You are on page 1of 7


HUMAN GENETICS populations have experienced high degrees of

isolation. Indeed, when autozygosity is inferred
using runs of homozygosity (ROH), all popula-
The genetics of Mexico recapitulates tions on average have long homozygous tracts,
with the Huichol, Lacandon, and Seri all having

Native American substructure and on average over 10% of the genome in ROH [figs.
S2 and S3 (9)]. These populations are relatively
small, increasing the effects of genetic drift and
affects biomedical traits driving some of the high FST values. In contrast,
the Mayan and Nahuan populations have much
smaller proportions of the genome in ROH, con-
Andrés Moreno-Estrada,1*† Christopher R. Gignoux,2†‡ Juan Carlos Fernández-López,3†
sistent with ROH levels found in Near Eastern
Fouad Zakharia,1 Martin Sikora,1 Alejandra V. Contreras,3 Victor Acuña-Alonzo,4,5
populations in HGDP (12). These populations
Karla Sandoval,1 Celeste Eng,6 Sandra Romero-Hidalgo,3 Patricia Ortiz-Tello,1
are the descendants of large Mesoamerican ci-
Victoria Robles,1 Eimear E. Kenny,1§ Ismael Nuño-Arana,7 Rodrigo Barquera-Lozano,4 vilizations, and concordant with large historical
Gastón Macín-Pérez,4 Julio Granados-Arriola,8 Scott Huntsman,6 Joshua M. Galanter,6,9 populations, have relatively low proportions of
Marc Via,6|| Jean G. Ford,10 Rocío Chapela,11 William Rodriguez-Cintron,12 ROH. The high degree of variance in ROH among
Jose R. Rodríguez-Santana,1,3 Isabelle Romieu,14 Juan José Sienra-Monge,15 populations is an additional indicator of popu-
Blanca del Rio Navarro,15 Stephanie J. London,16 Andrés Ruiz-Linares,5 lation substructure and suggests a large variance

Downloaded from on March 23, 2017

Rodrigo Garcia-Herrera,3 Karol Estrada,3¶ Alfredo Hidalgo-Miranda,3 in historical population sizes. Comparing the ob-
Gerardo Jimenez-Sanchez,3# Alessandra Carnevale,3 Xavier Soberón,3 served ROH patterns to those derived from coa-
Samuel Canizales-Quinteros,3,17 Héctor Rangel-Villalobos,7 Irma Silva-Zolezzi,3** lescent simulations, we find that Native American
Esteban Gonzalez Burchard,6,9* Carlos D. Bustamante1* groups within Mexico are characterized by small
effective population sizes under a model with a
Mexico harbors great cultural and ethnic diversity, yet fine-scale patterns of human strong bottleneck, in agreement with other studies
genome-wide variation from this region remain largely uncharacterized. We studied of Native American populations (13). The degree
genomic variation within Mexico from over 1000 individuals representing 20 indigenous of population size recovery to the current day is
and 11 mestizo populations. We found striking genetic stratification among indigenous consistent with the degree of isolation of the ex-
populations within Mexico at varying degrees of geographic isolation. Some groups were as tant populations, ranging from 1196 chromosomes
differentiated as Europeans are from East Asians. Pre-Columbian genetic substructure is [95% confidence interval (CI) 317 to 1548] for the
recapitulated in the indigenous ancestry of admixed mestizo individuals across the Seri in the Sonora desert, to 3669 (95% CI 2588 to
country. Furthermore, two independently phenotyped cohorts of Mexicans and Mexican 5522) for the Mayans from Quintana Roo (figs. S4
Americans showed a significant association between subcontinental ancestry and lung to S6; (9)).
function. Thus, accounting for fine-scale ancestry patterns is critical for medical and
population genetic studies within Mexico, in Mexican-descent populations, and likely in
many other populations worldwide. Department of Genetics, Stanford University School of
Medicine, Stanford, CA, USA. 2Department of Bioengineering
and Therapeutic Sciences, University of California, San
Francisco, CA, USA. 3Instituto Nacional de Medicina
nderstanding patterns of human popula- regions across Mexico (table S1). Standard prin- Genómica (INMEGEN), Mexico City, Mexico. 4Escuela

