Abstract
Recently, the number of Tibetan mastiffs, which is a precious germplasm resource and cultural heritage, is decreasing sharply. Therefore, the genetic diversity of Tibetan mastiffs needs to be studied to clarify its phylogenetics relationships and lay the foundation for resource protection, rational development and utilization of Tibetan mastiffs. We sequenced hypervariable region I of mitochondrial DNA (mtDNA) of 110 individuals from Tibet region and Gansu province. A total of 12 polymorphic sites were identified which defined eight haplotypes of which H4 and H8 were unique to Tibetan population with H8 being identified first. The haplotype diversity (Hd: 0.808), nucleotide diversity (Pi: 0.603%), the average number of nucleotide difference (K: 3.917) of Tibetan mastiffs from Gansu were higher than those from Tibet region (Hd: 0.794; Pi: 0.589%; K: 3.831), which revealed higher genetic diversity in Gansu. In terms of total population, the genetic variation was low. The median-joining network and phylogenetic tree based on the mtDNA hypervariable region I showed that Tibetan mastiffs originated from grey wolves, as the other domestic dogs and had different history of maternal origin. The mismatch distribution analysis and neutrality tests indicated that Tibetan mastiffs were in genetic equilibrium or in a population decline.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Explore related subjects
Discover the latest articles and news from researchers in related subjects, suggested using machine learning.References
Achilli A., Olivieri A., Soares P., Lancioni H., Hooshiar Kashani B., Perego U. A. et al. 2012 Mitochondrial genomes from modern horses reveal the major haplogroups that underwent domestication. Proc. Natl. Acad. Sci. USA 109, 2449–2454.
Ardalan A., Kluetsch C. F., Zhang A. B., Erdogan M. and Uhlén M. 2011 Houshmand M.others Comprehensive study of mtDNA among Southwest Asian dogs contradicts independent domestication of wolf, but implies dog–wolf hybridization. Ecol. Evol. 1, 373–385.
Bandelt H. -J., Forster P. and Röhl A. 1999 Median-joining networks for inferring intraspecific phylogenies. Mol. Biol. Evol. 16, 37–48.
Dadi H., Lee S. H., Jung K. S., Choi J. W., Ko M. S. and Han Y. 2012 Effect of population reduction on mtDNA diversity and demographic history of korean cattle populations. Asian-Australas J. Anim. Sci. 25, 1223–1228.
Fu Y. -X. 1997 Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147, 915–925.
Imes D. L., Wictum E. J., Allard M. W. and Sacks B. N. 2012 Identification of single nucleotide polymorphisms within the mtDNA genome of the domestic dog to discriminate individuals with common HVI haplotypes. Forensic Sci. Int. Genet. 6, 630–639.
Li Q., Liu Z., Li Y., Zhao X., Dong L., Pan Z. et al. 2008 Origin and phylogenetic analysis of Tibetan Mastiff based on the mitochondrial DNA sequence. J. Genet. Gen. 35, 335–340.
Li Y. and Zhang Y. 2012 High genetic diversity of tibetan mastiffs revealed by mtDNA sequences. Chine. Sci. Bull. 57, 1483–1487.
Li Y., Li Q., Zhao X., Xie Z. and Xu Y. 2011 Complete sequence of the Tibetan Mastiff mitochondrial genome and its phylogenetic relationship with other Canids (Canis, Canidae). Animal 5, 18–25.
Librado P. and Rozas J. 2009 DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25, 1451–1452.
Long J. R., Qiu X. P., Zeng F. T., Tang L. M. and Zhang Y. P. 2003 Origin of rabbit (Oryctolagus cuniculus) in China: evidence from mitochondrial DNA control region sequence analysis. Animal Genet. 34, 82–87.
Melo-Ferreira J., Boursot P., Carneiro M., Esteves P. J., Farelo L. and Alves P. C. 2012 Recurrent introgression of mitochondrial DNA among hares (Lepus spp.) revealed by species-tree inference and coalescent simulations. Syst. Biol. 61, 367–381.
