Y-chromosomal microsatellites and expansion from Africa

Abstract

Some diversities are thought to mark human expansion from Africa — they decline as distance from Africa accumulates, and suggest that the expansion originated from any of a range of locations which are only in Africa. Previously, a decline was found regarding Y-chromosomal microsatellite heterozygosity. However, this diversity has been noted to suggest a non-African starting point and, consequently, not appearing reflective of expansion from Africa. Declines have appeared in other variables derived through Y-chromosomal microsatellites, including effective population size, expansion time, and time to the most recent common ancestor. The present research inferred if these variables, and some Y-chromosomal diversities, indicate expansion from Africa; indicative variables could help with identifying which area of Africa the expansion started in. This research used variables derived previously from Y-chromosomal microsatellites for populations worldwide (effective population size, expansion time, and time to the most recent common ancestor) or only in Africa (haplotype and repeat unit diversities). Regarding populations worldwide, San were very high in each variable when considering distance from (southern) Africa. Without San, effective population size and time to the most recent common ancestor did not squarely indicate an African origin, and expansion time placed the origin wholly outside of Africa. When using San, each area was only in Africa. Amongst African populations, whilst both haplotype diversity and repeat unit diversity showed a geographical pattern of declining, only haplotype diversity suggested a completely African area of origin. Using Y-chromosomal haplotype diversity alongside some other genetic diversities, a southern African origin was broadly indicated.

The global expansion from southern Africa by modern humans? Its signal may be shown more through the cranial shape of males than females

“…In some preprints, there have been attempts to interpolate between estimates of origins from several biological variables in order to have a broad impression of which part of Africa the expansion originated, with the most plausible region appearing to be southern Africa (Cenac, 2022b, 2023). This has been done, for example in Cenac (2023), through ranking locations in Africa in terms of how well geographical distances from those locations are related to a variable (given a certain direction), and then pooling together those ranks from a number of variables in order to have an overall evaluation of where the origin is likely to be located. It seems that southern Africa (Choudhury et al, 2021) is given some further support by the ranks generated in the present study regarding the relationship between cranial and geographical distances concerning male crania (Figure 4A), including when these ranks are used to supplement the pooled estimate in Cenac (2023) (Figure 4B).…”

“…So, between Variables 1 and 2, a correlation coefficient was found using each African origin. The strengths of these associations were ranked as in Cenac (2023), with a rank of number 1 for the most negative, and these ranks are presented in Figure 4A. It should be reiterated that the area of origin was not 100% in Africa (see Figure 3A).…”

“…A new addition is the inclusion of red lines to indicate the geographical locations with BICs which are at values between the lowest BIC and (within) four BICs over the lowest. Figure 4 is, to some extent, based on Figure 4 of Cenac (2023) (who employed origins that are in a figure in Betti et al, 2013). Figure 5 modifies Figure 11A from Cenac (2022b), being produced from the relationship between cranial shape and geographical distances rather than (as in Cenac, 2022b) cranial shape diversity.…”

“…As with the association which diversity has with geographical distance from Africa (Balloux et al, 2009; Cenac, 2022b, 2023; Prugnolle et al, 2005; von Cramon-Taubadel & Lycett, 2008), it would be useful to use p -values to infer whether the strength of relationships (between cranial shape and geographical distances) is related to geographical distance from Africa. Yet, nonindependence was probably great enough to be an issue because the same populations contributed towards multiple correlation coefficients (see Forstmeier et al, 2017).…”

“…This study gave some thought as to whether relationships between cranial shape and geographical distances are of value for locating the origin of the global expansion. Like with other variables (e.g., Cenac, 2022b, 2023), to infer whether the relationship between cranial shape and geographical distances indicates the global expansion from Africa, the present research looked not only for an indication of this relationship going through a decline as geographical distance rises from Africa, but for the relationship to decline the most when geographical distance is from a location in Africa rather than in another continent (i.e., for the suggested area of origin to not go beyond Africa). In some preprints, research has generalised across various measures to estimate the region of Africa where the global expansion started, and the region suggested was the south (Cenac, 2022b, 2023); if the relationship between cranial shape and geographical distances (Hubbe et al, 2009) is indicative of the global expansion, then this opens up the avenue of including this relationship alongside the various measures when generally estimating the origin.…”