Haplogroup relationships between domestic and wild sheep resolved using a mitogenome panel

Abstract

Five haplogroups have been identified in domestic sheep through global surveys of mitochondrial (mt) sequence variation, however these group classifications are often based on small fragments of the complete mtDNA sequence; partial control region or the cytochrome B gene. This study presents the complete mitogenome from representatives of each haplogroup identified in domestic sheep, plus a sample of their wild relatives. Comparison of the sequence successfully resolved the relationships between each haplogroup and provided insight into the relationship with wild sheep. The five haplogroups were characterised as branching independently, a radiation that shared a common ancestor 920,000 ± 190,000 years ago based on protein coding sequence. The utility of various mtDNA components to inform the true relationship between sheep was also examined with Bayesian, maximum likelihood and partitioned Bremmer support analyses. The control region was found to be the mtDNA component, which contributed the highest amount of support to the tree generated using the complete data set. This study provides the nucleus of a mtDNA mitogenome panel, which can be used to assess additional mitogenomes and serve as a reference set to evaluate small fragments of the mtDNA.

Figure 1

Phylogenetic relationship between six wild and ten domestic sheep inferred using the (a) complete mitochondrial genome sequence, (b) 12s rRNA and (c) tRNA concatemer. The neighbour joining trees were generated using Baysian and maximum likelihood methods with bootstrap support values are given on the nodes and clade credibility scores in brackets. The time since divergence of haplogroups A–E was calculated after first estimating the time since the most recent common ancestor of argali and domestic sheep. This was used as a calibration point (CP) for timing the radiation of each haplogroup A–E (nodes 1–4).

Figure 2

Partitioned Bremmer support (PBS) for different components of the mitogenome. The graph shows the relative contribution to the tree presented in Figure 1a of 17 components of the mitogenome. Analysis was performed either with (blue bars) or without (green bars) inclusion of the six animals classified as ‘wild'. A full color version of this figure is available at the Heredity journal online.