Author
Francisco M. Salzano
Other affiliations: University of São Paulo, Federal University of Pará
Bio: Francisco M. Salzano is an academic researcher from Universidade Federal do Rio Grande do Sul. The author has contributed to research in topics: Population & Genetic variability. The author has an hindex of 53, co-authored 428 publications receiving 13617 citations. Previous affiliations of Francisco M. Salzano include University of São Paulo & Federal University of Pará.
Topics: Population, Genetic variability, Haplotype, Allele, Genetic variation
Papers published on a yearly basis
Papers
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Massachusetts Institute of Technology1, Harvard University2, University of Hong Kong3, University College London4, Aix-Marseille University5, University of Geneva6, University of Antioquia7, National Scientific and Technical Research Council8, University of Buenos Aires9, Universidade Federal do Rio Grande do Sul10, Federal University of Paraná11, National Autonomous University of Mexico12, Mexican Social Security Institute13, Instituto Politécnico Nacional14, Nestlé15, Universidad Autónoma de Nuevo León16, University of Santiago de Compostela17, Cayetano Heredia University18, University of Chicago19, Russian Academy of Sciences20, Université de Montréal21, University of Costa Rica22, University of Bern23, Swiss Institute of Bioinformatics24, University of Tarapacá25, Paul Sabatier University26, University of California, Berkeley27, Yale University28, Semel Institute for Neuroscience and Human Behavior29
TL;DR: It is shown that the initial peopling followed a southward expansion facilitated by the coast, with sequential population splits and little gene flow after divergence, especially in South America.
Abstract: The peopling of the Americas has been the subject of extensive genetic, archaeological and linguistic research; however, central questions remain unresolved. One contentious issue is whether the settlement occurred by means of a single migration or multiple streams of migration from Siberia. The pattern of dispersals within the Americas is also poorly understood. To address these questions at a higher resolution than was previously possible, we assembled data from 52 Native American and 17 Siberian groups genotyped at 364,470 single nucleotide polymorphisms. Here we show that Native Americans descend from at least three streams of Asian gene flow. Most descend entirely from a single ancestral population that we call 'First American'. However, speakers of Eskimo-Aleut languages from the Arctic inherit almost half their ancestry from a second stream of Asian gene flow, and the Na-Dene-speaking Chipewyan from Canada inherit roughly one-tenth of their ancestry from a third stream. We show that the initial peopling followed a southward expansion facilitated by the coast, with sequential population splits and little gene flow after divergence, especially in South America. A major exception is in Chibchan speakers on both sides of the Panama isthmus, who have ancestry from both North and South America.
696 citations
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TL;DR: Using DNA data from 50 nuclear loci sequenced in African, Asian and Native American samples, it is shown that a simple African replacement model with exponential growth has a higher probability as compared with alternative multiregional evolution or assimilation scenarios.
Abstract: An appropriate model of recent human evolution is not only important to understand our own history, but it is necessary to disentangle the effects of demography and selection on genome diversity. Although most genetic data support the view that our species originated recently in Africa, it is still unclear if it completely replaced former members of the Homo genus, or if some interbreeding occurred during its range expansion. Several scenarios of modern human evolution have been proposed on the basis of molecular and paleontological data, but their likelihood has never been statistically assessed. Using DNA data from 50 nuclear loci sequenced in African, Asian and Native American samples, we show here by extensive simulations that a simple African replacement model with exponential growth has a higher probability (78%) as compared with alternative multiregional evolution or assimilation scenarios. A Bayesian analysis of the data under this best supported model points to an origin of our species ≈141 thousand years ago (Kya), an exit out-of-Africa ≈51 Kya, and a recent colonization of the Americas ≈10.5 Kya. We also find that the African replacement model explains not only the shallow ancestry of mtDNA or Y-chromosomes but also the occurrence of deep lineages at some autosomal loci, which has been formerly interpreted as a sign of interbreeding with Homo erectus.
559 citations
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University College London1, University of Michigan2, Stanford University3, University of Bern4, University of Antioquia5, University of California, Los Angeles6, Cayetano Heredia University7, University of New Mexico8, Université de Montréal9, University of California, Berkeley10, University of Costa Rica11, Universidade Federal do Rio Grande do Sul12, Federal University of Paraná13, University of Chile14, University of Tarapacá15
TL;DR: Evidence is observed of a higher level of diversity and lower level of population structure in western South America compared to eastern South America, a relative lack of differentiation between Mesoamerican and Andean populations, and a partial agreement on a local scale between genetic similarity and the linguistic classification of populations.
