scholarly journals Effect of population structure and migration when investigating genetic continuity using ancient DNA

2016 ◽  
Author(s):  
NM Silva ◽  
S Kreutzer ◽  
C Papageorgopoulou ◽  
M Currat
Keyword(s):  
Population Structure ◽  
Ancient Dna ◽  
Isolated Populations ◽  
Hunter Gatherers ◽  
History Of ◽  
Genetic Continuity ◽  
Population Continuity ◽  
Local Hunter ◽  
And Migration ◽  
Genetic Pool

AbstractRecent advances in sequencing techniques provide means to access direct genetic snapshots from the past with ancient DNA data (aDNA) from diverse periods of human prehistory. Comparing samples taken in the same region but at different time periods may indicate if there is continuity in the peopling history of that area or if a large genetic input, such as an immigration wave, has occurred. Here we propose a new modeling approach for investigating population continuity using aDNA, including two fundamental elements in human evolution that were absent from previous methods: population structure and migration. The method also considers the extensive temporal and geographic heterogeneity commonly found in aDNA datasets. We compare our spatially-explicit approach to the previous non-spatial method and show that it is more conservative and thus suitable for testing population continuity, especially when small, isolated populations, such as prehistoric ones, are considered. Moreover, our approach also allows investigating partial population continuity and we apply it to a real dataset of ancient mitochondrial DNA. We estimate that 91% of the current genetic pool in central Europe entered the area with immigrant Neolithic farmers, but a genetic contribution of local hunter-gatherers as large as 83% cannot be entirely ruled out.

scholarly journals The Genomic History Of Southeastern Europe

2017 ◽  
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.

Isonymy and population structure of Irish isolates during the 1890s

1982 ◽  
Vol 14 (2) ◽  
pp. 241-247 ◽  
Author(s):  
John H. Relethford
Keyword(s):  
Population Structure ◽  
Genetic Variation ◽  
Isolation By Distance ◽  
Breeding Population ◽  
Isolated Populations ◽  
Estimated Parameters ◽  
Distance Model ◽  
Local Breeding ◽  
And Migration ◽  
Close Fit

SummaryThe estimation of genetic similarity from correspondence of surnames (isonymy) allows investigation of historical population structure. This study uses surname data from seven isolates located along the west coast of Ireland during the 1890s to assess geographic and historic influences on population structure. Observed genetic variation among populations shows a close fit with the expected isolation by distance model, with estimated parameters of isolation and migration being similar to those obtained in other studies of isolated populations. Local genetic variation appears to be due primarily to the size of the local breeding population, with deviations being explained in terms of recent emigration.

scholarly journals Andronovo Problem: Studies of Cultural Genesis in the Eurasian Bronze Age

2021 ◽  
Vol 7 (1) ◽  
pp. 3-36
Author(s):  
Stanislav Grigoriev
Keyword(s):  
Bronze Age ◽  
Early Stage ◽  
Forest Steppe ◽  
Scientific Terminology ◽  
Long Time ◽  
History Of ◽  
Genetic Continuity ◽  
And Migration ◽  
Cultural Genesis ◽  
The Bronze Age

Abstract Andronovo culture is the largest Eurasian formation in the Bronze Age, and it had a significant impact on neighboring regions. It is the important culture for understanding many historical processes, in particular, the origins and migration of Indo-Europeans. However, in most works there is a very simplified understanding of the scientific problems associated with this culture. The history of its study is full of opposing opinions, and all these opinions were based on reliable grounds. For a long time, the existence of the Andronovo problem was caused by the fact that researchers supposed they might explain general processes by local situations. In fact, the term “Andronovo culture” is incorrect. Another term “Andronovo cultural-historical commonality” also has no signs of scientific terminology. Under these terms a large number of cultures are combined, many of which were not related to each other. In the most simplified form, they can be combined into two blocks that existed during the Bronze Age: the steppe (Sintashta, Petrovka, Alakul, Sargari) and the forest-steppe (Fyodorovka, Cherkaskul, Mezhovka). Often these cultures are placed in vertical lines with genetic continuity. However, the problems of their chronology and interaction are very complicated. By Andronovo cultures we may understand only Fyodorovka and Alakul cultures (except for its early stage); however, it is better to avoid the use of this term.

