During the last couple of weeks, I have been asked by Matthew Collins (Department of Archaeology, University of Cambridge) to contribute two lectures to the module “Ancient Biomolecules”.
In my lecture “Climate and population genetics” I have discussed how to integrate climate into population genetics and genomics, which are the assumptions to take into account, and how to interpret the resulting information. In “The genetics of horse domestication”, I presented and explained a recent paper (Librado et al 2021, Nature) detailing the domestication and spread of Eurasian horses on the basis of ancient DNA data.
It was a lovely occasion, as my talks were followed by many questions and an interesting discussion. I hope there will be other opportunities to collaborate on these topics.
So excited to have contributed to this amazing new preprint!
In this study, we quantified the role of climate and mountains in shaping modern and ancient human genetic diversity.
Genomics shows that contemporary human populations result from the mixing of ancestral groups that are genetically distinct (ancestral genetic lineages) with unknown origins. In theory, ancient DNA could help disentangling their origin, but not in this case because we don’t have enough samples of the right age.
For this reason, we used a different strategy. We explicitly simulated the genetic history of humans in their spread out of Africa testing different values for demographic parameters and physiological responses to the changing climate. By doing so we could see if we can reconstruct the observed genetic diversity (spoiler alert: yes) and which parameters and climate variables shaped it.
For example, we find that aridity is the key factor controlling the timing for the out of Africa and mountains can be huge genetic barriers but only in some areas (e.g. Caucasus and Himalayas, not the Urals).
Thanks to this study, not only we could reconstruct such an important part of our genetic history, but we could also quantify the differential role of climate and topography through space and time in our spread out of Africa.
Preprint
Pierpaolo Maisano Delser, Mario Krapp, Robert Beyer, Eppie R Jones, Eleanor F Miller, Anahit Hovhannisyan, Michelle Parker, Veronika Siska, Maria Teresa Vizzari, Elizabeth J. Pearmain, Ivan Imaz-Rosshandler, Michela Leonardi, Gian Luigi Somma, Jason Hodgson, Eirlys Tysall, Zhe Xue, Lara Cassidy, Daniel G Bradley, Anders Eriksson, Andrea Manica Climate and mountains shaped human ancestral genetic lineages bioRxiv 2021.07.13.452067; doi: https://doi.org/10.1101/2021.07.13.452067
Abstract
Extensive sequencing of modern and ancient human genomes has revealed that contemporary populations can be explained as the result of recent mixing of a few distinct ancestral genetic lineages. But the small number of aDNA samples that predate the Last Glacial Maximum means that the origins of these lineages are not well understood. Here, we circumvent the limited sampling by modelling explicitly the effect of climatic changes and terrain on population demography and migrations through time and space, and show that these factors are sufficient to explain the divergence among ancestral lineages. Our reconstructions show that the sharp separation between African and Eurasian lineages is a consequence of only a few limited periods of connectivity through the arid Arabian peninsula, which acted as the gate out of the African continent. The subsequent spread across Eurasia was then mostly shaped by mountain ranges, and to a lesser extent deserts, leading to the split of Europeans and Asians, and the further diversification of these two groups. A high tolerance to cold climates allowed the persistence at high latitudes even during the Last Glacial Maximum, maintaining a pocket in Beringia that led to the later, rapid colonisation of the Americas. The advent of food production was associated with an increase in movement, but mountains and climate have been shown to still play a major role even in this latter period, affecting the mixing of the ancestral lineages that we have shown to be shaped by those two factors in the first place.
The Neolithic transition in Europe was driven by the rapid spread of Near Eastern farmers who, over a period of 3,500 years, brought food production to the far corners of the continent. However, this wave of expansion was far from homogeneous, with a marked slowdown observed at higher latitudes, which could be related to the different climatic conditions encountered by Neolithic farmers as they moved.
We tested this hypothesis. First, we calculated the expansion routes in the various areas using a large database collating archaeological dates of the first arrival of agriculture throughout Europe. We have identified four of them, shown in the image below.
The four Neolithic expansion routes identified via radiocarbon dates associated with the first appearance of agriculture in the various areas
Along three of these routes, we observed a slowdown (thicker lines in the image) where the value of Growing Degrees Days (reflects the quality of the growing season) exceeds a certain threshold (light green in the map). This suggests that crops that originated in the Near East may have struggled to grow in harsher climatic conditions, not allowing Neolithic populations to produce enough to support population increase and/or expansion.
Furthermore, the study of ancient DNA shows us that in conjunction with the same threshold in growing degree days, the level of admixture between farmers and hunter-gatherers increases, suggesting that unreliable harvests in these regions may have favoured the contact between the two groups.
Lia Betti, Robert M. Beyer, Eppie R. Jones, Anders Eriksson, Francesca Tassi, Veronika Siska, Michela Leonardi, Pierpaolo Maisano Delser, Lily K. Bentley, Philip R. Nigst, Jay T. Stock, Ron Pinhasi & Andrea Manica
Climate shaped how Neolithic farmers and European hunter-gatherers interacted after a major slowdown from 6,100 BCE to 4,500 BCE
The Neolithic transition in Europe was driven by the rapid dispersal of Near Eastern farmers who, over a period of 3,500 years, brought food production to the furthest corners of the continent. However, this wave of expansion was far from homogeneous, and climatic factors may have driven a marked slowdown observed at higher latitudes. Here, we test this hypothesis by assembling a large database of archaeological dates of first arrival of farming to quantify the expansion dynamics. We identify four axes of expansion and observe a slowdown along three axes when crossing the same climatic threshold. This threshold reflects the quality of the growing season, suggesting that Near Eastern crops might have struggled under more challenging climatic conditions. This same threshold also predicts the mixing of farmers and hunter-gatherers as estimated from ancient DNA, suggesting that unreliable yields in these regions might have favoured the contact between the two groups.
Next week, on the 2nd of February, I will be a speaker for “Spritz of Science”, the monthly aperitivo+outreach talk series organised by AIRIcerca Cambridge Chapter.
The title of the event is “Biology of the past”. Claudia Bonfio (Marie Curie Fellow at the MRC Laboratory of Molecular Biology) will discuss the origins of life on Earth, while I will show you the wonders of Ancient DNA.
The talks will be followed by Italian aperitivo at Signorelli La Piazza, in the Grafton Centre. Grab a ticket at this link and join us for an afternoon of spritz and science!
