On the Trail of Spatial Patterns of Genetic Variation

Evolutionary Biology ◽

10.1007/s11692-021-09552-y ◽

2021 ◽

Author(s):

José A. Peña ◽

Luis Gómez-Pérez ◽

Miguel A. Alfonso-Sánchez

Keyword(s):

Genetic Variation ◽

Evolutionary Biology ◽

Isolation By Distance ◽

Accurate Determination ◽

Data Entry ◽

Centroid Method ◽

Genome Wide ◽

Genome Wide Data ◽

History Of

AbstractThe accurate determination of the spatial trends on the variability of a species’ gene pool is essential to elucidate the underlying demographic-evolutionary events, thus helping to unravel the microevolutionary history of the population under study. Herein we present a new software called GenoCline, mainly addressed to detect genetic clines from allele, haplotype, and genome-wide data. This program package allows identifying the geographic orientation of clinal genetic variation through a system of iterative rotation of a virtual coordinate axis. Besides, GenoCline can perform complementary analyses to explore the potential origin of the genetic clines observed, including spatial autocorrelation, isolation by distance, centroid method, multidimensional scaling and Sammon projection. Among the advantages of this software is the ease in data entry and potential interconnection with other programs. Genetic and geographic data can be entered in spreadsheet table formatting (.xls), whereas genome-wide data can be imported in Eigensoft format. Genetic frequencies can also be exported in a format compatible with other programs dealing with population genetic and evolutionary biology analyses. All illustrations of results are saved in.svg format so that there will be high quality and easily editable vectorial graphs available for the researcher. Being implemented in Java, GenoCline is highly portable, thus working in different operating systems.

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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 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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Does Adaptive Protein Evolution Proceed by Large or Small Steps at the Amino Acid Level?

10.1101/379073 ◽

2018 ◽

Cited By ~ 1

Author(s):

Juraj Bergman ◽

Adam Eyre-Walker

Keyword(s):

Amino Acids ◽

Adaptive Evolution ◽

Evolutionary Biology ◽

Amino Acid Level ◽

Neutral Evolution ◽

Relative Contribution ◽

Mutational Step ◽

Genome Wide ◽

Genome Wide Data ◽

Evolution Of Proteins

AbstractA longstanding question in evolutionary biology is the relative contribution of large and small effect mutations to the adaptive process. We have investigated this question in proteins by estimating the rate of adaptive evolution between all pairs of amino acids separated by one mutational step using a McDonald-Kreitman type approach and genome-wide data from several Drosophila species. We find that the rate of adaptive evolution is higher amongst amino acids that are more similar. This is partly due to the fact that the proportion of mutations that are adaptive is higher amongst more similar amino acids. We also find that the rate of neutral evolution between amino acids is higher amongst similar amino acids. Overall our results suggest that both the adaptive and non-adaptive evolution of proteins is dominated by substitutions between amino acids that are more similar.

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Reconstructing the demographic history of divergence between European river and brook lampreys using approximate Bayesian computations

PeerJ ◽

10.7717/peerj.1910 ◽

2016 ◽

Vol 4 ◽

pp. e1910 ◽

Cited By ~ 17

Author(s):

Quentin Rougemont ◽

Camille Roux ◽

Samuel Neuenschwander ◽

Jerome Goudet ◽

Sophie Launey ◽

...

Keyword(s):

Gene Flow ◽

Life Histories ◽

Evolutionary Biology ◽

Demographic History ◽

Secondary Contact ◽

Isolation With Migration ◽

Genome Wide Data ◽

History Of ◽

Parameterized Model ◽

Approximate Bayesian

Inferring the history of isolation and gene flow during species divergence is a central question in evolutionary biology. The European river lamprey (Lampetra fluviatilis) and brook lamprey(L. planeri)show a low reproductive isolation but have highly distinct life histories, the former being parasitic-anadromous and the latter non-parasitic and freshwater resident. Here we used microsatellite data from six replicated population pairs to reconstruct their history of divergence using an approximate Bayesian computation framework combined with a random forest model. In most population pairs, scenarios of divergence with recent isolation were outcompeted by scenarios proposing ongoing gene flow, namely the Secondary Contact (SC) and Isolation with Migration (IM) models. The estimation of demographic parameters under the SC model indicated a time of secondary contact close to the time of speciation, explaining why SC and IM models could not be discriminated. In case of an ancient secondary contact, the historical signal of divergence is lost and neutral markers converge to the same equilibrium as under the less parameterized model allowing ongoing gene flow. Our results imply that models of secondary contacts should be systematically compared to models of divergence with gene flow; given the difficulty to discriminate among these models, we suggest that genome-wide data are needed to adequately reconstruct divergence history.

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

10.1101/003517 ◽

2014 ◽

Cited By ~ 1

Author(s):

Joseph Pickrell ◽

David Reich

Keyword(s):

Natural Selection ◽

Ancient Dna ◽

Population Replacement ◽

Local Conditions ◽

Geographic Locations ◽

Technological Advances ◽

Genome Wide ◽

Human Genes ◽

Genome Wide Data ◽

History Of

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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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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Extensive Ethnolinguistic Diversity in Vietnam Reflects Multiple Sources of Genetic Diversity

Molecular Biology and Evolution ◽

10.1093/molbev/msaa099 ◽

2020 ◽

Vol 37 (9) ◽

pp. 2503-2519 ◽

Cited By ~ 4

Author(s):

Dang Liu ◽

Nguyen Thuy Duong ◽

Nguyen Dang Ton ◽

Nguyen Van Phong ◽

Brigitte Pakendorf ◽

...

Keyword(s):

Genetic Diversity ◽

Southeast Asia ◽

Linguistic Diversity ◽

Published Data ◽

Multiple Sources ◽

Austronesian Languages ◽

Genome Wide ◽

Genome Wide Data ◽

History Of ◽

Mainland Southeast Asia

Abstract Vietnam features extensive ethnolinguistic diversity and occupies a key position in Mainland Southeast Asia. Yet, the genetic diversity of Vietnam remains relatively unexplored, especially with genome-wide data, because previous studies have focused mainly on the majority Kinh group. Here, we analyze newly generated genome-wide single-nucleotide polymorphism data for the Kinh and 21 additional ethnic groups in Vietnam, encompassing all five major language families in Mainland Southeast Asia. In addition to analyzing the allele and haplotype sharing within the Vietnamese groups, we incorporate published data from both nearby modern populations and ancient samples for comparison. In contrast to previous studies that suggested a largely indigenous origin for Vietnamese genetic diversity, we find that Vietnamese ethnolinguistic groups harbor multiple sources of genetic diversity that likely reflect different sources for the ancestry associated with each language family. However, linguistic diversity does not completely match genetic diversity: There have been extensive interactions between the Hmong-Mien and Tai-Kadai groups; different Austro-Asiatic groups show different affinities with other ethnolinguistic groups; and we identified a likely case of cultural diffusion in which some Austro-Asiatic groups shifted to Austronesian languages during the past 2,500 years. Overall, our results highlight the importance of genome-wide data from dense sampling of ethnolinguistic groups in providing new insights into the genetic diversity and history of an ethnolinguistically diverse region, such as Vietnam.

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