1
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Peng MS, Liu YH, Shen QK, Zhang XH, Dong J, Li JX, Zhao H, Zhang H, Zhang X, He Y, Shi H, Cui C, Ouzhuluobu, Wu TY, Liu SM, Gonggalanzi, Baimakangzhuo, Bai C, Duojizhuoma, Liu T, Dai SS, Murphy RW, Qi XB, Dong G, Su B, Zhang YP. Genetic and cultural adaptations underlie the establishment of dairy pastoralism in the Tibetan Plateau. BMC Biol 2023; 21:208. [PMID: 37798721 PMCID: PMC10557253 DOI: 10.1186/s12915-023-01707-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 09/20/2023] [Indexed: 10/07/2023] Open
Abstract
BACKGROUND Domestication and introduction of dairy animals facilitated the permanent human occupation of the Tibetan Plateau. Yet the history of dairy pastoralism in the Tibetan Plateau remains poorly understood. Little is known how Tibetans adapted to milk and dairy products. RESULTS We integrated archeological evidence and genetic analysis to show the picture that the dairy ruminants, together with dogs, were introduced from West Eurasia into the Tibetan Plateau since ~ 3600 years ago. The genetic admixture between the exotic and indigenous dogs enriched the candidate lactase persistence (LP) allele 10974A > G of West Eurasian origin in Tibetan dogs. In vitro experiments demonstrate that - 13838G > A functions as a LP allele in Tibetans. Unlike multiple LP alleles presenting selective signatures in West Eurasians and South Asians, the de novo origin of Tibetan-specific LP allele - 13838G > A with low frequency (~ 6-7%) and absence of selection corresponds - 13910C > T in pastoralists across eastern Eurasia steppe. CONCLUSIONS Results depict a novel scenario of genetic and cultural adaptations to diet and expand current understanding of the establishment of dairy pastoralism in the Tibetan Plateau.
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Affiliation(s)
- Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- Yunnan Key Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yan-Hu Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- Yunnan Key Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Quan-Kuan Shen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- Yunnan Key Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao-Hua Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, 650091, China
- Institute of Medical Biology, Chinese Academy of Medical Science, Peking Union Medical College, Kunming, 650118, China
| | - Jiajia Dong
- Key Laboratory of Western China's Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Jin-Xiu Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- Yunnan Key Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Hui Zhao
- State Key Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, 650091, China
| | - Hui Zhang
- State Key Laboratory of Primate Biomedical Research (LPBR), School of Primate Translational Medicine, Kunming University of Science and Technology (KUST), Kunming, 650000, China
| | - Xiaoming Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yaoxi He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hong Shi
- State Key Laboratory of Primate Biomedical Research (LPBR), School of Primate Translational Medicine, Kunming University of Science and Technology (KUST), Kunming, 650000, China
| | - Chaoying Cui
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa, 850000, China
| | - Ouzhuluobu
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa, 850000, China
| | - Tian-Yi Wu
- National Key Laboratory of High Altitude Medicine, High Altitude Medical Research Institute, Xining, 810000, China
| | - Shi-Ming Liu
- National Key Laboratory of High Altitude Medicine, High Altitude Medical Research Institute, Xining, 810000, China
| | - Gonggalanzi
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa, 850000, China
| | - Baimakangzhuo
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa, 850000, China
| | - Caijuan Bai
- The First People's Hospital of Gansu Province, Lanzhou, 730000, China
| | - Duojizhuoma
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa, 850000, China
| | - Ti Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, 650091, China
| | - Shan-Shan Dai
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- Yunnan Key Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, ON, M5S 2C6, Canada
| | - Xue-Bin Qi
- State Key Laboratory of Primate Biomedical Research (LPBR), School of Primate Translational Medicine, Kunming University of Science and Technology (KUST), Kunming, 650000, China.
- Tibetan Fukang Hospital, Lhasa, 850000, China.
| | - Guanghui Dong
- Key Laboratory of Western China's Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou, 730000, China.
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
- Yunnan Key Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- State Key Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, 650091, China.
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2
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Nguyen SN, Nguyen VDH, LE MVAN, Nguyen LT, Vo TDH, Vo BD, Che J, Murphy RW. A new snake of the genus Dendrelaphis Boulenger, 1890 (Squamata: Colubridae) from the coastal area of southern Vietnam. Zootaxa 2023; 5318:130-144. [PMID: 37518394 DOI: 10.11646/zootaxa.5318.1.6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Indexed: 08/01/2023]
Abstract
We describe a new species of Dendrelaphis from the coastal area in southern Vietnam based on morphological data and nucleotide sequences from one partial mitochondrial gene (Cytb). Dendrelaphis binhi sp. nov. is diagnosed by the following morphological characters: body scale rows 13 at neck and midbody, 9-11 before vent; vertebral scale row feebly enlarged; ventrals 154-158 in males and 161-170 in females; subcaudals 95-106 in males and 95-102 in females; one supralabial touching the eye; 18 or 19 maxillary teeth; hemipenis spinose, reaching 10th or 11th SC, with a slender papilla; cloacal plate divided; dorsum dark brown; and a white stripe along the lower flank. The new species differs from its congeners by an uncorrected p-distance in Cytb sequences of at least 8.1%.
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Affiliation(s)
- Sang Ngoc Nguyen
- Institute of Tropical Biology; Vietnam Academy of Science and Technology; 85 Tran Quoc Toan St.; Dist. 3; Ho Chi Minh City; Vietnam; Graduate University of Science and Technology; Vietnam Academy of Science and Technology; 18 Hoang Quoc Viet Road; Hanoi; Vietnam.
| | - Vu Dang Hoang Nguyen
- Institute of Tropical Biology; Vietnam Academy of Science and Technology; 85 Tran Quoc Toan St.; Dist. 3; Ho Chi Minh City; Vietnam.
| | - Manh VAN LE
- Institute of Tropical Biology; Vietnam Academy of Science and Technology; 85 Tran Quoc Toan St.; Dist. 3; Ho Chi Minh City; Vietnam.
| | - Luan Thanh Nguyen
- Indo-Myanmar Conservation; No. 1806; C14 Bac Ha Building; To Huu St.; Tu Liem Dist.; Hanoi; Vietnam.
| | - Thi-Dieu-Hien Vo
- Faculty of Environmental and Food Engineering; Nguyen Tat Thanh University; Ho Chi Minh City; Vietnam.
| | - Ba Dinh Vo
- Department of Biology; University of Science; Hue University; 77 Nguyen Hue St.; Hue City; Vietnam.
| | - Jing Che
- Laboratory of Herpetological Diversity and Evolution; Kunming Institute of Zoology; CAS; China.
| | - Robert W Murphy
- Reptilia Zoo and Education Centre; 2501 Rutherford Rd Vaughan; ON; Canada L4K 2N6.
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3
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Zhong H, Luo J, Tang L, Liao S, Lu Z, Lin G, Murphy RW, Liu L. Association filtering and generative adversarial networks for predicting lncRNA-associated disease. BMC Bioinformatics 2023; 24:234. [PMID: 37277721 DOI: 10.1186/s12859-023-05368-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 05/29/2023] [Indexed: 06/07/2023] Open
Abstract
BACKGROUND Long non-coding RNA (lncRNA) closely associates with numerous biological processes, and with many diseases. Therefore, lncRNA-disease association prediction helps obtain relevant biological information and understand pathogenesis, and thus better diagnose preventable diseases. RESULTS Herein, we offer the LDAF_GAN method for predicting lncRNA-associated disease based on association filtering and generative adversarial networks. Experimentation used two types of data: lncRNA-disease associated data without lncRNA sequence features, and fused lncRNA sequence features. LDAF_GAN uses a generator and discriminator, and differs from the original GAN by the addition of a filtering operation and negative sampling. Filtering allows the generator output to filter out unassociated diseases before being fed into the discriminator. Thus, the results generated by the model focuses only on lncRNAs associated with disease. Negative sampling takes a portion of disease terms with 0 from the association matrix as negative samples, which are assumed to be unassociated with lncRNA. A regular term is added to the loss function to avoid producing a vector with all values of 1, which can fool the discriminator. Thus, the model requires that generated positive samples are close to 1, and negative samples are close to 0. The model achieved a superior fitting effect; LDAF_GAN had superior performance in predicting fivefold cross-validations on the two datasets with AUC values of 0.9265 and 0.9278, respectively. In the case study, LDAF_GAN predicted disease association for six lncRNAs-H19, MALAT1, XIST, ZFAS1, UCA1, and ZEB1-AS1-and with the top ten predictions of 100%, 80%, 90%, 90%, 100%, and 90%, respectively, which were reported by previous studies. CONCLUSION LDAF_GAN efficiently predicts the potential association of existing lncRNAs and the potential association of new lncRNAs with diseases. The results of fivefold cross-validation, tenfold cross-validation, and case studies suggest that the model has great predictive potential for lncRNA-disease association prediction.
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Affiliation(s)
- Hua Zhong
- School of Information Science, Yunnan Normal University, Kunming, China
| | - Jing Luo
- State Key Laboratory for Conservation and Utilization of Bio-resource, School of Ecology and Environment and School of Life Sciences, Yunnan University, Kunming, China
| | - Lin Tang
- Key Laboratory of Educational lnformation for Nationalities Ministry of Education, Yunnan University, Kunming, China
| | - Shicheng Liao
- School of Information Science, Yunnan Normal University, Kunming, China
| | - Zhonghao Lu
- School of Information Science, Yunnan Normal University, Kunming, China
| | - Guoliang Lin
- School of Medicine, Yunnan University, Kunming, China
| | - Robert W Murphy
- Reptilia Zoo and Education Centre, 2501 Rutherford Rd., Vaughan, ON, L4K 2N6, Canada
| | - Lin Liu
- School of Information Science, Yunnan Normal University, Kunming, China.
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4
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Liu Y, Pu Y, Chen S, Wang X, Murphy RW, Wang X, Liao R, Tang K, Yue B, Liu S. Revalidation and expanded description of Mustela aistoodonnivalis (Mustelidae: Carnivora) based on a multigene phylogeny and morphology. Ecol Evol 2023; 13:e9944. [PMID: 37082328 PMCID: PMC10111237 DOI: 10.1002/ece3.9944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 03/02/2023] [Accepted: 03/13/2023] [Indexed: 04/22/2023] Open
Abstract
The lacked-teeth pygmy weasel, Mustela aistoodonnivalis Wu & Kao, 1991, was originally described as being from Taibai Mountain and Zhashui county, Shaanxi, China. Subsequently, it was considered a subspecies or synonym of Mustela nivalis. In a faunal survey of northwestern Sichuan, eight specimens of M. aistoodonnivalis were collected. A molecular phylogenetic analysis of one mitochondrial and six nuclear genes clustered the specimens as a distinct clade and not with M. nivalis. Morphologically, the lack of the second lower molar differentiated them from M. nivalis, and genetic distances were typical of discrete species. These analyses confirmed that M. aistoodonnivalis is an independent species in the genus Mustela.
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Affiliation(s)
- Yingxun Liu
- College of Life SciencesSichuan UniversityChengduSichuanChina
| | - Yingting Pu
- College of Life SciencesSichuan Normal UniversityChengduSichuanChina
| | - Shunde Chen
- College of Life SciencesSichuan Normal UniversityChengduSichuanChina
| | - Xuming Wang
- Sichuan Academy of ForestryChengduSichuanChina
| | | | - Xin Wang
- Sichuan Academy of ForestryChengduSichuanChina
| | - Rui Liao
- Sichuan Academy of ForestryChengduSichuanChina
| | - Keyi Tang
- College of Life SciencesSichuan Normal UniversityChengduSichuanChina
| | - Bisong Yue
- College of Life SciencesSichuan UniversityChengduSichuanChina
| | - Shaoying Liu
- Sichuan Academy of ForestryChengduSichuanChina
- Ecological Restoration and Conservation for Forest and Wetland Key Laboratory of Sichuan ProvinceSichuan Academy of ForestryChengduSichuanChina
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5
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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6
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Li Y, Wang S, Zhang Z, Luo J, Lin GL, Deng WD, Guo Z, Han FM, Wang LL, Li J, Wu SF, Liu HQ, He S, Murphy RW, Zhang ZJ, Cooper DN, Wu DD, Zhang YP. Large-Scale Chromosomal Changes Lead to Genome-Level Expression Alterations, Environmental Adaptation, and Speciation in the Gayal (Bos frontalis). Mol Biol Evol 2023; 40:6980758. [PMID: 36625089 PMCID: PMC9874039 DOI: 10.1093/molbev/msad006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 12/20/2022] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
Determining the functional consequences of karyotypic changes is invariably challenging because evolution tends to obscure many of its own footprints, such as accumulated mutations, recombination events, and demographic perturbations. Here, we describe the assembly of a chromosome-level reference genome of the gayal (Bos frontalis) thereby revealing the structure, at base-pair-level resolution, of a telo/acrocentric-to-telo/acrocentric Robertsonian translocation (2;28) (T/A-to-T/A rob[2;28]). The absence of any reduction in the recombination rate or genetic introgression within the fusion region of gayal served to challenge the long-standing view of a role for fusion-induced meiotic dysfunction in speciation. The disproportionate increase noted in the distant interactions across pro-chr2 and pro-chr28, and the change in open-chromatin accessibility following rob(2;28), may, however, have led to the various gene expression irregularities observed in the gayal. Indeed, we found that many muscle-related genes, located synthetically on pro-chr2 and pro-chr28, exhibited significant changes in expression. This, combined with genome-scale structural variants and expression alterations in genes involved in myofibril composition, may have driven the rapid sarcomere adaptation of gayal to its rugged mountain habitat. Our findings not only suggest that large-scale chromosomal changes can lead to alterations in genome-level expression, thereby promoting both adaptation and speciation, but also illuminate novel avenues for studying the relationship between karyotype evolution and speciation.
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Affiliation(s)
- Yan Li
- Corresponding authors: E-mails: ;
| | | | | | | | | | | | | | | | - Li-Li Wang
- Biomarker Technologies Corporation, Beijing, China
| | - Jie Li
- State Key Laboratory for Conservation and Utilization of Bio-resource in Yunnan and School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Shi-Fang Wu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - He-Qun Liu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Sheng He
- Nujiang Livestock Technology Promotion Station, Nujiang, China
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China,Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, ON, Canada
| | - Zi-Jie Zhang
- State Key Laboratory for Conservation and Utilization of Bio-resource in Yunnan and School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - David N Cooper
- Institute of Medical Genetics, Cardiff University, Cardiff, United Kingdom
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China,Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
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7
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Babarinde IA, Adeola AC, Djagoun CAMS, Nneji LM, Okeyoyin AO, Niba G, Wanzie NK, Oladipo OC, Adebambo AO, Bello SF, Ng'ang'a SI, Olaniyi WA, Okoro VMO, Adedeji BE, Olatunde O, Ayoola AO, Matouke MM, Wang YY, Sanke OJ, Oseni SO, Nwani CD, Murphy RW. Population structure and evolutionary history of the greater cane rat ( Thryonomys swinderianus) from the Guinean Forests of West Africa. Front Genet 2023; 14:1041103. [PMID: 36923796 PMCID: PMC10010571 DOI: 10.3389/fgene.2023.1041103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 02/07/2023] [Indexed: 03/02/2023] Open
Abstract
Grasscutter (Thryonomys swinderianus) is a large-body old world rodent found in sub-Saharan Africa. The body size and the unique taste of the meat of this major crop pest have made it a target of intense hunting and a potential consideration as a micro-livestock. However, there is insufficient knowledge on the genetic diversity of its populations across African Guinean forests. Herein, we investigated the genetic diversity, population structures and evolutionary history of seven Nigerian wild grasscutter populations together with individuals from Cameroon, Republic of Benin, and Ghana, using five mitochondrial fragments, including D-loop and cytochrome b (CYTB). D-loop haplotype diversity ranged from 0.571 (± 0.149) in Republic of Benin to 0.921 (± 0.013) in Ghana. Within Nigeria, the haplotype diversity ranged from 0.659 (± 0.059) in Cross River to 0.837 (± 0.075) in Ondo subpopulation. The fixation index (FST), haplotype frequency distribution and analysis of molecular variance revealed varying levels of population structures across populations. No significant signature of population contraction was detected in the grasscutter populations. Evolutionary analyses of CYTB suggests that South African population might have diverged from other populations about 6.1 (2.6-10.18, 95% CI) MYA. Taken together, this study reveals the population status and evolutionary history of grasscutter populations in the region.
