Towards a new history and geography of human genes informed by ancient DNA

Genetic information contains a record of the history of our species, and technological advances have transformed our ability to access this record. Many studies have used genome-wide data from populations today to learn about the peopling of the globe and subsequent adaptation to local conditions. Implicit in this research is the assumption that the geographic locations of people today are informative about the geographic locations of their ancestors in the distant past. However, it is now clear that long-range migration, admixture and population replacement have been the rule rather than the exception in human history. In light of this, we argue that it is time to critically re-evaluate current views of the peopling of the globe and the importance of natural selection in determining the geographic distribution of phenotypes. We specifically highlight the transformative potential of ancient DNA. By accessing the genetic make-up of populations living at archaeologically-known times and places, ancient DNA makes it possible to directly track migrations and responses to natural selection.

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Population Replacement in Early Neolithic Britain

10.1101/267443 ◽

2018 ◽

Cited By ~ 10

Author(s):

Selina Brace ◽

Yoan Diekmann ◽

Thomas J. Booth ◽

Zuzana Faltyskova ◽

Nadin Rohland ◽

...

Keyword(s):

Ancient Dna ◽

Genomic Data ◽

Early Neolithic ◽

Genetic Affinity ◽

Hunter Gatherers ◽

Population Replacement ◽

Neolithic Transition ◽

Genome Wide ◽

Genome Wide Data ◽

Neolithic Cultures

The roles of migration, admixture and acculturation in the European transition to farming have been debated for over 100 years. Genome-wide ancient DNA studies indicate predominantly Anatolian ancestry for continental Neolithic farmers, but also variable admixture with local Mesolithic hunter-gatherers1–9. Neolithic cultures first appear in Britain c. 6000 years ago (kBP), a millennium after they appear in adjacent areas of northwestern continental Europe. However, the pattern and process of the British Neolithic transition remains unclear10–15. We assembled genome-wide data from six Mesolithic and 67 Neolithic individuals found in Britain, dating from 10.5-4.5 kBP, a dataset that includes 22 newly reported individuals and the first genomic data from British Mesolithic hunter-gatherers. Our analyses reveals persistent genetic affinities between Mesolithic British and Western European hunter-gatherers over a period spanning Britain’s separation from continental Europe. We find overwhelming support for agriculture being introduced by incoming continental farmers, with small and geographically structured levels of additional hunter-gatherer introgression. We find genetic affinity between British and Iberian Neolithic populations indicating that British Neolithic people derived much of their ancestry from Anatolian farmers who originally followed the Mediterranean route of dispersal and likely entered Britain from northwestern mainland Europe.

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Ancient genomic time transect from the Central Asian Steppe unravels the history of the Scythians

Science Advances ◽

10.1126/sciadv.abe4414 ◽

2021 ◽

Vol 7 (13) ◽

pp. eabe4414

Author(s):

Guido Alberto Gnecchi-Ruscone ◽

Elmira Khussainova ◽

Nurzhibek Kahbatkyzy ◽

Lyazzat Musralina ◽

Maria A. Spyrou ◽

...

Keyword(s):

Bronze Age ◽

Iron Age ◽

Gene Pools ◽

Social Rules ◽

Eurasian Steppe ◽

Central Asian ◽

Genome Wide ◽

Genome Wide Data ◽

History Of ◽

First Millennium

The Scythians were a multitude of horse-warrior nomad cultures dwelling in the Eurasian steppe during the first millennium BCE. Because of the lack of first-hand written records, little is known about the origins and relations among the different cultures. To address these questions, we produced genome-wide data for 111 ancient individuals retrieved from 39 archaeological sites from the first millennia BCE and CE across the Central Asian Steppe. We uncovered major admixture events in the Late Bronze Age forming the genetic substratum for two main Iron Age gene-pools emerging around the Altai and the Urals respectively. Their demise was mirrored by new genetic turnovers, linked to the spread of the eastern nomad empires in the first centuries CE. Compared to the high genetic heterogeneity of the past, the homogenization of the present-day Kazakhs gene pool is notable, likely a result of 400 years of strict exogamous social rules.