scholarly journals Genetic characteristics and migration history of a bronze culture population in the West Liao-River valley revealed by ancient DNA

2011 ◽  
Vol 56 (12) ◽  
pp. 815-822 ◽  
Author(s):  
Hongjie Li ◽  
Xin Zhao ◽  
Yongbin Zhao ◽  
Chunxiang Li ◽  
Dayong Si ◽  
...  
Keyword(s):  
Ancient Dna ◽  
River Valley ◽  
The West ◽  
Genetic Characteristics ◽  
Migration History ◽  
History Of ◽  
And Migration

scholarly journals Population dynamics in the Japanese Archipelago since the Pleistocene

2021 ◽  
Author(s):  
Fuzuki Mizuno ◽  
Jun Gojobori ◽  
Masahiko Kumagai ◽  
Hisao Baba ◽  
Yasuhiro Taniguchi ◽  
...  
Keyword(s):  
Demographic History ◽  
Cultural Transition ◽  
Rice Agriculture ◽  
Hunter Gatherers ◽  
Japanese Archipelago ◽  
Mitogenome Sequence ◽  
History Of ◽  
Complete Mitogenome ◽  
Genetic Continuity ◽  
The Japanese Archipelago

Abstract The Japanese Archipelago is widely covered with acidic soil made of volcanic ash, an environment which is detrimental to the preservation of ancient biomolecules. More than 10,000 Palaeolithic and Neolithic sites have been discovered nationwide, but few skeletal remains exist and preservation of DNA is poor. Despite these challenging circumstances, we succeeded in obtaining a complete mitogenome sequence from Palaeolithic human remains. We also obtained those of Neolithic (hunting-gathering Jomon and the farming Yayoi cultures) remains, and over 2,000 present-day Japanese. The Palaeolithic mitogenome is potentially an ancestral type of haplogroup M, suggesting it is not only connected to present-day Japanese but also present-day East Asians. There were no changes in the gene pool from the hunting-gathering (Jomon) to the farming cultures (Yayoi), and this is different from in Europe, where there was no genetic continuity between hunter-gatherers and farmers. We also found that a vast increase of population size happened and has continued since the Yayoi period, characterized with paddy rice farming. It means that the cultural transition, i.e. rice agriculture, had significant impact on the demographic history of Japanese population.

scholarly journals Parallel paleogenomic transects reveal complex genetic history of early European farmers

2017 ◽  
Author(s):  
Mark Lipson ◽  
Anna Szécsényi-Nagy ◽  
Swapan Mallick ◽  
Annamária Pósa ◽  
Balázs Stégmár ◽  
...  
Keyword(s):  
Ancient Dna ◽  
Temporal Dynamics ◽  
Neolithic Period ◽  
Hunter Gatherers ◽  
Data Set ◽  
Open Questions ◽  
Dynamics Of Population ◽  
History Of ◽  
Population Interactions ◽  
Almost All

Ancient DNA studies have established that European Neolithic populations were descended from Anatolian migrants who received a limited amount of admixture from resident hunter-gatherers. Many open questions remain, however, about the spatial and temporal dynamics of population interactions and admixture during the Neolithic period. Using the highest-resolution genome-wide ancient DNA data set assembled to date—a total of 177 samples, 127 newly reported here, from the Neolithic and Chalcolithic of Hungary (6000–2900 BCE,n= 98), Germany (5500–3000 BCE,n= 42), and Spain (5500–2200 BCE,n= 37)—we investigate the population dynamics of Neolithization across Europe. We find that genetic diversity was shaped predominantly by local processes, with varied sources and proportions of hunter-gatherer ances try among the three regions and through time. Admixture between groups with different ancestry profiles was pervasive and resulted in observable population transformation across almost all cultural transitions. Our results shed new light on the ways that gene flow reshaped European populations throughout the Neolithic period and demonstrate the potential of time-series-based sampling and modeling approaches to elucidate multiple dimensions of historical population interactions.

