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The Y-chromosome has been widely used in ancestry inference based on its region-specific haplogroup distributions. However, there is always a debate on how informative such a single marker is for inferring an individual's genetic ancestry. Here, we compared genetic ancestry inferences at continental level made by Y-chromosomal haplogroups to those made by autosomal single-nucleotide polymorphisms in 1230 samples of Affymetrix Human Origins dataset. The highest ancestry proportions of a majority of individuals match the highest average continental-ancestry proportions in haplogroups A, B, D, H, I, K, L, T, O, and M. The high consistencies have not been observed in haplogroups E, C, G, J, N, Q, and R, but in some of their sublineages, such as E1a, E1b1a1, E1b1b1b1a, E2b1a, J1a2b, Q1a1a1, Q1a2a1a1, R1b1a2a1a, and R2. Although the consistencies of Y-chromosomal and autosomal continental ancestry vary among haplogroups, Y-chromosome could provide valuable clues for individual's continental ancestry.
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JOURNAL O F
FORENSIC SCIENCE AND MEDICINE
HIGHLIGHTS
Volume 2 | Issue 4 | October - December 2016
ISSN 2349-5014
E-ISSN 2455-0094
Institute of Evidence Law and Forensic Science,
China University of Political Science and Law
Collaborative Innovation Center of Judicial Civilization, China
Sponsored by : The “111 Plan” of China – Evidence Science Innovation and Talent Base
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BRIEF COMMUNICATION
The consistencies of Y chromosomal and
autosomal continental ancestry vary among
haplogroups
Journal of Forensic Science and Medicine • Volume 2 • Issue 4 • October - December 2016 • Pages 123-????
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© 2016 Journal of Forensic Science and Medicine | Published by Wolters Kluwer - Medknow 229
Brief Communication
IntroductIon
With the advantages of lack of recombination, strict paternal
inheritance, small effective population size, low mutation
rate, sufcient markers, and population‑specic haplotype
distribution, Y-chromosome has been widely used in
anthropology, population genetics, and forensic genetics to
understand population genetic structure, population history,
andforensicidentications.[1] Y-chromosome has also inspired
widespread public interest to trace paternal ancestors and
been commercially used by many companies. A very famous
example is the Y-chromosomal type of Genghis Khan,
which was supposed to belong to the “star cluster” under
haplogroup C3*-M217 (xM48)[2] and has gained extensive
attention and attracted numerous consumers to get tested.
However, as Y-chromosome is only a single marker and suffers
from severe genetic drift, such simple ancestry analyses tend to
overlook the contribution of the vast majority of an individual’s
ancestors to his/her genome.[3,4]
There are also many alternative ancestry inference
methods, such as testing mitochondrial DNA (mtDNA),[4]
genome-wide short tandem repeat (STR)[5] or single-nucleotide
polymorphism (SNP),[6] and ancestry informative
markers (AIMs).[7] The mtDNA is maternally inherited and
has been widely used to trace maternal history. Genome-wide
STRs, SNPs, and AIMs are usually applied to inferring a
detailed composition of an individual’s ancestry. However,
some recent genome-wide studies have revealed frequent
discrepancies between ancestry inferences using mtDNA
versus autosomal SNPs.[4,8] The mtDNA case reminds us to
rethink how much ancestry information that Y-chromosome
could give and the accuracy of Y-chromosomal ancestry
inference compared to that of genome-wide ancestry
The Consistencies of Y‑Chromosomal and Autosomal
Continental Ancestry Varying among Haplogroups
Chuan‑Chao Wang1,2, Lei Shang3, Hui‑Yuan Yeh4, Lan‑Hai Wei5
1Department of Genetics, Harvard Medical School, Boston, MA, USA, 2Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena,
Germany, 3Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing, China, 4School of Humanities and Social Sciences,
Nanyang Technological University, Singapore, 5State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology,
Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
Abstract
TheY‑chromosomehasbeenwidelyusedinancestryinferencebasedonitsregion‑specichaplogroupdistributions.However,thereisalwaysa
debate on how informative such a single marker is for inferring an individual’s genetic ancestry. Here, we compared genetic ancestry inferences
at continental level made by Y-chromosomal haplogroups to those made by autosomal single-nucleotide polymorphisms in 1230 samples of
Affymetrix Human Origins dataset. The highest ancestry proportions of a majority of individuals match the highest average continental-ancestry
proportions in haplogroups A, B, D, H, I, K, L, T, O, and M. The high consistencies have not been observed in haplogroups E, C, G, J, N, Q,
and R, but in some of their sublineages, such as E1a, E1b1a1, E1b1b1b1a, E2b1a, J1a2b, Q1a1a1, Q1a2a1a1, R1b1a2a1a, and R2. Although
the consistencies of Y-chromosomal and autosomal continental ancestry vary among haplogroups, Y-chromosome could provide valuable
clues for individual’s continental ancestry.
