Maternal ancestry and population history from whole mitochondrial genomes

Abstract

MtDNA has been a widely used tool in human evolutionary and population genetic studies over the past three decades. Its maternal inheritance and lack of recombination have offered the opportunity to explore genealogical relationships among individuals and to study the frequency differences of matrilineal clades among human populations at continental and regional scales. The whole mtDNA genome sequencing delivers molecular resolution that is sufficient to distinguish patterns that have arisen over thousands of years. However, mutation rate is highly variable among the functional and non-coding domains of mtDNA which makes it challenging to obtain accurate split dates of the mitochondrial clades. Due to the shallow coalescent time of mitochondrial TMRCA at approximately 100 to 200 thousand years (ky), mtDNA data have only limited power to inform us about the more distant past and the early stages of human evolutionary history. The variation shared by mitochondrial genomes of individuals drawn from different continents outside Africa has been used to illuminate the details of the colonization process of the Old World, whereas regional patterns of variation have been at the focus of studies addressing questions of a more recent time scale. In the era of whole nuclear genome sequencing, mitochondrial genomes are continuing to be informative as a unique tool for the assessment of female-specific aspects of the demographic history of human populations.

Keywords: Maternal ancestry; MtDNA; Population history.

Figure 1

Functional map of mtDNA. As in other vertebrates, human mtDNA is circular and characterized by high gene density and strand asymmetry. The heavy strand encodes all mtDNA genes except for the ND6 and has a high GT/AC ratio. Protein coding, rRNA and tRNA genes are shown in boxes distinguished by different colours. Adapted from Schon et al. [63].

Figure 2

mtDNA haplogroup tree and distribution map. Haplogroup labels are reported according to the http://www.phylotree.org/ nomenclature [14]. Only a single branch defining marker, preferably from the coding region, is shown. The main geographic features of haplogroup distribution are highlighted with colour.