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. 2019 May 9;9(12):6821-6832.
doi: 10.1002/ece3.5250. eCollection 2019 Jun.

Signals of positive selection in mitochondrial protein-coding genes of woolly mammoth: Adaptation to extreme environments?

Jacob Njaramba Ngatia  1 , Tian Ming Lan  2   3   4 , Thi Dao Dinh  1 , Le Zhang  1 , Ahmed Khalid Ahmed  1 , Yan Chun Xu  1   5   6
Affiliations

Signals of positive selection in mitochondrial protein-coding genes of woolly mammoth: Adaptation to extreme environments?

Jacob Njaramba Ngatia et al. Ecol Evol. .

Abstract

The mammoths originated in warm and equatorial Africa and later colonized cold and high-latitude environments. Studies on nuclear genes suggest that woolly mammoth had evolved genetic variations involved in processes relevant to cold tolerance, including lipid metabolism and thermogenesis, and adaptation to extremely varied light and darkness cycles. The mitochondria is a major regulator of cellular energy metabolism, thus the mitogenome of mammoths may also exhibit adaptive evolution. However, little is yet known in this regard. In this study, we analyzed mitochondrial protein-coding genes (MPCGs) sequences of 75 broadly distributed woolly mammoths (Mammuthus primigenius) to test for signatures of positive selection. Results showed that a total of eleven amino acid sites in six genes, namely ND1, ND4, ND5, ND6, CYTB, and ATP6, displayed strong evidence of positive selection. Two sites were located in close proximity to proton-translocation channels in mitochondrial complex I. Biochemical and homology protein structure modeling analyses demonstrated that five amino acid substitutions in ND1, ND5, and ND6 might have influenced the performance of protein-protein interaction among subunits of complex I, and three substitutions in CYTB and ATP6 might have influenced the performance of metabolic regulatory chain. These findings suggest metabolic adaptations in the mitogenome of woolly mammoths in relation to extreme environments and provide a basis for further tests on the significance of the variations on other systems.

Keywords: Mammuthus primigenius; mitochondrial genome; mitolineages; positive selection; woolly mammoth.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Sites locations of woolly mammoth mitochondrial genome samples included in this study. The samples are color‐coded by clade. The location of the five samples we collected and used for this study is shown as a blue square enclosed with a dotted circle, of which the latter represents the approximate diameter for their geographic range
Figure 2
Figure 2
Rooted phylogeny of Mammuthus primigenius based on mtDNA protein‐coding sequences estimated by Bayesian inference. All the nodes are well supported (PP > 0.9) unless indicated otherwise; mtDNA clades and the respective haplogroups labeled on the tree branches and on the right side of the tree respectively; the taxa names and codes are the individual sequence ID codes
Figure 3
Figure 3
Atomic level structure of the predicted mitochondrial complex I of M. primigenius. Residues with amino acid substitutions are displayed as orange spheres. The potentially active sites are enlarged images shown as red sticks. Letters before the residues indicate the amino acids and their corresponding substitutions
See this image and copyright information in PMC

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