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Genetic legacy of state centralization in the Kuba Kingdom of the Democratic Republic of the Congo

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1811211115 ◽

2018 ◽

Vol 116 (2) ◽

pp. 593-598 ◽

Cited By ~ 4

Author(s):

Lucy van Dorp ◽

Sara Lowes ◽

Jonathan L. Weigel ◽

Naser Ansari-Pour ◽

Saioa López ◽

...

Keyword(s):

Large Scale ◽

Democratic Republic ◽

Central Province ◽

Genome Wide ◽

Genetic Patterns ◽

Genetic Impact ◽

Genome Wide Data ◽

Republic Of The Congo ◽

History Of ◽

State Centralization

Few phenomena have had as profound or long-lasting consequences in human history as the emergence of large-scale centralized states in the place of smaller scale and more local societies. This study examines a fundamental, and yet unexplored, consequence of state formation: its genetic legacy. We studied the genetic impact of state centralization during the formation of the eminent precolonial Kuba Kingdom of the Democratic Republic of the Congo (DRC) in the 17th century. We analyzed genome-wide data from over 690 individuals sampled from 27 different ethnic groups from the Kasai Central Province of the DRC. By comparing genetic patterns in the present-day Kuba, whose ancestors were part of the Kuba Kingdom, with those in neighboring non-Kuba groups, we show that the Kuba today are more genetically diverse and more similar to other groups in the region than expected, consistent with the historical unification of distinct subgroups during state centralization. We also found evidence of genetic mixing dating to the time of the Kingdom at its most prominent. Using this unique dataset, we characterize the genetic history of the Kasai Central Province and describe the historic late wave of migrations into the region that contributed to a Bantu-like ancestry component found across large parts of Africa today. Taken together, we show the power of genetics to evidence events of sociopolitical importance and highlight how DNA can be used to better understand the behaviors of both people and institutions in the past.

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The Evolution of Lactose Tolerance in Dairying Populations

The Oxford Handbook of the Archaeology of Diet ◽

10.1093/oxfordhb/9780199694013.013.12 ◽

2017 ◽

Author(s):

Pascale Gerbault ◽

Catherine Walker ◽

Katherine Brown ◽

Ekaterina Yonova-Doing ◽

Mark G. Thomas

Keyword(s):

Natural Selection ◽

Ancient Dna ◽

Strong Correlation ◽

Simulation Modelling ◽

Lactase Persistence ◽

Lactose Tolerance ◽

Milk Sugar ◽

Genetic Patterns ◽

History Of

Among the biocultural innovations associated with the Neolithic, dairying and the evolution of lactose tolerance is the most studied. Expression of the enzyme lactase, which digests the milk sugar lactose, decreases after weaning in mammals, including most humans. However, some humans express lactase throughout adulthood—a trait known as lactase persistence (LP). Striking observations about LP evolution include: (i) a strong correlation between LP frequency and a history of herding and dairying; (ii) genetic patterns indicating LP-associated variants have increased in frequency through natural selection; (iii) two of these variants have been experimentally shown to affect lactase expression in adults; and (iv) archaeological and ancient DNA data indicate dairying pre-dated the rise of LP-associated variants. This chapter reviews the biology and archaeology of LP, examines some of the hypotheses formulated to explain its distribution, and outlines how simulation modelling has contributed to our understanding of its evolution.

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The genomic history of the Iberian Peninsula over the past 8000 years

Science ◽

10.1126/science.aav4040 ◽

2019 ◽

Vol 363 (6432) ◽

pp. 1230-1234 ◽

Cited By ~ 84

Author(s):

Iñigo Olalde ◽

Swapan Mallick ◽

Nick Patterson ◽

Nadin Rohland ◽

Vanessa Villalba-Mouco ◽

...

Keyword(s):

Iberian Peninsula ◽

Iron Age ◽

North Africa ◽

Eastern Mediterranean ◽

Hunter Gatherers ◽

Y Chromosomes ◽

Genome Wide ◽

Genome Wide Data ◽

History Of ◽

Genetic Substructure

We assembled genome-wide data from 271 ancient Iberians, of whom 176 are from the largely unsampled period after 2000 BCE, thereby providing a high-resolution time transect of the Iberian Peninsula. We document high genetic substructure between northwestern and southeastern hunter-gatherers before the spread of farming. We reveal sporadic contacts between Iberia and North Africa by ~2500 BCE and, by ~2000 BCE, the replacement of 40% of Iberia’s ancestry and nearly 100% of its Y-chromosomes by people with Steppe ancestry. We show that, in the Iron Age, Steppe ancestry had spread not only into Indo-European–speaking regions but also into non-Indo-European–speaking ones, and we reveal that present-day Basques are best described as a typical Iron Age population without the admixture events that later affected the rest of Iberia. Additionally, we document how, beginning at least in the Roman period, the ancestry of the peninsula was transformed by gene flow from North Africa and the eastern Mediterranean.

