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Journal ArticleDOI

Importance of the geographic barriers to promote gene drift and avoid pre- and post-Columbian gene flow in Mexican native groups: Evidence from forensic STR Loci.

TL;DR: Different dynamics of gene flow and drift were observed among Mexican Native groups, highlighting the geographic barriers as the main factor differentiating Pre-Hispanic populations, and eventually helping to avoid Post-European contact admixture and population bottleneck.
Abstract: Objective: To analyze the origin, structure,relationships, and recent admixture in Mexican Native groups basedon 15 STRs commonly used in human identification. Methods: We analyzed 39 Mexican Native population samples using STR databases based on the AmpFlSTRVRIdentifiler kit (n=3,135), including Mexican-Mestizos (admixed),European and African populations, as reference. Results: Based upon effective population size (Ne) differences, Native groups were clustered into three regions: i)Center-Southeast groups, characterized by larger Ne, migration rate (Nm), genetic diversity (He), and relative homo-geneity principally in the Yucatan Peninsula; ii) Isolated southern groups from Chiapas and Oaxaca, characterizedby lower Ne, Nm, and He (i.e. higher isolation and genetic differentiation); iii) North-Northwest groups, which aresimilar to the previous group but are characterized by generating the widest gene flow barrier in the Pre-HispanicMexican territory, and currently by elevated admixture in some northern Native groups. Despite the relative congru-ence between genetic relationships with cultural, linguistic, geographic criteria, these factors do not explain thepresent-day population structure of Native groups, excepting in those linguistically related to the Mayan that showhigher homogeneity. The Isolation by distance model was demonstrated at long distances (>1,500 km), whereas geo-graphic isolation stands as a determining factor to avoid both non-indigenous admixture and bottleneck processes. Conclusions: Different dynamics of gene flow and drift were observed among Mexican Native groups, highlight-ing the geographic barriers (mountains, canyons and jungle regions) as the main factor differentiating Pre-hispanicpopulations, and eventually helping to avoid Post-European contact admixture and population bottleneck.
Citations
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Journal ArticleDOI
TL;DR: This article performed a genome-wide analysis of 716 newly genotyped individuals from 60 of the 68 recognized ethnic groups in Mexico and found that the genetic structure of these populations is strongly influenced by geography, and their demographic reconstructions suggest a decline in the population size of all tested populations in the last 15-30 generations.
Abstract: The genetic makeup of Indigenous populations inhabiting Mexico has been strongly influenced by geography and demographic history. Here, we perform a genome-wide analysis of 716 newly genotyped individuals from 60 of the 68 recognized ethnic groups in Mexico. We show that the genetic structure of these populations is strongly influenced by geography, and our demographic reconstructions suggest a decline in the population size of all tested populations in the last 15-30 generations. We find evidence that Aridoamerican and Mesoamerican populations diverged roughly 4-9.9 ka, around the time when sedentary farming started in Mesoamerica. Comparisons with ancient genomes indicate that the Upward Sun River 1 (USR1) individual is an outgroup to Mexican/South American Indigenous populations, whereas Anzick-1 was more closely related to Mesoamerican/South American populations than to those from Aridoamerica, showing an even more complex history of divergence than recognized so far.

18 citations

Journal ArticleDOI
TL;DR: This study validates the confident use of the PowerPlex® 21 system for human identification purposes in Mestizo populations throughout the Mexican territory.
Abstract: We analyzed Mestizo (admixed) population samples from different geographic regions of Mexico (n = 1283) with 20 autosomal STRs (PowerPlex® 21, Promega Corp.). Allele frequencies and forensic parameters from the Northwest, Northeast, West, Center, and Southeast regions are reported, as well as from the pooled Mexican population sample. The combined PD and PE for this 20 STR system were > 0.9999999999 and > 0.99999996593% in all five population samples, respectively. Analysis of molecular variance (AMOVA) of these Mexican population samples, plus Monterrey (Northeast) and Mexico (Center) Cities, showed low but significant differences among Mexican-Mestizos from the seven populations (Fst = 0.20%; p = 0.0000). Structure analysis showed the highest proportion of Native American ancestry in Mexico City, Center, and Southeast regions, respectively, which was in agreement with the estimated genetic distances represented in a MDS plot and a NJ tree. The best fit of population clusters (K = 4) obtained with the Structure software indicates that Mexican-Mestizos are mainly composed by European, African, and two Native American ancestries. The European and Native American ancestries displayed a contrary gradient, increasing toward the North-West and South-Southeast, respectively. These 20 autosomal STR loci improved the admixture estimation regarding previous studies with the 13 CODIS-STRs, as supported by the higher similarity with previous estimates based on genome-wide SNP. In brief, this study validates the confident use of the PowerPlex® 21 system for human identification purposes in Mestizo populations throughout the Mexican territory.

