 ms and dominant frequency of 3,466–4,521 Hz) and translucent groin coloration in life. To facilitate the recognition and description of cryptic species previously hidden under the name P. ockendeni, we provide an amended diagnosis of this taxon based on external morphology and advertisement call of specimens recently collected nearby the type locality and additional localities in southwestern Amazonia.
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A New Species of the Genus Microhyla (Amphibia: Anura: Microhylidae) from the Dabie Mountains, China. Animals (Basel) 2022; 12:ani12212894. [DOI: 10.3390/ani12212894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/08/2022] [Accepted: 10/18/2022] [Indexed: 11/17/2022] Open
Abstract
Species belonging to the genus Microhyla are small-sized frogs that are widely distributed in southern, eastern, and south-eastern Asia. In China, the genus harbors many cryptic species, on two of which—M. beilunensis and M. fanjinshanensis—studies were recently published. In this study, we collected specimens from the Dabie Mountain range, which is at the junction of Anhui, Henan and Hubei Provinces, East China; these specimens belonged to a species previously identified as M. mixtura. Based on phylogenetic analyses, species delimitation analyses, morphological comparisons and advertisement calls comparisons, we found they were significantly different from other known congeners, and thus we describe them as a new species. This study enriches the diversity of Microhylidae, and clarifies the species of the genus Microhyla in the Dabie Mountains.
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Hong Y, He Y, Lin Z, Du Y, Chen S, Han L, Zhang Q, Gu S, Tu W, Hu S, Yuan Z, Liu X. Complex origins indicate a potential bridgehead introduction of an emerging amphibian invader (Eleutherodactylus planirostris) in China. NEOBIOTA 2022. [DOI: 10.3897/neobiota.77.83205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Identifying the origins of established alien species is important to prevent new introductions in the future. The greenhouse frog (Eleutherodactylus planirostris), native to Cuba, the Bahamas, and the Cayman Islands, has been widely introduced to the Caribbean, North and Central America, Oceania and Asia. This invasive alien amphibian was recently reported in Shenzhen, China, but the potential introduction sources remain poorly understood. Based on phylogenetic analysis using mitochondrial 16S, COI and CYTB sequences, we detected a complex introduction origin of this species, which may be from Hong Kong, China, the Philippines, Panama and Florida, USA, all pointing to a bridgehead introduction. In addition, the nursery trade between the four countries or regions and mainland China from 2011 to 2020 was also significantly higher than other areas with less likelihood of introductions, which supported the molecular results. Our study provides the first genetic evidence of the potential sources of this emerging amphibian invader in mainland China, which may help develop alien species control strategies in the face of growing trade through globalization.
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26
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Mondino A, Crovadore J, Lefort F, Ursenbacher S. Impact of invading species on biodiversity: Diet study of the green whip snake’s (Hierophis viridiflavus, L. 1789) in Switzerland. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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27
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Guo M, Yuan C, Tao L, Cai Y, Zhang W. Life barcoded by DNA barcodes. CONSERV GENET RESOUR 2022; 14:351-365. [PMID: 35991367 PMCID: PMC9377290 DOI: 10.1007/s12686-022-01291-2] [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: 07/15/2021] [Accepted: 08/05/2022] [Indexed: 11/15/2022]
Abstract
The modern concept of DNA-based barcoding for cataloguing biodiversity was proposed in 2003 by first adopting an approximately 600 bp fragment of the mitochondrial COI gene to compare via nucleotide alignments with known sequences from specimens previously identified by taxonomists. Other standardized regions meeting barcoding criteria then are also evolving as DNA barcodes for fast, reliable and inexpensive assessment of species composition across all forms of life, including animals, plants, fungi, bacteria and other microorganisms. Consequently, global DNA barcoding campaigns have resulted in the formation of many online workbenches and databases, such as BOLD system, as barcode references, and facilitated the development of mini-barcodes and metabarcoding strategies as important extensions of barcode techniques. Here we intend to give an overview of the characteristics and features of these barcode markers and major reference libraries existing for barcoding the planet’s life, as well as to address the limitations and opportunities of DNA barcodes to an increasingly broader community of science and society.
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28
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Vences M, Stützer D, Rasoamampionona Raminosoa N, Ziegler T. Towards a DNA barcode library for Madagascar’s threatened ichthyofauna. PLoS One 2022; 17:e0271400. [PMID: 35951642 PMCID: PMC9371263 DOI: 10.1371/journal.pone.0271400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 06/29/2022] [Indexed: 11/18/2022] Open
Abstract
In order to improve the molecular resources available for conservation management of Madagascar’s threatened ichthyofauna, we elaborated a curated database of 2860 mitochondrial sequences of the mitochondrial COI, 16S and ND2 genes of Malagasy fishes, of which 1141 sequences of freshwater fishes were newly sequenced for this data set. The data set is mostly composed of COI (2015 sequences) while 16S and ND2 sequences from partly the same samples were used to match the COI sequences to reliably identified reference sequences of these genes. We observed COI uncorrected pairwise genetic distances of 5.2‒31.0% (mean 20.6%) among species belonging to different genera, and 0.0‒22.4% (mean 6.4%) for species belonging to the same genus. Deeply divergent mitochondrial lineages of uncertain attribution were found among Malagasy freshwater eleotrids and gobiids, confirming these groups are in need of taxonomic revision. DNA barcodes assigned to introduced cichlids (tilapias) included Coptodon rendallii, C. zillii, Oreochromis aureus (apparently a new country record), O. cf. mossambicus, O. niloticus, and one undetermined species of Oreochromis, with sequences of up to three species found per location. In aplocheiloid killifishes of the genus Pachypanchax, most species from northern Madagascar had only low mitochondrial divergences, three of these species (P. omalonotus, P. patriciae, and P. varatraza) were not reciprocally monophyletic, and one genetically deviant lineage was discovered in a northern locality, suggesting a need for partial taxonomic revision of this genus. While the lack of voucher specimens for most of the samples sequenced herein precludes final conclusions, our first step towards a DNA barcoding reference library of Madagascar’s fishes already demonstrates the value of such a data set for improved taxonomic inventory and conservation management. We strongly suggest further exploration of Madagascar’s aquatic environments, which should include detailed photographic documentation and tissue sampling of large numbers of specimens, and collection of preserved voucher specimens as well as of living fish for the buildup of ex situ assurance populations of threatened species complying with the One Plan Approach proposed by the IUCN SSC Conservation Breeding Specialist Group (CBSG).
