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Admixture and genetic relationships of Mexican Mestizos regarding Latin American and Caribbean populations based on 13 CODIS-STRs

01 Feb 2015-Homo-journal of Comparative Human Biology (No longer published by Elsevier)-Vol. 66, Iss: 1, pp 44-59

TL;DR: CODIS-STRs allowed detecting significant population structure in Latin America based on greater presence of European, Amerindian, and African ancestries in Central/South America, Mexican Mestizos, and the Caribbean, respectively.

AbstractShort tandem repeats (STRs) of the combined DNA index system (CODIS) are probably the most employed markers for human identification purposes. STR databases generated to interpret DNA profiles are also helpful for anthropological purposes. In this work, we report admixture, population structure, and genetic relationships of Mexican Mestizos with respect to Latin American and Caribbean populations based on 13 CODIS-STRs. In addition, new STR population data were included from Tijuana, Baja California (Northwest, Mexico), which represents an interesting case of elevated genetic flow as a bordering city with the USA. Inter-population analyses included CODIS-STR data from 11 Mexican Mestizo, 12 Latin American and four Caribbean populations, in addition to European, Amerindian, and African genetic pools as ancestral references. We report allele frequencies and statistical parameters of forensic interest (PD, PE, Het, PIC, typical PI), for 15 STRs in Tijuana, Baja California. This Mexican border city was peculiar by the increase of African ancestry, and by presenting three STRs in Hardy–Weinberg disequilibrium, probably explained by recurrent gene flow. The Amerindian ancestry in Central and Southeast of Mexico was the greatest in Latin America (50.9–68.6%), only comparable with the North of Central America and Ecuador (48.8–56.4%), whereas the European ancestry was prevalent in South America (66.7–75%). The African ancestry in Mexico was the smallest (2.2–6.3%) in Latin America (≥2.6%), particularly regarding Brazil (21%), Honduras (62%), and the Caribbean (43.2–65.2%). CODIS-STRs allowed detecting significant population structure in Latin America based on greater presence of European, Amerindian, and African ancestries in Central/South America, Mexican Mestizos, and the Caribbean, respectively.

Topics: Latin Americans (55%)

Summary (4 min read)

Introduction

  • The microsatellites or short tandem repeats (STRs) have demonstrated to be useful for linkage and segregation analyses, and human and non-human (e.g. dogs and cattle) identification.
  • The inclusion of CODIS-STRs in commercial human identification kits has increased the number of population databases that can be used in molecular anthropology studies (Butler, 2006).
  • In Mexico, the European colonization began in 1519, when Spaniards arrived to the Southeast; they crossed the current state of Tabasco and settled in Veracruz.
  • Based on historical records, their origins are described as follows: 33% from Andalusia, 51% from Leon, Extremadura, the Old and New Castile, 14% from other regions of Spain, and some foreigners (6.2%) mainly from Portugal and Genoa, Italy (Grunberg, 2004).

DNA extraction and genotyping

  • DNA was extracted from buccal swabs or peripheral blood by standard phenol-chloroform method from 409 unrelated Mestizos resident of the Tijuana City, Mexico.
  • The individuals signed a written informed consent according to the Helsinki Declaration.
  • The amplicons and reference allelic ladders were analyzed by capillary electrophoresis in the genetic analyzer ABI-PRISM 310.
  • Results were interpreted using the software GeneMapper 3.2.

Statistical analysis

  • In the population sample from Tijuana, the authors estimated the following forensic parameters with the software PowerStats (Tereba, 2001): allele frequencies, heterozygosity (Het), power of discrimination (PD), power of exclusion (PE), polymorphic information content (PIC), typical paternity index (TPI), and minimum allele frequencies (MAF).
  • Furthermore, for each STR the authors tested the Hardy–Weinberg equilibrium (HWE) and linkage disequilibrium (LD) to check associations between pairs of loci.
  • Fisher exact tests based on 3200 simulations were carried out with the program Genetic Data Analysis (GDA 1.1) for these purposes (Lewis and Zaykin, 2001).

African

  • Six Central-American populations, 1026 persons from six South-American populations, and 628 individuals from four Caribbean populations (Table 1, Fig. 1).
  • In addition, the authors included into the analysis genetic datasets representing the three main ancestral components in Latin American populations: Amerindian, European and African (Table 1).
  • The software Arlequin 3.5.1.3 (Excoffier and Lischer, 2010) and the aforementioned population databases were employed to perform pairwise comparisons, Analysis Molecular of Variance , and FST genetic distances were plotted by multidimensional scaling (MDS) with optimum stress of 0.01 using the program SPSS 10.0 for Windows.
  • In addition, genetic distances of Nei (1978) were estimated with the software GDA 1.1, and were represented in a neighbor joining (NJ) tree by means of TreeView 3.2 (Page, 1996).
  • The coordinates (longitude and latitude) were obtained in Google earth (http://www.google.com/intl/es/earth/index.html).

Genetic relationships

  • Genetic distances and pairwise comparisons were estimated between all Mexican-Mestizo, Central American, South American, and Caribbean populations (Suplementary Table 1).
  • Nei and FST distances were represented in a NJ tree and a MDS plot, respectively (Fig. 2A and B).
  • In Mexico, the almost perfect similarity (p > 0.0019; after Bonferroni correction) between populations from the same region is noticeable when they are separated into Northwest and Central-Southeast regions, and differentiation between populations from the opposite region is visible, supporting the existence of two consistent population clusters of Mexican-Mestizos (Fig. 2A).

Population structure

  • Analysis molecular of variance showed a low but significant inter-population variability (p ≤ 0.0009).
  • In Mexican Mestizos, the inclusion of genetic and geographic criteria to cluster populations sequentially by means of the SAMOVA tests, showed in the first clusters the separation of southeastern populations (data not shown).
  • The most congruent population structure, characterized by significant differences between populations of different groups, but not between populations of the same group, indicated the existence of two main clusters: (1) North and West: Chihuahua, Nuevo León, and Nayarit; and (2) West and Center: Jalisco, Guanajuato, Mexico City and Veracruz.
  • The rest of Mexican Mestizo populations – principally from the Southeast – remained isolated (Tijuana, Puebla, Chiapas, and Yucatán) (Table 2).

