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Michela Leonardi

Natural History Museum, London, Life Sciences, Post-Doc

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I reconstruct species and population dynamics through time. I do so by integrating data and methods from different fields: ecology, archaeology, palaeoclimatology, and (less often), population genetics.

I developed two informatic tools (R packages) that facilitate palaeoecological analyses at a large scale.

pastclim (https://evolecolgroup.github.io/pastclim/) allows easy access and manipulation of several sets of palaeoclimatic reconstructions covering the whole world between 5 million years ago and future climate projections. It can also work on custom data, if properly formatted, and contains a set of functions to recover the climate for periods of interest for the whole world or specific areas; extract data from locations scattered in space and/or time; retrieve time series from individual sites; and visualise and handle the ice or land coverage.

tidysdm (https://evolecolgroup.github.io/tidysdm) is the first software to natively perform species distribution/habitat suitability/ecological niche modelling based on time-scattered data. Given a set of observations and the associated palaeoclimate, it identifies the relationship between the species of interest and the environment and reconstructs the potential distribution through time. The integration with pastclim allows hassle-free access and handling of palaeoclimatic data.

In my career, I have been working on a wide range of research questions focussing on both animals and humans. Here are a few projects I have carried out in recent years:

• Reconstruct culture-environmental relationships (European Acheulean)
• Reconstruct ecological niche dynamics through time using archaeological occurrences (late Pleistocene European ungulates)
• Species distribution modelling through time using modern occurrences (several holarctic bord species)
• How climate and migrations impacted human genetic diversity through time (Out of Africa, Palaeolithic demography, Neolithic diffusion, Migraine diffusion)
• Ancient DNA analysis (European Late Pleistocene/Holocene horses, North-Western humans from Tuscany)
Address: Cromwell Rd

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Papers by Michela Leonardi

The Acheulean niche: Climate and ecology predict handaxe production in Europe

bioRxiv, 2024

The Acheulean was the most spatially and temporally vast stone tool industry produced by early hu... more The Acheulean was the most spatially and temporally vast stone tool industry produced by early humans, persisting for >1.6 million years across three continents. Understanding how behavioral and artifactual variation in these populations relates to climate change and ecology is vital to correctly interpreting the archaeological record, especially given the major climatic and cultural fluctuations during the Pleistocene.

tidysdm: leveraging the flexibility of tidymodels for Species Distribution Modelling in R

bioRxiv (Cold Spring Harbor Laboratory), Jul 26, 2023

In species distribution modelling (SDM), it is common practice to explore multiple machine-learni... more In species distribution modelling (SDM), it is common practice to explore multiple machine-learning algorithms and combine their results into ensembles. This is no easy task in R: different algorithms were developed independently, with inconsistent syntax and data structures. Specialised SDM packages integrate multiple algorithms by creating a complex interface between the user (providing a unified input and receiving a unified output), and the back-end code (that tackles the specific needs depending on the algorithm). This requires a lot of work to create and maintain the right interface, and it prevents an easy integration of other methods that may become available.

Here we present tidysdm, an R package that solves this problem by taking advantage of the tidymodels universe. Being part of the tidyverse, (i) it has standardised grammar and data structures providing a coherent interface for modelling, (ii) includes packages designed for fitting, tuning, and validating various models, and (iii) allows easy integration of new algorithms and methods.

tidysdm allows easy, flexible and quick species distribution modelling by supporting standard algorithms, including additional SDM-oriented functions, and giving the opportunity of using any algorithm or procedure to fit, tune and validate a large number of different models. Additionally, it provides further functions to easily fit models based on paleo/time-scattered data.

