Demographic history inferred from genome-wide data reveals two lineages of sheldgeese endemic to a glacial refugium in the southern Atlantic

2016 ◽  
Vol 43 (10) ◽  
pp. 1979-1989 ◽  
Author(s):  
Cecilia Kopuchian ◽  
Leonardo Campagna ◽  
Adrián S. Di Giacomo ◽  
Robert E. Wilson ◽  
Mariana Bulgarella ◽  
...  
Keyword(s):  
Demographic History ◽  
Glacial Refugium ◽  
Genome Wide ◽  
Genome Wide Data

scholarly journals Demographic history shaped geographical patterns of deleterious mutation load in a broadly distributed Pacific Salmon

2019 ◽  
Author(s):  
Quentin Rougemont ◽  
Jean-Sébastien Moore ◽  
Thibault Leroy ◽  
Eric Normandeau ◽  
Eric B. Rondeau ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Coho Salmon ◽  
Pacific Salmon ◽  
Demographic History ◽  
Glacial Refugium ◽  
Human Populations ◽  
Deleterious Mutations ◽  
Effective Population ◽  
Geographical Patterns ◽  
Genome Wide Data

AbstractA thorough reconstruction of historical processes is essential for a comprehensive understanding the mechanisms shaping patterns of genetic diversity. Indeed, past and current conditions influencing effective population size have important evolutionary implications for the efficacy of selection, increased accumulation of deleterious mutations, and loss of adaptive potential. Here, we gather extensive genome-wide data that represent the extant diversity of the Coho salmon (Oncorhynchus kisutch) to address two objectives. We demonstrate that a single glacial refugium is the source of most of the present-day genetic diversity, with detectable inputs from a putative secondary micro-refugium. We found statistical support for a scenario whereby ancestral populations located south of the ice sheets expanded in postglacial time, swamping out most of the diversity from other putative micro-refugia. Demographic inferences revealed that genetic diversity was also affected by linked selection in large parts of the genome. Moreover, we demonstrate that the recent demographic history of this species generated regional differences in the load of deleterious mutations among populations, a finding that mirrors recent results from human populations and provides increased support for models of expansion load. We propose that insights from these historical inferences should be better integrated in conservation planning of wild organisms, which currently focuses largely on neutral genetic diversity and local adaptation, with the role of potentially maladaptive variation being generally ignored.

scholarly journals Genetic substructure and complex demographic history of South African Bantu speakers

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Dhriti Sengupta ◽  
◽  
Ananyo Choudhury ◽  
Cesar Fortes-Lima ◽  
Shaun Aron ◽  
...  
Keyword(s):  
South Africa ◽  
Population Structure ◽  
Iron Age ◽  
Association Studies ◽  
Demographic History ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Scale Population ◽  
Genome Wide Data ◽  
Genetic Substructure

AbstractSouth Eastern Bantu-speaking (SEB) groups constitute more than 80% of the population in South Africa. Despite clear linguistic and geographic diversity, the genetic differences between these groups have not been systematically investigated. Based on genome-wide data of over 5000 individuals, representing eight major SEB groups, we provide strong evidence for fine-scale population structure that broadly aligns with geographic distribution and is also congruent with linguistic phylogeny (separation of Nguni, Sotho-Tswana and Tsonga speakers). Although differential Khoe-San admixture plays a key role, the structure persists after Khoe-San ancestry-masking. The timing of admixture, levels of sex-biased gene flow and population size dynamics also highlight differences in the demographic histories of individual groups. The comparisons with five Iron Age farmer genomes further support genetic continuity over ~400 years in certain regions of the country. Simulated trait genome-wide association studies further show that the observed population structure could have major implications for biomedical genomics research in South Africa.

scholarly journals Novel insights on demographic history of tribal and caste groups from West Maharashtra (India) using genome-wide data

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Guilherme Debortoli ◽  
Cristina Abbatangelo ◽  
Francisco Ceballos ◽  
Cesar Fortes-Lima ◽  
Heather L. Norton ◽  
...  
Keyword(s):  
Demographic History ◽  
Genome Wide ◽  
Genome Wide Data ◽  
History Of ◽  
Caste Groups

scholarly journals Ancient genomes from the last three millennia support multiple human dispersals into Wallacea