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Affiliation(s)
- Miguel Vences
- Zoological Institute, Braunschweig, Germany
- * E-mail:
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29
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Banerjee P, Stewart KA, Dey G, Antognazza CM, Sharma RK, Maity JP, Saha S, Doi H, de Vere N, Chan MWY, Lin PY, Chao HC, Chen CY. Environmental DNA analysis as an emerging non-destructive method for plant biodiversity monitoring: a review. AOB PLANTS 2022; 14:plac031. [PMID: 35990516 PMCID: PMC9389569 DOI: 10.1093/aobpla/plac031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Environmental DNA (eDNA) analysis has recently transformed and modernized biodiversity monitoring. The accurate detection, and to some extent quantification, of organisms (individuals/populations/communities) in environmental samples is galvanizing eDNA as a successful cost and time-efficient biomonitoring technique. Currently, eDNA's application to plants remains more limited in implementation and scope compared to animals and microorganisms. This review evaluates the development of eDNA-based methods for (vascular) plants, comparing its performance and power of detection with that of traditional methods, to critically evaluate and advise best-practices needed to innovate plant biomonitoring. Recent advancements, standardization and field applications of eDNA-based methods have provided enough scope to utilize it in conservation biology for numerous organisms. Despite our review demonstrating only 13% of all eDNA studies focus on plant taxa to date, eDNA has considerable environmental DNA has considerable potential for plants, where successful detection of invasive, endangered and rare species, and community-level interpretations have provided proof-of-concept. Monitoring methods using eDNA were found to be equal or more effective than traditional methods; however, species detection increased when both methods were coupled. Additionally, eDNA methods were found to be effective in studying species interactions, community dynamics and even effects of anthropogenic pressure. Currently, elimination of potential obstacles (e.g. lack of relevant DNA reference libraries for plants) and the development of user-friendly protocols would greatly contribute to comprehensive eDNA-based plant monitoring programs. This is particularly needed in the data-depauperate tropics and for some plant groups (e.g., Bryophytes and Pteridophytes). We further advocate to coupling traditional methods with eDNA approaches, as the former is often cheaper and methodologically more straightforward, while the latter offers non-destructive approaches with increased discrimination ability. Furthermore, to make a global platform for eDNA, governmental and academic-industrial collaborations are essential to make eDNA surveys a broadly adopted and implemented, rapid, cost-effective and non-invasive plant monitoring approach.
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Affiliation(s)
- Pritam Banerjee
- Department of Biomedical Sciences, Graduate Institute of Molecular Biology, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
| | - Kathryn A Stewart
- Institute of Environmental Science, Leiden University, 2333 CC Leiden, The Netherlands
| | - Gobinda Dey
- Department of Biomedical Sciences, Graduate Institute of Molecular Biology, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
| | - Caterina M Antognazza
- Department of Theoretical and Applied Science, University of Insubria, Via J.H. Dunant, 3, 21100 Varese, Italy
| | - Raju Kumar Sharma
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
| | - Jyoti Prakash Maity
- Department of Chemistry, School of Applied Sciences, KIIT Deemed to be University, Bhubaneswar, Odisha 751024, India
| | - Santanu Saha
- Post Graduate Department of Botany, Bidhannagar College, Salt Lake City, Kolkata 700064, India
| | - Hideyuki Doi
- Graduate School of Information Science, University of Hyogo, 7-1-28 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Natasha de Vere
- Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K
| | - Michael W Y Chan
- Department of Biomedical Sciences, Graduate Institute of Molecular Biology, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
| | - Pin-Yun Lin
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
| | - Hung-Chun Chao
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
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Mullin KE, Rakotomanga MG, Dawson J, Glaw F, Rakotoarison A, Orozco-terWengel P, Scherz MD. An unexpected new red-bellied Stumpffia (Microhylidae) from forest fragments in central Madagascar highlights remaining cryptic diversity. Zookeys 2022; 1104:1-28. [PMID: 36761923 PMCID: PMC9848859 DOI: 10.3897/zookeys.1104.82396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 05/05/2022] [Indexed: 11/12/2022] Open
Abstract
The Madagascan endemic subfamily Cophylinae in the family Microhylidae, is an example of a taxonomic group for which much is still to be discovered. Indeed, the cophyline frogs present a large portion of Madagascar's cryptic and microendemic amphibian diversity, yet they remain understudied. A new red-bellied species of the microhylid frog genus Stumpffia is described from the central plateau of Madagascar. Visual encounter surveys in Ambohitantely and Anjozorobe in 2019 and 2020 identified this previously unknown Stumpffia species, which closely resembles Stumpffiakibomena known from Andasibe in the east. Stumpffialynnae sp. nov. adds another species to the red-bellied species complex, differing from S.kibomena by genetic differentiation in the mitochondrial 16S rRNA gene (3.6-3.9%) and distinct nuclear RAG1 haplotypes, as well as strongly by its advertisement call. The new species is known from across Ambohitantely Special Reserve and Anjozorobe Angavo protected area, but is known only from one complete specimen and eight individual tissue samples. Based on the rarity of the species, the small number of locations in which it has been found, and its disappearing forest habitat, its IUCN Red List classification is suggested as "Endangered". This species is the first Stumpffia described from Madagascar's central plateau, highlighting the importance of conserving the remnant forest fragments in this area and the ongoing need to survey and protect this threatened habitat type.
