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Title: Increasing phylogenetic resolution still informative for Y chromosomal studies on West-European populations
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G Model

FSIGEN-982; No. of Pages 7
Forensic Science International: Genetics xxx (2013) xxx–xxx

Contents lists available at SciVerse ScienceDirect

Forensic Science International: Genetics
journal homepage: www.elsevier.com/locate/fsig

Increasing phylogenetic resolution still informative for Y chromosomal
studies on West-European populations
M.H.D. Larmuseau a,b,c,*, N. Vanderheyden a, A. Van Geystelen a,d, M. van Oven e,
M. Kayser e, R. Decorte a,b
a

UZ Leuven, Laboratory of Forensic Genetics and Molecular Archaeology, Leuven, Belgium
KU Leuven, Forensic Medicine, Department of Imaging & Pathology, Leuven, Belgium
KU Leuven, Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, Leuven, Belgium
d
KU Leuven, Laboratory of Socioecology and Social Evolution, Department of Biology, Leuven, Belgium
e
Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
b
c

A R T I C L E I N F O

A B S T R A C T

Article history:

Many Y-chromosomal lineages which are defined in the latest phylogenetic tree of the human Y
chromosome by the Y Chromosome Consortium (YCC) in 2008 are distributed in (Western) Europe due to
the fact that a large number of phylogeographic studies focus on this area. Therefore, the question arises
whether newly discovered polymorphisms on the Y chromosome will still be interesting to study
Western Europeans on a population genetic level. To address this question, the West-European region of
Flanders (Belgium) was selected as study area since more than 1000 Y chromosomes from this area have
previously been genotyped at the highest resolution of the 2008 YCC-tree and coupled to in-depth
genealogical data. Based on these data the temporal changes of the population genetic pattern over the
last centuries within Flanders were studied and the effects of several past gene flow events were
identified. In the present study a set of recently reported novel Y-SNPs were genotyped to further
characterize all those Flemish Y chromosomes that belong to haplogroups G, R-M269 and T. Based on this
extended Y-SNP set the discrimination power increased drastically as previous large (sub-)haplogroups
are now subdivided in several non-marginal groups. Next, the previously observed population structure
within Flanders appeared to be the result of different gradients of independent sub-haplogroups.
Moreover, for the first time within Flanders a significant East–West gradient was observed in the
frequency of two R-M269 lineages, and this gradient is still present when considering the current
residence of the DNA donors. Our results thus suggest that an update of the Y-chromosomal tree based
on new polymorphisms is still useful to increase the discrimination power based on Y-SNPs and to study
population genetic patterns in more detail, even in an already well-studied region such as Western
Europe.
ß 2013 Elsevier Ireland Ltd. All rights reserved.

Keywords:
Discrimination power
Population structure
Y-SNPs
Flanders
Genetic genealogy
Y-chromosomal phylogeny

1. Introduction
The Y chromosome contains the largest non-recombining block
in the human genome and can be considered as one of the most
informative haplotypic systems [1,2]. Due to the lack of
recombination the history of mutational accumulation in the Y
chromosome can be described in a unique evolutionary haplogroup tree [3]. This Y-chromosomal phylogenetic tree is
currently becoming a resource with increasing importance in

* Corresponding author at: Katholieke Universiteit Leuven, Forensic Medicine,
Kapucijnenvoer 33, B-3000 Leuven, Belgium. Tel.: +32 0494397297;
fax: +32 016324575.
E-mail address: maarten.larmuseau@bio.kuleuven.be (M.H.D. Larmuseau).

