scholarly journals The genetic prehistory of the Andean highlands 7,000 Years BP though European contact

2018 ◽  
Author(s):  
John Lindo ◽  
Randall Haas ◽  
Courtney Hofman ◽  
Mario Apata ◽  
Mauricio Moraga ◽  
...  
Keyword(s):  
Pathogen Resistance ◽  
High Elevation ◽  
South American ◽  
European Contact ◽  
The Andes ◽  
Complex Modes ◽  
Genome Wide ◽  
Complex Process ◽  
Complex Picture ◽  
Andean Highlands

AbstractThe peopling of the Andean highlands above 2500m in elevation was a complex process that included cultural, biological and genetic adaptations. Here we present a time series of ancient whole genomes from the Andes of Peru, dating back to 7,000 calendar years before present (BP), and compare them to 64 new genome-wide genetic variation datasets from both high and lowland populations. We infer three significant features: a split between low and high elevation populations that occurred between 9200-8200 BP; a population collapse after European contact that is significantly more severe in South American lowlanders than in highland populations; and evidence for positive selection at genetic loci related to starch digestion and plausibly pathogen resistance after European contact. Importantly, we do not find selective sweep signals related to known components of the human hypoxia response, which may suggest more complex modes of genetic adaptation to high altitude.One Sentence SummaryAncient DNA from the Andes reveals a complex picture of human adaptation from early settlement to the colonial period.

scholarly journals The genetic prehistory of the Andean highlands 7000 years BP though European contact

2018 ◽  
Vol 4 (11) ◽  
pp. eaau4921 ◽  
Author(s):  
John Lindo ◽  
Randall Haas ◽  
Courtney Hofman ◽  
Mario Apata ◽  
Mauricio Moraga ◽  
...  
Keyword(s):  
Pathogen Resistance ◽  
High Elevation ◽  
South American ◽  
European Contact ◽  
The Andes ◽  
Complex Modes ◽  
Genome Wide ◽  
Complex Process ◽  
Whole Genomes ◽  
Andean Highlands

The peopling of the Andean highlands above 2500 m in elevation was a complex process that included cultural, biological, and genetic adaptations. Here, we present a time series of ancient whole genomes from the Andes of Peru, dating back to 7000 calendar years before the present (BP), and compare them to 42 new genome-wide genetic variation datasets from both highland and lowland populations. We infer three significant features: a split between low- and high-elevation populations that occurred between 9200 and 8200 BP; a population collapse after European contact that is significantly more severe in South American lowlanders than in highland populations; and evidence for positive selection at genetic loci related to starch digestion and plausibly pathogen resistance after European contact. We do not find selective sweep signals related to known components of the human hypoxia response, which may suggest more complex modes of genetic adaptation to high altitude.

Biogeographic origins and floristic affinities of the bryophytes of the Tota-Bijagual-Mamapacha complex in the Páramos of Boyacá, Colombia

Phytotaxa ◽  
2020 ◽  
Vol 477 (2) ◽  
pp. 171-193
Author(s):  
JORGE ENRIQUE GIL-NOVOA ◽  
MARÍA E. MORALES-PUENTES ◽  
JORGE D. MERCADO GÓMEZ
Keyword(s):  
Transition Zone ◽  
Plant Species ◽  
Endemic Species ◽  
High Elevation ◽  
Environmental Services ◽  
South American ◽  
The South ◽  
The Andes ◽  
Biogeographic Regionalization ◽  
Surface And Groundwater

Páramos are Neotropical high-elevation isolated ecosystems in the Andes. These areas are inhabited by many distinct plant species, such as bryophytes, which provide environmental services including the storage and regulation of surface and groundwater; however, the diversity and biogeographic affinities of bryophytes are still unknown. We used phytogeographic analysis and biogeographic regionalization approaches to determine the biogeographic origins and floristic affinities of this flora in the Tota-Bijagual-Mamapacha (TBM) páramos complex. We found 219 species of bryophytes, 145 mosses, and 75 liverworts. These species are mainly of Neotropical origin, although we also found relationships with Ethiopian, Nearctic, Australian, Antarctic, Palearctic and Oriental regions. According to Morrone (2014), the TBM is located in the South American Transition Zone, the Páramo province, and the Páramos de la cordillera Oriental biogeographic district. The TBM had important floristic relationships with the South Brazilian subregion and the Magdalena province. We found no endemic species to the TBM complex, but identified several endemic species for the Andean páramos.

