Andrea Manica

University of Cambridge | Cam · Department of Zoology

The Neolithic transition was a dynamic time in European prehistory of cultural, social, and technological change. Although this period has been well explored in central Europe using ancient nuclear DNA [1, 2], its genetic impact on northern and eastern parts of this continent has not been as extensively studied. To broaden our understanding of the...

We extend the scope of European palaeogenomics by sequencing the genomes of Late Upper Palaeolithic (13,300 years old, 1.4-fold coverage) and Mesolithic (9,700 years old, 15.4-fold) males from western Georgia in the Caucasus and a Late Upper Palaeolithic (13,700 years old, 9.5-fold) male from Switzerland. While we detect Late Palaeolithic–Mesolithi...

Ancient genomes have revolutionized our understanding of Holocene prehistory and, particularly, the Neolithic transition in western Eurasia. In contrast, East Asia has so far received little attention, despite representing a core region at which the Neolithic transition took place independently ~3 millennia after its onset in the Near East. We repo...

Characterizing genetic diversity in Africa is a crucial step for most analyses reconstructing the evolutionary history of anatomically modern humans. However, historic migrations from Eurasia into Africa have affected many contemporary populations, confounding inferences. Here, we present a 12.5× coverage ancient genome of an Ethiopian male (“Mota”...

The extent to which past climate change has dictated the pattern and timing of the out-of-Africa expansion by anatomically modern humans is currently unclear [Stewart JR, Stringer CB (2012) Science 335:1317-1321]. In particular, the incompleteness of the fossil record makes it difficult to quantify the effect of climate. Here, we take a different a...

The appearance of the oldest known animals during the late Ediacaran (~574 million years ago [Ma]) was followed by a phase of little change. This period, which lasted ~14 million years, ended with a burst of rapid diversification known as the Ediacaran Second Wave. The reasons for these diversity patterns are poorly understood. Here we investigate...

In the transition between the Middle Stone Age (MSA) and the Late Stone Age (LSA) in eastern Africa, the archaeological record shows a gradual and asynchronous decline in MSA features and an increase in LSA characteristics. A link between this pattern and climatic variations has not yet been tested in the region using lithic attribute analysis. To...

Although cumulative culture is a hallmark of hominin evolution, its origins can be traced back to our common ancestor with chimpanzees. Here, we investigated the evolutionary origins of chimpanzee cumulative culture and why it remained incipient. To trace cultural transmission among the four chimpanzee subspecies, we compared population networks ba...

Video of the talk: https://www.youtube.com/watch?v=4InGRZ05SmY&ab_channel=MethodsEcolEvol Abstract: By building on the modular infrastructure of tidymodels, tidysdm does not need to create complete solutions from scratch: objects created within tidysdm can be directly fed to functions from other packages. In addition to that, tidysdm facilitate...

In species distribution modelling (SDM), it is common practice to explore multiple machine learning (ML) algorithms and combine their results into ensembles. In R, many implementations of different ML algorithms are available but, as they were mostly developed independently, they often use inconsistent syntax and data structures. For this reason, r...

A variety of fish species have proven instrumental in the investigation of evolution, behavior, ecology, and physiology, among many other fields. Many model systems (e.g., zebrafish, guppies, and three-spined sticklebacks) have been maintained by institutions and have had protocols written with respect to their husbandry. Here we present the protoc...

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...

The reconstruction of past demographic histories relies on the pattern of genetic variation shown by the sampled populations; this means that an accurate estimation of genotypes is crucial for a reliable inference of past processes. A commonly adopted approach to reconstruct complex demographic dynamics is the Approximate Bayesian Computation (ABC)...

Both proxies and models provide key resources to explore how palaeoenvironmental changes may have impacted diverse biotic communities and cultural processes. Whilst proxies provide the gold standard in reconstructing the local environment, they only provide point estimates for a limited number of locations; on the other hand, models have the potent...

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 g...

Predator-prey interactions in marine ecosystems control population sizes, maintain species richness, and provide intermediate disturbance. Such ecosystem structuring interactions may be rare in Antarctic epibenthic communities, which are unique among marine ecosystems worldwide for their dominance of soft bodied fauna (sponges, soft and hard corals...

The driving forces behind the evolution of early metazoans are not well understood, but key insights into their ecology and evolution can be gained through ecological analyses of the in situ, sessile communities of the Avalon assemblage in the Ediacaran (~565 million years ago). Community structure in the Avalon is thought to be underpinned by epif...

The extinction of the woolly rhinoceros ( Coelodonta antiquitatis ) at the onset of the Holocene remains an enigma, with conflicting evidence regarding its cause and spatiotemporal dynamics. This partly reflects challenges in determining demographic responses of late Quaternary megafauna to climatic and anthropogenic causal drivers with available g...

Aim Competition is often proposed to drive niche segregation along multiple axes in speciose communities. Understanding spatial partitioning of foraging areas is particularly important in species that are constrained to a central place. We present a natural experiment examining variation in habitat preferences of congeneric Southern Ocean predators...