The package includes two vignettes detailing standard procedures for present-day and time-scattered data. These vignettes also showcase the integration with pastclim (Leonardi et al. 2023) to allow easier access to palaeoclimatic data series, if needed, but users can bring in their own climatic data in standard formats.

pastclim 1.2: an R package to easily access and use paleoclimatic reconstructions

Ecography

Author response for "pastclim 1.2: an R package to easily access and use paleoclimatic reconstructions

May contain traces of milk. Investigating the role of dairy farming and milk consumption in the European Neolithic

Niche conservatism in a generalist felid: low differentiation of the climatic niche among subspecies of the leopard(Panthera pardus)

AimSpecies distribution modelling can be used to reveal if the ecology of a species varies across... more AimSpecies distribution modelling can be used to reveal if the ecology of a species varies across its range, to investigate if range expansions entailed niche shifts, and to help assess ecological differentiation: the answers to such questions are vital for effective conservation. The leopard (Panthera pardus spp.) is a generalist species composed of one African and eight Asian subspecies, reflecting dispersal from an ancestral African range. This study uses species distribution models to compare the niches of leopard subspecies, to investigate if they conserved their niches when moving into new territories or adapted to local conditions and shifted niche.LocationAfrica and EurasiaMethodsWe assembled a database ofP. pardus spp. presences. We then associated them with bioclimatic variables to identify which are relevant in predicting the distribution of the leopard. We then constructed a species distribution model and compared the distribution predicted from models based on presences...

Ecography 2023 Leonardi pastclim 1 2 an R package to easily access and use paleoclimatic reconstructions

by Michela Leonardi and Emily Y Hallett

Ecography, 2022

The recent development of continuous paleoclimatic reconstructions covering hundreds of thousands... more The recent development of continuous paleoclimatic reconstructions covering hundreds of thousands of years paved the way for a large number of studies from disciplines ranging from paleoecology to archaeology, conservation to population genetics, macroevolution to anthropology and human evolution to linguistics. Unfortunately, (paleo)climatic data can be challenging to extract and analyze for scholars unfamiliar with such specific file formats. Here we present pastclim, an R package facilitating the access and use of paleoclimatic reconstructions. It currently includes two of such datasets, covering respectively the last 120 000 and 800 000 years, and a vignette provides instructions on how to include additional datasets. The package contains a set of functions to quickly and easily recover the climate for time periods of interest either for the whole world or specific areas, extract data from locations scattered in space and/or time, retrieve time series from individual sites, and manage the ice or land coverage, offering a handy platform to include the climate of the past into existing or new analyses and pipelines.

Following the niche: the differential impact of the last glacial maximum on four European ungulates

Communications Biology

Predicting the effects of future global changes on species requires a better understanding of the... more Predicting the effects of future global changes on species requires a better understanding of the ecological niche dynamics in response to climate; the large climatic fluctuations of the last 50,000 years can be used as a natural experiment to that aim. Here we test whether the realized niche of horse, aurochs, red deer, and wild boar changed between 47,000 and 7500 years ago using paleoecological modelling over an extensive archaeological database. We show that they all changed their niche, with species-specific responses to climate fluctuations. We also suggest that they survived the climatic turnovers thanks to their flexibility and by expanding their niche in response to the extinction of competitors and predators. Irrespective of the mechanism behind such processes, the fact that species with long generation times can change their niche over thousands of years cautions against assuming it to stay constant both when reconstructing the past and predicting the future.

Following the niche: the differential impact of the last glacial maximum on four European ungulates

by Michela Leonardi and Francesco Boschin

Communications Biology, 2022

Predicting the effects of future global changes on species requires a better understanding of the... more Predicting the effects of future global changes on species requires a better understanding of the ecological niche dynamics in response to climate; the large climatic fluctuations of the last 50,000 years can be used as a natural experiment to that aim. Here we test whether the realized niche of horse, aurochs, red deer, and wild boar changed between 47,000 and 7500 years ago using paleoecological modelling over an extensive archaeological database. We show that they all changed their niche, with species-specific responses to climate fluctuations. We also suggest that they survived the climatic turnovers thanks to their flexibility and by expanding their niche in response to the extinction of competitors and predators. Irrespective of the mechanism behind such processes, the fact that species with long generation times can change their niche over thousands of years cautions against assuming it to stay constant both when reconstructing the past and predicting the future.