Admixture components

  • In Mexican Mestizos, the European ancestry increases to the Northwest, and vice versa the Amerindian counterpart increases to the Southeast, whereas the African ancestry is low and constant throughout the Mexican territory (2.2–6.3%) (Fig. 3A).
  • Honduras2 and Nicaragua were the two major exceptions from the aforementioned pattern due to the sudden increment of African ancestry (13.6–62%).
  • In order to observe the admixture components variation, the authors plotted the standard deviation of individual ancestry for each population studied here (Fig. 4).
  • For most of the Latin American populations, the standard deviations of Amerindian and European ancestries were relatively homogeneous, about two to three times greater than the standard deviation of the African ancestry, except in Honduras2, Brazil, and Caribbean populations, where the African dispersion was higher (range 0.286–0.375), always at the expense of the Amerindian ancestry (Fig. 4).
  • Interestingly, the population of Tijuana, characterized by elevated gene flow, showed the highest African standard deviation (0.157) among the Mexican-Mestizo populations (range 0.04–0.094).

Forensic parameters for the 15 STRs in Tijuana

  • Allele frequencies and statistical parameters of forensic importance are presented in Table 3.
  • Five STRs were in Hardy–Weinberg disequilibrium (p < 0.05), but after applying the Bonferroni correction (p < 0.0033) only three loci remained in disequilibrium: TH01, D21S11, and FGA.
  • These cases implied the aforementioned loci in Hardy–Weinberg disequilibrium, which partially explain this finding and does not deserve further discussion (data not shown).

Discussion

  • The authors analyzed the genetic structure, relationships and admixture components of Mexican-Mestizos based on published CODIS-STR databases from a continental point of view, integrating Latin American and Caribbean populations.
  • A larger ancestral gene pool was obtained (Table 1), which theoretically improved the admixture component estimation regarding the previous study with CODIS-STRs (Rubi-Castellanos et al., 2009a).
  • Another essential issue is the forensic origin of a large number of population samples, because these commonly include both resident and native individuals from the populations that they represent.
  • Therefore, the authors can predict that Mestizo or Latin American populations with similar ancestral proportions will have similar prevalence of certain diseases; if this is not observed, they can imply environmental factors, which should be confirmed in each case.

Mexican Mestizo populations

  • In Mexico, CODIS-STRs allowed inferring a significant genetic structure similar to that described in the previous study of Rubi-Castellanos et al. (2009a).
  • The clearest picture of this structure was obtained from pairwise comparisons and genetic distances graphically represented (Fig. 2A), which allow suggesting two principal population clusters: Northwest (Tijuana, Chihuahua, Nuevo Leon, Jalisco, Nayarit and Guanajuato) and Center-Southeast (Mexico City, Puebla, Veracruz, Chiapas and Yucatan).
  • Supporting this interpretation, their results indicate that some Central American populations show greater African ancestry than that observed in Mexico, such as those observed in Honduras, El Salvador, Nicaragua and Costa Rica (Fig. 3).
  • The admixture component pattern obtained in Mexican Mestizo populations is similar to the previously described by genome-wide SNPs and CODIS-STRs (Rubi-Castellanos et al., 2009a; Silva-Zolezzi et al., 2009).
  • This is explained by software Leadmix employed before for that purpose (Wang, 2003), whereas in this study the program Structure was used (Falush et al., 2003).

Central America and the Caribbean

  • Interestingly, Mexico shows similarity between populations with elevated Amerindian ancestry (Guatemala, El Salvador and Honduras1), but this gradually decreases to the South (56.4–36.2%).
  • In addition, Honduras2 (Black Garifuna), Costa Rica, and Caribbean populations were characterized by greater differentiation (Fig. 2A), attributable to greater African component (Fig. 3A).
  • For the Caribbean, their results detect the elevated African genetic legacy received by the populations studied herein, and show a significant differentiation between some of them (Fig. 2, Table 2).
  • The prevalence of African component is attributable to the trans-Atlantic slave trade that entered the Bahamas from West Africa (Duncan et al., 1996).

South America

  • In South America, pairwise comparisons and genetic distances showed larger population structure than in Mexican Mestizos (Fst = 0.72%, Fig. 2A and B).
  • In most of the Latin American populations, standard deviations of Amerindian and European ancestries were two to three times larger than the African ancestry, except for Brazil, Honduras2 and Caribbean populations (Fig. 4).
  • The authors report allele frequencies and statistical parameters of forensic interest in Tijuana,. (3) The immigration of: (i) medical professionals, surgeons, and nurses to care for USA patients; (ii) tourists traveling for business; (iii) USA retired persons (∼250,000) living in the Tijuana-Ensenada coastal corridor (Ramírez de Arellano, 2006; Vargas-Hernández, 2011).
  • In brief, the effects here detected in Tijuana that could be attributed to elevated gene flow include Hardy–Weinberg disequilibrium in three of 15 STRs (20%), increment of the allele diversity and African ancestry.

Acknowledgments

  • The authors thank to Daniel Piñero and Quinto-Cortés et al. (2010) for the STR dataset of Amerindian groups from Oaxaca provided for admixture analysis.
  • The authors report no conflicts of interest.

