Author
Omar E. Cornejo
Other affiliations: Stanford University, Venezuelan Institute for Scientific Research, Emory University
Bio: Omar E. Cornejo is an academic researcher from Washington State University. The author has contributed to research in topics: Population & Plasmodium vivax. The author has an hindex of 23, co-authored 50 publications receiving 2956 citations. Previous affiliations of Omar E. Cornejo include Stanford University & Venezuelan Institute for Scientific Research.
Topics: Population, Plasmodium vivax, Biology, Genome, Medicine
Papers published on a yearly basis
Papers
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University of Copenhagen1, Texas A&M University2, Uppsala University3, Natural History Museum4, University of California, Berkeley5, Aarhus University6, Technical University of Denmark7, University of Chicago8, Montana State University9, Stanford University10, University of Montana11, Washington State University12, University of Tartu13, University of Cambridge14, King Abdullah University of Science and Technology15, Royal Holloway, University of London16, Southern Methodist University17, University College London18, University of Illinois at Urbana–Champaign19, Pennsylvania State University20, University of York21, Medical Research Council22
TL;DR: The genome sequence of a male infant recovered from the Anzick burial site in western Montana is sequenced and it is shown that the gene flow from the Siberian Upper Palaeolithic Mal’ta population into Native American ancestors is also shared by the AnZick-1 individual and thus happened before 12,600 years bp.
Abstract: Clovis, with its distinctive biface, blade and osseous technologies, is the oldest widespread archaeological complex defined in North America, dating from 11,100 to 10,700 C-14 years before present (BP) (13,000 to 12,600 calendar years BP)(1,2). Nearly 50 years of archaeological research point to the Clovis complex as having developed south of the North American ice sheets from an ancestral technology(3). However, both the origins and the genetic legacy of the people who manufactured Clovis tools remain under debate. It is generally believed that these people ultimately derived from Asia and were directly related to contemporary Native Americans(2). An alternative, Solutrean, hypothesis posits that the Clovis predecessors emigrated from southwestern Europe during the Last Glacial Maximum(4). Here we report the genome sequence of a male infant (Anzick-1) recovered from the Anzick burial site in western Montana. The human bones date to 10,705 +/- 35 C-14 years BP (approximately 12,707-12,556 calendar years BP) and were directly associated with Clovis tools. We sequenced the genome to an average depth of 14.4x and show that the gene flow from the Siberian Upper Palaeolithic Mal'ta population(5) into Native American ancestors is also shared by the Anzick-1 individual and thus happened before 12,600 years BP. We also show that the Anzick-1 individual is more closely related to all indigenous American populations than to any other group. Our data are compatible with the hypothesis that Anzick-1 belonged to a population directly ancestral to many contemporary Native Americans. Finally, we find evidence of a deep divergence in Native American populations that predates the Anzick-1 individual.
464 citations
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University of Copenhagen1, University of Massachusetts Amherst2, University of California, Berkeley3, Wellcome Trust Sanger Institute4, Technical University of Denmark5, Pennsylvania State University6, La Trobe University7, Stanford University8, King Abdullah University of Science and Technology9, University of Cambridge10, University of Tartu11, Estonian Biocentre12, University of California, San Francisco13, Washington State University14, University of Porto15, University of Illinois at Urbana–Champaign16, Carlos III Health Institute17, University of Utah18, Science for Life Laboratory19, Aarhus University20, University College London21, University of Reading22, University of Bristol23, University of Guadalajara24, University of Bologna25, Oregon State University26, University of Paris27, University of Zurich28, St. John's University29, Max Planck Society30, University of California, Irvine31, University of Tarapacá32, University of Toulouse33, Russian Academy of Sciences34, Novosibirsk State University35, Kemerovo State University36, Bashkir State University37, North-Eastern Federal University38, Western Washington University39, Northwest Community College40, University of Western Ontario41, Simon Fraser University42, Laboratory of Molecular Biology43, University of Kansas44, University of California, Davis45, Texas A&M University46, Santa Barbara Museum of Natural History47, Southern Methodist University48
TL;DR: The results suggest that there has been gene flow between some Native Americans from both North and South America and groups related to East Asians and Australo-Melanesians, the latter possibly through an East Asian route that might have included ancestors of modern Aleutian Islanders.