Genetic demography: What does it mean and how to interpret it, with a case study on the Neolithic transition

Words, Bones, Genes, Tools: DFG Center for Advanced Studies, 2021

The present work describes the basic principles underlying demographic reconstructions from genet... more The present work describes the basic principles underlying demographic reconstructions from genetic data, and reviews the studies using such methods with respect to the Neolithic Demographic Transition. It is intended as a tool for scholars outside the field of population genetics (e.g., archaeologists, anthropologists, etc.) to better understand the significance and intrinsic limitations of genetic demography, and to help integrate its results within the broader context of the reconstruction of the human past.

pastclim: an R package to easily access and use paleoclimatic reconstructions

The recent development of continuous paleoclimatic reconstructions covering hundreds of thousands... more The recent development of continuous paleoclimatic reconstructions covering hundreds of thousands of years paved the way to a large number of studies from disciplines ranging from paleoecology to linguistics, from archaeology to conservation and from population genetics to human evolution. Unfortunately, such climatic data can be challenging to extract and analyze for scholars unfamiliar with such specific climatic file formats.Here we present pastclim, an R package facilitating the access and use of two sets of paleoclimatic reconstructions covering respectively the last 120,000 and 800,000 years. The package contains a set of functions allowing to quickly and easily recover the climate for the whole world or specific areas for time periods of interest, extract data from locations scattered in space and/or time, retrieve time series from individual sites, and easily manage the ice or land coverage.The package can easily be adapted to paleoclimatic reconstructions different from the...

Data from: Evolutionary patterns and processes: lessons from ancient DNA

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

Nature Human Behaviour, 2020

The Neolithic transition in Europe was driven by the rapid dispersal of Near Eastern farmers who,... more 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. By synthesizing information on archaeological sites, palaeoclimate reconstructions and ancient DNA, Betti et al. show that the Neolithic expansion in Europe was not a continuous process of diffusion, but a series of climate-driven episodes of varying speeds.

Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series

Cell, 2019

An earlier revolution: genetic and genomic analyses reveal pre-existing cultural differences leading to Neolithization

Scientific Reports, 2017

Domestication and migrations: Using mitochondrial DNA to infer domestication processes of goats and horses

by Mark Thomas and Michela Leonardi

Population Dynamics in Prehistory and Early History, 2012

Lactase persistence and milk consumption in Europe: an interdisciplinary approach involving genetics and archaeology

Documenta Praehistorica, 2013

The ability to digest milk during adulthood (lactase persistence) is a genetically determined tra... more The ability to digest milk during adulthood (lactase persistence) is a genetically determined trait present only in humans. Its origin and diffusion are correlated with the development of pastoralism and the consumption of fresh milk. This work will present the genetic and archaeologi- cal data that allow the reconstruction of the co-evolutionary process between dairying culture and lactase persistence, as well as a discussion of the chronology and the way lactase persistence spread in Europe.

Evolutionary Patterns and Processes: Lessons from Ancient DNA

Systematic Biology, 2016

Following The Niche: Reconstructing 32,000 Years Of Niche Dynamics In Four European Ungulate Species

An understanding of how ecological niches can change through time is key to predicting the effect... more An understanding of how ecological niches can change through time is key to predicting the effect of future global change. Past climatic fluctuations provide a natural experiment to assess the extent to which species can change their niche. Here we use an extensive archaeological database to formally test whether the niche of four European ungulates changed between 40 and 8 kya (i.e. before major anthropogenic habitat modification and excluding the confounding effect of domestication). We find that niche change depended on habitat. Horse and aurochs, which are adapted to open environment, changed their niche after the Last Glacial Maximum, and it is unclear whether this was the result of adaptation, or an expansion of the realized niche as a response to the extinction of other megafauna (competitors and predators) that shared the same habitat preferences. On the other hand, red deer and wild boar, which prefer close and semi-close habitats, did not change their niche during the same...

Climate and mountains shaped human ancestral genetic lineages

bioRxiv, 2021

Extensive sequencing of modern and ancient human genomes has revealed that contemporary populatio... more 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 lineages1. 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 Arican continent. The subsequent spread across Eurasia was then mostly shaped by mountain ranges, and to a lesser extent deserts, leading to the split of European and Asia...

