http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.908373
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of Cervus elaphus songaricus (Cetartiodactyla: Cervinae) and a phylogenetic analysis with related species Yiqing Li1,2, Hengxing Ba1,2, and Fuhe Yang1,2
Mitochondrial DNA Downloaded from informahealthcare.com by Mcgill University on 10/18/14 For personal use only.
1
Institute of Special Economic Animals and Plants, Chinese Academy of Agricultural Sciences, Jilin, People’s Republic of China and 2State Key Laboratory for Molecular Biology of Special Economical Animals, Chinese Academy of Agricultural Sciences, Jilin, People’s Republic of China Abstract
Keywords
Complete mitochondrial genome of Tianshan wapiti, Cervus elaphus songaricus, is 16,419 bp in length and contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 1 control region. The phylogenetic trees were reconstructed with the concatenated nucleotide sequences of the 13 protein-coding genes using maximum parsimony (MP) and Bayesian inference (BI) methods. MP and BI phylogenetic trees here showed an identical tree topology. The monopoly of red deer, wapiti and sika deer was well supported, and wapiti was found to share a closer relationship with sika deer. Tianshan wapiti shared a closer relationship with xanthopygus than yarkandensis. Rusa unicolor and Rucervus eldi were given a basal phylogenetic position. Our phylogenetic analysis provided a robust phylogenetic resolution spanning the entire evolutionary relationship of the subfamily Cervinae.
Cervus elaphus songaricus, mitochondrial genome, phylogeny, Tianshan wapiti
The Tianshan wapiti (Cervus elaphus songaricus) can be found in the Tian Shan Mountains in eastern Kyrgyzstan, southeastern Kazakhstan, and North Central Xinjiang, China (Gao & Gu, 1985; Gao & Hu, 1993). It is the largest subspecies of Asian wapiti, both in body size and antlers. There are around 50,000 individuals left in the wild, and they are declining at a rapid rate. This species currently has Class IIProtected Status in China. To provide useful genetic resources that could be used in conservation and restoration projects for Tianshan wapiti, the complete mitochondrial genome (KJ025072) of this species was determined and the phylogenetic trees with related species were also constructed in this paper. The mitochondrial DNA of Tianshan wapiti has 16,419 bp in length, and consists of 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, 13 protein-coding genes and a non-coding region (D-loop). Most mitochondrial genes are encoded on the H strand, except the ND6 gene and eight tRNA genes. Phylogenetic analysis was based on the concatenated nucleotide sequences of 13 encoded protein genes. For the phylogenetic
Correspondence: Fuhe Yang, Institute of Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences, Jilin, People’s Republic of China. E-mail: [email protected]
History Received 19 March 2014 Accepted 23 March 2014 Published online 14 April 2014
analysis, a maximum parsimony (MP) tree with heuristic search using 10 stepwise additions of sequences and TBR branchswapping option was constructed using PAUP 4.0 (Swofford, 2002). Node support of the phylogenetic tree was assessed by 1000 bootstrap replicates. Bayesian inference (BI) tree was constructed in MrBayes v3.1.2 (Huelsenbeck & Ronquist, 2001) with two independent Markov chain Monte Carlo (MCMC) analyses. The best-fitting model (‘‘invgamma’’) for BI was chosen. Samples from the posterior were drawn every 1000 generations over a total of 10 million generations per MCMC run. The first 20% burn-in was discarded, and the resulting trees for each replicate were combined. Two methods of phylogenetic analyses yielded an essentially identical tree topology (Figure 1). All nodes in the phylogenetic tree were strong supported by statistical value. This result was in agreement with the view that a monophyly consists of red deer, wapiti and sika deer, and wapiti was found to share a closer relationship with sika deer (Kuwayama & Ozawa, 2000; Ludt et al., 2004; Mahmut et al., 2002). The phylogenetic relationships supported that Tianshan wapiti was grouped into wapiti clade and was closer to xanthopygus than yarkandensis, which were supported by previous data (Ludt et al., 2004; Mahmut et al., 2002). Rusa unicolor and Rucervus eldi were given a basal phylogenetic position, branching apparently earlier than sika deer, wapiti and red deer within the subfamily Cervinae. But the position of Rusa unicolor is in conflict with the previous studies (Pitra et al., 2004). Based on the 13 encoded protein genes, our phylogenetic analysis provided a robust phylogenetic resolution spanning the entire evolutionary relationship of the subfamily Cervinae.