2021 ◽  
Author(s):  
Sandra Oliveira ◽  
Kathrin Nägele ◽  
Selina Carlhoff ◽  
Irina Pugach ◽  
Toetik Koesbardiati ◽  
...  
Keyword(s):  
Southeast Asia ◽  
Demographic History ◽  
Island Southeast Asia ◽  
The North ◽  
Complex Interactions ◽  
Time Estimates ◽  
Continental Shelves ◽  
Genome Wide ◽  
Timor Leste ◽  
Genome Wide Data

Previous research indicates that the human genetic diversity found in Wallacea - islands in present-day Eastern Indonesia and Timor-Leste that were never part of the Sunda or Sahul continental shelves - has been shaped by complex interactions between migrating Austronesian farmers and indigenous hunter-gatherer communities. Here, we provide new insights into this region's demographic history based on genome-wide data from 16 ancient individuals (2600-250 yrs BP) from islands of the North Moluccas, Sulawesi, and East Nusa Tenggara. While the ancestry of individuals from the northern islands fit earlier views of contact between groups related to the Austronesian expansion and the first colonization of Sahul, the ancestry of individuals from the southern islands revealed additional contributions from Mainland Southeast Asia, which seems to predate the Austronesian admixture in the region. Admixture time estimates for the oldest individuals of Wallacea are closer to archaeological estimates for the Austronesian arrival into the region than are admixture time estimates for present-day groups. The decreasing trend in admixture times exhibited by younger individuals supports a scenario of multiple or continuous admixture involving Papuan- and Asian-related groups. Our results clarify previously debated times of admixture and suggest that the Neolithic dispersals into Island Southeast Asia are associated with the spread of multiple genetic ancestries.

scholarly journals More rule than exception: Parallel evidence of ancient migrations in grammars and genomes of Finno-Ugric speakers

2020 ◽  
Author(s):  
Patrícia Santos ◽  
Gloria Gonzalez-Fortes ◽  
Emiliano Trucchi ◽  
Andrea Ceolin ◽  
Guido Cordoni ◽  
...  
Keyword(s):  
Demographic History ◽  
Comparative Method ◽  
Population Level ◽  
Syntactic Analysis ◽  
Complex Relation ◽  
Human Demographic History ◽  
Genome Wide ◽  
Genome Wide Data ◽  
Demographic Processes ◽  
North Western

AbstractTo reconstruct aspects of human demographic history, linguistics and genetics complement each other, reciprocally suggesting testable hypotheses on population relationships and interactions. Relying on a linguistic comparative method exclusively based on syntactic data, here we focus on the complex relation of genes and languages among Finno-Ugric (FU) speakers, in comparison to their Indo-European (IE) and Altaic (AL) neighbors. Syntactic analysis supports three distinct clusters corresponding to these three Eurasian families; yet, the outliers of the FU group show linguistic convergence with their geographical neighbors. By analyzing genome-wide data in both ancient and contemporary populations, we uncovered remarkably matching patterns, with north-western FU speakers linguistically and genetically closer in parallel degrees to their IE-speaking neighbors, and eastern FU speakers to AL-speakers. Therefore, our study indicates plausible secondary convergence in the syntax of languages of different families, providing evidence that such interference effects were accompanied, and possibly caused, by recognizable processes at the population level. In particular, based on the comparison of modern and ancient genomes, our analysis identified the Pontic-Caspian steppes as the possible origin of the demographic processes that led to the expansion of the FU into Europe.

scholarly journals Demographic History of Oceania Inferred from Genome-wide Data

2010 ◽  
Vol 20 (22) ◽  
pp. 1983-1992 ◽  
Author(s):  
Andreas Wollstein ◽  
Oscar Lao ◽  
Christian Becker ◽  
Silke Brauer ◽  
Ronald J. Trent ◽  
...  
Keyword(s):  
Demographic History ◽  
Genome Wide ◽  
Genome Wide Data ◽  
History Of

scholarly journals More Rule than Exception: Parallel Evidence of Ancient Migrations in Grammars and Genomes of Finno-Ugric Speakers

Genes ◽  
2020 ◽  
Vol 11 (12) ◽  
pp. 1491
Author(s):  
Patrícia Santos ◽  
Gloria Gonzàlez-Fortes ◽  
Emiliano Trucchi ◽  
Andrea Ceolin ◽  
Guido Cordoni ◽  
...  
Keyword(s):  
Demographic History ◽  
Comparative Method ◽  
Syntactic Analysis ◽  
Interference Effects ◽  
Human Demographic History ◽  
Genome Wide ◽  
Linguistic Interference ◽  
Genome Wide Data ◽  
Demographic Processes ◽  
North Western