The Acheulean niche: Climate and ecology predict handaxe production in Europe

bioRxiv, 2024

The Acheulean was the most spatially and temporally vast stone tool industry produced by early hu... more The Acheulean was the most spatially and temporally vast stone tool industry produced by early humans, persisting for >1.6 million years across three continents. Understanding how behavioral and artifactual variation in these populations relates to climate change and ecology is vital to correctly interpreting the archaeological record, especially given the major climatic and cultural fluctuations during the Pleistocene.

tidysdm: leveraging the flexibility of tidymodels for Species Distribution Modelling in R

bioRxiv (Cold Spring Harbor Laboratory), Jul 26, 2023

In species distribution modelling (SDM), it is common practice to explore multiple machine-learni... more In species distribution modelling (SDM), it is common practice to explore multiple machine-learning algorithms and combine their results into ensembles. This is no easy task in R: different algorithms were developed independently, with inconsistent syntax and data structures. Specialised SDM packages integrate multiple algorithms by creating a complex interface between the user (providing a unified input and receiving a unified output), and the back-end code (that tackles the specific needs depending on the algorithm). This requires a lot of work to create and maintain the right interface, and it prevents an easy integration of other methods that may become available.

Here we present tidysdm, an R package that solves this problem by taking advantage of the tidymodels universe. Being part of the tidyverse, (i) it has standardised grammar and data structures providing a coherent interface for modelling, (ii) includes packages designed for fitting, tuning, and validating various models, and (iii) allows easy integration of new algorithms and methods.

tidysdm allows easy, flexible and quick species distribution modelling by supporting standard algorithms, including additional SDM-oriented functions, and giving the opportunity of using any algorithm or procedure to fit, tune and validate a large number of different models. Additionally, it provides further functions to easily fit models based on paleo/time-scattered data.

The package includes two vignettes detailing standard procedures for present-day and time-scattered data. These vignettes also showcase the integration with pastclim (Leonardi et al. 2023) to allow easier access to palaeoclimatic data series, if needed, but users can bring in their own climatic data in standard formats.

pastclim 1.2: an R package to easily access and use paleoclimatic reconstructions

Ecography

Author response for "pastclim 1.2: an R package to easily access and use paleoclimatic reconstructions

May contain traces of milk. Investigating the role of dairy farming and milk consumption in the European Neolithic

Niche conservatism in a generalist felid: low differentiation of the climatic niche among subspecies of the leopard(Panthera pardus)

AimSpecies distribution modelling can be used to reveal if the ecology of a species varies across... more AimSpecies distribution modelling can be used to reveal if the ecology of a species varies across its range, to investigate if range expansions entailed niche shifts, and to help assess ecological differentiation: the answers to such questions are vital for effective conservation. The leopard (Panthera pardus spp.) is a generalist species composed of one African and eight Asian subspecies, reflecting dispersal from an ancestral African range. This study uses species distribution models to compare the niches of leopard subspecies, to investigate if they conserved their niches when moving into new territories or adapted to local conditions and shifted niche.LocationAfrica and EurasiaMethodsWe assembled a database ofP. pardus spp. presences. We then associated them with bioclimatic variables to identify which are relevant in predicting the distribution of the leopard. We then constructed a species distribution model and compared the distribution predicted from models based on presences...

Ecography 2023 Leonardi pastclim 1 2 an R package to easily access and use paleoclimatic reconstructions

by Michela Leonardi and Emily Y Hallett

Ecography, 2022

The recent development of continuous paleoclimatic reconstructions covering hundreds of thousands... more The recent development of continuous paleoclimatic reconstructions covering hundreds of thousands of years paved the way for a large number of studies from disciplines ranging from paleoecology to archaeology, conservation to population genetics, macroevolution to anthropology and human evolution to linguistics. Unfortunately, (paleo)climatic data can be challenging to extract and analyze for scholars unfamiliar with such specific file formats. Here we present pastclim, an R package facilitating the access and use of paleoclimatic reconstructions. It currently includes two of such datasets, covering respectively the last 120 000 and 800 000 years, and a vignette provides instructions on how to include additional datasets. The package contains a set of functions to quickly and easily recover the climate for time periods of interest either for the whole world or specific areas, extract data from locations scattered in space and/or time, retrieve time series from individual sites, and manage the ice or land coverage, offering a handy platform to include the climate of the past into existing or new analyses and pipelines.

