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Yang X, Ni X, Fu C. Phylogeographical Analysis of the Freshwater Gudgeon Huigobio chenhsienensis (Cypriniformes: Gobionidae) in Southern China. Life (Basel) 2022; 12:1024. [PMID: 35888112 PMCID: PMC9318155 DOI: 10.3390/life12071024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/17/2022] [Accepted: 07/06/2022] [Indexed: 06/15/2023] Open
Abstract
The freshwater gudgeon Huigobio chenhsienensis (Cypriniformes: Gobionidae) is a small fish endemic to southern China. In this study, we used mitochondrial cytochrome b gene (Cytb), from wide-ranging samplings of H. chenhsienensis from the Ou River (the central of southern China) to the Yangtze River Basin (the northernmost part of southern China) to explore genetic variations and the evolutionary history of H. chenhsienensis in southern China. In total, 66 haplotypes were identified from Cytb sequences of 142 H. chenhsienensis individuals, which could be divided into lineages A, B, and C with divergence times of ~4.24 Ma and ~3.03 Ma. Lineage A was distributed in the lower reaches of the Yangtze River, the Oujiang River, and the Jiao River, lineage B was distributed in the Qiantang River and the Cao'e River, whereas lineage C was restricted to the Poyang Lake drainage from the middle reaches of the Yangtze River. Lineage A could be subdivided into sub-lineages A-I, A-II, A-III, and A-IV, with divergence times of 1.30, 0.97, and 0.44 Ma. Lineage C could be subdivided into sub-lineages C-I and C-II, with a divergence time of 0.85 Ma. Our findings indicate that climate change during the Pliocene and Pleistocene eras, as well as the limited dispersal ability of H. chenhsienensis, have been major drivers for shaping the phylogeographical patterns of H. chenhsienensis.
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Chen YJ, Zhu L, Wu QN, Hu CC, Qu YF, Ji X. Geological and climatic influences on population differentiation of the Phrynocephalus vlangalii species complex (Sauria: Agamidae) in the northern Qinghai-Tibet Plateau. Mol Phylogenet Evol 2022; 169:107394. [PMID: 35045310 DOI: 10.1016/j.ympev.2022.107394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 10/06/2021] [Accepted: 12/25/2021] [Indexed: 11/26/2022]
Abstract
Extremely heterogeneous topography and complex paleoclimate history of the Qinghai-Tibet Plateau (QTP) have a key role in promoting genetic divergence and lineage/species formation. Here, we sequenced one nuclear and three mitochondrial markers of 532 individuals from the entire range of the Phrynocephalus vlangalii species complex including two species, P. putjatai and P. vlangalii, endemic to the northern QTP. We integrated multilocus phylogeny, demographic analysis and geographic barrier detection to evaluate the population structure and dynamics. We found a new mitochondrial clade (PV-I) in the Gonghe County population of P. vlangalii, partial mitochondrial DNA replacement within P. vlangalii and complete mitochondrial DNA replacement between P. putjatai and P. vlangalii. Neutrality test, mismatch distribution analysis and Extended Bayesian Skyline Plot (EBSP) analysis all supported a significant expansion of the Qaidam Basin population of P. vlangalii (PV-II-2) from 0.091 to 0.026 Ma after Penultimate Glaciation. The uplift of the Arjin and Anyemanqen Mountains during the Kunhuang Movement (∼1.2 Ma) split populations of P. vlangalii in Akesai, Qaidam Basin and source of the Yellow River. The uplift of the Elashan Mountains during the second phase of the Qingzang Movement (∼2.5 Ma) contributed to the divergence of the Gonghe County population of P. vlangalii from other conspecific populations. The third phase of the Qingzang Movement (∼1.7 Ma) contributed to the divergence of the Xinghai population of P. vlangalii from P. putjatai and to the divergence of the northern populations of P. putjatai from the southern conspecific populations. Our data support the idea that the geological and climatic changes following the orogeny of the QTP may have promoted population differentiation and shaped the current population patterns of the P. vlangalii species complex in the northeastern QTP.
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Affiliation(s)
- Yi-Jing Chen
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu, China
| | - Lin Zhu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu, China
| | - Qian-Nian Wu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu, China
| | - Chao-Chao Hu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu, China
| | - Yan-Fu Qu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu, China.
| | - Xiang Ji
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu, China; College of Life and Environmental Sciences, Wenzhou University, Wenzhou 325035, Zhejiang, China.
