scholarly journals Evolutionary history of modern Samoans

2020 ◽  
Vol 117 (17) ◽  
pp. 9458-9465 ◽  
Author(s):  
Daniel N. Harris ◽  
Michael D. Kessler ◽  
Amol C. Shetty ◽  
Daniel E. Weeks ◽  
Ryan L. Minster ◽  
...  
Keyword(s):  
Population History ◽  
Capital City ◽  
High Coverage ◽  
Whole Genomes ◽  
Human Modification ◽  
European Colonization ◽  
Demographic Processes ◽  
History Of ◽  
European Colonialism ◽  
History Of Migration

Archaeological studies estimate the initial settlement of Samoa at 2,750 to 2,880 y ago and identify only limited settlement and human modification to the landscape until about 1,000 to 1,500 y ago. At this point, a complex history of migration is thought to have begun with the arrival of people sharing ancestry with Near Oceanic groups (i.e., Austronesian-speaking and Papuan-speaking groups), and was then followed by the arrival of non-Oceanic groups during European colonialism. However, the specifics of this peopling are not entirely clear from the archaeological and anthropological records, and is therefore a focus of continued debate. To shed additional light on the Samoan population history that this peopling reflects, we employ a population genetic approach to analyze 1,197 Samoan high-coverage whole genomes. We identify population splits between the major Samoan islands and detect asymmetrical gene flow to the capital city. We also find an extreme bottleneck until about 1,000 y ago, which is followed by distinct expansions across the islands and subsequent bottlenecks consistent with European colonization. These results provide for an increased understanding of Samoan population history and the dynamics that inform it, and also demonstrate how rapid demographic processes can shape modern genomes.

scholarly journals Insights into human genetic variation and population history from 929 diverse genomes

2019 ◽  
Author(s):  
Anders Bergström ◽  
Shane A. McCarthy ◽  
Ruoyun Hui ◽  
Mohamed A. Almarri ◽  
Qasim Ayub ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Central Africa ◽  
Population History ◽  
Human Populations ◽  
Genome Sequences ◽  
High Coverage ◽  
Geographical Regions ◽  
History Of ◽  
Different Populations ◽  
Source Populations

AbstractGenome sequences from diverse human groups are needed to understand the structure of genetic variation in our species and the history of, and relationships between, different populations. We present 929 high-coverage genome sequences from 54 diverse human populations, 26 of which are physically phased using linked-read sequencing. Analyses of these genomes reveal an excess of previously undocumented private genetic variation in southern and central Africa and in Oceania and the Americas, but an absence of fixed, private variants between major geographical regions. We also find deep and gradual population separations within Africa, contrasting population size histories between hunter-gatherer and agriculturalist groups in the last 10,000 years, a potentially major population growth episode after the peopling of the Americas, and a contrast between single Neanderthal but multiple Denisovan source populations contributing to present-day human populations. We also demonstrate benefits to the study of population relationships of genome sequences over ascertained array genotypes. These genome sequences are freely available as a resource with no access or analysis restrictions.

scholarly journals Full-genome evolutionary histories of selfing, splitting and selection in Caenorhabditis

2014 ◽  
Author(s):  
Cristel G. Thomas ◽  
Wei Wang ◽  
Richard Jovelin ◽  
Rajarshi Ghosh ◽  
Tatiana Lomasko ◽  
...  
Keyword(s):  
Population History ◽  
Population Variation ◽  
Population Divergence ◽  
Genomic Context ◽  
Size Change ◽  
High Coverage ◽  
C Elegans ◽  
Developmental Evolution ◽  
History Of ◽  
Rare Gene

