Strong population structure of Schizopygopsis chengi and the origin of S. chengi baoxingensis revealed by mtDNA and microsatellite markers

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• 作者：Dongqi Liu (1)
  Feixia Hou (1) (2)
  Qin Liu (3)
  Xiuyue Zhang (1)
  Taiming Yan (4)
  Zhaobin Song (1) (5)
  
  1. Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife ; College of Life Sciences ; Sichuan University ; Chengdu ; 610065 ; People鈥檚 Republic of China
  2. Pharmacy College ; Chengdu University of Traditional Chinese Medicine ; Chengdu ; 611137 ; People鈥檚 Republic of China
  3. College of Life Sciences and Food Engineering ; Yibin College ; Yibin ; 644000 ; People鈥檚 Republic of China
  4. Department of Aquaculture ; Sichuan Agricultural University ; Ya鈥檃n ; 625014 ; People鈥檚 Republic of China
  5. Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education ; College of Life Sciences ; Sichuan University ; Chengdu ; 610065 ; People鈥檚 Republic of China
  
• 关键词：Schizopygopsis chengi ; Microsatellite ; Control region ; Population structure ; Historical gene flow ; Phylogenetic analysis
• 刊名：Genetica
• 出版年：2015
• 出版时间：February 2015
• 年：2015
• 卷：143
• 期：1
• 页码：73-84
• 全文大小：1,379 KB
• 参考文献：1. Akaike H (1974) A new look at the statistical model identification. IEEE Trans Autom Control 19:716鈥?23 CrossRef
  2. Alpers DL, Van Vuuren BJ, Arctander P, Robinson TJ (2004) Population genetics of the roan antelope ( / Hippotragus equinus) with suggestions for conservation. Mol Ecol 13:1771鈥?784 CrossRef
  3. An B, Zhang LX, Browne S, Liu NF, Ruan LZ, Song S (2009) Phylogeography of Tibetan snowcock ( / Tetraogallus tibetanus) in Qinghai鈥揟ibetan Plateau. Mol Phylogenet Evol 50:526鈥?33 CrossRef
  4. Avise JC (1989) Gene trees and organismal histories: a phylogenetic approach to population biology. Evolution 43:1192鈥?208 CrossRef
  5. Bandelt HJ, Forster P, R枚hl A (1999) Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16:37鈥?8 CrossRef
  6. Bever JD, Felber F (1992) The theoretical population genetics of autotetraploidy. In: Antonovis J, Futuyma D (eds) Oxford surveys in evolutionary biology. Oxford University Press, New York, pp 185鈥?17
  7. Cao WX, Chen YY, Wu YF, Zhu SQ (1981) Origin and evolution of schizothoracine fishes in relation to the upheaval of the Xizang Plateau. Studies on the period, amplitude and type of the uplift of the Qinghai鈥揟ibetan Plateau. Science Press, Beijing, pp 118鈥?30 (in Chinese)
  8. Clark LV, Jasieniuk M (2011) POLYSAT: an R package for polyploidy microsatellite analysis. Mol Ecol Resour 11:562鈥?66 CrossRef
  9. Ding R (1994) The fishes of Sichuan, China. Sichuan Publishing House of Science and Technology, Chengdu, p 402
  10. Drummond AJ, Rambaut A (2007) Beast: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7:214 CrossRef
  11. Drummond AJ, Rambaut A, Shapiro B, Pybus OG (2005) Bayesian coalescent inference of past population dynamics from molecular sequences. Mol Biol Evol 22:1185鈥?192 CrossRef
  12. Dudgeon D (2000) The ecology of tropical Asian rivers and streams in relation to biodiversity conservation. Annu Rev Ecol Syst 31:239鈥?63 CrossRef
  13. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611鈥?620 CrossRef
  14. Excoffier L, Smouse P, Quattro J (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131:479鈥?91
  15. Excoffier L, Laval G, Schneidier S (2005) Arlequin Ver. 3.0: an integrated software package for population genetics data analysis. Evol Bioinform Online 1:47鈥?0
  16. Fang G, Sech TR (1995) Telomere proteins. In: Blackburn EH, Greider CW (eds) Telomeres. Cold Spring Harbor Laboratory Press, New York, pp 69鈥?06
  17. Fu Y (1997) Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147:915鈥?25
  18. He YF (2010) Structure of endemic fish assemblages in the upper Yangtze River basin and population differentiation of an endangered endemic fish ( / Gobiocypris ratus). Ph.D. thesis, L鈥橴niversit茅 Toulouse 3 Paul Sabatier (France) and l鈥橧nstitut d鈥橦ydrobiologie (Wuhan)
  19. He DK, Chen YF (2006) Biogeography and molecular phylogeny of the genus / Schizothorax (Teleostei: Cypriiinidae) in China inferred from cytochrome / b sequences. J Biogeogr 33:1448鈥?460 CrossRef
  20. He DK, Chen YF (2007) Molecualr phylogeny and biogeography of the highly specialized grade schizothoracine fishes (Teleostei: Cyprinidae) inferred from cytochrome / b sequences. Chin Sci Bull 52:777鈥?88 CrossRef
  21. He SP, Cao WX, Chen YY (2001) The uplift of Qinghai-Xizang (Tibet) Plateau and the vicariance speciation of glyptosternoid fishes (Siluriformes: Sisoridae). Sci China Ser C 44:44鈥?51
  22. He DK, Chen YX, Chen YF (2006) Molecular phylogeny and biogeography of the genus / Triplophysa (Osteichthyes: Nemacheilinae) in the Tibetan Plateau inferred from cytochrome / b DNA sequences. Prog Nat Sci 16:1395鈥?404
  23. Hewitt GM (2004) Genetic consequences of climatic oscillations in the Quaternary. Phil Trans R Soc B 359:183鈥?95 CrossRef
  24. Hey J (2010) Isolation with migration models for more than two populations. Mol Biol Evol 27:905鈥?20 CrossRef
  25. Hou FX, Zhang XY, Zhang XF, Yue BS, Song ZB (2012) High intra-population genetic variability and inter-population differentiation in a plateau specialized fish, / Triplophysa orientalis. Environ Biol Fish 93:519鈥?30 CrossRef
