Mitochondrial DNA variation reveals maternal origins and demographic dynamics of Ethiopian indigenous goats

Abstract

The Horn of Africa forms one of the two main historical entry points of domestics into the continent and Ethiopia is particularly important in this regard. Through the analysis of mitochondrial DNA (mtDNA) d‐loop region in 309 individuals from 13 populations, we reveal the maternal genetic variation and demographic dynamics of Ethiopian indigenous goats. A total of 174 variable sites that generated 231 haplotypes were observed. They defined two haplogroups that were present in all the 13 study populations. Reference haplotypes from the six globally defined goat mtDNA haplogroups show the two haplogroups present in Ethiopia to be A and G, the former being the most predominant. Although both haplogroups are characterized by an increase in effective population sizes (N e) predating domestication, they also have experienced a decline in N e at different time periods, suggesting different demographic histories. We observed seven haplotypes, six were directly linked to the central haplotypes of the two haplogroups and one was central to haplogroup G. The seven haplotypes were common between Ethiopia, Kenya, Egypt, and Saudi Arabia populations, suggesting common maternal history and the introduction of goats into East Africa via Egypt and the Arabian Peninsula, respectively. While providing new mtDNA data from a historically important region, our results suggest extensive intermixing of goats mediated by human socio‐cultural and economic interactions. These have led to the coexistence of the two haplogroups in different geographic regions in Ethiopia resulting in a large caprine genetic diversity that can be exploited for genetic improvement.

Mitochondrial DNA variation and phylogeography of native Mongolian goats

“…This study conducted the first assessments of genetic population structure, genetic diversity, phylogenetic status, and the origin of Mongolian goats using the most polymorphic HVI region in mtDNA. This highly polymorphic region (indeed, the complete D-loop) has been routinely used in previous studies that examined genetic diversity, phylogenetic relationships, and especially the maternal origin of most domesticated animals, including goats [14,[33][34][35][36][37]. Similar to previous results [17,38,39], goats from Mongolia investigated in this study showed high mtDNA diversity.…”

“…mismatch distribution pattern was multimodal for all MG while unimodal for haplogroup A, and highly significant and negative Fu's Fs values were observed for all MG (-24.06) and haplogroup A (-24.39). Relatively similar patterns of mismatch distribution and significant and negative Fu's Fs values were obtained in previous studies [37,39,42]. More recently, the number of goats in Mongolia has increased fivefold within the last 30 years, more specifically the goat population grew from 5.1 million in 1990 to 27.3 million by 2017 [18].…”

“…Mismatch distribution and the neutrality test of Fu's [33] Fs statistics are recognized as suitable approaches to examine past population expansion and were routinely used in previous studies [6,36,38,39]. Mismatch distribution is a frequency graph of pairwise differences between alleles, and it has two common patterns, including multimodal (populations at demographic equilibrium) and unimodal (populations passed through a recent demographic expansion) [29,43].…”

Genetic diversity estimation of Yunnan indigenous goat breeds using microsatellite markers

“…Currently, the abundant genetic diversity of goats has been assessed by using many different types of molecular markers, including microsatellites (Câmara, Nunes, Diniz, Silva, & Araújo, 2017;E et al, 2018), MHC region variants (Gowane, Akram, Misra, Prakash, & Kumar, 2018), mitochondrial DNA (E et al, 2018;Tarekegn et al, 2018), functional genes (Gowane et al, 2018;Pitarch et al, 2018), and genomewide SNPs (Ilie, Kusza, Sauer, & Gavojdian, 2018;Nicoloso et al, 2015;Onzima et al, 2018). Currently, the abundant genetic diversity of goats has been assessed by using many different types of molecular markers, including microsatellites (Câmara, Nunes, Diniz, Silva, & Araújo, 2017;E et al, 2018), MHC region variants (Gowane, Akram, Misra, Prakash, & Kumar, 2018), mitochondrial DNA (E et al, 2018;Tarekegn et al, 2018), functional genes (Gowane et al, 2018;Pitarch et al, 2018), and genomewide SNPs (Ilie, Kusza, Sauer, & Gavojdian, 2018;Nicoloso et al, 2015;Onzima et al, 2018).…”

“…Goats (Capra hircus) are economically important domestic animals worldwide. Currently, the abundant genetic diversity of goats has been assessed by using many different types of molecular markers, including microsatellites (Câmara, Nunes, Diniz, Silva, & Araújo, 2017;E et al, 2018), MHC region variants (Gowane, Akram, Misra, Prakash, & Kumar, 2018), mitochondrial DNA (E et al, 2018;Tarekegn et al, 2018), functional genes (Gowane et al, 2018;Pitarch et al, 2018), and genomewide SNPs (Ilie, Kusza, Sauer, & Gavojdian, 2018;Nicoloso et al, 2015;Onzima et al, 2018). The diversity of several indigenous goat breeds in China was assessed Liu et al, 2014;Wang et al, 2017).…”