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Wu H, Gu Q, Zhou C, Tang Y, Husemann M, Meng X, Zhang J, Nie G, Li X. Molecular phylogeny and biogeography of Triplophysa stone loaches in the Central Chinese Mountains. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa060] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
AbstractThe geological structure and history of mountains often cause highly complex patterns of evolution. The origin and diversity of the genus Triplophysa is considered to be closely associated with the rapid and persistent rise of the Qinghai-Tibet Plateau (QTP). Species of the genus are widely distributed in the QTP and adjacent regions, and are strongly adapted to its extreme environments. However, the Central Chinese Mountains (CCM), which are far apart from the QTP, also have many Triplophysa populations and yet their taxonomy, phylogeny and origin are unknown. We used three mitochondrial genes of 266 individuals from 29 sites in the CCM to shed light on the evolution of these Triplophysa populations. Phylogenetic analyses and species delimitation revealed seven distinct molecular operational taxonomic units (mOTUs) in the CCM, each with low genetic diversity. Molecular clock and biogeographic analyses suggested that vicariance events resulting from the rapid uplifting of the Qinling and Taihang Mountains initialized diversification in the Pliocene. During the early Pleistocene, dispersal events in the central parts of the Yellow River drainage altered genetic diversity and led to the currently observed biogeographic patterns. Our results suggest the presence of at least six species of Triplophysa in the CCM and more are likely to be discovered in the future.
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Affiliation(s)
- Huihui Wu
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, Henan, P.R. China
| | - Qianhong Gu
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, Henan, P.R. China
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, Hunan, P.R. China
| | - Chuanjiang Zhou
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, Henan, P.R. China
| | - Yongtao Tang
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, Henan, P.R. China
| | - Martin Husemann
- Centrum für Naturkunde, Universität Hamburg, Hamburg, Germany
| | - Xiaolin Meng
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, Henan, P.R. China
| | - Jianxin Zhang
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, Henan, P.R. China
| | - Guoxing Nie
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, Henan, P.R. China
| | - Xuejun Li
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, Henan, P.R. China
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Yang T, Meng W, Guo B. Population Genomic Analysis of Two Endemic Schizothoracins Reveals Their Genetic Differences and Underlying Selection Associated with Altitude and Temperature. Animals (Basel) 2020; 10:ani10030447. [PMID: 32156058 PMCID: PMC7142781 DOI: 10.3390/ani10030447] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/02/2020] [Accepted: 03/03/2020] [Indexed: 01/18/2023] Open
Abstract
Simple Summary Diptychus maculates and Gymnodiptychus dybowskii are two rare aboriginal fishes in the Xinjiang Uygur Autonomous Region. In recent years, due to overfishing and habitat fragmentation caused by construction of water conservancy and hydropower projects, the fishery resources have decreased sharply. Understanding the genetic background is of great significance for resource protection. In this study, we revealed the similar trends of population genetic diversities in these two species collected from the Tarim River and the Yili River. In addition, outlier SNPs associated with temperature and altitude were detected in both of them, indicating that Schizothoracinae fishes represented by D. maculates and G. dybowskii were still under the selection pressure of plateau environments. Abstract Schizothoracins are a group of cyprinid fishes distributed throughout the Qinghai–Tibet Plateau, which can be classified in three grades: primitive, specialised and highly specialised according to adaptation ability to plateau environments. As the only specialised schizothoracins in Xinjiang, China, Diptychus maculates and Gymnodiptychus dybowskii are ideal materials for adaptive evolution research. Based on single-nucleotide polymorphism (SNP) loci detected by specific-locus amplified fragment (SLAF) technology, the genome-wide genetic diversities of these two species from nine sites in Xinjiang were evaluated. D.maculates in the Muzat River (BM) and G. dybowskii in the Kaidu River (LKG) presented the lowest genetic diversity levels, whereas D. maculates in the Kumarik River (BK) and G.dybowskii in the Kashi River (LK) were just the opposite. Cluster and principal component analysis demonstrated a distant genetic affinity between D. maculates in the Tashkurgan River (BT) and other populations. Outlier SNP loci were discovered both in D. maculates and G. dybowskii. The coalescent Bayenv and latent factor mixed model (LFMM) methods showed that a total of thirteen and eighteen SNPs in D. maculates were associated with altitude and temperature gradient, respectively. No intersection was revealed in G. dybowskii. The results indicated that D. maculates was subject to much greater divergent selection pressure. A strong signal of isolation-by-distance (IBD) was detected across D. maculates (Mantel test, rs = 0.65; p = 0.05), indicating an evident geographical isolation in the Tarim River. Isolation-by-environment (IBE) analysis implied that temperature and altitude selections were more intensive in D. maculates, with greater environmental variation resulting in weak gene flow.