To reconstruct aspects of human demographic history, linguistics and genetics complement each other, reciprocally suggesting testable hypotheses on population relationships and interactions. Relying on a linguistic comparative method based on syntactic data, here we focus on the non-straightforward relation of genes and languages among Finno-Ugric (FU) speakers, in comparison to their Indo-European (IE) and Altaic (AL) neighbors. Syntactic analysis, in agreement with the indications of more traditional linguistic levels, supports at least three distinct clusters, corresponding to these three Eurasian families; yet, the outliers of the FU group show linguistic convergence with their geographical neighbors. By analyzing genome-wide data in both ancient and contemporary populations, we uncovered remarkably matching patterns, with north-western FU speakers linguistically and genetically closer in parallel degrees to their IE-speaking neighbors, and eastern FU speakers to AL speakers. Therefore, our analysis indicates that plausible cross-family linguistic interference effects were accompanied, and possibly caused, by recognizable demographic processes. In particular, based on the comparison of modern and ancient genomes, our study identified the Pontic-Caspian steppes as the possible origin of the demographic processes that led to the expansion of FU languages into Europe.

scholarly journals Exploring Cuba’s population structure and demographic history using genome-wide data

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Cesar Fortes-Lima ◽  
Jonas Bybjerg-Grauholm ◽  
Lilia Caridad Marin-Padrón ◽  
Enrique Javier Gomez-Cabezas ◽  
Marie Bækvad-Hansen ◽  
...  
Keyword(s):  
Population Structure ◽  
Demographic History ◽  
Genome Wide ◽  
Genome Wide Data

scholarly journals Genetic-substructure and complex demographic history of South African Bantu speakers

2020 ◽  
Author(s):  
Dhriti Sengupta ◽  
Ananyo Choudhury ◽  
Cesar Fortes-Lima ◽  
Shaun Aron ◽  
Gavin Whitelaw ◽  
...  
Keyword(s):  
South Africa ◽  
Population Structure ◽  
Iron Age ◽  
Association Studies ◽  
Demographic History ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Scale Population ◽  
Genome Wide Data ◽  
Genetic Substructure

AbstractSouth Eastern Bantu-speaking (SEB) groups constitute more than 80% of the population in South Africa. Despite clear linguistic and geographic diversity, the genetic differences between these groups have not been systematically investigated. Based on genome-wide data of over 5000 individuals, representing eight major SEB groups, we provide strong evidence for fine-scale population structure that broadly aligns with geographic distribution and is also congruent with linguistic phylogeny (separation of Nguni, Sotho-Tswana and Tsonga speakers). Although differential Khoe-San admixture plays a key role, the structure persists after Khoe-San ancestry-masking. The timing of admixture, levels of sex-biased gene flow and population size dynamics also highlight differences in the demographic histories of individual groups. The comparisons with five Iron Age farmer genomes further support genetic continuity over ∼400 years in certain regions of the country. Simulated trait genome-wide association studies further show that the observed population structure could have major implications for biomedical genomics research in South Africa.

scholarly journals Evolutionary and Medical Consequences of Archaic Introgression into Modern Human Genomes

Genes ◽  
2018 ◽  
Vol 9 (7) ◽  
pp. 358 ◽  
Author(s):  
Olga Dolgova ◽  
Oscar Lao
Keyword(s):  
Demographic History ◽  
Modern Human ◽  
Human Populations ◽  
Human Genomes ◽  
Fitness Consequences ◽  
Genome Wide ◽  
Anatomically Modern Humans ◽  
Genome Wide Data ◽  
History Of ◽  
Health And Disease

The demographic history of anatomically modern humans (AMH) involves multiple migration events, population extinctions and genetic adaptations. As genome-wide data from complete genome sequencing becomes increasingly abundant and available even from extinct hominins, new insights of the evolutionary history of our species are discovered. It is currently known that AMH interbred with archaic hominins once they left the African continent. Current non-African human genomes carry fragments of archaic origin. This review focuses on the fitness consequences of archaic interbreeding in current human populations. We discuss new insights and challenges that researchers face when interpreting the potential impact of introgression on fitness and testing hypotheses about the role of selection within the context of health and disease.

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