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Chen W, Hubert N, Li Y, Zhu S, Wang J, Xiang D, Gao S, Kou C, Wang J, Wang T, Liang Z, Wu J, Li X, Li J. Mitogenomic phylogeny, biogeography, and cryptic divergence of the genus Silurus (Siluriformes: Siluridae). Zool Res 2024; 45:711-723. [PMID: 38766761 PMCID: PMC11298680 DOI: 10.24272/j.issn.2095-8137.2023.311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 12/25/2023] [Indexed: 05/22/2024] Open
Abstract
The genus Silurus, an important group of catfish, exhibits heterogeneous distribution in Eurasian freshwater systems. This group includes economically important and endangered species, thereby attracting considerable scientific interest. Despite this interest, the lack of a comprehensive phylogenetic framework impedes our understanding of the mechanisms underlying the extensive diversity found within this genus. Herein, we analyzed 89 newly sequenced and 20 previously published mitochondrial genomes (mitogenomes) from 13 morphological species to reconstruct the phylogenetic relationships, biogeographic history, and species diversity of Silurus. Our phylogenetic reconstructions identified eight clades, supported by both maximum-likelihood and Bayesian inference. Sequence-based species delimitation analyses yielded multiple molecular operational taxonomic units (MOTUs) in several taxa, including the Silurus asotus complex (four MOTUs) and Silurus microdorsalis (two MOTUs), suggesting that species diversity is underestimated in the genus. A reconstructed time-calibrated tree of Silurus species provided an age estimate of the most recent common ancestor of approximately 37.61 million years ago (Ma), with divergences among clades within the genus occurring between 11.56 Ma and 29.44 Ma, and divergences among MOTUs within species occurring between 3.71 Ma and 11.56 Ma. Biogeographic reconstructions suggested that the ancestral area for the genus likely encompassed China and the Korean Peninsula, with multiple inferred dispersal events to Europe and Central and Western Asia between 21.78 Ma and 26.67 Ma and to Japan between 2.51 Ma and 18.42 Ma. Key factors such as the Eocene-Oligocene extinction event, onset and intensification of the monsoon system, and glacial cycles associated with sea-level fluctuations have likely played significant roles in shaping the evolutionary history of the genus Silurus.
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Affiliation(s)
- Weitao Chen
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China
- China Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Guangzhou, Guangdong 510380, China
- Key Laboratory of Prevention and Control for Aquatic Invasive Alien Species, Ministry of Agriculture and Rural Affairs, Guangzhou, Guangdong 510380, China
- Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou, Guangdong 510380, China
| | - Nicolas Hubert
- Institut de Recherche pour le Développement, Montpellier, UMR 226 ISEM (UM-CNRS-IRD), France. E-mail:
| | - Yuefei Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China
- China Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Guangzhou, Guangdong 510380, China
- Key Laboratory of Prevention and Control for Aquatic Invasive Alien Species, Ministry of Agriculture and Rural Affairs, Guangzhou, Guangdong 510380, China
- Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou, Guangdong 510380, China
| | - Shuli Zhu
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China
- China Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Guangzhou, Guangdong 510380, China
- Key Laboratory of Prevention and Control for Aquatic Invasive Alien Species, Ministry of Agriculture and Rural Affairs, Guangzhou, Guangdong 510380, China
- Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou, Guangdong 510380, China
| | - Jun Wang
- State Key Laboratory of Eco-hydraulic in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, Shaanxi 710048, China
| | - Denggao Xiang
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China
| | - Shang Gao
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China
| | - Chunni Kou
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China
| | - Jilong Wang
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, Heilongjiang 150076, China
| | - Tai Wang
- Gansu Fisheries Research Institute, Lanzhou, Gansu 730030, China
| | - Zhiqiang Liang
- Hunan Fisheries Science Institute, Changsha, Hunan 410153, China
| | - Junjie Wu
- Yunnan Institute of Fishery Sciences Research, Kunming, Yunnan 650111, China
| | - Xinhui Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China
| | - Jie Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China
- China Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Guangzhou, Guangdong 510380, China
- Key Laboratory of Prevention and Control for Aquatic Invasive Alien Species, Ministry of Agriculture and Rural Affairs, Guangzhou, Guangdong 510380, China
- Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou, Guangdong 510380, China. E-mail:
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Deng Q, Li M, Yu D, Chen L, Li W, Cai X, Liu H. Molecular phylogenetic analysis of the East Asian hemicultrine fishes (Teleostei: Cyprinidae: Xenocypridinae), with suggestions to their generic classification and redescription of the recently described species Hemiculter yungaoi Vasil'eva et al. 2022. JOURNAL OF FISH BIOLOGY 2024; 105:239-253. [PMID: 38712539 DOI: 10.1111/jfb.15776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/15/2024] [Accepted: 04/17/2024] [Indexed: 05/08/2024]
Abstract
The hemicultrine fishes are a group of small-sized cyprinids, widely distributed but endemic to East Asian rivers and lakes. Till now, the taxonomic boundaries and relationships within this group remain poorly explored. In the present study, we study the phylogeny of this group, providing suggestions for classification of the hemicultrine group. Using two mitochondrial and three nuclear genes, and samples representing all genera, our results showed that the group consists of seven major lineages, of which four (Hemiculterella, Hainania, Pseudolaubuca, and Anabarilius) were monophyletic and three (Hemiculter, Toxabramis, and Pseudohemiculter) were not. Based on the phylogenetic tree, we redefined the genera. We revive the genus Siniichthys, which has three species, Siniichthys bleekeri, Siniichthys lucidus, and S. varpachovskii, that were previously treated as members of the genus Hemiculter but showed distant relationships to the genus Hemiculter in our phylogenetic tree. With the new results, a diagnostic key for clades of the hemicultrine group is provided. Furthermore, we provide more detailed information on diagnostic features of the recently described species Hemiculter yungaoi (Vasil'eva et al., 2022). This work will facilitate future systematic studies, pave the way for evolutionary studies, and provide valuable information for the urgent conservation of hemicultrine fishes.
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Affiliation(s)
- Qiaoling Deng
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mingzheng Li
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Dan Yu
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Lin Chen
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wenjing Li
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Xingwei Cai
- Hainan Academy of Ocean and Fisheries Sciences, Haikou, China
| | - Huanzhang Liu
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
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Park CW, Kim JG. A Comparative Morphological Study on the Characteristics of Egg Envelopes of Three Cultrinae Fishes (Cyprinidae, Teleostei) in Korea. Life (Basel) 2024; 14:840. [PMID: 39063594 PMCID: PMC11277662 DOI: 10.3390/life14070840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 06/05/2024] [Accepted: 06/27/2024] [Indexed: 07/28/2024] Open
Abstract
Three species of subfamily Cultrinae currently live in Korea, but Erythroculter erythropterus has been introduced into the Nakdonggang River and has taken over the habitat, reducing the habitat of Culter brevicauda. Only the endangered species C. brevicauda still lives in the Yeongsangang River, and it is necessary to be careful not to introduce E. erythropterus in the future. Hemiculter eigenmanni is also found throughout the country. In order to effectively manage and conserve the species in its various habitats and against invasions, this study was initiated. The ultrastructure of the egg envelopes of three species of Cultrinae inhabiting the Geumgang and Yeongsangang Rivers-E. erythropterus, C. brevicauda, and H. eigenmanni-were observed. It was found that the zona radiata of the egg envelopes of all three species were divided into two layers, an outer and inner layer, with the outer surface having a non-structural form. This form is characteristic of fishes with muddy, stagnant habitats or spawning grounds. The number of pore canals on the surface of the egg envelopes was 83 for E. erythropterus, 75 for C. brevicauda, and 58 for H. eigenmanni per 10 μm2, and the thickness was 7.89 ± 0.34 μm, 12.27 ± 0.46 μm, and 7.42 ± 0.24 μm, respectively. The shape of the micropyle demonstrated a funnel shape narrowing toward the inner diameter in all three species, and the size of the inner diameter was 6.62 ± 0.29 μm in E. erythropterus, 4.19 ± 0.39 μm in C. brevicauda, and 3.98 ± 0.46 μm in H. eigenmanni. The differences between species were identified in the number of pore canals, thickness, and micropyle inner diameter of egg envelopes, which were species-specific. Our study reveals a morphological mechanism in the egg envelope that prevents the formation of interspecific hybrids, and these features can be taxonomic traits that clarify species names. It also provides useful data for the production (breeding) of the second generation in aquaculture.