Mitochondrial DNA Downloaded from informahealthcare.com by Mcgill University on 10/18/14 For personal use only.
2
Y. Li et al.
Mitochondrial DNA, Early Online: 1–2
Figure 1. Phylogenetic tree based on the nucleotide dataset of the 13 protein-coding genes. Branch lengths and topologies came from Bayesian analysis. The posterior probabilities of BI and bootstrap values of MP were shown beside nodes.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper. We would like to thank National Basic Condition Platform (2013), and Science and Technology Commission, Jilin (No. 201262514) for providing funds for this research.
References Gao X, Gu J. (1985). Red Deer in Xinjiang. Chinese Wildlife 2:24–6. Gao X, Hu D. (1993). Status of wild and farmed red deer in Xinjiang. In: Ohtaishi N, Sheng H, editors. Deer of China: Biology and management. Amsterdam: Elsevier Science Publishers. p 159–64. Huelsenbeck JP, Ronquist F. (2001). MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17:754–5.
Kuwayama R, Ozawa T. (2000). Phylogenetic relationships among European red deer, wapiti, and sika deer inferred from mitochondrial DNA sequences. Mol Phylogenet Evol 15:115–23. Ludt CJ, Schroeder W, Rottmann O, Kuehn R. (2004). Mitochondrial DNA phylogeography of red deer (Cervus elaphus). Mol Phylogenet Evol 31:1064–83. Mahmut H, Masuda R, Onuma M, Takahashi M, Nagata J, Suzuki M, Ohtaishi N. (2002). Molecular phylogeography of the red deer (Cervus elaphus) populations in Xinjiang of China: Comparison with other Asian, European, and North American populations. Zoolog Sci 19: 485–95. Pitra C, Fickel J, Meijaard E, Groves PC. (2004). Evolution and phylogeny of old world deer. Mol Phylogenet Evol 33:880–95. Swofford DL. (2002). PAUP*: Phylogenetic analysis using parsimony (* and other methods). version 4. Sunderland, MA: Sinauer.
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of Cervus elaphus songaricus (Cetartiodactyla: Cervinae) and a phylogenetic analysis with related species Yiqing Li1,2, Hengxing Ba1,2, and Fuhe Yang1,2
Mitochondrial DNA Downloaded from informahealthcare.com by Mcgill University on 10/18/14 For personal use only.
1
Institute of Special Economic Animals and Plants, Chinese Academy of Agricultural Sciences, Jilin, People’s Republic of China and 2State Key Laboratory for Molecular Biology of Special Economical Animals, Chinese Academy of Agricultural Sciences, Jilin, People’s Republic of China Abstract
Keywords
Complete mitochondrial genome of Tianshan wapiti, Cervus elaphus songaricus, is 16,419 bp in length and contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 1 control region. The phylogenetic trees were reconstructed with the concatenated nucleotide sequences of the 13 protein-coding genes using maximum parsimony (MP) and Bayesian inference (BI) methods. MP and BI phylogenetic trees here showed an identical tree topology. The monopoly of red deer, wapiti and sika deer was well supported, and wapiti was found to share a closer relationship with sika deer. Tianshan wapiti shared a closer relationship with xanthopygus than yarkandensis. Rusa unicolor and Rucervus eldi were given a basal phylogenetic position. Our phylogenetic analysis provided a robust phylogenetic resolution spanning the entire evolutionary relationship of the subfamily Cervinae.
