Paternal traces of Bantu expansion + African R1b1 mystery

It's good to see a paper which doesn't use an effective mutation rate to estimate ages, so the reported ages in this paper are more believable than the norm.

Expansion times and their standard deviations were calculated using eleven STRs (DYS19, DYS389I, DYS389II DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS460), whose mutation rates have been individually estimated (Gusmao et al. 2005). The allelic variance of each STR was divided by the estimated mutation rate, and the mean of the variances was multiplied by 25 (intergeneration time in years).

The main haplogroups found were:

Specifically, most of these lineages have been associated either to Bantu-speaking people - E1b1a (E3a according to The Y Chromosome Consortium (2002)), B2a, and E2 - or to Pygmy populations (haplogroup B2b). We also observed traces of haplogroups A, E*, E1a, and E1b1b1a (E3b1 according to The Y Chromosome Consortium (2002)), which are found at low frequencies across the African continent (Underhill et al. 2000; Underhill et al. 2001; Cruciani et al. 2002; Wood et al. 2005). Interestingly, almost 5% of the individuals here analyzed belonged to Eurasian haplogroup R1b1*.

If a correct mutation rate is used and a star-like signal of expansion is visible, then, not surprisingly, archaeology does correlate with haplogroup expansion:

The expansion date of the E1b1a haplogroup was estimated at 5,800 years (SD 7,200), in agreement with the expansion of Bantu languages.

The R1b1*-in-Africa mystery thickens. At first, these typically Eurasian chromosomes had been found in Cameroon, but they seem to be found in many populations

A remarkable finding of our study is the substantial number of individuals belonging to haplogroup R1b1* (5.2%). Surprisingly, it has been previously observed in northern Cameroon (40%) at high frequencies (Cruciani et al. 2002), and at lower frequencies in southern Cameroon (1.12%) (Cruciani et al. 2002), Oman (1%), Egypt
(2%), Hutu from Rwanda (1%) (Luis et al. 2004). The presence of this lineage in Africa has been claimed to be a genetic signature of a possible backflow migration from west Asia into Africa (Cruciani et al. 2002). Here we observe R1b1* in 12 Bantu
agriculturalist populations (ranging from 2% to 20%) and in two Pygmy individuals. A
network of R1b1* haplotypes performed using STR-data (Figure 2) shows two main
clusters, without any population structure. Interestingly, the estimated expansion time for these haplotypes – 7,000 years (SD 8,100) - precedes the time at which the Bantu expansion occurred.

...

It is noteworthy that the Fang population is the Bantu agriculturalist group presenting the highest frequency of R1b1*. The presence of the Fang in west Central Africa appears to be recent and they 20 are thought to have entered the region from the north-eastern open grassland plateau during the 17th and 18th centuries (Perrois 2006).

It would certainly be worthwhile for R1b1 experts to take a look at the haplotypes found in the region (Supplementary Table 1), and to see how they are related to R1b1 elsewhere.

Molecular Biology and Evolution, doi:10.1093/molbev/msp069

Genetic and demographic implications of the Bantu expansion: insights from human paternal lineages

Gemma Berniell-Lee et al.

Abstract

The expansion of Bantu languages, which started around 5,000 years before present (YBP) in west/central Africa and spread all throughout sub-Saharan Africa, may represent one of the major and most rapid demographic movements in the history of the human species. Although the genetic footprints of this expansion have been unmasked through the analyses of the maternally-inherited mitochondrial (mtDNA) lineages, information on the genetic impact of this massive movement and on the genetic composition of pre-Bantu populations is still scarce. Here we analyze an extensive collection of Y-chromosome markers - 41 SNPs and 18 STRs - in 883 individuals from 22 Bantu-speaking agriculturalist populations and 3 Pygmy hunter-gatherer populations from Gabon and Cameroon. Our data reveal a recent origin for most paternal lineages in west Central African populations most likely resulting from the expansion of Bantu-speaking farmers that erased the more ancient Y-chromosome diversity found in this area. However, some traces of ancient paternal lineages are observed in these populations, mainly among hunter-gatherers. These results are at odds with those obtained from mtDNA analyses, where high frequencies of ancient maternal lineages are observed, and substantial maternal gene flow from hunter-gatherers to Bantu farmers has been suggested. These differences are most likely explained by socio-cultural factors such as patrilocality. We also find the intriguing presence of paternal lineages belonging to Eurasian haplogroup R1b1*, which might represent footprints of demographic expansions in central Africa not directly related to the Bantu expansion.

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