scholarly journals Exploring Phonological Areality in the Circum-Andean Region Using a Naive Bayes Classifier

2014 ◽  
Vol 4 (1) ◽  
pp. 27-86 ◽  
Author(s):  
Lev Michael ◽  
Will Chang ◽  
Tammy Stark
Keyword(s):  
Naive Bayes ◽  
Naïve Bayes ◽  
South American ◽  
Naive Bayes Classifier ◽  
Bayes Classifier ◽  
Naïve Bayes Classifier ◽  
Statistical Tool ◽  
The Core ◽  
The Andes ◽  
Andean Highlands

This paper describes the Core and Periphery technique: a quantitative method for exploring areality that uses a naive Bayes classifier, a statistical tool for inferring class membership based on training sets assembled from members of the classes in question. The Core and Periphery technique is applied to the exploration of phonological areality in the Andes and surrounding lowland regions, based on the South American Phonological Inventory Database (SAPhon 1.1.3; Michael et al., 2013). Evidence is found for a phonological area centering on the Andean highlands, and extending to parts of the northern and central Andean foothills regions, the Chaco, and Patagonia. Evidence is also found for Southern and North-Central phonological sub-areas within this larger phonological area.

Radiocarbon Dating and Dietary Stable Isotope Analysis of Kwaday Dän Ts'inchí

2007 ◽  
Vol 72 (4) ◽  
pp. 719-734 ◽  
Author(s):  
Michael P. Richards ◽  
Sheila Greer ◽  
Lorna T. Corr ◽  
Owen Beattie ◽  
Alexander Mackie ◽  
...  
Keyword(s):  
Radiocarbon Dating ◽  
Isotope Analysis ◽  
Human Remains ◽  
Isotopic Analysis ◽  
High Elevation ◽  
Bone Collagen ◽  
Contact Period ◽  
European Contact ◽  
Ams Dating ◽  
The Individual

We report here on the results of AMS dating and isotopic analysis of the frozen human remains named Kwaday Dän Ts'inchí and associated materials recovered from a glacier located in Northwest British Columbia, Canada in 1999. The isotopic analysis of bone collagen (bulk and single amino acids) from the individual indicates a strongly marine diet, which was unexpected given the location of this find, more than 100 km inland eroding out of a high elevation glacier; however, bulk hair and bone cholesterol isotopic values indicate a shift in diet to include more terrestrial foods in the year before death. The radiocarbon dating is not straightforward, as there are difficulties in determining the appropriate marine correction for the human remains, and the spread of dates on the associated artifacts clearly indicates that this was not a single use site. By combining the most recent date on a robe worn by Kwaday Dän Ts'inchi with direct bone collagen dates we conclude that the individual likely dates to between cal A.D. 1670 to 1850, which is in the pre-(or early) European contact period for this region.

scholarly journals Geographical variability of bacterial communities of cryoconite holes of Andean glaciers

2021 ◽  
Author(s):  
Francesca Pittino ◽  
Michael Seeger ◽  
Roberto Azzoni ◽  
Roberto Ambrosini ◽  
Andrea Franzetti
Keyword(s):  
Bacterial Communities ◽  
High Elevation ◽  
Glacier Surface ◽  
Organic Matter Production ◽  
The Andes ◽  
Matter Production ◽  
O2 Concentration ◽  
The World ◽  
Water Ph ◽  
Andean Glaciers

AbstractCryoconite holes, ponds full of melting water with a sediment on the bottom, are hotspot of biodiversity of glacier surface. They host a metabolically active bacterial community that is involved in different dynamics concerning glacier ecosystems. Indeed, they are responsible of organic matter production and with other microorganisms establish a real microecosystem. Cryoconite holes have been described in different areas of the world (e.g., Arctic, Antarctic, Alps, Himalaya), and with this study we will provide the first description of bacterial communities of cryoconite holes of the Andes in South America. We collected samples on three high elevation glaciers of the Andes (Iver, Iver East and Morado glaciers) and two Patagonian glaciers located at sea level (Exploradores glacier and Perito Moreno). Results show that the most abundant orders are Burkholderiales, Cytophagales, Sphingobacteriales, Actinomycetales, Pseudomonadales, Rhodospiarillales, Rhizobiales, Sphingomonadales and Bacteroidales, which have been reported on glaciers of other areas of the world, Bacterial communities change from one glacier to another and both water pH and O2 concentration affect bacterial communities composition.