Following the niche: the differential impact of the last glacial maximum on four European ungulates

Communications Biology

Predicting the effects of future global changes on species requires a better understanding of the... more Predicting the effects of future global changes on species requires a better understanding of the ecological niche dynamics in response to climate; the large climatic fluctuations of the last 50,000 years can be used as a natural experiment to that aim. Here we test whether the realized niche of horse, aurochs, red deer, and wild boar changed between 47,000 and 7500 years ago using paleoecological modelling over an extensive archaeological database. We show that they all changed their niche, with species-specific responses to climate fluctuations. We also suggest that they survived the climatic turnovers thanks to their flexibility and by expanding their niche in response to the extinction of competitors and predators. Irrespective of the mechanism behind such processes, the fact that species with long generation times can change their niche over thousands of years cautions against assuming it to stay constant both when reconstructing the past and predicting the future.

Following the niche: the differential impact of the last glacial maximum on four European ungulates

by Michela Leonardi and Francesco Boschin

Communications Biology, 2022

Predicting the effects of future global changes on species requires a better understanding of the... more Predicting the effects of future global changes on species requires a better understanding of the ecological niche dynamics in response to climate; the large climatic fluctuations of the last 50,000 years can be used as a natural experiment to that aim. Here we test whether the realized niche of horse, aurochs, red deer, and wild boar changed between 47,000 and 7500 years ago using paleoecological modelling over an extensive archaeological database. We show that they all changed their niche, with species-specific responses to climate fluctuations. We also suggest that they survived the climatic turnovers thanks to their flexibility and by expanding their niche in response to the extinction of competitors and predators. Irrespective of the mechanism behind such processes, the fact that species with long generation times can change their niche over thousands of years cautions against assuming it to stay constant both when reconstructing the past and predicting the future.

Genetic demography: What does it mean and how to interpret it, with a case study on the Neolithic transition

Words, Bones, Genes, Tools: DFG Center for Advanced Studies, 2021

The present work describes the basic principles underlying demographic reconstructions from genet... more The present work describes the basic principles underlying demographic reconstructions from genetic data, and reviews the studies using such methods with respect to the Neolithic Demographic Transition. It is intended as a tool for scholars outside the field of population genetics (e.g., archaeologists, anthropologists, etc.) to better understand the significance and intrinsic limitations of genetic demography, and to help integrate its results within the broader context of the reconstruction of the human past.

pastclim: an R package to easily access and use paleoclimatic reconstructions

The recent development of continuous paleoclimatic reconstructions covering hundreds of thousands... more The recent development of continuous paleoclimatic reconstructions covering hundreds of thousands of years paved the way to a large number of studies from disciplines ranging from paleoecology to linguistics, from archaeology to conservation and from population genetics to human evolution. Unfortunately, such climatic data can be challenging to extract and analyze for scholars unfamiliar with such specific climatic file formats.Here we present pastclim, an R package facilitating the access and use of two sets of paleoclimatic reconstructions covering respectively the last 120,000 and 800,000 years. The package contains a set of functions allowing to quickly and easily recover the climate for the whole world or specific areas for time periods of interest, extract data from locations scattered in space and/or time, retrieve time series from individual sites, and easily manage the ice or land coverage.The package can easily be adapted to paleoclimatic reconstructions different from the...

Data from: Evolutionary patterns and processes: lessons from ancient DNA

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

Nature Human Behaviour, 2020

The Neolithic transition in Europe was driven by the rapid dispersal of Near Eastern farmers who,... more 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. By synthesizing information on archaeological sites, palaeoclimate reconstructions and ancient DNA, Betti et al. show that the Neolithic expansion in Europe was not a continuous process of diffusion, but a series of climate-driven episodes of varying speeds.

Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series

Cell, 2019

An earlier revolution: genetic and genomic analyses reveal pre-existing cultural differences leading to Neolithization

Scientific Reports, 2017

Domestication and migrations: Using mitochondrial DNA to infer domestication processes of goats and horses

by Mark Thomas and Michela Leonardi

Population Dynamics in Prehistory and Early History, 2012

Lactase persistence and milk consumption in Europe: an interdisciplinary approach involving genetics and archaeology

Documenta Praehistorica, 2013

The ability to digest milk during adulthood (lactase persistence) is a genetically determined tra... more The ability to digest milk during adulthood (lactase persistence) is a genetically determined trait present only in humans. Its origin and diffusion are correlated with the development of pastoralism and the consumption of fresh milk. This work will present the genetic and archaeologi- cal data that allow the reconstruction of the co-evolutionary process between dairying culture and lactase persistence, as well as a discussion of the chronology and the way lactase persistence spread in Europe.

