Andrea Manica

Andrea Manica
University of Cambridge | Cam · Department of Zoology

PhD Cantab

About

442
Publications
174,066
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18,847
Citations
Additional affiliations
October 2005 - present
University of Cambridge
Position
  • Professor (Full)

Publications

Publications (442)
Article
Full-text available
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...
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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...
Article
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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...
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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”...
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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...
Article
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...
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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....
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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...
Preprint
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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...
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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...
Article
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...
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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...
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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...
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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...
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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.
Article
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Migration allows animals to exploit spatially separated and seasonally available resources at a continental to global scale. However, responding to global climatic changes might prove challenging, especially for long-distance intercontinental migrants. During glacial periods, when conditions became too harsh for breeding in the north, avian migrant...
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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...
Chapter
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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...
Article
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...
Article
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...
Preprint
Full-text available
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...
Article
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...
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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...
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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...
Article
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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...
Preprint
Full-text available
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 ¹ . 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 cir...
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Increasing body and brain size constitutes a key macro-evolutionary pattern in the hominin lineage, yet the mechanisms behind these changes remain debated. Hypothesized drivers include environmental, demographic, social, dietary, and technological factors. Here we test the influence of environmental factors on the evolution of body and brain size i...
Article
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The gastric bacterium Helicobacter pylori shares a coevolutionary history with humans that predates the out-of-Africa diaspora, and the geographical specificities of H. pylori populations reflect multiple well-known human migrations. We extensively sampled H. pylori from 16 ethnically diverse human populations across Siberia to help resolve whether...
Preprint
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The evolutionary history of African hunter-gatherers holds key insights into modern human diversity. Here we combine ethnographic and genetic data on Central African hunter-gatherers (CAHG) to show that their current distribution and density is explained by ecology rather than by a displacement to marginal habitats due to recent farming expansions,...
Article
Attempts to identify a ‘homeland’ for our species from genetic data are widespread in the academic literature. However, even when putting aside the question of whether a ‘homeland’ is a useful concept, there are a number of inferential pitfalls in attempting to identify the geographic origin of a species from contemporary patterns of genetic variat...
Article
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During the Quaternary, large climate oscillations impacted the distribution and demography of species globally. Two approaches have played a major role in reconstructing changes through time: Bayesian Skyline Plots (BSP), which reconstruct population fluctuations based on genetic data, and Species Distribution Models, which allow us to back‐cast th...
Preprint
Full-text available
The first animals appear during the late Ediacaran (572 – 541 Ma); an initial diversity increase was followed by a drop, interpreted as catastrophic mass extinction. We investigate the processes underlying these changes using the “Elements of Metacommunity Structure” framework. The oldest metacommunity was characterized by taxa with wide environmen...
Preprint
Full-text available
During the glacial periods of the Pleistocene, swathes of the Northern Hemisphere were covered by ice sheets, tundra and permafrost leaving large areas uninhabitable for temperate and boreal species. The glacial refugia paradigm proposes that, during glaciations, species living in the Northern Hemisphere were forced southwards, forming isolated, in...
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Microplastic (MP) pollution is a key global environmental issue and laboratory exposure studies on aquatic biota are proliferating at an exponential rate. However, most research is limited to treatment-level effects, ignoring that there may be substantial within-population variation in responses to anthropogenic stressors. MP exposure experiments o...
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The impact of deteriorating climatic conditions on variability in the archaeological record towards the Last Glacial Maximum (LGM) remains uncertain. Partly as a result of poor-quality data, previous studies on Upper Palaeolithic (UP) societies of North-Western Europe prior to the LGM have focused on techno-typological traditions and diversificatio...
Article