Abstract: We examined genetic diversity and population structure in the American landmass using 678 autosomal microsatellite markers genotyped in 422 individuals representing 24 Native American populations sampled from North, Central, and South America. These data were analyzed jointly with similar data available in 54 other indigenous populations worldwide, including an additional five Native American groups. The Native American populations have lower genetic diversity and greater differentiation than populations from other continental regions. We observe gradients both of decreasing genetic diversity as a function of geographic distance from the Bering Strait and of decreasing genetic similarity to Siberians—signals of the southward dispersal of human populations from the northwestern tip of the Americas. We also observe evidence of: (1) a higher level of diversity and lower level of population structure in western South America compared to eastern South America, (2) a relative lack of differentiation between Mesoamerican and Andean populations, (3) a scenario in which coastal routes were easier for migrating peoples to traverse in comparison with inland routes, and (4) a partial agreement on a local scale between genetic similarity and the linguistic classification of populations. These findings offer new insights into the process of population dispersal and differentiation during the peopling of the Americas.
542 citations
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University College London1, University of Bern2, University of Antioquia3, Cayetano Heredia University4, University of New Mexico5, Universidad Autónoma de la Ciudad de México6, University of California, Berkeley7, University of Costa Rica8, University of California, Los Angeles9, Universidade Federal do Rio Grande do Sul10, Federal University of Paraná11, National University of Jujuy12, University of Chile13, University of Tarapacá14
TL;DR: An analysis of admixture in thirteen Mestizo populations from seven countries in Latin America based on data for 678 autosomal and 29 X-chromosome microsatellites found extensive variation in Native American and European ancestry among populations and individuals and evidence that admixture across Latin America has often involved predominantly European men and both Native and African women.
Abstract: The large and diverse population of Latin America is potentially a powerful resource for elucidating the genetic basis of complex traits through admixture mapping. However, no genome-wide characterization of admixture across Latin America has yet been attempted. Here, we report an analysis of admixture in thirteen Mestizo populations (i.e. in regions of mainly European and Native settlement) from seven countries in Latin America based on data for 678 autosomal and 29 X-chromosome microsatellites. We found extensive variation in Native American and European ancestry (and generally low levels of African ancestry) among populations and individuals, and evidence that admixture across Latin America has often involved predominantly European men and both Native and African women. An admixture analysis allowing for Native American population subdivision revealed a differentiation of the Native American ancestry amongst Mestizos. This observation is consistent with the genetic structure of pre-Columbian populations and with admixture having involved Natives from the area where the Mestizo examined are located. Our findings agree with available information on the demographic history of Latin America and have a number of implications for the design of association studies in population from the region.
431 citations
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University College London1, National Scientific and Technical Research Council2, University of Antioquia3, University of Tarapacá4, National Autonomous University of Mexico5, Universidade Federal do Rio Grande do Sul6, Institute for Fiscal Studies7, University of Geneva8, Cayetano Heredia University9
TL;DR: The geographic distribution of admixture proportions in this sample reveals extensive population structure, illustrating the continuing impact of demographic history on the genetic diversity of Latin America.
Abstract: The current genetic makeup of Latin America has been shaped by a history of extensive admixture between Africans, Europeans and Native Americans, a process taking place within the context of extensive geographic and social stratification. We estimated individual ancestry proportions in a sample of 7,342 subjects ascertained in five countries (Brazil, Chile, Colombia, Mexico and Peru). These individuals were also characterized for a range of physical appearance traits and for self-perception of ancestry. The geographic distribution of admixture proportions in this sample reveals extensive population structure, illustrating the continuing impact of demographic history on the genetic diversity of Latin America. Significant ancestry effects were detected for most phenotypes studied. However, ancestry generally explains only a modest proportion of total phenotypic variation. Genetically estimated and self-perceived ancestry correlate significantly, but certain physical attributes have a strong impact on self-perception and bias self-perception of ancestry relative to genetically estimated ancestry.
343 citations
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TL;DR: The main innovations of the new version of the Arlequin program include enhanced outputs in XML format, the possibility to embed graphics displaying computation results directly into output files, and the implementation of a new method to detect loci under selection from genome scans.
Abstract: We present here a new version of the Arlequin program available under three different forms: a Windows graphical version (Winarl35), a console version of Arlequin (arlecore), and a specific console version to compute summary statistics (arlsumstat). The command-line versions run under both Linux and Windows. The main innovations of the new version include enhanced outputs in XML format, the possibility to embed graphics displaying computation results directly into output files, and the implementation of a new method to detect loci under selection from genome scans. Command-line versions are designed to handle large series of files, and arlsumstat can be used to generate summary statistics from simulated data sets within an Approximate Bayesian Computation framework.
13,581 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
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TL;DR: For the next few weeks the course is going to be exploring a field that’s actually older than classical population genetics, although the approach it’ll be taking to it involves the use of population genetic machinery.
