Skip to main content
SpringerLink
Log in

Genetic variation and phylogenetic relationship between three serow species of the genus Capricornis based on the complete mitochondrial DNA control region sequences

  • Published:
Molecular Biology Reports Aims and scope Submit manuscript

Abstract

The molecular evidence of phylogenetic status regarding the Formosan serow (Capricornis swinhoei) is not robust and little is known about the genetic diversity of the Sumatran serow (Capricornis sumatraensis), which partly is due to the hardness in sample collection. Here we determined the sequences of the complete mitochondrial DNA control region (1,014 bp) of 19 Sumatran-serow individuals. Nine new haplotypes were defined based on 78 variable sites. Combined analysis with other 32 haplotypes downloaded from the public database, including 1 Sumatran-serow, 11 Formosan-serow and 20 Japanese-serow (Capricornis crispus) haplotypes, a relatively high level of nucleotide diversity was first observed in Sumatran serow (π = 0.0249). By comparative analysis with structural consensus sequences from other mammals, we have identified central, left and right domains and depicted the putative functional structure, including extend termination associated sequences and conserve sequence blocks, in mtDNA control region. The alignment of mtDNA control region revealed that both Sumatran and Japanese serow have two tandem repeats (TRs), but three TRs in Formosan serow. Phylogenetic analyses revealed that the Formosan serow is distinct species with the Japanese serow, but a sister group with the Sumatran serow. The divergence time estimated among three serow species revealed that Pleistocene climate changes and the uplift of Qinghai-Tibetan plateau might play an important role in the genetic differentiation of the serows. These results mainly provide the convinced evidence on the genetic relationship between three serow species.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  1. Wilson DE, Reeder DAM (2005) Mammal species of the world: a taxonomic and geographic reference, vol 2. Johns Hopkins University Press, Baltimore, Maryland, pp 313–743

    Google Scholar 

  2. Simpson GG (1945) The principles of classification and a classification of mammals. American Museum of Natural History, New York

    Google Scholar 

  3. Corbet GB (1978) The mammals of the Palaearctic region: a taxonomic review. Cornell University Press, New York, p 314

    Google Scholar 

  4. Ryder OA, Byrd ML, Benirschke K (1984) One medicine: a tribute to Kurt Benirschke. Springer, Berlin, pp 109–118

    Google Scholar 

  5. Nowak RM (1999) Walker’s mammals of the world, vol 2, 6th edn. Johns Hopkins University Press, Baltimore, pp 1129–1135

    Google Scholar 

  6. Soma H, Kada H, Matayoshi K (1987) Evolutionary pathways of karyotypes of the tribe Rupicaprini. In: Soma H (ed) The biology and management of Capricornis and related mountain antelopes. Croom Helm, London, pp 62–71

    Chapter  Google Scholar 

  7. Benirschke K, Soma H, Ito T (1972) The chromosomes of the Japanese serow, Capricornis crispus (Temminck). Proc Jpn Acad 48:608–612

    Google Scholar 

  8. Soma H, Kada H, Matayoshi K, Tsai MT, Kiyokawa T, Ito T, Wang KP, Chen BPC, Tseng SC (1981) Cytogenetic similarities between the Formosan Serow (Capricornis swinhoi) and the Japanese Serow: Capricornis crispus. Proc Jpn Acad B Phys Biol Sci 57:254–259

    Article  Google Scholar 

  9. Horng DC, Huang HW, Liang YC, Ou BR (2003) Two distinct phylogenetic groups of Formosan serow (Naemorhedus swinhoei Gray) population in Taiwan: based on mitochondrial D-loop region sequences. Endem Species Res 5:15–25

    Google Scholar 

  10. Okumura H (2004) Complete sequence of mitochondrial DNA control region of the Japanese serow Capricornis crispus (Bovidae: Caprinae). Mamm Stud 29:137–145

    Article  Google Scholar 

  11. Chikuni K, Mori Y, Tabata T, Saito M, Monma M, Kosugiyama M (1995) Molecular phylogeny based on the k-casein and cytochrome b sequences in the mammalian suborder Ruminantia. J Mol Evol 41:859–866

    Article  PubMed  CAS  Google Scholar 

  12. Hassanin A, Pasquet E, Vigne JD (1998) Molecular systematics of the subfamily Caprinae (Artiodactyla, Bovidae) as determined from Cytochrome b sequences. J Mamm Evol 5(3):217–236

    Article  Google Scholar 

  13. Min MS, Okumura H, Jo DJ, An JH, Kim KS, Kim CB, Shin NS, Lee MH, Han CH, Voloshina IV (2004) Molecular phylogenetic status of the Korean goral and Japanese serow based on partial sequences of the mitochondrial cytochrome b gene. Mol Cell 17:365–372

    CAS  Google Scholar 

  14. Hassanin A, Ropiquet A, Couloux A, Cruaud C (2009) Evolution of the mitochondrial genome in mammals living at high altitude: new insights from a study of the tribe Caprini (Bovidae, Antilopinae). J Mol Evol 68:293–310

