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. 2017 Jun 6;6:e25413.
doi: 10.7554/eLife.25413.

Palaeogenomes of Eurasian Straight-Tusked Elephants Challenge the Current View of Elephant Evolution

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Free PMC article

Palaeogenomes of Eurasian Straight-Tusked Elephants Challenge the Current View of Elephant Evolution

Matthias Meyer et al. Elife. .
Free PMC article

Abstract

The straight-tusked elephants Palaeoloxodon spp. were widespread across Eurasia during the Pleistocene. Phylogenetic reconstructions using morphological traits have grouped them with Asian elephants (Elephas maximus), and many paleontologists place Palaeoloxodon within Elephas. Here, we report the recovery of full mitochondrial genomes from four and partial nuclear genomes from two P. antiquus fossils. These fossils were collected at two sites in Germany, Neumark-Nord and Weimar-Ehringsdorf, and likely date to interglacial periods ~120 and ~244 thousand years ago, respectively. Unexpectedly, nuclear and mitochondrial DNA analyses suggest that P. antiquus was a close relative of extant African forest elephants (Loxodonta cyclotis). Species previously referred to Palaeoloxodon are thus most parsimoniously explained as having diverged from the lineage of Loxodonta, indicating that Loxodonta has not been constrained to Africa. Our results demonstrate that the current picture of elephant evolution is in need of substantial revision.

Keywords: Elephas antiquus; Palaeoloxodon antiquus; ancient DNA; evolutionary biology; genomics; paleogenomes.

Conflict of interest statement

The authors declare that no competing interests exist.

Figures

Figure 1.
Figure 1.. Palaeoloxodon antiquus, geographic range based on fossil finds (after Pushkina, 2007).
White dots indicate the locations of Weimar-Ehringsdorf and Neumark-Nord. DOI: http://dx.doi.org/10.7554/eLife.25413.003
Figure 2.
Figure 2.. Phylogenetic trees relating the mitochondrial and nuclear sequences of P.antiquus (NN and WE) to other elephantids.
(A) Maximum clade credibility (MCC) tree resulting from a BEAST (Drummond et al., 2012) analysis of 35 complete mitochondrial genomes using 15,447 sites. Node bars and numbers show the 95% highest posterior density estimates for node ages and clade support, respectively. Mitochondrial partitioning scheme and molecular and coalescent models are described in ‘Materials and methods’. (B) Pairwise-distance Neighbor-joining tree from between 210 million and 2.5 billion base pairs of nuclear shotgun sequence data. Bootstrap support values from 100 replicates are shown inside nodes. Summary statistics of the underlying sequence data are available in Figure 2—source data 1. DOI: http://dx.doi.org/10.7554/eLife.25413.004
Figure 2—figure supplement 1.
Figure 2—figure supplement 1.. Sequence coverage of the NN and WE mitochondrial genomes.
DOI: http://dx.doi.org/10.7554/eLife.25413.006
Figure 2—figure supplement 2.
Figure 2—figure supplement 2.. DNA fragment size distribution inferred from full-length mtDNA sequences.
DOI: http://dx.doi.org/10.7554/eLife.25413.007
Figure 2—figure supplement 3.
Figure 2—figure supplement 3.. Frequency of C to T substitutions for each position in the sequence alignments.
(A) Substitution frequencies in mitochondrial alignments. Substitution frequencies are depressed in the Neumark-Nord libraries due treatment with uracil-DNA-glycosylase (UDG). (B) In nuclear sequence alignments, the deamination signal could be partly restored by limiting analysis to cytosines in CpG content. Since the majority of cytosines in CpG dinucleotides are methylated in mammalian genomes, deamination leaves thymines, which are not excised by UDG. DOI: http://dx.doi.org/10.7554/eLife.25413.008
Figure 2—figure supplement 4.
Figure 2—figure supplement 4.. Maximum likelihood tree from concatenated nuclear protein-coding sequences with bootstrap support values shown inside nodes.
DOI: http://dx.doi.org/10.7554/eLife.25413.009
Figure 2—figure supplement 5.
Figure 2—figure supplement 5.. Amino acid racemization data.
D/L values of Asx, Glx, Ala and Val for the free amino acid (FAA, panels on the left) and total hydrolysable amino acid (THAA, panels on the right) fraction of bleached Bithynia tentaculata opercula from Amersfoort, Neumark-Nord 1 and 2. Ranges for samples from UK sites correlated with MIS 5e and MIS seven are indicative only, as effective diagenetic temperatures are likely to have differed significantly between Britain and continental Europe. The boundary of the box closest to zero indicates the 25th percentile, the dashed line within the box marks the mean and the boundary of the box farthest from zero indicates the 75th percentile. The 10th and 90th percentiles are represented by lines above and below the boxes. The results of each duplicate analysis are included in order to provide a statistically significant sample size. DOI: http://dx.doi.org/10.7554/eLife.25413.010
Figure 3.
Figure 3.. A revised tree of phylogenetic relationships among elephantids, color-coded by their presumed geographical range.
DOI: http://dx.doi.org/10.7554/eLife.25413.011

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