Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes

Abstract

We report five new complete mitochondrial DNA (mtDNA) genomes of Siberian woolly mammoth (Mammuthus primigenius), sequenced with up to 73-fold coverage from DNA extracted from hair shaft material. Three of the sequences present the first complete mtDNA genomes of mammoth clade II. Analysis of these and 13 recently published mtDNA genomes demonstrates the existence of two apparently sympatric mtDNA clades that exhibit high interclade divergence. The analytical power afforded by the analysis of the complete mtDNA genomes reveals a surprisingly ancient coalescence age of the two clades, approximately 1-2 million years, depending on the calibration technique. Furthermore, statistical analysis of the temporal distribution of the (14)C ages of these and previously identified members of the two mammoth clades suggests that clade II went extinct before clade I. Modeling of protein structures failed to indicate any important functional difference between genomes belonging to the two clades, suggesting that the loss of clade II more likely is due to genetic drift than a selective sweep.

Fig. 1.

Sites of recovery of the mammoth hair specimens whose complete mitochondrial genome sequences have been reported. Clade I mammoths are indicated as blue diamonds. Clade II mammoths are indicated by red circles. The exact locations of M1, M4, and M5 are not known but most probably originate from Northern Yakutia (c. 66–76°N, 106–160°E). “K,” “R,” and “P” indicate the Krause (4), Rogaev (5), and Poinar (6, 7) mammoth mtDNA genomes, respectively. This figure is modified from ref. .

Fig. 2.

Sequence differences found among the 18 mammoth mitochondrial genomes with respect to mammoth M1 (GenBank entry EU153444.1). Each vertical bar depicts a nucleotide difference from sample M1, which serves as a reference (and hence has no row). The rectangle labeled 591 shows the location of a 591-bp interval used to assess the diversity among the larger mammoth and modern elephant datasets. We have not tried to assemble the interval denoted by VNTR; thus, this section is absent from the alignment.

Fig. 3.

Phylogenetic trees inferred using Bayesian analysis of complete mitochondrial genomes, drawn to time scales, with mammoth clades indicated. Nodes of interest are labeled with posterior probabilities. Blue bars represent 95% highest posterior densities of nodal age estimates. Slanted double lines indicate that portions of lines or bars have been omitted because of space constraints. (a) Estimated phylogeny of 18 mammoths, mastodon, and African and Asian elephants, where divergence dates are estimated using fossil calibration. (b) Estimated genealogy of 14 mammoth specimens with finite radiocarbon dates, where divergence dates are derived using an internally calibrated molecular clock.

Fig. 4.

Temporal distribution of 43 ¹⁴C dated clade I and 11 clade II mammoths. For a number of individuals (5 clade I and 8 clade II, indicated by the extended timelines) finite dates could not be calculated; thus, the reported dates are only indicative of minimum bounds on the samples' ages. In this context, some aspects of the figure may be misleading—for example, the apparent absence of clade I mammoths between ≈50,000 and 60,000 ¹⁴C years ago. The apparently “older” minimum on the infinite dates of most of the hair (this study) as compared with bone samples (1) may reflect a superiority in hair over bone material with regard to long-term carbon preservation in the samples.