Abstract: How and when the Americas were populated remains contentious. Using ancient and modern genome-wide data, we found that the ancestors of all present-day Native Americans, including Athabascans and Amerindians, entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (ka) and after no more than an 8000-year isolation period in Beringia. After their arrival to the Americas, ancestral Native Americans diversified into two basal genetic branches around 13 ka, one that is now dispersed across North and South America and the other restricted to North America. Subsequent gene flow resulted in some Native Americans sharing ancestry with present-day East Asians (including Siberians) and, more distantly, Australo-Melanesians. Putative "Paleoamerican" relict populations, including the historical Mexican Pericues and South American Fuego-Patagonians, are not directly related to modern Australo-Melanesians as suggested by the Paleoamerican Model.
459 citations
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University of Copenhagen1, Pennsylvania State University2, University of Chicago3, Harvard University4, Uppsala University5, University of Toronto6, National Museum of Natural History7, Technical University of Denmark8, Aarhus University9, University of California, Irvine10, Max Planck Society11, St. John's University12, University of Western Ontario13, University of Cambridge14, University of Aberdeen15, University of Edinburgh16, University of Tartu17, Stanford University18, Washington State University19, University of California, Berkeley20, Ontario Institute for Cancer Research21, Bashkir State University22, Northwestern University23, University of Utah24, Russian Academy25, Stockholm University26, University of Kansas27
TL;DR: In this paper, the authors present genome-wide sequence data from ancient and present-day humans from Greenland, Arctic Canada, Alaska, Aleutian Islands, and Siberia, and show that a single Paleo-Eskimo metapopulation likely survived in near-isolation for more than 4000 years, only to vanish around 700 years ago.
Abstract: The New World Arctic, the last region of the Americas to be populated by humans, has a relatively well-researched archaeology, but an understanding of its genetic history is lacking. We present genome-wide sequence data from ancient and present-day humans from Greenland, Arctic Canada, Alaska, Aleutian Islands, and Siberia. We show that Paleo-Eskimos (~3000 BCE to 1300 CE) represent a migration pulse into the Americas independent of both Native American and Inuit expansions. Furthermore, the genetic continuity characterizing the Paleo-Eskimo period was interrupted by the arrival of a new population, representing the ancestors of present-day Inuit, with evidence of past gene flow between these lineages. Despite periodic abandonment of major Arctic regions, a single Paleo-Eskimo metapopulation likely survived in near-isolation for more than 4000 years, only to vanish around 700 years ago.
266 citations
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TL;DR: Theobroma cacao L. cultivar Matina 1-6 belongs to the most cultivated cacao type and the availability of its genome sequence and methods for identifying genes responsible for important cacao traits will aid cacao researchers and breeders as discussed by the authors.
Abstract: Background
Theobroma cacao L. cultivar Matina 1-6 belongs to the most cultivated cacao type. The availability of its genome sequence and methods for identifying genes responsible for important cacao traits will aid cacao researchers and breeders.
222 citations
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TL;DR: The phylogenetic relationships among 10 species of Plasmodium that infect primates are investigated by using three genes, two nuclear (beta-tubulin and cell division cycle 2) and a gene from the plastid genome (the elongation factor Tu) to find compelling evidence that P. vivax is derived from a species that inhabited macaques in Southeast Asia.
Abstract: The high prevalence of Duffy negativity (lack of the Duffy blood group antigen) among human populations in sub-Saharan Africa has been used to argue that Plasmodium vivax originated on that continent. Here, we investigate the phylogenetic relationships among 10 species of Plasmodium that infect primates by using three genes, two nuclear (β-tubulin and cell division cycle 2) and a gene from the plastid genome (the elongation factor Tu). We find compelling evidence that P. vivax is derived from a species that inhabited macaques in Southeast Asia. Specifically, those phylogenies that include P. vivax as an ancient lineage from which all of the macaque parasites could originate are significantly less likely to explain the data. We estimate the time to the most recent common ancestor at four neutral gene loci from Asian and South American isolates (a minimum sample of seven isolates per locus). Our analysis estimates that the extant populations of P. vivax originated between 45,680 and 81,607 years ago. The phylogeny and the estimated time frame for the origination of current P. vivax populations are consistent with an “out of Asia” origin for P. vivax as hominoid parasite. The current debate regarding how the Duffy negative trait became fixed in Africa needs to be revisited, taking into account not only human genetic data but also the genetic diversity observed in the extant P. vivax populations and the phylogeny of the genus Plasmodium.