Cervus elaphus songaricus, mitochondrial genome, phylogeny, Tianshan wapiti
The Tianshan wapiti (Cervus elaphus songaricus) can be found in the Tian Shan Mountains in eastern Kyrgyzstan, southeastern Kazakhstan, and North Central Xinjiang, China (Gao & Gu, 1985; Gao & Hu, 1993). It is the largest subspecies of Asian wapiti, both in body size and antlers. There are around 50,000 individuals left in the wild, and they are declining at a rapid rate. This species currently has Class IIProtected Status in China. To provide useful genetic resources that could be used in conservation and restoration projects for Tianshan wapiti, the complete mitochondrial genome (KJ025072) of this species was determined and the phylogenetic trees with related species were also constructed in this paper. The mitochondrial DNA of Tianshan wapiti has 16,419 bp in length, and consists of 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, 13 protein-coding genes and a non-coding region (D-loop). Most mitochondrial genes are encoded on the H strand, except the ND6 gene and eight tRNA genes. Phylogenetic analysis was based on the concatenated nucleotide sequences of 13 encoded protein genes. For the phylogenetic
Correspondence: Fuhe Yang, Institute of Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences, Jilin, People’s Republic of China. E-mail: [email protected]
History Received 19 March 2014 Accepted 23 March 2014 Published online 14 April 2014
analysis, a maximum parsimony (MP) tree with heuristic search using 10 stepwise additions of sequences and TBR branchswapping option was constructed using PAUP 4.0 (Swofford, 2002). Node support of the phylogenetic tree was assessed by 1000 bootstrap replicates. Bayesian inference (BI) tree was constructed in MrBayes v3.1.2 (Huelsenbeck & Ronquist, 2001) with two independent Markov chain Monte Carlo (MCMC) analyses. The best-fitting model (‘‘invgamma’’) for BI was chosen. Samples from the posterior were drawn every 1000 generations over a total of 10 million generations per MCMC run. The first 20% burn-in was discarded, and the resulting trees for each replicate were combined. Two methods of phylogenetic analyses yielded an essentially identical tree topology (Figure 1). All nodes in the phylogenetic tree were strong supported by statistical value. This result was in agreement with the view that a monophyly consists of red deer, wapiti and sika deer, and wapiti was found to share a closer relationship with sika deer (Kuwayama & Ozawa, 2000; Ludt et al., 2004; Mahmut et al., 2002). The phylogenetic relationships supported that Tianshan wapiti was grouped into wapiti clade and was closer to xanthopygus than yarkandensis, which were supported by previous data (Ludt et al., 2004; Mahmut et al., 2002). Rusa unicolor and Rucervus eldi were given a basal phylogenetic position, branching apparently earlier than sika deer, wapiti and red deer within the subfamily Cervinae. But the position of Rusa unicolor is in conflict with the previous studies (Pitra et al., 2004). Based on the 13 encoded protein genes, our phylogenetic analysis provided a robust phylogenetic resolution spanning the entire evolutionary relationship of the subfamily Cervinae.
Mitochondrial DNA Downloaded from informahealthcare.com by Mcgill University on 10/18/14 For personal use only.
2
Y. Li et al.
Mitochondrial DNA, Early Online: 1–2
Figure 1. Phylogenetic tree based on the nucleotide dataset of the 13 protein-coding genes. Branch lengths and topologies came from Bayesian analysis. The posterior probabilities of BI and bootstrap values of MP were shown beside nodes.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper. We would like to thank National Basic Condition Platform (2013), and Science and Technology Commission, Jilin (No. 201262514) for providing funds for this research.
References Gao X, Gu J. (1985). Red Deer in Xinjiang. Chinese Wildlife 2:24–6. Gao X, Hu D. (1993). Status of wild and farmed red deer in Xinjiang. In: Ohtaishi N, Sheng H, editors. Deer of China: Biology and management. Amsterdam: Elsevier Science Publishers. p 159–64. Huelsenbeck JP, Ronquist F. (2001). MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17:754–5.
Kuwayama R, Ozawa T. (2000). Phylogenetic relationships among European red deer, wapiti, and sika deer inferred from mitochondrial DNA sequences. Mol Phylogenet Evol 15:115–23. Ludt CJ, Schroeder W, Rottmann O, Kuehn R. (2004). Mitochondrial DNA phylogeography of red deer (Cervus elaphus). Mol Phylogenet Evol 31:1064–83. Mahmut H, Masuda R, Onuma M, Takahashi M, Nagata J, Suzuki M, Ohtaishi N. (2002). Molecular phylogeography of the red deer (Cervus elaphus) populations in Xinjiang of China: Comparison with other Asian, European, and North American populations. Zoolog Sci 19: 485–95. Pitra C, Fickel J, Meijaard E, Groves PC. (2004). Evolution and phylogeny of old world deer. Mol Phylogenet Evol 33:880–95. Swofford DL. (2002). PAUP*: Phylogenetic analysis using parsimony (* and other methods). version 4. Sunderland, MA: Sinauer.