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Affiliation(s)
- Cheol-Woo Park
- Alpha Research and Ecology Institute, Gunsan 54151, Republic of Korea;
- Department of Biological Science, College of Natural Sciences, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Jae-Goo Kim
- Alpha Research and Ecology Institute, Gunsan 54151, Republic of Korea;
- Department of Biological Science, College of Natural Sciences, Jeonbuk National University, Jeonju 54896, Republic of Korea
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Zhou M, Xia J, Li C. Divergence of the freshwater sleeper, Neodontobutishainanensis (Chen, 1985) (Teleostei, Odontobutidae), in the Pearl River basin and on Hainan Island of southern China. Zookeys 2024; 1197:183-196. [PMID: 38725537 PMCID: PMC11079591 DOI: 10.3897/zookeys.1197.110314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 03/14/2024] [Indexed: 05/12/2024] Open
Abstract
Study of divergence of freshwater fish populations between island and adjacent mainland areas can shed light on the phylogeographical relationships of these regions. Neodontobutishainanensis is a freshwater fish species restricted to Hainan Island and in Guangdong and Guangxi provinces in the southern mainland China. We examine the phylogenetic relationship and population structure of N.hainanensis based on 3,176 nuclear loci using a gene-capture method. STRUCTURE analysis and principal coordinate analyses (PCA) indicate that populations from Guangdong, Guangxi and Hainan are each distinct, except that some individuals of the Guangdong population share minor genetic components with individuals of the Guangxi population. In the concatenated gene tree, the Hainan population is grouped with the Guangdong population, but the coalescent tree groups the Hainan population as the sister to the Guangxi population. Finally, coalescent simulations confirmed the divergence pattern supported by the coalescent tree and revealed a one-way introgression from the Guangxi population to the Guangdong population, which can explain the discordant results supported by the concatenated and coalescent phylogenetic analyses. Due to recent decline of N.hainanensis populations and the genetic patterns in this species, as revealed in this study, the populations in the three areas should be treated as separate conservation units.
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Affiliation(s)
- Mingwei Zhou
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, China
| | - Jianhong Xia
- Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Shanghai Ocean University, Shanghai 201306, China
| | - Chenhong Li
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, China
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Ni X, Chen Y, Deng G, Fu C. Pleistocene Landscape Dynamics Drives Lineage Divergence of a Temperate Freshwater Fish Gobio rivuloides in Coastal Drainages of Northern China. Genes (Basel) 2023; 14:2146. [PMID: 38136969 PMCID: PMC10743038 DOI: 10.3390/genes14122146] [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: 10/26/2023] [Revised: 11/20/2023] [Accepted: 11/26/2023] [Indexed: 12/24/2023] Open
Abstract
Understanding historical processes underlying lineage distribution patterns is a primary goal of phylogeography. We selected Gobio rivuloides (Cypriniformes: Gobionidae) as a model to improve our knowledge about how intraspecific genetic divergence of freshwater fishes arises in coastal drainages of northern China via statistical analysis using cytochrome b gene. The time-calibrated phylogeny of G. rivuloides showed the divergence of two major lineages (I and II) at ~0.98 Ma (million years ago). Lineage I can be divided into two sub-lineages (I-A and I-B) with a divergence time of ~0.83 Ma. Sub-lineage I-A inhabits the Amur River, and sub-lineage I-B lives in the Luan River and Liao River. Lineage II is distributed in the Yellow River and Hai River, with close genetic relationships between the two drainages, and can be split into two sub-lineages (II-C and II-D) with a divergence time of ~0.60 Ma. Our findings indicate that the splitting of lineages and sub-lineages could be attributed to geographic isolation caused by the formation of the Bohai Sea, river capture, and the episodic hydrologic closing of a paleolake during the late Lower-Middle Pleistocene. It is also the first report we know of displaying a clear phylogeographic break for freshwater fishes across coastal drainages in northern China.
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Affiliation(s)
| | | | | | - Cuizhang Fu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of the Yangtze River Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai 200438, China; (X.N.); (Y.C.); (G.D.)
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Wu YH, Hou SB, Yuan ZY, Jiang K, Huang RY, Wang K, Liu Q, Yu ZB, Zhao HP, Zhang BL, Chen JM, Wang LJ, Stuart BL, Chambers EA, Wang YF, Gao W, Zou DH, Yan F, Zhao GG, Fu ZX, Wang SN, Jiang M, Zhang L, Ren JL, Wu YY, Zhang LY, Yang DC, Jin JQ, Yin TT, Li JT, Zhao WG, Murphy RW, Huang S, Guo P, Zhang YP, Che J. DNA barcoding of Chinese snakes reveals hidden diversity and conservation needs. Mol Ecol Resour 2023. [PMID: 36924341 DOI: 10.1111/1755-0998.13784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 02/25/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023]
Abstract
DNA barcoding has greatly facilitated studies of taxonomy, biodiversity, biological conservation, and ecology. Here, we establish a reliable DNA barcoding library for Chinese snakes, unveiling hidden diversity with implications for taxonomy, and provide a standardized tool for conservation management. Our comprehensive study includes 1638 cytochrome c oxidase subunit I (COI) sequences from Chinese snakes that correspond to 17 families, 65 genera, 228 named species (80.6% of named species) and 36 candidate species. A barcode gap analysis reveals gaps, where all nearest neighbour distances exceed maximum intraspecific distances, in 217 named species and all candidate species. Three species-delimitation methods (ABGD, sGMYC, and sPTP) recover 320 operational taxonomic units (OTUs), of which 192 OTUs correspond to named and candidate species. Twenty-eight other named species share OTUs, such as Azemiops feae and A. kharini, Gloydius halys, G. shedaoensis, and G. intermedius, and Bungarus multicinctus and B. candidus, representing inconsistencies most probably caused by imperfect taxonomy, recent and rapid speciation, weak taxonomic signal, introgressive hybridization, and/or inadequate phylogenetic signal. In contrast, 43 species and candidate species assign to two or more OTUs due to having large intraspecific distances. If most OTUs detected in this study reflect valid species, including the 36 candidate species, then 30% more species would exist than are currently recognized. Several OTU divergences associate with known biogeographic barriers, such as the Taiwan Strait. In addition to facilitating future studies, this reliable and relatively comprehensive reference database will play an important role in the future monitoring, conservation, and management of Chinese snakes.