U tion structure, where regional surveys are cipal components analysis (PCA) summarizes Nacional de Antropología e Historia (ENAH), Mexico City,
Mexico. 5Department of Genetics, Evolution and
key for delineating geographically restricted the major axes of genetic variation in the data Environment, University College London, London, UK.
variation, is important for the design and set [see (9)]. Whereas PC1 and PC2 separate 6
Department of Medicine, University of California, San
interpretation of medical genetic studies. Africans and Europeans from Native Mexicans, Francisco, CA, USA. 7Instituto de Investigación en Genética
In particular, we expect rare genetic variants, PC3 differentiates indigenous populations with- Molecular, Universidad de Guadalajara, Ocotlán, Mexico.
Instituto Nacional de Ciencias Médicas y Nutrición Salvador
including functionally relevant sites, to exhibit in Mexico, following a clear northwest-southeast Zubirán, Mexico City, Mexico. 9Department of Bioengineering
little sharing among diverged populations (1). cline (Fig. 1A). A total of 0.89% of the variation and Therapeutic Sciences, University of California, San
Native Americans display the lowest genetic is explained by PC3, nearly three times as much Francisco, CA, USA. 10The Brooklyn Hospital Center,
diversity of any continental group, but there is as the variation accounted for by the north-south Brooklyn, NY, USA. 11Instituto Nacional de Enfermedades
Respiratorias (INER), Mexico City, Mexico. 12Veterans
high divergence among subpopulations (2). As axis of differentiation within Europe [0.30%, in Caribbean Health Care System, San Juan, Puerto Rico.
a result, present-day American indigenous pop- (10)]. The northernmost (Seri) and southern- 13
Centro de Neumología Pediatrica, San Juan, Puerto Rico.
ulations (and individuals with indigenous an- most (Lacandon) populations define the extremes International Agency for Research on Cancer, Lyon, France.
cestry) may harbor local private alleles rare or of the distribution, with very clear clustering Hospital Infantil de México Federico Gomez, Mexico City,
Mexico. 16National Institute of Environmental Health
absent elsewhere, including functional and med- of individuals by population, indicating high Sciences, National Institutes of Health, Department of Health
ically relevant variants (3, 4). Mexico serves as levels of divergence among groups (fig. S1). and Human Services, Research Triangle Park, NC, USA.
an important focal point for such analyses, be- Seri and Lacandon show the highest level of Facultad de Química, Universidad Nacional Autónoma de
cause it harbors one of the largest sources of population differentiation as measured with México, Mexico City, Mexico.
*Corresponding author. E-mail:
pre-Columbian diversity and has a long history Wright’s fixation index FST (0.136, Fig. 1B and (C.D.B.); (A.M.-E.); esteban.burchard@
of complex civilizations with varying contribu- table S4), higher than the FST between Euro- (E.G.B.) †These authors contributed equally to this
tions to the present-day population. peans and Chinese populations in HapMap3 work. ‡Present address: Department of Genetics, Stanford University
Previous estimates of Native Mexican genetic (0.11) (11). Other populations within Mexico School of Medicine, Stanford, CA, USA. (C.R.G.) §Present address:
Center for Statistical Genetics, Mount Sinai School of Medicine, New
diversity examined single loci or were limited to also show extreme FST values; for example, the York, USA. (E.E.K.) ||Present address: Department of Psychiatry and
a reduced number of populations or small sam- Huichol and Tojolabal have a pairwise FST of Clinical Psychobiology - IR3C, Universitat de Barcelona, Spain. (M.V.).
ple sizes (5–8). We examined local patterns of 0.068, similar to that observed between the ¶Present address: Analytic and Translational Genetics Unit,
variation from nearly 1 million genome-wide Gujarati Indians and the Chinese in HapMap3 Massachusetts General Hospital, Boston, USA. (K.E.) #Present
address: Harvard School of Public Health and Global Biotech
autosomal single-nucleotode polymorphisms (0.076). Consulting Group. (G.J.-S.) **Present address: Nutrition and
(SNPs) for 511 Native Mexican individuals from The high degree of differentiation between Health Department Nestec Ltd, Nestle Research Center, Lausanne,
20 indigenous groups, covering most geographic populations measured by FST argues that these Switzerland. (I.S.-Z.)

1280 13 JUNE 2014 • VOL 344 ISSUE 6189 SCIENCE


Isolation also correlates with the degree of As seen with the ROH calculations, the Mayan gence and migration among the Native Amer-
relatedness within and between ethnic groups, ul- and Nahuan groups have fewer internal connec- ican populations (Fig. 1D). The inferred tree with
timately shaping the pattern of genetic relation- tions. The few between-population connections no migration paths recapitulates the north/south
ships among populations. We built a relatedness appear in populations close to each coastline, and east/west gradients of differentiation from
graph (Fig. 1C) of individuals sharing >13 cM of such as the connections between the Campeche the PCA and IBD analyses, with populations
the genome identically by descent (IBD) (cor- Mayans and populations to the west along the with high ROH values also exhibiting longer
responding to third/fourth cousins or closer Gulf of Mexico. tip branches. The primary branches divide pop-
relatives). Almost all the connections are within- The long-tract ROH and IBD analyses are es- ulations by geography. All northern populations
versus among-population, consistent with the pecially relevant to the recent history of isolation (dark blue) branch from the same initial split
populations being discrete rather than exhib- of Native American populations. We ran TreeMix at the root. We also find two additional major
iting large-scale gene flow [figs. S7 and S8 (9)]. (14) to generate a probabilistic model of diver- clades: a grouping of populations from the south-
ern states of Guerrero and Oaxaca (green labels)
and a “Mayan clade” composed of Mayan-speaking
populations from Chiapas and the Yucatan pe-
ninsula in the southeast (orange labels). Intro-
ducing migratory edges to the model connects
the Maya in Yucatan to a branch leading to the
Totonac, whose ancestors occupied the large pre-
Columbian city of El Tajin in Veracruz (15). This