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Affiliation(s)
- Isaac A Babarinde
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Adeniyi C Adeola
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Kunming, China.,Centre for Biotechnology Research, Bayero University, Kano, Nigeria
| | - Chabi A M S Djagoun
- Laboratory of Applied Ecology, Faculty of Agronomic Sciences, University of Abomey-Calavi, Cotonou, Benin
| | - Lotanna M Nneji
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, United States
| | - Agboola O Okeyoyin
- National Park Service Headquarters, Federal Capital Territory, Abuja, Nigeria
| | - George Niba
- National Centre for Animal Husbandry and Veterinary Training, Jakiri, North West Region, Cameroon
| | - Ndifor K Wanzie
- Department of Zoology, University of Douala, Douala, Cameroon.,Department of Zoology, Faculty of Life Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria
| | | | - Ayotunde O Adebambo
- Animal Genetics & Biotechnology, Federal University of Agriculture, Abeokuta, Nigeria
| | - Semiu F Bello
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Said I Ng'ang'a
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Wasiu A Olaniyi
- Department of Animal Science, Faculty of Agriculture, Adekunle Ajasin University, Akungba-Akoko, Ondo State, Nigeria
| | - Victor M O Okoro
- Department of Animal Science and Technology, School of Agriculture and Agricultural Technology, Federal University of Technology, Owerri, Nigeria
| | | | - Omotoso Olatunde
- Department of Zoology, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Adeola O Ayoola
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Kunming, China
| | - Moise M Matouke
- Department of Fisheries and Aquatic Resources Management, University of Buea, Buea, Cameroon
| | | | - Oscar J Sanke
- Taraba State Ministry of Agriculture and Natural Resources, Jalingo, Nigeria
| | - Saidu O Oseni
- Department of Animal Sciences, Faculty of Agriculture, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Christopher D Nwani
- Department of Zoology and Environmental Biology, Faculty of Biological Sciences, University of Nigeria, Nsukka, Nigeria
| | - Robert W Murphy
- Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, ON, Canada
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8
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Liu S, Zhou C, Meng G, Wan T, Tang M, Yang C, Murphy RW, Fan Z, Liu Y, Zeng T, Zhao Y, Liu S. Evolution and diversification of Mountain voles (Rodentia: Cricetidae). Commun Biol 2022; 5:1417. [PMID: 36572770 PMCID: PMC9792541 DOI: 10.1038/s42003-022-04371-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 12/13/2022] [Indexed: 12/27/2022] Open
Abstract
The systematics of the Cricetid genus Neodon have long been fraught with uncertainty due to sampling issues and a lack of comprehensive datasets. To gain better insights into the phylogeny and evolution of Neodon, we systematically sampled Neodon across the Hengduan and Himalayan Mountains, which cover most of its range in China. Analyses of skulls, teeth, and bacular structures revealed 15 distinct patterns corresponding to 15 species of Neodon. In addition to morphological analyses, we generated a high-quality reference genome for the mountain vole and generated whole-genome sequencing data for 47 samples. Phylogenomic analyses supported the recognition of six new species, revealing a long-term underestimation of Neodon diversity. We further identified positively selected genes potentially related to high-elevation adaptation. Together, our results illuminate how climate change caused the plateau to become the centre of Neodon origin and diversification and how mountain voles have adapted to the hypoxic high-altitude plateau environment.
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Affiliation(s)
- Shaoying Liu
- grid.464457.00000 0004 0445 3867Sichuan Academy of Forestry, No.18, Xinhui xilu, Chengdu, 610081 China
| | - Chengran Zhou
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, 518083 China ,grid.13291.380000 0001 0807 1581Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 China
| | - Guanliang Meng
- grid.452935.c0000 0001 2216 5875Zoological Research Museum Alexander Koenig, D-53113 Bonn, Germany
| | - Tao Wan
- grid.464457.00000 0004 0445 3867Sichuan Academy of Forestry, No.18, Xinhui xilu, Chengdu, 610081 China
| | - Mingkun Tang
- grid.464457.00000 0004 0445 3867Sichuan Academy of Forestry, No.18, Xinhui xilu, Chengdu, 610081 China
| | - Chentao Yang
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, 518083 China
| | - Robert W. Murphy
- Reptilia Sanctuary and Education Centre, Concord, ON L4K 2N6 Canada ,grid.421647.20000 0001 2197 9375Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, ON M5S 2C6 Canada
| | - Zhenxin Fan
- grid.13291.380000 0001 0807 1581Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 China
| | - Yang Liu
- grid.464457.00000 0004 0445 3867Sichuan Academy of Forestry, No.18, Xinhui xilu, Chengdu, 610081 China
| | - Tao Zeng
- grid.13291.380000 0001 0807 1581Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 China
| | - Yun Zhao
- grid.13291.380000 0001 0807 1581Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 China
| | - Shanlin Liu
- grid.22935.3f0000 0004 0530 8290Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, 100193 China
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9
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French CM, Berezin CT, Overcast I, Méndez De La Cruz FR, Basu S, Martínez Bernal RL, Murphy RW, Hickerson MJ, Blair C. Forest cover and geographical distance influence fine-scale genetic structure of leaf-toed geckos in the tropical dry forests of western Mexico. Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blac118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
The biodiversity within tropical dry forests (TDFs) is astounding and yet poorly catalogued due to inadequate sampling and the presence of cryptic species. In the Mexican TDF, endemic species are common, and the landscape has been continually altered by geological and anthropogenic changes. To understand how landscape and environmental variables have shaped the population structure of endemic species, we studied the recently described species of leaf-toed gecko, Phyllodactylus benedettii, in coastal western Mexico. Using double-digest restriction site-associated DNA sequencing data, we first explore population structure and estimate the number of ancestral populations. The results indicate a high degree of genetic structure with little admixture, and patterns corresponding to both latitudinal and altitudinal gradients. We find that genetic structure cannot be explained purely by geographical distance, and that ecological corridors may facilitate dispersal and gene flow. We then model the spatial distribution of P. benedettii in the TDF through time and find that the coastline has been climatically suitable for the species since the Last Glacial Maximum. Landscape genetic analyses suggest that the combination of isolation by distance (IBD) and isolation by resistance (IBR; forest cover) has influenced the spatial genetic structure of the species. Overall, our genomic data demonstrate fine-scale population structure in TDF habitat, a complex colonization history, and spatial patterns consistent with both IBD and other ecological factors. These results further highlight the Mexican TDF as a diversity hotspot and suggest that continued anthropogenic changes are likely to affect native fauna.
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Affiliation(s)
- Connor M French
- Biology PhD Program, CUNY Graduate Center , 365 5th Avenue, New York, NY 10016 , USA
| | - Casey-Tyler Berezin
- Department of Biology, City College of New York , 160 Convent Avenue, New York, NY 10031 , USA
| | - Isaac Overcast
- Biology PhD Program, CUNY Graduate Center , 365 5th Avenue, New York, NY 10016 , USA
- Institut de Biologie de l’Ecole Normale Superieure , 46 Rue d’Ulm, 75005 Paris , France
- Division of Vertebrate Zoology, American Museum of Natural History , 200 Central Park West, New York, NY 10024 , USA
| | | | - Saptarsi Basu
- Department of Biological Sciences, New York City College of Technology, The City University of New York , 285 Jay Street, Brooklyn, NY 11201 , USA
| | | | - Robert W Murphy
- Centre for Biodiversity, Royal Ontario Museum , 100 Queen’s Park, Toronto, ON M5S 2C6 , Canada
| | - Michael J Hickerson
- Biology PhD Program, CUNY Graduate Center , 365 5th Avenue, New York, NY 10016 , USA
- Department of Biology, City College of New York , 160 Convent Avenue, New York, NY 10031 , USA
| | - Christopher Blair
- Biology PhD Program, CUNY Graduate Center , 365 5th Avenue, New York, NY 10016 , USA
- Department of Biological Sciences, New York City College of Technology, The City University of New York , 285 Jay Street, Brooklyn, NY 11201 , USA
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10
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LaFond J, Martin KR, Dahn H, Richmond JQ, Murphy RW, Rollinson N, Savage AE. Invasive Bullfrogs Maintain MHC Polymorphism Including Alleles Associated with Chytrid Fungal Infection. Integr Comp Biol 2022; 62:262-274. [PMID: 35588059 DOI: 10.1093/icb/icac044] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/19/2022] [Accepted: 05/16/2022] [Indexed: 11/14/2022] Open
Abstract
Maintenance of genetic diversity at adaptive loci may facilitate invasions by non-native species by allowing populations to adapt to novel environments, despite the loss of diversity at neutral loci that typically occurs during founder events. To evaluate this prediction, we compared genetic diversity at major histocompatibility complex (MHC) and cytochrome b (cytb) loci from 20 populations of the American bullfrog (Rana catesbeiana) across theinvasive and native ranges in North America and quantified the presence of the pathogen Batrachochytrium dendrobatidis (Bd). Compared to native populations, invasive populations had significantly higher Bd prevalence and intensity, significantly higher pairwise MHC and cytb FST, and significantly lower cytb diversity, but maintained similar levels of MHC diversity. The two most common MHC alleles (LiCA_B and Rapi_33) were associated with a significant decreased risk of Bd infection, and we detected positive selection acting on four peptide binding residues. Phylogenetic analysis suggested invasive populations likely arose from a single founding population in the American Midwest with a possible subsequent invasion in the northwest. Overall, our study suggests that the maintenance of diversity at adaptive loci may contribute to invasion success and highlights the importance of quantifying diversity at functional loci to assess the evolutionary potential of invasive populations.
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Affiliation(s)
- Jacob LaFond
- Department of Biology, University of Central Florida, Orlando, FL 32816, USA
- Department of Biology, University of Tampa, Tampa, FL 33606, USA
| | - Katherine R Martin
- Department of Biology, University of Central Florida, Orlando, FL 32816, USA
| | - Hollis Dahn
- Department of Biology, University of Toronto, Toronto, ON, Canada
| | - Jonathan Q Richmond
- U.S. Geological Survey, 4165 Spruance Rd. Suite 200, San Diego, CA 92101, USA
| | - Robert W Murphy
- Department of Biology, University of Toronto, Toronto, ON, Canada
| | - Njal Rollinson
- Department of Biology, University of Toronto, Toronto, ON, Canada
| | - Anna E Savage
- Department of Biology, University of Central Florida, Orlando, FL 32816, USA
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11
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Dahn HA, Mountcastle J, Balacco J, Winkler S, Bista I, Schmitt AD, Pettersson OV, Formenti G, Oliver K, Smith M, Tan W, Kraus A, Mac S, Komoroske LM, Lama T, Crawford AJ, Murphy RW, Brown S, Scott AF, Morin PA, Jarvis ED, Fedrigo O. Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing. Gigascience 2022; 11:6659719. [PMID: 35946988 PMCID: PMC9364683 DOI: 10.1093/gigascience/giac068] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 01/26/2022] [Accepted: 06/16/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Studies in vertebrate genomics require sampling from a broad range of tissue types, taxa, and localities. Recent advancements in long-read and long-range genome sequencing have made it possible to produce high-quality chromosome-level genome assemblies for almost any organism. However, adequate tissue preservation for the requisite ultra-high molecular weight DNA (uHMW DNA) remains a major challenge. Here we present a comparative study of preservation methods for field and laboratory tissue sampling, across vertebrate classes and different tissue types. RESULTS We find that storage temperature was the strongest predictor of uHMW fragment lengths. While immediate flash-freezing remains the sample preservation gold standard, samples preserved in 95% EtOH or 20-25% DMSO-EDTA showed little fragment length degradation when stored at 4°C for 6 hours. Samples in 95% EtOH or 20-25% DMSO-EDTA kept at 4°C for 1 week after dissection still yielded adequate amounts of uHMW DNA for most applications. Tissue type was a significant predictor of total DNA yield but not fragment length. Preservation solution had a smaller but significant influence on both fragment length and DNA yield. CONCLUSION We provide sample preservation guidelines that ensure sufficient DNA integrity and amount required for use with long-read and long-range sequencing technologies across vertebrates. Our best practices generated the uHMW DNA needed for the high-quality reference genomes for phase 1 of the Vertebrate Genomes Project, whose ultimate mission is to generate chromosome-level reference genome assemblies of all ∼70,000 extant vertebrate species.
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Affiliation(s)
| | | | | | - Sylke Winkler
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Saxony 01307, Germany
| | - Iliana Bista
- Tree of Life Program, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
- Department of Genetics, University of Cambridge, Cambridge, Cambridgeshire CB2 3EH, UK
| | | | | | | | - Karen Oliver
- Tree of Life Program, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Michelle Smith
- Tree of Life Program, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Wenhua Tan
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Saxony 01307, Germany
| | - Anne Kraus
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Saxony 01307, Germany
| | - Stephen Mac
- Arima Genomics, Inc., San Diego, CA 92121, USA
| | - Lisa M Komoroske
- Department of Environmental Conservation, University of Massachusetts Amherst, Amherst, MA 01003-9285, USA
| | - Tanya Lama
- Department of Environmental Conservation, University of Massachusetts Amherst, Amherst, MA 01003-9285, USA
| | - Andrew J Crawford
- Department of Biological Sciences, Universidad de los Andes, Bogotá 111711, Colombia
| | - Robert W Murphy
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Samara Brown
- The Rockefeller University, New York, NY 10065, USA
| | - Alan F Scott
- Department of Medicine, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Phillip A Morin
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA 92037, USA
| | - Erich D Jarvis
- The Rockefeller University, New York, NY 10065, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Olivier Fedrigo
- Correspondence address. Olivier Fedrigo, Vertebrate Genome Laboratory, The Rockefeller University, 1230 York Avenue, Box 366, New York, NY 10065, USA. E-mail:
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12
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Tu F, Zhao L, Murphy RW, Zhai X, Wang J. Phylogeography of the Hong Kong Whipping Frog (<i>Polypedates megacephalus</i>) throughout Hainan Island, China. RUSS J HERPETOL 2022. [DOI: 10.30906/1026-2296-2022-29-3-137-148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The Hong Kong Whipping Frog (Polypedates megacephalus) is widespread on Hainan Island and yet nothing is known about its history. To investigate this, we use sequences of a partial fragment of mitochondrial ND1 and its flanking region from 248 individuals taken from 30 localities. Analyses reveal low genetic diversity and commonly shared haplotypes. Montane areas exhibit a significantly greater genetic diversity than lowland areas (P 0.01). The origin of P. megacephalus on Hainan Island dates to 1.06 Ma in the Pleistocene. Population expansion events were associated with the transition from the last interglacial period to the last glacial maximum. The matrilineal history indicates dispersal from the montane to the lowland. Bidirectional dispersion occurs between northeastern and southwestern parts of the island. Low FCT values for the northeastern and the southwestern areas associate with rivers, whereas the highest values occur among two geographical groups. Thus, mountains and rivers appear to have effected dispersal. Pleistocene climatic cooling and the creation of a landbridge with mainland China owing to lowered sea levels best explains the occurrence of P. megacephalus on Hainan Island. The analyses provide insights into the effects of Pleistocene climatic fluctuations on an amphibian on Hainan Island.
