The Evolution of Human Genetic and Phenotypic Variation in Africa

Campbell, Michael C.; Tishkoff, Sarah A.

doi:10.1016/j.cub.2009.11.050

Cited by 177 publications

(120 citation statements)

References 77 publications

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“…Despite both archaeological (27,28) and genetic evidence (28)(29)(30)(31)(32) for ancient population structure in Africa, none of the genetic models used so far to study the geographic patterns of similarity has incorporated structure in Africa. Currat and Excoffier (5) used a spatial framework to investigate admixture with Neanderthals, but concentrated on the role of gene surfing during the expansion wave in affecting the distribution of polymorphisms unique to Neanderthals across Eurasia, provided admixture did happen.…”

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confidence: 99%

Effect of ancient population structure on the degree of polymorphism shared between modern human populations and ancient hominins

Eriksson

Manica

2012

Proc. Natl. Acad. Sci. U.S.A.

208

144

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Recent comparisons between anatomically modern humans and ancient genomes of other hominins have raised the tantalizing, and hotly debated, possibility of hybridization. Although several tests of hybridization have been devised, they all rely on the degree to which different modern populations share genetic polymorphisms with the ancient genomes of other hominins. However, spatial population structure is expected to generate genetic patterns similar to those that might be attributed to hybridization. To investigate this problem, we take Neanderthals as a case study, and build a spatially explicit model of the shared history of anatomically modern humans and this hominin. We show that the excess polymorphism shared between Eurasians and Neanderthals is compatible with scenarios in which no hybridization occurred, and is strongly linked to the strength of population structure in ancient populations. Thus, we recommend caution in inferring admixture from geographic patterns of shared polymorphisms, and argue that future attempts to investigate ancient hybridization between humans and other hominins should explicitly account for population structure.ABBA-BABA | D statistic | Neanderthal introgression | stepping stone model |

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Effect of ancient population structure on the degree of polymorphism shared between modern human populations and ancient hominins

Eriksson

Manica

2012

Proc. Natl. Acad. Sci. U.S.A.

208

144

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“…Previous studies (Voight et al 2006;Sabeti et al 2007;Jarvis et al 2012;Lachance et al 2012) have reported strong signals of positive selection in African populations. Local adaptation is expected to be common within Africa, as African populations practice a range of subsistence strategies and inhabit diverse environments to which adaptation may have occurred (deMenocal 2004;Campbell and Tishkoff 2010;deMenocal 2011). Selection may also have acted more efficiently in African populations, many of which have maintained large effective population sizes for the past 50,000 years, in contrast to populations outside of Africa (Tenesa et al 2007;Lambert and Tishkoff 2009;Campbell and Tishkoff 2010;Henn et al 2011).…”

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confidence: 99%

“…Local adaptation is expected to be common within Africa, as African populations practice a range of subsistence strategies and inhabit diverse environments to which adaptation may have occurred (deMenocal 2004;Campbell and Tishkoff 2010;deMenocal 2011). Selection may also have acted more efficiently in African populations, many of which have maintained large effective population sizes for the past 50,000 years, in contrast to populations outside of Africa (Tenesa et al 2007;Lambert and Tishkoff 2009;Campbell and Tishkoff 2010;Henn et al 2011). While African populations would appear ideal for understanding the extent of positive selection in humans, they have usually been underrepresented in such studies.…”

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Limited Evidence for Classic Selective Sweeps in African Populations

et al. 2012

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While hundreds of loci have been identified as reflecting strong-positive selection in human populations, connections between candidate loci and specific selective pressures often remain obscure. This study investigates broader patterns of selection in African populations, which are underrepresented despite their potential to offer key insights into human adaptation. We scan for hard selective sweeps using several haplotype and allele-frequency statistics with a data set of nearly 500,000 genome-wide singlenucleotide polymorphisms in 12 highly diverged African populations that span a range of environments and subsistence strategies. We find that positive selection does not appear to be a strong determinant of allele-frequency differentiation among these African populations. Haplotype statistics do identify putatively selected regions that are shared across African populations. However, as assessed by extensive simulations, patterns of haplotype sharing between African populations follow neutral expectations and suggest that tails of the empirical distributions contain false-positive signals. After highlighting several genomic regions where positive selection can be inferred with higher confidence, we use a novel method to identify biological functions enriched among populations' empirical tail genomic windows, such as immune response in agricultural groups. In general, however, it seems that current methods for selection scans are poorly suited to populations that, like the African populations in this study, are affected by ascertainment bias and have low levels of linkage disequilibrium, possibly old selective sweeps, and potentially reduced phasing accuracy. Additionally, population history can confound the interpretation of selection statistics, suggesting that greater care is needed in attributing broad genetic patterns to human adaptation. E LUCIDATING the selective pressures that human populations have encountered, as well as the means by which they have adapted to them, is a central aim of evolutionary biology and anthropology. Recently, statistical methods in population genetics have been applied to genome-wide polymorphism data to identify genetic loci that may have experienced natural selection. Such inferences have primarily been made under the model of a hard selective sweep, where a new allele rapidly rises to fixation within a population due to positive selection (Sabeti et al. 2002(Sabeti et al. , 2005(Sabeti et al. , 2006Voight et al. 2006;Sabeti et al. 2007;Williamson et al. 2007;Akey 2009;Pickrell et al. 2009;. While these genome-wide scans have detected hundreds of loci as focal sites of selective sweeps, most connections between the loci and their selective pressures remain unknown. Lack of phenotypic or functional information, the relative effect of background selection, demography, and statistical noise have been suggested as some of the causes of the lack of agreement between studies (Teshima et al. 2006;Akey 2009;Hermisson 2009;Hernandez et al. 2011).In light of these issues, it ...