Meyer S., Weiss G. and von Haeseler A. 1999 Pattern of nucleotide substitution and rate heterogeneity in the hypervariable regions I and II of human mtDNA. Genetics 152, 1103–1110.
Pang J. F., Kluetsch C., Zou X. J., Zhang A. B., Luo L. Y., Angleby H. et al. 2009 mtDNA data indicate a single origin for dogs south of Yangtze River, less than 16,300 years ago, from numerous wolves. Mol. Biol. Evol. 26, 2849–2864.
Pérez-Pardal L., Grizelj J., Traore A., Cubric-Curik V., Arsenos G., Dovenski T. et al. 2014 Lack of mitochondrial DNA structure in Balkan donkey is consistent with a quick spread of the species after domestication. Animal Genet. 45, 144–147.
Picornell A., Gomez-Barbeito L., Tomas C., Castro J. A. and Ramon M. M. 2005 Mitochondrial DNA HVRI variation in Balearic populations. Am. J. Phys. Anthropol. 128, 119–130.
Ray N., Currat M. and Excoffier L. 2003 Intra-deme molecular diversity in spatially expanding populations. Mol. Biol. Evol. 20, 76–86.
Ren D., Yang Q., Ye J., Xu L., Zhao H. and Wu X. 2009 Strong heterozygote deficit in tibetan mastiff of China based on microsatellite loci. Animal 3, 1213–1215.
Rogers A. R. and Harpending H. 1992 Population growth makes waves in the distribution of pairwise genetic differences. Mol. Biol. Evol. 9, 552–569.
Rout P., Thangraj K., Mandal A. and Roy R. 2012 Genetic variation and population structure in jamunapari goats using microsatellites, mitochondrial DNA, and milk protein genes. Scientific World J. 2012.
Santos C., Sierra B., Alvarez L., Ramos A., Fernandez E., Nogues R. et al. 2008 Frequency and pattern of heteroplasmy in the control region of human mitochondrial DNA. J. Mol. Evol. 67, 191–200.
Savolainen P., Zhang Y. -p., Luo J., Lundeberg J. and Leitner T. 2002 Genetic evidence for an East Asian origin of domestic dogs. Science 298, 1610–1613.
Savolainen P., Leitner T., Wilton A. N., Matisoo-Smith E. and Lundeberg J. 2004 A detailed picture of the origin of the Australian dingo, obtained from the study of mitochondrial DNA. Proc. Natl. Acad. Sci. USA 101, 12387–12390.
Sugiyama S., Chong Y. H., Shito M., Kasuga M., Kawakami T., Udagawa C. et al. 2013 Analysis of mitochondrial DNA HVR1 haplotype of pure-bred domestic dogs in Japan. Leg. Med. 15, 303–309.
Tajima F. 1989 Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123, 585–595.
Tamura K., Peterson D., Peterson N., Stecher G., Nei M. and Kumar S. 2011 MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28, 2731–2739.
Theyab J. B., Al-Bustan S. and Crawford M. H. 2012 The genetic structure of the Kuwaiti population: mtDNA inter-and intra-population variation. Hum. Biol. 84, 379–403.
Zhao E., Yu Q., Zhang N., Kong D. and Zhao Y. 2013 Mitochondrial DNA diversity and the origin of Chinese indigenous sheep. Trop. Animal Health Prod. 45, 1715–1722.
Acknowledgement
We thank Dr Chuzhao Lei for his kind help in manuscript improvement.
Author information
Authors and Affiliations
Corresponding author
Additional information
Corresponding editor: N. G. PRASAD
[Ren Z., Chen H., Yang X. and Zhang C. 2017 Phylogenetic analysis of Tibetan mastiffs based on mitochondrial hypervariable region I. J. Genet. 96, xx–xx]
Rights and permissions
About this article
Cite this article
REN, Z., CHEN, H., YANG, X. et al. Phylogenetic analysis of Tibetan mastiffs based on mitochondrial hypervariable region I. J Genet 96, 119–125 (2017). https://doi.org/10.1007/s12041-017-0753-3
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12041-017-0753-3