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Affiliation(s)
- Katherine E. Mullin
- Cardiff University, School of Biosciences, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UKCardiff UniversityCardiffUnited Kingdom
| | - Manoa G. Rakotomanga
- Conservation Action Plan for Madagascar (‘C.A.P. Mada’), Antananarivo, MadagascarConservation Action Plan for Madagascar (‘C.A.P. Mada’)AntananarivoMadagascar
| | - Jeff Dawson
- Durrell Wildlife Conservation Trust, Les Augrès Manor, La Profonde Rue, Trinity, Jersey, JE3 5BP, Channel Islands, UKDurrell Wildlife Conservation Trust, Les Augrès ManorJerseyUnited Kingdom
| | - Frank Glaw
- Zoologische Staatssammlung München (ZSM-SNSB), Münchhausenstr. 21, 81247 München, GermanyZoologische Staatssammlung München (ZSM-SNSB)MunichGermany
| | - Andolalao Rakotoarison
- Department of Animal Biology, University of Antananarivo, MadagascarUniversity of AntananarivoAntananarivoMadagascar,School for International Training, VN 41A Bis Ambohitsoa Ankazolava, 101 Antananarivo, MadagascarSchool for International TrainingAntananarivoMadagascar
| | - Pablo Orozco-terWengel
- Cardiff University, School of Biosciences, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UKCardiff UniversityCardiffUnited Kingdom
| | - Mark D. Scherz
- Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen Ø, DenmarkUniversity of CopenhagenCopenhagenDenmark
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Li P, Li D, Hong Y, Chen M, Zhang X, Hu L, Liu C. Combining DNA Mini-Barcoding and Species-Specific Primers PCR Technology for Identification of Heosemys grandis. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.822871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Heosemys grandis, a species of Asian water turtle, that has a wide range of applications in the food and pharmaceutical industries. Since some processed products cannot be identified exclusively by morphological and microscopic identification, a reliable and quick approach to guarantee authenticity is critical. Thus, we fostered an effective and stable molecular identification system to identify Heosemys grandis based on DNA mini-barcoding and species-specific primers PCR technology. A total of 48 turtle samples from 16 different species were collected. To distinguish Heosemys grandis from its counterfeits, DNA mini-barcoding and a pair of species-specific primers were designed and verified by PCR after analyzing the COI sequences of samples. The results showed that only Heosemys grandis samples could generate a single clear band following amplification using species-specific primers. Employing DNA mini-barcoding to amplify samples can verify authenticity by sequence alignment. These findings indicated that species-specific primers PCR technology combined with DNA mini-barcoding could accurately detect the authenticity of Heosemys grandis. This technology broadens the application of molecular biology techniques in the food and pharmaceutical industries. It provides a reliable and convenient method for identifying raw materials to standardize the market and protect customers’ rights and interests.
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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: 9] [Impact Index Per Article: 4.5] [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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33
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Ergül Kalaycı T, Gümüşsoy K. Genetic diversity of the Caucasian Parsley Frog, Pelodytes caucasicus (Anura: Pelodytidae). ZOOLOGY IN THE MIDDLE EAST 2022. [DOI: 10.1080/09397140.2022.2051917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
| | - Kafiye Gümüşsoy
- Department of Biology, Recep Tayyip Erdoğan University, Rize, Turkey
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Li S, Liu J, Yang G, Wei G, Su H. A new toad species of the genus Brachytarsophrys Tian & Hu, 1983 (Anura, Megophryidae) from Guizhou Province, China. Biodivers Data J 2022; 10:e79984. [PMID: 35233171 PMCID: PMC8881434 DOI: 10.3897/bdj.10.e79984] [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: 12/31/2021] [Accepted: 02/17/2022] [Indexed: 11/21/2022] Open
Abstract
Background The toads of the genus Brachytarsophrys Tian & Hu, 1983 are distributed in southern China, Myanmar, Vietnam, Laos and northern Thailand. Seven species of the genus have been recognised, of which five of them are known from China so far. New information Brachytarsophrysqiannanensis sp. nov., a new species of the short-legged toad genus is here described from southern Guizhou Province, China. Diagnostic characters of the new species are illustrated and comparisons with its congeners are provided. Its validity is also affirmed by its distinct mitochondrial gene sequence divergence with all congeners and its monophyly recovered in the mitochondrial gene-based phylogenetic analyses.
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35
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Yuan Z, Wu D, Wen Y, Xu W, Gao W, Dahn HA, Liu X, Jin J, Yu C, Xiao H, Che J. Historical mitochondrial genome introgression confounds species delimitation: Evidence from phylogenetic inference in the odorrana grahami species complex. Curr Zool 2022; 69:82-90. [PMID: 36974146 PMCID: PMC10039181 DOI: 10.1093/cz/zoac010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 02/11/2022] [Indexed: 11/12/2022] Open
Abstract
Abstract
Species delimitation is essential to informing conservation policy and understanding ecological and evolutionary processes. Most of our recent gains in knowledge on animal diversity rely on morphological characteristics and mitochondrial (mt) DNA variation. Concordant results based on both have led to an unprecedented acceleration in the identification of new species and enriched the field of taxonomy. However, discordances are also found commonly between morphological and mtDNA evidence. This confounds species delimitation, especially when gene flow or mitochondrial genome introgression has occurred. Here we illustrate how mitochondrial genome introgression among species of the Odorrana grahami complex confounds species delimitation using the combined evidence of morphological characters, mitochondrial variation, and thousands of nuclear single nucleotide polymorphisms (SNPs) from genotyping-by-sequencing (GBS). Fifty-eight samples across the distribution of the O. grahami complex were included. The mtDNA matrilineal genealogy indicated two clades, with O. grahami and O. junlianensis clustered together. In contrast, all nuclear evidence including gene trees, species trees, and genetic structure analyses based on GBS data support three species with distinct genetic clusters. These three distinct genetic clusters also correspond to distinct morphological characters. They affirm the distinct taxonomic entities of both O. grahami and O. junlianensis, as well as a third clade distinct from either. Which species the third clade belongs to remains unclear and will require further testing. The nuclear genomic loci contradict the COI evidence, with indications of rampant historical mitochondrial genome introgression among the species of the O. grahami complex. These discordant signals previously confused species delimitation efforts in this group. Based on these findings, we recommend the integration of independent data, especially nuclear genomic evidence, in species delimitation so as to be robust against the pitfalls of mitochondrial introgression.