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13
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Gao W, Yu CX, Zhou WW, Zhang BL, Chambers EA, Dahn HA, Jin JQ, Murphy RW, Zhang YP, Che J. Species persistence with hybridization in toad-headed lizards driven by divergent selection and low recombination. Mol Biol Evol 2022; 39:6561330. [PMID: 35356979 PMCID: PMC9007161 DOI: 10.1093/molbev/msac064] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Speciation plays a central role in evolutionary studies, and particularly how reproductive isolation (RI) evolves. The origins and persistence of RI are distinct processes that require separate evaluations. Treating them separately clarifies the drivers of speciation and then it is possible to link the processes to understand large-scale patterns of diversity. Recent genomic studies have focused predominantly on how species or RI originate. However, we know little about how species persist in face of gene flow. Here, we evaluate a contact zone of two closely related toad-headed lizards (Phrynocephalus) using a chromosome-level genome assembly and population genomics. To some extent, recent asymmetric introgression from Phrynocephalus putjatai to P. vlangalii reduces their genomic differences. However, their highly divergent regions (HDRs) have heterogeneous distributions across the genomes. Functional gene annotation indicates that many genes within HDRs are involved in reproduction and RI. Compared with allopatric populations, contact areas exhibit recent divergent selection on the HDRs and a lower population recombination rate. Taken together, this implies that divergent selection and low genetic recombination help maintain RI. This study provides insights into the genomic mechanisms that drive RI and two species persistence in the face of gene flow during the late stage of speciation.
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Affiliation(s)
- 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, China
| | - Chuan-Xin 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, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Wei-Wei Zhou
- 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, China
| | - Bao-Lin Zhang
- 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, China
| | - E Anne Chambers
- Department of Integrative Biology and Biodiversity Center, University of Texas at Austin, Austin, USA.,Department of Environmental Science, Policy, and Management, Univerity of California, Berkeley, USA
| | - Hollis A Dahn
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Jie-Qiong 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, China
| | - Robert W Murphy
- 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, China.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada.,Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, Ontario, Canada
| | - Ya-Ping Zhang
- 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, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 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, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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14
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Yuan ZY, Wu YK, Yan F, Murphy RW, Papenfuss TJ, Wake DB, Zhang YP, Che J. Comparative multi-locus assessment of modern Asian newts (<i>Cynops</i>, <i>Paramesotriton</i>, and <i>Pachytriton</i>: Salamandridae) in southern China suggests a shared biogeographic history. Zool Res 2022; 43:706-718. [PMID: 35927393 PMCID: PMC9486527 DOI: 10.24272/j.issn.2095-8137.2022.080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- Zhi-Yong Yuan
- 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, Yunnan 650223, China
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Yun-Ke Wu
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca 14850, USA
| | - Fang Yan
- College of Life Science, Yunnan University, Kunming, Yunnan 650091, China
| | - Robert W Murphy
- 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, Yunnan 650223, China
- Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, Ontario M5S 2C6, Canada
| | | | - David B Wake
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
| | - Ya-Ping Zhang
- 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, Yunnan 650223, China. E-mail:
| | - 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, Yunnan 650223, China. E-mail:
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15
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Chai J, Lu CQ, Yi MR, Dai NH, Weng XD, Di MX, Peng Y, Tang Y, Shan QH, Wang K, Liu HZ, Zhao HP, Jin JQ, Cao RJ, Lu P, Luo LC, Murphy RW, Zhang YP, Che J. Discovery of a wild, genetically pure Chinese giant salamander creates new conservation opportunities. Zool Res 2022; 43:469-480. [PMID: 35514224 PMCID: PMC9113980 DOI: 10.24272/j.issn.2095-8137.2022.101] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Effective conservation of threatened biota relies on accurate assessments and scientific guidance. As an unfortunate example, Chinese giant salamanders (Andrias, CGS) remain critically endangered in nature. Misguided conservation efforts, e.g., commercial propagation and releasing of millions of likely non-indigenous or interspecific hybrids, have further compromised conservation initiatives. Limited information on wild populations of CGS poses a significant conservation challenge. Following 18-month long field monitoring, we now report the discovery of a wild population of CGS in a closed nature reserve in Jiangxi Province, China. Genomic assessments reveal its genetic distinctiveness and do not detect genetic admixture with other species. Based on morphological and molecular evidences, we describe this CGS as a new species Andrias jiangxiensissp. nov. This is the only known species of CGS today with a genetically pure, reproducing, in situ population. This discovery emphasizes the important role that closed nature reserves play in protecting species, and the necessity of integrating long-term field monitoring and genetic assessments. It sets a new pathway for discovering and conserving endangered species, especially for those biotas that are similarly being extirpated by anthropogenic translocations and overexploitation.
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Affiliation(s)
- Jing Chai
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Chen-Qi Lu
- State Key Laboratory of Genetic Resources and Evolution, 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
| | - Mu-Rong Yi
- State Key Laboratory of Genetic Resources and Evolution, 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
| | - Nian-Hua Dai
- Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, Jiangxi 330096, China
| | - Xiao-Dong Weng
- Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, Jiangxi 330096, China
| | - Ming-Xiao Di
- Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, Jiangxi 330096, China
| | - Yong Peng
- Jiangxi Jiulingshan National Nature Reserve, Jing'an, Jiangxi 330600, China
| | - Yong Tang
- Jiangxi Jiulingshan National Nature Reserve, Jing'an, Jiangxi 330600, China
| | - Qing-Hua Shan
- Jiangxi Jiulingshan National Nature Reserve, Jing'an, Jiangxi 330600, China
| | - Kai Wang
- Sam Noble Oklahoma Museum of Natural History & Department of Biology, University of Oklahoma, Norman 73072, USA
| | - Huan-Zhang Liu
- The Key Laboratory of Biodiversity and Conservation of Aquatic Organisms, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
| | - Hai-Peng Zhao
- School of Life Science, Henan University, Kaifeng, Henan 475001, China
| | - Jie-Qiong Jin
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Ru-Jun Cao
- State Key Laboratory of Genetic Resources and Evolution, 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
| | - Ping Lu
- Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, Jiangxi 330096, China
| | - Lai-Chun Luo
- Jing'an County Bureau of Agriculture and Rural Affairs, Jing'an, Jiangxi 330600, China
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, Ontario M5S 2C6, Canada. E-mail:
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China. E-mail:
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China. E-mail:
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16
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Smart U, Ingrasci MJ, Sarker GC, Lalremsanga H, Murphy RW, Ota H, Tu MC, Shouche Y, Orlov NL, Smith EN. A comprehensive appraisal of evolutionary diversity in venomous Asian coralsnakes of the genus
Sinomicrurus
(Serpentes: Elapidae) using Bayesian coalescent inference and supervised machine learning. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Utpal Smart
- Center for Human Identification University of North Texas Health Science Center Fort Worth Texas USA
- Department of Biology The Amphibian and Reptile Diversity Research Center The University of Texas at Arlington Arlington Texas USA
| | - Matthew J. Ingrasci
- Department of Biology The Amphibian and Reptile Diversity Research Center The University of Texas at Arlington Arlington Texas USA
| | - Goutam C. Sarker
- Department of Biology The Amphibian and Reptile Diversity Research Center The University of Texas at Arlington Arlington Texas USA
| | | | - Robert W. Murphy
- Royal Ontario Museum Centre for Biodiversity and Conservation Biology Toronto ON Canada
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Kunming China
| | - Hidetoshi Ota
- Institute of Natural and Environmental Sciences Museum of Nature and Human Activities University of Hyogo Sanda Japan
| | - Ming Chung Tu
- Department of Life Sciences National Taiwan Normal University Taipei City Taiwan
| | - Yogesh Shouche
- National Centre for Microbial ResourceNational Center for Cell Science Pune India
| | - Nikolai L. Orlov
- Zoological Institute Russian Academy of SciencesSaint Petersburg Russia
| | - Eric N. Smith
- Department of Biology The Amphibian and Reptile Diversity Research Center The University of Texas at Arlington Arlington Texas USA
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17
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Zhang T, Chen J, Zhang J, Guo YT, Zhou X, Li MW, Zheng ZZ, Zhang TZ, Murphy RW, Nevo E, Shi P. Phenotypic and genomic adaptations to the extremely high elevation in plateau zokor (Myospalax baileyi). Mol Ecol 2021; 30:5765-5779. [PMID: 34510615 DOI: 10.1111/mec.16174] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 08/07/2021] [Accepted: 08/31/2021] [Indexed: 12/31/2022]
Abstract
The evolutionary outcomes of high elevation adaptation have been extensively described. However, whether widely distributed high elevation endemic animals adopt uniform mechanisms during adaptation to different elevational environments remains unknown, especially with respect to extreme high elevation environments. To explore this, we analysed the phenotypic and genomic data of seven populations of plateau zokor (Myospalax baileyi) along elevations ranging from 2,700 to 4,300 m. Based on whole-genome sequencing data and demographic reconstruction of the evolutionary history, we show that two populations of plateau zokor living at elevations exceeding 3,700 m diverged from other populations nearly 10,000 years ago. Further, phenotypic comparisons reveal stress-dependent adaptation, as two populations living at elevations exceeding 3,700 m have elevated ratios of heart mass to body mass relative to other populations, and the highest population (4,300 m) displays alterations in erythrocytes. Correspondingly, genomic analysis of selective sweeps indicates that positive selection might contribute to the observed phenotypic alterations in these two extremely high elevation populations, with the adaptive cardiovascular phenotypes of both populations possibly evolving under the functional constrains of their common ancestral population. Taken together, phenotypic and genomic evidence demonstrates that heterogeneous stressors impact adaptations to extreme elevations and reveals stress-dependent and genetically constrained adaptation to hypoxia, collectively providing new insights into the high elevation adaptation.
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Affiliation(s)
- Tao Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Jie Chen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Jia Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yuan-Ting Guo
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Xin Zhou
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Meng-Wen Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Zhi-Zhong Zheng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Tong-Zuo Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, ON, Canada
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Peng Shi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,School of Future Technology, University of Chinese Academy of Sciences, Beijing, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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18
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Shen QK, Peng MS, Adeola AC, Kui L, Duan S, Miao YW, Eltayeb NM, Lichoti JK, Otecko NO, Strillacci MG, Gorla E, Bagnato A, Charles OS, Sanke OJ, Dawuda PM, Okeyoyin AO, Musina J, Njoroge P, Agwanda B, Kusza S, Nanaei HA, Pedar R, Xu MM, Du Y, Nneji LM, Murphy RW, Wang MS, Esmailizadeh A, Dong Y, Ommeh SC, Zhang YP. Erratum to: Genomic analyses unveil helmeted guinea fowl (Numida meleagris) domestication in West Africa. Genome Biol Evol 2021; 13:6355925. [PMID: 34417609 PMCID: PMC8379371 DOI: 10.1093/gbe/evab174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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19
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Yan F, Nneji LM, Jin JQ, Yuan ZY, Chen JM, Mi X, Chen HM, Murphy RW, Che J. Multi-locus genetic analyses of Quasipaa from throughout its distribution. Mol Phylogenet Evol 2021; 163:107218. [PMID: 34082130 DOI: 10.1016/j.ympev.2021.107218] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 02/24/2021] [Accepted: 05/27/2021] [Indexed: 11/16/2022]
Abstract
Montane frogs of the genus Quasipaa Dubois, 1992 occur from southern China to Southeast Asia (Frost 2021). Analyses of mtDNA (Cytb) and nuDNA data (Rag1, Rag2, Rhod, Tyr) for samples from 93 localities throughout its distribution yield a phylogeny. Clades A and B occur in Southeast Asia, clade C in northern Yangtze River, China, clade D in southwestern China, and clades E and F in southeastern China. Results place Q. yei within monophyletic Quasipaa and identify two new species. Based on nuDNA data, the basal split of clade A and B indicates an Indochinese origin of Quasipaa. The west-east diversification of five species across South China (Q. spinosa, Q. exilispinosa, Q. jiulongensis, Q. shini, Q. boulengeri) corresponds to topographic terrains II and III of China. Divergence of species from southeastern China (Q. shini, Q. jiulongensis, Q. spinosa, Q. exilispinosa) and southwestern China (Q. boulengeri) dates to 15.30-16.56 Ma (million years ago). A principal component analysis (PCA) and t-test involving 19 bioclimatic variables identifies significantly different environmental conditions between the two regions. Species' distribution models (SDM) for Q. spinosa and Q. boulengeri identify the best areas to be eastern and western South China, respectively. Thus, environmental variation appears to have influenced the genetic divergence and distributions of Quasipaa in South China. Mito-nuclear discordance indicates that some individuals of Q. exilispinosa and Q. spinosa hybridized historically.
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Affiliation(s)
- Fang Yan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Lotanna M Nneji
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Jie-Qiong Jin
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Zhi-Yong Yuan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; College of Forestry, Southwest Forestry University, Kunming 650224, Yunnan, China
| | - Jin-Min Chen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Xue Mi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Hong-Man Chen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, 100 Queen's Park, Toronto, Ontario M5S 2C6, Canada
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
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20
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Lam NQ, Thu TTA, Nguyen LT, Murphy RW, Nguyen SN. A new species of Ahaetulla Link, 1807 (Squamata: Colubridae) from the Mekong Delta, Vietnam. Zootaxa 2021; 4966:290304. [PMID: 34186616 DOI: 10.11646/zootaxa.4966.3.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Indexed: 11/04/2022]
Abstract
A new vine snake, genus Ahaetulla, from Soc Trang Province, southern Vietnam is described based on morphological data and nucleotide sequences from COI and Cytb. Ahaetulla rufusoculara sp. nov. is diagnosed by the following morphological characters: bright red eyes; snout without dermal appendage; internasal separated from supralabial by loreal; body scale rows 15-15-13; ventrals 186190 in males and 182185 in females; subcaudals 143153 in males and 128 or 129 in females; 8 (rarely 9) supralabials, fourth and fifth or fourth to sixth entering orbit; 1214 maxillary teeth; hemipenis short, reaching 6th or 7th SC; cloacal plate divided; dorsum bright green; and yellow or white stripe along the lower flank. The new species differs from its congeners by an uncorrected p-distance in COI and Cytb sequences of at least 7.7% and 7.5%, respectively.
