The mixed genetic origin of the first farmers of Europe

SummaryWhile the Neolithic expansion in Europe is well described archaeologically, the genetic origins of European first farmers and their affinities with local hunter-gatherers (HGs) remain unclear. To infer the demographic history of these populations, the genomes of 15 ancient individuals located between Western Anatolia and Southern Germany were sequenced to high quality, allowing us to perform population genomics analyses formerly restricted to modern genomes. We find that all European and Anatolian early farmers descend from the merging of a European and a Near Eastern group of HGs, possibly in the Near East, shortly after the Last Glacial Maximum (LGM). Western and Southeastern European HG are shown to split during the LGM, and share signals of a very strong LGM bottleneck that drastically reduced their genetic diversity. Early Neolithic Central Anatolians seem only indirectly related to ancestors of European farmers, who probably originated in the Near East and dispersed later on from the Aegean along the Danubian corridor following a stepwise demic process with only limited (2-6%) but additive input from local HGs.Our analyses provide a time frame and resolve the genetic origins of early European farmers. They highlight the impact of Late Pleistocene climatic fluctuations that caused the fragmentation, merging and reexpansion of human populations in SW Asia and Europe, and eventually led to the world's first agricultural populations.

Download Full-text

Mycobacterium ulcerans Population Genomics To Inform on the Spread of Buruli Ulcer across Central Africa

mSphere ◽

10.1128/msphere.00472-18 ◽

2019 ◽

Vol 4 (1) ◽

Cited By ~ 6

Author(s):

Koen Vandelannoote ◽

Delphin Mavinga Phanzu ◽

Kapay Kibadi ◽

Miriam Eddyani ◽

Conor J. Meehan ◽

...

Keyword(s):

Disease Control ◽

Population Genomics ◽

Demographic History ◽

Buruli Ulcer ◽

Central Africa ◽

Mycobacterium Ulcerans ◽

Evolutionary Trajectory ◽

Content Type ◽

Mode Of Transmission ◽

The Impact

ABSTRACT Buruli ulcer is a neglected tropical disease of skin and subcutaneous tissue caused by infection with the pathogen Mycobacterium ulcerans. Many critical issues for disease control, such as understanding the mode of transmission and identifying source reservoirs of M. ulcerans, are still largely unknown. Here, we used genomics to reconstruct in detail the evolutionary trajectory and dynamics of M. ulcerans populations at a central African scale and at smaller geographical village scales. Whole-genome sequencing (WGS) data were analyzed from 179 M. ulcerans strains isolated from all Buruli ulcer foci in the Democratic Republic of the Congo, The Republic of Congo, and Angola that have ever yielded positive M. ulcerans cultures. We used both temporal associations and the study of the mycobacterial demographic history to estimate the contribution of humans as a reservoir in Buruli ulcer transmission. Our phylogeographic analysis revealed one almost exclusively predominant sublineage of M. ulcerans that arose in Central Africa and proliferated in its different regions of endemicity during the Age of Discovery. We observed how the best sampled endemic hot spot, the Songololo territory, became an area of endemicity while the region was being colonized by Belgium (1880s). We furthermore identified temporal parallels between the observed past population fluxes of M. ulcerans from the Songololo territory and the timing of health policy changes toward control of the Buruli ulcer epidemic in that region. These findings suggest that an intervention based on detecting and treating human cases in an area of endemicity might be sufficient to break disease transmission chains, irrespective of other reservoirs of the bacterium. IMPORTANCE Buruli ulcer is a destructive skin and soft tissue infection caused by Mycobacterium ulcerans. The disease is characterized by progressive skin ulceration, which can lead to permanent disfigurement and long-term disability. Currently, the major hurdles facing disease control are incomplete understandings of both the mode of transmission and environmental reservoirs of M. ulcerans. As decades of spasmodic environmental sampling surveys have not brought us much closer to overcoming these hurdles, the Buruli ulcer research community has recently switched to using comparative genomics. The significance of our research is in how we used both temporal associations and the study of the mycobacterial demographic history to estimate the contribution of humans as a reservoir in Buruli ulcer transmission. Our approach shows that it might be possible to use bacterial population genomics to assess the impact of health interventions, providing valuable feedback for managers of disease control programs in areas where health surveillance infrastructure is poor.