scholarly journals Revisiting the demographic history of Central African populations from a genetic perspective

2021 ◽  
pp. 1-29
Author(s):  
Gwenna Breton ◽  
Cesar Fortes-Lima ◽  
Carina M. Schlebusch
Keyword(s):  
Ancient Dna ◽  
Central African Republic ◽  
Genetic Distances ◽  
Population History ◽  
African History ◽  
Hunter Gatherers ◽  
African Populations ◽  
Pilot Investigation ◽  
History Of ◽  
African Pygmies

Africa is the continent of our species’ origin and the deep history of humans is represented by African genetic variation. Through genetic studies, it has become evident that deep African population history is captured by relationships among African hunter-gatherers and that the world’s deepest population divergences occur among these groups. In this review, we look back at a study published by Cavalli-Sforza and colleagues in 1969 entitled “Studies on African Pygmies. I. A pilot investigation of Babinga Pygmies in the Central African Republic (with an analysis of genetic distances)”. The study analyzed 19 classical polymorphisms and found that the deepest divergences in African populations were represented by hunter-gatherer groups such as the southern African San and the central African rainforest hunter-gatherers. We repeated the original analyses from Cavalli-Sforza et al. [1] with about 22 thousand times more genome-wide genetic markers in populations similar to those included in the original study. Our high-resolution analyses gave similar results regarding the relationships of early-diverging African populations compared to the classical polymorphism analyses. This finding, however, does not imply that research has stagnated and that developments in technology and genetic methods over the last fifty years delivered no additional information regarding African history and adaptation. We review how technology and population genetic methods have advanced to give more detailed inferences about population structure, migrations, admixture patterns, timing of admixture, sex-biased admixture, and inferences of selection and adaptive introgression in rainforest hunter-gatherers and other African populations. We also comment on how sequencing of ancient DNA has influenced findings and deliberate on the progress and development of more complex models of African history, including alternatives to tree-models and the inference of possible archaic admixture in African populations. We review the growing complexity of our picture of population history in central Africa and Africa as a whole, emerging from genomic studies and other disciplines investigating human population history and adaptation. While data and knowledge are accumulating, certain populations and areas remain underrepresented in genomic research. Their inclusion, possibly also through ancient DNA studies, together with new methods of analysis and the testing of representative models of deep population history in Africa, will help to build a more complete picture of past population history in Africa. Based on “Cavalli-Sforza LL, Zonta LA, Nuzzo F, Bernini L, de Jong WW, Meera Khan P, Ray AK, Went LN, Siniscalco M, Nijenhuis LE, van Loghem E, Modiano G. Studies on African Pygmies. I. A pilot investigation of Babinga Pygmies in the Central African Republic (with an analysis of genetic distances). Am J Hum Genet. 1969 May;21(3):252-274”.

Historical population structure of two Tasmanian communities using surname analyses

1983 ◽  
Vol 15 (3) ◽  
pp. 367-376 ◽  
Author(s):  
M. Kosten ◽  
J. Williams ◽  
R. J. Mitchell
Keyword(s):  
Nineteenth Century ◽  
Population Structure ◽  
Sex Ratio ◽  
Census Data ◽  
Political History ◽  
Short History ◽  
Vital Records ◽  
History Of ◽  
Genetic Continuity ◽  
Very High