Downloaded from on March 23, 2017

result points to an Atlantic coastal corridor of
gene flow between the Yucatan peninsula and
central/northern Mexico (fig. S9), consistent with
our IBD analysis. Indeed, the only Mayan lan-
guage outside the Mayan territory is spoken by
the Huastec, nearby in northern Veracruz, sup-
porting a shared history (16).
These signals remain today as a legacy of the
pre-Columbian diversity of Mexican populations.
Over the past 500 years, population dynamics
have changed drastically. Today, the majority of
Mexicans are admixed and can trace their an-
cestry back not only to indigenous groups but
also to Europe and Africa. To investigate patterns
of admixture, we combined data from continental
source populations (including the 20 native
Mexican groups, 16 European populations, and
50 West African Yorubas) with 500 admixed
mestizo individuals from 10 Mexican states
recruited by the National Institute of Genomic
Medicine (INMEGEN) for this study, Mexicans
from Guadalajara in the POPRES collection (17),
and individuals of Mexican descent from Los
Angeles in the HapMap Phase 3 project (table
S1). We ran the unsupervised mixture model al-
gorithm ADMIXTURE (18) to estimate ancestry
proportions for individuals in our combined data
set (Fig. 2, fig. S10, and table S5). Allowing for
three ancestral clusters (K = 3), we find that most
individuals have a large amount of Native and
European ancestry, with a small (typically <5%)
amount of African ancestry. At the best-fit mod-
el for K = 9, the Native American cluster breaks
down into six separate components (Fig. 2B).
Three of these are mostly restricted to isolated
Fig. 1. Genetic differentiation of Native Mexican populations. (A) PCA of Native Mexicans with populations (Seri, navy blue; Lacandon, yellow;
HapMap YRI and CEU samples. Population labels as in table S1. (B) Pairwise FST values among Native and Tojolabal, brown). The other three show a
Mexican populations ordered geographically (see also table S4). (C) Relatedness graph of individuals wider but geographically well-defined distribu-
sharing more than 13 cM of the genome as measured by the total of segments IBD. Each node tion: A northern component (light blue) repre-
represents a haploid genome, and edges within clusters attract nodes proportionally to shared IBD. sented by Tarahumara, Tepehuano, and Huichol,
The spread of each cluster is thus indicative of the level of relatedness in each population, as deter- gradually decreases southward. Corresponding-
mined by a force-directed algorithm. Only the layout of nodes within each cluster is the result of the ly, a southern component (blue), which includes
algorithm, as populations are localized to their approximate sampling locations to ease interpreta- Triqui, Zapotec, and Mazatec, gradually decreases
tion. Parentheses indicate the number of individuals represented out of the total sample size (2N). northward. In the Yucatan peninsula and the
The full range of IBD thresholds are shown in fig. S8. (D) TreeMix graph representing population neighboring state of Chiapas, we found what we
splitting patterns of the 20 Native Mexican groups studied. The length of the branch is proportional termed the “Mayan component” (orange in Fig.
to the drift of each population. African, European, and Asian samples were used as outgroups to root 2B, bottom panel), found primarily in Mayan-
the tree (fig. S9). speaking groups. This Mayan component is also

SCIENCE 13 JUNE 2014 • VOL 344 ISSUE 6189 1281


Fig. 2. Mexican population structure. (A) Map of sampled pop-

ulations (detailed in table S1) and admixture average proportions
(table S5). Dots correspond to Native Mexican populations color-
coded according to K = 9 clusters identified in (B) (bottom), and
shaded areas denote states in which cosmopolitan populations
were sampled. Pie charts summarize per-state average propor-
tions of cosmopolitan samples at K = 3 (European in red, West
African in green, and Native American in gray). Bars show the
total Native American ancestry decomposed into average propor-
tions of the native subcomponents identified at K = 9. (B) Global
ancestry proportions at K = 3 (top) and K = 9 (bottom) estimated
with ADMIXTURE, including African, European, Native Mexican, and
cosmopolitan Mexican samples (tables S1 and S2). From left to right,
Mexican populations are displayed north-to-south. (C) Interpola-
tion maps showing the spatial distribution of the six native com-
ponents identified at K = 9. Contour intensities are proportional to
ADMIXTURE values observed in Native Mexican samples, with crosses indi-
cating sampling locations. Scatter plots with linear fits show ADMIXTURE
values observed in cosmopolitan samples versus a distance metric summariz-

Downloaded from on March 23, 2017

ing latitude and longitude (long axis) for the sampled states. From left to right:
Yucatan, Campeche, Oaxaca, Veracruz, Guerrero, Tamaulipas, Guanajuato,
Zacatecas, Jalisco, Durango, and Sonora. Values are adjusted relative to
the total Native American ancestry of each individual (9).