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Affiliation(s)
- Yun-He Wu
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Shao-Bing Hou
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, Yunnan, 650204, China
| | - Zhi-Yong Yuan
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Ke Jiang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Ru-Yi Huang
- Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Kai Wang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Qin Liu
- Faculty of Agriculture, Forest and Food Engineering, Yibin University, Yibin, Sichuan, 644007, China
| | - Zhong-Bin Yu
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Hai-Peng Zhao
- School of Life Science, Henan University, Kaifeng, Henan, 475001, China
| | - Bao-Lin Zhang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Jin-Min Chen
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Li-Jun Wang
- School of Life Sciences, Hainan Normal University, Haikou, Hainan, 571158, China
| | - Bryan L Stuart
- Section of Research & Collections, North Carolina Museum of Natural Sciences, Raleigh, North Carolina, 27601, USA
| | - E Anne Chambers
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, California, 94720, USA
| | - Yu-Fan Wang
- Zhejiang Forest Resource Monitoring Center, Hangzhou, Zhejiang, 310020, China
| | - Wei Gao
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Da-Hu Zou
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- College of Science, Tibet University, Lhasa, Tibet, 850000, China
| | - Fang Yan
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Gui-Gang Zhao
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Zhong-Xiong Fu
- Yunnan Senye Biotechnology Co., Ltd, Xishuangbanna, Yunnan, 666100, China
| | - Shao-Neng Wang
- Bureau of Guangxi Mao'er Mountain Nature Reserve, Guilin, Guangxi, 541316, China
| | - Ming Jiang
- Gongshan Bureau of Gaoligongshan National Nature Reserve, Gongshan, Yunnan, 650224, China
| | - Liang Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, Guangdong, 510260, China
| | - Jin-Long Ren
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, 610041, China
| | - Ya-Yong Wu
- Faculty of Agriculture, Forest and Food Engineering, Yibin University, Yibin, Sichuan, 644007, China
| | - Lu-Yang Zhang
- Beijing Mountains & Seas Eco Technology Co. Ltd, Beijing, 101100, China
| | - Dian-Cheng Yang
- Anhui Province Key Laboratory of the Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, 241000, China
| | - Jie-Qiong Jin
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Ting-Ting Yin
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Jia-Tang Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, 610041, China
| | - Wen-Ge Zhao
- College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang, 150025, China
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- Reptilia Zoo and Education Centre, Vaughn, Ontario, L4K 2N6, Canada
| | - Song Huang
- Anhui Province Key Laboratory of the Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, 241000, China
| | - Peng Guo
- Faculty of Agriculture, Forest and Food Engineering, Yibin University, Yibin, Sichuan, 644007, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
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7
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Panthum T, Ariyaphong N, Wattanadilokchatkun P, Singchat W, Ahmad SF, Kraichak E, Dokkaew S, Muangmai N, Han K, Duengkae P, Srikulnath K. Quality control of fighting fish nucleotide sequences in public repositories reveals a dark matter of systematic taxonomic implication. Genes Genomics 2023; 45:169-181. [PMID: 36512198 DOI: 10.1007/s13258-022-01353-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 12/02/2022] [Indexed: 12/15/2022]
Abstract
BACKGROUND The number of nucleotide sequences in public repositories has exploded recently. However, the data contain errors, leading to incorrect species identification. Several fighting fish (Betta spp.) are poorly described, with unresolved cryptic species complexes masking undescribed species. Here, DNA barcoding was used to detect erroneous sequences in public repositories. OBJECTIVE This study reflects the current quantitative and qualitative status of DNA barcoding in fighting fish and provides a rapid and reliable identification tool. METHODS A total of 1034 barcode sequences were analyzed from mitochondrial cytochrome c oxidase I (COI) and cytochrome b (Cytb) genes from 71 fighting fish species. RESULTS The nearest neighbor test showed the highest percentage of intraspecific nearest neighbors at 93.41% for COI and 91.67% for Cytb, which can be used as reference barcodes for certain taxa. Intraspecific variation was usually less than 13%, while most species differed by more than 54%. The barcoding gap, calculated from the difference between inter- and intraspecific sequence divergences, was negative in the COI data set indicating overlapping intra- and interspecific sequence divergence. Sequence saturation was observed in the Cytb data set but not in the COI data set. CONCLUSION The COI gene should thus be used as the main barcoding marker for fighting fish.
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Affiliation(s)
- Thitipong Panthum
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Faculty of Science, Interdisciplinary Graduate Program in Bioscience, Kasetsart University, Bangkok, 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Nattakan Ariyaphong
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Pish Wattanadilokchatkun
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Master of Science Program in Fishery Science and Technology (International Program), Faculty of Fisheries, Kasetsart University, Bangkok, 10900, Thailand
| | - Worapong Singchat
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Syed Farhan Ahmad
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Ekaphan Kraichak
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Department of Botany, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Sahabhop Dokkaew
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Narongrit Muangmai
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Kyudong Han
- Department of Microbiology, Dankook University, Cheonan, 31116, Korea
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, 31116, Korea
| | - Prateep Duengkae
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Faculty of Science, Interdisciplinary Graduate Program in Bioscience, Kasetsart University, Bangkok, 10900, Thailand.
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Master of Science Program in Fishery Science and Technology (International Program), Faculty of Fisheries, Kasetsart University, Bangkok, 10900, Thailand.
- Amphibian Research Center, Hiroshima University, 1-3-1, Kagamiyama, Higashihiroshima, 739-8526, Japan.
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8
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Li M, Yang X, Ni X, Fu C. The role of landscape evolution in the genetic diversification of a stream fish Sarcocheilichthys parvus from Southern China. Front Genet 2023; 13:1075617. [PMID: 36685913 PMCID: PMC9853433 DOI: 10.3389/fgene.2022.1075617] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 12/22/2022] [Indexed: 01/09/2023] Open
Abstract
Sarcocheilichthys parvus (Cypriniformes: Gobionidae) is a stream fish which is endemic to sub-tropical coastal drainages in southern China, thus offering a valuable model for understanding how genetic divergence arises in stream-adapting freshwater fishes in this region. Using the mitochondrial Cyt b gene, integrative analyses of phylogeny, population demography, and ancestral area and paleo-drainage reconstructions are carried out to explicitly explore the role of landscape evolution in genetic diversification of S. parvus. The time-calibrated phylogeny of S. parvus indicates the splitting of two major lineages (A and B) at ∼3.66 Ma. Lineage A inhabits the Poyang Lake sub-drainage of the middle Yangtze River, Han River and Pearl River, and can be split into two sub-lineages (A-I and A-II), where sub-lineage A-II can be further sub-divided into three infra-sub-lineages (A-IIa, A-IIb and A-IIc). Except for the infra-sub-lineage A-IIc, which is restricted to the Han River and Pearl River, the other sub-lineages and infra-sub-lineages live exclusively in the Poyang Lake sub-drainage. Lineage B lives in the lower Yangtze River, Qiantang River, Jiaojiang River and Ou River, displaying close genetic relationships among the drainages. Rapid population expansion has occurred since the Late Pleistocene. Our findings indicate that the splitting of lineages A and B could be attributed to geographic isolation due to the Zhe-Min Uplift, acting as a biogeographic barrier before the late Early Pleistocene. Furthermore, the strong genetic divergence within Lineage A could be explained by the isolation role of the Nanling Mountains and Poyang Lake acting as an ecological barrier; while the lack of phylogenetic structure within Lineage B may have been the result of paleo-drainage connections or episodic freshwater connections during the eustatic low stand of sea level in the late Middle-Late Pleistocene.