Download Full-text

The impact of recent population history on the deleterious mutation load in humans and close evolutionary relatives

10.1101/073635 ◽

2016 ◽

Author(s):

Yuval B. Simons ◽

Guy Sella

Keyword(s):

Demographic History ◽

Population History ◽

Human Populations ◽

Data Sets ◽

Loss Of Function ◽

Mutation Load ◽

Synonymous Mutations ◽

Show Evidence ◽

Out Of Africa ◽

The Impact

AbstractOver the past decade, there has been both great interest and confusion about whether recent demographic events—notably the Out-of-Africa-bottleneck and recent population growth—have led to differences in mutation load among human populations. The confusion can be traced to the use of different summary statistics to measure load, which lead to apparently conflicting results. We argue, however, that when statistics more directly related to load are used, the results of different studies and data sets consistently reveal little or no difference in the load of non-synonymous mutations among human populations. Theory helps to understand why no such differences are seen, as well as to predict in what settings they are to be expected. In particular, as predicted by modeling, there is evidence for changes in the load of recessive loss of function mutations in founder and inbred human populations. Also as predicted, eastern subspecies of gorilla, Neanderthals and Denisovans, who are thought to have undergone reductions in population sizes that exceed the human Out-of-Africa bottleneck in duration and severity, show evidence for increased load of non-synonymous mutations (relative to western subspecies of gorillas and modern humans, respectively). A coherent picture is thus starting to emerge about the effects of demographic history on the mutation load in populations of humans and close evolutionary relatives.

Download Full-text

Cultural Innovations Influence Patterns of Genetic Diversity in Northwestern Amazonia

10.1101/347336 ◽

2018 ◽

Author(s):

Leonardo Arias ◽

Roland Schröder ◽

Alexander Hübner ◽

Guillermo Barreto ◽

Mark Stoneking ◽

...

Keyword(s):

Genetic Diversity ◽

Native American ◽

Cultural Practices ◽

Demographic History ◽

Population History ◽

Human Populations ◽

Effective Population ◽

Trade Networks ◽

Males And Females ◽

The Impact

ABSTRACTHuman populations often exhibit contrasting patterns of genetic diversity in the mtDNA and the non-recombining portion of the Y-chromosome (NRY), which reflect sex-specific cultural behaviors and population histories. Here, we sequenced 2.3 Mb of the NRY from 284 individuals representing more than 30 Native-American groups from Northwestern Amazonia (NWA) and compared these data to previously generated mtDNA genomes from the same groups, to investigate the impact of cultural practices on genetic diversity and gain new insights about NWA population history. Relevant cultural practices in NWA include postmarital residential rules and linguistic-exogamy, a marital practice in which men are required to marry women speaking a different language.We identified 2,969 SNPs in the NRY sequences; only 925 SNPs were previously described. The NRY and mtDNA data showed that males and females experienced different demographic histories: the female effective population size has been larger than that of males through time, and both markers show an increase in lineage diversification beginning ~5,000 years ago, with a male-specific expansion occurring ~3,500 years ago. These dates are too recent to be associated with agriculture, therefore we propose that they reflect technological innovations and the expansion of regional trade networks documented in the archaeological evidence. Furthermore, our study provides evidence of the impact of postmarital residence rules and linguistic exogamy on genetic diversity patterns. Finally, we highlight the importance of analyzing high-resolution mtDNA and NRY sequences to reconstruct demographic history, since this can differ considerably between males and females.

Download Full-text

Demographic history and admixture dynamics in African Sahelian populations

Human Molecular Genetics ◽

10.1093/hmg/ddaa239 ◽

2020 ◽

Author(s):

Viktor Černý ◽

Cesar Fortes-Lima ◽

Petr Tříska

Keyword(s):

Demographic History ◽

Distribution Patterns ◽

Human Populations ◽

African Region ◽

Genetic Studies ◽

Genomic Studies ◽

History Of ◽

Sub Saharan ◽

High Degree ◽

The Impact

Abstract The Sahel/Savannah belt of Africa is a contact zone between two subsistence systems (nomadic pastoralism and sedentary farming) and of two groups of populations, namely Eurasians penetrating from northern Africa southwards and sub-Saharan Africans migrating northwards. Because pastoralism is characterised by a high degree of mobility, it leaves few significant archaeological traces. Demographic history seen through the lens of population genetic studies complements our historical and archaeological knowledge in this African region. In this review, we highlight recent advances in our understanding of demographic history in the Sahel/Savannah belt as revealed by genetic studies. We show the impact of food-producing subsistence strategies on population structure as well as the somewhat different migration patterns in the western and eastern part of the region. Genomic studies show that the gene pool of various groups of Sahelians consists in a complex mosaic of several ancestries. We also touch upon various signals of genetic adaptations such as lactase persistence, taste sensitivity, and malaria resistance, all of which have different distribution patterns among Sahelian populations. Overall, genetic studies contribute to gain a deeper understanding about the demographic and adaptive history of human populations in this specific African region and beyond.

Download Full-text

The genetic structure of the world’s first farmers

10.1101/059311 ◽

2016 ◽

Cited By ~ 3

Author(s):

Iosif Lazaridis ◽

Dani Nadel ◽

Gary Rollefson ◽

Deborah C. Merrett ◽

Nadin Rohland ◽

...