1282 13 JUNE 2014 • VOL 344 ISSUE 6189 SCIENCE


present at ~10 to 20% in central Mexican na- hidden population structure within Native Am- (32). Due to differences in protocols and geno-
tives, consistent with the IBD and migration edges erican ancestry beyond that found solely in ex- typing platforms, we calculated ASPCA values
connecting the regions. This relationship between tant indigenous groups (Fig. 3A). Consistent for the two studies independently (fig. S17) using
the Yucatan peninsula and central Mexico, seen with the previous PCA analyses, we observed the the same reference populations described above,
in both recent shared IBD and genetic drift– most diverged indigenous populations defining then used fixed-effects meta-analysis to combine
based models of allele frequencies (TreeMix and the extremes of the top PCs due to high levels of the results (9).
ADMIXTURE), suggests that gene flow between genetic drift and isolation. However, including First, in GALA I we looked for significant
the two regions has been ongoing for a long all the indigenous groups in the plot masks the ancestry-specific differences between Mexico City
time. In contrast, Mayan admixture is not found signal contained in the indigenous segments and the San Francisco Bay Area, the two recruit-
at appreciable levels in highlanders of the south- of the Mexican mestizos. When plotting the ment sites. ASPCA values were associated with
ern state of Oaxaca (Triqui and Zapotec), where ASPCA values for the admixed individuals only, recruitment location, with the receiver-operator
mountain ranges may have acted as geographic we discovered a strong correlation between Na- characteristic curve from the Native American
barriers to gene flow. tive American ancestry and geography within ancestry dimensions resulting in an area under
Patterns of Native American population sub- Mexico (Fig. 3B), with ASPC1 representing a west- the curve (AUC) of 80% (fig. S17). After we ad-
structure are recapitulated in the genomes of to-east dimension and ASPC2 one from north justed for overall ancestry proportions (here both
Mexican mestizos from cosmopolitan popula- to south. Both of these correlations are highly African and Native American), both ASPCs were
tions throughout Mexico. Sonora and neighbor- significant and linearly predictive of geographic significant in a logistic regression: ASPC1 OR per
ing northern states show the highest average location (Pearson’s r2 of 72% and 38% for ASPC1 SD: 0.44 (95% CI 0.22 to 0.68), P = 3.8 × 10−4,
proportions of the northern native component and 2, respectively, both P values < 10−5). The cor- ASPC2 OR per SD: 1.68 (95% CI 1.03 to 2.76), P =

