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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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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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Wang Y, Wang Y, Zhao Y, Kravchenko AY, Merilä J, Guo B. Phylogenomics of Northeast Asian
Pungitius
sticklebacks. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13423] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Yingnan Wang
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
| | - Yu Wang
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
| | - Yahui Zhao
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Alexandra Yu Kravchenko
- A. V. Zhirmunsky National Scientific Center of Marine Biology Far Eastern Branch Russian Academy of Sciences Vladivostok Russia
| | - Juha Merilä
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme Faculty of Biological and Environmental Sciences University of Helsinki Helsinki Finland
- Research Division for Ecology and Biodiversity, School of Biological Sciences Faculty of Science The University of Hong Kong Hong Kong SAR China
| | - Baocheng Guo
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
- Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Kunming China
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Phylogeography of Triplophysa stenura (Nemacheilidae): Responded to the Mid-Pleistocene Climate Transition in the Qinghai-Tibetan Plateau. Zool Stud 2021; 59:e67. [PMID: 34140984 DOI: 10.6620/zs.2020.59-67] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 10/22/2020] [Indexed: 11/18/2022]
Abstract
Pleistocene climatic oscillations have greatly influenced the evolutionary histories and distribution patterns of most extant species. In this study, the phylogeographic patterns and evolutionary history of Triplophysa stenura were investigated. A total of 359 individuals from 19 locations covering the species' distribution range were collected, and two mitochondrial genes (COI and Cyt b) and the recombination activating protein 1 gene (Rag1) were analyzed. Two deeply divergent lineages, corresponding geographically to the northern and southern Tanggula Mountain, were observed, and shallow divergences were found within the southern and central Qinghai-Tibetan plateau (QTP). The estimated divergence time between the northern and southern Tanggula lineages was around 1.07 Mya. Within the southern Tanggula Mountain lineages, the Nu and Subansiri rivers populations were split about 0.74 Mya, and the southwestern and central QTP populations were divided with the southeastern QTP ones approximately 0.67 Mya. The divergence times of the lineages were matched with two major glaciations in QTP (the Xixiabangma Glaciation, 1.17-0.80 Mya and Kunlun Glaciation, 0.72-0.62 Mya). Together with demographic history analyses, our results highlighted that major glacial cycles during the mid-Pleistocene played a major role in sculpting the distribution pattern of T. stenura, and led to the gene homogenization crossing the drainage populations in the southwestern and central QTP.
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Population genetic pattern of the freshwater fish Amur sleeper (Perccottus glenii) across its native distribution area in China. CONSERV GENET 2021. [DOI: 10.1007/s10592-020-01323-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Souza MS, Thomaz AT, Fagundes NJR. River capture or ancestral polymorphism: an empirical genetic test in a freshwater fish using approximate Bayesian computation. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa140] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Abstract
A headwater or river capture is a phenomenon commonly invoked to explain the absence of reciprocal monophyly of genetic lineages among isolated hydrographic basins in freshwater fish. Under the assumption of river capture, a secondary contact between populations previously isolated in different basins explains the observed genetic pattern. However, the absence of reciprocal monophyly could also arise under population isolation through the retention of ancestral of polymorphisms. Here, we applied an approximate Bayesian computation (ABC) framework for estimating the relative probability of scenarios with and without secondary contact. We used Cnesterodon decemmaculatus as a study model because of the multiple possible cases of river capture and the demographic parameters estimated in a previous mitochondrial DNA study that are useful for simulating scenarios to test both hypotheses using the ABC framework. Our results showed that, in general, mitochondrial DNA is useful for distinguishing between these alternative demographic scenarios with reasonable confidence, but in extreme cases (e.g. recent divergence or large population size) there is no power to discriminate between scenarios. Testing hypotheses of drainage rearrangement under a statistically rigorous framework is fundamental for understanding the evolution of freshwater fish fauna as a complement to, or in the absence of, geological evidence.