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Affiliation(s)
- Ngon Quang Lam
- Indo-Myanmar Conservation, No. 1806, C14 Bac Ha Building, To Huu St., Tu Liem Dist., Hanoi, Vietnam..
| | - Tran Thi Anh Thu
- Can Tho University, 3/2 St., Ninh Kieu Dist., Can Tho, Vietnam..
| | - Luan Thanh Nguyen
- Indo-Myanmar Conservation, No. 1806, C14 Bac Ha Building, To Huu St., Tu Liem Dist., Hanoi, Vietnam..
| | - Robert W Murphy
- Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, 100 Queen's Park, Toronto, Canada M5S 2C6..
| | - Sang Ngoc Nguyen
- Institute of Tropical Biology, Vietnam Academy of Science and Technology, 85 Tran Quoc Toan St., Dist. 3, Ho Chi Minh City, Vietnam..
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21
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Nguyen VDH, Nguyen LT, Orlov NL, Murphy RW, Nguyen SN. Gekko phuyenensis sp. nov. (Squamata: Gekkonidae), a new species from southern Vietnam. Zootaxa 2021; 4966:175186. [PMID: 34186624 DOI: 10.11646/zootaxa.4966.2.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Indexed: 11/04/2022]
Abstract
A new species of the genus Gekko Laurenti, 1768 is described from Phu Yen Province, southern Vietnam based on morphological and molecular evidence. Gekko phuyenensis sp. nov. differs from other congeners by its moderate size, with a snout-vent length of 90.292.8 mm; nares in contact with rostral; internasal 1; interorbitals 35 or 36; ventrals 3032; dorsal tubercle rows 9 or 10; precloacal pores 12 or 13 in males and precloacal pits 13 in female; subdigital lamellae under first finger 1821, fourth finger 19 or 20, first toe 1820, and fourth toe 2123; subcaudals median enlarged; no webbing between toes; and the absence of tubercles on hind limbs. Molecular phylogenetic analyses of mitochondrial gene COI (681 bp) using the geckos from Phu Yen and its congeners in southern Vietnam resolve the new species as the sister lineage to G. cf. grossmanni from Khanh Hoa Province. Genetic distances between G. phuyenensis sp. nov. and its congeners in southern Vietnam range from 16.924.2%. The discovery of this new species raises the number of known species of Gekko in Vietnam to 14.
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Affiliation(s)
- Vu Dang Hoang Nguyen
- Institute of Tropical Biology, Vietnam Academy of Science and Technology, 85 Tran Quoc Toan St., Dist. 3, Ho Chi Minh City, Department of Biology, Ho Chi Minh City University of Education, 280 An Duong Vuong St., Dist. 5, Ho Chi Minh City, Vietnam.
| | - Luan Thanh Nguyen
- Asian Turtle Program Indo-Myanmar Conservation, R.1806, 18th F., CT1 Bac Ha C14 Building To Huu St., Nam Tu Liem Dist., Ha Noi, Vietnam..
| | - Nikolai L Orlov
- Zoological Institute, Russian Academy of Sciences, Universitetskaya nab. 1, St. Petersburg 199034, Russia..
| | - Robert W Murphy
- Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, 100 Queen's Park, Toronto, Canada..
| | - Sang Ngoc Nguyen
- Institute of Tropical Biology, Vietnam Academy of Science and Technology, 85 Tran Quoc Toan St., Dist. 3, Ho Chi Minh City, Vietnam..
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22
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Shen QK, Peng MS, Adeola AC, Kui L, Duan S, Miao YW, Eltayeb NM, Lichoti JK, Otecko NO, Strillacci MG, Gorla E, Bagnato A, Charles OS, Sanke OJ, Dawuda PM, Okeyoyin AO, Musina J, Njoroge P, Agwanda B, Kusza S, Nanaei HA, Pedar R, Xu MM, Du Y, Nneji LM, Murphy RW, Wang MS, Esmailizadeh A, Dong Y, Ommeh SC, Zhang YP. Genomic Analyses of Unveil Helmeted Guinea Fowl (Numida meleagris) Domestication in West Africa. Genome Biol Evol 2021; 13:6261762. [PMID: 34009300 PMCID: PMC8214406 DOI: 10.1093/gbe/evab090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2021] [Indexed: 12/22/2022] Open
Abstract
Domestication of the helmeted guinea fowl (HGF; Numida meleagris) in Africa remains elusive. Here we report a high-quality de novo genome assembly for domestic HGF generated by long- and short-reads sequencing together with optical and chromatin interaction mapping. Using this assembly as the reference, we performed population genomic analyses for newly sequenced whole-genomes for 129 birds from Africa, Asia, and Europe, including domestic animals (n = 89), wild progenitors (n = 34), and their closely related wild species (n = 6). Our results reveal domestication of HGF in West Africa around 1,300-5,500 years ago. Scanning for selective signals characterized the functional genes in behavior and locomotion changes involved in domestication of HGF. The pleiotropy and linkage in genes affecting plumage color and fertility were revealed in the recent breeding of Italian domestic HGF. In addition to presenting a missing piece to the jigsaw puzzle of domestication in poultry, our study provides valuable genetic resources for researchers and breeders to improve production in this species.
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Affiliation(s)
- Quan-Kuan Shen
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Nairobi, Kenya.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Nairobi, Kenya.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Adeniyi C Adeola
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Nairobi, Kenya.,Centre for Biotechnology Research, Bayero University, Kano, Nigeria
| | - Ling Kui
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Yong-Wang Miao
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Nada M Eltayeb
- Department of Animal breeding and Reproduction Technology, College of Animal Production, University of Bahri, Khartoum, Sudan
| | - Jacqueline K Lichoti
- State Department of Livestock, Ministry of Agriculture Livestock Fisheries and Irrigation, Nairobi, Kenya
| | - Newton O Otecko
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Nairobi, Kenya.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | | | - Erica Gorla
- Department of Veterinary Medicine, Università degli Studi di Milano, Italy
| | - Alessandro Bagnato
- Department of Veterinary Medicine, Università degli Studi di Milano, Italy
| | | | - Oscar J Sanke
- Taraba State Ministry of Agriculture and Natural Resources, Jalingo, Nigeria
| | - Philip M Dawuda
- Department of Veterinary Surgery and Theriogenology, College of Veterinary Medicine, University of Agriculture, Makurdi, Nigeria
| | - Agboola O Okeyoyin
- National Park Service Headquarter, Federal Capital Territory, Abuja, Nigeria
| | - John Musina
- Department of Zoology, National Museums of Kenya, Nairobi, Kenya
| | - Peter Njoroge
- Department of Zoology, National Museums of Kenya, Nairobi, Kenya
| | - Bernard Agwanda
- Department of Zoology, National Museums of Kenya, Nairobi, Kenya
| | - Szilvia Kusza
- Centre for Agricultural Genomics and Biotechnology, University of Debrecen, Debrecen, Hungary
| | | | - Rana Pedar
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Iran
| | - Ming-Min Xu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Nairobi, Kenya.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Yuan Du
- Nowbio Biotechnology Company, Kunming, China
| | - Lotanna M Nneji
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Nairobi, Kenya
| | - Robert W Murphy
- Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, Ontario, Canada
| | - Ming-Shan Wang
- Howard Hughes Medical Institute, University of California Santa Cruz, California, USA.,Department of Ecology and Evolutionary Biology, University of California Santa Cruz, California, USA
| | - Ali Esmailizadeh
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Iran
| | - Yang Dong
- College of Biological Big Data, Yunnan Agriculture University, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China.,Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Sheila C Ommeh
- Department of Zoology, National Museums of Kenya, Nairobi, Kenya.,Institute of Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Nairobi, Kenya.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Yunnan University, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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23
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Ramírez‐Reyes T, Flores‐Villela O, Piñero D, Lathrop A, Murphy RW. Genomic assessment of the
Phyllodactylus tuberculosus
complex (Reptilia: Phyllodactylidae) in America. ZOOL SCR 2021. [DOI: 10.1111/zsc.12492] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tonatiuh Ramírez‐Reyes
- Posgrado en Ciencias Biológicas Universidad Nacional Autónoma de México México City México
- Museo de Zoología Facultad de Ciencias Universidad Nacional Autónoma de Méxic México City México
- Departamento de Ecología Evolutiva Instituto de EcologíaUniversidad Nacional Autónoma de México México City México
| | - Oscar Flores‐Villela
- Museo de Zoología Facultad de Ciencias Universidad Nacional Autónoma de Méxic México City México
| | - Daniel Piñero
- Departamento de Ecología Evolutiva Instituto de EcologíaUniversidad Nacional Autónoma de México México City México
| | - Amy Lathrop
- Centre for Biodiversity and Conservation Biology Royal Ontario Museum Toronto ON Canada
| | - Robert W. Murphy
- Centre for Biodiversity and Conservation Biology Royal Ontario Museum Toronto ON Canada
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24
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LE MVAN, Nguyen VDH, Phan HT, Rujirawan A, Aowphol A, Vo TDH, Murphy RW, Nguyen SN. A new skink of the genus emSubdoluseps/em Freitas, Datta-Roy, Karanth, Grismer amp; Siler, 2019 (Squamata: Scincidae) from southern Vietnam. Zootaxa 2021; 4952:zootaxa.4952.2.3. [PMID: 33903367 DOI: 10.11646/zootaxa.4952.2.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Indexed: 11/04/2022]
Abstract
We describe a new species of the genus Subdoluseps Freitas, Datta-Roy, Karanth, Grismer Siler from a coastal area in southern Vietnam. Subdoluseps vietnamensis sp. nov. is characterized by the following morphological characters: medium size in adults (snout-vent length up to 48.7 mm); tail length/snout-vent length ratio 1.04; toes not reaching finger when limbs adpressed; 27-30 midbody scale rows, smooth; 55-57 paravertebral scales; 55-62 ventral scale rows; 64-74 subcaudal scales; frontoparietal scale single; four supraoculars; prefrontals not in contact with one another; two loreal scales; seven supralabials; ear-opening with two lobules on the anterior border; smooth lamellae beneath finger III 9 or 10 and toe IV 12-15; six enlarged precloacal scales; and four distinct black stripes on dorsum. The new species differs genetically from its closest congeners, S. bowringii (Günther) and S. frontoparietale (Taylor), by uncorrected p-distances of 10.0% and 9.5%, respectively in ND1 sequences, and clusters into the same matriline with these two congeners on the phylogenetic trees.
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Affiliation(s)
- Manh VAN LE
- University of Science and Education, University of Danang, 459 Ton Duc Thang St., Lien Chieu District, Danang City, Vietnam..
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25
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Peng C, Ren JL, Deng C, Jiang D, Wang J, Qu J, Chang J, Yan C, Jiang K, Murphy RW, Wu DD, Li JT. The Genome of Shaw's Sea Snake (Hydrophis curtus) Reveals Secondary Adaptation to Its Marine Environment. Mol Biol Evol 2021; 37:1744-1760. [PMID: 32077944 DOI: 10.1093/molbev/msaa043] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The transition of terrestrial snakes to marine life ∼10 Ma is ideal for exploring adaptive evolution. Sea snakes possess phenotype specializations including laterally compressed bodies, paddle-shaped tails, valvular nostrils, cutaneous respiration, elongated lungs, and salt glands, yet, knowledge on the genetic underpinnings of the transition remains limited. Herein, we report the first genome of Shaw's sea snake (Hydrophis curtus) and use it to investigate sea snake secondary marine adaptation. A hybrid assembly strategy obtains a high-quality genome. Gene family analyses date a pulsed coding-gene expansion to ∼20 Ma, and these genes associate strongly with adaptations to marine environments. Analyses of selection pressure and convergent evolution discover the rapid evolution of protein-coding genes, and some convergent features. Additionally, 108 conserved noncoding elements appear to have evolved quickly, and these may underpin the phenotypic changes. Transposon elements may contribute to adaptive specializations by inserting into genomic regions around functionally related coding genes. The integration of genomic and transcriptomic analyses indicates independent origins and different components in sea snake and terrestrial snake venom; the venom gland of the sea snake harbors the highest PLA2 (17.23%) expression in selected elapids and these genes may organize tandemly in the genome. These analyses provide insights into the genetic mechanisms that underlay the secondary adaptation to marine and venom production of this sea snake.
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Affiliation(s)
- Changjun Peng
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Jin-Long Ren
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Cao Deng
- Department of Bioinformatics, DNA Stories Bioinformatics Center, Chengdu, China
| | - Dechun Jiang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Jichao Wang
- College of Life Sciences, Hainan Normal University, Haikou, Hainan, China
| | - Jiangyong Qu
- College of Life Sciences, Yantai University, Yantai, Shandong, China
| | - Jiang Chang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Chaochao Yan
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Ke Jiang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Robert W Murphy
- Center for Biodiversity, Royal Ontario Museum, Toronto, Ontario, Canada
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Jia-Tang Li
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China.,University of Chinese Academy of Sciences, Beijing, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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26
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Rhie A, McCarthy SA, Fedrigo O, Damas J, Formenti G, Koren S, Uliano-Silva M, Chow W, Fungtammasan A, Kim J, Lee C, Ko BJ, Chaisson M, Gedman GL, Cantin LJ, Thibaud-Nissen F, Haggerty L, Bista I, Smith M, Haase B, Mountcastle J, Winkler S, Paez S, Howard J, Vernes SC, Lama TM, Grutzner F, Warren WC, Balakrishnan CN, Burt D, George JM, Biegler MT, Iorns D, Digby A, Eason D, Robertson B, Edwards T, Wilkinson M, Turner G, Meyer A, Kautt AF, Franchini P, Detrich HW, Svardal H, Wagner M, Naylor GJP, Pippel M, Malinsky M, Mooney M, Simbirsky M, Hannigan BT, Pesout T, Houck M, Misuraca A, Kingan SB, Hall R, Kronenberg Z, Sović I, Dunn C, Ning Z, Hastie A, Lee J, Selvaraj S, Green RE, Putnam NH, Gut I, Ghurye J, Garrison E, Sims Y, Collins J, Pelan S, Torrance J, Tracey A, Wood J, Dagnew RE, Guan D, London SE, Clayton DF, Mello CV, Friedrich SR, Lovell PV, Osipova E, Al-Ajli FO, Secomandi S, Kim H, Theofanopoulou C, Hiller M, Zhou Y, Harris RS, Makova KD, Medvedev P, Hoffman J, Masterson P, Clark K, Martin F, Howe K, Flicek P, Walenz BP, Kwak W, Clawson H, Diekhans M, Nassar L, Paten B, Kraus RHS, Crawford AJ, Gilbert MTP, Zhang G, Venkatesh B, Murphy RW, Koepfli KP, Shapiro B, Johnson WE, Di Palma F, Marques-Bonet T, Teeling EC, Warnow T, Graves JM, Ryder OA, Haussler D, O'Brien SJ, Korlach J, Lewin HA, Howe K, Myers EW, Durbin R, Phillippy AM, Jarvis ED. Towards complete and error-free genome assemblies of all vertebrate species. Nature 2021; 592:737-746. [PMID: 33911273 PMCID: PMC8081667 DOI: 10.1038/s41586-021-03451-0] [Citation(s) in RCA: 591] [Impact Index Per Article: 197.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 03/12/2021] [Indexed: 02/02/2023]
Abstract
High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species1-4. To address this issue, the international Genome 10K (G10K) consortium5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences.