Evolutionary Patterns and Processes: Lessons from Ancient DNA

Systematic Biology, 2016

Following The Niche: Reconstructing 32,000 Years Of Niche Dynamics In Four European Ungulate Species

An understanding of how ecological niches can change through time is key to predicting the effect... more An understanding of how ecological niches can change through time is key to predicting the effect of future global change. Past climatic fluctuations provide a natural experiment to assess the extent to which species can change their niche. Here we use an extensive archaeological database to formally test whether the niche of four European ungulates changed between 40 and 8 kya (i.e. before major anthropogenic habitat modification and excluding the confounding effect of domestication). We find that niche change depended on habitat. Horse and aurochs, which are adapted to open environment, changed their niche after the Last Glacial Maximum, and it is unclear whether this was the result of adaptation, or an expansion of the realized niche as a response to the extinction of other megafauna (competitors and predators) that shared the same habitat preferences. On the other hand, red deer and wild boar, which prefer close and semi-close habitats, did not change their niche during the same...

Climate and mountains shaped human ancestral genetic lineages

bioRxiv, 2021

Extensive sequencing of modern and ancient human genomes has revealed that contemporary populatio... more 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 lineages1. 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 Arican continent. The subsequent spread across Eurasia was then mostly shaped by mountain ranges, and to a lesser extent deserts, leading to the split of European and Asia...

Domestication and migrations: using mitochondrial DNA to infer domestication processes of goats and horses

by Michela Leonardi, Mark Thomas, and Christine Weber

In: Kaiser E, Schier W, Burger J (eds), Population dynamics in Prehistory and Early History. New Approaches by Stable Isotopes and Genetics, DE GRUYTER, 2012

Die weiße revolution der Jungsteinzeit

in J. Reinhard (ed.): “Milch! Nahrung - Mythos - Politikum”, Jexhof Bauernhof Museum, Fürstenfeldbruck, 2011

The history inside us, how genetic diversity tells us our history

in Feulner F. et al., "May contain traces of milk, investigating the role of dairy farming and milk consumption in the European Neolithic". University of York, 2012

Lactase persistence and milk consumption in Europe: an interdisciplinary approach between genetics and archaeology.

Simulating horse domestication with the help of ancient DNA.

by Michela Leonardi and Mark Thomas

Ancient DNA and horse domestication.

Preliminary analyses of five population samples across 5,000 years in Northwestern Tuscany (Italy)

pastclim and tidysdm: two new R packages to integrate palaeoecological analyses in archaeology

poster, 2024

In recent years, the release of large datasets of archaeological occurrences and palaeoclimatic d... more In recent years, the release of large datasets of archaeological occurrences and palaeoclimatic data series covering hundreds of thousands of years opened the door to exciting new possibilities for integrating palaeoclimate in archaeological analyses. Here, we will present two new R packages released by our lab that facilitate the use and analyses of archaeological "big data" with a palaeoecological perspective.

pastclim (Leonardi et al. 2023a, https://evolecolgroup.github.io/pastclim/) allows easy access and manipulation of several sets of palaeoclimatic reconstructions covering the whole world between 5 million years ago and future climate projections. It can also work on custom data, if properly formatted, and contains a set of functions to recover the climate for periods of interest for the whole world or specific areas; extract data from locations scattered in space and/or time; retrieve time series from individual sites; and visualise and handle the ice or land coverage.

tidysdm (Leonardi et al. 2023b, https://evolecolgroup.github.io/tidysdm) is the first software to natively perform species distribution/habitat suitability/ecological niche modelling based on time-scattered data. Given a set of observations and the associated palaeoclimate, it identifies the relationship between the species of interest and the environment; and reconstruct the potential distribution through time. The integration with pastclim allows hassle-free access and handling of palaeoclimatic data. These easy-to-use and freely available tools can offer exciting new possibilities to test for the role of palaeoclimate in cultural or biological processes to scholars studying the past from any field (archaeology, palaeoecology, palaeoanthropology, archaeozoology, archaeobotany, linguistics, etc.).