Proboscidean mitogenomics: chronology and mode of elephant evolution using mastodon as outgroup - PubMed (original) (raw)

Proboscidean mitogenomics: chronology and mode of elephant evolution using mastodon as outgroup

Nadin Rohland et al. PLoS Biol. 2007 Aug.

Abstract

We have sequenced the complete mitochondrial genome of the extinct American mastodon (Mammut americanum) from an Alaskan fossil that is between 50,000 and 130,000 y old, extending the age range of genomic analyses by almost a complete glacial cycle. The sequence we obtained is substantially different from previously reported partial mastodon mitochondrial DNA sequences. By comparing those partial sequences to other proboscidean sequences, we conclude that we have obtained the first sequence of mastodon DNA ever reported. Using the sequence of the mastodon, which diverged 24-28 million years ago (mya) from the Elephantidae lineage, as an outgroup, we infer that the ancestors of African elephants diverged from the lineage leading to mammoths and Asian elephants approximately 7.6 mya and that mammoths and Asian elephants diverged approximately 6.7 mya. We also conclude that the nuclear genomes of the African savannah and forest elephants diverged approximately 4.0 mya, supporting the view that these two groups represent different species. Finally, we found the mitochondrial mutation rate of proboscideans to be roughly half of the rate in primates during at least the last 24 million years.

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Conflict of interest statement

Competing interests. The authors have declared that no competing interests exist.

Figures

Figure 1

Figure 1. Appearance and Location of Origin of the Mastodon Tooth (IK-99–237) Used for Sequencing of the mtDNA Genome

The scale bar shows centimeters.

Figure 2

Figure 2. Ratio of the Number of Transitions to the Number of Transversions

The six points correspond to the ratio between species of Elephantidae (first two points), between Elephantidae and Mammut, between Proboscidea and (Dugong, Procavia), between Uranotheria and Bos, and between Mammalia and Struthio. The corresponding divergence times for proboscideans are given in Table 2. Dugong and hyrax diverged from Proboscidea 65 mya [5,9]. We used 105 mya for the Uranotheria–ruminant split ([9] and citations therein). The mammalian–bird divergence was set to 313 mya (the mean value of the confidence interval of [62]; but see also [63,65]). The arrows indicate the points of interest. The uncertainty of the divergence times is not taken into account because the goal was to show the general trend.

Figure 3

Figure 3. Gene-by-Gene Topology

Colored bars indicate the posterior probabilities for each respective topology. Blue indicates a Mammuthus–Elephas sister group relationship, green indicates a Mammuthus–Loxodonta sister group relationship, and yellow indicates an Elephas–Loxodonta sister group relationship. Black bars show the length of the respective genes in base pairs.

Figure 4

Figure 4. Data Saturation as Determined by the 95% CI Width as a Function of Posterior Mean Time

The high correlation coefficient of this plot suggests that the sequence data are highly informative. However, it cannot be excluded that the accuracy of divergence time estimates could be further improved by additional sequence data. The graph corresponds to the whole genome analysis. The partitioned data give a slightly higher correlation coefficient of 0.89 (not shown).

Figure 5

Figure 5. Phylogeny and Divergence Times Determined by This Study for the Four Proboscidean Species Analyzed

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