Capturing goats: documenting two hundred years of mitochondrial DNA diversity among goat populations from Britain and Ireland

Abstract

The domestic goat (Capra hircus) plays a key role in global agriculture, being especially prized in regions of marginal pasture. However, the advent of industrialized breeding has seen a dramatic reduction in genetic diversity within commercial populations, while high extinction rates among feral herds have further depleted the reservoir of genetic variation available. Here, we present the first survey of whole mitochondrial genomic variation among the modern and historical goat populations of Britain and Ireland using a combination of mtDNA enrichment and high throughput sequencing. Fifteen historical taxidermy samples, representing the indigenous 'Old Goat' populations of the islands, were sequenced alongside five modern Irish dairy goats and four feral samples from endangered populations in western Ireland. Phylogenetic and network analyses of European mitochondrial variation revealed distinct groupings dominated by historical British and Irish samples, which demonstrate a degree of maternal genetic structure between the goats of insular and continental Europe. Several Irish modern feral samples also fall within these clusters, suggesting continuity between these dwindling populations and the ancestral 'Old Goats' of Ireland and Britain.

Keywords: Capra hircus; conservation; mtDNA Capture; next generation sequencing; taxidermy samples.

Figure 1.

Whole mitochondrion maximum-likelihood phylogeny of 76 domestic goats from Europe and Turkey. Goats from this study are coloured in green or blue depending on their geographical origin—Ireland and Britain, respectively. Bootstrap values and haplogroup (Hg) divisions are displayed along branches. Dashed lines represent branches scaled to a fifth of their true length. (Online version in colour.)

Figure 2.

HV1 control region diversity in 154 goats from indigenous populations of western and central Europe. Individuals from Ireland and Britain are labelled. Groupings containing a majority of insular samples are highlighted in red. (a) A HV1 control region maximum-likelihood phylogeny. Dashed lines represent branches scaled to a fifth of their true length. The composition of each collapsed subclade is represented with a pie chart, sized according to number of samples within the clade and coloured according to the geographical origins of these samples. (b) A median-joining network following the same colour key. Branch lengths are not proportional to genetic distance. Mutations between nodes are represented through hatch marks. (Online version in colour.)