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HOMO
-
Journal
of
Comparative
Human
Biology
66
(2015)
44–59
Contents
lists
available
at
ScienceDirect
HOMO
-
Journal
of
Comparative
Human
Biology
j
o
u
rnal
homepage:
www.elsevier.com/locate/jchb
Admixture
and
genetic
relationships
of
Mexican
Mestizos
regarding
Latin
American
and
Caribbean
populations
based
on
13
CODIS-STRs
J.
Salazar-Flores
a,
1
,
F.
Zu
˜
niga-Chiquette
b,
1
,
R.
Rubi-Castellanos
c
,
J.L.
Álvarez-Miranda
b
,
A.
Zetina-Hérnandez
b
,
V.M.
Martínez-Sevilla
a
,
F.
González-Andrade
d
,
D.
Corach
e
,
C.
Vullo
f
,
J.C.
Álvarez
g
,
J.A.
Lorente
g
,
P.
Sánchez-Diz
h
,
R.J.
Herrera
i
,
R.M.
Cerda-Flores
j
,
J.F.
Mu
˜
noz-Valle
k
,
H.
Rangel-Villalobos
a,
a
Instituto
de
Investigación
en
Genética
Molecular,
Centro
Universitario
de
la
Ciénega,
Universidad
de
Guadalajara
(CUCI-UdeG),
Av.
Universidad
#1115,
CP
47810
Ocotlán,
Jalisco,
Mexico
b
Laboratorio
de
Genética
Forense,
Servicios
Periciales
de
la
Procuraduría
General
de
Justicia
del
Estado
de
Baja
California,
BC,
Mexico
c
Laboratorio
de
Genética-CIR
Biomédicas,
Universidad
Autónoma
de
Yucatán
(UADY),
Mérida,
Yucatán,
Mexico
d
Escuela
de
Medicina,
Universidad
Central
del
Ecuador,
Quito,
Ecuador
e
Servicio
de
Huellas
Digitales
Genéticas,
Facultad
de
Farmacia
y
Bioquímica,
Universidad
de
Buenos
Aires,
Buenos
Aires,
Argentina
f
Equipo
Argentino
de
Antropología
Forense,
Independencia
644
5C,
Edif.
EME1,
Córdoba,
Argentina
g
Laboratory
of
Genetic
Identification,
Department
of
Legal
Medicine,
University
of
Granada,
Granada,
Spain
h
Genomics
Medicine
Group,
Galician
Foundation
of
Genomic
Medicine
and
University
of
Santiago
de
Compostela,
CIBERER,
Santiago
de
Compostela,
Spain
i
Department
of
Biological
Sciences,
Florida
International
University,
Miami,
FL
33199,
USA
j
Facultad
de
Enfermería,
Universidad
Autónoma
de
Nuevo
León
(UANL),
Monterrey,
Nuevo
León,
Mexico
k
Instituto
de
Investigación
en
Ciencias
Biomédicas,
Centro
Universitario
de
Ciencias
de
la
Salud,
Universidad
de
Guadalajara
(CUCS-UdeG),
Guadalajara,
Jalisco,
Mexico
a
r
t
i
c
l
e
i
n
f
o
Article
history:
Received
25
August
2013
Accepted
28
August
2014
a
b
s
t
r
a
c
t
Short
tandem
repeats
(STRs)
of
the
combined
DNA
index
sys-
tem
(CODIS)
are
probably
the
most
employed
markers
for
human
identification
purposes.
STR
databases
generated
to
interpret
DNA
profiles
are
also
helpful
for
anthropological
purposes.
In
this
work,
Corresponding
author.
Tel.:
+52
392
9257112;
fax:
+52
392
9257112.
E-mail
address:
hrangel13@hotmail.com
(H.
Rangel-Villalobos).
1
These
authors
contributed
equally
to
this
work.
http://dx.doi.org/10.1016/j.jchb.2014.08.005
0018-442X/©
2014
Elsevier
GmbH.
All
rights
reserved.