scholarly journals Genome-wide Association Study of Non-syndromic Orofacial Clefts in a Multiethnic Sample of Families and Controls Identifies Novel Regions

2020 ◽  
Author(s):  
Nandita Mukhopadhyay ◽  
Eleanor Feingold ◽  
Lina Moreno-Uribe ◽  
George Wehby ◽  
Luz Consuelo Valencia-Ramirez ◽  
...  
Keyword(s):  
Native American ◽  
Cleft Lip ◽  
Genome Wide Association Study ◽  
Population Level ◽  
Allele Frequencies ◽  
Genome Wide Association ◽  
South American ◽  
Orofacial Clefts ◽  
Public Health Burden ◽  
Genome Wide

AbstractOrofacial clefts (OFCs) are among the most prevalent craniofacial birth defects worldwide and create a significant public health burden. The majority of OFCs are non-syndromic and vary in prevalence by ethnicity. Africans have the lowest prevalence of OFCs (∼ 1/2,500), Asians have the highest prevalence (∼1/500), European and Latin Americans lie somewhere in the middle (∼1/800 and 1/900 respectively). Thus, ethnicity appears to be a major determinant of the risk of developing OFC. The Pittsburgh Orofacial Clefts Multiethnic study was designed to explore this ethnic variance, comprising a large number of families and individuals (∼12,000 individuals) from multiple populations worldwide: US and Europe, Asians, mixed Native American/Caucasians, and Africans. In this current study, we analyzed 2,915 OFC cases, 6,044 unaffected individuals related to the OFC cases, and 2,685 controls with no personal or family history of OFC. Participants were grouped by their ancestry into African, Asian, European, and Central and South American subsets, and genome-wide association run on the combined sample as well as the four ancestry-based groups. We observed 22 associations to cleft lip with or without cleft palate at 18 distinct loci with p-values < 1e-06, including 10 with genome-wide significance (< 5e-08), in the combined sample and within ancestry groups. Three loci - 2p12 (rs62164740, p=6.27e-07), 10q22.2 (rs150952246, p=3.14e-07), and 10q24.32 (rs118107597, p=8.21e-07) are novel. Nine were in or near known OFC loci - PAX7, IRF6, FAM49A, DCAF4L2, 8q24.21, NTN1, WNT3-WNT9B, TANC2, and RHPN2. The majority of the associations were observed only in the combined sample, European, and Central and South American groups. We investigated whether the observed differences in association strength were a) purely due to sample sizes, b) due to systematic allele frequency difference at the population level, or (c) due to the fact certain OFC-causing variants confer different amounts of risk depending on ancestral origin, by comparing effect sizes to observed allele frequencies of the effect allele in our ancestry-based groups. While some of the associations differ due to systematic differences in allele frequencies between groups, others show variation in effect size despite similar frequencies across ancestry groups.

scholarly journals Comparative Analysis of Chlamydia psittaci Genomes Reveals the Recent Emergence of a Pathogenic Lineage with a Broad Host Range

mBio ◽  
2013 ◽  
Vol 4 (2) ◽  
Author(s):  
Timothy D. Read ◽  
Sandeep J. Joseph ◽  
Xavier Didelot ◽  
Brooke Liang ◽  
Lisa Patel ◽  
...  
Keyword(s):  
Chlamydia Trachomatis ◽  
New World ◽  
Evolutionary Dynamics ◽  
Chlamydia Psittaci ◽  
South American ◽  
Content Type ◽  
Sexually Transmitted ◽  
Genome Wide ◽  
Life Threatening ◽  
History Of