forensic studies, evolutionary population studies, medical genetics, and genealogical reconstruction [2,4,5]. The latest ‘official’
phylogenetic tree of the human Y chromosome was published by
the Y Chromosome Consortium (YCC) in 2008 [6]. This tree
contains 311 distinct haplogroups and incorporates 599 binary
markers. Many Y-chromosomal lineages which are defined in this
tree are mostly distributed in (Western) Europe due to the fact that
most research projects focus on this area, including present-day
Americans of European descent [6]. An increasing number of Ychromosomal SNPs are becoming available in addition to the set of
SNPs which were included by Karafet et al. [6] as a result of whole
genome projects such as the 1000 Genomes project [7]. Therefore,
novel lineages continue to be discovered and the phylogeny is
under constant revision [8,9]. However, as many Y-chromosomal
lineages are already studied in considerable detail in (Western)

1872-4973/$ – see front matter ß 2013 Elsevier Ireland Ltd. All rights reserved.
http://dx.doi.org/10.1016/j.fsigen.2013.04.002

Please cite this article in press as: M.H.D. Larmuseau, et al., Increasing phylogenetic resolution still informative for Y chromosomal
studies on West-European populations, Forensic Sci. Int. Genet. (2013), http://dx.doi.org/10.1016/j.fsigen.2013.04.002

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2

Europe the question arises if those newly discovered polymorphisms on the Y chromosome will still be informative within
Western Europe on a population genetic level.
To answer this question the West-European region of Flanders
(Belgium) together with the provinces of Noord-Brabant and
Limburg of the Netherlands was selected as study area since its Ychromosomal variation and distribution are already well known in
detail [10–12]. In this region more than 1000 Y chromosomes
which were genotyped at the highest resolution of the 2008 YCC
tree were coupled to the in-depth genealogical data of the
autochthonous DNA donors. Based on these data the temporal
changes of the population genetic pattern within Flanders over the
last centuries, namely the North–South gradient for sub-haplogroup R-U106 in Brabant, have been studied in detail [10,12].
Moreover, the effects of several past gene-flow events in this WestEuropean region were identified based on surname origin [11]. By
including recently published and newly developed Y-SNPs to
characterize the Flemish Y chromosomes the aim of the present
study was to investigate the effect of these new Y-SNPs on the
discrimination power and on the detection of population structure
within the Flemish population.
2. Materials and methods
2.1. Sampling procedure
Samples were obtained via genealogical societies from Belgium,
the Netherlands and the Grand Duchy of Luxembourg through the
open genealogical project ‘DNA Brabant/Belgium’. All samples
were collected with written consent from the donors who gave
their permission for DNA analyses, storage of the samples and
scientific publication of their anonymized DNA results. The
genealogical and genetic data of all donors of this genealogical
project are available in Van den Cloot [13,14].
In addition to a DNA sample the requirement for participation
was the availability of patrilineal genealogical data with an oldest
reported paternal ancestor (ORPA) born before 1800. After
receiving all genealogical data two different datasets were
composed: a genealogical (GD) and a present (PD) dataset. In

order to avoid a family bias only one individual per family (defined
as a group of relatives with maximum fourth degree relatedness)
was retained when multiple of such close relatives had participated. Each participant was assigned to one of the six defined regions
based on the birth place of their ORPA for the GD or based on their
actual living place at the time of sample collection (during the
period 2009–2013) for the PD. The six defined regions are NoordBrabant (Dutch province ‘Noord-Brabant’; number 1 in Fig. 1),
Antwerp (Belgian province ‘Antwerpen’, number 2 in Fig. 1),
Vlaams-Waals Brabant (Belgian provinces ‘Vlaams Brabant’ and
‘Brabant Wallon’, and the ‘Brussels region’; number 3 in Fig. 1),
West-Flanders (Belgian province ‘West-Vlaanderen’; number 4 in
Fig. 1), East-Flanders (Belgian province ‘Oost-Vlaanderen’; number
5 in Fig. 1) and Limburg (Belgian province ‘Limburg’ and the Dutch
province ‘Limburg’; number 6 in Fig. 1). As such there is a microgeographical North–South range and East–West range in this
study. To have a representative East–West range for Flanders, the
region ‘Belgian Brabant’ was defined as the sum of the regions
Antwerp and Vlaams-Waals Brabant.
For GD an ideal autochthonous sample of the population needs
to fulfill several extra criteria according to the recommendations
for sampling on micro-geographical scale defined in Larmuseau
et al. [15]. First, pairs of DNA-donors with a common documented
ancestor in paternal lineage but with a different Y-chromosomal
sub-haplogroup or Y-STR-haplotypes with more than six differences (out of 38 Y-STRs) were excluded from the dataset. Based on
the overall Y-STR mutation rate more than six differences out of 38
Y-STRs is not likely to occur between genuine genealogical
relatives. Furthermore, one individual from each pair which (i)
showed no difference in surname or which are close variants, (ii)
belonged to the same Y-chromosomal sub-haplogroup and (iii) had
a related Y-haplotype, meaning less than six mutations in the 38
genotyped Y-STRs, was excluded from the analysis. Next, also
participants who are known descendants of a foundling or a child
with an unknown biological father were excluded from this
dataset. Finally, participants were also excluded based on
the anthroponymical analysis of the surname of their ORPA. The
language (including dialect) and the etymology of the surnames
were scientifically examined as defined by standard sources [16]