Keyword(s):

Bronze Age ◽

Near East ◽

Zagros Mountains ◽

Hunter Gatherers ◽

Near Eastern ◽

Eurasian Steppe ◽

Neanderthal Admixture ◽

Eurasian Lineage ◽

Early Farmers ◽

The Impact

We report genome-wide ancient DNA from 44 ancient Near Easterners ranging in time between ~12,000-1,400 BCE, from Natufian hunter-gatherers to Bronze Age farmers. We show that the earliest populations of the Near East derived around half their ancestry from a ‘Basal Eurasian’ lineage that had little if any Neanderthal admixture and that separated from other non-African lineages prior to their separation from each other. The first farmers of the southern Levant (Israel and Jordan) and Zagros Mountains (Iran) were strongly genetically differentiated, and each descended from local hunter-gatherers. By the time of the Bronze Age, these two populations and Anatolian-related farmers had mixed with each other and with the hunter-gatherers of Europe to drastically reduce genetic differentiation. The impact of the Near Eastern farmers extended beyond the Near East: farmers related to those of Anatolia spread westward into Europe; farmers related to those of the Levant spread southward into East Africa; farmers related to those from Iran spread northward into the Eurasian steppe; and people related to both the early farmers of Iran and to the pastoralists of the Eurasian steppe spread eastward into South Asia.

Download Full-text

The impact of biases in mobile phone ownership on estimates of human mobility

Journal of The Royal Society Interface ◽

10.1098/rsif.2012.0986 ◽

2013 ◽

Vol 10 (81) ◽

pp. 20120986 ◽

Cited By ~ 87

Author(s):

Amy Wesolowski ◽

Nathan Eagle ◽

Abdisalan M. Noor ◽

Robert W. Snow ◽

Caroline O. Buckee

Keyword(s):

Mobile Phone ◽

Human Mobility ◽

Population Level ◽

Time Frame ◽

Data Sources ◽

Mobile Phone Data ◽

Human Populations ◽

Mobility Patterns ◽

Wide Range ◽

The Impact

Mobile phone data are increasingly being used to quantify the movements of human populations for a wide range of social, scientific and public health research. However, making population-level inferences using these data is complicated by differential ownership of phones among different demographic groups that may exhibit variable mobility. Here, we quantify the effects of ownership bias on mobility estimates by coupling two data sources from the same country during the same time frame. We analyse mobility patterns from one of the largest mobile phone datasets studied, representing the daily movements of nearly 15 million individuals in Kenya over the course of a year. We couple this analysis with the results from a survey of socioeconomic status, mobile phone ownership and usage patterns across the country, providing regional estimates of population distributions of income, reported airtime expenditure and actual airtime expenditure across the country. We match the two data sources and show that mobility estimates are surprisingly robust to the substantial biases in phone ownership across different geographical and socioeconomic groups.

Download Full-text

The demographic history and mutational load of African hunter-gatherers and farmers

10.1101/131219 ◽

2017 ◽

Author(s):

Marie Lopez ◽

Athanasios Kousathanas ◽

Hélène Quach ◽

Christine Harmant ◽

Patrick Mouguiama-Daouda ◽

...

Keyword(s):

Genetic Variation ◽

Gene Flow ◽

Demographic History ◽

Purifying Selection ◽

Human Populations ◽

Mutational Load ◽

Sequencing Data ◽

Hunter Gatherers ◽

African Populations ◽

The Impact

AbstractThe distribution of deleterious genetic variation across human populations is a key issue in evolutionary biology and medical genetics. However, the impact of different modes of subsistence on recent changes in population size, patterns of gene flow, and deleterious mutational load remains unclear. Here, we report high-coverage exome sequencing data from various populations of rainforest hunter-gatherers and farmers from central Africa. We find that the recent demographic histories of hunter-gatherers and farmers differed considerably, with population collapses for hunter-gatherers and expansions for farmers, accompanied by increased gene flow. We show that purifying selection against deleterious alleles is of similar efficiency across African populations, in contrast with Europeans where we detect weaker purifying selection. Furthermore, the per-individual mutation load of rainforest hunter-gatherers is similar to that of farmers, under both additive and recessive models. Our results indicate that differences in the cultural practices and demographic regimes of African populations have not resulted in large differences in mutational burden, and highlight the beneficial role of gene flow in reshaping the distribution of deleterious genetic variation across human populations.