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Affiliation(s)
- Zhiyong Yuan
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Southwest University, Chongqing, 400715, China
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Southwest Forestry University, Kunming, 650224, China
| | - Dongyi Wu
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Southwest Forestry University, Kunming, 650224, China
| | - Yang Wen
- School of Life Sciences, Yunnan University, Kunming, 650091, China
- School of Ecology and Environment Sciences, Yunnan University, Kunming, 650091, China
| | - Wei Xu
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Wei Gao
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Hollis A Dahn
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Xiaolong Liu
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Southwest Forestry University, Kunming, 650224, China
| | - Jieqiong Jin
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Chuanxin Yu
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Heng Xiao
- School of Ecology and Environment Sciences, Yunnan University, Kunming, 650091, China
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
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Landscape Genetics and Species Delimitation in the Andean Palm Rocket Frog (Aromobatidae, Rheobates). J ZOOL SYST EVOL RES 2022. [DOI: 10.1155/2022/6774225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The complex topography of the species-rich northern Andes creates heterogeneous environmental landscapes that are hypothesized to have promoted population fragmentation and diversification by processes such as vicariance or local adaptation. Previous phylogenetic work on the palm rocket frog (Anura: Aromobatidae: Rheobates spp.), endemic to midelevation forests of Colombia, suggested that valleys were important in promoting divergence between lineages. In this study, we first evaluated previous hypotheses of species-level diversity, then fitted an isolation-with-migration (IM) historical demographic model, and tested two landscape genetic models to explain genetic divergence within Rheobates: isolation by distance and isolation by environment. The data consisted of two mitochondrial and four nuclear genes from 24 samples covering most of the geographic range of the genus. Species delimitation by Bayesian Phylogenetics and Phylogeography recovered five highly divergent genetic lineages within Rheobates, among which few to no migrants are exchanged according to IM. We found that isolation by environment provided the only variable significantly correlated with genetic distances for both mitochondrial and nuclear genes, suggesting that local adaptation may have a role in driving the genetic divergence within this frog genus. Thus, genetic divergence in Rheobates may be driven more by variation among the local environments where these frogs live rather than by geographic distance.
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37
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Walhidayah T. Characteristics Evaluation of a Barcode Sequence of Two Limnonectes (Anura) Sympatric Populations from Kendari, Southeast Sulawesi. Pak J Biol Sci 2022; 25:732-740. [PMID: 36098199 DOI: 10.3923/pjbs.2022.732.740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
<b>Background and Objective:</b> Cytochrome c oxidase gene subunit-I (COI) has conserved and variable regions and along with the 658 nucleotide base pairs at the '5 of these have been used as animal barcode, species identification and evolutionary studies of several vertebrates, especially Anura. This research was conducted to characterize the nucleotides of the COI sequence gene of (<i>Limnonectes cf. grunniens</i>) that live sympatrically with <i>L. modestus</i> on several headwater streams in Kendari, Southeast Sulawesi. <b>Materials and Methods:</b> This research is explorative, samples of frogs were obtained from the Lahundape and Moramo headwater streams. A total of 16 frogs were sampled and the genomic DNA of frog samples was extracted and, then amplified using the PCR method. The next steps are sequencing and analysis using MEGA 7. <b>Results:</b> The result showed nucleotides along 688 to 705 base pairs. There were two haplotypes of <i>L. cf. grunniens</i> and three <i>L. modestus</i>. <i>L. cf. grunniens </i>consist of 32.6% Thymine (Uracil), 32.3% Cytisine, 17.9% Adenine and 17.9% Guanine. While <i>L. modestus</i> is 37.6% Thymine, 26.0% Cytosine, 20.7% Adenine and 15.8% Guanine. Based on Kimura-2 parameter, the genetic distance between genera ranges from 0.25-0.26 while the genetic distance between species is 0.00-0.01. <b>Conclusion:</b> Phylogeny trees based on partial sequences of COI frog genes showed that <i>L. cf. grunniens</i> and <i>L. modestus</i> are monophyletic with bootstrapped values ranging from 86-100% and differentiated between species. There is a genetic variability of COI sequences of <i>Limnonectes cf. grunniens</i> and <i>L. modestus</i> from Kendari, Southeast Sulawesi.
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38
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Suzuki T, Nishikawa K, Sato Y, Toda M. Development and evaluation of a loop-mediated isothermal amplification (LAMP) assay for quick identification of the Japanese salamander Hynobius tokyoensis. Genes Genet Syst 2021; 96:247-252. [PMID: 34744097 DOI: 10.1266/ggs.21-00046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Species identification using molecular techniques has recently become common for various taxa. Loop-mediated isothermal amplification (LAMP) is one of the easiest and least expensive molecular identification methods. Although few studies have developed LAMP assays for amphibians, we believe that LAMP is also useful for identifying endangered amphibians. Hynobius tokyoensis and H. lichenatus occur in Honshu, Japan, and have parapatric distributions. They are similar morphologically, especially at early developmental stages, including eggs and larvae. Hynobius tokyoensis has been listed as a national endangered species in Japan since 2020, and unambiguous identification of these species is therefore important for their conservation and management. In this study, we developed a LAMP primer set for the mitochondrial cytochrome b region to detect H. tokyoensis, and we evaluated the LAMP assay using total genomic DNA from four H. tokyoensis and three H. lichenatus individuals from across most of their ranges. Our LAMP primer set could distinguish these two species. This study should help to establish LAMP assays for other endangered species and morphologically similar species.