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Affiliation(s)
| | | | - Xiaomin Ni
- *Correspondence: Xiaomin Ni, ; Cuizhang Fu,
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9
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Zeng Q, Sun Y, Zhong H, Yang C, Qin Q, Gu Q. Population Genomic Evidence for the Diversification of Bellamya aeruginosa in Different River Systems in China. BIOLOGY 2022; 12:biology12010029. [PMID: 36671722 PMCID: PMC9855799 DOI: 10.3390/biology12010029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 12/18/2022] [Accepted: 12/20/2022] [Indexed: 12/28/2022]
Abstract
Clarifying the genetic structure can facilitate the understanding of a species evolution history. It is crucial for the management of germplasm resources and providing useful guidance for effective selective breeding. Bellamya is an economically and ecologically important freshwater snail for fish, birds and even humans. Population genetic structures of the Bellamya species, however, were unknown in previous studies. Population genomics approaches with tens to hundreds of thousands of single nucleotide polymorphisms (SNPs) make it possible to detect previously unidentified structures. The population genomic study of seven populations of B. aeruginosa across three river systems (Yellow River, Yangtze River and Pearl River) in China was conducted by SLAF-seq. SLAF-seq obtained a total of 4737 polymorphisms SLAF-tags and 25,999 high-consistency genome-wide SNPs. The population genetic structure showed a clear division among populations from the Yellow River basin (YH and WL) and the Pearl River basin (QSH and LB), as well as population YC from the Yangtze River basin using the SNPs data. However, there existed no distinct population structure using the mitochondrial DNA (mtDNA). The anthropogenic translocation from the Yangtze River basin to the Pearl River basin and the passive dispersion from the Yangtze River basin to the Yellow River basin by flooding have weakened the phylogeographic pattern of B. aeruginosa. The divergence of B. aeruginosa in the three river systems suggests that the anthropogenic dispersal for aquaculture and breeding requires serious consideration of the population structure for the preservation of genetic diversity and effective utilization of germplasm resources.
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10
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Wang J, Zhang W, Wu J, Li C, Ju YM, Lin HD, Zhao J. Multilocus Phylogeography and Population Genetic Analyses of Opsariichthys hainanensis Reveal Pleistocene Isolation Followed by High Gene Flow around the Gulf of Tonkin. Genes (Basel) 2022; 13:genes13101908. [PMID: 36292792 PMCID: PMC9602001 DOI: 10.3390/genes13101908] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/08/2022] [Accepted: 10/14/2022] [Indexed: 11/21/2022] Open
Abstract
The ichthyofauna of continental islands is characterized by immigration through a land bridge due to fluctuating sea levels. Hainan Island is adjacent to the southern margin of mainland China and provides opportunities for understanding the origin and diversification of freshwater fishes. The aim of our study was to evaluate the level of genetic variation and phylogeographic structure of Opsariichthys hainanensis on Hainan Island and mainland China, using mtDNA cyt b gene (1140 bp) and D-loop (926 bp), nuclear RAG1 gene (1506 bp), and 12 microsatellite loci. Mitochondrial phylogenetic analysis identified five major lineages according to the geographical distribution from different populations. We suggested that two dispersal events occurred: the population in the Changhua River migrated to the Red River (Lineage B), and the populations in the South Hainan region moved northwards to the North Hainan region. However, populations in Northwest Hainan Island dispersed to the populations around the Gulf of Tonkin (Lineage A1) and populations in Northeast Hainan Island dispersed to the populations in mainland China (Lineage A2). Our results indicated that the populations of O. hainanensis suffered a bottleneck event followed by a recent population expansion supported by the ABC analysis. We suggest that O. hainanensis populations were found mostly in the lowlands and a lack of suitable freshwater habitat in southern mainland China and Hainan during the Last Interglacial period, and then expansion occurred during the Last Glacial Maximum.
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Affiliation(s)
- Junjie Wang
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally-Friendly Aquaculture, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Wenjun Zhang
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally-Friendly Aquaculture, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Jinxian Wu
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally-Friendly Aquaculture, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Chao Li
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally-Friendly Aquaculture, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Yu-Min Ju
- National Museum of Marine Biology and Aquarium, Pingtung 94401, Taiwan
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - Hung-Du Lin
- The Affiliated School of National Tainan First Senior High School, Tainan 701, Taiwan
- Correspondence: (H.-D.L.); (J.Z.); Tel.: +886-6-2097821 (H.-D.L.); +86-020-85211372 (J.Z.)
| | - Jun Zhao
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally-Friendly Aquaculture, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China
- Correspondence: (H.-D.L.); (J.Z.); Tel.: +886-6-2097821 (H.-D.L.); +86-020-85211372 (J.Z.)
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11
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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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12
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Luo C, Chen P, Zhu J, Ma Z. The complete mitogenome of Hemiculter leucisculus (Basilewsky, 1855) in Hainan Island and its phylogenetic status. Mitochondrial DNA B Resour 2022; 7:396-398. [PMID: 35224195 PMCID: PMC8865130 DOI: 10.1080/23802359.2022.2040390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The sharpbelly, Hemiculter leucisculus (Basilewsky, 1855) is a small cyprinid fish that has a wide distribution in East Asia. In this study, we characterized the complete mitochondrial genome of H. leucisculus in Hainan Island using Illumina MiSeq platform. The mitogenome contained 16,621 bp with AT content of 56.2%. The mitogenome of H. leucisculus comprised 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and one control region (D-loop). Phylogenetic analyses indicated that H. leucisculus in the Hainan Island formed independent lineage and the species of H. leucisculus might be a paraphyletic taxon.
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Affiliation(s)
- Congqiang Luo
- Changde Research Center for Agricultural Biomacromolecule, Hunan University of Arts and Science, Changde, China
| | - Peng Chen
- Changde Win-win Environmental Consul Ting Service Co. LTD, Changde, China
| | - Jibin Zhu
- Changde Municipal Waterworks Co. LTD, Changde, China
| | - Zemin Ma
- Changde Research Center for Agricultural Biomacromolecule, Hunan University of Arts and Science, Changde, China
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13
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Guo J, Mo J, Qi Q, Peng J, Qi G, Kanerva M, Iwata H, Li Q. Prediction of adverse effects of effluents containing phenolic compounds in the Ba River on the ovary of fish (Hemiculter leucisculus) using transcriptomic and metabolomic analyses. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 801:149554. [PMID: 34467927 DOI: 10.1016/j.scitotenv.2021.149554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 07/22/2021] [Accepted: 08/05/2021] [Indexed: 06/13/2023]
Abstract
The aim of this work was to evaluate the endocrine disrupting effects on the ovarian development of sharpbelly (Hemiculter leucisculus) caused by effluents containing phenolic compounds. This was achieved using integrated transcriptomic and metabolomic analyses, along with histopathological examinations. Sharpbelly, an indigenous freshwater fish widely distributed in East Asia, were collected by pole fishing from three sampling sites in the Ba River. These sampling sites include a mid-stream site near a wastewater outfall and a reference site located upstream and a far field comparison site located downstream. In sharpbelly collected near the wastewater discharge, the oocyte development was activated, compared to the other two sites. Histopathological alterations in the fish ovaries were likely due to the upregulated steroid hormone biosynthesis process, as suggested by the differentially expressed genes (e.g., hsd3b, hsd17b1) and differentially accumulated metabolites (e.g., pregnenolone). Additionally, under the stress of effluents containing phenolic compounds, genes related to the signaling pathways for oxidative phosphorylation and leukocyte transendothelial migration were dysregulated, suggesting the potential induction of inflammation and several ovarian diseases. Overall, these findings suggest that effluents containing phenolic compounds influence ovary development and reproductive function of female sharpbelly. Whether there is any resulting dysfunction of folliculogenesis, abnormality of ovulation, production of premature eggs and/or potential induction of ovarian cancers remains to be determined by further studies, for a better evaluation on effluents containing phenolic compounds to the fish fertility and the health of their offspring, and even the stability of the wild fish population. Notably, the integration of transcriptomics and metabolomics can complement the routine chemical analysis to comprehensively monitor the effects of wastewater treatment plant effluents on the health of wild fish.
