African human diversity, origins and migrations

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The continent of Africa is thought to be the site of origin of all modern humans and is the more recent origin of millions of African Americans. Although Africa has the highest levels of human genetic diversity both within and between populations, it is under-represented in studies of human genetics. Recent advances have been made in understanding the origins of modern humans within Africa, the rate of adaptations due to positive selection, the routes taken in the first migrations of modern humans out of Africa, and the degree of admixture with archaic populations. Africa is also in dire need of effective medical interventions, and studies of genetic variation in Africans will shed light on the genetic basis of diseases and resistance to infectious diseases. Thus, we have tremendous potential to learn about human variation and evolutionary history and to positively impact human health care from studies of genetic diversity in Africa.

Introduction

Africa contains a considerable amount of diversity, not only in regard to genetic diversity but also in regard to cultural, linguistic and phenotypic diversity [1]. The continent of Africa has been estimated to contain over 2000 distinct ethno-linguistic groups — speaking languages that constitute nearly a third of the worlds living languages (http://www.ethnologue.com/). Primary subsistence patterns within Africa include various modes of agriculture, pastoralism and some of the last remnants of the world's hunter-gatherers. Africans live in climates that range from those of the world's largest desert and second largest tropical rainforest to those of savanna, swamps and mountain highlands, and these climates have, in some cases, undergone dramatic shifts in the past 10 000 years [2]. In addition to high levels of genetic variation within populations, Africa also has high levels of genetic divergence between populations (reviewed in [1, 3]). Patterns of genetic variation in Africa have been influenced by several short-range, in addition to long-range, migration events (e.g. the migration of agricultural Bantu-speakers from West Africa throughout Sub-Saharan Africa within the past 4000 years; summarized in [1, 3]). Africa is the more recent site of origin of millions of African Americans, many of whom are now turning to genetic studies to infer their ancestry. The continent of Africa also has an extremely high mortality rate from infectious disease, with malaria and HIV alone responsible for millions of deaths per year (http://www.cdc.gov/malaria/index.htm) [4]. Studies of genetic variation in Africans and African descendants in the Americas might shed light on the genetic basis of resistance to these infectious diseases, as well as revealing more about the role of pharmacogenetic variation on effectiveness of drugs used to treat them. Thus, the richness of Africa for human genetic, anthropological and medical studies is unparalleled.

Here, we review some recent advances in understanding the demographic and selective history of our species in Africa, with particular attention paid to the possible role of inversion polymorphisms and how this might confound recent inferences. We also discuss the recent interest and limitations in using genetic studies to infer personal ancestries and examine the potential impact that studies in Africa can have on medical intervention and understanding the genetic basis of infectious and complex diseases.

Section snippets

Modern human origins in Africa

Human paleontology has established that humans have spread at least twice from Africa to Eurasia; early events involved archaic populations such as Homo erectus and Homo heidelbergensis, whereas a later event, occurring within the past 100 000 years, involved the migration of anatomically modern humans out of Africa and across the rest of the globe [5]. The transition to modern humans was unlikely to be sudden; rather, the paleobiological record indicates an irregular mosaic of modern, archaic

Evidence for admixture of archaic and modern Homo populations?

Overall, the weight of evidence from both genetic and paleobiological studies supports a recent common origin of all modern humans from a population originating from the continent of Africa — probably from East Africa — within the past 100 kya (summarized in [4]). Although analyses of ancient mtDNA obtained from 24 Neanderthal and 40 early modern human remains do not support high levels of admixture between archaic and modern humans [17], the possibility of limited gene flow is difficult to rule

A single African origin for non-African populations?

Estimates vary for the time of the first migration of modern humans from Africa to Eurasia. Paleontological data show modern humans in the Levant 90–130 kya, but it is not clear that this was a continuous occupation to the present. In general, age ranges inferred from mitochondrial DNA (mtDNA) suggest migrations out of Africa ∼45–75 kya [10•, 29], broadly consistent with dates inferred from paleontological [5], X chromosome [30], Y chromosome [31] and autosomal [32] data. However, inferences

Genetic adaptations

There have been some conflicting results regarding the relative amounts of recent positive selection in African versus non-African populations. It is easy to imagine an increase in positive selection as a species migrates into and adapts to new environments. Indeed, in addition to founder effects, novel selective demands have been suggested as a contributor to reductions of human genetic diversity outside of Africa [38]. Several studies in the past few years have reported more evidence for

The African diaspora

In the United States alone, more than 36 million African Americans have recent origins in Africa (http://www.census.gov/population/www/socdemo/race/ppl-186.html), the majority of their ancestors having been forcibly brought to the Americas as slaves. Exact estimates vary, but according to analyses of historical records, the majority of the people brought to the Americas from Africa, approximately eight million, originated in western Africa, with a lesser amount, approximately four million, from

Biomedical implications

The continent of Africa is in dire need of safe and effective medical interventions. Deaths due to infectious disease are disproportionately higher in Africa then in any other region of the world. In addition to the one million deaths per year from malaria (http://www.cdc.gov/malaria/index.htm), the poor state of medical care in Africa has contributed to high rates of HIV infection, which in turn are promoting the spread of other serious diseases such as tuberculosis [58]. Furthermore, very

Prospects

More comprehensive population sampling, maximizing both ethnic and geographic diversity, is needed to fully appreciate and study the genetic diversity contained in Africa. Eventually, publicly available cell lines should be established, under the appropriate ethical protocols, so that these samples can become a broad resource for the scientific community to complement the CEPH–HGDP.

A shift toward multilocus datasets, away from single-locus studies, holds great potential to refine our

References and recommended reading

Papers of particular interest, published within the annual period of review, have been highlighted as:

  • • of special interest

  • •• of outstanding interest

Acknowledgements

Supported by a National Science Foundation grant BSC0552486 and National Institutes of Health (NIH) grant R01GM076637 to SAT, and NIH grant F32HG003801 to FAR.

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