Human Genetic Data Reveal Contrasting Demographic Patterns between Sedentary and Nomadic Populations That Predate the Emergence of Farming

Aimé, Carla; Laval, Guillaume; Patin, Étienne; Verdu, Paul; Ségurel, Laure; Chaix, Raphaëlle; Hegay, Tatyana; Quintana-Murci, Lluı́s; Heyer, Évelyne; Austerlitz, Frédéric

doi:10.1093/molbev/mst156

Cited by 41 publications

(40 citation statements)

References 70 publications

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“…This suggests that strong Paleolithic expansions may have ultimately favored the emergence of agriculture in some populations. 17 However, as ancient expansions could have masked potential signals of more recent expansions, these findings do not preclude the possibility of a second expansion event resulting from the Neolithic transition. Indeed, strong ancient demographic events are more easily detected with coalescent-based methods, and, in some cases, they can mask the signals of more recent events, especially if the population has not yet reached genetic equilibrium.…”

Section: Introductionmentioning

confidence: 87%

“…16 Similarly, our previous work on HVS-1 data demonstrated strong signals of expansion in both African and Eurasian sedentary farmer populations, weaker expansion signals in Eurasian herders and no signal in African hunter-gatherers. 17 All these studies reported expansions that started during the Paleolithic. Here, using autosomal microsatellite data, although confidence intervals were quite large, we inferred modal estimates for the expansion onsets during or after the Neolithic transition for all farmer populations in Africa and Eurasia, as well as for herder populations in Central Asia.…”

Section: Contrasted Demographic Histories Associated With Different Lmentioning

confidence: 99%

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Microsatellite data show recent demographic expansions in sedentary but not in nomadic human populations in Africa and Eurasia

et al. 2014

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The transition from hunting and gathering to plant and animal domestication was one of the most important cultural and technological revolutions in human history. According to archeologists and paleoanthropologists, this transition triggered major demographic expansions. However, few genetic studies have found traces of Neolithic expansions in the current repartition of genetic polymorphism, pointing rather toward Paleolithic expansions. Here, we used microsatellite autosomal data to investigate the past demographic history of 87 African and Eurasian human populations with contrasted lifestyles (nomadic huntergatherers, semi-nomadic herders and sedentary farmers). Likely due to the combination of a higher mutation rate and the possibility to analyze several loci as independent replicates of the coalescent process, the analysis of microsatellite data allowed us to infer more recent expansions than previous genetic studies, potentially resulting from the Neolithic transition. Despite the variability in their location and environment, we found consistent expansions for all sedentary farmers, while we inferred constant population sizes for all hunter-gatherers and most herders that could result from constraints linked to a nomadic or semi-nomadic lifestyle and/or competition for land between herders and farmers. As an exception, we inferred expansions for Central Asian herders. This might be linked with the arid environment of this area that may have been more favorable to nomadic herders than to sedentary farmers. Alternatively, current Central Asian herders may descent from populations who have first experienced a transition from hunter-gathering to sedentary agropastoralism, and then a second transition to nomadic herding.

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Section: Introductionmentioning

confidence: 87%

Section: Contrasted Demographic Histories Associated With Different Lmentioning

confidence: 99%

Microsatellite data show recent demographic expansions in sedentary but not in nomadic human populations in Africa and Eurasia

et al. 2014

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“…We show that the effective population size of RHG is B30% lower than that of AGR, at least in Western Central Africa, as a result of a bottleneck and an expansion occurring earlier than 7,000 YBP in the ancestors of RHG and AGR, respectively. Previous studies have indeed estimated that the ancestors of African farmers started to expand B10,000-30,000 YBP using other aspects of the data such as the allele frequency spectrum [58][59][60] . Our analyses of LD levels thus reinforce these findings, and support the notion that the expansions of Bantu-speaking peoples 3,000-5,000 YBP are not sufficient to explain the signal of population growth observed in present-day AGR.…”

Section: Discussionmentioning

confidence: 99%

The impact of agricultural emergence on the genetic history of African rainforest hunter-gatherers and agriculturalists

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The emergence of agriculture in West-Central Africa approximately 5,000 years ago, profoundly modified the cultural landscape and mode of subsistence of most sub-Saharan populations. How this major innovation has had an impact on the genetic history of rainforest hunter-gatherers-historically referred to as 'pygmies'-and agriculturalists, however, remains poorly understood. Here we report genome-wide SNP data from these populations located west-to-east of the equatorial rainforest. We find that hunter-gathering populations present up to 50% of farmer genomic ancestry, and that substantial admixture began only within the last 1,000 years. Furthermore, we show that the historical population sizes characterizing these communities already differed before the introduction of agriculture. Our results suggest that the first socio-economic interactions between rainforest hunter-gatherers and farmers introduced by the spread of farming were not accompanied by immediate, extensive genetic exchanges and occurred on a backdrop of two groups already differentiated by their specialization in two ecotopes with differing carrying capacities.