13 citations

Journal ArticleDOI
18 Aug 2018-Gene
TL;DR: Assessment of which genetic risk variants could be involved in the high rates of T2D in 92 individuals with Maya ancestry proposes 24 candidate SNPs associated with T1D for replication studies and one for protective association with T2d.

12 citations

Journal ArticleDOI
TL;DR: Heterogeneity in craniometrically-derived estimates of admixture is investigated in order to reveal population substructure in a sample of Black, White, Hispanic, and Native American individuals from the FDB and its findings agree with census trends and speak broadly to admixture dynamics and ancestral diversity among contemporary Americans.
Abstract: Objectives This study investigates heterogeneity in craniometrically-derived estimates of admixture in order to reveal population substructure in a sample of Black, White, Hispanic, and Native American individuals from the FDB. It reports evidence of spatial trends in population-specific patterns of admixture and contextualizes its results in terms of demographic diversity in the United States. Materials and Methods The FDB was sampled to capture the population variation within forensic casework, skeletal collections, and the U.S. population-at-large. Individuals were selected for the availability of population identifier, sex, and geographic information. Variation in inferred admixture proportions was evaluated, per population and by sex, for evidence of geographic substructure. Comparative data was sourced from the U.S. Census. Results This analysis identifies significant associations between the estimated Black, Native American and White component memberships and place of birth and recovery. The sampled populations differ significantly in admixture proportions, in a systematic way. Admixture patterns vary in accordance with the densities and relative proportions of the U.S. census populations. Discussion There is considerable variation in admixture estimates, not just between, but notably within, all four of the populations. This substructure can be explained by differences in geography, including regions, divisions, and states. This article's findings agree with census trends and speak broadly to admixture dynamics and ancestral diversity among contemporary Americans. They are also specifically relevant to those cases in the FDB. The presence of subpopulations has implications for cranial research, forensic identification, and studies of biological variation in the United States.

11 citations

Journal ArticleDOI
TL;DR: Interpopulation variability in the observed frequencies of ABCB1 polymorphisms among Mexican Mestizos and Amerindians allow predicting diverse drug responses toABCB1 substrates in these populations.
Abstract: The most widely studied polymorphisms of the ABCB1 gene are rs1128503 (c.1236C>T), rs2032582 (c.2677G>T/A), and rs1045642 (c.3435C>T). Although variation in ABCB1 allele frequencies among Mexican Mestizos (admixed) from different regions has been observed, Mexican Amerindians have been poorly studied. We aimed to describe the genetic variability of these three ABCB1 polymorphisms in a total sample of 273 Mexican volunteers that included Mestizos from the state of Yucatan, and Amerindians from seven populations (Tarahumara, Mayo, Huichol, Purepecha, Nahua, Tojolabal, and Maya). Genotypes were determined by means of Taq Man probes (qPCR). Genotype distribution was in Hardy–Weinberg equilibrium for all three ABCB1polymorphisms in the eight Mexican populations analyzed. For c.1236C>T and c.3435C>T, the heterozygous C/T was the most frequent genotype in the majority of the studied Mexican populations (range 30.8–65.4%), while heterozygous G/T was the most common genotype for c.2677G>T/A (range 25.9–51.2%), mainly followed by G/G (range 3.2–47.1%) and T/T (range 7.0–35.5%). 12 haplotypes were estimated from the three ABCB1 polymorphisms analyzed, with TTT the most frequent haplotype (mean, 37.0%). Genetic differentiation was demonstrated among the studied Mexican populations (Fst p value < 0.0001), which could imply a diverse drug response or a risk for adverse drug reactions to ABCB1 substrates. Although differences among Amerindians are probably due to genetic drift effects, for Mestizos this could imply variation in admixture composition. In conclusion, interpopulation variability in the observed frequencies of ABCB1 polymorphisms among Mexican Mestizos and Amerindians allow predicting diverse drug responses to ABCB1 substrates in these populations.

8 citations

References
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Journal ArticleDOI
01 Jun 2000-Genetics
TL;DR: Pritch et al. as discussed by the authors proposed a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations, which can be applied to most of the commonly used genetic markers, provided that they are not closely linked.
Abstract: We describe a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations. We assume a model in which there are K populations (where K may be unknown), each of which is characterized by a set of allele frequencies at each locus. Individuals in the sample are assigned (probabilistically) to populations, or jointly to two or more populations if their genotypes indicate that they are admixed. Our model does not assume a particular mutation process, and it can be applied to most of the commonly used genetic markers, provided that they are not closely linked. Applications of our method include demonstrating the presence of population structure, assigning individuals to populations, studying hybrid zones, and identifying migrants and admixed individuals. We show that the method can produce highly accurate assignments using modest numbers of loci— e.g. , seven microsatellite loci in an example using genotype data from an endangered bird species. The software used for this article is available from http://www.stats.ox.ac.uk/~pritch/home.html.