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Affiliation(s)
- Tianyan Yang
- College of Fishery, Zhejiang Ocean University, Zhoushan 316022, China;
| | - Wei Meng
- Marine Fisheries Research Institute of Zhejiang, Key Laboratory of Sustainable Utilization of Technology Research for Fisheries Resources of Zhejiang Province, Scientific Observing and Experimental Station of Fishery Resources for Key Fishing Grounds, Ministry of Agriculture, Zhoushan 316021, China
- Correspondence: (W.M.); (B.G.); Tel.: +86-580-229-9888 (W.M.); +86-10-6480-7978 (B.G.)
| | - Baocheng Guo
- Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (W.M.); (B.G.); Tel.: +86-580-229-9888 (W.M.); +86-10-6480-7978 (B.G.)
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Feng C, Tang Y, Liu S, Tian F, Zhang C, Zhao K. Multiple convergent events created a nominal widespread species: Triplophysa stoliczkae (Steindachner, 1866) (Cobitoidea: Nemacheilidae). BMC Evol Biol 2019; 19:177. [PMID: 31484504 PMCID: PMC6724303 DOI: 10.1186/s12862-019-1503-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 08/26/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Triplophysa stoliczkae is the most widespread species in the genus Triplophysa and may have originated from morphological convergence. To understand the evolutionary history of T. stoliczkae, we employed a multilocus approach to investigate the phylogenetics and the morphological evolution of T. stoliczkae on the Qinghai-Tibetan Plateau. RESULTS All phylogenetic analyses (two mitochondrial and five nuclear loci), a genealogical sorting index and species tree inferences suggested that T. stoliczkae consists of distinct lineages that were not closest relatives. The time estimation indicated that the divergence events between "T. stoliczkae" and other Triplophysa species occurred from approximately 0.10 to 4.51 Ma. The ancestral state analyses supported the independent evolution of T. stoliczkae morphology in distinct lineages. The morphometric analysis and convergence estimates demonstrated significant phenotypic convergence among "T. stoliczkae" lineages. CONCLUSIONS Triplophysa stoliczkae includes 4 different lineages with similar morphologies. The increasingly harsh environments that have occurred since the Pliocene have driven the occurrences of scrape-feeding fish in the genus Triplophysa. Morphological adaptations associated with scrape-feeding behavior resulted in convergences and the artificial lumping of four different species in the nominal taxon T. stoliczkae. A taxonomic revision for T. stoliczkae is needed.
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Affiliation(s)
- Chenguang Feng
- Key Laboratory of Adaptation and Evolution of Plateau Biota, and Laboratory of Plateau Fish Evolutionary and Functional Genomics, and Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, No. 23 Xinning Road, Xining, 810008, Qinghai, China.,Center for Ecological and Environmental Sciences, Key Laboratory for Space Bioscience and Biotechnology, Northwestern Polytechnical University, Xi'an, 710072, Shaanxi, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yongtao Tang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, and Laboratory of Plateau Fish Evolutionary and Functional Genomics, and Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, No. 23 Xinning Road, Xining, 810008, Qinghai, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Sijia Liu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, and Laboratory of Plateau Fish Evolutionary and Functional Genomics, and Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, No. 23 Xinning Road, Xining, 810008, Qinghai, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fei Tian
- Key Laboratory of Adaptation and Evolution of Plateau Biota, and Laboratory of Plateau Fish Evolutionary and Functional Genomics, and Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, No. 23 Xinning Road, Xining, 810008, Qinghai, China
| | - Cunfang Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, and Laboratory of Plateau Fish Evolutionary and Functional Genomics, and Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, No. 23 Xinning Road, Xining, 810008, Qinghai, China
| | - Kai Zhao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, and Laboratory of Plateau Fish Evolutionary and Functional Genomics, and Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, No. 23 Xinning Road, Xining, 810008, Qinghai, China.