Downloaded from on March 23, 2017

(15%, light blue in Fig. 2B, bottom), whereas relation is strong enough that the overall distri- 0.039. The ASPCs defined similar east-west and
only traces are detected in Oaxaca and the bution of mestizo-derived indigenous haplotypes north-south axes as in the previous analysis (fig.
Yucatan peninsula. Conversely, the southern in ASPCA space resembles a geographic map of S17) and show that Mexican-Americans in the San
native component is the most prevalent across Mexico (Fig. 3B and fig. S15). This finding sug- Francisco Bay Area tend to have increased Na-
states, reaching maximum values in Oaxaca gests that the genetic composition of present-day tive American ancestry from northwest Mexico
and decreasing northward. Cosmopolitan sam- Mexicans recapitulates ancient Native American as compared to individuals from Mexico City
ples from the Yucatan peninsula have Native substructure, despite the potential homogeniz- (joint logistic regression likelihood ratio test
American fractions of the genome dominated ing effect of postcolonial admixture. Fine-scale P = 6.4 × 10−5).
by the Mayan component, which diminishes in population structure going back centuries is not We then used the ASPCA values for both
northward populations. Likewise, Mayan-related merely a property of isolated or rural indigenous studies to test for an association with FEV1 as
local components, Tojolabal and Lacandon, are communities. Cosmopolitan populations still re- transformed to percentile of predicted “normal”
detected above 1% exclusively among individ- flect the underlying genetic ancestry of local na- function via the standard set of reference equa-
uals from the states neighboring the Yucatan tive populations, arguing for a strong relationship tions (28) for individuals of Mexican descent.
peninsula. In contrast, Mexican-Americans sam- between the indigenous and the Mexican mes- These equations use population-specific demo-
pled in Los Angeles (MXL) do not show a homog- tizo population, albeit without the extreme drift graphic characteristics to account for age, sex,
eneous pattern, consistent with their diverse exhibited in some current indigenous groups. and height in estimates of lung function. Ad-
origins within Mexico. Overall, the continuous Having found these hidden patterns of ances- justing for overall ancestry proportions in linear
geographic distribution of each Native American try in the native component of Mexican mestizos, regressions, we observed a significant associa-
component across Mexico (fig. S12) demonstrates we investigated whether this structure could tion between FEV1 and the east-west component
a high correlation of individual admixture pro- have potential biomedical applications. Over (ASPC1) in both studies, with a meta-analysis
portions with geography, even in individuals of the past decade, genetic ancestry has been as- P value of 0.0045 (2.2% decrease in FEV1 per
mixed ancestry (Fig. 2C, NW-SE axis F-test for sociated with numerous clinical endpoints and 1 SD, 95% CI 0.69 to 3.74). The effect sizes
all native clusters, P <10−16). disease risks in admixed populations, including were homogeneous (Fig. 3C and table S6) de-
To further test whether ancestral popula- neutrophil counts (25), creatinine levels (26), and spite differences in recruitment strategy, geog-
tion structure is recapitulated in the genomes breast cancer susceptibility (27). Similarly, an- raphy, and genotyping platform (9). In contrast,
of mestizos, we used an ancestry-specific PCA cestral background is especially important in ASPC2 showed no association with FEV1. Where-
(ASPCA) approach [fig. S13 (9, 19)]. We estimated pulmonary medicine, where different reference as FEV1 has previously been associated with over-
local ancestry using PCAdmix (20) to identify equations are used for different ethnicities, de- all ancestry in several populations, the effect seen
segments of the genome belonging to Native fining normative predicted volumes and identify- here is not correlated with overall admixture
American, European, or African ancestries. We ing thresholds for disease diagnosis in standard proportions, because we adjusted for those in the
focused on the European and Native American clinical practice (28). That is, depending on one’s regression model. The combined results here in-
components of ancestry, given the low propor- ethnic background, the same value of forced ex- dicate that subcontinental ancestry as measured
tions of African ancestry overall. We would expect piratory volume in 1 s (FEV1, a standard measure by ASPCA is important for characterizing clinical
the history of Spanish occupation and coloniza- of lung function) could be either within the nor- measurements.
tion in Mexico to be reflected in the European mal range or indicative of pulmonary disease. To estimate how variation in genetic ancestry
segments of Mexican mestizos, as has been seen Previous work has shown that the proportion of within Mexico may affect FEV1, we used the re-
previously (21). ASPCA of the European haplo- African and European ancestry was associated sults from GALA I and MCCAS to predict trait
types in present-day Mexicans confirms this, with FEV1 in African Americans (29) and Mexicans values by state (Fig. 3D) for the INMEGEN
as individuals cluster tightly with present-day (30), respectively, establishing the importance mestizo samples. We found that difference in
Iberians even with a dense set of European pop- of genomic ancestry in lung function prediction subcontinental Native American ancestry as
ulations (17, 22) (fig. S14). equations. measured by ASPC1 results in an expected
In contrast, given the complex demographic To investigate possible associations between 7.3% change in FEV1, moving from the state of
history of Native Americans, high isolation, and ancestral structure in Mexicans and FEV1, we Sonora in the west to the state of Yucatan in
limited characterization of regional ancestry applied our ASPCA approach to two studies mea- the east. These results suggest that fine-scale
patterns (23, 24), it remains unknown whether suring lung function in Mexican or Mexican- patterns of native ancestry alone could have
the correlation between genes and geography ob- American children: the Mexico City Childhood significant impacts on clinical measurements
served in Europe (10) can be similarly recapitu- Asthma Study (MCCAS) (31) and the Genetics of of lung function in admixed individuals with-
lated within Mexico. We used ASPCA to uncover Asthma in Latino Americans (GALA I) Study in Mexico.

SCIENCE 13 JUNE 2014 • VOL 344 ISSUE 6189 1283


These changes due to ancestry are compar- thresholds. This finding indicates that diagnoses by existing reference panels [figs. S18 to 20 (9)].
able to other factors affecting lung function. Com- of diseases such as asthma and chronic obstruc- Although Mexican-American samples (MXL) were
paring the expected effect of ancestry across tive pulmonary disease (COPD) relying on spe- included in both the HapMap and 1000 Ge-
Mexico with the known effects of age in the cific lung function thresholds may benefit from nomes catalogs, average haplotype sharing for
standard Mexican-American reference equa- taking finer-scale ancestry into consideration. the INMEGEN mestizo samples is limited to
tions (28), the inferred 7.3% change in FEV1 An important implication of our work is that 81.2 and 90.5% when combined with all conti-
associated with subcontinental ancestry is sim- multi- and transethnic mapping efforts will nental HapMap populations. It is only after in-
ilar to the decline in FEV1 that a 30-year-old benefit from including individuals of Mexican cluding the Native American samples genotyped
Mexican-American individual of average height ancestry, because the Mexican population har- here that nearly 100% of haplotypes are shared,
would experience by aging 10.3 years if male bors rich amounts of genetic variation that may maximizing the chances of capturing most of the
and 11.8 years if female. Similarly, comparing underlie important biomedical phenotypes. A variation in Mexico.
our results from the Mexican data with the key question in this regard is whether existing Much effort has been invested in detecting
model incorporating ancestry in African Amer- catalogs of human genome variation capture common genetic variants associated with com-
icans, a difference of 7.3% in FEV1 would corre- the genetic variation present in the samples plex disease and replicating associations across
spond to a 33% difference in African ancestry analyzed here. We performed targeted SNP tag- populations. However, functional and medically
(29). The association between FEV1 and ASPC1 ging and genome-wide haplotype sharing anal- relevant variation may be rare or population-
is not an indicator of impaired lung function ysis within 100-kb sliding windows to assess specific, requiring studies of diverse human
on its own–rather, it contributes to the distribu- the degree to which haplotype diversity in the populations to identify new risk factors (4).
tion of FEV1 values and would modify clinical Mexican mestizo samples could be captured Without detailed knowledge of the geographic