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Affiliation(s)
- Mateus S Souza
- Postgraduate Program in Animal Biology, Institute of Biosciences, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
- Laboratory of Medical Genetics and Evolution, Department of Genetics, Institute of Biosciences, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Andréa T Thomaz
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
| | - Nelson J R Fagundes
- Postgraduate Program in Animal Biology, Institute of Biosciences, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
- Laboratory of Medical Genetics and Evolution, Department of Genetics, Institute of Biosciences, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
- Postgraduate Program in Genetics and Molecular Biology, Institute of Biosciences, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
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Grabowska J, Kvach Y, Rewicz T, Pupins M, Kutsokon I, Dykyy I, Antal L, Zięba G, Rakauskas V, Trichkova T, Čeirāns A, Grabowski M. First insights into the molecular population structure and origins of the invasive Chinese sleeper, Perccottus glenii, in Europe. NEOBIOTA 2020. [DOI: 10.3897/neobiota.57.48958] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The aim of our study was to provide a first overview of the population genetic structure of the invasive Chinese sleeper,Perccottus glenii, (Actinopterygii: Odontobutidae) in European water bodies. This species originates from inland waters of north-eastern China, northern North Korea and the Russian Far East. The 1172 bp long portion of the cytochrome b gene was sequenced from Chinese sleeper specimens collected from a variety of water bodies in Belarus, Bulgaria, Hungary, Germany, Latvia, Lithuania, Poland, Russia (European part) and Ukraine. Our study revealed that the invasive Chinese sleeper in Europe consists of at least three distinct haplogroups that may represent independent introduction events from different parts of its native area; i.e. three founding populations: (1) Baltic haplogroup that may originate either from fish introduced inadvertent from Russia or from some unidentified source (release by aquarists). So far, this haplogroup has been found only in the Daugava basin in Latvia. (2) East-European haplogroup that may originate from an unintentional introduction to the Volga basin in Russia and has expanded westward. So far, this group was recorded in the Volga, Upper Dnieper and Neman drainages in Belarus, Lithuania, and Russia. (3) Carpathian haplogroup, that originated from individuals unintentionally introduced with Asian cyprinid fishes to Lviv region in Ukraine and are now widely distributed in Central Europe.
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Jeon HB, Kim DY, Lee YJ, Bae HG, Suk HY. The genetic structure of Squalidus multimaculatus revealing the historical pattern of serial colonization on the tip of East Asian continent. Sci Rep 2018; 8:10629. [PMID: 30006507 PMCID: PMC6045656 DOI: 10.1038/s41598-018-28340-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 06/19/2018] [Indexed: 11/28/2022] Open
Abstract
Separated river systems could create confluences via two geological processes, estuary coalescence in response to decreasing sea levels and headwater capture, allowing primary freshwater species to disperse across rivers. Squalidus multimaculatus, is an endemic and primary freshwater species restricted to the southeast coast of the Korean Peninsula. The distribution of this species is unique, given that other congeneric species, including its closely related S. gracilis majimae, as well as other cyprind species are observed throughout the peninsula except for the east coast. Phylogeographic analyses were conducted using three mitochondrial loci to identify the origin of S. multimaculatus and the historical pathways of dispersal. A strong phylogenetic affinity between S. multimaculatus and S. g. majimae and the genetic structure among populations indicated that S. multimaculatus originated from the eastward colonization of the common ancestor between S. g. majimae and S. multimaculatus via headwater capture through fault zones within successive mountain range. Following colonization, the ancestral S. multimaculatus likely migrated towards north via estuary coalescence along a well-developed continental shelf. Our study was the first empirical attempt providing insights into how freshwater organisms dispersed to the southernmost tip of East Asia, despite the potential loss of such historical imprints with anthropogenic interference.
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Affiliation(s)
- Hyung-Bae Jeon
- Department of Life Sciences, Yeungnam University, 280 Daehak-ro, Gyeongsan, Gyeongsangbuk-do, 38541, South Korea
| | - Dong-Young Kim
- Department of Life Sciences, Yeungnam University, 280 Daehak-ro, Gyeongsan, Gyeongsangbuk-do, 38541, South Korea
| | - Yoon Jeong Lee
- Department of Life Sciences, Yeungnam University, 280 Daehak-ro, Gyeongsan, Gyeongsangbuk-do, 38541, South Korea
| | - Han-Gyu Bae
- Department of Life Sciences, Yeungnam University, 280 Daehak-ro, Gyeongsan, Gyeongsangbuk-do, 38541, South Korea
| | - Ho Young Suk
- Department of Life Sciences, Yeungnam University, 280 Daehak-ro, Gyeongsan, Gyeongsangbuk-do, 38541, South Korea.
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