ABSTRACT Chlamydia psittaci is an obligate intracellular bacterium. Interest in Chlamydia stems from its high degree of virulence as an intestinal and pulmonary pathogen across a broad range of animals, including humans. C. psittaci human pulmonary infections, referred to as psittacosis, can be life-threatening, which is why the organism was developed as a bioweapon in the 20th century and is listed as a CDC biothreat agent. One remarkable recent result from comparative genomics is the finding of frequent homologous recombination across the genome of the sexually transmitted and trachoma pathogen Chlamydia trachomatis. We sought to determine if similar evolutionary dynamics occurred in C. psittaci. We analyzed 20 C. psittaci genomes from diverse strains representing the nine known serotypes of the organism as well as infections in a range of birds and mammals, including humans. Genome annotation revealed a core genome in all strains of 911 genes. Our analyses showed that C. psittaci has a history of frequently switching hosts and undergoing recombination more often than C. trachomatis. Evolutionary history reconstructions showed genome-wide homologous recombination and evidence of whole-plasmid exchange. Tracking the origins of recombinant segments revealed that some strains have imported DNA from as-yet-unsampled or -unsequenced C. psittaci lineages or other Chlamydiaceae species. Three ancestral populations of C. psittaci were predicted, explaining the current population structure. Molecular clock analysis found that certain strains are part of a clonal epidemic expansion likely introduced into North America by South American bird traders, suggesting that psittacosis is a recently emerged disease originating in New World parrots. IMPORTANCE Chlamydia psittaci is classified as a CDC biothreat agent based on its association with life-threatening lung disease, termed psittacosis, in humans. Because of the recent remarkable findings of frequent recombination across the genome of the human sexually transmitted and ocular trachoma pathogen Chlamydia trachomatis, we sought to determine if similar evolutionary dynamics occur in C. psittaci. Twenty C. psittaci genomes were analyzed from diverse strains that may play a pathogenic role in human disease. Evolution of the strains revealed genome-wide recombination occurring at a higher rate than for C. trachomatis. Certain strains were discovered to be part of a recent epidemic clonal expansion originating in South America. These strains may have been introduced into the United States from South American bird traders, suggesting that psittacosis is a recently emerged disease originating in New World parrots. Our analyses indicate that C. psittaci strains have a history of frequently switching hosts and undergoing recombination.

scholarly journals On the Pleistocene Snow-Line Depression in the Arid Regions of the South American Andes

1971 ◽  
Vol 10 (59) ◽  
pp. 255-267
Author(s):  
Stefan L. Hastenrath
Keyword(s):  
Arid Regions ◽  
South American ◽  
The South ◽  
Temperate Latitude ◽  
The Andes ◽  
Western Cordillera ◽  
Snow Line ◽  
The Pacific ◽  
The Arid Regions ◽  
June July

AbstractField observations during a journey through the arid regions of the South American Andes in June-July 1969 are evaluated in conjunction with available air photographs and reports from adjacent regions of the High Andes. Results indicate an increase of the Pleistocene snow-line depression in the western Cordillera from about 700 m at lat. 12° S. to more than 1 500 m at lat. 30° S. The Pleistocene snow-line depression decreases from the Pacific to the Atlantic side of the Andes, but particularly strongly so on the poleward fringe of the arid region. From this geomorphic evidence it is suggested that the atmospheric circulation during the glacial period was characterized by an Equatorward displacement of the boundary between tropical easterlies and temperate-latitude westerlies.

scholarly journals Analysis of Brachypodium genomes with genome-wide optical maps

Genome ◽  
2018 ◽  
Vol 61 (8) ◽  
pp. 559-565 ◽  
Author(s):  
Tingting Zhu ◽  
Zhaorong Hu ◽  
Juan C. Rodriguez ◽  
Karin R. Deal ◽  
Jan Dvorak ◽  
...  
Keyword(s):  
Genetic Model ◽  
Brachypodium Distachyon ◽  
Pairwise Alignment ◽  
Whole Genome ◽  
Structural Variants ◽  
Genome Wide ◽  
Complex Process ◽  
Optical Maps ◽  
Lines Of Evidence ◽  
Detection And Quantification

Brachypodium distachyon (n = 5) is a diploid and has been widely used as a genetic model. Brachypodium stacei (n = 10) and B. hybridum (n = 15) are species that are related to B. distachyon, leading to an hypothesis that they are part of a polyploid series based on x = 5. Several lines of evidence suggest that this hypothesis is incorrect and that the genomes of the three taxa may have evolved by a more complex process. We constructed an optical whole-genome BioNano genome (BNG) map for each species and did pairwise alignment of the BNG maps. The maps showed that B. distachyon and B. stacei are both diploid, in spite of B. stacei having twice as many chromosomes as B. distachyon, and that B. hybridum is an allopolyploid formed from hybridization between B. distachyon and B. stacei. This study also demonstrated the use of BNG maps in the detection and quantification of structural variants among the genomes.

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