Download Full-text

The Late Glacial ancestry of Europeans: combining genetic and archaeological evidence

Documenta Praehistorica ◽

10.4312/dp.33.1 ◽

2006 ◽

Vol 33 ◽

pp. 1-10 ◽

Cited By ~ 5

Author(s):

Clive Gamble ◽

William Davies ◽

Paul Pettitt ◽

Lee Hazelwood ◽

Martin Richards

Keyword(s):

Western Europe ◽

Demographic History ◽

Ice Core ◽

Late Glacial ◽

Ice Age ◽

Human Populations ◽

Fine Grained ◽

The North ◽

Archaeological Cultures ◽

The Impact

Chronometric attention in the Late Glacial of Western Europe is turning from the dating of archaeological cultures to studying how the continent was re-populated at the end of the last ice age. We present results from a survey of all available radiocarbon determinations (the S2AGES database) which show that when calibrated, and compared to the GRIP stratotype of climatic events, the data can be interpreted as five population events in the 15ka prior to the onset of the Holocene. The fine-grained climate record provides an opportunity to study the impact of environmental factors on a human dispersal process that not only shaped subsequent European prehistory, but also the genetic makeup of modern Europeans. The population events have implications for archaeologists and molecular geneticists concerning the timing, direction, speed and scale of processes in Western European demographic history. The results also bear on the role of climatic forcing on the expansion and contraction of human populations and in particular the correlation of ice core and terrestrial records for the onset of warming in the North Atlantic.

Download Full-text

Coming-of-Age Cinema in New Zealand

10.3366/edinburgh/9781474429443.001.0001 ◽

2017 ◽

Author(s):

Alistair Fox

Keyword(s):

Coming Of Age ◽

Belief Systems ◽

Time Frame ◽

New Wave ◽

Art Cinema ◽

Literary Sources ◽

French New Wave ◽

Significant Phenomenon ◽

The Impact ◽

New Zealanders

This book investigates the coming-of-age genre as a significant phenomenon in New Zealand’s national cinema, tracing its development from the 1970s to the present day. A preliminary chapter identifies the characteristics of the coming-of-age film as a genre, tracing its evolution and the influence of the French New Wave and European Art Cinema, and speculating on the role of the genre in the output of national cinemas. Through case studies of fifteen significant films, including The God Boy, Sleeping Dogs, The Scarecrow, Vigil, Mauri, An Angel at My Table, Heavenly Creatures, Once Were Warriors, Rain, Whale Rider, In My Father’s Den, 50 Ways of Saying Fabulous, Boy, Mahana, and Hunt for the Wilderpeople, subsequent chapters examine thematic preoccupations of filmmakers such as the impact of repressive belief systems and social codes, the experience of cultural dislocation, the expression of a Māori perspective through an indigenous “Fourth Cinema,” bicultural relationships, and issues of sexual identity, arguing that these films provide a unique insight into the cultural formation of New Zealanders. Given that the majority of films are adaptations of literary sources, the book also explores the dialogue each film conducts with the nation’s literature, showing how the time frame of each film is updated in a way that allows these films to be considered as a register of important cultural shifts that have occurred as New Zealanders have sought to discover their emerging national identity.

Download Full-text

Systematic benchmark of ancient DNA read mapping

Briefings in Bioinformatics ◽

10.1093/bib/bbab076 ◽

2021 ◽

Author(s):

Adrien Oliva ◽

Raymond Tobler ◽

Alan Cooper ◽

Bastien Llamas ◽

Yassine Souilmi

Keyword(s):

Ancient Dna ◽

Dna Sequences ◽

Population Genetic ◽

Reference Genome ◽

Population Data ◽

Human Populations ◽

Current Standard ◽

Read Mapping ◽

Reference Bias ◽

The Impact

Abstract The current standard practice for assembling individual genomes involves mapping millions of short DNA sequences (also known as DNA ‘reads’) against a pre-constructed reference genome. Mapping vast amounts of short reads in a timely manner is a computationally challenging task that inevitably produces artefacts, including biases against alleles not found in the reference genome. This reference bias and other mapping artefacts are expected to be exacerbated in ancient DNA (aDNA) studies, which rely on the analysis of low quantities of damaged and very short DNA fragments (~30–80 bp). Nevertheless, the current gold-standard mapping strategies for aDNA studies have effectively remained unchanged for nearly a decade, during which time new software has emerged. In this study, we used simulated aDNA reads from three different human populations to benchmark the performance of 30 distinct mapping strategies implemented across four different read mapping software—BWA-aln, BWA-mem, NovoAlign and Bowtie2—and quantified the impact of reference bias in downstream population genetic analyses. We show that specific NovoAlign, BWA-aln and BWA-mem parameterizations achieve high mapping precision with low levels of reference bias, particularly after filtering out reads with low mapping qualities. However, unbiased NovoAlign results required the use of an IUPAC reference genome. While relevant only to aDNA projects where reference population data are available, the benefit of using an IUPAC reference demonstrates the value of incorporating population genetic information into the aDNA mapping process, echoing recent results based on graph genome representations.

Download Full-text