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Affiliation(s)
- Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Shane A McCarthy
- Department of Genetics, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Cambridge, UK
| | - Olivier Fedrigo
- Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA
| | - Joana Damas
- The Genome Center, University of California Davis, Davis, CA, USA
| | - Giulio Formenti
- Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Marcela Uliano-Silva
- Leibniz Institute for Zoo and Wildlife Research, Department of Evolutionary Genetics, Berlin, Germany
- Berlin Center for Genomics in Biodiversity Research, Berlin, Germany
| | | | | | - Juwan Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Chul Lee
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Byung June Ko
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Mark Chaisson
- University of Southern California, Los Angeles, CA, USA
| | - Gregory L Gedman
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
| | - Lindsey J Cantin
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
| | - Francoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, USA
| | - Leanne Haggerty
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Iliana Bista
- Department of Genetics, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Cambridge, UK
| | | | - Bettina Haase
- Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA
| | | | - Sylke Winkler
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- DRESDEN-concept Genome Center, Dresden, Germany
| | - Sadye Paez
- Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
| | | | - Sonja C Vernes
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
- School of Biology, University of St Andrews, St Andrews, UK
| | - Tanya M Lama
- University of Massachusetts Cooperative Fish and Wildlife Research Unit, Amherst, MA, USA
| | - Frank Grutzner
- School of Biological Science, The Environment Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Wesley C Warren
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | | | - Dave Burt
- UQ Genomics, University of Queensland, Brisbane, Queensland, Australia
| | - Julia M George
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
| | - Matthew T Biegler
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
| | - David Iorns
- The Genetic Rescue Foundation, Wellington, New Zealand
| | - Andrew Digby
- Kākāpō Recovery, Department of Conservation, Invercargill, New Zealand
| | - Daryl Eason
- Kākāpō Recovery, Department of Conservation, Invercargill, New Zealand
| | - Bruce Robertson
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | | | - Mark Wilkinson
- Department of Life Sciences, Natural History Museum, London, UK
| | - George Turner
- School of Natural Sciences, Bangor University, Gwynedd, UK
| | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Andreas F Kautt
- Department of Biology, University of Konstanz, Konstanz, Germany
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Paolo Franchini
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - H William Detrich
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, MA, USA
| | - Hannes Svardal
- Department of Biology, University of Antwerp, Antwerp, Belgium
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Maximilian Wagner
- Institute of Biology, Karl-Franzens University of Graz, Graz, Austria
| | - Gavin J P Naylor
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Martin Pippel
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology, Dresden, Germany
| | - Milan Malinsky
- Wellcome Sanger Institute, Cambridge, UK
- Zoological Institute, University of Basel, Basel, Switzerland
| | | | | | | | - Trevor Pesout
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | | | | | | | | | | | - Ivan Sović
- Pacific Biosciences, Menlo Park, CA, USA
- Digital BioLogic, Ivanić-Grad, Croatia
| | | | - Zemin Ning
- Wellcome Sanger Institute, Cambridge, UK
| | | | - Joyce Lee
- Bionano Genomics, San Diego, CA, USA
| | | | - Richard E Green
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
- Dovetail Genomics, Santa Cruz, CA, USA
| | | | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Jay Ghurye
- Dovetail Genomics, Santa Cruz, CA, USA
- Department of Computer Science, University of Maryland College Park, College Park, MD, USA
| | - Erik Garrison
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Ying Sims
- Wellcome Sanger Institute, Cambridge, UK
| | | | | | | | | | | | | | - Dengfeng Guan
- Department of Genetics, University of Cambridge, Cambridge, UK
- School of Computer Science and Technology, Center for Bioinformatics, Harbin Institute of Technology, Harbin, China
| | - Sarah E London
- Department of Psychology, Institute for Mind and Biology, University of Chicago, Chicago, IL, USA
| | - David F Clayton
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA
| | - Claudio V Mello
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, USA
| | - Samantha R Friedrich
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, USA
| | - Peter V Lovell
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, USA
| | - Ekaterina Osipova
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology, Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Farooq O Al-Ajli
- Monash University Malaysia Genomics Facility, School of Science, Selangor Darul Ehsan, Malaysia
- Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia, Selangor Darul Ehsan, Malaysia
- Qatar Falcon Genome Project, Doha, Qatar
| | | | - Heebal Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- eGnome, Inc., Seoul, Republic of Korea
| | | | - Michael Hiller
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt, Germany
- Senckenberg Research Institute, Frankfurt, Germany
- Goethe-University, Faculty of Biosciences, Frankfurt, Germany
| | | | - Robert S Harris
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Kateryna D Makova
- Department of Biology, Pennsylvania State University, University Park, PA, USA
- Center for Medical Genomics, Pennsylvania State University, University Park, PA, USA
- Center for Computational Biology and Bioinformatics, Pennsylvania State University, University Park, PA, USA
| | - Paul Medvedev
- Center for Medical Genomics, Pennsylvania State University, University Park, PA, USA
- Center for Computational Biology and Bioinformatics, Pennsylvania State University, University Park, PA, USA
- Department of Computer Science and Engineering, Pennsylvania State University, University Park, PA, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Jinna Hoffman
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, USA
| | - Patrick Masterson
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, USA
| | - Karen Clark
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, USA
| | - Fergal Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Kevin Howe
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Brian P Walenz
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Woori Kwak
- eGnome, Inc., Seoul, Republic of Korea
- Hoonygen, Seoul, Korea
| | - Hiram Clawson
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Mark Diekhans
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Luis Nassar
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Robert H S Kraus
- Department of Biology, University of Konstanz, Konstanz, Germany
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany
| | - Andrew J Crawford
- Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, NTNU, Trondheim, Norway
| | - Guojie Zhang
- China National Genebank, BGI-Shenzhen, Shenzhen, China
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Byrappa Venkatesh
- Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore, Singapore
| | - Robert W Murphy
- Centre for Biodiversity, Royal Ontario Museum, Toronto, Ontario, Canada
| | - Klaus-Peter Koepfli
- Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Washington, DC, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Warren E Johnson
- Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Washington, DC, USA
- The Walter Reed Biosystematics Unit, Museum Support Center MRC-534, Smithsonian Institution, Suitland, MD, USA
- Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Federica Di Palma
- Department of Biological Sciences, Earlham Institute, University of East Anglia, Norwich, UK
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Emma C Teeling
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Tandy Warnow
- Department of Computer Science, The University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | - Oliver A Ryder
- San Diego Zoo Global, Escondido, CA, USA
- Department of Evolution, Behavior, and Ecology, University of California San Diego, La Jolla, CA, USA
| | - David Haussler
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Stephen J O'Brien
- Laboratory of Genomics Diversity-Center for Computer Technologies, ITMO University, St. Petersburg, Russian Federation
- Guy Harvey Oceanographic Center, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale, FL, USA
| | | | - Harris A Lewin
- The Genome Center, University of California Davis, Davis, CA, USA
- Department of Evolution and Ecology, University of California Davis, Davis, CA, USA
- John Muir Institute for the Environment, University of California Davis, Davis, CA, USA
| | | | - Eugene W Myers
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
- Center for Systems Biology, Dresden, Germany.
- Faculty of Computer Science, Technical University Dresden, Dresden, Germany.
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Cambridge, UK.
- Wellcome Sanger Institute, Cambridge, UK.
| | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Erich D Jarvis
- Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA.
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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27
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Borzée A, Kielgast J, Wren S, Angulo A, Chen S, Magellan K, Messenger KR, Hansen-Hendrikx CM, Baker A, Santos MMD, Kusrini M, Jiang J, Maslova IV, Das I, Park D, Bickford D, Murphy RW, Che J, Van Do T, Nguyen TQ, Chuang MF, Bishop PJ. Using the 2020 global pandemic as a springboard to highlight the need for amphibian conservation in eastern Asia. Biol Conserv 2021; 255:108973. [PMID: 35125500 PMCID: PMC8798316 DOI: 10.1016/j.biocon.2021.108973] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 12/28/2020] [Accepted: 01/11/2021] [Indexed: 05/26/2023]
Abstract
UNLABELLED Emerging infectious diseases are on the rise in many different taxa, including, among others, the amphibian batrachochytrids, the snake fungal disease and the Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) virus, responsible for Coronavirus disease 2019 (COVID-19) in mammals. Following the onset of the pandemic linked to COVID-19, eastern Asia has shown strong leadership, taking actions to regulate the trade of potential vector species in several regions. These actions were taken in response to an increase in public awareness, and the need for a quick reaction to mitigate against further pandemics. However, trade restrictions rarely affect amphibians, despite the risk of pathogen transmission, directly, or indirectly through habitat destruction and the loss of vector consumption. Thus, species that help alleviate the risk of zoonoses or provide biological control are not protected. Hence, in view of the global amphibian decline and the risk of zoonoses, we support the current wildlife trade regulations and support measures to safeguard wildlife from overexploitation. The current period of regulation overhaul should be used as a springboard for amphibian conservation. To mitigate risks, we suggest the following stipulations specifically for amphibians. I) Restrictions to amphibian farming in eastern Asia, in relation to pathogen transmission and the establishment of invasive species. II) Regulation of the amphibian pet trade, with a focus on potential vector species. III) Expansion of the wildlife trade ban, to limit the wildlife-human-pet interface. The resulting actions will benefit both human and wildlife populations, as they will lead to a decrease in the risk of zoonoses and better protection of the environment. SIGNIFICANCE STATEMENT There is an increasing number of emerging infectious diseases impacting all species, including amphibians, reptiles and mammals. The latest threat to humans is the virus responsible for COVID-19, and the resulting pandemic. Countries in eastern Asia have taken steps to regulate wildlife trade and prevent further zoonoses thereby decreasing the risk of pathogens arising from wild species. However, as amphibians are generally excluded from regulations we support specific trade restrictions: I) Restrictions to amphibian farming; II) regulation of the amphibian pet trade; III) expansion of the wildlife trade ban. These restrictions will benefit both human and wildlife populations by decreasing the risks of zoonoses and better protecting the environment.
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Affiliation(s)
- Amaël Borzée
- Laboratory of Animal Behaviour and Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, People's Republic of China
- IUCN SSC Amphibian Specialist Group, 3701 Lake Shore Blvd W, P.O. Box 48586, Toronto, Ontario M8W 1P5, Canada
| | - Jos Kielgast
- IUCN SSC Amphibian Specialist Group, 3701 Lake Shore Blvd W, P.O. Box 48586, Toronto, Ontario M8W 1P5, Canada
- Section for Freshwater Biology, Department of Biology, University of Copenhagen, Universitetsparken 4, DK-2100, Denmark
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, Universitetsparken, 15, DK-2100, Denmark
| | - Sally Wren
- IUCN SSC Amphibian Specialist Group, 3701 Lake Shore Blvd W, P.O. Box 48586, Toronto, Ontario M8W 1P5, Canada
- Department of Zoology, University of Otago, 340 Great King Street, Dunedin 9016, New Zealand
| | - Ariadne Angulo
- IUCN SSC Amphibian Specialist Group, 3701 Lake Shore Blvd W, P.O. Box 48586, Toronto, Ontario M8W 1P5, Canada
| | - Shu Chen
- Zoological Society of London, London NW1 4RY, United Kingdom
| | | | - Kevin R Messenger
- Herpetology and Applied Conservation Laboratory, College of Biology and the Environment, Nanjing Forestry University, Nanjing, People's Republic of China
| | | | - Anne Baker
- Amphibian Ark, Conservation Planning Specialist Group, Apple Valley, USA
| | - Marcileida M Dos Santos
- IUCN SSC Amphibian Specialist Group, 3701 Lake Shore Blvd W, P.O. Box 48586, Toronto, Ontario M8W 1P5, Canada
- Department of Zoology, University of Otago, 340 Great King Street, Dunedin 9016, New Zealand
| | - Mirza Kusrini
- Department of Forest Resources Conservation and Ecotourism, IPB University, Bogor, Indonesia
| | - Jianping Jiang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, People's Republic of China
| | - Irina V Maslova
- Federal Scientific Center of the East Asia Terrestrial Biodiversity Far Eastern Branch of Russian Academy of Sciences, Vladivostok 690022, Russia
| | - Indraneil Das
- Institute of Biodiversity and Environmental Conservation, Universiti Malaysia Sarawak, Kota Samarahan 94300, Malaysia
| | - Daesik Park
- Division of Science Education, Kangwon National University, Chuncheon, Kangwon 24341, Republic of Korea
| | | | - Robert W Murphy
- Centre for Biodiversity, Royal Ontario Museum, Toronto, Canada
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, People's Republic of China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, People's Republic of China
| | - Tu Van Do
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Viet Nam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Viet Nam
| | - Truong Quang Nguyen
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Viet Nam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Viet Nam
| | - Ming-Feng Chuang
- Department of Life Sciences and Research Center for Global Change Biology, National Chung Hsing University, Taichung, Taiwan
| | - Phillip J Bishop
- IUCN SSC Amphibian Specialist Group, 3701 Lake Shore Blvd W, P.O. Box 48586, Toronto, Ontario M8W 1P5, Canada
- Department of Zoology, University of Otago, 340 Great King Street, Dunedin 9016, New Zealand
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Nguyen SN, Nguyen VDH, Nguyen LT, Murphy RW. A new skink of the genus Scincella Mittleman, 1950 (Squamata: Scincidae) from southern Vietnam. Zootaxa 2020; 4868:zootaxa.4868.3.6. [PMID: 33311393 DOI: 10.11646/zootaxa.4868.3.6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Indexed: 11/04/2022]
Abstract
A new skink of the genus Scincella Mittleman, 1950, from Binh Phuoc Province, southern Vietnam is described based on morphological data, including hemipenial characters, and nucleotide sequences from COI. The following morphological characters diagnose Scincella baraensis sp. nov.: relatively small size in adults (snout-vent length up to 49.2 mm); when limbs adpressed, toes do not or just reach fingers; 30 smooth midbody scale rows and dorsal scales not enlarged; 66-70 paravertebral scales; 64-66 ventral scale rows; 7 supralabials, the fifth and sixth below the center of the eye; enlarged temporal scales 1+2; nuchals present; ear with small auricular lobules; 18-20 smooth lamellae beneath toe IV; hemipenis smooth, short, and unforked; dorsum with faint black dots. The new species differs from its congeners by an uncorrected p-distance in COI sequences of at least 16.2%.
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Affiliation(s)
- Sang Ngoc Nguyen
- Institute of Tropical Biology, Vietnam Academy of Science and Technology, 85 Tran Quoc Toan St., Dist. 3, Ho Chi Minh City, Vietnam. Faculty of Environmental and Food Engineering, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam.