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6
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Wang T, Qi D, Sun S, Liu Z, Du Y, Guo S, Ma J. DNA barcodes and their characteristic diagnostic sites analysis of Schizothoracinae fishes in Qinghai province. Mitochondrial DNA A DNA Mapp Seq Anal 2019; 30:592-601. [PMID: 30952197 DOI: 10.1080/24701394.2019.1580273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The Qinghai-Tibetan Plateau (QTP), the source and upper reaches of many Asian rivers, are crisscrossed by rivers and dotted with lakes. Schizothoracinae fishes, species native to the QTP, are distributed widely through these rivers and lakes. Over the past decades, ecological protection has become increasingly intense. The rapid acquisition of the genetic information and accurate gene sequence database are assumed to play an important role in the conservation of species diversity and biodiversity. In this study, 153 COI sequences (648bp in length) covering 13 species in 8 genera of Schizothoracinae fishes in Qinghai Province were used to determine whether barcode could identify Schizothoracinae species accurately. The average Kimura two parameter (K2P) genetic distances within and among species were 0.35% and 8.83%, respectively. The maximum K2P distance within species was observed in Gymnocypris eckloni (1.36%) while minimum K2P distance among species was observed between Chuanchia labiosa and Schizopygopsis pylzovi (0.23%). Overlaps existed in K2P distance intra- and inter- species based on both the genes. Eleven groups with 9 single-species groups and 2 multi-species groups were identified through Automatic Barcode Gap Discovery System, which were consistent with the overlaps of K2P distance. 96.7% as the accurate ratio for COI barcode was calculated and high solution was observed in the phylogenetic trees based on COI gene and Cyt b gene. Except for the similar results based on two genes above, COI barcode was more economical than Cyt b gene. The SOM model successfully predicted characteristic-diagnostic sites at species level: 36 characteristic-diagnostic sites from eight species, in which 12 from Gmnodiptychus pachycgeilus, 2 from Platypharodon extremus, 7 from Ptychobarbus kaznakovi, 2 from Schizopygopsis anteroventris, 2 from Schizopygopsis malacanthus, 3 from Schizopygopsis malacanthus chengi, 3 from Schizothorax dolichonema and 5 from Schizothorax lantsangensis. Our results show that Schizothoracinae fishes can be identified validly by using COI DNA barcode. Thirty-six characteristic-diagnostic sites were proposed to be applied into works of species identification for the Schizothoracinae fishes in Qinghai Province.
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Affiliation(s)
- Ting Wang
- a College of Life Sciences , Qinghai Normal University , Xining , China.,b Key Laboratory of Medicinal Plant and Animal Resources of Qinghai-Tibetan Plateau in Qinghai Province , Xining , China
| | - Desheng Qi
- a College of Life Sciences , Qinghai Normal University , Xining , China.,b Key Laboratory of Medicinal Plant and Animal Resources of Qinghai-Tibetan Plateau in Qinghai Province , Xining , China
| | - Shihao Sun
- a College of Life Sciences , Qinghai Normal University , Xining , China.,b Key Laboratory of Medicinal Plant and Animal Resources of Qinghai-Tibetan Plateau in Qinghai Province , Xining , China
| | - Zhonghao Liu
- a College of Life Sciences , Qinghai Normal University , Xining , China.,b Key Laboratory of Medicinal Plant and Animal Resources of Qinghai-Tibetan Plateau in Qinghai Province , Xining , China
| | - Yurong Du
- a College of Life Sciences , Qinghai Normal University , Xining , China.,b Key Laboratory of Medicinal Plant and Animal Resources of Qinghai-Tibetan Plateau in Qinghai Province , Xining , China
| | - Songchang Guo
- c College of Animal Science and Technology , Hunan Agricultural University , Changsha , China
| | - Jianbin Ma
- a College of Life Sciences , Qinghai Normal University , Xining , China.,b Key Laboratory of Medicinal Plant and Animal Resources of Qinghai-Tibetan Plateau in Qinghai Province , Xining , China
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Convergent evolution misled taxonomy in schizothoracine fishes (Cypriniformes: Cyprinidae). Mol Phylogenet Evol 2019; 134:323-337. [PMID: 30641272 DOI: 10.1016/j.ympev.2019.01.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 12/26/2018] [Accepted: 01/07/2019] [Indexed: 12/23/2022]
