African genetic diversity- Kittles and Keita

Rick Kitties1 and S. O. Y. Keita2
Interpreting African Genetic Diversity
African Archaeological Review, Vol. 16, No. 2, 1999
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Explanations of human biological variation in extant African populations have
historically been shaped by a racial paradigm. In this paradigm deep genetic differences
are assumed to exist between so-called "racial" groups or types, which are
viewed as being composed of nearly uniform individuals and are taken as "natural"
fundamental taxonomic units of Homo sapiens. These types were originally based
on specific aspects of external morphology. Carleton Coon (1962), a physical
anthropologist who contributed to this paradigm, proposed a theory of human
evolution which postulated the independent emergence of five primordial races or
subspecies from distinct, separate, Homo erectus ancestors. Two of these purported
primordial races originated in Africa. They were called Congoid ("Pygmies") and
Capoid (Khoisan or "Bushmen"). In Coon's conception other continental Africans,
which exhibit a broad range of biological diversity, were considered to be primarily
or only the result of various levels of admixture between these two groups with
each other or with immigrants deemed to be of European or Asian origin and generally
called "Caucasian." Although the causal aspects of Coon's theory have been
rejected, racial thinking still persists today using Coon's categories and is quite
evident in the methods and interpretation of genetic studies of African populations
(Keita and Kittles, 1997). 

Here we briefly discuss the implications of modern genetic studies of African and 
world populations for understanding African biohistory.
We propose an evolutionary biogeographical model as an alternative to
"racial" explanatory models of African biological diversity. A rational definition
of African in a biological sense should be derived from biogeography and not be
based on uninformed (and biased) traditions of practice.

Racial models, as traditionally presented, are static, and obligate one to postulate
gene flow as the primary explanation for variation. The racial paradigm
is manifested in the early writings on Africa by Seligman (1930) and Coon
(1962,1965) and is still operationalized in varying degrees by anthropologists and
geneticists, who otherwise reject Coon's thinking, to explain the vast biological
diversity observed in the continent. While it is a formidable task to evaluate the
extent of genetic diversity in Africa, it is quite evident that in many of these studies
there is the lack of an evolutionary perspective. This is especially the case when
northern Africa and the Horn are considered. The variation in these regions has
generally been explained as being due primarily to admixture between "Africans"
and "non-Africans." In fact, supra-Saharan African populations have frequently
been conceptualized as being derived from "European" ancestors and, hence, non-
African (see Seligman, 1930). The genetic profiles of supra-Saharan populations
are indeed in a relative sense "intermediate" to those of various sub-Saharan groups
(stereotypically defined) and "Eurasians" (see Guglielmino et al., 1987; Chibani
et al., 1985; Tartaglia et al., 1996; Merghoub et al., 1997). But is this genetic
"intermediateness" due primarily to supra-Saharan populations being foundationally
an admixed group (the result of gene flow between two distinct "races")? Or
is their biology reflective of factors acting on indigenous modern Homo sapien
populations in Africa?


Invoking admixture to explain human variation is related to another polemic
generally seen in many genetic studies of African populations. This is the persistence
of the socially constructed normative view of the African as only the "Forest
Negro" type, or the so-called "Pygmy" from Central Africa, in line with Coon's
(1962, 1965) thinking. These populations are used as the representative African
in many studies (see Bowcock et al., 1991, 1994; Cavalli-Sforza et al., 1994).
Northern African populations are rarely used in research under the designation
"African." Also, studies which utilize pooled samples of individuals from distinct
African populations as a representative "race" are problematic. If modern humans
evolved in Africa 150,000 to 200,000 years ago, and dispersed outside of Africa
only about 100,000 years ago, why should it be assumed that those populations
which remained in Africa became stagnant and homogeneous? While African populations
share a common ancestry, they also have evolved separately for a long time.
Evidence for isolation by distance operating in Africa is seen by genetic distinctions
among eastern, western, northern, central, and southern Africa (Excoffier
et al., 1987). 