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Lovich JE, Edwards T, Berry KH, Puffer SR, Cummings KL, Ennen JR, Agha M, Woodard R, Brundige KD, Murphy RW. Refining genetic boundaries for Agassiz’s desert tortoise (Gopherus agassizii) in the western Sonoran Desert: the influence of the Coachella Valley on gene flow among populations in southern California. Frontiers of Biogeography 2020. [DOI: 10.21425/f5fbg46888] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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Ananjeva NB, Ermakov OA, Nguyen SN, Nguyen TT, Murphy RW, Lukonina SA, Orlov NL. A New Species of Acanthosaura Gray, 1831 (Squamata: Agamidae) from Central Highlands, Vietnam. RUSS J HERPETOL 2020. [DOI: 10.30906/1026-2296-2020-27-4-217-230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Herein, we describe a new agamid species of the genus Acanthosaura from Central Highlands of Vietnam: Gia Lai Province, Kon Chu Rang NR, and Kon Tum Province: Kon Plông and Ngoc Linh Mountain based on morphological and molecular data. Acanthosaura prasina sp. nov. is distinguished from all congeners by a combination of the following morphological characters. Acanthosaura prasina sp. nov. differs from A. capra, A. murphyi, and A. nataliae by the presence of a short spine on each side of the neck and a smaller body size. From the known species of «lepidogaster» complex and A. coronata it differs in the arrangement of dorsal crests with a distinct double row of vertebral scales, from A. brachypoda in a smaller body size, longer tail and limbs, fewer supra- and infralabials and coloration patterns with a white area on lips and shoulders; from A. lepidogaster by lacking a dark marking on the nape and the absence of a distinct diastema; from A. phongdienensis by lacking a dark marking on the nape. We provide a cyt b-based estimation of diversity of the genus Acanthosaura. A. prasina sp. nov. differs from A. phongdiensis, A. coronata, A. lepidogaster, A. armata, A. crucigera, A. nataliae, A. phuketensis, and Acanthosaura sp. SK in p-distances of 15.4, 24.5, 14.7, 14.6, 16.3, 14.6, 15.4, and 24.4%, respectively. The new species currently known from three localities from Central Highlands was recorded from 800 to 1700 m a.s.l. in the evergreen polydominant forests in the mountainous regions of Gia Lai and Kon Tum provinces. This is the 16th species of Acanthosaura and the ninth species of the genus from Vietnam.
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31
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Sánchez-Pacheco SJ, Kong S, Pulido-Santacruz P, Murphy RW, Kubatko L. Median-joining network analysis of SARS-CoV-2 genomes is neither phylogenetic nor evolutionary. Proc Natl Acad Sci U S A 2020; 117:12518-12519. [PMID: 32381733 PMCID: PMC7293637 DOI: 10.1073/pnas.2007062117] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
| | - Sungsik Kong
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH 43210;
| | - Paola Pulido-Santacruz
- Programa Ciencias de la Biodiversidad, Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Bogotá, 111311, Colombia
| | - Robert W Murphy
- Centre for Biodiversity, Royal Ontario Museum, Toronto, ON M5S 2C6, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
| | - Laura Kubatko
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH 43210
- Department of Statistics, The Ohio State University, Columbus, OH 43210
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Vergun AA, Girnyk AE, Korchagin VI, Semyenova SK, Arakelyan MS, Danielyan FD, Murphy RW, Ryskov AP. Origin, clonal diversity, and evolution of the parthenogenetic lizard Darevskia unisexualis. BMC Genomics 2020; 21:351. [PMID: 32393253 PMCID: PMC7216553 DOI: 10.1186/s12864-020-6759-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 04/28/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The hybridization of female D. raddei and male D. valentini gave rise to the parthenogenetic Caucasian rock lizard Darevskia unisexualis. A previously identified genetic polymorphism in the species consisted of one common and two allozyme clones. Analysis of microsatellites and single nucleotide polymorphisms (SNPs) from the three species yields estimates of clonal diversity and tests the hypothesis of a single origin for D. unisexualis. RESULTS Genotyping and sequencing of four microsatellite-containing loci for 109 specimens of D. unisexualis, 17 D. valentini, and 45 D. raddei nairensis identified 12 presumptive clones, including one widespread and 11 rare clones. Most individuals in some localities had a rare clone. Clone-specific alleles in D. unisexualis were compared with those of the parental species. The results inferred a single hybridization event. Post-formation mutations best explain the less common clones. CONCLUSIONS Interspecific analyses identify alleles inherited by D. unisexualis from its bisexual ancestors. SNP analyses fail to reject the hypothesis of a single interspecific origin of D. unisexualis, followed by microsatellite mutations in this initial clone. Microsatellites detect higher clonal diversity in D. unisexualis compared to allozymes and identify the likely origins of clones. Our approach may be applicable to other unisexual species whose origins involve interspecific hybridization.
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Affiliation(s)
- Andrey A Vergun
- Laboratory of Genome Organization, Institute of Gene Biology of the Russian Academy of Sciences, Vavilova Str., 34/5, Moscow, 119334, Russia
- Department of Biochemistry, Molecular Biology and Genetics, Moscow State Pedagogical University, M. Pirogovskaya Str., 1/1, Moscow, 119991, Russia
| | - Anastasiya E Girnyk
- Laboratory of Genome Organization, Institute of Gene Biology of the Russian Academy of Sciences, Vavilova Str., 34/5, Moscow, 119334, Russia
| | - Vitaly I Korchagin
- Laboratory of Genome Organization, Institute of Gene Biology of the Russian Academy of Sciences, Vavilova Str., 34/5, Moscow, 119334, Russia
| | - Seraphima K Semyenova
- Laboratory of Genome Organization, Institute of Gene Biology of the Russian Academy of Sciences, Vavilova Str., 34/5, Moscow, 119334, Russia
| | - Marine S Arakelyan
- Faculty of Biology, Yerevan State University, 1 Alex Manoogian, 0025, Yerevan, Armenia
| | - Felix D Danielyan
- Faculty of Biology, Yerevan State University, 1 Alex Manoogian, 0025, Yerevan, Armenia
| | - Robert W Murphy
- Department of Natural History, Royal Ontario Museum, 100 Queen's Park, Toronto, ON, M5S 2C6, Canada
| | - Alexey P Ryskov
- Laboratory of Genome Organization, Institute of Gene Biology of the Russian Academy of Sciences, Vavilova Str., 34/5, Moscow, 119334, Russia.
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33
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Luo J, Chai J, Wen Y, Tao M, Lin G, Liu X, Ren L, Chen Z, Wu S, Li S, Wang Y, Qin Q, Wang S, Gao Y, Huang F, Wang L, Ai C, Wang X, Li L, Ye C, Yang H, Luo M, Chen J, Hu H, Yuan L, Zhong L, Wang J, Xu J, Du Z, Ma Z(S, Murphy RW, Meyer A, Gui J, Xu P, Ruan J, Chen ZJ, Liu S, Lu X, Zhang YP. From asymmetrical to balanced genomic diversification during rediploidization: Subgenomic evolution in allotetraploid fish. Sci Adv 2020; 6:eaaz7677. [PMID: 32766441 PMCID: PMC7385415 DOI: 10.1126/sciadv.aaz7677] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 03/20/2020] [Indexed: 05/27/2023]
Abstract
A persistent enigma is the rarity of polyploidy in animals, compared to its prevalence in plants. Although animal polyploids are thought to experience deleterious genomic chaos during initial polyploidization and subsequent rediploidization processes, this hypothesis has not been tested. We provide an improved reference-quality de novo genome for allotetraploid goldfish whose origin dates to ~15 million years ago. Comprehensive analyses identify changes in subgenomic evolution from asymmetrical oscillation in goldfish and common carp to diverse stabilization and balanced gene expression during continuous rediploidization. The homoeologs are coexpressed in most pathways, and their expression dominance shifts temporally during embryogenesis. Homoeolog expression correlates negatively with alternation of DNA methylation. The results show that allotetraploid cyprinids have a unique strategy for balancing subgenomic stabilization and diversification. Rediploidization process in these fishes provides intriguing insights into genome evolution and function in allopolyploid vertebrates.
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Affiliation(s)
- Jing Luo
- State Key Laboratory for Conservation and Utilization of Bio-resource and School of Life Sciences, Yunnan University, Kunming, 650091 Yunnan, China
| | - Jing Chai
- State Key Laboratory for Conservation and Utilization of Bio-resource and School of Life Sciences, Yunnan University, Kunming, 650091 Yunnan, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223 Yunnan, China
| | - Yanling Wen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223 Yunnan, China
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Min Tao
- State Key Laboratory of Developmental Biology of Freshwater Fish and College of Life Sciences, Hunan Normal University, Changsha, 410081 Hunan, China
| | - Guoliang Lin
- State Key Laboratory for Conservation and Utilization of Bio-resource and School of Life Sciences, Yunnan University, Kunming, 650091 Yunnan, China
| | - Xiaochuan Liu
- State Key Laboratory for Conservation and Utilization of Bio-resource and School of Life Sciences, Yunnan University, Kunming, 650091 Yunnan, China
| | - Li Ren
- State Key Laboratory of Developmental Biology of Freshwater Fish and College of Life Sciences, Hunan Normal University, Changsha, 410081 Hunan, China
| | - Zeyu Chen
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Shigang Wu
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Shengnan Li
- State Key Laboratory of Developmental Biology of Freshwater Fish and College of Life Sciences, Hunan Normal University, Changsha, 410081 Hunan, China
| | - Yude Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish and College of Life Sciences, Hunan Normal University, Changsha, 410081 Hunan, China
| | - Qinbo Qin
- State Key Laboratory of Developmental Biology of Freshwater Fish and College of Life Sciences, Hunan Normal University, Changsha, 410081 Hunan, China
| | - Shi Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish and College of Life Sciences, Hunan Normal University, Changsha, 410081 Hunan, China
| | - Yun Gao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223 Yunnan, China
| | - Feng Huang
- State Key Laboratory for Conservation and Utilization of Bio-resource and School of Life Sciences, Yunnan University, Kunming, 650091 Yunnan, China
| | - Lu Wang
- State Key Laboratory for Conservation and Utilization of Bio-resource and School of Life Sciences, Yunnan University, Kunming, 650091 Yunnan, China
| | - Cheng Ai
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Xiaobo Wang
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Lianwei Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223 Yunnan, China
| | - Chengxi Ye
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223 Yunnan, China
- Department of Computer Science, University of Maryland, College Park, MD 20742, USA
| | - Huimin Yang
- State Key Laboratory for Conservation and Utilization of Bio-resource and School of Life Sciences, Yunnan University, Kunming, 650091 Yunnan, China
| | - Mi Luo
- State Key Laboratory of Developmental Biology of Freshwater Fish and College of Life Sciences, Hunan Normal University, Changsha, 410081 Hunan, China
| | - Jie Chen
- State Key Laboratory of Developmental Biology of Freshwater Fish and College of Life Sciences, Hunan Normal University, Changsha, 410081 Hunan, China
| | - Hong Hu
- State Key Laboratory of Developmental Biology of Freshwater Fish and College of Life Sciences, Hunan Normal University, Changsha, 410081 Hunan, China
| | - Liujiao Yuan
- State Key Laboratory of Developmental Biology of Freshwater Fish and College of Life Sciences, Hunan Normal University, Changsha, 410081 Hunan, China
| | - Li Zhong
- State Key Laboratory for Conservation and Utilization of Bio-resource and School of Life Sciences, Yunnan University, Kunming, 650091 Yunnan, China
| | - Jing Wang
- State Key Laboratory for Conservation and Utilization of Bio-resource and School of Life Sciences, Yunnan University, Kunming, 650091 Yunnan, China
| | - Jian Xu
- Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China
| | - Zhenglin Du
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhanshan (Sam) Ma
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223 Yunnan, China
| | - Robert W. Murphy
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223 Yunnan, China
- Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, ON M5S 2C6, Canada
| | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz 78457, Germany
| | - Jianfang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Innovation Academy for Seed Design, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Wuhan 430072, China
| | - Peng Xu
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102 Fujian, China
| | - Jue Ruan
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Peng Cheng Laboratory, Shenzhen 518052, China
| | - Z. Jeffrey Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 Jiangsu, China
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712-0159, USA
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish and College of Life Sciences, Hunan Normal University, Changsha, 410081 Hunan, China
| | - Xuemei Lu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223 Yunnan, China
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- CAS Center for Excellence in Animal Evolution and Genetics, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223 Yunnan, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ya-ping Zhang
- State Key Laboratory for Conservation and Utilization of Bio-resource and School of Life Sciences, Yunnan University, Kunming, 650091 Yunnan, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223 Yunnan, China
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Affiliation(s)
- Chenqi Lu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223 Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, 650204 Kunming, China
| | - Jing Chai
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223 Kunming, China
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223 Kunming, China.,Centre for Biodiversity, Royal Ontario Museum, Toronto, ON M5S 2C6, Canada
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223 Kunming, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223 Kunming, China
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Rahman MM, Chen JM, Wu YH, Chen HM, Lwin YH, Murphy RW, Li GG, Che J. New country records for three species of frog from Myanmar including two genera (Nasutixalus and Oreolalax). Zootaxa 2020; 4742:zootaxa.4742.3.7. [PMID: 32230368 DOI: 10.11646/zootaxa.4742.3.7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Indexed: 11/04/2022]
Abstract
Myanmar, a biodiversity hotspot, harbors a striking diversity and endemism of species. Despite this, its herpetofauna remains one of the least explored in continental Asia due to restrictions of crossing political boundaries and infrastructure in remote regions. Many species in adjacent China and India are hypothesized to occur in Myanmar but records are wanting. Recent fieldwork found the frogs Polypedates braueri, Nasutixalus jerdonii and Oreolalax jingdongensis there, and the latter two species represent new generic records for Myanmar. All major morphological characters of these populations match the original descriptions. In addition, our matrilineal genealogy based on DNA barcoding confirms their identities. Overall, these findings confirm that the amphibian diversity is underestimated and this has important implications for conservation. Analyses indicate that northern Myanmar is a biogeographic corridor for the Himalayas, southern China, and northeastern India.
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Affiliation(s)
- Md Mizanur Rahman
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China.