Abstract
Highly specialized grade (HSG; genera Gymnocypris, Oxygymnocypris, Schizopygopsis, Platypharodon and Chuanchia) of the Schizothoracinae (Cypriniformes: Cyprinidae) are endemic to the Qinghai-Tibet Plateau (QTP). Previously, two distinct ecomorphs were recognized according to trophic traits. One was a limnetic omnivore with normal lower jaw morphology, terminal mouth, and moderate or dense gill rakers, mostly inhabiting in open water of lakes, including Gymnocypris and Oxygymnocypris. Another was a benthic feeder with inferior mouth, sparse gill rakers and sharp horny sheath on the lower jaw for scraping of attached prey off hard substrates, including Schizopygopsis, Platypharodon and Chuanchia. However, traditional taxonomy of HSG based on these trophic traits presented extensive conflicts with the molecular studies in recent years. The possible cause could be convergent evolution in morphology, retention of ancestral polymorphisms or mitochondrial introgression, but these hypotheses could not be assessed due to incomplete taxon sampling and only mitochondrial data employed in previous works. Here, we conducted the most comprehensive molecular analysis on HSG fishes to date, using four mitochondrial loci and 152,464 genome-wide SNPs, and including 21 of 24 putative species and one undescribed Schizopygopsis species. Both SNP and mtDNA trees confirmed extensive paraphyly of genera Gymnocypris and Schizopygopsis, where species often were clustered together by watershed instead of by genus. Basal split into the north clade B and the south clade C (ca. 3.03 Ma) approximately by the Tanggula-Tanitawen Mountains in SLAF tree coincided with a violent uplift of the QTP during the phase A of 'Qingzang movement' (ca. 3.6 Ma). Ancestral state reconstruction of the trophic ecomorph showed that the limnetic omnivore ecomorph had evolved repeatedly in clade B and C. Furthermore, we presented a striking case of convergent evolution between two 'subspecies' Gymnocypris chui chui and G. chui longimandibularis, which had diverged as early as two million years ago (ca. 2.42 Ma). Ecological analyses revealed that similar food utilization, particularly in zooplankton, was the main underlying driving force. This work showed an example of taxonomy with the most extensive errors at the genus/species levels due to convergent evolution and suggested that trophic traits could be misleading in fish taxonomy. Therefore, we propose a major generic revision for HSG species.
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Wanghe K, Tang Y, Tian F, Feng C, Zhang R, Li G, Liu S, Zhao K. Phylogeography of Schizopygopsis stoliczkai (Cyprinidae) in Northwest Tibetan Plateau area. Ecol Evol 2017; 7:9602-9612. [PMID: 29187993 PMCID: PMC5696390 DOI: 10.1002/ece3.3452] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 08/14/2017] [Accepted: 08/17/2017] [Indexed: 11/27/2022] Open
Abstract
Schizopygopsis stoliczkai (Cyprinidae, subfamily Schizothoracinae) is one of the major freshwater fishes endemic to the northwestern margin of the Tibetan Plateau. In the current study, we used mitochondrial DNA markers cytochrome b (Cyt b) and 16S rRNA (16S), as well as the nuclear marker, the second intron of the nuclear beta-actin gene (Act2), to uncover the phylogeography of S. stoliczkai. In total, we obtained 74 haplotypes from 403 mitochondrial concatenated sequences. The mtDNA markers depict the phylogenetic structures of S. stoliczkai, which consist of clade North and clade South. The split time of the two clades is dated back to 4.27 Mya (95% HPD = 1.96-8.20 Mya). The estimated split time is earlier than the beginning of the ice age of Pleistocene (2.60 Mya), suggesting that the northwestern area of the Tibetan Plateau probably contain at least two glacial refugia for S. stoliczkai. SAMOVA supports the formation of four groups: (i) the Karakash River group; (ii) The Lake Pangong group; (iii) the Shiquan River group; (iv) the Southern Basin group. Clade North included Karakash River, Lake Pangong, and Shiquan River groups, while seven populations of clade South share the haplotypes. Genetic diversity, star-like network, BSP analysis, as well as negative neutrality tests indicate recent expansions events of S. stoliczkai. Conclusively, our results illustrate the phylogeography of S. stoliczkai, implying the Shiquan River is presumably the main refuge for S. stoliczkai.