These genetic differences broadly correlate with geographic distances.
Various populations in Africa have interacted via migrations during past
history. One striking and most apparent signature of migration is the dramatic
eastern-to-western Africa cline of mitochondrial DNA (mtDNA) haplogroup L3a
frequencies (Watson et al., 1997). Haplogroup L3a is closely related to a mtDNA
haplotype common in European populations [the Cambridge Reference Sequence
(Anderson et al., 1981)]. A subgroup of related mtDNA haplotypes appears to be
East African specific and may represent a common ancestral sequence for most of
Europe and Eurasia. In other words, the mtDNA diversity observed in non-African
populations is a subset of African mtDNA variation. We note that while this group
of mtDNA haplotypes is common in Eastern Africa, it represents only a subset of
the total mtDNA diversity observed throughout the African continent. A similar
pattern is observed for nuclear (Tishkoff et al., 1996, 1998) and Y chromosome
(Passarino et al., 1998) variation in Eastern Africa. There are several implications
for these observations. First, it provides evidence for an African (specifically,
Eastern African) origin for Eurasians. Second it suggests that before major migrations
occurred out of the continent, populations were diverging. These observations
deconstruct racial thinking, especially the concept of "racial divergence."

The term racial divergence fails to describe the process responsible for producing
the variation that exists as a continuum in the human species. So-called
racial divergence dates reflect the times of differentiation of genes within populations
used in a given analysis and should be interpreted as such. "Racial divergence"
time estimates have been used to infer the age of the common ancestor between
sampled groups, but this is definitely not the time of origin for the so-called "racial
groups," which traditionally have been defined by morphology, nor is it the time
of "origin" for the sampled populations. Time, geography, and other data help elucidate 
the larger meaning of genetic studies. A date of 156,000 years ago has been
suggested by Goldstein etal. (1995) for the separation of African (stereotypically
defined) and non-African populations. Given that there is no fossil evidence for
modern humans anywhere at 150,000 years ago except in Africa, this does not
represent an African/non-African "split." This date is actually an estimate of the
initial genetic divergence that occurred within the continent of Africa among our
modern human ancestors. After the expansion of modern humans out of Africa,
subsets of the resultant genetic variation were distributed throughout the other
continents. Most genetic variants observed outside of Africa are also found within
Africa at various frequencies (and are of indigenous origin); this clearly indicates
that "Africans" are not monomorphic. Northern African genetics, when this information
is considered carefully with palaeontological data, would not seem to be
explicable as simply "hybrids" or lost Eurasians. A different perspective, having
more explanatory power and consistent with the available data, is that northern and
Horn of Africa populations constitute gradients of differentiation largely reflective
of African biohistorical processes.


The data of Tishkoff et al. (1996, 1998) are best interpreted as suggesting
that a model of in situ evolutionary differentiation explains the bulk of variation in
Africa (which includes supra-Saharan, Saharan, and sub-Saharan regions). Markers
from mitochondrial DNA and the Y chromosome, which define maternal and
paternal lineages, respectively, also reveal significant differentiation of ancestral
African populations (Watson et al., 1996,1997; Passarino et al., 1998; Malaspina
et al., 1998). Another likely example of internal differentiation within Africa is to
be found in the "unusual" genetic makeup of the Khoisan, a southern African population
with a high frequency of purported "Asian" alleles (Cavalli-Sforza et al.,
1994). Some suggest admixture with Asians to explain the Khoisan genetic profile.
However, the Khoisan speakers may be descendants of a generalized ancestral human
population from which modern Asian and African populations were ultimately
derived. The Khoisan have been shown to be less diverse than other African populations
for a variety of genetic loci (Excoffier et al., 1987). This may be due to two
reasons: historical isolation and a smaller effective population size. The Khoisan
have historically remained relatively isolated from other African populations due
to cultural and linguistic differences. Also, the smaller effective population size is
likely the result of the hunter-gatherer culture of the Khoisan. These cultural and
subsistence patterns could promote significant differentiation of the population.