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Affiliation(s)
- Jiahua Guo
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an 710127, China
| | - Jiezhang Mo
- State Key Laboratory of Marine Pollution and Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong, SAR, China
| | - Qianju Qi
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an 710127, China
| | - Jianglin Peng
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an 710127, China
| | - Guizeng Qi
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an 710127, China
| | - Mirella Kanerva
- Center for Marine Environmental Studies, Ehime University, Bunkyo-cho 2-5, Matsuyama 790-8577, Ehime prefecture, Japan
| | - Hisato Iwata
- Center for Marine Environmental Studies, Ehime University, Bunkyo-cho 2-5, Matsuyama 790-8577, Ehime prefecture, Japan
| | - Qi Li
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an 710127, China.
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14
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Shao WH, Cheng JL, Zhang E. Eight in One: Hidden Diversity of the Bagrid Catfish Tachysurus albomarginatus s.l. (Rendhal, 1928) Widespread in Lowlands of South China. Front Genet 2021; 12:713793. [PMID: 34868198 PMCID: PMC8635968 DOI: 10.3389/fgene.2021.713793] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 10/19/2021] [Indexed: 11/17/2022] Open
Abstract
There is increasing evidence that species diversity is underestimated in the current taxonomy of widespread freshwater fishes. The bagrid species T. albomarginatus s.l. is mainly distributed in the lowlands of South China, as currently identified. A total of 40 localities (including the type locality), which covers most of its known range, were sampled. Molecular phylogenetic analyses based on concatenated mtDNA and nuclear genes recover nine highly supported lineages clustering into eight geographic populations. The integration of molecular evidence, morphological data, and geographic distribution demonstrates the delineation of T. albomarginatus s.l. as eight putative species. Four species, namely, T. albomarginatus, T. lani, T. analis, and T. zhangfei sp. nov. and the T. similis complex are taxonomically recognized herein. Moreover, T. zhangfei sp. nov. comprises two genetically distinct lineages with no morphological and geographical difference. This study also reveals aspects of estimation of divergence time, distribution, and ecological adaption within the T. albomarginatus group. The unraveling of the hidden species diversity of this lowland bagrid fish highlights the need for not only the molecular scrutiny of widely distributed species of South China but also the adjustment of current biodiversity conservation strategies to protect the largely overlooked diversity of fishes from low-elevation rapids.
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Affiliation(s)
- Wei-Han Shao
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jian-Li Cheng
- School of Life Sciences, Jinggangshan University, Ji'an, China
| | - E Zhang
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
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15
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Zhang XL, Liu P, Xu SL, Rizo EZ, Zhang Q, Dumont HJ, Han BP. Geographic Variation of Phyllodiaptomus tunguidus Mitogenomes: Genetic Differentiation and Phylogeny. Front Genet 2021; 12:711992. [PMID: 34531896 PMCID: PMC8439380 DOI: 10.3389/fgene.2021.711992] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 08/03/2021] [Indexed: 12/04/2022] Open
Abstract
Phyllodiaptomus tunguidus (Copepoda: Calanoida) is largely endemic to and widespread in freshwater in southern China, where it inhabits a complex landscape from lowland to highland across an elevation gradient of 2000m. A deep genetic differentiation can be expected between its most distant geographic populations. Here, we sequenced nine mitogenomes from diverse populations. All mitogenomes contained 37 genes, including 13 protein-coding genes (PCG), two rRNA genes, 22 tRNA genes and one control region. Their base composition, genetic distance and tRNA structure indeed revealed a wide differentiation between mitogenomes. Two P. tunguidus from Guangxi near Vietnam differed from the other seven by up to 10.1%. Their tRNA-Arg had a complete clover-leaf structure, whereas that of the others did not contain an entire dihydrouridine arm. The nine mitogenomes also differed in the length of rRNA. NJ, ML, and Bayesian analyses all split them into two clades, viz. the two P. tunguidus from Guangxi (Clade 1), and the other seven (Clade 2). Both the structure and phylogeny of the mitogenomes suggest that P. tunguidus has complex geographic origin, and its populations in Clade 1 have long lived in isolation from those in Clade 2. They currently reach the level of subspecies or cryptic species. An extensive phylogenetic analysis of Copepoda further verified that Diaptomidae is the most recently diverging family in Calanoida and that P. tunguidus is at the evolutionary apex of the family.
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Affiliation(s)
- Xiao-Li Zhang
- Department of Ecology, Jinan University, Guangzhou, China
| | - Ping Liu
- Department of Ecology, Jinan University, Guangzhou, China
| | - Shao-Lin Xu
- Department of Ecology, Jinan University, Guangzhou, China
| | - Eric Zeus Rizo
- Department of Ecology, Jinan University, Guangzhou, China.,Division of Biological Sciences, College of Arts and Sciences, University of the Philippines Visayas, Iloilo, Philippines
| | - Qun Zhang
- Department of Ecology, Jinan University, Guangzhou, China
| | - Henri J Dumont
- Department of Ecology, Jinan University, Guangzhou, China.,Department of Biology, Ghent University, Ghent, Belgium
| | - Bo-Ping Han
- Department of Ecology, Jinan University, Guangzhou, China
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16
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Carvalho AF, Menezes RST, Miranda EA, Costa MA, Del Lama MA. Comparative phylogeography and palaeomodelling reveal idiosyncratic responses to climate changes in Neotropical paper wasps. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blaa215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
The impact of the broad disjunction between Amazonia and the Atlantic Forest on biodiversity has been the theme of several discussions in recent decades. Here, we evaluate the effects of dependence on humid environments and the role of historical factors on the level, distribution and structuring of genetic variation in widely distributed Neotropical insects. For such, we test whether climatically stable zones (i.e. refuges) in both Amazonia and the Atlantic Forest concentrate higher genetic diversity in the social paper wasps Angiopolybia pallens and Synoeca surinama. We found that historical events have avoided the interchange of A. pallens between both rainforests at least since the Early Pliocene and that ancient colonization in north-western Amazonia and the Bahia refuge significantly predicts genetic diversity in populations of this species. Conversely, the split between the Atlantic Forest and remaining western populations of S. surinama is more recent (Plio-Pleistocene); this species has considerably lower genetic diversity than A. pallens and such diversity is mostly concentrated in Amazonia and in the cerrado biome (savanna) than in the Atlantic Forest. Finally, we propose that the occurrence of species that exhibit such distribution patterns should be taken into consideration when establishing areas for conservation.