    Article  PubMed  CAS  Google Scholar 

  15. An J, Okumura H, Lee YS, Kim KS, Min MS, Lee H (2010) Organization and variation of the mitochondrial DNA control region in five Caprinae species. Genes Genom 32:335–344

    Article  CAS  Google Scholar 

  16. Hassanin A, Delsuc F, Ropiquet A, Hammer C, Jansen van Vuuren B, Matthee C, Ruiz-Garcia M, Catzeflis F, Areskoug V, Nguyen TT, Couloux A (2012) Pattern and timing of diversification of Cetartiodactyla (Mammalia, Laurasiatheria), as revealed by a comprehensive analysis of mitochondrial genomes. C R Biol 335(1):32–50

    Article  PubMed  Google Scholar 

  17. He L, Dai B, Zeng B, Zhang X, Chen B, Yue B, Li J (2009) The complete mitochondrial genome of the Sichuan Hill Partridge (Arborophila rufipectus) and a phylogenetic analysis with related species. Gene 435:23–28

    Article  PubMed  CAS  Google Scholar 

  18. Peng R, Zeng B, Meng X, Yue B, Zhang Z, Zou F (2007) The complete mitochondrial genome and phylogenetic analysis of the giant panda (Ailuropoda melanoleuca). Gene 397:76–83

    Article  PubMed  CAS  Google Scholar 

  19. Smith DG, McDonough J (2005) Mitochondrial DNA variation in Chinese and Indian rhesus macaques (Macaca mulatta). Am J Primatol 65:1–25

    Article  PubMed  CAS  Google Scholar 

  20. Xu S, Luosang J, Hua S, He J, Ciren A, Wang W, Tong X, Liang Y, Wang J, Zheng X (2007) High altitude adaptation and phylogenetic analysis of Tibetan horse based on the mitochondrial genome. J Genet Genom 34:720–729

    Article  CAS  Google Scholar 

  21. Brown J, Beckenbach A, Smith M (1992) Mitochondrial DNA length variation and heteroplasmy in populations of white sturgeon (Acipenser transmontanus). Genetics 132:221–228

    PubMed  CAS  Google Scholar 

  22. Castro A, Stewart B, Wilson S, Hueter R, Meekan M, Motta P, Bowen B, Karl S (2007) Population genetic structure of Earth’s largest fish, the whale shark (Rhincodon typus). Mol Ecol 16:5183–5192

    Article  PubMed  CAS  Google Scholar 

  23. Jia S, Chen H, Zhang G, Wang Z, Lei C, Yao R, Han X (2007) Genetic variation of mitochondrial D-loop region and evolution analysis in some Chinese cattle breeds. J Genet Genom 34:510–518

    Article  CAS  Google Scholar 

  24. Li D, Li D, Fan L, Li D, Fan L, Ran J, Yin H, Wang H, Wu S, Yue B (2008) Genetic diversity analysis of Macaca thibetana based on mitochondrial DNA control region sequences. Mitochondrial DNA 19:446–452

    Article  PubMed  CAS  Google Scholar 

  25. Loehr J, Worley K, Grapputo A, Carey J, Veitch A, Coltman DW (2005) Evidence for cryptic glacial refugia from North American mountain sheep mitochondrial DNA. J Evol Biol 19:419–430

    Article  Google Scholar 

  26. Hassan A, El Nahas S, Kumar S, Godithala P, Roushdy K (2009) Mitochondrial D-loop nucleotide sequences of Egyptian river buffalo: variation and phylogeny studies. Livest Sci 125:37–42

    Article  Google Scholar 

  27. Saccone C, Pesole G, Sbisá E (1991) The main regulatory region of mammalian mitochondrial DNA: structure-function model and evolutionary pattern. J Mol Evol 33:83–91

    Article  PubMed  CAS  Google Scholar 

  28. Walberg MW, Clayton DA (1981) Sequence and properties of the human KB cell and mouse L cell D-loop regions of mitochondrial DNA. Nucleic Acids Res 9:5411–5421

    Article  PubMed  CAS  Google Scholar 

  29. Singh VK, Mangalam A, Dwivedi S, Naik S (1998) Primer premier: program for design of degenerate primers from a protein sequence. Biotechniques 24:318–319

    PubMed  CAS  Google Scholar 

  30. McCarthy C (1996) Chromas, v. 1.45. Griffith University, Queensland

    Google Scholar 

  31. Hall TA (1999) In BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp 41:95–98

    CAS  Google Scholar 

  32. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739

    Article  PubMed  CAS  Google Scholar 

  33. Sbisà E, Tanzariello F, Reyes A, Pesole G, Saccone C (1997) Mammalian mitochondrial D-loop region structural analysis: identification of new conserved sequences and their functional and evolutionary implications. Gene 205:125–140

    Article  PubMed  Google Scholar 

  34. Nei M, Kumar S (2000) Molecular evolution and phylogenetics. Oxford University Press, USA

    Google Scholar 

  35. Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451–1452

    Article  PubMed  CAS  Google Scholar 

  36. Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585–595

    PubMed  CAS  Google Scholar 

  37. Excoffier L, Laval G, Schneider S (2005) Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol Bioinform Online 1:47