Downloaded from on March 23, 2017

Fig. 3. Subcontinental ancestry of admixed Mexican genomes and bio- subcontinental origin of admixed genomes (prefixed by MEX). Each circle
medical implications. (A) ASPCA of Native American segments from Mexican represents the combined set of haplotypes called Native American along
cosmopolitan samples (colored circles) together with 20 indigenous Mexican the haploid genome of each sample with >25% of Native American an-
populations (population labels). Samples with >10% of non-native ad- cestry. The inset map shows the geographic origin of cosmopolitan sam-
mixture were excluded from the reference panel, as well as population ples per state, color-coded by region (9). (C) Coefficients and 95% CIs for
outliers such as Seri, Lacandon, and Tojolabal. (B) Zoomed detail of the associations between ASPC1 and lung function (FEV1) from Mexican
distribution of the Native American fraction of cosmopolitan samples participants in the GALA I study, and the MCCAS, as well as both studies
throughout Mexico. Native ancestral populations were used to define PCA combined (table S6 and fig. S17) (9). (D) Means and CIs of predicted
space (prefixed by NAT) but removed from the background to highlight the change in FEV1 by state, extrapolated from the model in (C).

1284 13 JUNE 2014 • VOL 344 ISSUE 6189 SCIENCE


stratification of genetic variation, negative results Foundation; the American Asthma Foundation (to E.G.B.); dbGaP through accession number phs000145.v1.p1. Access to the
and lack of replication are likely to dominate the CONACYT grant 129693 (to H.R.-V.); BBSRC grant BB/I021213/1 MCCAS data set may be obtained under the terms of a data transfer
(to A.R.-L.); the National Institutes of Health (NIH) (grants agreement with the National Institute of Environmental Health
outcome of genetic studies in uncharacterized R01GM090087, R01HG003229, ES015794, GM007546, Sciences; the contact is S.J.L.. Individual-level genotypes for new data
populations. Here we have demonstrated a high GM061390, HL004464, HL078885, HL088133, HL111636, presented in this study are available, through a data access
degree of fine-scale genomic structure across RR000083, P60MD006902, and ZIA ES49019); and National agreement to respect the privacy of the participants for the transfer
Mexico, shaped by pre-Columbian population Science Foundation award DMS-1201234. This work was supported of genetic data, by contacting C.D.B., A.M.-E., and INMEGEN
in part by the Intramural Research Program of NIH, National (
dynamics and affecting the present-day genomes Institute of Environmental Health Sciences (to S.J.L.). Some
of Mexican mestizos, which is of both anthro- computations were performed using the UCSF Biostatistics High SUPPLEMENTARY MATERIALS
pological and biomedical relevance. Studies such Performance Computing System. We also thank B. Henn,
as this one are crucial for enabling precision med- S. Gravel, and J. Byrnes for helpful discussions; C. Gunter and
Materials and Methods
M. Carpenter for editing the manuscript; and M. Morales for
icine, providing novel data resources, empowering informatics and programming support. C.D.B. is on the advisory
Supplementary Text
the next generation of genetic studies, and dem- Figs. S1 to S20
board of a project at 23andMe; and on the scientific advisory
Tables S1 to S6
onstrating the importance of understanding and boards of Personalis, Inc.; InVitae; Etalon, Inc.; and
References (33–64)
measuring fine-scale population structure and The collections and methods for the Population Reference Sample
(POPRES) are described by Nelson et al. (2008). The POPRES data 3 February 2014; accepted 21 May 2014
its associations with biomedical traits. sets used for the analyses described here were obtained from 10.1126/science.1251688