220 citations
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TL;DR: It is suggested that the natural selection against large insertion/deletion is so weak that a large amount of variation is maintained in a population.
11,521 citations
01 Jan 1980
TL;DR: In this article, the influence of diet on the distribution of nitrogen isotopes in animals was investigated by analyzing animals grown in the laboratory on diets of constant nitrogen isotopic composition and found that the variability of the relationship between the δ^(15)N values of animals and their diets is greater for different individuals raised on the same diet than for the same species raised on different diets.
Abstract: The influence of diet on the distribution of nitrogen isotopes in animals was investigated by analyzing animals grown in the laboratory on diets of constant nitrogen isotopic composition.
The isotopic composition of the nitrogen in an animal reflects the nitrogen isotopic composition of its diet. The δ^(15)N values of the whole bodies of animals are usually more positive than those of their diets. Different individuals of a species raised on the same diet can have significantly different δ^(15)N values. The variability of the relationship between the δ^(15)N values of animals and their diets is greater for different species raised on the same diet than for the same species raised on different diets. Different tissues of mice are also enriched in ^(15)N relative to the diet, with the difference between the δ^(15)N values of a tissue and the diet depending on both the kind of tissue and the diet involved. The δ^(15)N values of collagen and chitin, biochemical components that are often preserved in fossil animal remains, are also related to the δ^(15)N value of the diet.
The dependence of the δ^(15)N values of whole animals and their tissues and biochemical components on the δ^(15)N value of diet indicates that the isotopic composition of animal nitrogen can be used to obtain information about an animal's diet if its potential food sources had different δ^(15)N values. The nitrogen isotopic method of dietary analysis probably can be used to estimate the relative use of legumes vs non-legumes or of aquatic vs terrestrial organisms as food sources for extant and fossil animals. However, the method probably will not be applicable in those modern ecosystems in which the use of chemical fertilizers has influenced the distribution of nitrogen isotopes in food sources.
The isotopic method of dietary analysis was used to reconstruct changes in the diet of the human population that occupied the Tehuacan Valley of Mexico over a 7000 yr span. Variations in the δ^(15)C and δ^(15)N values of bone collagen suggest that C_4 and/or CAM plants (presumably mostly corn) and legumes (presumably mostly beans) were introduced into the diet much earlier than suggested by conventional archaeological analysis.
5,548 citations
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3,213 citations
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TL;DR: Some of the key events in the peopling of the world in the light of the findings of work on ancient DNA are reviewed.
Abstract: Ancient DNA research is revealing a human history far more complex than that inferred from parsimonious models based on modern DNA. Here, we review some of the key events in the peopling of the world in the light of the findings of work on ancient DNA.
1,365 citations
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TL;DR: Genomic signatures of selection and domestication are associated with positively selected genes (PSGs) for fiber improvement in the A subgenome and for stress tolerance in the D subgenomes, suggesting asymmetric evolution.
Abstract: Upland cotton is a model for polyploid crop domestication and transgenic improvement. Here we sequenced the allotetraploid Gossypium hirsutum L. acc. TM-1 genome by integrating whole-genome shotgun reads, bacterial artificial chromosome (BAC)-end sequences and genotype-by-sequencing genetic maps. We assembled and annotated 32,032 A-subgenome genes and 34,402 D-subgenome genes. Structural rearrangements, gene loss, disrupted genes and sequence divergence were more common in the A subgenome than in the D subgenome, suggesting asymmetric evolution. However, no genome-wide expression dominance was found between the subgenomes. Genomic signatures of selection and domestication are associated with positively selected genes (PSGs) for fiber improvement in the A subgenome and for stress tolerance in the D subgenome. This draft genome sequence provides a resource for engineering superior cotton lines.
1,221 citations