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Genome-wide scans provide evidence for positive selection of genes implicated in Lassa fever

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2011.0299 ◽

2012 ◽

Vol 367 (1590) ◽

pp. 868-877 ◽

Cited By ~ 74

Author(s):

Kristian G. Andersen ◽

Ilya Shylakhter ◽

Shervin Tabrizi ◽

Sharon R. Grossman ◽

Christian T. Happi ◽

...

Keyword(s):

Natural Selection ◽

Positive Selection ◽

Lassa Fever ◽

West African ◽

Lassa Virus ◽

Genome Wide ◽

African Populations ◽

Genome Wide Data ◽

Differential Gene ◽

Selection Of

Rapidly evolving viruses and other pathogens can have an immense impact on human evolution as natural selection acts to increase the prevalence of genetic variants providing resistance to disease. With the emergence of large datasets of human genetic variation, we can search for signatures of natural selection in the human genome driven by such disease-causing microorganisms. Based on this approach, we have previously hypothesized that Lassa virus (LASV) may have been a driver of natural selection in West African populations where Lassa haemorrhagic fever is endemic. In this study, we provide further evidence for this notion. By applying tests for selection to genome-wide data from the International Haplotype Map Consortium and the 1000 Genomes Consortium, we demonstrate evidence for positive selection in LARGE and interleukin 21 ( IL21 ), two genes implicated in LASV infectivity and immunity. We further localized the signals of selection, using the recently developed composite of multiple signals method, to introns and putative regulatory regions of those genes. Our results suggest that natural selection may have targeted variants giving rise to alternative splicing or differential gene expression of LARGE and IL21 . Overall, our study supports the hypothesis that selective pressures imposed by LASV may have led to the emergence of particular alleles conferring resistance to Lassa fever, and opens up new avenues of research pursuit.

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A dynamic 6,000-year genetic history of Eurasia’s Eastern Steppe

10.1101/2020.03.25.008078 ◽

2020 ◽

Cited By ~ 4

Author(s):

Choongwon Jeong ◽

Ke Wang ◽

Shevan Wilkin ◽

William Timothy Treal Taylor ◽

Bryan K. Miller ◽

...

Keyword(s):

Bronze Age ◽

Population History ◽

Complex Interplay ◽

Cultural Changes ◽

Genetic History ◽

Nomadic Pastoralists ◽

Eurasian Steppe ◽

Genome Wide ◽

Genome Wide Data ◽

History Of

SummaryThe Eastern Eurasian Steppe was home to historic empires of nomadic pastoralists, including the Xiongnu and the Mongols. However, little is known about the region’s population history. Here we reveal its dynamic genetic history by analyzing new genome-wide data for 214 ancient individuals spanning 6,000 years. We identify a pastoralist expansion into Mongolia ca. 3000 BCE, and by the Late Bronze Age, Mongolian populations were biogeographically structured into three distinct groups, all practicing dairy pastoralism regardless of ancestry. The Xiongnu emerged from the mixing of these populations and those from surrounding regions. By comparison, the Mongols exhibit much higher Eastern Eurasian ancestry, resembling present-day Mongolic-speaking populations. Our results illuminate the complex interplay between genetic, sociopolitical, and cultural changes on the Eastern Steppe.

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Killer whale genomes reveal a complex history of recurrent admixture and vicariance

10.1101/520718 ◽

2019 ◽

Author(s):

Andrew D. Foote ◽

Michael D. Martin ◽

Marie Louis ◽

George Pacheco ◽

Kelly M. Robertson ◽

...