27,454 citations

Journal Article

16,851 citations

Journal ArticleDOI
TL;DR: Genalex is a user-friendly cross-platform package that runs within Microsoft Excel, enabling population genetic analyses of codominant, haploid and binary data.
Abstract: genalex is a user-friendly cross-platform package that runs within Microsoft Excel, enabling population genetic analyses of codominant, haploid and binary data. Allele frequency-based analyses include heterozygosity, F statistics, Nei's genetic distance, population assignment, probabilities of identity and pairwise relatedness. Distance-based calculations include amova, principal coordinates analysis (PCA), Mantel tests, multivariate and 2D spatial autocorrelation and twogener. More than 20 different graphs summarize data and aid exploration. Sequence and genotype data can be imported from automated sequencers, and exported to other software. Initially designed as tool for teaching, genalex 6 now offers features for researchers as well. Documentation and the program are available at http://www.anu.edu.au/BoZo/GenAlEx/

15,786 citations


"Importance of the geographic barrie..." refers methods in this paper

  • ...For the 39 Mexican Native American groups, the following genetic diversity statistics were calculated using the Excel complement GeneAlEx 6.5 (Peakall and Smouse, 2006, 2012): number of alleles (Na), number effective of alleles (Ne), observed heterozygosity (Ho), expected heterozygosity (He),…...

    [...]

  • ...We evaluated the genetic relationships among Mexican Native groups by means of the following methods: 1) pairwise Fst distances using the program GeneAlEx 6.5 (Peakall and Smouse, 2006, 2012) and GDA 1.1 (Weir, 1996)....

    [...]

Journal ArticleDOI
TL;DR: Arlequin ver 3.0 as discussed by the authors is a software package integrating several basic and advanced methods for population genetics data analysis, like the computation of standard genetic diversity indices, the estimation of allele and haplotype frequencies, tests of departure from linkage equilibrium, departure from selective neutrality and demographic equilibrium, estimation or parameters from past population expansions, and thorough analyses of population subdivision under the AMOVA framework.
Abstract: Arlequin ver 3.0 is a software package integrating several basic and advanced methods for population genetics data analysis, like the computation of standard genetic diversity indices, the estimation of allele and haplotype frequencies, tests of departure from linkage equilibrium, departure from selective neutrality and demographic equilibrium, estimation or parameters from past population expansions, and thorough analyses of population subdivision under the AMOVA framework. Arlequin 3 introduces a completely new graphical interface written in C++, a more robust semantic analysis of input files, and two new methods: a Bayesian estimation of gametic phase from multi-locus genotypes, and an estimation of the parameters of an instantaneous spatial expansion from DNA sequence polymorphism. Arlequin can handle several data types like DNA sequences, microsatellite data, or standard multi-locus genotypes. A Windows version of the software is freely available on http://cmpg.unibe.ch/software/arlequin3.

14,271 citations

Journal ArticleDOI
TL;DR: TreeView is a simple, easy to use phylogenetic tree viewing utility that runs under both MacOS (on Apple Macintosh computers) and under Microsoft Windows on Intel based computers, the two most common personal computers used by biologists.
Abstract: TreeView is a simple, easy to use phylogenetic tree viewing utility that runs under both MacOS (on Apple Macintosh computers) and under Microsoft Windows on Intel based computers, the two most common personal computers used by biologists. Some phylogeny programs, such as PAUP (Swofford, 1993) and MacClade (Maddison and Maddison, 1992) already provide excellent tree drawing and printing facilities, however at present these programs are restricted to Apple Macintosh computers. Furthermore, they require the user to load a data set before any trees can be displayed which is inconvenient if the user simply wants to view the trees. More portable programs, such as DRAWGRAM and DRAWTREE in the PHYLIP package (Felsenstein, 1993) can run on both MacOS and Windows computers, but make little, if any use of the graphical interface features available under those operating systems. TreeView runs as a native application on either MacOS or Windows computers, enables the user to use the standard fonts installed on their machine, their printer, and supports the relevant native graphics format (PICT and Windows metafile) for either creating graphics files or pasting pictures to other applications via the clipboard. The program also supports standard file operations, such as 'drag and drop' whereby dragging a file's icon onto the program opens that file. TreeView can read a range of tree file formats (see below) and can display trees in a range of styles (Fig. 1). Additional information, such as edge lengths and internal node labels can also be displayed. The order of the terminal taxa in the tree can be altered, and the tree can be rerooted. If the tree file contains more than one tree the user can view each tree in turn. The program can also save trees in a variety of file formats, so that it can be used to move trees between programs that use different file formats.

10,368 citations