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Affiliation(s)
- Kunyuan Wanghe
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau BiologyChinese Academy of SciencesXiningQinghaiChina
- Laboratory of Plateau Fish Evolutionary and Functional GenomicsNorthwest Institute of Plateau BiologyChinese Academy of SciencesXiningQinghaiChina
- Qinghai Key Laboratory of Animal Ecological GenomicsXiningQinghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yongtao Tang
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau BiologyChinese Academy of SciencesXiningQinghaiChina
- Laboratory of Plateau Fish Evolutionary and Functional GenomicsNorthwest Institute of Plateau BiologyChinese Academy of SciencesXiningQinghaiChina
- Qinghai Key Laboratory of Animal Ecological GenomicsXiningQinghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Fei Tian
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau BiologyChinese Academy of SciencesXiningQinghaiChina
- Laboratory of Plateau Fish Evolutionary and Functional GenomicsNorthwest Institute of Plateau BiologyChinese Academy of SciencesXiningQinghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Chenguang Feng
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau BiologyChinese Academy of SciencesXiningQinghaiChina
- Laboratory of Plateau Fish Evolutionary and Functional GenomicsNorthwest Institute of Plateau BiologyChinese Academy of SciencesXiningQinghaiChina
- Qinghai Key Laboratory of Animal Ecological GenomicsXiningQinghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | | | - Guogang Li
- Xishuangbanna Tropical Botanical GardenChinese Academy of SciencesMenglaChina
| | - Sijia Liu
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau BiologyChinese Academy of SciencesXiningQinghaiChina
- Laboratory of Plateau Fish Evolutionary and Functional GenomicsNorthwest Institute of Plateau BiologyChinese Academy of SciencesXiningQinghaiChina
- Qinghai Key Laboratory of Animal Ecological GenomicsXiningQinghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Kai Zhao
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau BiologyChinese Academy of SciencesXiningQinghaiChina
- Laboratory of Plateau Fish Evolutionary and Functional GenomicsNorthwest Institute of Plateau BiologyChinese Academy of SciencesXiningQinghaiChina
- University of Chinese Academy of SciencesBeijingChina
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Cheng J, Lv X, Xia L, Ge D, Zhang Q, Lu L, Yang Q. Impact of Orogeny and Environmental Change on Genetic Divergence and Demographic History of Dipus sagitta (Dipodoidea, Dipodinae) since the Pliocene in Inland East Asia. J MAMM EVOL 2017. [DOI: 10.1007/s10914-017-9397-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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10
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Wang X, Gan X, Li J, Chen Y, He S. Cyprininae phylogeny revealed independent origins of the Tibetan Plateau endemic polyploid cyprinids and their diversifications related to the Neogene uplift of the plateau. SCIENCE CHINA-LIFE SCIENCES 2016; 59:1149-1165. [PMID: 27646682 DOI: 10.1007/s11427-016-0007-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 07/13/2016] [Indexed: 11/28/2022]
Abstract
Origin and diversification of the Tibetan polyploid cyprinids (schizothoracins) may help us to explore relationships between diversification of the cyprinids and the Tibetan Plateau uplift. Cyprininae phylogeny was analyzed using mitochondrial and nuclear DNA sequences to trace origins of polyploidy and diversifications of schizothoracins. Ancestral states reconstruction for ploidy levels indicated that the Cyprininae was diploid origin and the schizothoracin clades tetraploid origins. There were two diversification rate shifts along with diversification of the cyprinine fishes in response to the Tibetan uplift. The unusual diversification shifts were located to branches subtending the clades of Tibetan polyploid cyprinids. Our analyses suggested that (i) phylogeny of Cyprininae recovered two independent origins of the Tibetan polyploidy schizothoracins; (ii) diversifications of the schizothoracins were closely related to the Neogene uplift of the Tibetan plateau in the following ways: the relatively ancient Late Oligocene-Middle Miocene adaptive radiation may be associated with the uplift of the southern Tibet and Himalaya; the Middle Miocene-Early Pleistocene lineage-specific diversification broadly coincident with major phase of the Neogene Tibetan uplift; and the most recent Pleistocene diversification shift in Schizothorax closely coincident with the successive Kunlun-Huanghe and Gonghe movements of the Tibetan uplift and the glaciation-induced climate oscillations on the plateau.
