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A Multi-Calibrated Mitochondrial Phylogeny of Extant Bovidae (Artiodactyla, Ruminantia) and the Importance of the Fossil Record to Systematics

A Multi-Calibrated Mitochondrial Phylogeny of Extant Bovidae (Artiodactyla, Ruminantia) and the Importance of the Fossil Record to Systematics

Faysal Bibi. BMC Evol Biol.

Abstract

Background: Molecular phylogenetics has provided unprecedented resolution in the ruminant evolutionary tree. However, molecular age estimates using only one or a few (often misapplied) fossil calibration points have produced a diversity of conflicting ages for important evolutionary events within this clade. I here identify 16 fossil calibration points of relevance to the phylogeny of Bovidae and Ruminantia and use these, individually and together, to construct a dated molecular phylogeny through a reanalysis of the full mitochondrial genome of over 100 ruminant species.

Results: The new multi-calibrated tree provides ages that are younger overall than found in previous studies. Among these are young ages for the origin of crown Ruminantia (39.3-28.8 Ma), and crown Bovidae (17.3-15.1 Ma). These are argued to be reasonable hypotheses given that many basal fossils assigned to these taxa may in fact lie on the stem groups leading to the crown clades, thus inflating previous age estimates. Areas of conflict between molecular and fossil dates do persist, however, especially with regard to the base of the rapid Pecoran radiation and the sister relationship of Moschidae to Bovidae. Results of the single-calibrated analyses also show that a very wide range of molecular age estimates are obtainable using different calibration points, and that the choice of calibration point can influence the topology of the resulting tree. Compared to the single-calibrated trees, the multi-calibrated tree exhibits smaller variance in estimated ages and better reflects the fossil record.

Conclusions: The use of a large number of vetted fossil calibration points with soft bounds is promoted as a better approach than using just one or a few calibrations, or relying on internal-congruency metrics to discard good fossil data. This study also highlights the importance of considering morphological and ecological characteristics of clades when delimiting higher taxa. I also illustrate how phylogeographic and paleoenvironmental hypotheses inferred from a tree containing only extant taxa can be problematic without consideration of the fossil record. Incorporating the fossil record of Ruminantia is a necessary step for future analyses aiming to reconstruct the evolutionary history of this clade.

Figures

Figure 1
Figure 1
Tree resulting from Bayesian analysis of the full mitochondrial genome of 127 ruminants using 16 fossil calibration points (yellow circles). Calibrations along branches indicate stem calibrations. Node bars represent 95% intervals and node values are posterior probabilities. Names of terminal taxa follow those in ref. [8].
Figure 2
Figure 2
Median age estimates by node for each of the 16 single-calibrated analyses and the analysis using all 16 fossil calibrations (data in Table 2 ), covering the tree root (far left) and the 16 calibrated nodes. A large range of ages is obtainable with the use of different calibration points. The multi-calibrated analysis (blue with circles) provides estimates that are intermediate in age for older nodes, and towards the younger end of the range for younger nodes (<10 Ma).
Figure 3
Figure 3
A large number of morphological, ecological, and behavioral characteristics distinguish Bovini (A-C) from their sister taxon the saola (D, Pseudoryx nghetinhensis). A, European bison (Bos (Bison) bonasus), B, African buffalo (Syncerus caffer), and C, domestic cattle (Bos taurus). All images from Wikimedia Commons, user credits: Michael Gäbler (A), Haplochromis (B), DFoidl (C), Silviculture (D).

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