Expansion and Contraction of Lake Basin Shape the Genetic Structure of (Osteichthyes: Cypriniformes: Cyprinidae) Populations in Central Yunnan, China

Overview

Journal Ecol Evol

Date 2024 Jan 22

PMID 38250223

Authors

Xing-Jin Che

Yuan-Wei Zhang

An-Li Wu

Xiao-Fu Pan

Mo Wang

Jun-Xing Yang

Xiao-Ai Wang

Affiliations

Soon will be listed here.

Abstract

Geological events can strongly affect the genetic structures and differentiation of fish populations. Especially, as an endemic fish of the genus in the Yunnan-Guizhou Plateau, the effects of key geological events on the distributions and genetic structures remain poorly understood. Examining the phylogeographic patterns of fishes can be useful for elucidating the spatio-temporal dynamics of their population size, dispersal history and extent of geographical isolation, thereby providing a theoretical basis for their protection. Here, we used single nucleotide polymorphisms (SNP) method to investigate the phylogeographic patterns of fishes. Our analysis supports the endemicity of , but the samples of different regions of contain multiple ancestral components, which displayed more admixed and diversified genetic components, this may be due to the polymorphism of the ancestors themselves, or gene infiltration caused by hybridization between adjacent species of . We estimate that the most recent common ancestor (MRCA) of fish in the Central Yunnan Basin at approximately 3.75~3.11 Ma, and infer that the evolution of in the central Yunnan Basin is closely related to the formation of plateau lakes (around 4.0~0.02 Ma), and identifies the formation of Dianchi Lake and Fuxian Lake as key geological events shaping population structure. It is also the first time to prove that the altitude change has a great influence on the genetic variation among the populations of

Citing Articles

Expansion and contraction of lake basin shape the genetic structure of (Osteichthyes: Cypriniformes: Cyprinidae) populations in Central Yunnan, China.

Che X, Zhang Y, Wu A, Pan X, Wang M, Yang J Ecol Evol. 2024; 14(1):e10840.

PMID: 38250223 PMC: 10797211. DOI: 10.1002/ece3.10840.

References

Chen S, Zhang R, Feng J, Xiao H, Li W, Zan R . Exploring factors shaping population genetic structure of the freshwater fish Sinocyclocheilus grahami (Teleostei, Cyprinidae). J Fish Biol. 2010; 74(8):1774-86. DOI: 10.1111/j.1095-8649.2009.02204.x. View

Li H, Durbin R . Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009; 25(14):1754-60. PMC: 2705234. DOI: 10.1093/bioinformatics/btp324. View

Rambaut A, Drummond A, Xie D, Baele G, Suchard M . Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7. Syst Biol. 2018; 67(5):901-904. PMC: 6101584. DOI: 10.1093/sysbio/syy032. View

Mao T, Liu Y, Meegaskumbura M, Yang J, Ellepola G, Senevirathne G . Evolution in Sinocyclocheilus cavefish is marked by rate shifts, reversals, and origin of novel traits. BMC Ecol Evol. 2021; 21(1):45. PMC: 7968296. DOI: 10.1186/s12862-021-01776-y. View

Xiang K, Erst A, Yang J, Peng H, Ortiz R, Jabbour F . Biogeographic diversification of (Ranunculaceae) reflects the geological history of the three great Asian plateaus. Proc Biol Sci. 2021; 288(1948):20210281. PMC: 8059577. DOI: 10.1098/rspb.2021.0281. View

Gutierrez E, Helgen K . Mammalogy: Outdated taxonomy blocks conservation. Nature. 2013; 495(7441):314. DOI: 10.1038/495314e. View

Drummond A, Suchard M, Xie D, Rambaut A . Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol. 2012; 29(8):1969-73. PMC: 3408070. DOI: 10.1093/molbev/mss075. View

Danecek P, Auton A, Abecasis G, Albers C, Banks E, DePristo M . The variant call format and VCFtools. Bioinformatics. 2011; 27(15):2156-8. PMC: 3137218. DOI: 10.1093/bioinformatics/btr330. View

Mao T, Liu Y, Vasconcellos M, Pie M, Ellepola G, Fu C . Evolving in the darkness: Phylogenomics of Sinocyclocheilus cavefishes highlights recent diversification and cryptic diversity. Mol Phylogenet Evol. 2022; 168:107400. DOI: 10.1016/j.ympev.2022.107400. View

10.

Malinsky M, Challis R, Tyers A, Schiffels S, Terai Y, Ngatunga B . Genomic islands of speciation separate cichlid ecomorphs in an East African crater lake. Science. 2015; 350(6267):1493-1498. PMC: 4700518. DOI: 10.1126/science.aac9927. View

11.

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N . The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009; 25(16):2078-9. PMC: 2723002. DOI: 10.1093/bioinformatics/btp352. View

12.

Jiang W, Li J, Lei X, Wen Z, Han Y, Yang J . , a new blind fish from the Three Gorges of Yangtze River provides insights into speciation of Chinese cavefish. Zool Res. 2019; 40(6):552-557. PMC: 6822930. DOI: 10.24272/j.issn.2095-8137.2019.065. View

13.

Yang J, Chen X, Bai J, Fang D, Qiu Y, Jiang W . The Sinocyclocheilus cavefish genome provides insights into cave adaptation. BMC Biol. 2016; 14:1. PMC: 4698820. DOI: 10.1186/s12915-015-0223-4. View

14.

Zachos F . Taxonomy: Species splitting puts conservation at risk. Nature. 2013; 494(7435):35. DOI: 10.1038/494035c. View

15.

Guo P, Liu Q, Zhu F, Zhong G, Che J, Wang P . Multilocus phylogeography of the brown-spotted pitviper Protobothrops mucrosquamatus (Reptilia: Serpentes: Viperidae) sheds a new light on the diversification pattern in Asia. Mol Phylogenet Evol. 2018; 133:82-91. DOI: 10.1016/j.ympev.2018.12.028. View

16.

Zhao Z, Li S . Extinction vs. Rapid Radiation: The Juxtaposed Evolutionary Histories of Coelotine Spiders Support the Eocene-Oligocene Orogenesis of the Tibetan Plateau. Syst Biol. 2017; 66(6):988-1006. DOI: 10.1093/sysbio/syx042. View

17.

Jocelyn P, Knight T, Ferguson M . Nonequilibrium conditions following landscape rearrangement: the relative contribution of past and current hydrological landscapes on the genetic structure of a stream-dwelling fish. Mol Ecol. 2005; 14(5):1321-31. DOI: 10.1111/j.1365-294X.2005.02500.x. View

18.

Che X, Zhang Y, Wu A, Pan X, Wang M, Yang J . Expansion and contraction of lake basin shape the genetic structure of (Osteichthyes: Cypriniformes: Cyprinidae) populations in Central Yunnan, China. Ecol Evol. 2024; 14(1):e10840. PMC: 10797211. DOI: 10.1002/ece3.10840. View

19.

Shu S, Jiang W, Whitten T, Yang J, Chen X . Drought and China's cave species. Science. 2013; 340(6130):272. DOI: 10.1126/science.340.6130.272-a. View

20.

Burridge C, Craw D, Waters J . An empirical test of freshwater vicariance via river capture. Mol Ecol. 2007; 16(9):1883-95. DOI: 10.1111/j.1365-294X.2006.03196.x. View