A View of Modern Human Origins from Y Chromosome Microsatellite Variation

Abstract

The idea that all modern humans share a recent (within the last 150,000 years) African origin has been proposed and supported on the basis of three observations. Most genetic loci examined to date have (1) shown greater diversity in African populations than in others, (2) placed the first branch between African and all non-African populations in phylogenetic trees, and (3) indicated recent dates for either the molecular coalescence (with the exception of some autosomal and X-chromosomal loci) or for the time of separation between African and non-African populations. We analyze variation at 10 Y chromosome microsatellite loci that were typed in 506 males representing 49 populations and every inhabited continent and find significantly greater Y chromosome diversity in Africa than elsewhere, find the first branch in phylogenetic trees of the continental populations to fall between African and all non-African populations, and date this branching with the (δμ)2 distance measure to 5800–17,400 or 12,800–36,800 years BP depending on the mutation rate used. The magnitude of the excess Y chromosome diversity in African populations appears to result from a greater antiquity of African populations rather than a greater long-term effective population size. These observations are most consistent with a recent African origin for all modern humans.

Modern human expansion from (southern?) Africa: Origin, non-African ancestry, and linearity

“…When using a combined African population and a number of non-African populations, a phylogenetic tree (arising from Y-chromosomal microsatellites) has its root located between Africans and non-Africans (Seielstad et al, 1999), hence Table 1 and Figure 5C and 5D may be surprising. Nevertheless, studies are congruent with there being migration back into Africa (e.g., Henn, Botigué et al, 2012; Hodgson et al, 2014).…”

“…Nonetheless, despite Y-chromosomal microsatellite heterozygosity being related to geographical distance from Africa (Balloux et al, 2009), that type of diversity was not indicated to signal the expansion. Yet that diversity was from six Y-chromosomal microsatellites (Balloux et al, 2009), i.e., not many (given Seielstad et al, 1999), so it really is not clear if the signal is present in the heterozygosity of Y-chromosomal microsatellites. As for where in Africa the expansion originated, the location of a geographical centroid (determined through a number of expansion indicators) and locations of peak points (using populations worldwide) adds weight to southern Africa being the origin (Figure 6).…”

“…When using a combined African population and a number of non-African populations, a phylogenetic tree (arising from Y-chromosomal microsatellites) has its root located between Africans and non-Africans (Seielstad et al, 1999), hence Table 1 and Figure 5C and 5D may be surprising.…”

“…Nevertheless, in Balloux et al (2009), Y-chromosomal diversity was calculated from six microsatellites, whilst X-chromosomal and autosomal microsatellite diversities were determined from 36 and 783 microsatellites respectively. Ten Y-chromosomal microsatellites is few (Seielstad et al, 1999). A tally of six microsatellites could be described similarly.…”

“…Using heterozygosities within each of 51 populations in Balloux et al (2009), averages (means) were calculated by continent. Also, see estimates of Y-chromosomal diversity elsewhere (e.g., Hammer et al, 2001;Seielstad et al, 1999), for instance, in Jorde et al (2000), microsatellite diversity was numerically higher in Africa than in Asia or Europe (other continents were not featured). Balloux et al (2009) did not explore where origin areas are located regarding genetic diversities; they did not determine if mitochondrial, and X-and Y-chromosomal diversities suggest an origin area entirely within Africa.…”