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Affiliation(s)
- Tomoya Suzuki
- Graduate School of Global Environmental Studies, Kyoto University
| | - Kanto Nishikawa
- Graduate School of Global Environmental Studies, Kyoto University.,Graduate School of Human and Environmental Studies, Kyoto University
| | - Yukuto Sato
- Research Laboratory Center, Faculty of Medicine, University of the Ryukyus.,Tropical Biosphere Research Center, University of the Ryukyus.,Center for Strategic Research Project, University of the Ryukyus
| | - Mamoru Toda
- Tropical Biosphere Research Center, University of the Ryukyus
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39
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Seo Y, Shin N, Nam HH, Song J, Cheol Moon B, Choi G, Shin I, Kim J. Effects of larval extracts from identified Protaetia brevitarsis seulensis against benign prostatic hyperplasia induced by testosterone in rats. Food Sci Nutr 2021; 9:5361-5369. [PMID: 34646508 PMCID: PMC8498080 DOI: 10.1002/fsn3.2460] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 06/03/2021] [Accepted: 06/29/2021] [Indexed: 01/15/2023] Open
Abstract
Protaetia brevitarsis seulensis is an animal-based medicine used traditionally in China, Japan, and Korea to treat hepatic disorders; it has been shown to possess various pharmacological effects such as antibacterial and antioxidant activities. In this study, we investigated the effects of P. brevitarsis on a testosterone-induced benign prostatic hyperplasia (BPH) rat model. To establish the BPH model, the animals were administered a subcutaneous injection of testosterone daily for 28 days. P. brevitarsis was administered by oral gavage at doses of 12.5, 25, and 50 mg/kg for 28 days, along with testosterone injection. P. brevitarsis treatment markedly decreased the absolute and relative prostate weight of BPH animals. The levels of dihydrotestosterone was reduced in P. brevitarsis-treated animals compared to those in the BPH animals. Histological analysis of the prostate showed that P. brevitarsis treatment effectively suppressed the testosterone-induced hyperplasia of prostatic epithelial cells, which was accompanied by reductions in the PCNA and Ki-67 expressions in prostatic tissues. These results indicate that P. brevitarsis effectively suppresses testosterone-induced development of BPH, and thus, is a potential therapeutic agent for BPH.
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Affiliation(s)
- Yun‐Soo Seo
- Herbal Medicine Resources Research CenterKorea Institute of Oriental MedicineNaju‐siKorea
| | - Na‐Rea Shin
- College of Veterinary Medicine and BK21 Plus Project TeamChonnam National UniversityGwangjuKorea
| | - Hyeon Hwa Nam
- Herbal Medicine Resources Research CenterKorea Institute of Oriental MedicineNaju‐siKorea
| | - Jun‐Ho Song
- Herbal Medicine Resources Research CenterKorea Institute of Oriental MedicineNaju‐siKorea
| | - Byeong Cheol Moon
- Herbal Medicine Resources Research CenterKorea Institute of Oriental MedicineNaju‐siKorea
| | - Goya Choi
- Herbal Medicine Resources Research CenterKorea Institute of Oriental MedicineNaju‐siKorea
| | - In‐Sik Shin
- College of Veterinary Medicine and BK21 Plus Project TeamChonnam National UniversityGwangjuKorea
| | - Joong‐Sun Kim
- Herbal Medicine Resources Research CenterKorea Institute of Oriental MedicineNaju‐siKorea
- College of Veterinary Medicine and BK21 Plus Project TeamChonnam National UniversityGwangjuKorea
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40
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Stöck M, Dedukh D, Reifová R, Lamatsch DK, Starostová Z, Janko K. Sex chromosomes in meiotic, hemiclonal, clonal and polyploid hybrid vertebrates: along the 'extended speciation continuum'. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200103. [PMID: 34304588 PMCID: PMC8310718 DOI: 10.1098/rstb.2020.0103] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/12/2021] [Indexed: 12/15/2022] Open
Abstract
We review knowledge about the roles of sex chromosomes in vertebrate hybridization and speciation, exploring a gradient of divergences with increasing reproductive isolation (speciation continuum). Under early divergence, well-differentiated sex chromosomes in meiotic hybrids may cause Haldane-effects and introgress less easily than autosomes. Undifferentiated sex chromosomes are more susceptible to introgression and form multiple (or new) sex chromosome systems with hardly predictable dominance hierarchies. Under increased divergence, most vertebrates reach complete intrinsic reproductive isolation. Slightly earlier, some hybrids (linked in 'the extended speciation continuum') exhibit aberrant gametogenesis, leading towards female clonality. This facilitates the evolution of various allodiploid and allopolyploid clonal ('asexual') hybrid vertebrates, where 'asexuality' might be a form of intrinsic reproductive isolation. A comprehensive list of 'asexual' hybrid vertebrates shows that they all evolved from parents with divergences that were greater than at the intraspecific level (K2P-distances of greater than 5-22% based on mtDNA). These 'asexual' taxa inherited genetic sex determination by mostly undifferentiated sex chromosomes. Among the few known sex-determining systems in hybrid 'asexuals', female heterogamety (ZW) occurred about twice as often as male heterogamety (XY). We hypothesize that pre-/meiotic aberrations in all-female ZW-hybrids present Haldane-effects promoting their evolution. Understanding the preconditions to produce various clonal or meiotic allopolyploids appears crucial for insights into the evolution of sex, 'asexuality' and polyploidy. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)'.
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Affiliation(s)
- Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries - IGB (Forschungsverbund Berlin), Müggelseedamm 301, 12587 Berlin, Germany
- Amphibian Research Center, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Dmitrij Dedukh
- Institute of Animal Physiology and Genetics, Laboratory of Fish Genetics, The Czech Academy of Sciences, 277 21 Libechov, Czech Republic
| | - Radka Reifová
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, Prague 2, 128 00, Czech Republic
| | - Dunja K. Lamatsch
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Zuzana Starostová
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, Prague 2, 128 00, Czech Republic
| | - Karel Janko
- Institute of Animal Physiology and Genetics, Laboratory of Fish Genetics, The Czech Academy of Sciences, 277 21 Libechov, Czech Republic
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, 701 03 Ostrava, Czech Republic
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Malik S, Javid A, Hamidullah, Iqbal MA, Hussain A, Bukhari SM, Chaber AL, Hemmatzadeh F, Ismat N, Ali A, Azam SM, Mustafa G, Hussain S, Ahmad U, Ahmad A, Ali W. Phylogeography of cliff racer (Platyceps rhodorachis Jan, 1865) from Punjab, Pakistan. BRAZ J BIOL 2021; 83:e246243. [PMID: 34468516 DOI: 10.1590/1519-6984.246243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 01/20/2021] [Indexed: 11/22/2022] Open
Abstract
The present study reports the existence of cliff racer, Platyceps rhodorachis from the plains of Punjab, Pakistan. A total of 10 specimens were captured during the field surveys from June to September, 2018 from different sites of Punjab. Platyceps rhodorachis was identify on the basis of morphology and confirmed through COI gene sequences. The obtained DNA sequences have shown reliable and exact species identification. Newly produced DNA sequences of Platyceps rhodorachis were submitted to GenBank and accession numbers were obtained (MK936174.1, MK941839.1 and MT790210.1). N-J tree based on COI sequences of Platyceps rhodorachis clearly separated as out-group with other members of family Colubridae based on p-distance. The intra-specific genetic variation ranges from 12% to 18%. The DNA sequences of Platyceps rhodorachis kashmirensis, Platyceps rhodorachis ladacensis, Platyceps ventromaculatus, Platyceps ventromaculatus bengalensis and Platyceps ventromaculatus indusai are not available at NCBI to validate their taxonomic positions. In our recommendations, a large scale molecular based identification of Pakistan's herpetofauna is required to report more new or subspecies from country.