J.
Salazar-Flores
et
al.
/
HOMO
-
Journal
of
Comparative
Human
Biology
66
(2015)
44–59
45
we
report
admixture,
population
structure,
and
genetic
relation-
ships
of
Mexican
Mestizos
with
respect
to
Latin
American
and
Caribbean
populations
based
on
13
CODIS-STRs.
In
addition,
new
STR
population
data
were
included
from
Tijuana,
Baja
California
(Northwest,
Mexico),
which
represents
an
interesting
case
of
elevated
genetic
flow
as
a
bordering
city
with
the
USA.
Inter-
population
analyses
included
CODIS-STR
data
from
11
Mexican
Mestizo,
12
Latin
American
and
four
Caribbean
populations,
in
addi-
tion
to
European,
Amerindian,
and
African
genetic
pools
as
ancestral
references.
We
report
allele
frequencies
and
statistical
parame-
ters
of
forensic
interest
(PD,
PE,
Het,
PIC,
typical
PI),
for
15
STRs
in
Tijuana,
Baja
California.
This
Mexican
border
city
was
peculiar
by
the
increase
of
African
ancestry,
and
by
presenting
three
STRs
in
Hardy–Weinberg
disequilibrium,
probably
explained
by
recur-
rent
gene
flow.
The
Amerindian
ancestry
in
Central
and
Southeast
of
Mexico
was
the
greatest
in
Latin
America
(50.9–68.6%),
only
compa-
rable
with
the
North
of
Central
America
and
Ecuador
(48.8–56.4%),
whereas
the
European
ancestry
was
prevalent
in
South
Amer-
ica
(66.7–75%).
The
African
ancestry
in
Mexico
was
the
smallest
(2.2–6.3%)
in
Latin
America
(2.6%),
particularly
regarding
Brazil
(21%),
Honduras
(62%),
and
the
Caribbean
(43.2–65.2%).
CODIS-STRs
allowed
detecting
significant
population
structure
in
Latin
America
based
on
greater
presence
of
European,
Amerindian,
and
African
ancestries
in
Central/South
America,
Mexican
Mestizos,
and
the
Caribbean,
respectively.
©
2014
Elsevier
GmbH.
All
rights
reserved.
Introduction
The
microsatellites
or
short
tandem
repeats
(STRs)
have
demonstrated
to
be
useful
for
linkage
and
segregation
analyses,
and
human
and
non-human
(e.g.
dogs
and
cattle)
identification.
This
is
due
to
their
elevated
heterozygosity,
genome
abundance,
high
mutation
rate,
and
simple
analysis
based
on
the
polymerase
chain
reaction
(PCR)
(Butler,
2006).
For
anthropological
purposes,
their
high
mutation
rate
allows
approaching
historical
questions
such
as
admixture,
structure,
and
migratory
events,
among
others
(Wang
et
al.,
2008).
Probably,
STRs
used
in
forensic
and
paternity
testing
are
the
most
commonly
employed
markers,
specifically
the
core
of
13
STRs
that
comprise
the
combined
DNA
index
system
(CODIS).
The
inclusion
of
CODIS-STRs
in
commercial
human
identification
kits
has
increased
the
number
of
population
databases
that
can
be
used
in
molecular
anthropology
studies
(
Butler,
2006).
The
admixture
process
presupposes
the
contact
of
ancestral
populations
that
have
been
previously
in
relative
isolation
from
each
other
and
generated
hybrid
populations,
whereas
the
population
struc-
ture
implies
differences
between
individuals
of
one
or
more
populations.
This
knowledge
is
essential
in
tasks
such
as
association
mapping,
forensic
casework,
disease
susceptibility
prediction,
wildlife
man-
agement,
and
evolutionary
studies
(Sans,
2000).
In
Latin-America,
hybrid
populations
have
emerged
since
the
European
contact
with
the
New
World
in
1492,
and
currently
reflect
a
complex
genetic
struc-
ture
from
old
and
recent
admixture
processes
(Bryc
et
al.,
2010;
Wang
et
al.,
2008).
In
Mexico,
the
European
colonization
began
in
1519,
when
Spaniards
arrived
to
the
Southeast;
they
crossed
the
cur-
rent
state
of
Tabasco
and
settled
in
Veracruz.
After
the
conquest,
about
85%
of
the
Spaniards
remained
in
conquered
territory.
Based
on
historical
records,
their
origins
are
described
as
follows:
33%
from
Andalusia,
51%
from
Leon,
Extremadura,
the
Old
and
New
Castile,
14%
from
other
regions
of
Spain,
and
some
foreigners
(6.2%)
mainly
from
Portugal
and
Genoa,
Italy
(Grunberg,
2004).
In
Mexico,
in
addition
to
the
European
component,
African
ancestry
was
incorporated
subsequently
by
means
of
slave
trad-
ing
from
various
African
countries,
such
as
Cabo
Verde,
Guinea,
and
Congo
(Aguirre-Beltrán,
1989).

46
J.
Salazar-Flores
et
al.
/
HOMO
-
Journal
of
Comparative
Human
Biology
66
(2015)
44–59
In
fact,
studies
of
mitochondrial
DNA
(mtDNA)
suggest
that
West
and
West-Central
Africa
regions
are
the
most
important
providers
of
African
ancestry
in
Central
America
and
North
America
(Salas
et
al.,
2004).
Nevertheless,
African
genes
could
have
also
arrived
in
Mexico
by
Spanish
migrants
with
Moorish
ancestry,
which
in
turn,
was
a
result
of
the
Islamic
occupation
of
Iberian
Peninsula
(Gerard
et
al.,
2006).
Currently,
most
of
the
Mexican
population
speaks
Spanish
and
is
the
result
of
admixture
between
Spaniards,
Native
Americans
and
African
populations
through
approx.
500
years.
They
are
called
Mes-
tizos
and
predominantly
disclose
the
European
and
Native
American
components,
with
low
levels
of
African
ancestry
(<5%)
(Bryc
et
al.,
2010;
Silva-Zolezzi
et
al.,
2009).
However,
a
Mexican
Mestizo
is
defined
as
a
person
born
in
the
country,
having
a
Spanish-derived
last
name,
with
family
antecedents
of
Mexican
ancestors,
at
least
back
to
the
third
generation
(Sánchez-Serrano,
1996).
A
tri-hybrid
model
has
been
used
to
explain
the
biological
diversity
of
Mexican-Mestizos,
where
specific
ancestral
com-
ponents
increase
in
different
geographical
areas:
European
in
the
North,
Amerindian
in
the
Center
and
Southeast,
and
the
African
in
the
coast.
This
model
has
been
illustrated
in
a
tripolar
diagram
where
the
edges
are
very
narrow,
indicating
a
negligible
number
of
individuals
“genetically
pure”
of
any
of
the
three
ancestries
(Gorodezky
et
al.,
2001).
The
admixture
analysis
in
Latin
America
shows
a
complex
genetic
structure
and
high
variation
of
the
Amerindian
and
European
components,
principally.
These
studies
have
included
genome-wide
SNPs
(Silva-Zolezzi
et
al.,
2009;
Bryc
et
al.,
2010)
and
autosomal
STRs
in
different
Latin
American
populations
(Godinho
et
al.,
2008;
Marino
et
al.,
2006
Wang
et
al.,
2008),
and
particularly
CODIS-STRs
in
Mexican
populations
(Rubi-Castellanos
et
al.,
2009a).
However,
during
the
last
years
further
STR
datasets
used
in
forensic
casework
have
been
reported
in
Mexican-Mestizo
populations
(Table
1),
and
the
current
inter-populational
analyses
have
not
included
the
continental
context.
In
this
study,
we
analyzed
the
ancestry,
structure,
and
genetic
relationship
of
Mexican
Mestizos
with
respect
to
Latin
America
and
the
Caribbean,
based
on
13
CODIS-STRs
population
datasets.
For
that
purpose,
we
included
reference
genetic
pools
representing
the
European,
Amerindian,
and
African
ancestries.
In
addition,
we
included
new
STR
genotype
data
of
Tijuana,
Baja
California
(BC),
the
border
city
located
in
the
North
of
Mexico
where
thousands
of
migrants
pass
to
the
United
States
of
America.
Interestingly,
this
human
mobility
comes
from
various
countries,
principally
Mexico
but
also
Salvador,
Guatemala,
Honduras,
Nicaragua,
Panama,
Costa
Rica,
and
Belize,
respectively
(Brick
et
al.,
2011).
Therefore,
Tijuana
border
city
represents
an
interesting
case
to
analyze
gene
flow
effects
in
human
populations
(INEGI,
2010).
Materials
and
methods
DNA
extraction
and
genotyping
DNA
was
extracted
from
buccal
swabs
or
peripheral
blood
by
standard
phenol-chloroform
method
from
409
unrelated
Mestizos
resident
of
the
Tijuana
City,
Mexico.
The
individuals
signed
a
written
informed
consent
according
to
the
Helsinki
Declaration.
We
amplified
15
STRs
markers
(D3S1358,
TH01,
D21S11,
D18S51,
D5S818,
D13S317,
D7S820,
D16S539,
CSF1PO,
vWA,
D8S1179,
TPOX,
FGA,
D2S1338
and
D19S433)
as
recommended
in
the
PCR
AmpFlSTR
Identifiler
kit
(Applied
Biosystems,
Foster
City,
CA).
The
amplicons
and
reference
allelic
ladders
were
analyzed
by
capillary
electrophoresis
in
the
genetic
analyzer
ABI-PRISM
310.
Results
were
interpreted
using
the
software
GeneMapper
3.2.
Statistical
analysis
In
the
population
sample
from
Tijuana,
we
estimated
the
following
forensic
parameters
with
the
software
PowerStats
(Tereba,
2001):
allele
frequencies,
heterozygosity
(Het),
power
of
discrimination
(PD),
power
of
exclusion
(PE),
polymorphic
information
content
(PIC),
typical
paternity
index
(TPI),
and
minimum
allele
frequencies
(MAF).
Furthermore,
for
each
STR
we
tested
the
Hardy–Weinberg
equi-
librium
(HWE)
and
linkage
disequilibrium
(LD)
to
check
associations
between
pairs
of
loci.
Fisher
exact
tests
based
on
3200
simulations
were
carried
out
with
the
program
Genetic
Data
Analysis
(GDA
1.1)
for
these
purposes
(Lewis
and
Zaykin,
2001).
Inter-population
analysis
was
based
on
13
CODIS-STR
datasets
including
2221
Mestizos
from
11
Mexican
populations,
1125
individuals
from