Key words: Ancestry inference, autosomal single-nucleotide polymorphism, Y-chromosome
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DOI:
10.4103/2349-5014.197925
Address for correspondence: Dr. Chuan‑Chao Wang,
Department of Genetics, Harvard Medical School,
Boston, MA, USA.
Department of Archaeogenetics, Max Planck Institute for the Science of
Human History, Jena, Germany.
E‑Mail: wang@shh.mpg.de
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How to cite this article: Wang CC, Shang L, Yeh HY, Wei LH. The
Consistencies of Y-Chromosomal and Autosomal Continental Ancestry
Varying among Haplogroups. J Forensic Sci Med 2016;2:229-32.
Received: 08-05-2016
Revised: 10-08-2016
Accepted: 11-09-2016
Wang, et al.: Y Chromosomal and Autosomal Ancestry
Journal of Forensic Science and Medicine ¦ October 2016 ¦ Volume 2 ¦ Issue 4
230
estimation. Here, we presented a comprehensive analysis using
Y-chromosomal and genome-wide autosomal SNP data of more
than 1200 male individuals from Affymetrix Human Origins
dataset[6] to directly and quantitatively assess the consistency
of Y-chromosomal and autosomal continental ancestry.
MaterIals and Methods
The Y-chromosomal and autosomal genotype data for
1230 male individuals were extracted from Affymetrix
Human Origins dataset[6] using EIGENSOFT[9] and PLINK.[10]
Y‑chromosomal haplogroups were classied based on the
International Society of Genetic Genealogy phylogenetic
tree at January 28, 2015 (http://www.isogg.org/). We used
ADMIXTURE v. 1.23[11] to estimate ancestry proportions
for 1230 males with 594,924 autosomal SNPs. Each run
involved 100 replicates with different random starting seeds,
default 5-fold cross-validation, and varying the number
of ancestral populations K from 2 to 12. At K = 8, the
samples were well assigned to eight continental regions:
Africa, Middle East, Europe, South Asia, East Asia, Siberia,
Oceania, and Americas. The average continental-ancestry
proportions within each Y-chromosomal haplogroup, standard
deviation (SD) of individual continental-ancestry percentages
for each continental region in each haplogroup, mean pairwise
Euclidean distance (d) within each haplogroup, and consistency
scores were all calculated according to Emery et al.[4] The
graphical displays for ancestry plot were carried out in
R statistical software v3.0.2.[12]
results
The Human Origin dataset contained male samples of
worldwide lineages from Y-chromosomal haplogroups A, B,
C, D, E, F, G, H, I, J, K, L, M, N, O, Q, R, S, and T [Table S1].