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Affiliation(s)
- S Malik
- University of Veterinary and Animal Sciences, Department of Wildlife and Ecology, Lahore, Pakistan
| | - A Javid
- University of Veterinary and Animal Sciences, Department of Wildlife and Ecology, Lahore, Pakistan
| | - Hamidullah
- Islamia University Bahawalpur, Department of Zoology, Sub Campus Bahawalnagur, Bahawalpur, Pakistan
| | - M A Iqbal
- Gomal University Sub Campus Tank, Department of Zoology, Dera Ismail Khan, Pakistan
| | - A Hussain
- University of Veterinary and Animal Sciences, Department of Wildlife and Ecology, Lahore, Pakistan
| | - S M Bukhari
- University of Veterinary and Animal Sciences, Department of Wildlife and Ecology, Lahore, Pakistan
| | - A L Chaber
- The University of Adelaide, School of Animal and Veterinary Sciences, Adelaide, Australia
| | - F Hemmatzadeh
- The University of Adelaide, School of Animal and Veterinary Sciences, Adelaide, Australia
| | - N Ismat
- The University of Lahore, Department of Molecular Biology, Lahore, Pakistan
| | - A Ali
- The Islamia University of Bahawalpur, Department of Zoology, Bahawalpur, Pakistan
| | - S M Azam
- University of Education, Department of Zoology, Lahore, Pakistan
| | - G Mustafa
- University of Veterinary and Animal Sciences, Department of Wildlife and Ecology, Lahore, Pakistan
| | - S Hussain
- University of Veterinary and Animal Sciences, Department of Wildlife and Ecology, Lahore, Pakistan
| | - U Ahmad
- University of Veterinary and Animal Sciences, Department of Wildlife and Ecology, Lahore, Pakistan
| | - A Ahmad
- University of Veterinary & Animal Sciences, Para-Veterinary Institute, Karor, Layyah, (Sub-Campus), Lahore, Pakistan
| | - W Ali
- University of Veterinary and Animal Sciences, Department of Wildlife and Ecology, Lahore, Pakistan
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42
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Li KE, Wu YY, Xu RY, Zhu F, Ren JL, Guo P, Dong BJ. A new species of the Achalinus rufescens complex (Xenodermidae: Achalinus) from Fujian Province, China. Zootaxa 2021; 5026:239-254. [PMID: 34810931 DOI: 10.11646/zootaxa.5026.2.5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Indexed: 11/04/2022]
Abstract
A new species of the xenodermid snake genus Achalinus Peters, 1869 is described from Fujian Province, China, based on six specimens. Bayesian inference and maximum likelihood analyses based on a mitochondrial DNA fragment (CO1) indicated the new taxon is different from its congeners (pdistance ≥ 18.5%). Morphologically, the new species can be diagnosed from the other species by a combination of following characters: (1) dorsal scales 23 rows throughout, strongly keeled, the most outer rows on both sides also keeled and slightly enlarged; (2) tail relatively longer, TaL/TL ratio 0.260.29 in males, 0.210.22 in females; (3) maxillary teeth 3033; (4) length of suture between internasals significantly longer than that between prefrontals; (5) nasal divided into two sections by nasal cleft; (6) a single loreal; (7) SPO 1, seldom 2; (8) SPL 6, the fourth and fifth contacting eye; (9) IFL5, rarely 6, the first three touching the first pair of chin shields; (10) TMP 79, arranged in three rows; (11) VS 142149 in males, VS 152154 in females; (12) SC 7481 in males, SC 6365 in females, arranged in a single row; (13) cloacal entire; (14) greyish brown above, pale yellow beneath; (15) dorsum with an indistinct longitudinal vertebral stripe. The description of the new species brings the total species of Achalinus to 19.
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Affiliation(s)
- K E Li
- College of Life Sciences, Shenyang Normal University, Shenyang 110034, China. Faculty of Agriculture, Forest and Food Engineering, Yibin University, Yibin 644007, China..
| | - Ya-Yong Wu
- Faculty of Agriculture, Forest and Food Engineering, Yibin University, Yibin 644007, China..
| | - Rui-Ying Xu
- Faculty of Agriculture, Forest and Food Engineering, Yibin University, Yibin 644007, China..
| | - Fei Zhu
- Collegel of Life Science, Guizhou Normal University, Guiyang 550025, China..
| | - Jin-Long Ren
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China..
| | - Peng Guo
- Faculty of Agriculture, Forest and Food Engineering, Yibin University, Yibin 644007, China..
| | - Bing-Jun Dong
- College of Life Sciences, Shenyang Normal University, Shenyang 110034, China..