J.
Salazar-Flores
et
al.
/
HOMO
-
Journal
of
Comparative
Human
Biology
66
(2015)
44–59
47
Table
1
Geographic
region,
abbreviation,
sample
size
and
reference
of
the
admixed
population
analyzed
in
this
study.
Admixed
population
Abbr.
Sample
Reference
Mexico
(Region) Size
Tijuana
(Northwest) Tij
409
This
study
Chihuahua
(North
Center) Chi
162
Martínez-González
et
al.
(2005)
Nuevo
León
(Northeast) NL
143
Cerda-Flores
et
al.
(2002)
Jalisco
(West)
Jal
200
Rubi-Castellanos
et
al.
(2009a,b)
Nayarit
(West) Nay
200
González-Herrera
et
al.
(2010)
Guanajuato
(Center
West) Gto
200
Rangel-Villalobos
et
al.
(2010)
Mexico
City
(Center) Mex
200
Luna-Vázquez
et
al.
(2005)
Puebla
(Center)
Pue
200
Rubi-Castellanos
et
al.,
2009
Veracruz
(Center-East)
Ver
200
Rangel-Villalobos
et
al.
(2010)
Chiapas
(South) Chia
107
Sánchez
et
al.,
2005
Yucatán
(Southeast) Yuc
200
Rubi-Castellanos
et
al.
(2009a,b)
Central
America
Guatemala
Gua
200
Martinez-Espín
et
al.
(2006)
El
Salvador
Sal
200
Monterrosa
et
al.
(2006)
Honduras1
(Center-South)
Hon1
176
Matamoros
et
al.
(2008)
Honduras2
(Caribbean
coast,
Black
Garifuna) Hon2
198
Herrera-Paz
et
al.
(2008)
Nicaragua
Nic
151
Gutiérrez
et
al.
(2011)
Costa
Rica
CR
200
Rodríguez
et
al.
(2007)
South
America
Venezuela
Ven
45
Bernal
et
al.
(2006)
Colombia
Col
200
Porras
et
al.
(2008)
Ecuador
Ecu
200
González-Andrade
et
al.
(2003)
Brazil
Bra
200
Fridman
et
al.
(2008)
Paraguay
Par
181
Martínez-Espin
et
al.
(2003)
Argentina
Arg
200
Marino
et
al.
(2006)
The
Caribbean
Bahamas
Bha
162
Budowle
et
al.
(1999)
Nueva
Providencia
NP
221
Simms
et
al.
(2008)
Jamaica
Jam
160
Budowle
et
al.
(1999)
Trinidad
and
Tobago
TT
85
Budowle
et
al.
(1999)
Ancestral
Pools
Amerindian
From
Mexico
(Purepechas,
Huastecos,
Otomíes,
Tepehuas,
Amuzgos,
Chinantecos,
Choles,
Chontales,
Huaves,
Mixes,
Mixtecos,
Mazatecos,
Triquis,
Zapotecos
Zoques,
and
Mayas)
and
Ecuador
(Woaranis
and
Kichuas)
Amer
915
González-Martín
et
al.
(2008),
Quinto-Cortés
et
al.
(2010),
Ibarra-Rivera
et
al.
(2008),
González-Andrade
et
al.
(2007)
European
From
Iberian
Peninsula
(Spain
and
Portugal)
Eur
642
Camacho
et
al.
(2007),
Coudray
et
al.
(2007)
,
Lopes
et
al.
(2009)
African
From
West
Africa
(Guinea
Bissau,
Equatorial
Guinea,
and
Angola)
Afr
265
Calzada
et
al.
(2005),
Alves
et
al.
(2005)
six
Central-American
populations,
1026
persons
from
six
South-American
populations,
and
628
indi-
viduals
from
four
Caribbean
populations
(Table
1,
Fig.
1).
In
addition,
we
included
into
the
analysis
genetic
datasets
representing
the
three
main
ancestral
components
in
Latin
American
populations:
Amerindian,
European
and
African
(Table
1).
The
software
Arlequin
3.5.1.3
(Excoffier
and
Lischer,
2010)
and
the
aforementioned
population
databases
were
employed
to
perform
pairwise
comparisons,
Analysis
Molecular
of
Variance
(AMOVA),
and
F
ST
genetic
distances
were
plotted
by
multidimensional
scaling
(MDS)
with
optimum
stress
of
0.01
using
the
program
SPSS
10.0
for
Windows.
In
addition,
genetic
distances
of
Nei
(1978)
were
esti-
mated
with
the
software
GDA
1.1,
and
were
represented
in
a
neighbor
joining
(NJ)
tree
by
means
of
TreeView
3.2
(Page,
1996).
Different
population
groups
were
established
considering
genetic
and
geo-
graphical
criteria
using
the
software
SAMOVA
1.0
(Dupanloup
et
al.,
2002).
The
coordinates
(longitude
and
latitude)
were
obtained
in
Google
earth
(http://www.google.com/intl/es/earth/index.html).
The