All the haplogroups, except A, B, K, M, and S, were found
in more than one continent. Haplogroups A and B were only
discovered in Africa whereas K, M, and S were only presented
in Oceania. Likewise, haplogroups A and B had predominately
African ancestry whereas K, M, and S had predominately
Oceanian ancestry [Table S2 and Figure 1]. Haplogroups C,
D, and O were frequent in populations from East Asia. The
East Asian ancestry proportions in haplogroups D and O were
extremely higher than those of other continents. East Asian and
Siberian ancestry seemed to contribute equally to individuals of
haplogroup C [Table S2 and Figure 1]. Haplogroup E reached
high frequencies in Africa and Middle East. The African and
Middle Eastern ancestries are also the two main components
for individuals of haplogroup E. Haplogroups L, H, and R
were frequent in South Asia, and R was also found at very high
frequency in Europe. Haplogroups L and H had predominately
South Asian ancestry. The maximum ancestry proportion
of haplogroup R was from Europe, and the second- and
third-highest ancestry proportions were from South Asia and
Middle East, respectively. The frequencies of haplogroups I,
Q, and T were enriched in Europe, Americas, and Middle East,
respectively. Similarly, the ancestry proportions of the above
three regions also reached highest in haplogroups I, Q, and T,
respectively. Haplogroups G, J, and N were found in various
regions [Table S1] and their genetic ancestries also varied.
Collectively, we found a good correlation between haplogroup
frequencies and continental-ancestry proportions.
We then estimated the SD of individual continental-ancestry
percentages within each haplogroup. The continental-ancestry
proportions varied considerably among individuals in the
majority of haplogroups, especially in haplogroups E, N, K,
Q, and R (SD > 0.3) [Table S3]. We also calculated the mean
pairwise Euclidean distance between continental-ancestry
proportions among individuals within each haplogroup,
which is a quantitative measure of the inter-individual
variability.[4] Consistent with the SD results, the mean pairwise
Euclidean distances in haplogroups E, C, K, N, Q, and R were
high (>0.5) [Table S4], suggesting that these haplogroups are
not very informative for inferring individual’s continental
ancestry. In contrary, the distance in haplogroups A, B, D,
K, O, and M were relatively low [Table S4], indicating a
strong association between geographic-ancestry compositions
and a certain haplogroup. To directly and quantitatively
assess how informative Y-chromosome is in inferring an
individual’s genetic ancestry, we calculated the consistency
score within each haplogroup. The score was the proportion
of individuals with continental ancestry >50% matching
highest continental-ancestry component of the haplogroup
in our dataset. The consistency ranged from 0.333 to 1.000
with a mean of 0.697 in major haplogroups from A to
R, and about 65% of Y-chromosomal haplogroups had a
consistency score >50% [Table S4]. The high consistency
had been observed in haplogroups A, B, D, H, I, K, L, T, O,
and M, meaning that these haplogroups could be regarded as
having substantial genetic ancestry from their corresponding
continents. The consistency values in haplogroups C, G, J, N,
Q,andRwererelativelylow,whichmakeitdifculttoassign
each of these haplogroups to a certain continent.
The haplogroups with high SD, high Euclidean distance,
and low consistency are all continent-wide distributed
lineages. However, some of their sublineages are regional
specic.Forinstance,Q1a2a1a1‑M3 is almost exclusively
distributed in Americas. It is very likely that these sublineages
also have exclusive continental ancestry. The frequency of
Q1a2a1a1 in our dataset reached 36.2% of all Q individuals.
This lineage, with more than 90% of American ancestry
and a consistency value of 0.88, could be undisputedly
classied intoAmericas. Haplogroups E1a, E1b1a1, and
E2b1a, comprising more than half of all haplogroup E
individuals, had exclusive African ancestry with extremely
high consistency scores (nearly 1) and low Euclidean
distance and SD. In addition, haplogroup E1b1b1b1a,
accounting for 12% of all haplogroup E individuals, could
be reasonably assigned to Middle East with a consistency
value of 0.87. Haplogroup R1b1a2a1a, making up 32.6% of
all R individuals, had a strong association with Europe, while
R2 samples had substantial South Asian genetic ancestry.
