michelaleonardi Articles, Research

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

michelaleonardi Articles, Research

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

michelaleonardi Articles, Research

The female ancestor’s tale: Long‐term matrilineal continuity in a nonisolated region of Tuscany

Lucca_GEarth
The city of Lucca as seen from satellite. Source: Google Earth.

It just come out in American Journal of Physical Anthropology our new paper (behind paywall) The female ancestor’s tale: Long‐term matrilineal continuity in a nonisolated region of Tuscany, in collaboration with Guido Barbujani, Silvia Ghirotto and Francesca Tassi, in Ferrara, and David Caramelli, Stefania Vai and colleagues in Florence. Open-access link to the PDF (read-only).

North-Western Tuscany (roughly Lucca and Massa Carrara provinces) has always been a corridor of exchange between Central and North-Western Italy. The region was disputed between the Etruscans and Ligurians, it has been then conquered by the Romans, and in the following centuries underwent several changes of rulers.

We tried to define if and when such complex history entailed matrilinear discontinuity in the local population. We did so by analysing a portion of the mitochondrial DNA in 119 samples from the region, dated from the Copper age (around 5,000 years ago) the Roman period, the Renaissance, modern-day and including some Etruscan sequences from the whole of Tuscany.

tuscany

Using computer simulations we found out that the better explanation for the genetic diversity in our samples is that they belong to the same population, in continuity through time. This is a quite surprising result since similar degrees of long-term continuity have been mostly observed in isolated areas.

A possible explanation of those results is that either the historical changes observed in north-western Tuscany (conquers, immigration etc.) mainly lead to foreign males arriving and marrying local females. It is also possible that the rulers from outside (Romans, Lombards, French) and the local population did not mix significantly because they were part of different social groups. Whatever the region may be, modern-day Lucca inhabitants appear to be the direct descendants of the women living in the regions millennia ago, teaching us that genetic continuity can not only be found in isolated communities.

Michela Leonardi, Anna Sandionigi, Annalisa Conzato, Stefania Vai, Martina Lari, Francesca Tassi, Silvia Ghirotto, David Caramelli, Guido Barbujani

The female ancestor’s tale: Long‐term matrilineal continuity in a nonisolated region of Tuscany

Objectives: With the advent of ancient DNA analyses, it has been possible to disentangle the contribution of ancient populations to the genetic pool of the modern inhabitants of many regions. Reconstructing the maternal ancestry has often highlighted genetic continuity over several millennia, but almost always in isolated areas. Here we analyze North‐western Tuscany, a region that was a corridor of exchanges between Central Italy and the Western Mediterranean coast.

Materials and methods: We newly obtained mitochondrial HVRI sequences from 28 individuals, and after gathering published data, we collected genetic information for 119 individuals from the region. Those span five periods during the last 5,000 years: Prehistory, Etruscan age, Roman age, Renaissance, and Present‐day. We used serial coalescent simulations in an approximate Bayesian computation framework to test for continuity between the mentioned groups.

Results: Our analyses always favor continuity over discontinuity for all groups considered, with the Etruscans being part of the genealogy. Moreover, the posterior distributions of the parameters support very small female effective population sizes.

Conclusions: The observed signals of long‐term genetic continuity and isolation are in contrast with the history of the region, conquered several times (Etruscans, Romans, Lombards, and French). While the Etruscans appear as a local population, intermediate between the prehistoric and the other samples, we suggest that the other conquerors—arriving from far—had a consistent social or sex bias, hence only marginally affecting the maternal lineages. At the same time, our results show that long‐term genealogical continuity is not necessarily linked to geographical isolation.

Am J Phys Anthropol. 2018;1–10. https://doi.org/10.1002/ajpa.23679 

Read-only pdf

michelaleonardi Articles, Research

Late Quaternary horses in Eurasia in the face of climate and vegetation change

Horses in Camargue, France. Photo by Michela Leonardi
Horses in Camargue, France. Photo by Michela Leonardi

It just came out in Science Advances our paper “Late Quaternary horses in Eurasia in the face of climate and vegetation change“, done in collaboration with Ludovic Orlando (Copenhagen/Toulouse), David Nogues-Bravo (Copenhagen), Andrea Manica (Cambridge), Francesco Boschin and Paolo Boscato (Siena), and many other excellent scientists!

This study represents the most ambitious effort so far to reconstruct the palaeoecology of the horse in Eurasia through more than 40 thousand years to gain a better understanding of their population dynamics through space and time. Our results suggest that European and Asian horses show different climatic adaptations;  allow a better understanding of the progressive reduction in European horse remains during the Holocene, and shed new light on potential domestication centres.

Michela Leonardi, Francesco Boschin, Konstantinos Giampoudakis, Robert M. Beyer, Mario Krapp, Robin Bendrey, Robert Sommer, Paolo Boscato, Andrea Manica, David Nogues-Bravo and Ludovic Orlando

Late Quaternary horses in Eurasia in the face of climate and vegetation change

Wild horses thrived across Eurasia until the Last Glacial Maximum to collapse after the beginning of the Holocene. The interplay of climate change, species adaptability to different environments, and human domestication in horse history is still lacking coherent continental-scale analysis integrating different lines of evidence. We assembled temporal and geographical information on 3070 horse occurrences across Eurasia, frequency data for 1120 archeological layers in Europe, and matched them to paleoclimatic and paleoenvironmental simulations for the Late Quaternary. Climate controlled the distribution of horses, and they inhabited regions in Europe and Asia with different climates and ecosystem productivity, suggesting plasticity to populate different environments. Their decline in Europe during the Holocene appears associated with an increasing loss and fragmentation of open habitats. Europe was the most likely source for the spread of horses toward more temperate regions, and we propose both Iberia and central Asia as potential centers of domestication.

Science Advances, Vol. 4, no. 7, eaar5589