  26. Hou FX, Zhang HB, Wu B, Zhang XY, Song ZB (2013) Characterization of microsatellite loci in S / chizopygopsis chengi chengi and their utilization in assessment of the genetic diversity in / Schizopygopsis chengi baoxingensis. Biochem Syst Ecol 46:50鈥?4 CrossRef
  27. Hudson RR, Slatkin M, Maddison WP (1992) Estimation of levels of gene flow from DNA sequence data. Genetics 132:583鈥?89
  28. Jensen JL, Bohonak AJ, Kelley ST (2005) Isolation by distance, web service. BMC Genet 6:6 CrossRef
  29. Li CA, Ying HF, Yu QW (2000) Evolution of drainage systems and its developing trend in connection with tectonic uplift of Eastern Kunlun Mt. Chin Sci Bull 45:1904鈥?908 CrossRef
  30. Liu Q (2010) Genetic diversity of two subspecies of / Schizopygopsis chengi and the origin of / S. c. baoxingensis. MS Dissertation. Sichuan: Sichuan University
  31. Liu H, Tzeng CS, Teng HY (2002) Sequence variations in the mitochondrial DNA control region and their implications for the phylogeny of the Cypriniformes. Can J Zool 80:569鈥?81 CrossRef
  32. Liu Q, Wang S, Zhang XY, Yue BS, Song ZB (2009) Limited genetic diversity of an endemic subspecies / Schizopygopsis chengi baoxingensis as inferred from the mitochondrial DNA control region. Hydrobiologia 632:371鈥?76 CrossRef
  33. McCauley DE (1991) Genetic consequences of local population extinction and recolonization. Trends Ecol Evol 6:5鈥? CrossRef
  34. Moritz C (1994) Defining 鈥榚volutionarily significant units鈥?for conservation. Trends Ecol Evol 9:373鈥?75 CrossRef
  35. Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York City
  36. Park YS, Chang JB, Lek S, Cao WX, Brosse S (2003) Conservation strategies for endemic fish species threatened by the Three Gorges Dam. Conserv Biol 17:1748鈥?758 CrossRef
  37. Peng ZG, Ho SYW, Zhang YG, He SP (2006) Uplift of the Tibetan Plateau: evidence from divergence times of glyposternoid catfishes. Mol Phylogenet Evol 39:568鈥?72 CrossRef
  38. Posada D (2008) jModelTest: phylogenetic model averaging. Mol Biol Evol 25:1253鈥?256 CrossRef
  39. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945鈥?59
  40. Qi DL, Guo SC, Zhao XQ, Yang J, Tang WJ (2007) Genetic diversity and historical population structure of / Schizopygopsis pylzovi (Teleostei: Cyprinidae) in the Qinghai鈥揟ibetan Plateau. Freshw Biol 52:1090鈥?104 CrossRef
  41. Rambaut A, Drummond AJ (2007) Tracer v1.5 (Accessed 10 Nov 2010). http://beast.bio.ed.ac.uk/Tracer
  42. Rogers AR, Harpending H (1992) Population growth makes waves in the distribution of pairwise genetic differences. Mol Biol Evol 9:552鈥?69
  43. Ronfort JL, Jenczewski E, Bataillon T, Rousset F (1998) Analysis of population strcuture in autotetraploid species. Genetics 150:921鈥?30
  44. Ronquist F, Huelsenbeck JP (2003) MyBayes 3: Bayesian phylogenetic inference under mixed models. Bioniformatics 19:1572鈥?574 CrossRef
  45. Rozas J, S谩nchez DJC, Messeguer X, Rozas R (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19:2496鈥?497 CrossRef
  46. Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual, 3rd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor
  47. Schilt CR (2007) Developing fish passage and protection at hydropower dams. Appl Anim Behav Sci 104:295鈥?25 CrossRef
  48. Song ZB (2006) Final report for WWF small grant: impacts of hydropower construction on fish population on the Baoxing River, Sichuan. Sichuan University, Chengdu, pp 1鈥?0
  49. Sun HL (2008) Ecological and environmental problems in the upper Yangtze River. China Environmental Science Press, Beijing
  50. Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585鈥?95
  51. Tang QY, Liu HZ, Mayden R, Xiong BX (2006) Comparison of evolutionary rates in the mitochondrial DNA cytochrome / b gene and control region and their implications for phylogeny of the Cobitoidea (Teleostei: Cypriniformes). Mol Phylogenet Evol 39:347鈥?57 CrossRef
  52. Thrall PH, Yong A (2000) AUTOTET: a program for analysis of autotetraploid genotypic data. J Hered 91:348鈥?49 CrossRef
  53. Wu YF, Wu CZ (1991) The fishes of the Qinghai鈥揦izang Plateau. Sichuan Publishing House of Science and Technology, Chengdu
  54. Xiao WH, Zhang YP, Liu HZ (2001) Molecular systmeatics of Xenocyprinae (Teleostei: Cyprinidae): taxonomy, biogeography, and coevolution of a special group restricted in East Asia. Mol Phylogenet Evol 18:163鈥?73 CrossRef
  55. Yang X, Rost KT, Lehmkuhl F, Zhou Z, Dodson J (2004) The evolution of dry lands in northern China and in Republic of Mongolia since the last glacial maximum. Quat Int 118鈥?19:69鈥?5 CrossRef
  56. Yu CJ, Song ZB, Yue BS (2006) Taxonomic implications from phylogenetic relationships of subspecies of / Schizopygopsis malacanthus (Pisces: Cyprinidae) based on sequence analysis of cytochrome / b and mitochondrial DNA control region. J Nat Hist 40:44鈥?6 CrossRef
  57. Zaccara S, Stefani F, Crosa G (2005) Diversity of mitochondrial DNA of the endangered white-clawed crayfish ( / Austropotamobius italicus) in the Po River catchment. Freshw Biol 50:1262鈥?272 CrossRef
  58. Zhu XM, Kang A, Han DX, Wang YB, Kang Q (2003) Relation among quaternary environmental evolution, tectonic deformation in the Qiadam basin and uplifting of the Qinghai鈥揟ibet plateau. Chin J Geol 38:413鈥?24
  