48
J.
Salazar-Flores
et
al.
/
HOMO
-
Journal
of
Comparative
Human
Biology
66
(2015)
44–59
Fig.
1.
Geographic
location
of
the
Mexican,
Central
America,
South
American,
and
Caribbean
populations
analyzed
here.
Shadow
areas
indicate
the
Mexican
states
and
countries
included
in
this
study.
Abbreviation
meaning
can
be
consulted
in
Table
1.
components
of
admixture
were
estimated
in
individuals
and
populations
with
the
software
Struc-
ture
2.3.3
(Falush
et
al.,
2003),
with
a
burn-in-period
of
10,000
iterations
in
each
parameter
and
25
repetitions
for
each
run
(K),
using
the
mixture
model,
allele
frequency
correlation,
and
-value
sepa-
rated
for
populations,
with
three
populations
groups
identified
as
the
ancestral
references
(supervised
analysis).
Results
Genetic
relationships
Genetic
distances
and
pairwise
comparisons
were
estimated
between
all
Mexican-Mestizo,
Central
American,
South
American,
and
Caribbean
populations
(Suplementary
Table
1).
Nei
and
F
ST
distances
were
represented
in
a
NJ
tree
and
a
MDS
plot,
respectively
(Fig.
2A
and
B).
In
Mexico,
the
almost
per-
fect
similarity
(p
>
0.0019;
after
Bonferroni
correction)
between
populations
from
the
same
region
is
noticeable
when
they
are
separated
into
Northwest
and
Central-Southeast
regions,
and
differentiation
between
populations
from
the
opposite
region
is
visible,
supporting
the
existence
of
two
consistent
population
clusters
of
Mexican-Mestizos
(Fig.
2A).
In
Central
America,
Honduras2
(Black
Garifuna),

Figures (7)
Citations
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Journal ArticleDOI
TL;DR: The findings are consistent with the hypothesis that differences in cognitive ability are passed on along lineages and that they explain some of the global variation in socioeconomic outcomes and are dubbed the racial-cognitive ability-socioeconomic (R~CA-S) hypothesis.
Abstract: We conducted novel analyses regarding the association between continental racial ancestry, cognitive ability and socioeconomic outcomes across 6 datasets: states of Mexico, states of the United States, states of Brazil, departments of Colombia, sovereign nations and all units together. We find that European ancestry is consistently and usually strongly positively correlated with cognitive ability and socioeconomic outcomes (mean r for cognitive ability = .708; for socioeconomic well-being = .643) (Sections 3-8). In most cases, including another ancestry component, in addition to European ancestry, did not increase predictive power (Section 9). At the national level, the association between European ancestry and outcomes was robust to controls for natural-environmental factors (Section 10). This was not always the case at the regional level (Section 18). It was found that genetic distance did not have predictive power independent of European ancestry (Section 10). Automatic modeling using best subset selection and lasso regression agreed in most cases that European ancestry was a non-redundant predictor (Section 11). Results were robust across 4 different ways of weighting the analyses (Section 12). It was found that the effect of European ancestry on socioeconomic outcomes was mostly mediated by cognitive ability (Section 13). We failed to find evidence of international colorism or culturalism (i.e., neither skin reflectance nor self-reported race/ethnicity showed incremental predictive ability once genomic ancestry had been taken into account) (Section 14). The association between European ancestry and cognitive outcomes was robust across a number of alternative measures of cognitive ability (Section 15). It was found that the general socioeconomic factor was not structurally different in the American sample as compared to the worldwide sample, thus justifying the use of that measure. Using Jensen's method of correlated vectors, it was found that the association between European ancestry and socioeconomic outcomes was stronger on more S factor loaded outcomes, r = .75 (Section 16). There was some evidence that tourist expenditure helped explain the relatively high socioeconomic performance of Caribbean states (Section 17).

29 citations


Cites methods from "Admixture and genetic relationships..."

  • ...Admixture estimates were copied from Salzano and Sans (2014), MorenoEstrada et al. (2014) and Salazar-Flores et al. (2015)....

    [...]


Journal ArticleDOI
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.