The overall pattern of genetic variation that exists within and outside of Africa
suggests an African origin of modern humans and a recent common origin of non-
African populations. The pattern of human genetic diversity supportive of this
position is observed in studies which examine genetic signatures left behind from
population expansions and population bottlenecks (Rogers and Harpending, 1992;
Harpending et al., 1993, 1998; Shriver et al., 1997; Reich and Goldstein, 1998;
Kimmel etal., 1998; Jorde et al., 1997). These studies consistently reveal an initial
population expansion within Africa prior to out-migration into other continents.
What is actually a population expansion has been mistakenly termed "racial divergence,"
which implies morphological differentiation into the recognizable entities
now labeled "races." In reality, it represents the early genetic divergence of ancestral
Homo sapiens. From the genetic data we find evidence of in situ differentiation
(or genetic divergence) of mid-Pleistocene populations in Africa and subsequent
migrations out of Africa into Europe and Asia, with continued drift due to isolation
by distance and founder effects, which abruptly end when expansion in population
size and frequent migrations occurred. Also, numerous environmental zones
exerted their own selective pressures on the populations. The populations remaining
in Africa are the primary ancestors of present Africans. This model is more
consistent with archaeological and molecular evidence and can be tested using various
data sets. This biogeographical perspective better explains the main source of
variation within Africa and obviates the need for racial thinking and its associated
baggage.



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Modern DNA analysis debunks simplistic "race" models

quote:

"It also does not mean that no differences whatsoever exist between continental groups. In fact, what Rosenberg et al. (2002) have shown is that given enough markers and the extraordinary power of Structure, the tiny amounts of genetic differences that exist between continents can also be discerned. However, this should not obscure the fact that on a worldwide scale, clines are a better representation of the human diversity than clades, and that continents do not represent more substantial discontinuities in such clines than many other geographical and cultural barriers. That clines are a more adequate representation of human genetic diversity than clades is not unexpected in view of earlier works that show that most genetic variation is found among individuals rather than among continents (e.g., Boyd 1950; Livingstone 1962; Lewontin 1972; Cavalli-Sforza et al. 1994). 

In fact, also in the current data set, 87.6% percent of the total diversity is found among individuals and only 9.2% among continents (Excoffier and Hamilton 2003), in agreement with many previous studies (e.g. Lewontin 1972; Owens and King 1999; but see also Edwards 2003). The current results are also not unexpected in view of the fact that identical DNA sequences of several kilobases are found on different continents (Kaessmann et al. 1999; Gabriel et al. 2002). In fact, as much as a third of the entire human diversity of common haplotypes may be contained within single individuals (Pääbo 2003). However, in spite of this, there is a great tendency in the literature to use a few populations from the extremes of continental landmasses (such as in Fig. 1A) to make worldwide inferences about substructures in the human gene pool. In fact, because human genetic diversity tends to be distributed clinally, it is especially problematic to sample the extremes of continents because this will create the impression of sharp discontinuities in the distribution of genetic variants... 

Clustering in the human gene pool is of practical importance. It has recently been claimed that “the greatest genetic structure that exists in the human population occurs at the racial level” (Risch et al. 2002). Our results show that this is not the case, and we see no reason to assume that “races” represent any units of relevance for understanding human genetic history. In clinical practice, the “classification” of people into “races,” as recently suggested (Risch et al. 2002; Burchard et al. 2003), could perhaps have some justification as a proxy for differences in environmental and other factors of relevance for public health or to help identify rare disease alleles (Phimister 2003). However, in the absence of other knowledge, most alleles influencing susceptibility to disease or outcome of medical interventions cannot be expected to show significantly different frequencies between “races.” 

An exception may be genes where different selection regimes have acted in different geographical regions. .. even in those cases, the genetic discontinuities seen are generally not “racial” or continental in nature but depend on historical and cultural factors that are more local in nature. For example, the hemoglobin S allele that causes resistance to malaria occurs not only in sub-Saharan Africa but also in southern Europe, the Middle East, and India (Cavalli-Sforza et al. 1994). Lactose tolerance occurs both in Europe and in Africa (Sahi 1994), and the deleted allele of CCR5 that confers resistance to human immunodeficiency virus occurs in Europe as well as in Asia (Martinson et al. 1997). Thus, even for a rapid and rough evaluation of genetic risk factors, “racial” background is of limited use, and direct analysis of the relevant gene is the only reliable way to evaluate genetic risk in an individual (Cooper et al. 2003). "

Source: 
-- Evidence for Gradients of Human Genetic Diversity Within and Among Continents -- David Serre and Svante Pääbo Genome Research. (2004) 14: 1679-1685

mtDNA DATA in North Africa and Egypt