The nematode Caenorhabditis briggsae is a model for comparative developmental evolution with C. elegans. Worldwide collections of C. briggsae have implicated an intriguing history of divergence among genetic groups separated by latitude, or by restricted geography, that is being exploited to dissect the genetic basis to adaptive evolution and reproductive incompatibility. And yet, the genomic scope and timing of population divergence is unclear. We performed high-coverage whole-genome sequencing of 37 wild isolates of the nematode C. briggsae and applied a pairwise sequentially Markovian coalescent (PSMC) model to 703 combinations of genomic haplotypes to draw inferences about population history, the genomic scope of natural selection, and to compare with 40 wild isolates of C. elegans. We estimate that a diaspora of at least 6 distinct C. briggsae lineages separated from one another approximately 200 thousand generations ago, including the ???Temperate??? and ???Tropical??? phylogeographic groups that dominate most samples from around the world. Moreover, an ancient population split in its history 2 million generations ago, coupled with only rare gene flow among lineage groups, validates this system as a model for incipient speciation. Low versus high recombination regions of the genome give distinct signatures of population size change through time, indicative of widespread effects of selection on highly linked portions of the genome owing to extreme inbreeding by self-fertilization. Analysis of functional mutations indicates that genomic context, owing to selection that acts on long linkage blocks, is a more important driver of population variation than are the functional attributes of the individually encoded genes.

scholarly journals Estimation of coalescence probabilities and population divergence times from SNP data

Heredity ◽  
2021 ◽  
Author(s):  
Kristy Mualim ◽  
Christoph Theunert ◽  
Montgomery Slatkin
Keyword(s):  
Demographic History ◽  
Population History ◽  
Divergence Times ◽  
Population Divergence ◽  
High Coverage ◽  
Snp Data ◽  
Population Sizes ◽  
History Of ◽  
Relationship Of ◽  
The Relationship

AbstractWe present a method called the G(A|B) method for estimating coalescence probabilities within population lineages from genome sequences when one individual is sampled from each population. Population divergence times can be estimated from these coalescence probabilities if additional assumptions about the history of population sizes are made. Our method is based on a method presented by Rasmussen et al. (2014) to test whether an archaic genome is from a population directly ancestral to a present-day population. The G(A|B) method does not require distinguishing ancestral from derived alleles or assumptions about demographic history before population divergence. We discuss the relationship of our method to two similar methods, one introduced by Green et al. (2010) and called the F(A|B) method and the other introduced by Schlebusch et al. (2017) and called the TT method. When our method is applied to individuals from three or more populations, it provides a test of whether the population history is treelike because coalescence probabilities are additive on a tree. We illustrate the use of our method by applying it to three high-coverage archaic genomes, two Neanderthals (Vindija and Altai) and a Denisovan.

scholarly journals Insights into human genetic variation and population history from 929 diverse genomes

Science ◽  
2020 ◽  
Vol 367 (6484) ◽  
pp. eaay5012 ◽  
Author(s):  
Anders Bergström ◽  
Shane A. McCarthy ◽  
Ruoyun Hui ◽  
Mohamed A. Almarri ◽  
Qasim Ayub ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Central Africa ◽  
Population History ◽  
Human Populations ◽  
Genome Sequences ◽  
High Coverage ◽  
Geographical Regions ◽  
History Of ◽  
Different Populations ◽  
Source Populations

Genome sequences from diverse human groups are needed to understand the structure of genetic variation in our species and the history of, and relationships between, different populations. We present 929 high-coverage genome sequences from 54 diverse human populations, 26 of which are physically phased using linked-read sequencing. Analyses of these genomes reveal an excess of previously undocumented common genetic variation private to southern Africa, central Africa, Oceania, and the Americas, but an absence of such variants fixed between major geographical regions. We also find deep and gradual population separations within Africa, contrasting population size histories between hunter-gatherer and agriculturalist groups in the past 10,000 years, and a contrast between single Neanderthal but multiple Denisovan source populations contributing to present-day human populations.

scholarly journals Magnaporthe oryzae populations in Sub-Saharan Africa are diverse and show signs of local adaptation

2020 ◽  
Author(s):  
Geoffrey Onaga ◽  
Worrawit Suktrakul ◽  
Margaret Wanjiku ◽  
Ian Lorenzo Quibod ◽  
Jean-Baka Domelevo Entfellner ◽  
...  
Keyword(s):  
Local Adaptation ◽  
Magnaporthe Oryzae ◽  
Management Strategies ◽  
Haplotype Diversity ◽  
Population History ◽  
Sub Saharan Africa ◽  
Demographic Processes ◽  
History Of ◽  
Sub Saharan ◽  
Genetic Pools