25 citations


Journal ArticleDOI
TL;DR: The results showed that the FST panel performed slightly better for population resolution based on principal component analysis (PCA) clustering than did the δ panel and both performed better than the In panel, and indicated that individuals could be correctly assigned to the major population categories.
Abstract: Ancestry informative markers (AIMs) can be used to detect and adjust for population stratification and predict the ancestry of the source of an evidence sample. Autosomal single nucleotide polymorphisms (SNPs) are the best candidates for AIMs. It is essential to identify the most informative AIM SNPs across relevant populations. Several informativeness measures for ancestry estimation have been used for AIMs selection: absolute allele frequency differences (δ), F statistics (F ST), and informativeness for assignment measure (In). However, their efficacy has not been compared objectively, particularly for determining affiliations of major US populations. In this study, these three measures were directly compared for AIMs selection among four major US populations, i.e., African American, Caucasian, East Asian, and Hispanic American. The results showed that the F ST panel performed slightly better for population resolution based on principal component analysis (PCA) clustering than did the δ panel and both performed better than the In panel. Therefore, the 23 AIMs selected by the F ST measure were used to characterize the four major American populations. Genotype data of nine sample populations were used to evaluate the efficiency of the 23-AIMs panel. The results indicated that individuals could be correctly assigned to the major population categories. Our AIMs panel could contribute to the candidate pool of AIMs for potential forensic identification purposes.

23 citations


Journal ArticleDOI
Abstract: Motivated by the humanitarian crisis along the US–Mexico border and the need for more integrative approaches to migrant death investigations, we employ both biological and cultural anthropology perspectives to provide insight into these deaths and the forensic identification process. We propose that structural vulnerabilities linked to ethnicity impact the success of identifying deceased migrants. Using forensic genetic data, we examine the relationships among identification status, case year, and ancestry, demonstrating how Native American and European ancestry proportions differ between identified and unidentified migrant fatalities, revealing an otherwise unrecognized identification bias. We find that Mexican migrants with more European ancestry are more often successfully identified in recent years. We attribute this bias in identification to the layers of structural vulnerability that uniquely affect indigenous Mexican migrants. By demonstrating the impact that social processes like structural violence can have on the relative success of forensic casework along the US–Mexico border, our work underscores the fact that forensic casework is itself a social process. Research undertaken with the intent to improve forensic identification protocols should consider social context, a factor that could significantly impact identification rates. This study shows the need for collaboration between forensic practitioners and those working closely with affected communities. [US–Mexico border, forensic anthropology, migration, admixture, DNA]

23 citations


Journal ArticleDOI
TL;DR: Results of this study confirm frequent rates of misclassification among Hispanic and Japanese groups and identify a close morphological relationship that may stem from similar population histories reflected in ancestral Native American and East Asian populations.
Abstract: It has been brought to the attention of the authors of Fordisc 3.1 that Hispanic samples will often misclassify as Japanese when Asian population samples are included. This study examined this problem in an effort to better document the occurrence and deduce possible causes via comparative analyses. Asian and Hispanic samples were first compared utilizing the existing samples from the University of Tennessee's Forensic Data Bank. Additional modern Japanese, Thai, and Korean samples collected by the first author that have previously not been utilized in analyses were subsequently included. Results of this study confirm frequent rates of misclassification among Hispanic and Japanese groups. Furthermore, a close morphological relationship is identified through further group comparisons and the addition of data used in conjunction with Fordisc samples. Similarities identified among Hispanic and Japanese crania may stem from similar population histories reflected in ancestral Native American and East Asian populations.

20 citations


Cites methods from "Admixture and genetic relationships..."

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References
More filters

Journal ArticleDOI
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.

11,882 citations


"Admixture and genetic relationships..." refers methods in this paper

  • ...3 (Excoffier and Lischer, 2010) and the aforementioned population databases were employed to perform pairwise comparisons, Analysis Molecular of Variance (AMOVA), and FST genetic distances were plotted by multidimensional scaling (MDS) with optimum stress of 0....

    [...]

  • ...The software Arlequin 3.5.1.3 (Excoffier and Lischer, 2010) and the aforementioned population databases were employed to perform pairwise comparisons, Analysis Molecular of Variance (AMOVA), and FST genetic distances were plotted by multidimensional scaling (MDS) with optimum stress of 0.01 using…...

    [...]


Journal ArticleDOI
01 Aug 2003-Genetics
TL;DR: Extensions to the method of Pritchard et al. for inferring population structure from multilocus genotype data are described and methods that allow for linkage between loci are developed, which allows identification of subtle population subdivisions that were not detectable using the existing method.
Abstract: We describe extensions to the method of Pritchard et al. for inferring population structure from multilocus genotype data. Most importantly, we develop methods that allow for linkage between loci. The new model accounts for the correlations between linked loci that arise in admixed populations (“admixture linkage disequilibium”). This modification has several advantages, allowing (1) detection of admixture events farther back into the past, (2) inference of the population of origin of chromosomal regions, and (3) more accurate estimates of statistical uncertainty when linked loci are used. It is also of potential use for admixture mapping. In addition, we describe a new prior model for the allele frequencies within each population, which allows identification of subtle population subdivisions that were not detectable using the existing method. We present results applying the new methods to study admixture in African-Americans, recombination in Helicobacter pylori , and drift in populations of Drosophila melanogaster . The methods are implemented in a program, structure , version 2.0, which is available at http://pritch.bsd.uchicago.edu.

7,202 citations


"Admixture and genetic relationships..." refers methods in this paper

  • ...This is explained by software Leadmix employed before for that purpose (Wang, 2003), whereas in this study the program Structure was used (Falush et al., 2003)....

    [...]

  • ...3 (Falush et al., 2003), with a burn-in-period of 10,000 iterations in each parameter and 25 repetitions for each run (K), using the mixture model, allele frequency correlation, and -value separated for populations, with three populations groups identified as the ancestral references (supervised analysis)....

    [...]