    CAS  Google Scholar 

  38. Bandelt HJ, Forster P, Röhl A (1999) Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16:37–48

    Article  PubMed  CAS  Google Scholar 

  39. Swofford DL (2003) PAUP*, v. 4. Phylogenetic analysis using Parsimony and other methods

  40. Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572–1574

    Article  PubMed  CAS  Google Scholar 

  41. Darriba D, Taboada GL, Doallo R, Posada D (2012) jModelTest 2: more models, new heuristics and parallel computing. Nat Methods 9(8):772

    Article  PubMed  CAS  Google Scholar 

  42. Hasegawa M, Kishino H, Yano T (1985) Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 22(2):160–174

    Article  PubMed  CAS  Google Scholar 

  43. Stoneking M, Sherry ST, Redd AJ, Vigilant L (1992) New approaches to dating suggest a recent age for the human mtDNA ancestor. Philos Trans R Soc Lond B 337:167–175

    Article  CAS  Google Scholar 

  44. Drummond AJ, Suchard MA, Xie D, Rambaut A (2012) Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol 29(8):1969–1973

    Article  PubMed  CAS  Google Scholar 

  45. Hoelzel AR, Lopez JV, Dover GA, O’Brien SJ (1994) Rapid evolution of a heteroplasmic repetitive sequence in the mitochondrial DNA control region of carnivores. J Mol Evol 39:191–199

    PubMed  CAS  Google Scholar 

  46. Buroker N, Brown J, Gilbert T, O’hara P, Beckenbach A, Thomas W, Smith M (1990) Length heteroplasmy of sturgeon mitochondrial DNA: an illegitimate elongation model. Genetics 124:157–163

    PubMed  CAS  Google Scholar 

  47. Doda JN, Wright CT, Clayton DA (1981) Elongation of displacement-loop strands in human and mouse mitochondrial DNA is arrested near specific template sequences. Proc Natl Acad Sci USA 78:6116–6120

    Article  PubMed  CAS  Google Scholar 

  48. Li M, Meng SJ, Wei FW, Wang J, Yong YG (2003) Genetic diversity and population genetic structure of takin (Budorcas taxicolor). Acta Theriol Sinica 23(1):10–16

    Google Scholar 

  49. Walsh PD (2000) Sample size for the diagnosis of conservation units. Conserv Biol 14(5):1533–1537

    Article  Google Scholar 

  50. Yasukochi Y, Nishida S, Han SH, Kurosaki T, Yoneda M, Koike H (2009) Genetic structure of the Asiatic black bear in Japan using mitochondrial DNA analysis. J Hered 100:297–308

    Article  PubMed  CAS  Google Scholar 

  51. Millar C, Libby W (1991) Strategies for conserving clinal, Ccotypic, Ana disjunct population diversity in widespread species. In: Fald DA, Holsinger KE (eds) Genetics and conservation of rare plants. Oxford University Press, New York, pp 140–170

    Google Scholar 

  52. Bossart J, Pashley Prowell D (1998) Genetic estimates of population structure and gene flow: limitations, lessons and new directions. Trends Ecol Evol 13:202–206

    Article  PubMed  CAS  Google Scholar 

  53. Nei M, Maruyama T, Chakraborty R (1975) The bottleneck effect and genetic variability in populations. Evolution 29:1–10

    Article  Google Scholar 

  54. Kimura M (1962) On the probability of fixation of mutant genes in a population. Genetics 47:713

    PubMed  CAS  Google Scholar 

Download references

Acknowledgments

This work was supported by the National Natural Science Foundation of China (No. 30970383) and Natural Science Foundation of Educational Commission of Sichuan Province of China (No. 08ZA076).

Conflict of interest

The authors declare no any potential conflict of interest.

Author information

Authors and Affiliations

  1. College of Animal Science and Technology, Sichuan Agricultural University, Ya’an, 625014, People’s Republic of China

    Wei Liu, Yong-fang Yao, Qin Yu, Qing-yong Ni, Ming-wang Zhang, Jian-dong Yang, Miao-miao Mai & Huai-liang Xu

  2. Forestry College, Sichuan Agricultural University, Ya’an, 625014, China

    Wei Liu, Yong-fang Yao, Ming-wang Zhang, Jian-dong Yang & Huai-liang Xu

Authors
  1. Wei Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yong-fang Yao
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Qin Yu
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Qing-yong Ni
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Ming-wang Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Jian-dong Yang
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Miao-miao Mai
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Huai-liang Xu
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Huai-liang Xu.

Additional information

Wei Liu and Yong-fang Yao have contributed equally to this work.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (PDF 70 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Liu, W., Yao, Yf., Yu, Q. et al. Genetic variation and phylogenetic relationship between three serow species of the genus Capricornis based on the complete mitochondrial DNA control region sequences. Mol Biol Rep 40, 6793–6802 (2013). https://doi.org/10.1007/s11033-013-2796-8

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11033-013-2796-8

Keywords

Search

Navigation