AbstractRice blast caused by Magnaporthe oryzae is one of the most economically damaging diseases of rice worldwide. The disease originated in Asia but was detected for the first time in Sub-Saharan Africa (SSA) around 100 years ago. Despite its importance, the evolutionary processes involved in shaping the population structure of M. oryzae in SSA remain unclear. In this study, we investigate the population history of M. oryzae using a combined dataset of 180 genomes. Our results show that SSA populations are more diverse than earlier perceived, and harbor all genetic groups previously reported in Asia. While M. oryzae populations in SSA and Asia draw from the same genetic pools, both are experiencing different evolutionary trajectories resulting from unknown selection pressures or demographic processes. The distribution of rare alleles, measured as Tajima’s D values, show significant differences at the substructure level. Genome-wide analysis indicates potential events of population contraction strongly affecting M. oryzae in SSA. In addition, the distribution and haplotype diversity of effectors might suggest a process of local adaptation to SSA conditions. These findings provide additional clues about the evolutionary history of M. oryzae outside the center of origin and help to build customized disease management strategies.

Mining Language

2020 ◽  
Author(s):  
Allison Margaret Bigelow
Keyword(s):  
Print Culture ◽  
Scientific Practices ◽  
Metallic Materials ◽  
The Andes ◽  
Northern European ◽  
Mineral Wealth ◽  
Gonzalo Fernandez De Oviedo ◽  
European Colonization ◽  
History Of ◽  
European Colonialism

Mineral wealth from the Americas underwrote and undergirded European colonization of the New World; American gold and silver enriched Spain, funded the slave trade, and spurred Spain's northern European competitors to become Atlantic powers. Building upon works that have narrated this global history of American mining in economic and labor terms, Mining Language is the first book-length study of the technical and scientific vocabularies that miners developed in the sixteenth and seventeenth centuries as they engaged with metallic materials. This language-centric focus enables Allison Bigelow to document the crucial intellectual contributions Indigenous and African miners made to the very engine of European colonialism. By carefully parsing the writings of well-known figures such as Cristóbal Colón and Gonzalo Fernández de Oviedo y Valdés and lesser-known writers such Álvaro Alonso Barba, a Spanish priest who spent most of his life in the Andes, Bigelow uncovers the ways in which Indigenous and African metallurgists aided or resisted imperial mining endeavors, shaped critical scientific practices, and offered imaginative visions of metalwork. Her creative linguistic and visual analyses of archival fragments, images, and texts in languages as diverse as Spanish and Quechua also allow her to reconstruct the processes that led to the silencing of these voices in European print culture.

scholarly journals Digging into the Genomic Past of Swiss Honey Bees by Whole-Genome Sequencing Museum Specimens

2020 ◽  
Vol 12 (12) ◽  
pp. 2535-2551
Author(s):  
Melanie Parejo ◽  
David Wragg ◽  
Dora Henriques ◽  
Jean-Daniel Charrière ◽  
Andone Estonba
Keyword(s):  
Genetic Diversity ◽  
Apis Mellifera ◽  
Honey Bee ◽  
Honey Bees ◽  
Population History ◽  
History Museum ◽  
Whole Genomes ◽  
History Of ◽  
Commercial Breeding

Abstract Historical specimens in museum collections provide opportunities to gain insights into the genomic past. For the Western honey bee, Apis mellifera L., this is particularly important because its populations are currently under threat worldwide and have experienced many changes in management and environment over the last century. Using Swiss Apis mellifera mellifera as a case study, our research provides important insights into the genetic diversity of native honey bees prior to the industrial-scale introductions and trade of non-native stocks during the 20th century—the onset of intensive commercial breeding and the decline of wild honey bees following the arrival of Varroa destructor. We sequenced whole-genomes of 22 honey bees from the Natural History Museum in Bern collected in Switzerland, including the oldest A. mellifera sample ever sequenced. We identify both, a historic and a recent migrant, natural or human-mediated, which corroborates with the population history of honey bees in Switzerland. Contrary to what we expected, we find no evidence for a significant genetic bottleneck in Swiss honey bees, and find that genetic diversity is not only maintained, but even slightly increased, most probably due to modern apicultural practices. Finally, we identify signals of selection between historic and modern honey bee populations associated with genes enriched in functions linked to xenobiotics, suggesting a possible selective pressure from the increasing use and diversity of chemicals used in agriculture and apiculture over the last century.