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“…Using Simcoal version 2.1.2, 26 we simulated here both DNA sequences (mitochondrial or autosomal) and microsatellite (autosomal or from the Y chromosome) data sets under several scenarios involving either one or two successive expansion events, starting at different points in time, consistent with either a Paleolithic or a Neolithic expansion. These data sets were similar to those used in Aimé et al 4,20,25 in terms of numbers of loci.…”

Section: Introductionmentioning

confidence: 87%

“…For the autosomal sequences, we simulated 20 unlinked diploid sequences of 1300 base pairs (bp) to be consistent with existing short neutral sequence marker sets, such as the one developed by Patin et al 28 used in Aimé et al 20 We assumed a mutation rate of 2.5 × 10 − 8 per generation and per site. 29 For the mitochondrial sequences, we simulated a haploid sequence of 400 bp, corresponding to the HVS-I region, assuming a mutation rate of 10 − 5 per generation per site.…”

Section: Data Simulationmentioning

confidence: 99%

Different kinds of genetic markers permit inference of Paleolithic and Neolithic expansions in humans

Aimé¹,

Austerlitz²

2016

Eur J Hum Genet

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Recent population genetic studies have provided valuable insights on the demographic history of our species. However, some issues such as the dating of the first demographic expansions in human populations remain puzzling. Indeed, although a few genetic studies argued that the first human expansions were concomitant with the Neolithic transition, many others found signals of expansion events starting during the Palaeolithic. Here we performed a simulation study to show that these contradictory findings may result from the differences in the genetic markers used, especially if two successive expansion events occurred. For a large majority of replicates for each scenario tested, microsatellite data allow only detecting the recent expansion event in that case, whereas sequence data allow only detecting the ancient expansion. Combined with previous real data analyses, our results bring support to the ideas that (i) a first human expansions started during the Palaeolithic period, (ii) a second expansion event occurred later, concomitantly with the Neolithic transition. INTRODUCTIONDemographic changes are known to leave footprints on allelic frequencies. Together with the increased availability of large genetic data sets, numerical methods stemming from Kingman's coalescent theory 1 allow inferring the past demography of populations from their present-day patterns of genetic diversity. 2,3 Several types of genetic markers can be used, each category of markers having its own specificities. For instance, as they are uni-parentally transmitted, mitochondrial sequences are informative only about maternal lineages, whereas the Y-chromosome provides information about paternal lineages. In Aimé et al., 4 it has been shown that these two types of markers sometimes provide different inferences on the demographic history of human populations, especially as females generally exhibit higher effective population sizes and higher migration rates than males. 5,6 Conversely, autosomal markers provide synthetic information about both maternal and paternal lineages. When these loci are carefully selected in order to avoid pairwise linkage disequilibria, they also offer the possibility to consider each of them as an independent replicate. Among these autosomal markers, sequences or microsatellites data also exhibit contrasted properties. In particular, microsatellites have higher mutation rates than sequences. 7,8 Moreover, microsatellites are subject to strong homoplasy, which can lead to false signals when using models where this phenomenon is not efficiently controlled for. One simulation-based study 9 showed that when microsatellites are included into an Approximate Bayesian Computation analysis, 10 they provide substantially better estimation for recent admixture events than sequence data. However, they did not investigate the question of inferring other kind of demographic events such as expansions. Moreover, an empirical study on a non-human species (the black sea porpoise) showed that integrating microsatellites in an ABC analy...

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Human Genetic Data Reveal Contrasting Demographic Patterns between Sedentary and Nomadic Populations That Predate the Emergence of Farming

Cited by 41 publications

References 70 publications

Microsatellite data show recent demographic expansions in sedentary but not in nomadic human populations in Africa and Eurasia

Microsatellite data show recent demographic expansions in sedentary but not in nomadic human populations in Africa and Eurasia

The impact of agricultural emergence on the genetic history of African rainforest hunter-gatherers and agriculturalists

Different kinds of genetic markers permit inference of Paleolithic and Neolithic expansions in humans

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