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Affiliation(s)
- Xuzhen Wang
- Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Xiaoni Gan
- Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Junbing Li
- Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Yiyu Chen
- Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Shunping He
- Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
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Li G, Tang Y, Zhang R, Zhao K. Phylogeography of Diptychus maculatus (Cyprinidae) endemic to the northern margin of the QTP and Tien Shan region. BMC Evol Biol 2016; 16:186. [PMID: 27613240 PMCID: PMC5017051 DOI: 10.1186/s12862-016-0756-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 08/26/2016] [Indexed: 11/11/2022] Open
Abstract
Background Phylogeography and historical demography of the cyprinid fish Diptychus maculatus (subfamily Schizothoracinae) are evaluated across three river systems in the Northern Qinghai-Tibetan Plateau (QTP) and Tien Shan range: the Indus River, Tarim River and Ili River. Results Results from both mtDNA (16S rRNA, Cyt b and D-loop) and nucDNA (RAG-2) resolved four reciprocally monophyletic clades, representing populations from Indus River, South Tarim River, North Tarim River and Ili River, respectively. The divergence times was estimated to be 1.5–2.5 Mya. It is consistent with the hypothesis that the split of four clades is the consequence of vicariance resulting from both the intensive uplift of QTP and Tien Shan as well as the resultant expansion of the Taklimakan Desert. Several lines of evidences indicate dynamic demographic histories for the populations, with late Pleistocene and Holocene population bottlenecks and expansions except the Indus River. Conclusions Our results clearly depicted the phylogenetic relationship of D. maculatus from Indus River, Tarim River and Ili River. The analyses implicated the relationship among the distribution of D. maculatus, paleo-drainages and geographic events, and implied the existence of the South Tarim River in history. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0756-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Guogang Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, No. 23 Xinning Road, Xining, Qinghai, 810001, China.,Laboratory of Plateau Fish Evolutionary and Functional Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, No. 23 Xinning Road, Xining, Qinghai, 810001, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yongtao Tang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, No. 23 Xinning Road, Xining, Qinghai, 810001, China.,Laboratory of Plateau Fish Evolutionary and Functional Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, No. 23 Xinning Road, Xining, Qinghai, 810001, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Renyi Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, No. 23 Xinning Road, Xining, Qinghai, 810001, China.,Laboratory of Plateau Fish Evolutionary and Functional Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, No. 23 Xinning Road, Xining, Qinghai, 810001, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Kai Zhao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, No. 23 Xinning Road, Xining, Qinghai, 810001, China. .,Laboratory of Plateau Fish Evolutionary and Functional Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, No. 23 Xinning Road, Xining, Qinghai, 810001, China.
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Li G, Peng Z, Zhang R, Tang Y, Tong C, Feng C, Zhang C, Zhao K. Mito-nuclear phylogeography of the cyprinid fishGymnodiptychus dybowskiiin the arid Tien Shan region of Central Asia. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12724] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Guogang Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xining Qinghai China
- Laboratory of Plateau Fish Evolutionary and Functional Genomics; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xining Qinghai China
- University of Chinese Academy of Sciences; Beijing China
| | - Zuogang Peng
- Key Laboratory of Freshwater Fish; Reproduction and Development (Ministry of Education); Southwest University School of Life Sciences; Chongqing China
| | - Renyi Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xining Qinghai China
- Laboratory of Plateau Fish Evolutionary and Functional Genomics; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xining Qinghai China
- University of Chinese Academy of Sciences; Beijing China
| | - Yongtao Tang
- Key Laboratory of Adaptation and Evolution of Plateau Biota; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xining Qinghai China
- Laboratory of Plateau Fish Evolutionary and Functional Genomics; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xining Qinghai China
- University of Chinese Academy of Sciences; Beijing China
| | - Chao Tong
- Key Laboratory of Adaptation and Evolution of Plateau Biota; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xining Qinghai China
- Laboratory of Plateau Fish Evolutionary and Functional Genomics; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xining Qinghai China
- University of Chinese Academy of Sciences; Beijing China
| | - Chenguang Feng
- Key Laboratory of Adaptation and Evolution of Plateau Biota; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xining Qinghai China
- Laboratory of Plateau Fish Evolutionary and Functional Genomics; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xining Qinghai China
- University of Chinese Academy of Sciences; Beijing China
| | - Cunfang Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xining Qinghai China
- Laboratory of Plateau Fish Evolutionary and Functional Genomics; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xining Qinghai China
| | - Kai Zhao
- Key Laboratory of Adaptation and Evolution of Plateau Biota; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xining Qinghai China
- Laboratory of Plateau Fish Evolutionary and Functional Genomics; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xining Qinghai China
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