New paper: Climate shaped how Neolithic farmers and European hunter-gatherers interacted after a major slowdown from 6,100 BCE to 4,500 BCE

Crops. Photo by Michela Leonardi
Crops. Photo by Michela Leonardi

It just came out in Nature Human Behaviour a new paper to which I collaborated: Climate shaped how Neolithic farmers and European hunter-gatherers interacted after a major slowdown from 6,100 BCE to 4,500 BCE. The article is behind paywall, but there is a read-only version and the publisher added the full text in Researchgate.

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.

Nat Hum Behav (2020). https://doi.org/10.1038/s41562-020-0897-7

New release: Climate change – the board game

I have just released Climate Change – the board game: a free educational board game about evolution and climate change. The aim is to “put yourself in the paws” of animal species, and to experience both their evolution and their struggles in the current climate emergency.

Climate change - the board game

Each player is a medium/large mammal species, living in a word where climate changes unexpectedly. Every species has its DNA and collects mutations through time, allowing it to adapt to new habitats. Sometimes evolving is not an option, and the species must migrate or go extinct. It is also possible to integrate human-associated climate changes.

It has been designed as an educational resource for schools (groups of 4-5 people, with an approximate duration of 30 minutes to leave space for discussion and questions): we have used it successfully to do outreach at the Museum of Zoology, University of Cambridge. Still, it can also be played with friends and family.

Climate change the board game activity at the Zoology Museum, Cambridge

New preprint: mtDNA-based reconstructions of change in effective population sizes of Holarctic birds do not agree with their reconstructed range sizes based on paleoclimates

European robin (Erithacus rubecula), picture by Michela Leonardi
European robin (Erithacus rubecula), one of the species analysed in the study.
Picture by Michela Leonardi

A new preprint to which I collaborated was just submitted to BioRxiv: mtDNA-based reconstructions of change in effective population sizes of Holarctic birds do not agree with their reconstructed range sizes based on paleoclimates. The work is led by Eleanor Miller, and was performed under the supervision of Andrea Manica and Bill Amos (University of Cambridge).  

Eleanor F. Miller, Rhys E. Green, Andrew Balmford, Robert Beyer, Marius Somveille, Michela Leonardi, William Amos, Andrea Manica

mtDNA-based reconstructions of change in effective population sizes of Holarctic birds do not agree with their reconstructed range sizes based on paleoclimates

During the Quaternary, large climate oscillations had profound impacts on the distribution, demography and diversity of species globally. Birds offer a special opportunity for studying these impacts because surveys of geographical distributions, publicly-available genetic sequence data, and the existence of species with adaptations to life in structurally different habitats, permit large-scale comparative analyses. We use Bayesian Skyline Plot (BSP) analysis of mitochondrial DNA to reconstruct profiles depicting how effective population size (Ne) may have changed over time, focussing on variation in the effect of the last deglaciation among 102 Holarctic species. Only 3 species showed a decline in Ne since the Last Glacial Maximum (LGM) and 7 showed no sizeable change, whilst 92 profiles revealed an increase in Ne. Using bioclimatic Species Distribution Models (SDMs), we also estimated changes in species potential range extent since the LGM. Whilst most modelled ranges also increased, we found no correlation across species between the magnitude of change in range size and change in Ne. The lack of correlation between SDM and BSP reconstructions could not be reconciled even when range shifts were considered. We suggest the lack of agreement between these measures might be linked to changes in population densities which can be independent of range changes. We caution that interpreting either SDM or BSPs independently is problematic and potentially misleading. Additionally, we found that Ne of wetland species tended to increase later than species from terrestrial habitats, possibly reflecting a delayed increase in the extent of this habitat type after the LGM.

bioRxiv 2019.12.13.870410; doi: https://doi.org/10.1101/2019.12.13.870410

New paper: Tracking five millennia of horse management with extensive ancient genome time series

A herd of Kazakh horses in the Pavlodar region of Kazakhstan in August 2016. Credit: Ludovic Orlando
A herd of Kazakh horses in the Pavlodar region of Kazakhstan in August 2016.
Credit: Ludovic Orlando

A new paper to which I collaborated just came out, “Tracking five millennia of horse management with extensive ancient genome time series“, which is the result of a huge collaboration between more than a hundred scientists from many different research centres around the world. The lead authors are Antoine Fages, Kristian Hanghøj and Naveed Khan, and the senior author Ludovic Orlando (University of Toulouse and University of Copenhagen).