  • ...components of admixture were estimated in individuals and populations with the software Structure 2.3.3 (Falush et al., 2003), with a burn-in-period of 10,000 iterations in each parameter and 25 repetitions for each run (K), using the mixture model, allele frequency correlation, and -value…...

    [...]


Journal ArticleDOI
TL;DR: The samova algorithm was applied to a set of European roe deer populations examined for their mitochondrial DNA (mtDNA) HVRI diversity and the inferred genetic structure seemed to confirm the hypothesis that some Italian populations were recently reintroduced from a Balkanic stock.
Abstract: We present a new approach for defining groups of populations that are geographically homogeneous and maximally differentiated from each other. As a by-product, it also leads to the identification of genetic barriers between these groups. The method is based on a simulated annealing procedure that aims to maximize the proportion of total genetic variance due to differences between groups of populations (spatial analysis of molecular variance; samova). Monte Carlo simulations were used to study the performance of our approach and, for comparison, the behaviour of the Monmonier algorithm, a procedure commonly used to identify zones of sharp genetic changes in a geographical area. Simulations showed that the samova algorithm indeed finds maximally differentiated groups, which do not always correspond to the simulated group structure in the presence of isolation by distance, especially when data from a single locus are available. In this case, the Monmonier algorithm seems slightly better at finding predefined genetic barriers, but can often lead to the definition of groups of populations not differentiated genetically. The samova algorithm was then applied to a set of European roe deer populations examined for their mitochondrial DNA (mtDNA) HVRI diversity. The inferred genetic structure seemed to confirm the hypothesis that some Italian populations were recently reintroduced from a Balkanic stock, as well as the differentiation of groups of populations possibly due to the postglacial recolonization of Europe or the action of a specific barrier to gene flow.

1,718 citations


"Admixture and genetic relationships..." refers methods in this paper

  • ...3 (Excoffier and Lischer, 2010) and the aforementioned population databases were employed to perform pairwise comparisons, Analysis Molecular of Variance (AMOVA), and FST genetic distances were plotted by multidimensional scaling (MDS) with optimum stress of 0.01 using the program SPSS 10.0 for Windows. In addition, genetic distances of Nei (1978) were estimated with the software GDA 1....

    [...]

  • ...Different population groups were established considering genetic and geographical criteria using the software SAMOVA 1.0 (Dupanloup et al., 2002)....

    [...]

  • ...0 (Dupanloup et al., 2002)....

    [...]


Journal ArticleDOI
TL;DR: Significant nonrandom association between two markers located 22 cM apart (FY-null and AT3) is detected, most likely due to admixture linkage disequilibrium created in the interbreeding of the two parental populations, emphasize the importance of admixed populations as a useful resource for mapping traits with different prevalence in two parental population.
Abstract: We analyzed the European genetic contribution to 10 populations of African descent in the United States (Maywood, Illinois; Detroit; New York; Philadelphia; Pittsburgh; Baltimore; Charleston, South Carolina; New Orleans; and Houston) and in Jamaica, using nine autosomal DNA markers. These markers either are population-specific or show frequency differences >45% between the parental populations and are thus especially informative for admixture. European genetic ancestry ranged from 6.8% (Jamaica) to 22.5% (New Orleans). The unique utility of these markers is reflected in the low variance associated with these admixture estimates (SEM 1.3%-2.7%). We also estimated the male and female European contribution to African Americans, on the basis of informative mtDNA (haplogroups H and L) and Y Alu polymorphic markers. Results indicate a sex-biased gene flow from Europeans, the male contribution being substantially greater than the female contribution. mtDNA haplogroups analysis shows no evidence of a significant maternal Amerindian contribution to any of the 10 populations. We detected significant nonrandom association between two markers located 22 cM apart (FY-null and AT3), most likely due to admixture linkage disequilibrium created in the interbreeding of the two parental populations. The strength of this association and the substantial genetic distance between FY and AT3 emphasize the importance of admixed populations as a useful resource for mapping traits with different prevalence in two parental populations.

756 citations


"Admixture and genetic relationships..." refers background in this paper

  • ...However, our preliminary admixture estimates could be helpful in the biomedical area for complex disease analysis (i.e. case–control studies) where population genetic composition and dynamics of the admixture processes should be clearly understood (Parra et al., 1998)....

    [...]


Journal ArticleDOI
TL;DR: The physical location of each STR locus in the human genome is delineated and allele ranges and variants observed in human populations are summarized as are mutation rates observed from parentage testing.
Abstract: Over the past decade, the human identity testing community has settled on a set of core short tandem repeat (STR) loci that are widely used for DNA typing applications. A variety of commercial kits enable robust amplification of these core STR loci. A brief history is presented regarding the selection of core autosomal and Y-chromosomal STR markers. The physical location of each STR locus in the human genome is delineated and allele ranges and variants observed in human populations are summarized as are mutation rates observed from parentage testing. Internet resources for additional information on core STR loci are reviewed. Additional topics are also discussed, including potential linkage of STR loci to genetic disease-causing genes, probabilistic predictions of sample ethnicity, and desirable characteristics for additional STR loci that may be added in the future to the current core loci. These core STR loci, which form the basis for DNA databases worldwide, will continue to play an important role in forensic science for many years to come.

576 citations


"Admixture and genetic relationships..." refers background or methods in this paper

  • ...The inclusion of CODIS-STRs in commercial human identification kits has increased the number of population databases that can be used in molecular anthropology studies (Butler, 2006)....

    [...]

  • ...We amplified 15 STRs markers (D3S1358, TH01, D21S11, D18S51, D5S818, D13S317, D7S820, D16S539, CSF1PO, vWA, D8S1179, TPOX, FGA, D2S1338 and D19S433) as recommended in the PCR AmpFlSTR Identifiler kit (Applied Biosystems, Foster City, CA)....

    [...]

  • ...This is due to their elevated heterozygosity, genome abundance, high mutation rate, and simple analysis based on the polymerase chain reaction (PCR) (Butler, 2006)....

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