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43
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Patel NG, Garg S, Das A, Stuart BL, Biju S. Phylogenetic position of the poorly known montane cascade frog Amolops monticola (Ranidae) and description of a new closely related species from Northeast India. J NAT HIST 2021. [DOI: 10.1080/00222933.2021.1946185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Naitik G. Patel
- Department of Endangered Species Management, Wildlife Institute of India, Dehradun, India
| | - Sonali Garg
- Systematics Lab, Department of Environmental Studies, University of Delhi, Delhi, India
| | - Abhijit Das
- Department of Endangered Species Management, Wildlife Institute of India, Dehradun, India
| | - Bryan L. Stuart
- Section of Research & Collections, North Carolina Museum of Natural Sciences, Raleigh, NC, USA
| | - S.D. Biju
- Systematics Lab, Department of Environmental Studies, University of Delhi, Delhi, India
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Jang‐Liaw N. A barcoding-based scat-analysis assessment of Eurasian otter Lutra lutra diet on Kinmen Island. Ecol Evol 2021; 11:8795-8813. [PMID: 34257929 PMCID: PMC8258194 DOI: 10.1002/ece3.7712] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 03/24/2021] [Accepted: 05/04/2021] [Indexed: 11/25/2022] Open
Abstract
While it is well known that Eurasian otters principally feed on fishes and crustaceans, their detailed diet taxonomies are not fully understood. This is partly due to their nocturnal behavior and the limited resolving power of traditional morphological identification from scat. A suitable, reliable molecular method for diet studies is therefore needed.I performed a series of Sanger-sequencing reactions, utilizing nine primer sets for Eurasian otter diet research. These are mainly based on the barcoding concept to determine the taxonomic composition of spraints. The primer sets target different types of animals, amplifying each separately. This procedure was used to detect the prey contents of 64 spraint samples collected from Kinmen Island. Through high-resolution gel electrophoresis and sequencing, it was evident that PCR products could be successfully amplified by the different primer sets and from spraint samples comprising multiple prey species.Extracted DNA from all spraint samples was PCR-amplified with 9 primer sets. In total, 16 prey types were identified across all 64 samples. Fourteen were identified at the species level.The aim of this study was to develop and apply a novel diet research method to Eurasian otters. Eight of the primers are universal primers designed for COI segments of different animal groups, and one primer set was designed specifically for tilapia groups. This method can be applied to study the diets of not only Kinmen Eurasian otter populations, but also other Eurasian otter populations and other small carnivorous animals.
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Affiliation(s)
- Nian‐Hong Jang‐Liaw
- Conservation Genetics LaboratoryConservation and Research CenterTaipei ZooTaipei CityTaiwan
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Luo T, Wang Y, Wang S, Lu X, Wang W, Deng H, Zhou J. A species of the genus Panophrys (Anura, Megophryidae) from southeastern Guizhou Province, China. Zookeys 2021; 1047:27-60. [PMID: 34248365 PMCID: PMC8249361 DOI: 10.3897/zookeys.1047.61097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 04/19/2021] [Indexed: 11/22/2022] Open
Abstract
Herein, we describe Panophryscongjiangensissp. nov. obtained from the Yueliangshan Nature Reserve, Congjiang County, Guizhou Province, China. Phylogenetic analyses based on the mitochondrial genes 16S rRNA and COI indicated that this new species represented an independent lineage, closely related to P.leishanensis. The uncorrected genetic distances between the new species and its closest congener, P.leishanensis, were 3.0% for 16S rRNA and 8.4% for COI. The new species is distinguished from its congeners by a combination of the following morphological characteristics (1) medium body size (SVL 28.6–33.4 mm in males and 38.4–40.2 mm in females); (2) a small horn-like tubercle at the edge of each upper eyelid; (3) the tympanum distinctly visible (TD/ED ratio 0.47–0.66); (4) vomerine teeth absent; (5) the tongue not notched behind; (6) a narrow and unobvious lateral fringe on toes; (7) relative finger lengths II < I < V < III; (8) rudimentary webs on toes; (9) hindlimbs slender, heels overlapping when thighs are positioned at right angles to the body; (10) two metacarpal tubercles on the palm, with the inner metatarsal tubercle long and oval-shaped; (11) the tibiotarsal articulation reaching the nostril when the leg is adpressed and stretched forward; (12) dorsal skin rough with numerous orange–red granules, ventral surface smooth; (13) a single internal subgular vocal sac present in males; and (14) in breeding males, weak gray-black nuptial pads with black nuptial spines present on the dorsal surface of the bases of the first and second fingers. To date, the new species is only known from the type locality.
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Affiliation(s)
- Tao Luo
- School of Karst Sciences, Guizhou Normal University, Guiyang 550001, Guizhou, China Guizhou Normal University Guiyang China
| | - Yali Wang
- School of Karst Sciences, Guizhou Normal University, Guiyang 550001, Guizhou, China Guizhou Normal University Guiyang China
| | - Siwei Wang
- School of Karst Sciences, Guizhou Normal University, Guiyang 550001, Guizhou, China Guizhou Normal University Guiyang China
| | - Xueli Lu
- School of Karst Sciences, Guizhou Normal University, Guiyang 550001, Guizhou, China Guizhou Normal University Guiyang China
| | - Weifeng Wang
- School of Karst Sciences, Guizhou Normal University, Guiyang 550001, Guizhou, China Guizhou Normal University Guiyang China
| | - Huaiqing Deng
- School of Life Sciences, Guizhou Normal University, Guiyang 550001, Guizhou, China Guizhou Normal University Guiyang China
| | - Jiang Zhou
- School of Karst Sciences, Guizhou Normal University, Guiyang 550001, Guizhou, China Guizhou Normal University Guiyang China
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Li S, Wei G, Liu J, Xu H. Mitochondrial DNA phylogeography of the Guizhou odorous frog: limited population genetic structure and evidence for recent population size expansion. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:1592-1596. [PMID: 34212081 PMCID: PMC8218851 DOI: 10.1080/23802359.2021.1914215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The Guizhou odorous frog Odorrana kweichowensis is endemic to Guizhou Province, China. In this study, a comparative analysis of the mitochondrial COI and ND2 gene sequences was performed to examine genetic diversity in 109 individuals from ten localities across the geographic range of the species. Haplotype diversity and nucleotide diversity were 0.576 and 0.00055, respectively. Phylogenetic analyses almost nested all haplotypes into one lineage. AMOVA indicated that total variation was mainly derived from variation within individual populations. Neutral tests indicated that a recent expansion occurred in the total population. Fst estimations indicated that genetic divergence was not correlated with geographic distance. Accordingly, the species probably experienced a recent population expansion, and there no obvious population genetic structure is apparent. The findings provide useful information for the conservation of this species.