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36
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Chen S, Qing J, Liu Z, Liu Y, Tang M, Murphy RW, Pu Y, Wang X, Tang K, Guo K, Jiang X, Liu S. Multilocus phylogeny and cryptic diversity of white-toothed shrews (Mammalia, Eulipotyphla, Crocidura) in China. BMC Evol Biol 2020; 20:29. [PMID: 32059644 PMCID: PMC7023792 DOI: 10.1186/s12862-020-1588-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 01/27/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Crocidura, the most speciose mammalian genus, occurs across much of Asia, Europe and Africa. The taxonomy of Chinese representatives has been studied primarily based on cursory morphological comparisons and their molecular phylogenetic analyses remain unexplored. In order to understand the phylogeny of this group in China, we estimated the first multilocus phylogeny and conducted species delimitation, including taxon sampling throughout their distribution range. RESULTS We obtained one mitochondrial gene (cytb) (~ 1, 134 bp) and three nuclear genes (ApoB, BRCA1, RAG1) (~ 2, 170 bp) for 132 samples from 57 localities. Molecular analyses identified at least 14 putative species that occur within two major well-supported groups in China. Polyphyletic C. wuchihensis appears to be composed of two putative species. Two subspecies, C. rapax rapax and C. rapax kurodai should be elevated to full species status. A phylogenetic tree based on mitochondrial gene from Asian Crocidura species showed that the C. rapax rapax is embedded within C. attenuata, making the latter a paraphyletic group. Three strongly supported undescribed species (C. sp.1, C. sp.2 and C. sp.3) are revealed from Zada County of Tibet (Western China), Hongjiang County of Hunan Province (Central China) and Dongyang County of Zhejiang Province (Eastern China), Motuo County of Tibet, respectively. The divergence time estimation suggested that China's Crocidura species began to diversify during the late Pliocene (3.66 Ma) and the Early Pleistocene (2.29 Ma), followed by a series of diversifications through the Pleistocene. CONCLUSIONS The cryptic diversity found in this study indicated that the number of species is strongly underestimated under the current taxonomy. We propose that the three undescribed species should be evaluated using extensive taxon sampling and comprehensive morphological and morphometric approaches. Climate change since the late Pliocene and the uplift of the Qinghai-Tibet Plateau may result in the diversification and speciation of China's Crocidura species. In short, the underestimated diversity underlines the need for a taxonomic revision of Chinese Crocidura species.
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Affiliation(s)
- Shunde Chen
- College of Life Sciences, Sichuan Normal University, Chengdu, 610066, China.,Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Jiao Qing
- College of Life Sciences, Sichuan Normal University, Chengdu, 610066, China
| | - Zhu Liu
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, 157011, China
| | - Yang Liu
- Sichuan Academy of Forestry, Chengdu, 610081, China
| | - Mingkun Tang
- Sichuan Academy of Forestry, Chengdu, 610081, China
| | - Robert W Murphy
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, 100 Queen's Park, Toronto, M5S 2C6, Canada
| | - Yingting Pu
- College of Life Sciences, Sichuan Normal University, Chengdu, 610066, China
| | - Xuming Wang
- College of Life Sciences, Sichuan Normal University, Chengdu, 610066, China.,Sichuan Academy of Forestry, Chengdu, 610081, China
| | - Keyi Tang
- College of Life Sciences, Sichuan Normal University, Chengdu, 610066, China
| | - Keji Guo
- Central South Forest Inventory and Planning Institute of State Forestry Administration, Changsha, 410014, China
| | - Xuelong Jiang
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Shaoying Liu
- Sichuan Academy of Forestry, Chengdu, 610081, China.
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Liu Q, Yan JW, Hou SB, Wang P, Nguyen SN, Murphy RW, Che J, Guo P. A new species of the genus <italic>Sinomicrurus</italic> (Serpentes: Elapidae) from China and Vietnam. Zool Res 2020; 41:194-198. [PMID: 32125101 PMCID: PMC7109021 DOI: 10.24272/j.issn.2095-8137.2020.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Qin Liu
- College of Life Sciences and Food Engineering, Yibin University, Yibin, Sichuan 644007, China
| | - Jiao-Wen Yan
- Fisheries, Animal & Veterinary Sciences Bureau of Cangwu County, Wuzhou, Guangxi 543115, China
| | - Shao-Bing Hou
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Ping Wang
- College of Life Sciences and Food Engineering, Yibin University, Yibin, Sichuan 644007, China
| | - Sang Ngoc Nguyen
- Institute of Tropical Biology, Vietnam Academy of Science and Technology (VAST), Ho Chi Minh City, Vietnam
| | - Robert W Murphy
- Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, Ontario M5S 2C6, Canada
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China. E-mail:
| | - Peng Guo
- College of Life Sciences and Food Engineering, Yibin University, Yibin, Sichuan 644007, China. E-mail:
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Kilunda FK, Conradie W, Wasonga DV, Jin JQ, Peng MS, Murphy RW, Malonza PK, Che J. Revalidation and resurrection of Panaspis massaiensis (Angel, 1924) and the description of a new species of Panaspis Cope (Squamata: Scincidae) from south-eastern Kenya. Zootaxa 2019; 4706:zootaxa.4706.2.3. [PMID: 32230541 DOI: 10.11646/zootaxa.4706.2.3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Indexed: 11/04/2022]
Abstract
Historically Panaspis wahlbergi (Smith, 1849) has been the only assignable species present in Kenya. Recent studies have shown that it comprises multiple cryptic species and the nominal species is now restricted to southern Africa. Newly collected mitochondrial data (16S rRNA) helped to resolve the status of the Kenyan populations, which revealed the presence of two distant related species. Pairwise distances show average 5.87% differences between the two Kenyan species, and 3.58-5.27% and 8.62-9.15% to nominal P. wahlbergi and P. maculicollis Jacobsen Broadley, 2000 respectively. Ablepharus massaiensis Angel, 1924 was described from the Maasai plains near Nairobi, but has long been considered a junior synonym of P. wahlbergi. We herein resurrect Panaspis massaiensis comb. nov. as a valid species and describe a new species, Panaspis tsavoensis sp. nov. from the Tsavo Conservation Area in south-eastern Kenya. Morphological examinations of specimens reveal minor differences from each other as well as nominal forms of P. wahlbergi and P. maculicollis. Panaspis massaiensis comb. nov. shares with the P. wahlbergi group a white ventrolateral stripe but can be distinguished by the presence of 26 midbody scale rows versus 24. Panaspis tsavoensis sp. nov. on the other hand, lacks the white ventrolateral stripe, most similar to the P. maculicollis group but differs in that P. maculicollis breeding males have a black patch on the neck with diagonal rows of white spots. Panaspis massaiensis comb. nov. is widespread in the Kenyan and northern Tanzanian highlands, isolated dryland montane forests and rocky hills, while P. tsavoensis sp. nov. occur in the expansive arid lowlands of Tsavo Conservation Area and should be present in similar arid lowlands in northern Kenya as well as in adjacent Tanzania.
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Affiliation(s)
- Felista Kasyoka Kilunda
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223 Kunming, China Sino-African Joint Research Center, Chinese Academy of Sciences, Kunming Institute of Zoology, Kunming, 650223, China Kunming College of Life Science, University of Chinese Academy of Sciences, 650204 Kunming, China National Museums of Kenya, Department of Zoology, Herpetology section, 40658-00100 Nairobi, Kenya.
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Abstract
Species of Xenophrys are conserved morphologically and live primarily in forests. In Thailand, the genus harbors many cryptic species. Herein we report the collection of specimens from Doi Inthanon, Chiang Mai Province, northern Thailand, which were identified previously as X. minor. Molecular and morphological analyses find that these specimens differ significantly from other known congeners, and therefore we describe a new species. Further, our phylogenetic analyses indicate that X. latidactyla is a junior synonym of X. palpebralespinosa.
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Affiliation(s)
- Yun-He Wu
- State Key Laboratory of Genetic Resources and Evolution State, 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.,Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin Nay Pyi Taw 05282, Myanmar
| | | | - Nikolay A Poyarkov
- Department of Vertebrate Zoology, Biological Faculty, Lomonosov Moscow State University, Moscow 119991, Russia.,Joint Russian-Vietnamese Tropical Research and Technological Center, 63 Nguyen Van Huyen Road, Nghia Do, Cau Giay, Hanoi, Vietnam
| | - Parinya Pawangkhanant
- School of Agriculture and Natural Resources, University of Phayao, Phayao 56000, Thailand
| | - Kai Xu
- State Key Laboratory of Genetic Resources and Evolution State, 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
| | - Jie-Qiong Jin
- State Key Laboratory of Genetic Resources and Evolution State, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution State, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China.,Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto M5S 2C6, Canada
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution State, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China, E-mail:.,Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin Nay Pyi Taw 05282, Myanmar
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Wu YH, Suwannapoom C, Xu K, Chen JM, Jin JQ, Chen HM, Murphy RW, Che J. A new species of the genus Raorchestes (Anura: Rhacophoridae) from Yunnan Province, China. Zool Res 2019; 40:558-563. [PMID: 31631588 PMCID: PMC6822928 DOI: 10.24272/j.issn.2095-8137.2019.066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Yun-He Wu
- State Key Laboratory of Genetic Resources and Evolution State, 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
| | | | - Kai Xu
- State Key Laboratory of Genetic Resources and Evolution State, 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
| | - Jin-Min Chen
- State Key Laboratory of Genetic Resources and Evolution State, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
| | - Jie-Qiong Jin
- State Key Laboratory of Genetic Resources and Evolution State, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
| | - Hong-Man Chen
- State Key Laboratory of Genetic Resources and Evolution State, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
| | - Robert W Murphy
- Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto Ontario M5S 2C6, Canada
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution State, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China, E-mail:
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Abstract
Elucidating the closest living relatives of extant primates is essential for fully understanding important biological processes related to the genomic and phenotypic evolution of primates, especially of humans. However, the phylogenetic placement of these primate relatives remains controversial, with three primary hypotheses currently espoused based on morphological and molecular evidence. In the present study, we used two algorithms to analyze differently partitioned genomic datasets consisting of 45.4 Mb of conserved non-coding elements and 393 kb of concatenated coding sequences to test these hypotheses. We assessed different genomic histories and compared with other molecular studies found solid support for colugos being the closest living relatives of primates. Our phylogeny showed Cercopithecinae to have low levels of nucleotide divergence, especially for Papionini, and gibbons to have a high rate of divergence. The MCMCtree comprehensively updated divergence dates of early evolution of Primatomorpha and Primates.
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Affiliation(s)
- Mei-Ling Zhang
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Centre for Disease Control and Prevention, Kunming Yunnan 650022, China
| | - Ming-Li Li
- State Key Laboratory of Genetic Resources and Evolution, 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 650223, China
| | - Adeola Oluwakemi Ayoola
- State Key Laboratory of Genetic Resources and Evolution, 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 650223, China
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China.,Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto M5S 2C6, Canada
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China, E-mail:
| | - Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China, E-mail:
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Burbrink FT, Grazziotin FG, Pyron RA, Cundall D, Donnellan S, Irish F, Keogh JS, Kraus F, Murphy RW, Noonan B, Raxworthy CJ, Ruane S, Lemmon AR, Lemmon EM, Zaher H. Interrogating Genomic-Scale Data for Squamata (Lizards, Snakes, and Amphisbaenians) Shows no Support for Key Traditional Morphological Relationships. Syst Biol 2019; 69:502-520. [DOI: 10.1093/sysbio/syz062] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 09/05/2019] [Accepted: 09/10/2019] [Indexed: 12/15/2022] Open
Abstract
Abstract
Genomics is narrowing uncertainty in the phylogenetic structure for many amniote groups. For one of the most diverse and species-rich groups, the squamate reptiles (lizards, snakes, and amphisbaenians), an inverse correlation between the number of taxa and loci sampled still persists across all publications using DNA sequence data and reaching a consensus on the relationships among them has been highly problematic. In this study, we use high-throughput sequence data from 289 samples covering 75 families of squamates to address phylogenetic affinities, estimate divergence times, and characterize residual topological uncertainty in the presence of genome-scale data. Importantly, we address genomic support for the traditional taxonomic groupings Scleroglossa and Macrostomata using novel machine-learning techniques. We interrogate genes using various metrics inherent to these loci, including parsimony-informative sites (PIS), phylogenetic informativeness, length, gaps, number of substitutions, and site concordance to understand why certain loci fail to find previously well-supported molecular clades and how they fail to support species-tree estimates. We show that both incomplete lineage sorting and poor gene-tree estimation (due to a few undesirable gene properties, such as an insufficient number of PIS), may account for most gene and species-tree discordance. We find overwhelming signal for Toxicofera, and also show that none of the loci included in this study supports Scleroglossa or Macrostomata. We comment on the origins and diversification of Squamata throughout the Mesozoic and underscore remaining uncertainties that persist in both deeper parts of the tree (e.g., relationships between Dibamia, Gekkota, and remaining squamates; among the three toxicoferan clades Iguania, Serpentes, and Anguiformes) and within specific clades (e.g., affinities among gekkotan, pleurodont iguanians, and colubroid families).
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Affiliation(s)
- Frank T Burbrink
- Department of Herpetology, The American Museum of Natural History, 79th Street at Central Park West, New York, NY 10024, USA
| | - Felipe G Grazziotin
- Laboratório de Coleções Zoológicas, Instituto Butantan, Av. Vital Brasil, 1500—Butantã, São Paulo—SP 05503-900, Brazil
| | - R Alexander Pyron
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
| | - David Cundall
- Department of Biological Sciences, 1 W. Packer Avenue, Lehigh University, Bethlehem, PA 18015, USA
| | - Steve Donnellan
- South Australian Museum, North Terrace, Adelaide SA 5000, Australia
- School of Biological Sciences, University of Adelaide, SA 5005 Australia
| | - Frances Irish
- Department of Biological Sciences, Moravian College, 1200 Main St, Bethlehem, PA 18018, US
| | - J Scott Keogh
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Fred Kraus
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Robert W Murphy
- Department of Natural History, Royal Ontario Museum, 100 Queens Park, Toronto, ON M5S 2C6, Canada
| | - Brice Noonan
- Department of Biology, University of Mississippi, Oxford, MS 38677, USA
| | - Christopher J Raxworthy
- Department of Herpetology, The American Museum of Natural History, 79th Street at Central Park West, New York, NY 10024, USA
| | - Sara Ruane
- Department of Biological Sciences, 206 Boyden Hall, Rutgers University, 195 University Avenue, Newark, NJ 07102, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL 32306-4102, USA
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306-4295, USA
| | - Hussam Zaher
- Museu de Zoologia da Universidade de São Paulo, São Paulo, Brazil CEP 04263-000, Brazil
- Centre de Recherche sur la Paléobiodiversité et les Paléoenvironnements (CR2P), UMR 7207 CNRS/MNHN/Sorbonne Université, Muséum national d’Histoire naturelle, 8 rue Buffon, CP 38, 75005 Paris, France
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43
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Guo X, Li YQ, Wang MS, Wang ZB, Zhang Q, Shao Y, Jiang RS, Wang S, Ma CD, Murphy RW, Wang GQ, Dong J, Zhang L, Wu DD, Du BW, Peng MS, Zhang YP. A parallel mechanism underlying frizzle in domestic chickens. J Mol Cell Biol 2019; 10:589-591. [PMID: 29868726 DOI: 10.1093/jmcb/mjy037] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 06/04/2018] [Indexed: 01/27/2023] Open
Affiliation(s)
- Xing Guo
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yan-Qing Li
- College of Agricultural, Guangdong Ocean University, Zhanjiang, China
| | - Ming-Shan Wang
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Zhi-Bin Wang
- College of Agricultural, Guangdong Ocean University, Zhanjiang, China
| | - Quan Zhang
- College of Agricultural, Guangdong Ocean University, Zhanjiang, China
| | - Yong Shao
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Run-Shen Jiang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Sheng Wang
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Chen-Dong Ma
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, Canada
| | - Guang-Qin Wang
- Jinsheng Animal Husbandry Technology Co. Ltd, Zhanjiang, China
| | - Jing Dong
- College of Agricultural, Guangdong Ocean University, Zhanjiang, China
| | - Li Zhang
- College of Agricultural, Guangdong Ocean University, Zhanjiang, China
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Bing-Wang Du
- College of Agricultural, Guangdong Ocean University, Zhanjiang, China
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming, China
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Turvey ST, Marr MM, Barnes I, Brace S, Tapley B, Murphy RW, Zhao E, Cunningham AA. Historical museum collections clarify the evolutionary history of cryptic species radiation in the world's largest amphibians. Ecol Evol 2019; 9:10070-10084. [PMID: 31624538 PMCID: PMC6787787 DOI: 10.1002/ece3.5257] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 04/02/2019] [Accepted: 04/13/2019] [Indexed: 11/06/2022] Open
Abstract
Inaccurate taxonomic assessment of threatened populations can hinder conservation prioritization and management, with human-mediated population movements obscuring biogeographic patterns and confounding reconstructions of evolutionary history. Giant salamanders were formerly distributed widely across China, and are interpreted as a single species, Andrias davidianus. Previous phylogenetic studies have identified distinct Chinese giant salamander lineages but were unable to associate these consistently with different landscapes, probably because population structure has been modified by human-mediated translocations for recent commercial farming. We investigated the evolutionary history and relationships of allopatric Chinese giant salamander populations with Next-Generation Sequencing methods, using historical museum specimens and late 20th-century samples, and retrieved partial or near-complete mitogenomes for 17 individuals. Samples from populations unlikely to have been affected by translocations form three clades from separate regions of China, spatially congruent with isolation by either major river drainages or mountain ranges. Pliocene-Pleistocene divergences for these clades are consistent with topographic modification of southern China associated with uplift of the Qinghai-Tibet Plateau. General Mixed Yule Coalescent model analysis indicates that these clades represent separate species: Andrias davidianus (Blanchard, 1871) (northern Yangtze/Sichuan), Andrias sligoi (Boulenger, 1924) (Pearl/Nanling), and an undescribed species (Huangshan). Andrias sligoi is possibly the world's largest amphibian. Inclusion of additional reportedly wild samples from areas of known giant salamander exploitation and movement leads to increasing loss of biogeographic signal. Wild Chinese giant salamander populations are now critically depleted or extirpated, and conservation actions should be updated to recognize the existence of multiple species.
