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Lan G, Yu J, Liu J, Zhang Y, Ma R, Zhou Y, Zhu B, Wei W, Liu J, Qi G. Complete Mitochondrial Genome and Phylogenetic Analysis of Tarsiger indicus (Aves: Passeriformes: Muscicapidae). Genes (Basel) 2024; 15:90. [PMID: 38254979 PMCID: PMC10815732 DOI: 10.3390/genes15010090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/26/2023] [Accepted: 12/26/2023] [Indexed: 01/24/2024] Open
Abstract
Tarsiger indicus (Vieillot, 1817), the White-browed Bush Robin, is a small passerine bird widely distributed in Asian countries. Here, we successfully sequenced its mitogenome using the Illumina Novaseq 6000 platform (Illumina, San Diego, CA, USA) for PE 2 × 150 bp sequencing. Combined with other published mitogenomes, we conducted the first comprehensive comparative mitogenome analysis of Muscicapidae birds and reconstructed the phylogenetic relationships between Muscicapidae and related groups. The T. indicus mitogenome was 16,723 bp in size, and it possessed the typical avian mitogenome structure and organization. Most PCGs of T. indicus were initiated strictly with the typical start codon ATG, while COX1 and ND2 were started with GTG. RSCU statistics showed that CUA, CGA, and GCC were relatively high frequency in the T. indicus mitogenome. T. cyanurus and T. indicus shared very similar mitogenomic features. All 13 PCGs of Muscicapidae mitogenomes had experienced purifying selection. Specifically, ATP8 had the highest rate of evolution (0.13296), whereas COX1 had the lowest (0.01373). The monophylies of Muscicapidae, Turdidae, and Paradoxornithidae were strongly supported. The clade of ((Muscicapidae + Turdidae) + Sturnidae) in Passeriformes was supported by both Bayesian Inference and Maximum likelihood analyses. The latest taxonomic status of many passerine birds with complex taxonomic histories were also supported. For example, Monticola gularis, T. indicus, and T. cyanurus were allocated to Turdidae in other literature; our phylogenetic topologies clearly supported their membership in Muscicapidae; Paradoxornis heudei, Suthora webbiana, S. nipalensis, and S. fulvifrons were formerly classified into Muscicapidae; we supported their membership in Paradoxornithidae; Culicicapa ceylonensis was originally classified as a member of Muscicapidae; our results are consistent with a position in Stenostiridae. Our study enriches the genetic data of T. indicus and provides new insights into the molecular phylogeny and evolution of passerine birds.
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Affiliation(s)
- Guanwei Lan
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, China; (G.L.); (W.W.)
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China; (J.Y.); (R.M.); (Y.Z.)
| | - Jiaojiao Yu
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China; (J.Y.); (R.M.); (Y.Z.)
| | - Juan Liu
- Administrative Bureau of Baihe National Nature Reserve, Ngawa 623400, China; (J.L.); (Y.Z.); (B.Z.)
| | - Yue Zhang
- Administrative Bureau of Baihe National Nature Reserve, Ngawa 623400, China; (J.L.); (Y.Z.); (B.Z.)
| | - Rui Ma
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China; (J.Y.); (R.M.); (Y.Z.)
| | - Yanshan Zhou
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China; (J.Y.); (R.M.); (Y.Z.)
| | - Biqing Zhu
- Administrative Bureau of Baihe National Nature Reserve, Ngawa 623400, China; (J.L.); (Y.Z.); (B.Z.)
| | - Wei Wei
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, China; (G.L.); (W.W.)
| | - Jiabin Liu
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China; (J.Y.); (R.M.); (Y.Z.)
- Institute of Wildlife Conservation, Central South University of Forestry and Technology, Changsha 410004, China
| | - Guilan Qi
- Animal Husbandry Institute, Chengdu Academy of Agriculture and Forestry Sciences, Chengdu 611130, China
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Yuan J, Sun G, Xiao B, Hu J, Wang L, Taogetongqimuge, Bao L, Hou Y, Song S, Jiang S, Wu Y, Pan D, Liu Y, Westbury MV, Lai X, Sheng G. Ancient mitogenomes reveal a high maternal genetic diversity of Pleistocene woolly rhinoceros in Northern China. BMC Ecol Evol 2023; 23:56. [PMID: 37752413 PMCID: PMC10521388 DOI: 10.1186/s12862-023-02168-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 09/18/2023] [Indexed: 09/28/2023] Open
Abstract
BACKGROUND Woolly rhinoceros (Coelodonta antiquitatis) is a typical indicator of cold-stage climate that was widely distributed in Northern Hemisphere during the Middle-Late Pleistocene. Although a plethora of fossils have been excavated from Northern China, their phylogenetic status, intraspecific diversity and phylogeographical structure are still vague. RESULTS In the present study, we generated four mitogenomes from Late Pleistocene woolly rhinoceros in Northern China and compared them with published data. Bayesian and network analyses indicate that the analyzed individuals contain at least four maternal haplogroups, and Chinese samples fall in three of them. One of our samples belongs to a previously unidentified early diverging clade (haplogroup D), which separated from other woolly rhinoceros around 0.57 Ma (95% CI: 0.76-0.41 Ma). The timing of this clade's origin coincides with the first occurrence of woolly rhinoceros, which are thought to have evolved in Europe. Our other three samples cluster in haplogroup C, previously only identified from one specimen from Wrangel Island (ND030) and initially considered to be an isolated clade. Herein, our findings suggest that ND030 is likely descended from a northward dispersal of the individuals carrying haplogroup C from Northern China. Additionally, Chinese woolly rhinoceros specimens exhibit higher nucleotide diversity than those from Siberia. CONCLUSION Our findings highlight Northern China as a possible refugium and a key evolution center of the Pleistocene woolly rhinoceros.
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Affiliation(s)
- Junxia Yuan
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430078, China.
- Bioarchaeology Laboratory, Jilin University, Changchun, 130012, China.
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430078, China.
| | - Guojiang Sun
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430078, China
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430078, China
| | - Bo Xiao
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430078, China
- School of Earth Science, China University of Geosciences, Wuhan, 430074, China
| | - Jiaming Hu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430078, China
- School of Earth Science, China University of Geosciences, Wuhan, 430074, China
| | - Linying Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430078, China
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430078, China
- College of Earth and Environmental Science, Lanzhou University, Lanzhou, 730099, China
| | | | - Lei Bao
- Ordos Institute of Cultural Relics and Archaeology, Ordos, 017010, China
| | - Yamei Hou
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China
| | - Shiwen Song
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430078, China
- School of Environmental Studies, China University of Geosciences, Wuhan, 430078, China
| | - Shan Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430078, China
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430078, China
| | - Yong Wu
- The Third Geological and Mineral Exploration Institute of Gansu Bureau of Geology and Mineral Resources, Lanzhou, 730050, China
| | - Dong Pan
- Palaeontological Fossil Conservation Center, Qinggang County, Suihua, 151600, China
| | - Yang Liu
- School of Sociology & Anthropology, Sun Yat-sen University, Guangzhou, 510275, China
| | | | - Xulong Lai
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430078, China
- School of Earth Science, China University of Geosciences, Wuhan, 430074, China
| | - Guilian Sheng
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430078, China.
- School of Environmental Studies, China University of Geosciences, Wuhan, 430078, China.
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