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1. Many seabirds dive to forage, and the ability to use this hunting technique varies according to such factors as morphology, physiology, prey availability, and ambient light levels. Proficient divers are more able to seize sinking baits deployed by longline fishing vessels and may return them to the surface, increasing exposure of other species....
Article
Leopards are the only big cats still widely distributed across the continents of Africa and Asia. They occur in a wide range of habitats and are often found in close proximity to humans. But despite their ubiquity, leopard phylogeography and population history have not yet been studied with genomic tools. Here, we present population-genomic data fr...
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Background Today an unprecedented amount of genetic sequence data is stored in publicly available repositories. For decades now, mitochondrial DNA (mtDNA) has been the workhorse of genetic studies, and as a result, there is a large volume of mtDNA data available in these repositories for a wide range of species. Indeed, whilst whole genome sequenci...
Article
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Predicting how populations may respond to climate change and anthropogenic pressures requires detailed knowledge of demographic traits, such as survival and reproduction. However, the availability of these data varies greatly across space and taxa. Therefore, it is common practice to conduct population assessments by filling in missing values from...
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Diving is an ecologically important behaviour that provides air-breathing predators with opportunities to capture prey, but that also increases their exposure to incidental mortality (bycatch) in commercial fisheries. In this study, we characterised the diving behaviour of 26 individuals of three species, the black-browed albatross Thalassarche mel...
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Many organisms avoid habitats posing risks of parasitism. Parasites are not generally conspicuous, however, which raises the question of what cues individuals use to detect parasitism risk. Here, we provide evidence in alpine newts (Ichthyosaura alpestris) that non-visual cues from parasite-exposed conspecifics inform habitat avoidance. Alpine newt...
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The destruction of natural habitat for cropland and pastures represents a major threat to global biodiversity. Despite widespread societal concern about biodiversity loss associated with food production, consumers access to quantitative estimates of the impact of crop production on the world's species has been very limited compared to assessments o...
Preprint
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Processes leading to the megafauna extinctions of the late Pleistocene and early-Holocene are uncertain, with intense debate on the roles of human hunting and climatic change. Using process-explicit simulations of climate-human-woolly mammoth interactions, which integrate spatiotemporal evidence from fossils and ancient DNA, we show that humans acc...
Article
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The Welfare Genome Project (WGP) provided 1,000 healthy Korean volunteers with detailed genetic and health reports to test the social perception of integrating personal genetic and healthcare data at a large-scale. WGP was launched in 2016 in the Ulsan Metropolitan City as the first large-scale genome project with public participation in Korea. The...
Article
Bats are the likely zoonotic origin of several coronaviruses (CoVs) that infect humans, including SARS-CoV-1 and SARS-CoV-2, both of which have caused large-scale epidemics. The number of CoVs that are present in an area is strongly correlated with local bat species richness, which in turn is affected by local climatic conditions that drive the geo...
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Domesticator-domesticate relationships are specialized mutualisms where one species provides multigenerational support to another in exchange for a resource or service, and through which both partners gain an advantage over individuals outside the relationship. While this ecological innovation has profoundly reshaped the world’s landscapes and bio-...
Preprint
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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 ungulate...
Article
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Infectious diseases are considered major threats to biodiversity, however strategies to mitigate their impacts in the natural world are scarce and largely unsuccessful. Chytridiomycosis is responsible for the decline of hundreds of amphibian species worldwide, but an effective disease management strategy that could be applied across natural habitat...
Article
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Species’ vulnerability to extinction is strongly impacted by their geographical range size. Formulating effective conservation strategies therefore requires a better understanding of how the ranges of the world’s species have changed in the past, and how they will change under alternative future scenarios. Here, we use reconstructions of global lan...
Article
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Environmental DNA (eDNA) provides a promising supplement to traditional sampling methods for population genetic inferences, but current studies have almost entirely focused on short mitochondrial markers. Here, we develop one mitochondrial and one nuclear set of target capture probes for the whale shark (Rhincodon typus) and test them on seawater s...
Article
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Understanding and predicting the distribution of organisms in heterogeneous envi- ronments is a fundamental ecological question and a requirement for sound management. To implement effective conservation strategies for white shark Carcharodon carcharias populations, it is imperative to define drivers of their movement and occurrence patterns and to...
Preprint
Full-text available
Over the last few years, genome-wide data for a large number of ancient human samples have been collected. Whilst datasets of capture SNPs have been collated, high coverage shotgun genomes (which are relatively few but allow certain type of analyses not possible with ascertained captured SNPs) have to be reprocessed by individual groups from raw re...
Preprint
Full-text available
Upward Sun River 1, an individual from a unique burial of the Denali tradition in Alaska (11500 calBP), is considered a type representative of Ancient Beringians who split from other First Americans 22000–18000 calBP in Beringia. Using a new admixture graph model-comparison approach resistant to overfitting, we show that Ancient Beringians do not f...
Article
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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...