Wang, et al.: Y Chromosomal and Autosomal Ancestry
Journal of Forensic Science and Medicine ¦ October 2016 ¦ Volume 2 ¦ Issue 4 231
Figure 1: (a) Haplogroup‑averaged continental‑ancestry proportions; (b) Individual continental‑ancestry proportions in the male individuals of Affymetrix
Human Origins Dataset
b
a
Wang, et al.: Y Chromosomal and Autosomal Ancestry
Journal of Forensic Science and Medicine ¦ October 2016 ¦ Volume 2 ¦ Issue 4
232
Similarly, haplogroup J1a2b was associated with Middle East,
and Q1a1a1 could be assigned into East Asia.
dIscussIon
We directly compared the genetic ancestry revealed by
Y-chromosomal haplogroups to those inferred from
genome-wide autosomal SNPs in a worldwide dataset. The
continental-ancestry compositions varied among individuals
of the same Y-chromosomal haplogroup judging from high
SDs. About 70% of the Y-chromosomal haplogroups could
be assigned to be associated with certain continents due to
thehighcontinent‑specicancestryproportions.Thehighest
ancestry proportions of a majority of individuals match
the highest average continental-ancestry proportions in
haplogroups A, B, D, H, I, K, L, T, O, and M. Although the
high consistencies have not been observed in haplogroups E,
C, G, J, N, Q, and R, some of their sublineages, such as E1a,
E1b1a1, E1b1b1b1a, E2b1a, J1a2b, Q1a1a1, Q1a2a1a1,
R1b1a2a1a, and R2 corresponded well with certain continents.
The Y-chromosome seemed like to give higher prediction
accuracy for individual ancestries than the mtDNA.[4] This
phenomenon might be caused by sex-biased migrations,
which refers to a higher female migration rate in human
populations.[13] A series of studies have revealed that the
among-population components of genetic variation are higher
for the Y-chromosome than for the mtDNA, indicating that the
Y-chromosomes tend to be more localized geographically.[13,14]
The Y-chromosome in a way could provide valuable clues for
individual’s continental ancestry, but it probably neglected
many other detailed ancestry information. One, or at most
two, top ancestry components could be well represented
by majority of Y-chromosomal haplogroups, whereas other
ancestry information is lost. For instance, the highest South
Asian ancestry proportions have been detected in individuals
of haplogroup H. Meanwhile, East Asia, Europe, and Middle
East each have contributed more than 10% of genetic
ancestry to many individuals of haplogroup H, which could
notbereectedbysuchasingleY‑chromosomalmarker.In
addition, the Y‑chromosomal haplogroup classications in
this study were not very informative. The rough assignment
might lose some information of a certain lineage and probably
have resulted in bias conclusion. For example, sublineages
of haplogroup C have distinct geographic distributions.[15]
However, we do not have enough markers in this dataset to
identify the detailed phylogeny of haplogroup C individuals,
resulting in the inconclusive ancestry inference of this
haplogroup.
Acknowledgments
CCW is supported by the Max Planck Society and Harvard
Medical School.
Financial support and sponsorship
Nil.
Conflicts of interest
Therearenoconictsofinterest.
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The association between a geographical region and an mtDNA haplogroup(s) has provided the basis for using mtDNA haplogroups to infer an individual's place of origin and genetic ancestry. Although it is well known that ancestry inferences using mtDNA haplogroups and those using genome-wide markers are frequently discrepant, little empirical information exists on the magnitude and scope of such discrepancies between multiple mtDNA haplogroups and worldwide populations. We compared genetic-ancestry inferences made by mtDNA-haplogroup membership to those made by autosomal SNPs in ∼940 samples of the Human Genome Diversity Panel and recently admixed populations from the 1000 Genomes Project. Continental-ancestry proportions often varied widely among individuals sharing the same mtDNA haplogroup. For only half of mtDNA haplogroups did the highest average continental-ancestry proportion match the highest continental-ancestry proportion of a majority of individuals with that haplogroup. Prediction of an individual's mtDNA haplogroup from his or her continental-ancestry proportions was often incorrect. Collectively, these results indicate that for most individuals in the worldwide populations sampled, mtDNA-haplogroup membership provides limited information about either continental ancestry or continental region of origin. Copyright © 2015 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.
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Genome-wide association (GWA) studies are an effective approach for identifying genetic variants associated with disease risk. GWA studies can be confounded by population stratification--systematic ancestry differences between cases and controls--which has previously been addressed by methods that infer genetic ancestry. Those methods perform well in data sets in which population structure is the only kind of structure present but are inadequate in data sets that also contain family structure or cryptic relatedness. Here, we review recent progress on methods that correct for stratification while accounting for these additional complexities.