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Affiliation(s)
- Shize Li
- Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Collaborative Innovation Center for Mountain Ecology and Agro-Bioengineering (CICMEAB), College of Life Sciences, Guizhou University, Guiyang, China.,Key Laboratory of Animal Genetics Breeding of Guizhou Province, Guizhou University, Guiyang, China.,Department of Food Science and Engineering, Moutai Institute, Renhuai, China
| | - Gang Wei
- Biodiversity Conservation Key Laboratory, Guiyang College, Guiyang, China
| | - Jing Liu
- Biodiversity Conservation Key Laboratory, Guiyang College, Guiyang, China
| | - Houqiang Xu
- Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Collaborative Innovation Center for Mountain Ecology and Agro-Bioengineering (CICMEAB), College of Life Sciences, Guizhou University, Guiyang, China.,Key Laboratory of Animal Genetics Breeding of Guizhou Province, Guizhou University, Guiyang, China
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Ge Y, Xia C, Wang J, Zhang X, Ma X, Zhou Q. The efficacy of DNA barcoding in the classification, genetic differentiation, and biodiversity assessment of benthic macroinvertebrates. Ecol Evol 2021; 11:5669-5681. [PMID: 34026038 PMCID: PMC8131818 DOI: 10.1002/ece3.7470] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 02/26/2021] [Accepted: 03/05/2021] [Indexed: 11/19/2022] Open
Abstract
Macroinvertebrates have been recognized as key ecological indicators of aquatic environment and are the most commonly used approaches for water quality assessment. However, species identification of macroinvertebrates (especially of aquatic insects) proves to be very difficult due to the lack of taxonomic expertise in some regions and can become time-consuming. In this study, we evaluated the feasibility of DNA barcoding for the classification of benthic macroinvertebrates and investigated the genetic differentiation in seven orders (Insecta: Ephemeroptera, Plecoptera, Trichoptera, Diptera, Hemiptera, Coleoptera, and Odonata) from four large transboundary rivers of northwest China and further explored its potential application to biodiversity assessment. A total of 1,144 COI sequences, belonging to 176 species, 112 genera, and 53 families were obtained and analyzed. The barcoding gap analysis showed that COI gene fragment yielded significant intra- and interspecific divergences and obvious barcoding gaps. NJ phylogenetic trees showed that all species group into monophyletic species clusters whether from the same population or not, except two species (Polypedilum. laetum and Polypedilum. bullum). The distance-based (ABGD) and tree-based (PTP and MPTP) methods were utilized for grouping specimens into Operational Taxonomic Units (OTUs) and delimiting species. The ABGD, PTP, and MPTP analysis were divided into 177 (p = .0599), 197, and 195 OTUs, respectively. The BIN analysis generated 186 different BINs. Overall, our study showed that DNA barcoding offers an effective framework for macroinvertebrate species identification and sheds new light on the biodiversity assessment of local macroinvertebrates. Also, the construction of DNA barcode reference library of benthic macroinvertebrates in Eurasian transboundary rivers provides a solid backup for bioassessment studies of freshwater habitats using modern high-throughput technologies in the near future.
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Affiliation(s)
- Yihao Ge
- Key Laboratory of Freshwater Animal BreedingMinistry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of FisheriesHuazhong Agricultural UniversityWuhanChina
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic BeltMinistry of EducationWuhanChina
- The Key Laboratory of Aquatic Biodiversity and ConservationInstitute of HydrobiologyChinese Academy of SciencesWuhanChina
| | - Chengxing Xia
- Key Laboratory of Freshwater Animal BreedingMinistry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of FisheriesHuazhong Agricultural UniversityWuhanChina
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic BeltMinistry of EducationWuhanChina
| | - Jun Wang
- Key Laboratory of Freshwater Animal BreedingMinistry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of FisheriesHuazhong Agricultural UniversityWuhanChina
- The Key Laboratory of Aquatic Biodiversity and ConservationInstitute of HydrobiologyChinese Academy of SciencesWuhanChina
| | - Xiujie Zhang
- Key Laboratory of Freshwater Animal BreedingMinistry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of FisheriesHuazhong Agricultural UniversityWuhanChina
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic BeltMinistry of EducationWuhanChina
| | - Xufa Ma
- Key Laboratory of Freshwater Animal BreedingMinistry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of FisheriesHuazhong Agricultural UniversityWuhanChina
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic BeltMinistry of EducationWuhanChina
| | - Qiong Zhou
- Key Laboratory of Freshwater Animal BreedingMinistry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of FisheriesHuazhong Agricultural UniversityWuhanChina
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic BeltMinistry of EducationWuhanChina
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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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49
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de Medeiros LA, Ribas CC, Lima AP. Genetic Diversification of Adelphobates quinquevittatus (Anura: Dendrobatidae) and the Influence of Upper Madeira River Historical Dynamics. Evol Biol 2021. [DOI: 10.1007/s11692-021-09536-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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50
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Tapley B, Cutajar T, Nguyen LT, Portway C, Mahony S, Nguyen CT, Harding L, Luong HV, Rowley JJL. A new potentially Endangered species of Megophrys (Amphibia: Megophryidae) from Mount Ky Quan San, north-west Vietnam. J NAT HIST 2021. [DOI: 10.1080/00222933.2020.1856952] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
| | - Timothy Cutajar
- Australian Museum Research Institute, Australian Museum, Sydney, Australia
| | - Luan Thanh Nguyen
- Indo-Myanmar Conservation, London, UK
- EDGE of Existence Programme, Zoological Society of London, London, UK
| | | | - Stephen Mahony
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- Department of Life Sciences, The Natural History Museum, London, UK
| | | | | | | | - Jodi J. L. Rowley
- Australian Museum Research Institute, Australian Museum, Sydney, Australia
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
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