September 25, 2013

Pre-farming population expansions (Aimé et al. 2013)

Mol Biol Evol (2013) doi: 10.1093/molbev/mst156

Human genetic data reveal contrasting demographic patterns between sedentary and nomadic populations that predate the emergence of farming.

C. Aimé et al.

Demographic changes are known to leave footprints on genetic polymorphism. Together with the increased availability of large polymorphism datasets, coalescent-based methods allow inferring the past demography of populations from their present-day patterns of genetic diversity. Here, we analyzed both nuclear (20 non-coding regions) and mitochondrial (HVS-I) re-sequencing data to infer the demographic history of 66 African and Eurasian human populations presenting contrasting life-styles (nomadic hunter-gatherers, nomadic herders and sedentary farmers). This allowed us to investigate the relationship between life-style and demography, and to address the long-standing debate about the chronology of demographic expansions and the Neolithic transition. In Africa, we inferred expansion events for farmers, but constant population sizes or contraction events for hunter-gatherers. In Eurasia, we inferred higher expansion rates for farmers than herders with HVS-I data, except in Central Asia and Korea. Although isolation and admixture processes could have impacted our demographic inferences, these processes alone seem unlikely to explain the contrasted demographic histories inferred in populations with different life-styles. The small expansion rates or constant population sizes inferred for herders and hunter-gatherers may thus result from constraints linked to nomadism. However, autosomal data revealed contraction events for two sedentary populations in Eurasia, which may be caused by founder effects. Finally, the inferred expansions likely predated the emergence of agriculture and herding. This suggests that human populations could have started to expand in Paleolithic times, and that strong Paleolithic expansions in some populations may have ultimately favored their shift towards agriculture during the Neolithic.



eurologist said...

Very interesting paper with fascinating dates.

The ~124,550 YBP expansion time (assuming μ= 1.2x10-8 /generation /site) of Mozambican "farmers" matches well the generally assumed expansion in NE Africa during the-then favorable climate, and ensuing ooA. At least one HVS-I has a somewhat similar time frame ~90,638 YBP. The ~15,950 YBP for Yoruba seems to match post-LGM expansion.

I am not surprised that Danes and Japanese show no expansion phase, since they are mixed paleolithic/ neolithic peoples, which probably wiped out any neolithic expansion signature, and since then live in a confined area. Interestlingly, the ~72,050 YBP Han expansion matches the post-Toba expansion I always envision (it cleared enough jungle and possibly killed natives to make expansion into China from India much easier). The ~42,700 YBP contraction event of Japanese fits the known time for the first populating of the region and may indicate the decoupling of the island and adjacent northern coastal population from the much larger central E Asian population. Again, the ~52,880 YBP contraction of the Danes might reflect the decoupling of the first Europeans (or those en route) from the much larger Pakistan/India population.

The ~27,720 - 33,092 YBP expansion dates for Central Asia matches well the know E -> W expansion in S Siberia during that time (and the likely arrival at, and perhaps even trigger for the Gravettian onset).

The relatively poor correlation with mtDNA signatures could be explained with the generally very high spatial diffusion rate of female haplogroups.

Unknown said...

"the inferred expansions likely predated the emergence of agriculture and herding. "

So either agriculture/herding happened earlier than we think, or the observed population expansions were more about climate change than the neolithic.

IMO mostly climate change, with a a little "folk knew how to do this agriculture stuff from way back, but in most places (that had the skills) the climate did not favour agriculture"

Mark Moore (Moderator) said...

"the inferred expansions likely predated the emergence of agriculture and herding. "

Scratching my head on that one. What is the mechanism? Why did some populations of hunter-gatherers undergo great expansion, and then only those became farmers/herders, while other populations that stayed the same size were still hunters? Seems to me the expanding populations had an edge, that is why they expanded.

Either, as has been suggested, many groups knew how to farm already but just did not feel the need to while game was abundant in a low-population density situation, or maybe even the dates are off. Maybe the expansion dates look older than they were due to some wrong assumptions about mutation rates or population sizes or something.

Jim said...

"What is the mechanism?"

Sometimes it is just a new food technolgy that has nothing to do with agriculture or herding. The population of California blew up about 4,000 years ago when Penutian-speakers figured out how to leach the tannins out of the super-abundant acorns in the Central Valley and turn them into food.

Mark Moore (Moderator) said...

That is a possibility I suppose, but I find it strange that for the most part only those populations who later took up farming and herding took advantage of this mysterious new food technology that was not farming or herding.

Carla said...

Thank you for talking about my paper on your blog ! Don't hesitate if you have any question to ask to me. About the fact that "only those populations who later took up farming and herding took advantage of this mysterious new food technology that was not farming or herding" (previous commentary from Mark Moore), perhaps we have to think differently. Paleolithic expansions could result from a new food technology that was not farming or herding in some populations, and, later, the fact that these populations was in expansion and had higher population sizes may have favored the emergence of farming in these populations. In this case, the results that I have found in this paper are those expected.

Carla Aimé (first author of this paper)