scholarly journals Sejarah Lokal Riau untuk Pengembangan Materi Ajar Sejarah Indonesia Kelas XI SMA

Diakronika ◽  
2019 ◽  
Vol 19 (1) ◽  
pp. 35
Author(s):  
Asyrul Fikri
Keyword(s):  
United Kingdom ◽  
Learning Strategies ◽  
20Th Century ◽  
Local History ◽  
Learning Material ◽  
National History ◽  
Learning History ◽  
European Colonization ◽  
History Of ◽  
European Colonialism

Results of the study aims to integrate local history that is in the Riau into festive the history of Indonesia material of class XI. The method used is the analysis of documents, namely documents the history of Indonesia syllabus of class XI. Historical events that happened in Riau are integrated and analyzed to each basic competence in accordance with the learning material. Results of the study are, among others, the local people's struggle history of Riau do resistance to colonization a foreign nation such as the people's resistance war Guntung, war Reteh, war Mondang Kumango, resistance Tuanku Tambusai, resistance Datuk Tabano, Resistance Raja Haji, Sultan Zainal Abidin, War and resistance Manggris and Pirates in waters of Riau can be integrated into the basic competence to analyze the process of entry and the development of European colonization (Portugal, Spain, Netherlands, United Kingdom) to Indonesia with the material of Learning Strategies of resistance against Indonesia nation of European colonialism until the beginning of the 20th century. Integration of the study of local history in the process of learning history in class is expected to improve the understanding and awareness of the students against the local local history and its relationship with national history.

The Population History of Britain and Ireland 1500-1750

1996 ◽  
Vol 50 (2) ◽  
pp. 284-285
Author(s):  
Eilidh Garrett
Keyword(s):  
Population History ◽  
History Of

Mau-Mau Rebels’ Doctor in Mount Kenya East Forest (1952–1960): Retrieving the Revolutionary History of Milton Munene Gachau

2018 ◽  
Vol 5 (1) ◽  
Author(s):  
Julius M. Gathogo
Keyword(s):  
National Level ◽  
Medical Doctor ◽  
Capital City ◽  
Revolutionary Movement ◽  
Armed Struggle ◽  
War Of Independence ◽  
Mau Mau ◽  
History Of ◽  
Revolutionary History ◽  
Second World

The Kenya Land and Freedom Army (KLFA), otherwise known as Mau-Mau revolutionary movement was formed after returnees of the Second World War (1939–1945) ignited the African populace to militarily fight for land and freedom (wiyathi nai thaka). John Walton’s theory of reluctant rebels informs this article theoretically, as it is indeed the political elites who inspired this armed struggle. To do this, they held several meetings in the capital city of Nairobi, drew the war structures from the national level to the sub-location level, especially in the central region of Kenya, and tasked locals with filling in the leadership vacuums that were created. In view of this, the article seeks to unveil the revolutionary history of the Mau-Mau medical Doctor, also known as Major Judge Munene Gachau (born in 1935), whose contribution in the Kenyan war of independence (1952–1960) remains unique. This uniqueness can be attested to by considering various factors. First, he is one of the few surviving leaders who joined the guerrilla forest war while he was relatively young. Normally, the Mau-Mau War Council did not encourage people below the age of 25 to join the rebels in the forest of Mt. Kenya, Aberdare Mountains and/or other places. Nor did they encourage adults past the age of 35 to join as combatants in the forest fight. Second, he is the only known Mau-Mau rebel in Kirinyaga county of Kenya to have gone back to school after the war had ended, traveled abroad, and studied up to a Masters degree level. Third, Munene Gachau belongs in the category that joined the rebels while still relatively educated and eventually got promoted to the rank of Major, upon being confirmed as the Mau-Mau Doctor.

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