Keyword(s):

Evolutionary History ◽

Killer Whale ◽

Natural Populations ◽

Major Axis ◽

Glacial Cycle ◽

Genome Wide ◽

Complex Population ◽

Genome Wide Data ◽

History Of ◽

Global Population

AbstractReconstruction of the demographic and evolutionary history of populations assuming a consensus tree-like relationship can mask more complex scenarios, which are prevalent in nature. An emerging genomic toolset, which has been most comprehensively harnessed in the reconstruction of human evolutionary history, enables molecular ecologists to elucidate complex population histories. Killer whales have limited extrinsic barriers to dispersal and have radiated globally, and are therefore a good candidate model for the application of such tools. Here, we analyse a global dataset of killer whale genomes in a rare attempt to elucidate global population structure in a non-human species. We identify a pattern of genetic homogenisation at lower latitudes and the greatest differentiation at high latitudes, even between currently sympatric lineages. The processes underlying the major axis of structure include high drift at the edge of species’ range, likely associated with founder effects and allelic surfing during post-glacial range expansion. Divergence between Antarctic and non-Antarctic lineages is further driven by ancestry segments with up to four-fold older coalescence time than the genome-wide average; relicts of a previous vicariance during an earlier glacial cycle. Our study further underpins that episodic gene flow is ubiquitous in natural populations, and can occur across great distances and after substantial periods of isolation between populations. Thus, understanding the evolutionary history of a species requires comprehensive geographic sampling and genome-wide data to sample the variation in ancestry within individuals.

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The Genomic History Of Southeastern Europe

10.1101/135616 ◽

2017 ◽

Cited By ~ 5

Author(s):

Iain Mathieson ◽

Songül Alpaslan Roodenberg ◽

Cosimo Posth ◽

Anna Szécsényi-Nagy ◽

Nadin Rohland ◽

...

Keyword(s):

Genetic Structure ◽

Ancient Dna ◽

Western Europe ◽

Southeastern Europe ◽

Hunter Gatherers ◽

The North ◽

Genome Wide ◽

History Of ◽

East And West ◽

Local Hunter

AbstractFarming was first introduced to southeastern Europe in the mid-7thmillennium BCE – brought by migrants from Anatolia who settled in the region before spreading throughout Europe. To clarify the dynamics of the interaction between the first farmers and indigenous hunter-gatherers where they first met, we analyze genome-wide ancient DNA data from 223 individuals who lived in southeastern Europe and surrounding regions between 12,000 and 500 BCE. We document previously uncharacterized genetic structure, showing a West-East cline of ancestry in hunter-gatherers, and show that some Aegean farmers had ancestry from a different lineage than the northwestern Anatolian lineage that formed the overwhelming ancestry of other European farmers. We show that the first farmers of northern and western Europe passed through southeastern Europe with limited admixture with local hunter-gatherers, but that some groups mixed extensively, with relatively sex-balanced admixture compared to the male-biased hunter-gatherer admixture that prevailed later in the North and West. Southeastern Europe continued to be a nexus between East and West after farming arrived, with intermittent genetic contact from the Steppe up to 2,000 years before the migration that replaced much of northern Europe’s population.

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Ancient DNA

The Science of Roman History ◽

10.23943/princeton/9780691195988.003.0007 ◽

2019 ◽

pp. 205-223

Author(s):

Noreen Tuross ◽

Michael G. Campana

Keyword(s):

Human Genome ◽

Real Time ◽

Case Studies ◽

Ancient Dna ◽

Roman History ◽

Ancient History ◽

Technological Advances ◽

Before And After ◽

History Of ◽

Adna Analysis

This chapter examines how ancient DNA (aDNA) analysis has helped reconstruct ancient history. It focuses in particular on cases investigating Roman history. History leaves traces in the human genome as well as those of pathogens and domesticates. While much can be gleaned from the genetic fossils preserved in extant genomes, genomes are palimpsests, with more recent events overwriting previous ones in part. The study of aDNA—DNA preserved in archaeological, paleontological, and museum sources—permits investigations into the genome before and after historic events and observations into how it evolves in real time. The field of aDNA also has a palimpsestic nature in which older results are not only extended and revised, but totally discarded due to rapid technological advances. The chapter briefly describes biochemistry of ancient DNA and the history of its research. Through several key case studies, it shows the potential for aDNA research to clarify the course of ancient history, and also highlights some of its weaknesses and limitations.

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