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Affiliation(s)
- Antônio F Carvalho
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
- Instituto Nacional da Mata Atlântica, Santa Teresa, Espírito Santo, Brazil
| | - Rodolpho S T Menezes
- Departamento de Biologia, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, Brazil
| | - Elder A Miranda
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, Brazil
- Observatório UniFG do Semiárido Nordestino, Núcleo de Pesquisa da Conservação e Biodiversidade do Semiárido – CONBIOS, Centro Universitário de Guanambi – UniFG, Guanambi, Guanambi, Bahia, Brazil
| | - Marco A Costa
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, Brazil
| | - Marco A Del Lama
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
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17
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Characterization of two complete mitochondrial genomes of Pterocryptis anomala (Siluridae) and its phylogeny and cryptic diversity. Biologia (Bratisl) 2021. [DOI: 10.2478/s11756-020-00582-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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18
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Xue X, Jia J, Yue X, Guan Y, Zhu L, Wang Z. River contamination shapes the microbiome and antibiotic resistance in sharpbelly (Hemiculter leucisculus). ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 268:115796. [PMID: 33120330 DOI: 10.1016/j.envpol.2020.115796] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 09/28/2020] [Accepted: 10/07/2020] [Indexed: 06/11/2023]
Abstract
Animals living in urban river systems play critical roles in the dissemination of microbiome and antibiotic resistance that poses a strong threat to public health. This study provides a comprehensive profile of microbiota and antibiotic resistance genes (ARGs) of sharpbelly (Hemiculter leucisculus) and the surrounding water from five sites along the Ba River. Results showed Proteobacteria, Firmicutes and Fusobacteria were the dominant bacteria in gut of H. leucisculus. With the aggravation of water pollution, bacterial biomass of fish gut significantly decreased and the proportion of Proteobacteria increased to become the most dominant phylum eventually. To quantify the contributions of influential factors on patterns of gut microbiome with structural equation model (SEM), water bacteria were confirmed to be the most stressors to perturb fish gut microbiome. SourceTracker model indicated that deteriorating living surroundings facilitated the invasion of water pathogens to fish gut eco-environments. Additionally, H. leucisculus gut is an important reservoir of ARGs in Ba River with relative abundance up to 9.86 × 10-1/copies. Among the ARGs, tetracycline and quinolone resistance genes were detected in dominant abundance. Deterioration of external environments elicited the accumulation of ARGs in fish gut. Intestinal class I integron, environmental heavy metal residues and gut bacteria were identified as key drivers of intestinal ARGs profiles in H. leucisculus. Analysis of SEM and co-occurrence patterns between ARGs and bacterial hosts indicated that class I integron and bacterial community played vital roles in ARGs transmission through water-fish pathway. In general, this study highlighted hazards of water contamination to microbiome and ARGs in aquatic animals and provided a new perspective to better understand the bacteria and ARGs dissemination in urban river ecosystems.
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Affiliation(s)
- Xue Xue
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jia Jia
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiaoya Yue
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yongjing Guan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Long Zhu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zaizhao Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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19
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Chen W, Li C, Yang J, Zhu S, Li J, Li Y, Li X. Temporal species-level composition of larvae resources in the lower Pearl River drainage and implications for species' reproductive cycles. Gene 2020; 776:145351. [PMID: 33333226 DOI: 10.1016/j.gene.2020.145351] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/04/2020] [Accepted: 12/01/2020] [Indexed: 11/30/2022]
Abstract
Resolving the temporal community composition of a larvae population can not only further our understanding of the regional species composition but also help us to infer the reproductive times of regional fish taxa, which can have implications on the development of effective monitoring and conservation policies for the regional fish stock. Nevertheless, correctly diagnosing the fish larvae is extremely challenging due to the paucity of diagnostic morphological characters at the species level. Based on daily larval samplings during March and October in 2018, this study combined morphological features with a DNA barcode technique to determine the species composition of fish larvae in the lower Pearl River drainage (LPR) and evaluate the spawning periods of identified species. Due to an absence of reference barcodes for LPR fishes, a DNA barcode library of adult fishes in the LPR was built for 384 individuals representing 78 morphological species. Analyses demonstrated the usability of the barcode library and uncovered many undetected mitochondrial lineages in 12 species. Morphological analyses performed on 81 temporal larval samples revealed 25 morphotypes and assigned 9 morphotypes into the species level. A total of 1624 larvae from 96 temporal larval samples were selected for molecular identification, and high quality barcoding sequences were obtained from 1391 larvae. We accurately assigned 1078 larvae to 37 species using our barcode library and published database. Among the identified species, a critically endangered species, namely, Ochetobius elongatus, and several invasive species were examined, providing a new perspective to assess the stock of regional endangered and invasive species. Furthermore, this study found high species diversity occurred primarily between May and September, and clarified the spawning periods of identified species inferred from the temporal occurrences of larvae. Above all, our study highlights the applicability to fish larval ecology to assist conservation and fishery management efforts.
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Affiliation(s)
- Weitao Chen
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, China; Experimental Station for Scientific Observation on Fishery Resources and Environment in the Middle and Lower Reaches of Pearl River, Zhaoqing, China
| | - Ce Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, China
| | - Jiping Yang
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, China; Experimental Station for Scientific Observation on Fishery Resources and Environment in the Middle and Lower Reaches of Pearl River, Zhaoqing, China
| | - Shuli Zhu
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, China; Experimental Station for Scientific Observation on Fishery Resources and Environment in the Middle and Lower Reaches of Pearl River, Zhaoqing, China
| | - Jie Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, China; Experimental Station for Scientific Observation on Fishery Resources and Environment in the Middle and Lower Reaches of Pearl River, Zhaoqing, China
| | - Yuefei Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, China; Experimental Station for Scientific Observation on Fishery Resources and Environment in the Middle and Lower Reaches of Pearl River, Zhaoqing, China.
| | - Xinhui Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, China; Experimental Station for Scientific Observation on Fishery Resources and Environment in the Middle and Lower Reaches of Pearl River, Zhaoqing, China.
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Li C, Jiang S, Schneider K, Jin J, Lin H, Wang J, Elmer KR, Zhao J. Cryptic species in White Cloud Mountain minnow, Tanichthys albonubes: Taxonomic and conservation implications. Mol Phylogenet Evol 2020; 153:106950. [PMID: 32889137 DOI: 10.1016/j.ympev.2020.106950] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 08/19/2020] [Accepted: 08/24/2020] [Indexed: 10/23/2022]
Abstract
Cryptic species describe two or more species that had mistakenly been considered to be a single species, a phenomenon that has been found throughout the tree of life. Recognizing cryptic species is key to estimating the real biodiversity of the world and understanding evolutionary processes. Molecular methods present an unprecedented opportunity for biologists to question whether morphologically similar populations are actually cryptic species. The minnow Tanichthys albonubes is a critically endangered freshwater fish and was classified as a second-class state-protected animal in China. Previous studies have revealed highly divergent lineages with similar morphological characters in this species. Herein, we tested for cryptic species across the ranges of all known wild populations of this minnow. Using multilocus molecular (one mitochondrial gene, two nuclear genes and 13 microsatellite loci) and morphological data for 230 individuals from eight populations, we found deep genetic divergence among these populations with subtle morphological disparity. Morphological examination found variance among these populations in the number of branched anal-fin rays. Based on genetic data, we inferred eight monophyletic groups that were well supported by haplotype network and population clustering analyses. Species delimitation methods suggested eight putative species in the T. albonubes complex. Molecular dating suggested that these cryptic species diverged in the period from the Pliocene to the Pleistocene. Based on these findings, we propose the existence of seven cryptic species in the T. albonubes complex. Our results highlight the need for a taxonomic revision of Tanichthys. What is more, the conservation status of and conservation strategies for the T. albonubes complex should be reassessed as soon as possible.
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Affiliation(s)
- Chao Li
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally Friendly Aquaculture, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China; Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland, UK
| | - Shuying Jiang
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally Friendly Aquaculture, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Kevin Schneider
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland, UK
| | - Jinjin Jin
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally Friendly Aquaculture, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Hungdu Lin
- The Affiliated School of National Tainan First Senior High School, Tainan, Taiwan
| | - Junjie Wang
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally Friendly Aquaculture, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Kathryn R Elmer
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland, UK
| | - Jun Zhao
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally Friendly Aquaculture, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China.