Antoine Fages, Kristian Hanghøj, Naveed Khan, Charleen Gaunitz, Andaine Seguin-Orlando, Michela Leonardi, [116 more authors] and Ludovic Orlando

Tracking five millennia of horse management with extensive ancient genome time series
Highlights
  • Two now-extinct horse lineages lived in Iberia and Siberia some 5,000 years ago
  • Iberian and Siberian horses contributed limited ancestry to modern domesticates
  • Oriental horses have had a strong genetic influence within the last millennium
  • Modern breeding practices were accompanied by a significant drop in genetic diversity
Graphical abstract
Graphical abstract

Horse domestication revolutionized warfare and accelerated travel, trade, and the geographic expansion of languages. Here, we present the largest DNA time series for a non-human organism to date, including genome-scale data from 149 ancient animals and 129 ancient genomes (≥1-fold coverage), 87 of which are new. This extensive dataset allows us to assess the modern legacy of past equestrian civilizations. We find that two extinct horse lineages existed during early domestication, one at the far western (Iberia) and the other at the far eastern range (Siberia) of Eurasia. None of these contributed significantly to modern diversity. We show that the influence of Persian-related horse lineages increased following the Islamic conquests in Europe and Asia. Multiple alleles associated with elite-racing, including at the MSTN “speed gene,” only rose in popularity within the last millennium. Finally, the development of modern breeding impacted genetic diversity more dramatically than the previous millennia of human management.

Cell, Volume 177, Issue 6, 30 May 2019, Pages 1419-1435.e31
DOI: https://doi.org/10.1016/j.cell.2019.03.049

New paper: Did Going North Give Us Migraine? An Evolutionary Approach on Understanding Latitudinal Differences in Migraine Epidemiology

Figure 1 from Key et al 2018, showing the populations analysed, their allele frequencies for the variant associated with migraine (in colour), the average temperature, and FST signaturess.
Figure 1 from Key et al 2018, showing the populations analysed, their allele frequencies for the variant associated with migraine (in colour), the average temperature, and FST signatures.

It just came out in Headache our commentary “Did Going North Give Us Migraine? An Evolutionary Approach on Understanding Latitudinal Differences in Migraine Epidemiology”. We discuss a recent publication (Key et al. 2018, Human local adaptation of the TRPM8 cold receptor along a latitudinal cline, PLoS Genet, 14 (5), e1007298) reconstructing the evolutionary history of a genetic polymorphism strongly associated with migraine. We collaborated with Alessandro Viganò and Vittorio di Piero, two medical doctors from the Sapienza University of Rome, to offer to the medical community a commentary piece on the importance of integrating an evolutionary approach into epidemiological studies of migraine, and other potentially genetic-associated diseases.

Alessandro Viganò, Andrea Manica, Vittorio Di Piero, Michela Leonardi

Did Going North Give Us Migraine? An Evolutionary Approach on Understanding Latitudinal Differences in Migraine Epidemiology

This commentary discusses a recent publication by evolutionary biologists with strong implications for migraine experts. The Authors showed that a gene polymorphism associated with migraine gave our ancestors an evolutionary advantage when colonizing northern, and thus colder, territories. They then highlight that the prevalence of migraine may differ among countries because of climatic adaptation. These results may prove useful in planning both epidemiological and physiological studies in the field of migraine.

Headache, 59 (4), 632-634 https://doi.org/10.1111/head.13520