Control Region Length Dynamics Potentially Drives Amino Acid Evolution in Tarsier Mitochondrial Genomes
- 337 Downloads
Patterns and processes of molecular evolution critically influence inferences in phylogeny and phylogeography. Within primates, a shift in evolutionary rates has been identified as the rationale for contrasting findings from mitochondrial and nuclear DNA studies as to the position of Tarsius. While the latter now seems settled, we sequenced complete mitochondrial genomes of three Sulawesi tarsiers (Tarsius dentatus, T. lariang, and T. wallacei) and analyzed substitution rates among tarsiers and other primates to infer driving processes of molecular evolution. We found substantial length polymorphism of the D-loop within tarsier individuals, but little variation of predominant lengths among them, regardless of species. Length variation was due to repetitive elements in the CSB domain—minisatellite motifs of 35 bp length and microsatellite motifs of 6 bp length. Amino acid evolutionary rates were second highest among major primate taxa relative to nucleotide substitution rates. We observed many radical possibly function-altering amino acid changes that were rarely driven by positive selection and thus potentially slightly deleterious or neutral. We hypothesize that the observed pattern of an increased amino acid evolutionary rate in tarsier mitochondrial genomes may be caused by hitchhiking of slightly deleterious mutations with favored D-loop length variants selected for maximizing replication success within the cell or the mitochondrion.
KeywordsHeteroplasmy Multilevel selection Primates Sulawesi Tandem repeats Tarsius
We thank the Indonesian authorities LIPI, RISTEK, PHKA, and BKSDA for granting research, capture, and export permits and the Primate Research Center at Bogor Agricultural University for providing administrative support. Nicolas Galtier and an anonymous reviewer provided valuable comments on an earlier draft of the manuscript. Sample collection, molecular analyses, and manuscript submission were supported through research grants from the Deutsche Forschungsgemeinschaft (DFG, Me2730/1-2, Me2730/1-3, and Me2730/2-1); the molecular work was partly supported by the research-funding program “LOEWE—Landes-Offensive zur Entwicklung Wissenschaftlich-ökonomischer Exzellenz” of Hesse’s Ministry of Higher Education, Research, and the Arts.
Conflict of interest
The authors declare that they have no conflict of interest.
- Drummond AJ, Ashton B, Buxton S, Cheung M, Cooper A, et al (2011) Geneious v5.4. http://www.geneious.com. Accessed 30 Dec 2013
- Hall R (2001) Cenozoic reconstructions of SE Asia and the SW Pacific: changing patterns of land and sea. In: Metcalfe I, Smith JMB, Morwood M, Davidson I (eds) Faunal and floral migrations and evolution in SE Asia-Australasia. A.A. Balkema, Lisse, pp 35–56Google Scholar
- Merker S, Driller C, Dahruddin H, Wirdateti, Sinaga W et al (2010) Tarsius wallacei: a new tarsier species from central Sulawesi occupies a discontinuous range. Int J Primatol 31:1107–1122Google Scholar
- Rozen S, Skaletsky HJ (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics methods and protocols: methods in molecular biology. Humana Press, Totowa, pp 365–386Google Scholar
- Shekelle M, Leksono SM (2004) Strategi konservasi di Pulau Sulawesi dengan menggunakan Tarsius sebagai flagship species [Conservation strategy in Sulawesi Island using Tarsius as flagship species]. Biota 9:1–10Google Scholar
- Shekelle M, Morales JC, Niemitz C, Ichwan LL, Melnick D (2008b) Distribution of tarsier haplotypes for some parts of northern and central Sulawesi. In: Shekelle M, Maryanto I, Groves C, Schulze H, Fitch-Snyder H (eds) Primates of the oriental night. LIPI Press, Jakarta, pp 51–69Google Scholar