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21
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Coexistence of Two Closely Related Cyprinid Fishes (Hemiculter bleekeri and Hemiculter leucisculus) in the Upper Yangtze River, China. DIVERSITY 2020. [DOI: 10.3390/d12070284] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Species coexistence is one of the most important concepts in ecology for understanding how biodiversity is shaped and changed. In this study, we investigated the mechanism by which two small cyprinid fishes (H. leucisculus and H. bleekeri) coexist by analyzing their niche segregation and morphological differences in the upper Yangtze River. Morphological analysis indicated that H. leucisculus has posteriorly located dorsal fins, whereas H. bleekeri has a more slender body, bigger eyes, longer anal fin base, and a higher head. Niche segregation analysis showed spatial and trophic niche segregation between these two species: on the spatial scale, H. leucisculus was more widely distributed than H. bleekeri, indicating that H. leucisculus is more of a generalist in the spatial dimension; on the trophic scale, H. bleekeri had a wider niche than H. leucisculus. Therefore, these two species adopt different adaptation mechanisms to coexist
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22
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Ding XH, Hsu KC, Tang WQ, Liu D, Ju YM, Lin HD, Yang JQ. Genetic diversity and structure of the Chinese lake gudgeon ( Sarcocheilichthys sinensis). Mitochondrial DNA A DNA Mapp Seq Anal 2020; 31:228-237. [PMID: 32723222 DOI: 10.1080/24701394.2020.1779239] [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: 10/24/2022]
Abstract
Mitochondrial DNA cytochrome b and d-loop sequences (2,137 bp) in 65 specimens of Sarcocheilichthys sinensis from five populations were identified as two lineages (I and II). The pairwise genetic distance between lineages I and II was 1.94%. SAMOVA analyses suggested that the best grouping occurred at three groups, Yangtze, Qiantang and Minjiang Rivers. High haplotype diversity (0.949) and low nucleotide diversity (θ π = 1.067%) were detected. The results of the neutrality tests, mismatch distribution and approximate Bayesian computation (ABC) did not support demographic expansions. The results of phylogenetic analysis, statistical dispersal-vicariance analysis (S-DIVA), ABC, MIGRATE-N and the time to the most recent common ancestor (TMRCA) indicated two colonization routes. First, before the Wuyi Mountains lifted, S. sinensis dispersed from the Yangtze River to the Minjiang River. Second, during glaciation, the continental shelf was exposed, which contributed to the dispersion of populations from the Yangtze River.
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Affiliation(s)
- Xin-Hua Ding
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, China.,Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China.,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Kui-Ching Hsu
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China
| | - Wen-Qiao Tang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, China.,Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China.,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Dong Liu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, China.,Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China.,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Yu-Min Ju
- Department of Biology, National Museum of Marine Biology and Aquarium, Pingtung, Taiwan.,Graduate Institute of Marine Biology, National Dong Hwa University, Pingtung, Taiwan
| | - Hung-Du Lin
- Department of Biology, The Affiliated School of National Tainan First Senior High School, Tainan, Taiwan
| | - Jin-Quan Yang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, China.,Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China.,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
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23
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Inconspicuous genetic and morphological patterns challenge the taxonomic status of endemic species Bodianus insularis (Labridae). ZOOL ANZ 2020. [DOI: 10.1016/j.jcz.2020.03.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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24
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Zhang WJ, Wang JJ, Li C, Chen JQ, Li W, Jiang SY, Hsu KC, Zhao M, Lin HD, Zhao J. Spatial genetic structure of Opsariichthys hainanensis in South China. Mitochondrial DNA A DNA Mapp Seq Anal 2020; 31:98-107. [PMID: 32186219 DOI: 10.1080/24701394.2020.1741564] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
South China presents an excellent opportunity to build a phylogeographic paradigm for complex geological history, including mountain lifting, climate change, and river capture/reversal events. The phylogeography of cyprinids, particularly Opsariichthys hainanensis, an endemic species restricted to South China, was examined to explore the relationship between the populations in Red River, Hainan Island and its adjacent mainland China. A total of 37 haplotypes were genotyped for the mitochondrial cytochrome b (Cyt b) gene in 115 specimens from 11 river systems. Relatively high levels of haplotype diversity (h = 0.946) and low levels of nucleotide diversity (π = 0.014) were detected in O. hainanensis. Four major phylogenetic haplotype groups revealed a relationship between phylogeny and geography. Our results found that (i) the ancestral populations of O. hainanensis were distributed south of the Wuzhishan and Yinggeling mountains, including the Changhua River on Hainan Island, and then spread to the surrounding areas, (ii) the admixtures within lineages occurred between the Red River in North Vietnam and the Changhua River in western Hainan Island and (iii) indicated that the exposure of straits and shelves under water retreat, provides opportunities for population dispersion during glaciations.
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Affiliation(s)
- Wen-Jun Zhang
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally-friendly Aquaculture, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou, China
| | - Jun-Jie Wang
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally-friendly Aquaculture, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou, China
| | - Chao Li
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally-friendly Aquaculture, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou, China
| | - Jia-Qi Chen
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally-friendly Aquaculture, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou, China
| | - Wei Li
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally-friendly Aquaculture, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou, China
| | - Shu-Ying Jiang
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally-friendly Aquaculture, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou, China
| | - Kui-Ching Hsu
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China
| | - Meiting Zhao
- Department of Geography, South China Normal University, Guangzhou, China
| | - Hung-Du Lin
- The Affiliated School of National Tainan First Senior High School, Tainan, Taiwan
| | - Jun Zhao
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally-friendly Aquaculture, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou, China
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25
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Chen Z, Li H, Zhai X, Zhu Y, He Y, Wang Q, Li Z, Jiang J, Xiong R, Chen X. Phylogeography, speciation and demographic history: Contrasting evidence from mitochondrial and nuclear markers of the Odorrana graminea sensu lato (Anura, Ranidae) in China. Mol Phylogenet Evol 2020; 144:106701. [DOI: 10.1016/j.ympev.2019.106701] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 11/21/2019] [Accepted: 12/03/2019] [Indexed: 10/25/2022]
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26
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Seed germination schedule and environmental context shaped the population genetic structure of subtropical evergreen oaks on the Yun-Gui Plateau, Southwest China. Heredity (Edinb) 2019; 124:499-513. [PMID: 31772317 DOI: 10.1038/s41437-019-0283-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 11/02/2019] [Accepted: 11/05/2019] [Indexed: 11/08/2022] Open
Abstract
The evergreen broadleaved forests (EBLFs) of Southwest China have a long-term stable environment and support a diverse flora, thus forming a global biodiversity hotspot. However, the key drivers that have shaped the genetic diversity patterns of species in these EBLFs are not well understood. Quercus delavayi, Q. schottkyana, and Q. kerrii are sympatric oak species with different seed biological traits that are typical for these EBLFs. This study combined multilocus phylogeography and ecological niche modeling to screen 33 Q. delavayi populations. Their population genetic structure was inferred in comparison with previous studies on Q. schottkyana and Q. kerrii. The seed germination traits of all three species were also investigated. cpDNAs showed a significant phylogeographic structure in Q. delavayi, which was not detected in Q. schottkyana or Q. kerrii. Quercus delavayi, Q. kerrii, and Q. schottkyana exhibited different pollen-to-seed migration ratios (r = 219, 117, and 22, respectively), which are linked to the germination schedules of acorns. The distributions of Q. delavayi and Q. schottkyana remained long-term stable since the last glacial maximum (LGM) with a similar nSSR genetic gradient change along latitude. Instead, Q. kerrii experienced a prominent range expansion since the LGM with genetic diversification between the East and the West of the Tanaka line due to environmental heterogeneity. These results identify seed traits and environmental heterogeneity as two key drivers that shape the population genetic structure of EBLF trees in Southwest China. These should be considered in regional forestry conservation and management.