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“…African pygmies share roots at the base of human history with Khoisan and Hadza (Henn et al 2011;Verdu and Destro-Bisol 2012) but exhibit distinct polymorphisms associated with immune function, metabolism, growth, and skeletal turnover, critical for lacta-tion (Campbell and Tishkoff 2010;Mendizabal et al 2012;Schuh-Huerta and Pera 2011). Less apparent is the phylogenetic, ecological, and cultural diversity of pygmies (Bahuchet 2012;Hewlett 1996), as eastern (e.g., Efé, Mbuti) and western (e.g., Aka, Bofi) populations diverged with fragmentation of Congo forests around 27,000 BP, with little subsequent admixture between them (Batini et al 2011).…”

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confidence: 99%

Allomaternal Nursing in Humans

Hewlett

Winn²

2014

Current Anthropology

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Few studies exist of allomaternal nursing in humans. It is relatively common among some cultures, such as the Aka and Efé hunter-gatherers of the Congo Basin, but it does not occur in other foragers such as the !Kung and Hadza of Southern and East Africa. This paper utilizes focal follow observations of Aka and Efé infants, interviews with Aka mothers, ethnographic reports from researchers working with hunter-gatherers, and a survey of the eHRAF cultures to try to answer the following questions: how often does allomaternal nursing occur, who provides it, and under what contexts does it take place? The study indicates that it occurs in many cultures (93% of cultures with data) but that it is normative in relatively few cultures; biological kin, especially grandmothers, frequently provide allomaternal nursing and that infant age, mother's condition, and culture (e.g., cultural models about if and when women other than the mother can nurse an infant or colostrum taboos) impact the nature and frequency of allomaternal nursing. The empirical results of this exploratory study are discussed in the context of existing hypotheses used to explain allomaternal nursing.Anthropologists have conducted several studies of breastfeeding from a variety of perspectives (Fouts, Hewlett, and Lamb 2012;Gottlieb 2004;Sellen 2007) and have occasionally described allomaternal nursing, that is, women other than mother nursing infants, but quantitative studies on the topic do not exist. Nutritional and health benefits of breast-feeding for mothers and infants are well documented (see American Academy of Pediatrics [2005] and Field [2005] for reviews), but what about infants who are breast-fed by women other than mother? Lactation is energetically costly, and allomaternal nursing may increase pathogen transmission between mothers and other infants. La Leche League, a global organization that promotes and assists women with breast-feeding, discourages both wet nursing (nursing another woman's infant, often for pay) and cross-nursing (the occasional nursing of another woman's infant while the mother continues to nurse her own child, often in a child-care situation), because the other women may transmit infectious diseases to the infant or cause the infant to be psychologically confused (Lawrence and Lawrence 2011;Minami 1995). Exceptions exist if the mother has health or other issues that lead to breast-feeding difficulties. 1 Allomaternal nursing occurs in many cultures. Our review of cultures in the electronic Human Relations Area Files (eHRAF), a digital database of 258 cultures from around the world, found that it existed in 97 of 104 cultures with ethnographic data about Barry S. Hewlett is a Professor in the Department of Anthropology of Washington State University, Vancouver (Vancouver, Washington 98686, U.S.A. [hewlett@vancouver.wsu.edu]). Steve Winn is Senior Vice President at the Behavioral Health Network (417 Liberty Street, Springfield, Massachusetts 01104, U.S.A.). This paper was submitted 8 VI 11, accepted 18 I 13, and ele...

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The Evolution of Human Genetic and Phenotypic Variation in Africa

Cited by 177 publications

References 77 publications

Effect of ancient population structure on the degree of polymorphism shared between modern human populations and ancient hominins

Effect of ancient population structure on the degree of polymorphism shared between modern human populations and ancient hominins

Limited Evidence for Classic Selective Sweeps in African Populations

Allomaternal Nursing in Humans

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