scholarly journals Ancient mitochondrial DNA provides high-resolution time scale of the peopling of the Americas

2016 ◽  
Vol 2 (4) ◽  
pp. e1501385 ◽  
Author(s):  
Bastien Llamas ◽  
Lars Fehren-Schmitz ◽  
Guido Valverde ◽  
Julien Soubrier ◽  
Swapan Mallick ◽  
...  
Keyword(s):  
Native Americans ◽  
Small Population ◽  
Phylogeographic Structure ◽  
Data Sets ◽  
Extinction Rate ◽  
Low Genetic Diversity ◽  
Coalescent Simulations ◽  
Peopling Of The Americas ◽  
European Colonization ◽  
Limited Gene Flow

The exact timing, route, and process of the initial peopling of the Americas remains uncertain despite much research. Archaeological evidence indicates the presence of humans as far as southern Chile by 14.6 thousand years ago (ka), shortly after the Pleistocene ice sheets blocking access from eastern Beringia began to retreat. Genetic estimates of the timing and route of entry have been constrained by the lack of suitable calibration points and low genetic diversity of Native Americans. We sequenced 92 whole mitochondrial genomes from pre-Columbian South American skeletons dating from 8.6 to 0.5 ka, allowing a detailed, temporally calibrated reconstruction of the peopling of the Americas in a Bayesian coalescent analysis. The data suggest that a small population entered the Americas via a coastal route around 16.0 ka, following previous isolation in eastern Beringia for ~2.4 to 9 thousand years after separation from eastern Siberian populations. Following a rapid movement throughout the Americas, limited gene flow in South America resulted in a marked phylogeographic structure of populations, which persisted through time. All of the ancient mitochondrial lineages detected in this study were absent from modern data sets, suggesting a high extinction rate. To investigate this further, we applied a novel principal components multiple logistic regression test to Bayesian serial coalescent simulations. The analysis supported a scenario in which European colonization caused a substantial loss of pre-Columbian lineages.

scholarly journals Les catastrophes naturelles dans les romans caribéens d’expression française

Il Tolomeo ◽  
2020 ◽  
Author(s):  
Alessia Vignoli
Keyword(s):  
Native Americans ◽  
Natural Hazards ◽  
Caribbean Literature ◽  
Common Origin ◽  
Caribbean Region ◽  
Common Features ◽  
African Slaves ◽  
European Colonization ◽  
The Common ◽  
The Caribbean

The notion of ‘disaster’ pervades the Caribbean thought. The common origin of the Caribbean region, the European colonization, caused two disasters: the extermination of Native Americans and the deportation of African slaves. The union between nature and the oppressed people against the oppressor resulted in the creation of an environmental conscience that the Caribbean literature has often expressed. This essay will investigate the common points shared by some Haitian, Martinican and Guadeloupean authors in the writing of natural hazards. It will show that, despite the diversity that marks the Caribbean, there is a repetition of common features that proves its geopoetic unity.

scholarly journals Early human dispersals within the Americas

Science ◽  
2018 ◽  
Vol 362 (6419) ◽  
pp. eaav2621 ◽  
Author(s):  
J. Víctor Moreno-Mayar ◽  
Lasse Vinner ◽  
Peter de Barros Damgaard ◽  
Constanza de la Fuente ◽  
Jeffrey Chan ◽  
...  
Keyword(s):  
Native Americans ◽  
South America ◽  
Late Pleistocene ◽  
Early Diversification ◽  
Human Genomes ◽  
Peopling Of The Americas ◽  
Genetic Signal ◽  
Dynamic Population ◽  
Early Human

Studies of the peopling of the Americas have focused on the timing and number of initial migrations. Less attention has been paid to the subsequent spread of people within the Americas. We sequenced 15 ancient human genomes spanning from Alaska to Patagonia; six are ≥10,000 years old (up to ~18× coverage). All are most closely related to Native Americans, including those from an Ancient Beringian individual and two morphologically distinct “Paleoamericans.” We found evidence of rapid dispersal and early diversification that included previously unknown groups as people moved south. This resulted in multiple independent, geographically uneven migrations, including one that provides clues of a Late Pleistocene Australasian genetic signal, as well as a later Mesoamerican-related expansion. These led to complex and dynamic population histories from North to South America.

scholarly journals GenomegaMap: Within-Species Genome-Wide dN/dS Estimation from over 10,000 Genomes

2020 ◽  
Vol 37 (8) ◽  
pp. 2450-2460 ◽  
Author(s):  
Daniel J Wilson ◽  
Derrick W Crook ◽  
Timothy E A Peto ◽  
A Sarah Walker ◽  
Sarah J Hoosdally ◽  
...  
Keyword(s):  
Protein A ◽  
Large Data ◽  
Large Data Sets ◽  
Data Sets ◽  
Protein Coding ◽  
Dead Box ◽  
Coalescent Simulations ◽  
Genome Wide ◽  
Signature Of Selection ◽  
Signatures Of Selection

