Correlating Bayesian date estimates with climatic events and domestication using a bovine case study

Abstract

The tribe Bovini contains a number of commercially and culturally important species, such as cattle. Understanding their evolutionary time scale is important for distinguishing between post-glacial and domestication-associated population expansions, but estimates of bovine divergence times have been hindered by a lack of reliable calibration points. We present a Bayesian phylogenetic analysis of 481 mitochondrial D-loop sequences, including 228 radiocarbon-dated ancient DNA sequences, using a multi-demographic coalescent model. By employing the radiocarbon dates as internal calibrations, we co-estimate the bovine phylogeny and divergence times in a relaxed-clock framework. The analysis yields evidence for significant population expansions in both taurine and zebu cattle, European aurochs and yak clades. The divergence age estimates support domestication-associated expansion times (less than 12 kyr) for the major haplogroups of cattle. We compare the molecular and palaeontological estimates for the Bison-Bos divergence.

Interrogation of modern and ancient genomes reveals the complex domestic history of cattle

“…Similarly to taurine mtDNA, zebu haplotype sequences fall into two major haplogroups (I1 and I2), comprised of two ancestral haplotypes (also called I1 and I2), through which all other sequences in the phylogeny root ( Figures 1C and 2). Comparable to taurine mtDNA variation, the dual star cluster motif within these clusters suggests that they are each signatures of domestication-induced population expansion; the estimated time-depths of the expansions are compatible with zebu domestic history as determined from archaeological studies (Ho et al, 2008). The I1 and I2 haplogroups display some geographic distribution across south Asia, with haplogroup I1 predominating in cattle that have moved eastwards to Southeast Asia from the Indus Valley, the most likely center of origin for this haplogroup.…”

“…Notably, the quantitative difference between the five major taurine ancestral haplotypes is small, with a coalescence time around the central T haplotype estimated at ~16,000 YBP (Troy et al, 2001;Achilli et al, 2008;Ho et al, 2008;Achilli et al, 2009). Thus, the shallow mtDNA sequence divergence observed in modern taurine populations suggests that the population of wild aurochs from which B. taurus was derived was itself limited in diversity.…”

Meta-Analysis of Mitochondrial DNA Reveals Several Population Bottlenecks during Worldwide Migrations of Cattle

“…It is not clear yet how to explain the overrepresentation in Africa of different sub-haplogroups exclusively from the T1 haplogroup. Possible explanations include positive selection of T1 mtDNA (see below), inherent uncertainties in time estimates and overestimations of the divergence times for recent taxa [28,29]. Shorter divergence times would allow an alternative scenario of a small herd with a high frequency of T1 reaching Africa, expanding and only then splitting into the different T1 sub-haplogroups.…”

Looking backwards to look forwards: conservation genetics in a changing world

“…Ancient DNA together with coalescent methods can improve estimates of historical demographic patterns, historical connectivity, splitting times among populations, directional migration (both in equilibrium and since the time of splitting; e.g. Hey and Nielsen 2004), and crucially, substitution rates relevant to the time frame under consideration (see discussion in Ho et al 2008). All other estimates related to the timing of historical events and effective population size based on genetic data depend on accurate substitution rates, and it is therefore encouraging that rates calculated in this way have allowed the derivation of very credible demographic patterns in the context of well known geologic time points (see examples discussed above).…”

“…This requires the assumption of a molecular clock, and therefore, an accurate interpretation of the mutation rate. However, although there are established estimates of mutation rate calculated by the phylogenetic method using geologic calibration points, more recent studies suggest that these estimates may be much too slow for intraspecific studies (see Ho et al 2008; though considerable discussion continues in the literature on this topic).…”