Human evolutionary history in Central Africa reflects a deep history of population connectivity. However, Central African hunter-gatherers (CAHGs) currently speak languages acquired from their neighbouring farmers. Hence it remains unclear which aspects of CAHG cultural diversity results from long-term evolution preceding agriculture and which refl...

Human evolutionary history in Central Africa reflects a deep history of population connectivity. However, Central African hunter-gatherers (CAHGs) currently speak languages acquired from their neighbouring farmers. Hence it remains unclear which aspects of CAHG cultural diversity results from long-term evolution preceding agriculture, and which ref...

Cooperative social behaviors, such as parental care, have long been hypothesized to relax selection leading to the accumulation of genetic variation in populations. Although the idea has been discussed for decades, there has been relatively little experimental work to investigate how social behavior contributes to genetic variation in populations....

While cumulative culture is a hallmark of hominin evolution, its origins can be traced back to our common ancestor with chimpanzees. Here we investigate the evolutionary origins of chimpanzee cumulative culture, and why it remained incipient. To trace cultural transmission among the four chimpanzee subspecies, we built between-populations networks...

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 comp...

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 conservation, archaeology to population genetics, macroevolution to anthropology, and human evolution to linguistics. The downside to this process is tha...

Climatic variations through time are one of the key drivers of evolutionary dynamics in animal species, leading to changes in distribution, migration, adaptation, or extinction. While specialists are aware of how the different factors involved interact in complex and variable ways, most often the general public fails to grasp the overall complexity...

Plastic pollution is distributed patchily around the world’s oceans. Likewise, marine organisms that are vulnerable to plastic ingestion or entanglement have uneven distributions. Understanding where wildlife encounters plastic is crucial for targeting research and mitigation. Oceanic seabirds, particularly petrels, frequently ingest plastic, are h...

The Ihò Eléérú (or Iho Eleru) rock shelter, located in Southwest Nigeria, is the only site from which Pleistocene-age hominin fossils have been recovered in western Africa. Excavations at Iho Eleru revealed regular human occupations ranging from the Later Stone Age (LSA) to the present day. Here, we present chronometric, archaeobotanical, and paleo...

Aim: Species 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 compose...

Cooperative social behaviours, such as parental care, have long been hypothesized to relax selection leading to the accumulation of genetic variation in populations. Although the idea has been discussed for decades, there has been relatively little experimental work to investigate how social behaviour contributes to genetic variation in populations...

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...

Knowledge of the 3-dimensional space use of large marine predators is central to our understanding of ecosystem dynamics and for the development of management recommendations. Horizontal movements of white sharks, Carcharodon carcharias, in eastern Australian and New Zealand waters have been relatively well studied, yet vertical habitat use is less...

Investigating resource partitioning of marine predators is essential for understanding coexistence of sympatric species and the functional role they play in marine ecosystems. Baleen whales are a key component of sub-Antarctic ecosystems, foraging predominantly on zooplankton and small forage fish. During the twentieth century, baleen whales were u...

Reconstructions of the spatiotemporal dynamics of human dispersal away from evolutionary origins in Africa are important for determining the ecological consequences of the arrival of anatomically modern humans in naïve landscapes and interpreting inferences from ancient genomes on indigenous population history. While efforts have been made to indep...

Central African hunter-gatherers (CAHGs) are widely seen as isolated populations displaced into the forest by the expansion of Bantu-speaking farmers. By contrast, recent studies revealed various genetic signs of long-term adaptation of CAHGs to forest environments and independence from Bantu demography. It remains unclear whether cultural diversit...

Foraging niche specialisation is thought to occur when different members of speciose communities divide resources in either time or space. Here we compared habitat preferences of the congeneric Grey Petrel Procellaria cinerea and White‐chinned Petrel P. aequinoctialis, tracked in the same calendar year using GPS loggers from Gough Island and Bird I...

Metagenomic data generated from environmental samples is increasingly common in the analysis of modern and ancient biological communities. To obtain taxonomic profiles from this type of data, DNA sequences are aligned against large genomic reference databases and the lowest common ancestor (LCA) needs to be inferred for each sequence with multiple...

The source–sink paradigm predicts that populations in poorer‐quality habitats (‘sinks') persist due to continued immigration from more‐productive areas (‘sources'). However, this categorisation of populations assumes that habitat quality is fixed through time. Globally, we are in an era of wide‐spread habitat degradation, and consequently there is...

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 betwe...

Recent decades have seen the rapid expansion of scholarship that identifies societal responses to past climatic fluctuations. This fast-changing scholarship, which was recently synthesized as the History of Climate and Society (HCS), is today undertaken primary by archaeologists, economists, geneticists, geographers, and paleoclimatologists. This r...

The level of detail on host communities needed to understand multihost parasite invasions is an unresolved issue in disease ecology. Coarse community metrics that ignore functional differences between hosts, such as host species richness, can be good predictors of invasion outcomes. Yet if host species vary in the extent to which they maintain and...