Abstract The dN/dS ratio provides evidence of adaptation or functional constraint in protein-coding genes by quantifying the relative excess or deficit of amino acid-replacing versus silent nucleotide variation. Inexpensive sequencing promises a better understanding of parameters, such as dN/dS, but analyzing very large data sets poses a major statistical challenge. Here, I introduce genomegaMap for estimating within-species genome-wide variation in dN/dS, and I apply it to 3,979 genes across 10,209 tuberculosis genomes to characterize the selection pressures shaping this global pathogen. GenomegaMap is a phylogeny-free method that addresses two major problems with existing approaches: 1) It is fast no matter how large the sample size and 2) it is robust to recombination, which causes phylogenetic methods to report artefactual signals of adaptation. GenomegaMap uses population genetics theory to approximate the distribution of allele frequencies under general, parent-dependent mutation models. Coalescent simulations show that substitution parameters are well estimated even when genomegaMap’s simplifying assumption of independence among sites is violated. I demonstrate the ability of genomegaMap to detect genuine signatures of selection at antimicrobial resistance-conferring substitutions in Mycobacterium tuberculosis and describe a novel signature of selection in the cold-shock DEAD-box protein A gene deaD/csdA. The genomegaMap approach helps accelerate the exploitation of big data for gaining new insights into evolution within species.

Blood group O alleles in Native Americans: Implications in the peopling of the Americas

2009 ◽  
pp. NA-NA
Author(s):  
Benito Estrada-Mena ◽  
F. Javier Estrada ◽  
Raúl Ulloa-Arvizu ◽  
Miriam Guido ◽  
Rocío Méndez ◽  
...  
Keyword(s):  
Native Americans ◽  
Blood Group ◽  
Peopling Of The Americas

The Disappearing Turnout Gap between Native Americans and Non-Native Americans

2014 ◽  
Vol 38 (2) ◽  
pp. 1-16 ◽  
Author(s):  
Tracy Skopek ◽  
Andrew Garner
Keyword(s):  
Native American ◽  
Native Americans ◽  
Political Parties ◽  
American Indians ◽  
Past Research ◽  
Data Sets ◽  
Political Values ◽  
Indian Gaming ◽  
The Past

Past research has consistently found that American Indians have traditionally turned out to vote at lower rates than do other citizens. Using two separate data sets, we examine this "turnout gap" over the past several decades. We find that not only has Native American turnout increased generally, but that the "gap" between Native Americans and non-Native Americans has declined substantially, and that in recent elections this "gap" has largely disappeared. We then provide a preliminary and tentative examination of possible causes for the decline, including the role of Indian gaming, mobilization by political parties and candidates, and shifting political values among Native Americans.

scholarly journals Phylogeographic Analysis Suggests a Recent Population Bottleneck in the Rare Red Sea Tridacna squamosina

2021 ◽  
Vol 8 ◽  
Author(s):  
Kah Kheng Lim ◽  
Susann Rossbach ◽  
Nathan R. Geraldi ◽  
Ester A. Serrão ◽  
Carlos M. Duarte
Keyword(s):  
Genetic Diversity ◽  
Red Sea ◽  
Coastal Zone Management ◽  
Small Population ◽  
Zone Management ◽  
Low Genetic Diversity ◽  
Giant Clams ◽  
Management Plans ◽  
Tridacna Maxima ◽  
Distribution And Ecology

Giant clams are an important ecological component of coral reefs in the Red Sea, as they enhance the reef’s productivity and provide habitat that can increase diversity. Three species of giant clams, namely Tridacna maxima, T. squamosa, and T. squamosina have been described within the Red Sea. However, due to its scarcity, information about the distribution and ecology of T. squamosina in the Saudi Arabian Red Sea is still lacking. This study used DNA barcoding to confirm the identity of the rare T. squamosina in the Farasan Banks. Six mtCOI fragments (500 bp) of T. squamosina were successfully amplified using the SQUA-primers for the first time. We used our data along with 18 reference sequences (16S) from the online database to assess the genetic diversity and population structure of T. squamosina. Low genetic diversity among the T. squamosina populations inferred from the 16S sequences implies a recent bottleneck for this species, which is supported by their historically higher diversity based on the coalescent-based estimator. Given the small population abundance and limited genetic variation of T. squamosina, it may warrant immediate local protections such as biobanking and fertility preservation programs as well as effective integrated coastal zone management plans.

scholarly journals Classification of Genus Acanthopanax in Korea and Genetic Diversity Using Allozymes

2005 ◽  
Vol 54 (1-6) ◽  
pp. 206-210 ◽  
Author(s):  
M. K. Huh ◽  
H. W. Huh
Keyword(s):  
Genetic Diversity ◽  
Representative Sample ◽  
Genetic Relationships ◽  
Woody Species ◽  
Small Population ◽  
Geographic Ranges ◽  
Low Level ◽  
Low Genetic Diversity ◽  
Population Sizes