SummaryThis paper reports the first data on historical population structure in white Australians. Vital records and census data from two Tasmanian registration districts, Oatlands and Bothwell, were examined using surname analysis to investigate population structure in the nineteenth century. Both were colonising populations and therefore initially had massive immigration and a very high sex ratio. Inbreeding, as measured by marital isonymy, was relatively high in Oatlands, especially in the context of its short history. Although genetic continuity, measured by surname constancy, was relatively low, a small but distinct core was detectable. Bothwell, the smaller community, exhibited very little inbreeding and, concomitantly, low surname constancy. The coefficient of relationship by isonymy between Oatlands and Bothwell was extremely low. These findings are discussed in the context of the known socio-political history of this region of Tasmania.

scholarly journals Ancient genomes from North Africa evidence prehistoric migrations to the Maghreb from both the Levant and Europe

2018 ◽  
Vol 115 (26) ◽  
pp. 6774-6779 ◽  
Author(s):  
Rosa Fregel ◽  
Fernando L. Méndez ◽  
Youssef Bokbot ◽  
Dimas Martín-Socas ◽  
María D. Camalich-Massieu ◽  
...  
Keyword(s):  
North Africa ◽  
Eastern Mediterranean ◽  
Early Neolithic ◽  
Late Neolithic ◽  
Hunter Gatherers ◽  
Adoption Of Innovations ◽  
Neolithic Culture ◽  
Southern Iberia ◽  
Genetic Continuity ◽  
Genetic Pool

The extent to which prehistoric migrations of farmers influenced the genetic pool of western North Africans remains unclear. Archaeological evidence suggests that the Neolithization process may have happened through the adoption of innovations by local Epipaleolithic communities or by demic diffusion from the Eastern Mediterranean shores or Iberia. Here, we present an analysis of individuals’ genome sequences from Early and Late Neolithic sites in Morocco and from Early Neolithic individuals from southern Iberia. We show that Early Neolithic Moroccans (∼5,000 BCE) are similar to Later Stone Age individuals from the same region and possess an endemic element retained in present-day Maghrebi populations, confirming a long-term genetic continuity in the region. This scenario is consistent with Early Neolithic traditions in North Africa deriving from Epipaleolithic communities that adopted certain agricultural techniques from neighboring populations. Among Eurasian ancient populations, Early Neolithic Moroccans are distantly related to Levantine Natufian hunter-gatherers (∼9,000 BCE) and Pre-Pottery Neolithic farmers (∼6,500 BCE). Late Neolithic (∼3,000 BCE) Moroccans, in contrast, share an Iberian component, supporting theories of trans-Gibraltar gene flow and indicating that Neolithization of North Africa involved both the movement of ideas and people. Lastly, the southern Iberian Early Neolithic samples share the same genetic composition as the Cardial Mediterranean Neolithic culture that reached Iberia ∼5,500 BCE. The cultural and genetic similarities between Iberian and North African Neolithic traditions further reinforce the model of an Iberian migration into the Maghreb.

Intraocular tuberculosis, a challenge in diagnosis and treatment

2020 ◽  
Vol 3 ◽  
pp. 4
Author(s):  
Martina Larroude ◽  
Gustavo Ariel Budmann
Keyword(s):  
Developing Countries ◽  
Clinical Signs ◽  
Steady Increase ◽  
Ocular Tuberculosis ◽  
Industrial Countries ◽  
Choroidal Granuloma ◽  
History Of ◽  
And Migration ◽  
Ocular Tb

Ocular tuberculosis (TB) is an extrapulmonary tuberculous condition and has variable manifestations. The incidence of TB is still high in developing countries, and a steady increase in new cases has been observed in industrial countries as a result of the growing number of immunodeficient patients and migration from developing countries. Choroidal granuloma is a rare and atypical location of TB. We present a case of a presumptive choroidal granuloma. This case exposes that diagnosis can be remarkably challenging when there is no history of pulmonary TB. The recognition of clinical signs of ocular TB is extremely important since it provides a clinical pathway toward tailored investigations and decision making for initiating anti-TB therapy and to ensure a close follow-up to detect the development of any complication.

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