1. S. Gravel et al., Proc. Natl. Acad. Sci. U.S.A. 108, 11983–11988

Downloaded from on March 23, 2017

2. S. Wang et al., PLOS Genet. 3, e185 (2007).
3. V. Acuña-Alonzo et al., Hum. Mol. Genet. 19, 2877–2885
4. A. L. Williams et al., Nature 506, 97–101 (2014).
5. R. Lisker, E. Ramírez, V. Babinsky, Hum. Biol. 68, 395–404
Interactions between RNA
6. K. Sandoval et al., Am. J. Phys. Anthropol. 148, 395–405
polymerase and the “core recognition
7. A. Gorostiza et al., PLOS ONE 7, e44666 (2012).
8. D. Reich et al., Nature 488, 370–374 (2012).
9. See supplementary materials on Science Online.
element” counteract pausing
10. J. Novembre et al., Nature 456, 98–101 (2008).
11. D. M. Altshuler et al., Nature 467, 52–58 (2010). Irina O. Vvedenskaya,1* Hanif Vahedian-Movahed,2* Jeremy G. Bird,1,2*
12. B. M. Henn et al., PLOS ONE 7, e34267 (2012).
13. J. Hey, PLOS Biol. 3, e193 (2005).
Jared G. Knoblauch,1 Seth R. Goldman,1 Yu Zhang,2
14. J. K. Pickrell, J. K. Pritchard, PLOS Genet. 8, e1002967 (2012). Richard H. Ebright,2† Bryce E. Nickels1†
15. A. Pascual Soto, El Tajín. En Busca de los Orígenes de una
Civilización (UNAM-INAH, Mexico, 2006). Transcription elongation is interrupted by sequences that inhibit nucleotide addition and
16. L. Campbell, T. Kaufman, Annu. Rev. Anthropol. 14, 187–198
cause RNA polymerase (RNAP) to pause. Here, by use of native elongating transcript
17. M. R. Nelson et al., Am. J. Hum. Genet. 83, 347–358 (2008). sequencing (NET-seq) and a variant of NET-seq that enables analysis of mutant RNAP
18. D. H. Alexander, J. Novembre, K. Lange, Genome Res. 19, derivatives in merodiploid cells (mNET-seq), we analyze transcriptional pausing
1655–1664 (2009). genome-wide in vivo in Escherichia coli. We identify a consensus pause-inducing sequence
19. A. Moreno-Estrada et al., PLOS Genet. 9, e1003925 (2013).
20. A. Brisbin et al., Hum. Biol. 84, 343–364 (2012).
element, G–10Y–1G+1 (where –1 corresponds to the position of the RNA 3′ end). We
21. N. A. Johnson et al., PLOS Genet. 7, e1002410 (2011). demonstrate that sequence-specific interactions between RNAP core enzyme and a core
22. L. R. Botigué et al., Proc. Natl. Acad. Sci. U.S.A. 110, recognition element (CRE) that stabilize transcription initiation complexes also occur in
11791–11796 (2013). transcription elongation complexes and facilitate pause read-through by stabilizing
23. S. Wang et al., PLOS Genet. 4, e1000037 (2008).
24. I. Silva-Zolezzi et al., Proc. Natl. Acad. Sci. U.S.A. 21, 8611–8616
RNAP in a posttranslocated register. Our findings identify key sequence determinants of
(2009). transcriptional pausing and establish that RNAP-CRE interactions modulate pausing.
25. M. A. Nalls et al., Am. J. Hum. Genet. 82, 81–87 (2008).
egulation of gene expression during tran- occupancy of the TEC at a given position is cor-