Fig. 1. Geographical location of the six – for this study selected – regions within Western Europe. (1) Noord-Brabant (Province in the Netherlands); (2) Antwerp (Province in
Belgium); (3) Vlaams-Waals Brabant (Provinces ‘Vlaams Brabant’ and ‘Brabant Wallon’, and the Brussels Region, all in Belgium); (4) West-Vlaanderen (Province in Belgium);
(5) Oost-Vlaanderen (Province in Belgium) and (6) Limburg (Provinces ‘Limburg’ in the Netherlands and Belgium). The region ‘Belgian Brabant’ is the sum of regions 2 and 3.

Please cite this article in press as: M.H.D. Larmuseau, et al., Increasing phylogenetic resolution still informative for Y chromosomal
studies on West-European populations, Forensic Sci. Int. Genet. (2013), http://dx.doi.org/10.1016/j.fsigen.2013.04.002

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3

Fig. 2. Phylogenetic relationships of all studied binary markers within the Y-chromosomal subhaplogroup R-M269. The nomenclature of the sub-haplogroups is based on the
terminal mutation that defined them.

and the Meertens Institute (Royal Netherlands Academy of Arts
and Sciences; http://www.meertens.knaw.nl). All surnames with
an indication for a toponym which does not match the assigned
geographic region for the DNA-donor were excluded as well as
foreign surnames which may be the result of pre-ORPA migrations.
The only exception on this rule is the FRS (French/Roman Surname)
group of samples which have a French or Roman Surname
associated with the recently reported past gene flow event at
the end of the 16th century from Northern France to Flanders [11].
In contrast to FRS all samples of individuals with a Flemish
surname that was already present in Flanders before the year 1500
were assigned to the autochthonous Flemish surname (AFS) group.
The FRS and AFS are surname-based samples within the GD next to
the six geographical samples.
2.2. Y chromosome genotyping
A buccal swab sample from each participant was collected for
DNA extraction by using the Maxwell 16 System (Promega,
Madison, WI, USA) followed by real-time PCR quantification
(Quantifiler Human DNA kit, Applied Biosystems, Foster City, CA,
USA). Thirty-eight Y-STR loci were genotyped for all samples as
previously described in [11]. The whole process was repeated with
new primer sets for all individuals that showed non-amplified loci
in order to exclude technical errors or allelic dropouts due to
mutations in the standard primer positions.
All haplotypes were submitted to Whit Athey’s Haplogroup
Predictor [17] to obtain probabilities for the inferred haplogroups.
Based on these results the samples were further genotyped
with specific Y-chromosomal single-nucleotide polymorphisms
(Y-SNPs) assays to confirm the predicted haplogroup and to assign
the sub-haplogroup at the highest resolution level of the latest Ychromosomal tree reported by Karafet et al. [6]. A set of recently
characterized Y-SNPs that improved the phylogenetic resolution
within haplogroup G [18], haplogroup T [19] and sub-haplogroup
R-M269 [8,9] were included. The positions of the new Y-SNPs
were verified that they do not lie in a gene-conversion hotspot

