A mitogenomic timetree for Darwin's enigmatic South American mammal Macrauchenia patachonica

Abstract

The unusual mix of morphological traits displayed by extinct South American native ungulates (SANUs) confounded both Charles Darwin, who first discovered them, and Richard Owen, who tried to resolve their relationships. Here we report an almost complete mitochondrial genome for the litoptern Macrauchenia. Our dated phylogenetic tree places Macrauchenia as sister to Perissodactyla, but close to the radiation of major lineages within Laurasiatheria. This position is consistent with a divergence estimate of ∼66 Ma (95% credibility interval, 56.64-77.83 Ma) obtained for the split between Macrauchenia and other Panperissodactyla. Combined with their morphological distinctiveness, this evidence supports the positioning of Litopterna (possibly in company with other SANU groups) as a separate order within Laurasiatheria. We also show that, when using strict criteria, extinct taxa marked by deep divergence times and a lack of close living relatives may still be amenable to palaeogenomic analysis through iterative mapping against more distant relatives.

Figure 1. Map of sites yielding specimens of Toxodon and Macrauchenia.

MAC002 Macrauchenia, the sample from which mitogenomic data were successfully collected, came from a metapodial recovered at the locality Baño Nuevo-1 Cave (in red). For locality context, see Supplementary Note 1 and Supplementary Fig. 8. Map generated using QGIS 2.8 (QGIS Development Team, 2016. QGIS Geographic Information System. Open Source Geospatial Foundation Project. http://www.qgis.org/).

Figure 2. Contamination check using pairwise sliding-window comparisons.

Comparisons were undertaken in 500 bp windows with 50 bp overlaps. X axis represents the sliding window number. Approximate gene locations within sliding windows are indicated by pink coloured boxes, and the control region is indicated by a blue box. Five sliding window pairwise comparisons are shown: MAC002-human (blue), MAC002-rhino (black), MAC002-guanaco (yellow), MAC002-tapir (orange) and MAC002-horse (red).

Figure 3. Dated mitogenomic phylogenetic tree.

Posterior probabilities and bootstrap values are indicated on the tree branches. The purple node bar represents the 95% CI for the Panperissodactyla clade divergence date based on the combination of all four calibrations used in this study. Scale bar represents time in millions of years. Grey vertical lines represent five million year intervals.