• 刊物类别：Biomedical and Life Sciences
• 刊物主题：Life Sciences
  Life Sciences
  Animal Genetics and Genomics
  Plant Genetics and Genomics
  Human Genetics
  Microbial Genetics and Genomics
  
• 出版者：Springer Netherlands
• ISSN：1573-6857

文摘

The Tibetan Plateau underwent dramatic geological and climatic changes, which had important implications for genetic divergence and population dynamics of freshwater fish populations. Fluctuations of the ecogeographical environment and major hydrographic formations might have promoted the formation of new subspecies or species. In order to understand the impact of plateau uplift on freshwater fish evolutionary history, we estimated the genetic diversity and population structure in two subspecies of Schizopygopsis chengi (S. c. chengi and S. c. baoxingensis) in upper Yangtze River in Tibetan Plateau area using mitochondrial DNA control region and eight microsatellite markers, which suggested that there was a close genetic relationship. S. chengi showed some significant genetic structure that did not correlate with geographic distance. Bayesian assignment tests indicated that S. chengi samples in the study could be divided into four populations: upstream population, midstream population, tributary population and S. c. baoxingensis population. S. c. chengi and S. c. baoxingensis showed significant genetic divergence. However, phylogenetic analysis, population structure analysis and historical gene flow estimation suggested that there was close genetic relationship between S. c. baoxingensis and the Dawei population which belongs to populations of S. c. chengi. The time that Dawei population suffered from a bottleneck and S. c. baoxingensis underwent population expansion was congruent with the last glacial period on the Tibetan Plateau. The results confirmed the hypothesis that the Dawei River and Baoxing River were once connected, and the Dawei and Baoxing populations originated from a single population, but were isolated into separate populations because of crustal movements and the Baoxing population evolved as S. c. baoxingensis.