within the Y chromosome. Also the possibility for back-mutations
of these Y-SNPs were analyzed based on an extended AMY-tree
analysis [20]. The most recent phylogeny and nomenclature of all
R-M269 sub-haplogroups are visualized in Fig. 2. The nomenclature of the sub-haplogroups is in accord with the updated tree of
AMY-tree [20]. A total of 17 multiplex systems with 120 Y-SNPs
were developed using SNaPshot mini-sequencing assays (Applied
Biosystems) according to previously published protocols [21,22]
and new protocols (van Oven et al., in preparation).
2.3. Statistical analysis
Sub-haplogroup frequencies are estimated for each defined
region for both the genealogical (GD) and the present dataset
(PD). FST values between the regions were estimated using
ARLEQUIN v.3.1 [23]. Significance of population subdivision was
tested using a permutation test implemented in R (The R
Foundation for Statistical Computing, 2011), as developed in
Larmuseau et al. [11]. In the case of pairwise tests the Bonferroni
correction was applied to all p-values [24]. No further tests to
observe population differentiation based on the Y-STRs were
done because of the insufficient power of the used set of Y-STRs
to detect population structure as a consequence of the high
homoplasy associated with these markers [10,11]. Statistically
significant differences of frequencies for the main sub-haplogroups between the several provinces and between AFS and
FRS were tested using chi-square tests in R. Finally, to test
differences in frequency gradients of the main sub-haplogroups
between GD and PD were tested with the Cochran-Armitagetrend test in R by using the Coin package [25].
3. Results
In total 1035 DNA donors contributed their genealogical records.
For the genealogical dataset (GD) 773 individuals (including 65
individuals within the FRS group) were selected. For the present
dataset (PD) 948 individuals were selected. Y-chromosomal

Please cite this article in press as: M.H.D. Larmuseau, et al., Increasing phylogenetic resolution still informative for Y chromosomal
studies on West-European populations, Forensic Sci. Int. Genet. (2013), http://dx.doi.org/10.1016/j.fsigen.2013.04.002

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4

data genotyped for this study have been submitted to the open access
Y-STR Haplotype Reference Database (YHRD, www.yhrd.org):
accession numbers YA003651-YA003652-YA003653-YA003738YA003739-YA003740-YA003741-YA003742. Almost all individuals
were correctly assigned to a basal haplogroup using the Whit Athey’s
Haplogroup Predictor. The single exception was a Y chromosome
belonging to haplogroup A which is not included in the predictor tool.
However, according to a recent study on the root of the human Ychromosomal phylogenetic tree by Scozzari et al. [26] haplogroup A is
not monophyletic and therefore this Y chromosome is further
referred to as belonging to paragroup Y*(xBT). All newly reported YSNPs are lying in one of the unique regions of the Y chromosome
according to [27,28]. However, two new markers L2 and L48 are lying
in one of the large ampliconic regions of the Y-chromosome. Based on

the most recent AMY-tree analyses these two markers are not lying in
gene conversion hotspots as there were no back-mutations found for
these markers along the whole Y-chromosomal phylogenetic tree.
In total 50 and 53 different sub-haplogroups were observed
within the GD and PD respectively. The number of samples per
sub-haplogroup and the relative frequencies are given in Table 1
for the full GD and in Supplementary Table S1 (see Supplementary
materials) for the full PD. There are six sub-haplogroups with a
frequency higher than 5% in the total dataset: R1b1b2a1a1b2 (RL48) with 12.5% and 12.2% for the GD and PD respectively, I1* (IM253*) with 12.0% and 11.6%, R1b1b2a1a2* (R-P312*) with 10.9%
and 10.4%, R1b1b2a1a1b* (R-Z381*) with 8.9% and 9.3%,
R1b1b2a1a2e* (R-M529*) with 7.1% and 7.6%, and R1b1b2a1a2g3
(R-L2) with 5.6% and 5.7%.