Abstract Genus Acanthopanax is a long-lived woody species that is primarily distributed throughout Asia. Many species of this genus are regarded as medically and ecologically important. We evaluated a representative sample of the nine taxa with allozymes to estimate genetic relationships within the genus. As some Korean populations were isolated and patchily distributed, they exhibited a low level of genetic diversity. The narrow geographic ranges, artificial distribution of habitats, and small population sizes are proposed as factors contributing to low genetic diversity. Acanthopanax seoulense was similar to A. sessiliflorus, while a cluster of the A. rufinerve population is distant from any other species. A. senticosus is closely related to A. seoulense and A. sessiliflorus, whereas other species (A. koreanum) are more distinct from the Korean populations. Korean species are clustered together and clearly differentiated from the Chinese and Russian Acanthopanax taxa, genus Acanthopanax

The fisher as a model organism

2018 ◽  
Author(s):  
Roger A. Powell ◽  
Aaron N. Facka ◽  
Mourad W. Gabriel ◽  
Jonathan H. Gilbert ◽  
J. Mark Higley ◽  
...  
Keyword(s):  
Climate Change ◽  
Native Americans ◽  
North American ◽  
Complex Structure ◽  
Model Organism ◽  
Generalist Predators ◽  
Ecological Knowledge ◽  
Population Recovery ◽  
Fragmented Habitats ◽  
European Colonization

The literature on fishers - medium-sized, North American carnivores - is broad, despite being limited, and traditional ecological knowledge of Native Americans contributes to our understanding of fishers. Fishers are generalist predators but also specialized predators of North American porcupines. Over trapping, habitat loss and climate change reduced fisher populations after European colonization of North America. Protection and reintroductions led to general but not to universal population recovery, contributing to the understanding of reintroduction science, including population genetics of both rare and expanding populations. Although adapted to live in old forests with complex structure, some fishers have colonized fragmented habitats, including suburbs. Models of fisher habitat, energetics, sexual dimorphism, genetics, and use of space illustrate the diversity of approaches possible for carnivore studies. Thus, the fisher has become a model organism for ecological and conservation research on mammalian carnivores.

Discrimination and resentment: examining American attitudes about Native Americans

2021 ◽  
pp. 1-28
Author(s):  
Raymond Foxworth ◽  
Carew Boulding
Keyword(s):  
Native American ◽  
Public Opinion ◽  
Native Americans ◽  
Race And Ethnicity ◽  
Political Ideology ◽  
Minority Groups ◽  
Original Data ◽  
Small Population ◽  
Factual Knowledge

Abstract What shapes Americans' attitudes toward and about Native Americans? Public opinion research acknowledges that race and ethnicity are a factor in shaping US public opinion. Native Americans have been almost entirely excluded from this research. But we do know that, despite being a relatively small population, the general public holds stereotypes and false narratives about Native Americans that have been perpetuated by popular culture, education curriculum, and national myths. In this paper, we use new and original data collected under the Reclaiming Native Truth project to examine the factors that shape attitudes toward Native Americans. More specifically, we examine individual and contextual factors that shape views of discrimination against Native Americans and resentment toward Native Americans. We find that political ideology (liberal versus conservative) and the reliance on Native American stereotypes are factors most consistently associated with resentment and attitudes about Native American discrimination, although direct personal experiences and factual knowledge also matter. Our findings contribute to conversations about attitudes toward racial and ethnic minority groups and emerging scholarship on the role of political attitudes in settler-colonial societies.

scholarly journals Ancient nuclear genomes enable repatriation of Indigenous human remains

2018 ◽  
Vol 4 (12) ◽  
pp. eaau5064 ◽  
Author(s):  
Joanne L. Wright ◽  
Sally Wasef ◽  
Tim H. Heupink ◽  
Michael C. Westaway ◽  
Simon Rasmussen ◽  
...  
Keyword(s):  
Population Structure ◽  
Native Americans ◽  
Indigenous People ◽  
Geographic Location ◽  
Museum Collections ◽  
High Coverage ◽  
Aboriginal Australians ◽  
Ancient Population ◽  
European Colonization ◽  
Nuclear Genomes

After European colonization, the ancestral remains of Indigenous people were often collected for scientific research or display in museum collections. For many decades, Indigenous people, including Native Americans and Aboriginal Australians, have fought for their return. However, many of these remains have no recorded provenance, making their repatriation very difficult or impossible. To determine whether DNA-based methods could resolve this important problem, we sequenced 10 nuclear genomes and 27 mitogenomes from ancient pre-European Aboriginal Australians (up to 1540 years before the present) of known provenance and compared them to 100 high-coverage contemporary Aboriginal Australian genomes, also of known provenance. We report substantial ancient population structure showing strong genetic affinities between ancient and contemporary Aboriginal Australian individuals from the same geographic location. Our findings demonstrate the feasibility of successfully identifying the origins of unprovenanced ancestral remains using genomic methods.

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