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Affiliation(s)
| | | | - Ian Barnes
- Earth Sciences DepartmentNatural History MuseumLondonUK
| | - Selina Brace
- Earth Sciences DepartmentNatural History MuseumLondonUK
| | | | - Robert W. Murphy
- Centre for Biodiversity and Conservation BiologyRoyal Ontario MuseumTorontoOntarioCanada
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
| | - Ermi Zhao
- Chengdu Institute of BiologyChinese Academy of SciencesChengduChina
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Nguyen SN, Nguyen VDH, Nguyen LT, Murphy RW. A new skink of the genus Scincella Mittleman, 1950 (Squamata: Scincidae) from Ba Den Mountain, Tay Ninh Province, southern Vietnam. Zootaxa 2019; 4648:zootaxa.4648.2.4. [PMID: 31716948 DOI: 10.11646/zootaxa.4648.2.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Indexed: 11/04/2022]
Abstract
Ba Den is an isolated mountain in southern Vietnam and home to two endemic species of lizards. Herein, we describe another endemic species, a new skink of the genus Scincella Mittleman, 1950, from the area based on morphological data, including hemipenial characters and nucleotide sequences of COI. The following morphological characters diagnose Scincella badenensis sp. nov.: medium size in adults (snout-vent length up to 64.4 mm); toes reach to fingers when limbs adpressed; midbody scale rows 32-36, smooth; paravertebral scales 67-71; dorsal scales not enlarged; ventral scale rows 68-74; supraoculars four; prefrontals in broad contact with one another; loreal scales two; tympanum deeply sunk, without auricular lobules; two enlarged anterior temporal scales; smooth lamellae beneath toe IV 18-20; pair of enlarged precloacal scales; hemipenes short, smooth and forked near the tip with two short lobes and two small terminal papillae; no dorsal pattern in males; and females with black interruptive vertebral line. The new species differs from its congeners by at least 10.4% uncorrected p-distance in COI sequences.
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Affiliation(s)
- Sang Ngoc Nguyen
- Institute of Tropical Biology, Vietnam Academy of Science and Technology, 85 Tran Quoc Toan St., Dist. 3, Ho Chi Minh City, Vietnam. NTT Institute of Hi-Technology, Nguyen Tat Thanh University, 300A Nguyen Tat Thanh St., Dist. 4, Ho Chi Minh City, Vietnam.
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46
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Zaher H, Murphy RW, Arredondo JC, Graboski R, Machado-Filho PR, Mahlow K, Montingelli GG, Quadros AB, Orlov NL, Wilkinson M, Zhang YP, Grazziotin FG. Correction: Large-scale molecular phylogeny, morphology, divergence-time estimation, and the fossil record of advanced caenophidian snakes (Squamata: Serpentes). PLoS One 2019; 14:e0217959. [PMID: 31150527 PMCID: PMC6544309 DOI: 10.1371/journal.pone.0217959] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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47
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Nguyen SN, Jin JQ, Vo BD, Nguyen LT, Zhou WW, Che J, Murphy RW, Zhang YP. A new species of Acanthosaura Gray 1831 (Reptilia: Agamidae) from central Vietnam. Zootaxa 2019; 4612:zootaxa.4612.4.7. [PMID: 31717043 DOI: 10.11646/zootaxa.4612.4.7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Indexed: 11/04/2022]
Abstract
Herein, we describe the new agamid species Acanthosaura phongdienensis sp. nov. from central Vietnam based on morphological and genetic data. Males of the new medium-sized species have a snout-vent length of up to 77.4 mm and females up to 64.7 mm. In both genders, the tail is longer than the snout-vent length. A spine occurs on each side of the neck, the rostral scute is entire, and the nuchal and dorsal crests are continuous. A postorbital spine is about half as long as the diameter of the eye-ball, and small lateral scales intermix with large, keeled scales whose tips point backwards and upwards. The new species differs genetically from the closely related species A. brachypoda, A. coronata, and A. lepidogaster by uncorrected p-distances of 13.6%, 21.7%, and 12.8%, respectively. This is the 13th species of Acanthosaura and the eighth species in the genus from Vietnam.
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Affiliation(s)
- Sang Ngoc Nguyen
- Institute of Tropical Biology, Vietnam Academy of Science and Technology, 85 Tran Quoc Toan St., District 3, Ho Chi Minh City, Vietnam. State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming 650223, Yunnan, China.
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48
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Zaher H, Murphy RW, Arredondo JC, Graboski R, Machado-Filho PR, Mahlow K, Montingelli GG, Quadros AB, Orlov NL, Wilkinson M, Zhang YP, Grazziotin FG. Large-scale molecular phylogeny, morphology, divergence-time estimation, and the fossil record of advanced caenophidian snakes (Squamata: Serpentes). PLoS One 2019; 14:e0216148. [PMID: 31075128 PMCID: PMC6512042 DOI: 10.1371/journal.pone.0216148] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 04/15/2019] [Indexed: 11/29/2022] Open
Abstract
Caenophidian snakes include the file snake genus Acrochordus and advanced colubroidean snakes that radiated mainly during the Neogene. Although caenophidian snakes are a well-supported clade, their inferred affinities, based either on molecular or morphological data, remain poorly known or controversial. Here, we provide an expanded molecular phylogenetic analysis of Caenophidia and use three non-parametric measures of support-Shimodaira-Hasegawa-Like test (SHL), Felsentein (FBP) and transfer (TBE) bootstrap measures-to evaluate the robustness of each clade in the molecular tree. That very different alternative support values are common suggests that results based on only one support value should be viewed with caution. Using a scheme to combine support values, we find 20.9% of the 1265 clades comprising the inferred caenophidian tree are unambiguously supported by both SHL and FBP values, while almost 37% are unsupported or ambiguously supported, revealing the substantial extent of phylogenetic problems within Caenophidia. Combined FBP/TBE support values show similar results, while SHL/TBE result in slightly higher combined values. We consider key morphological attributes of colubroidean cranial, vertebral and hemipenial anatomy and provide additional morphological evidence supporting the clades Colubroides, Colubriformes, and Endoglyptodonta. We review and revise the relevant caenophidian fossil record and provide a time-calibrated tree derived from our molecular data to discuss the main cladogenetic events that resulted in present-day patterns of caenophidian diversification. Our results suggest that all extant families of Colubroidea and Elapoidea composing the present-day endoglyptodont fauna originated rapidly within the early Oligocene-between approximately 33 and 28 Mya-following the major terrestrial faunal turnover known as the "Grande Coupure" and associated with the overall climate shift at the Eocene-Oligocene boundary. Our results further suggest that the caenophidian radiation originated within the Caenozoic, with the divergence between Colubroides and Acrochordidae occurring in the early Eocene, at ~ 56 Mya.
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Affiliation(s)
- Hussam Zaher
- Museu de Zoologia, Universidade de São Paulo, São Paulo, São Paulo,
Brazil
- CR2P –Centre de Recherche en Paléontologie – Muséum national d’Histoire
naturelle – Sorbonne Université, Paris, France
| | - Robert W. Murphy
- Centre for Biodiversity, Royal Ontario Museum, Toronto, Ontario,
Canada
- State Key Laboratory of Genetic Resources and Evolution, Kunming
Institute of Zoology, Kunming, China
| | | | - Roberta Graboski
- Museu de Zoologia, Universidade de São Paulo, São Paulo, São Paulo,
Brazil
- Laboratório de Herpetologia, Museu Paraense Emílio Goeldi, Belém, Pará,
Brazil
| | | | - Kristin Mahlow
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity
Science, Berlin, Germany
| | | | - Ana Bottallo Quadros
- Museu de Zoologia, Universidade de São Paulo, São Paulo, São Paulo,
Brazil
- CR2P –Centre de Recherche en Paléontologie – Muséum national d’Histoire
naturelle – Sorbonne Université, Paris, France
| | - Nikolai L. Orlov
- Zoological Institute, Russian Academy of Sciences, Saint Petersburg,
Russia
| | - Mark Wilkinson
- Department of Life Sciences, The Natural History Museum, London, United
Kingdom
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming
Institute of Zoology, Kunming, China
- Laboratory for Conservation and Utilization of Bio-resources, Yunnan
University, Kunming, China
| | - Felipe G. Grazziotin
- Laboratório de Coleções Zoológicas, Instituto Butantan, São Paulo, São
Paulo, Brazil
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Luo W, Tian L, Huang C, Li J, Shen X, Murphy RW, Liao M, Shen Y. The codon usage bias of avian influenza A viruses. J Infect 2019; 79:174-187. [PMID: 31075292 DOI: 10.1016/j.jinf.2019.05.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 05/04/2019] [Indexed: 12/25/2022]
Affiliation(s)
- Wen Luo
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Lin Tian
- Guangdong Provincial Hospital of Chinese Medicine, Zhuhai 519015, China
| | - Chuqi Huang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Jiayu Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Xuejuan Shen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Robert W Murphy
- Center for Biodiversity, Royal Ontario Museum, Toronto, M5S 2C6, Canada
| | - Ming Liao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
| | - Yongyi Shen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China.
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Nneji LM, Adeola AC, Yan F, Okeyoyin AO, Oladipo OC, Saidu Y, Samuel D, Nneji IC, Adeyi AO, Onadeko AB, Olagunju TE, Omotoso O, Oladipo SO, Iyiola OA, Usongo JY, Auta T, Usman AD, Abdullahi H, Ikhimiukor OO, Zhou WW, Jin JQ, Ugwumba OA, Ugwumba AAA, Peng MS, Murphy RW, Che J. Genetic variation and cryptic lineage diversity of the Nigerian red-headed rock agama Agama agama associate with eco-geographic zones. Curr Zool 2019; 65:713-724. [PMID: 31857818 PMCID: PMC6911843 DOI: 10.1093/cz/zoz002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Accepted: 01/28/2019] [Indexed: 11/14/2022] Open
Abstract
Nigeria is an Afrotropical region with considerable ecological heterogeneity and levels of biotic endemism. Among its vertebrate fauna, reptiles have broad distributions, thus, they constitute a compelling system for assessing the impact of ecological variation and geographic isolation on species diversification. The red-headed rock agama, Agama agama, lives in a wide range of habitats and, thus, it may show genetic structuring and diversification. Herein, we tested the hypothesis that ecology affects its genetic structure and population divergence. Bayesian inference phylogenetic analysis of a mitochondrial DNA (mtDNA) gene recovered four well-supported matrilines with strong evidence of genetic structuring consistent with eco-geographic regions. Genetic differences among populations based on the mtDNA also correlated with geographic distance. The ecological niche model for the matrilines had a good fit and robust performance. Population divergence along the environmental axes was associated with climatic conditions, and temperature ranked highest among all environmental variables for forest specialists, while precipitation ranked highest for the forest/derived savanna, and savanna specialists. Our results cannot reject the hypothesis that niche conservatism promotes geographic isolation of the western populations of Nigerian A. agama. Thus, ecological gradients and geographic isolation impact the genetic structure and population divergence of the lizards. This species might be facing threats due to recent habitat fragmentation, especially in western Nigeria. Conservation actions appear necessary.
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Affiliation(s)
- Lotanna M Nneji
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, China
| | - Adeniyi C Adeola
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, China
| | - Fang Yan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Agboola O Okeyoyin
- National Park Service Headquarters, Federal Capital Territory, Abuja, Nigeria
| | | | - Yohanna Saidu
- Gashaka Gumti National Park, Serti, Taraba State, Nigeria
| | - Dinatu Samuel
- Gashaka Gumti National Park, Serti, Taraba State, Nigeria
| | - Ifeanyi C Nneji
- Department of Biological Sciences, University of Abuja, FCT, Abuja, Nigeria
| | - Akindele O Adeyi
- Department of Zoology, University of Ibadan, Ibadan, Oyo State, Nigeria
| | | | | | - Olatunde Omotoso
- Department of Zoology, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Segun O Oladipo
- Department of Biosciences and Biotechnology, Kwara State University, Malete, Kwara State, Nigeria
| | - Oluyinka A Iyiola
- Department of Zoology, Faculty of Life Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria
| | - John Y Usongo
- Department of Zoology, Modibbo Adama University of Technology, Yola, Nigeria
| | - Timothy Auta
- Department of Biological Sciences, Federal University Dutsin-Ma, Katsina State, Nigeria
| | - Abbas D Usman
- Department of Biology, Kashim Ibrahim College of Education, Maiduguri, Borno State, Nigeria
| | - Halima Abdullahi
- Department of Biology, Kashim Ibrahim College of Education, Maiduguri, Borno State, Nigeria
| | - Odion O Ikhimiukor
- Department of Microbiology, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Wei-Wei Zhou
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Jie-Qiong Jin
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Obih A Ugwumba
- Department of Zoology, University of Ibadan, Ibadan, Oyo State, Nigeria
| | | | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, China
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, Ontario, Canada
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
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