Abstract: So far in this course we have dealt entirely with the evolution of characters that are controlled by simple Mendelian inheritance at a single locus. There are notes on the course website about gametic disequilibrium and how allele frequencies change at two loci simultaneously, but we didn’t discuss them. In every example we’ve considered we’ve imagined that we could understand something about evolution by examining the evolution of a single gene. That’s the domain of classical population genetics. For the next few weeks we’re going to be exploring a field that’s actually older than classical population genetics, although the approach we’ll be taking to it involves the use of population genetic machinery. If you know a little about the history of evolutionary biology, you may know that after the rediscovery of Mendel’s work in 1900 there was a heated debate between the “biometricians” (e.g., Galton and Pearson) and the “Mendelians” (e.g., de Vries, Correns, Bateson, and Morgan). Biometricians asserted that the really important variation in evolution didn’t follow Mendelian rules. Height, weight, skin color, and similar traits seemed to
9,847 citations
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TL;DR: The Discriminant Analysis of Principal Components (DAPC) is introduced, a multivariate method designed to identify and describe clusters of genetically related individuals that performs generally better than STRUCTURE at characterizing population subdivision.
Abstract: The dramatic progress in sequencing technologies offers unprecedented prospects for deciphering the organization of natural populations in space and time. However, the size of the datasets generated also poses some daunting challenges. In particular, Bayesian clustering algorithms based on pre-defined population genetics models such as the STRUCTURE or BAPS software may not be able to cope with this unprecedented amount of data. Thus, there is a need for less computer-intensive approaches. Multivariate analyses seem particularly appealing as they are specifically devoted to extracting information from large datasets. Unfortunately, currently available multivariate methods still lack some essential features needed to study the genetic structure of natural populations. We introduce the Discriminant Analysis of Principal Components (DAPC), a multivariate method designed to identify and describe clusters of genetically related individuals. When group priors are lacking, DAPC uses sequential K-means and model selection to infer genetic clusters. Our approach allows extracting rich information from genetic data, providing assignment of individuals to groups, a visual assessment of between-population differentiation, and contribution of individual alleles to population structuring. We evaluate the performance of our method using simulated data, which were also analyzed using STRUCTURE as a benchmark. Additionally, we illustrate the method by analyzing microsatellite polymorphism in worldwide human populations and hemagglutinin gene sequence variation in seasonal influenza. Analysis of simulated data revealed that our approach performs generally better than STRUCTURE at characterizing population subdivision. The tools implemented in DAPC for the identification of clusters and graphical representation of between-group structures allow to unravel complex population structures. Our approach is also faster than Bayesian clustering algorithms by several orders of magnitude, and may be applicable to a wider range of datasets.
3,770 citations
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TL;DR: For several years the study of social behavior has been undergoing a revolution with far-reaching consequences for the social and biological sciences, partly due to growing acceptance of the evidence that the potency of natural selection is overwhelmingly concentrated at levels no higher than that of the individual.
Abstract: For several years the study of social behavior has been undergoing a revolution with far-reaching consequences for the social and biological sciences. Partly responsible are three recent changes in the attitudes of evolutionary biologists. First was growing acceptance of the evidence that the potency of natural selection is overwhelmingly concentrated at levels no higher than that of the individual. Second was revival of the comparative method, especially as applied to behavior and life histories. Third was spread of the realization that not only are all aspects of structure and function of organisms to be understood solely as products of selection, but because of their peculiarly direct relationship to the forces of selection, behavior and life history phenomena, long neglected by the evolutionists, may be among the most predictable of all phenotypic attributes. These ideas have been appreciated by a few biologists for a long time, but they have only recently begun to characterize the science as a whole. Darwin’s discussion of sterility between species as an incidental effect of evolutionary adaptation (41, p. 260) and his refusal to deal with sex ratio selection (42, p. 399) suggest awareness of the difficult problem of determining the levels at which selection is most powerful. Yet significant clarification of this basic issue did not really commence until publication of Wynne-Edwards’ massive volume (179) championing group selection and inadvertently exposing its unlikelihood. As late as 1958, Fisher felt constrained to add to the revised edition of his 1929 classic, The Genetical Theory of Natural Selection, the admonishment (53, p. 49) that his fundamental theorem and its associated considerations, already misused then by decades of population geneticists dealing (as they saw it) with the fitness of populations, refer strictly to "the progressive modification of structure or function only in so far as variations in these are ofadvantage to the individual... [and afford] no corresponding explanation for any properties of animals and plants.., supposed to be of service to the species to which they belong." Williams’ critique (171) provided a significant turning point. Nevertheless, one has only to pick up any biological journal or attend any biological meeting to realize that this question has not yet been settled for all
3,216 citations