26. C. A. Peralta et al., Am. J. Nephrol. 31, 202–208 (2010).
27. L. Fejerman et al., Cancer Res. 68, 9723–9728 (2008). scription elongation often involves sequences related with the tendency of the TEC to pause
28. J. L. Hankinson, J. R. Odencrantz, K. B. Fedan, Am. J. Respir. in DNA that cause the transcription elon- at the position. Accordingly, NET-seq analysis
Crit. Care Med. 159, 179–187 (1999).
29. R. Kumar et al., N. Engl. J. Med. 363, 321–330 (2010).
gation complex (TEC) to pause. Pausing enables identification of pause sites. To per-
30. K. Salari et al., Genet. Epidemiol. 29, 76–86 (2005). can affect gene expression by facilitat- form NET-seq in Escherichia coli, cells carrying
31. D. B. Hancock et al., PLOS Genet. 5, e1000623 (2009). ing engagement of regulatory factors, influenc- a chromosomal rpoC-3xFLAG gene, encoding
32. D. G. Torgerson et al., J. Allergy Clin. Immunol. 130, 76, e12 ing formation of RNA secondary structures, and RNAP b′ subunit with a C-terminal 3xFLAG tag
enabling synchronization of transcription and were grown to midexponential phase; cells were
ACKN OW LEDG MEN TS translation. flash-frozen and lysed; 3xFLAG-tagged TECs were
We thank all volunteers for generously donating DNA samples and Several lines of evidence suggest that pausing immunoprecipitated with an antibody against
participating in the study. This project was possible with the joint involves specific sequence signals that inhibit FLAG; RNAs were extracted from TECs; and RNA
support from multiple Institutions in Mexico and the United States. nucleotide addition (1–11). To define key sequence 3′ ends were converted to cDNAs and analyzed
Stanford University supported C.D.B. with funding from the
Department of Genetics. INMEGEN received support from the
determinants for pausing, we used native elongat- using high-throughput sequencing. We defined
Federal Government of Mexico, particularly the Ministry of Health, ing transcript sequencing (NET-seq), which permits pause sites as positions where TEC occupancy
the Mexican Health Foundation (FUNSALUD), and the Gonzalo Río occupancies of TECs to be mapped genome-wide exceeded TEC occupancy at each position 25 base
Arronte Foundation. State governments and universities of with base-pair resolution (12, 13) (fig. S1). The pairs (bp) upstream and downstream. We iden-
Durango, Campeche, Guanajuato, Guerrero, Oaxaca, Sonora,
Tamaulipas, Veracruz, Yucatan, and Zacatecas contributed
tified 15,553 pause sites, which corresponds to
significantly to this work. This research was also supported by the 1
Department of Genetics and Waksman Institute, Rutgers ~19,800 total pause sites, given the estimated
George Rosenkranz Prize for Health Care Research in Developing University, Piscataway, NJ 08854, USA. 2Department of ~78% saturation of the analysis (tables S1 to
Countries awarded to A.M.-E.; University of California San Chemistry and Waksman Institute, Rutgers University, S7). Alignment of pause-site sequences revealed
Francisco (UCSF) Chancellor’s Research Fellowship, Dissertation Piscataway, NJ 08854, USA.
Year Fellowship, and NIH Training Grants T32GM007175 and *These authors contributed equally. †Corresponding author. E-mail:
a clear consensus pause element (PE): G–10Y–1G+1,
T32HG000044 (to C.R.G.); the Robert Wood Johnson Foundation (B.E.N.); ebright@waksman.rutgers. where position –1 corresponds to the position
Amos Medical Faculty Development Award; the Sandler edu (R.H.E.) of the RNA 3′ end (Fig. 1A and fig. S2). Of the

SCIENCE 13 JUNE 2014 • VOL 344 ISSUE 6189 1285

The genetics of Mexico recapitulates Native American
substructure and affects biomedical traits
Andrés Moreno-Estrada, Christopher R. Gignoux, Juan Carlos
Fernández-López, Fouad Zakharia, Martin Sikora, Alejandra V.
Contreras, Victor Acuña-Alonzo, Karla Sandoval, Celeste Eng,
Sandra Romero-Hidalgo, Patricia Ortiz-Tello, Victoria Robles,
Eimear E. Kenny, Ismael Nuño-Arana, Rodrigo Barquera-Lozano,
Gastón Macín-Pérez, Julio Granados-Arriola, Scott Huntsman,
Joshua M. Galanter, Marc Via, Jean G. Ford, Rocío Chapela,
William Rodriguez-Cintron, Jose R. Rodríguez-Santana, Isabelle
Romieu, Juan José Sienra-Monge, Blanca del Rio Navarro,
Stephanie J. London, Andrés Ruiz-Linares, Rodrigo Garcia-Herrera,
Karol Estrada, Alfredo Hidalgo-Miranda, Gerardo Jimenez-Sanchez,
Alessandra Carnevale, Xavier Soberón, Samuel
Canizales-Quinteros, Héctor Rangel-Villalobos, Irma Silva-Zolezzi,
Esteban Gonzalez Burchard and Carlos D. Bustamante (June 12,

Downloaded from on March 23, 2017

Science 344 (6189), 1280-1285. [doi: 10.1126/science.1251688]
Editor's Summary

The population structure of Native Mexicans

The genetics of indigenous Mexicans exhibit substantial geographical structure, some as
divergent from each other as are existing populations of Europeans and Asians. By performing
genome-wide analyses on Native Mexicans from differing populations, Moreno-Estrada et al.
successfully recapitulated the pre-Columbian substructure of Mexico. This ancestral structure is evident
among cosmopolitan Mexicans and is correlated with subcontinental origins and medically relevant
aspects of lung function. These findings exemplify the importance of understanding the genetic
contributions of admixed individuals.
Science, this issue p. 1280

This copy is for your personal, non-commercial use only.

Article Tools Visit the online version of this article to access the personalization and
article tools:

Permissions Obtain information about reproducing this article:

Science (print ISSN 0036-8075; online ISSN 1095-9203) is published weekly, except the last week
in December, by the American Association for the Advancement of Science, 1200 New York
Avenue NW, Washington, DC 20005. Copyright 2016 by the American Association for the
Advancement of Science; all rights reserved. The title Science is a registered trademark of AAAS.