Animals can gain large benefits from living in groups but must coordinate with their groupmates in order to do so. Social interactions between groupmates drive overall group coordination and are influenced by the characteristics of individual group members. In particular, consistent inter-individual differences in behaviour (e.g. boldness) and fami...

The relationships between avian brood parasites and their hosts are widely recognised as model systems for studying coevolution. However, while most brood parasites are known to parasitise multiple species of host and hosts are often subject to parasitism by multiple brood parasite species, the examination of multispecies interactions remains rare....

Significance We combined ethnographic, archaeological, genetic, and paleoclimatic data to model the dynamics of Central African hunter-gatherer populations over the past 120,000 years. We show, against common assumptions, that their distribution and density are explained by changing environments rather than by a displacement following recent farmin...

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 ext...

The first animals appear during the late Ediacaran (572 to 541 Ma); an initial diversity increase was followed reduction in diversity, often interpreted as catastrophic mass extinction. We investigate Ediacaran ecosystem structure changes over this time period using the “Elements of Metacommunity Structure” framework to assess whether this diversit...

Optimal selection of foraging habitats is key to survival, but it remains unclear how naïve individuals are able to locate patchily‐distributed resources and maximize energy gain in completely new environments. In most animals, juveniles disperse unaccompanied by their parents, and hence their movements are likely guided, at least at fine scales, b...

African paleoanthropological studies typically focus on regions of the continent such as Eastern, Southern and Northern Africa, which hold the highest density of Pleistocene archaeological sites. Nevertheless, lesser known areas such as West Africa also feature a high number of sites. Here, we present a high-resolution map synthesising all well con...

Agricultural production has replaced natural ecosystems across the planet, becoming a major driver of carbon emissions, biodiversity loss, and freshwater consumption. Here we combined global crop yield and environmental data in a ~1-million-dimensional mathematical optimisation framework to determine how optimising the spatial distribution of globa...

Eastern Africa has played a prominent role in debates about human evolution and dispersal due to the presence of rich archaeological, palaeoanthropological and palaeoenvironmental records. However, substantial disconnects occur between the spatial and temporal resolutions of these data that complicate their integration. Here, we apply high-resoluti...

The cover image is based on the Letter Process‐explicit models reveal pathway to extinction for woolly mammoth using pattern‐oriented validation by Damien A. Fordham et al., https://doi.org/10.1111/ele.13911. Image Credit: Mauricio Anton.

Significance We combine tracks of a long-distance migratory bird with high–temporal resolution climate data to reconstruct habitat availability month by month for the past 120,000 y. The seasonal changes of suitable habitat in the past imply that continued seasonal migration was necessary during the glacial maxima. Genomic-based estimates of effect...

Anthropogenic land use and climate change in the Industrial age have had substantial impacts on the geographic ranges of the world’s terrestrial animal species. How do these impacts compare against those in the millennia preceding the Industrial era? Here, we combine reconstructions of global climate and land use from 6000 BCE to 1850 CE with empir...

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 t...

Pathways to extinction start long before the death of the last individual. However, causes of early stage population declines and the susceptibility of small residual populations to extirpation are typically studied in isolation. Using validated process-explicit models, we disentangle the ecological mechanisms and threats that were integral in the...

Climate change influences population demography by altering patterns of gene flow and reproductive isolation. Direct mutation rates offer the possibility for accurate dating on the within-species level but are currently only available for a handful of vertebrate species. Here, we use the first directly estimated mutation rate in birds to study the...

Coronavirus disease, COVID-19 (coronavirus disease 2019), caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), has a higher case fatality rate in European countries than in others, especially East Asian ones. One potential explanation for this regional difference is the diversity of the viral infection efficiency. Here, we analyz...

Eastern Africa has played a prominent role in debates about human evolution and dispersal due to the presence of rich archaeological, palaeoanthropological and palaeoenvironmental records. However, substantial disconnects occur between the spatial and temporal resolutions of these data that complicate their integration. Here, we apply high-resoluti...

Fisheries bycatch is a major threat to marine megafauna such as seabirds. Population monitoring has revealed low survival of juvenile seabirds over recent decades, potentially because naïve individuals are more susceptible to bycatch than adults. However, major gaps remain in our knowledge of behavior and interaction of juveniles with fisheries. He...

Curated global climate data have been generated from climate model outputs for the last 120,000 years, whereas reconstructions going back even further have been lacking due to the high computational cost of climate simulations. Here, we present a statistically-derived global terrestrial climate dataset for every 1,000 years of the last 800,000 year...

Whilst an African origin of modern humans is well established, the timings and routes of their expansions into Eurasia are the subject of heated debate, due to the scarcity of fossils and the lack of suitably old ancient DNA. Here, we use high-resolution palaeoclimate reconstructions to estimate how difficult it would have been for humans in terms...

Over the last few years, genome-wide data for a large number of ancient human samples have been collected. Whilst datasets of captured SNPs have been collated, high coverage shotgun genomes (which are relatively few but allow certain types of analyses not possible with ascertained captured SNPs) have to be reprocessed by individual groups from raw...