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Zhong J, Yi S, Ma L, Wang W. Evolution and phylogeography analysis of diploid and polyploid Misgurnus anguillicaudatus populations across China. Proc Biol Sci 2019; 286:20190076. [PMID: 31014220 PMCID: PMC6501937 DOI: 10.1098/rspb.2019.0076] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 04/03/2019] [Indexed: 12/14/2022] Open
Abstract
The origin and evolution of polyploid organisms have been extensively studied in plants, but this topic remains only partially understood in vertebrates, where polyploidy is relatively rare. In this study, we used Misgurnus anguillicaudatus, a fish that comprises five ploidy levels in nature, as a model animal to improve our understanding of biogeographic history and evolution of polyploid vertebrates. After collecting samples from different geographical populations in China, their ploidy levels were determined using flow cytometry. Two mitochondrial markers ( cytochrome b and control region) were then used for phylogeographic analyses to unravel the possible origins of diploids and tetraploids in China. The results showed that diploids have wider geographical distribution than tetraploids and triploids. There was no clear allopatric geographical range or boundary to divide diploid and polyploid populations. Rather, the analysis of mitochondrial DNA sequences indicated that tetraploids were autopolyploids, with lower genetic diversity than diploids. This suggests that tetraploids originated from sympatric diploids via multiple independent polyploidization events. Genetic structure patterns were similar between diploids and tetraploids, whereas complex genetic differentiation was found among different regions. The potential origin of M. anguillicaudatus was deduced to be in the Pearl River basin, which exhibited the highest nucleotide diversity and genetic differentiation. These findings provide insights into the evolution of polyploidy in vertebrates.
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Affiliation(s)
| | | | | | - Weimin Wang
- College of Fisheries, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
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28
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Du X, Zhang X, Bu H, Zhang T, Lao Y, Dong W. Molecular Analysis of Evolution and Origins of Cultivated Hawthorn ( Crataegus spp.) and Related Species in China. FRONTIERS IN PLANT SCIENCE 2019; 10:443. [PMID: 31024604 PMCID: PMC6465762 DOI: 10.3389/fpls.2019.00443] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 03/25/2019] [Indexed: 06/09/2023]
Abstract
Hawthorn is of high economic value owing to its medicinal properties and health benefits. Crataegus is a member of the Rosaceae family; the genus has a complicated taxonomic history, and several theories on its origin have been proposed. In this study, 53 accessions from seven Crataegus taxa native to China and accessions of exotic Crataegus species (two from Europe and one from North America) were analyzed by specific locus amplified fragment sequencing (SLAF-seq). In total, 933,450 single-nucleotide polymorphisms were identified after filtering and used to investigate the species' genomic evolution. Phylogenetic trees derived from nuclear simple sequence repeats (SSRs) and SLAF-seq data showed the same topology, in which Crataegus maximowiczii and Crataegus sanguineae formed a closely related cluster that was clearly separated from the cluster composed of Crataegus hupehensis, Crataegus pinnatifida, Crataegus pinnatifida var. major, Crataegus bretschneideri and Crataegus scabrifolia. Phylogenetic and structure analysis indicated that the seven Chinese Crataegus taxa had two separate speciation events. Plants that evolved the southwestern route shared the genepool with the European species, whereas plants along the northeastern route shared the genepool with the North American species. TreeMix genetic analysis revealed that C. bretschneideri may have a hybrid origin. This study provides valuable information on the origins of Chinese Crataegus and suggests an evolutionary model for the main Crataegus species that native to China.
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Affiliation(s)
- Xiao Du
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Xiao Zhang
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Haidong Bu
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
- Mudanjiang Branch of Heilongjiang Academy of Agricultural Sciences, Mudanjiang, China
| | - Ticao Zhang
- College of Chinese Material Medica, Yunnan University of Traditional Chinese Medicine, Kunming, China
| | - Yongchun Lao
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Wenxuan Dong
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
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29
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Wang S, Zhu Z, He J, Yue X, Pan J, Wang Z. Steroidal and phenolic endocrine disrupting chemicals (EDCs) in surface water of Bahe River, China: Distribution, bioaccumulation, risk assessment and estrogenic effect on Hemiculter leucisculus. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 243:103-114. [PMID: 30172116 DOI: 10.1016/j.envpol.2018.08.063] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 08/17/2018] [Accepted: 08/20/2018] [Indexed: 06/08/2023]
Abstract
This study investigated selected steroidal and phenolic endocrine disrupting compounds (EDCs) in the surface water of the Bahe River (China) using gas chromatography mass spectrometry (GC-MS). Their effect on the wild sharpbelly Hemiculter leucisculus was investigated. The concentrations of 4-t-octylphenol, nonylphenol, bisphenol-A, estrone, 17 β-estradiol, 17 α-Ethinylestradiol, and estriol were up to 126.0, 634.8, 1573.1, 55.9, 23.9, 31.5, and 5.2 ng L-1 in the surface water, and up to 26.4, 103.5, 146.9, 14.2, 9.3, 13.8, and 1.3 ng g-1 in the fish muscle tissue, respectively. High estrogen equivalent levels and hazard quotients were found in the middle and lower reaches of the river, and the pollution in these regions caused enhanced growth conditions, inhibition of gonad growth, and suppression of spermatogenesis in H. leucisculus. The up-regulation of Vitellogenin mRNA expression in male fish, collected from relatively heavily EDCs contaminated areas, indicates a potential estrogenic effect. The differential expression profiles of genes related to steroidogenesis at all sampling sites suggests that these endpoints may play an important role for the pollution monitoring of estrogenic EDCs in the Bahe River.
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Affiliation(s)
- Song Wang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, China
| | - Zeliang Zhu
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, China
| | - Jiafa He
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, China
| | - Xiaoya Yue
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, China
| | - Jianxiong Pan
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, China
| | - Zaizhao Wang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, China.
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30
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Evolution of Trichobaris (Curculionidae) in relation to host plants: Geometric morphometrics, phylogeny and phylogeography. Mol Phylogenet Evol 2018; 124:37-49. [PMID: 29486237 DOI: 10.1016/j.ympev.2018.02.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 01/31/2018] [Accepted: 02/16/2018] [Indexed: 11/22/2022]
Abstract
The family Curculionidae (Coleoptera), the "true" weevils, have diversified tightly linked to the evolution of flowering plants. Here, we aim to assess diversification at a lower taxonomic level. We analyze the evolution of the genus Trichobaris in association with their host plants. Trichobaris comprises eight to thirteen species; their larvae feed inside the fruits of Datura spp. or inside the stem of wild and cultivated species of Solanaceae, such as potato, tobacco and tomato. We ask the following questions: (1) does the rostrum of Trichobaris species evolve according to the plant tissue used to oviposit, i.e., shorter rostrum to dig in stems and longer to dig in fruits? and (2) does Trichobaris diversify mainly in relation to the use of Datura species? For the first question, we estimated the phylogeny of Trichobaris based on four gene sequences (nuclear 18S and 28S rRNA genes and mitochondrial 16S rRNA and COI genes). Then, we carried out morphogeometric analyses of the Trichobaris species using 75 landmarks. For the second question, we calibrated a COI haplotype phylogeny using a constant rate of divergence to infer the diversification time of Trichobaris species, and we traced the host plant species on the haplotype network. We performed an ancestral state reconstruction analysis to infer recent colonization events and conserved associations with host plant species. We found that ancestral species in the Trichobaris phylogeny use the stem of Solanum plants for oviposition and display weak sexual dimorphism of rostrum size, whereas other, more recent species of Trichobaris display sexual dimorphism in rostrum size and use the fruits of Datura species, and a possible reversion to use the stem of Solanaceae was detected in one Trichobaris species. The use of Datura species by Trichobaris species is widely distributed on haplotype networks and restricted to Trichobaris species that originated ca. 5 ± 1.5 Ma. Given that the origin of Trichobaris is estimated to be ca. 6 ± 1.5 Ma, it is likely that Datura has played a role in its diversification.
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