Table 1
Distribution (N) and frequency (f) of the Y-chromosomal sub-haplogroups within the six selected regions within Western Europe based on the ‘genealogical dataset’ (GD),
including the French/Roman Surname Group (FRS). The sub-haplogroups with a frequency of more than 5% in the total GD are given in bold.
(Sub-)haplogroup

Y* (xBT)
E1b1b1a1a* (E-V12*)
E1b1b1a1b* (E-V13*)
E1b1b1a1c* (E-V22*)
E1b1b1b1* (E-M81*)
E1b1b1c* (E-M123*)
E1b1b1c1* (E-M34*)
G2a* (G-P15*)
G2a3* (G-U8*)
G2a3a1 (G-Page19)
G2a3b1a1* (G-U13*)
I1* (I-M253*)
I1c (I-P109)
I2* (I-P215*)
I2a* (I-P37.2*)
I2b1* (I-M223*)
I2b1a (I-M284)
I2b1c (I-P78)
I2b1d (I-P95)
J1* (J-M267*)
J1e* (J-P58*)
J2a* (J-M410*)
J2a2* (J-M67*)
J2a2a* (J-M92*)
J2a8 (J-M319)
J2b2* (J-M241*)
L1* (L-M27*)
L2* (L-M317*)
Q1* (Q-P36.2*)
R1* (R-M173*)
R1a1a* (R-M198*)
R1b1* (R-P25*)
R1b1b* (R-P297*)
R1b1b2* (R-M269*)
R1b1b2a1a* (R-P310*)
R1b1b2a1a1* (R-U106*)
R1b1b2a1a1a (R-Z18)
R1b1b2a1a1b* (R-Z381*)
R1b1b2a1a1b1 (R-U198)
R1b1b2a1a1b2 (R-L48)
R1b1b2a1a2* (R-P312*)
R1b1b2a1a2d (R-SRY2627)
R1b1b2a1a2e (R-M529)
R1b1b2a1a2g* (R-U152*)
R1b1b2a1a2g3 (R-L2)
R1b1b2a1a2g4 (R-L20)
R1b1b2a1a2h (R-Z195)
T1a2 (T-P77)
T1a4* (T-P321*)
T1b* (T-L131*)
Total

Total

NoordBrabant

Antwerp

VlaamsWaals
Brabant

WestVlaanderen

OostVlaanderen

Limburg

FRS

N

f

N

f

N

f

N

f

N

f

N

f

N

f

N

f

1
1
19
4
2
1
9
2
20
3
1
93
6
8
12
26
2
2
3
3
6
21
4
3
2
6
1
1
3
2
27
1
1
14
5
15
12
69
10
97
84
8
55
27
43
9
24
1
1
3
773

0.1
0.1
2.5
0.5
0.3
0.1
1.2
0.3
2.6
0.4
0.1
12.0
0.8
1.0
1.6
3.4
0.3
0.3
0.4
0.4
0.8
2.7
0.5
0.4
0.3
0.8
0.1
0.1
0.4
0.3
3.5
0.1
0.1
1.8
0.6
1.9
1.6
8.9
1.3
12.5
10.9
1.0
7.1
3.5
5.6
1.2
3.1
0.1
0.1
0.4

0
0
2
1
0
0
1
0
3
2
0
13
0
0
2
4
0
0
1
1
1
6
1
2
0
1
0
0
0
0
2
0
0
1
2
2
2
17
3
19
14
3
8
3
6
1
7
0
0
1
132

0.0
0.0
1.5
0.8
0.0
0.0
0.8
0.0
2.3
1.5
0.0
9.8
0.0
0.0
1.5
3.0
0.0
0.0
0.8
0.8
0.8
4.5
0.8
1.5
0.0
0.8
0.0
0.0
0.0
0.0
1.5
0.0
0.0
0.8
1.5
1.5
1.5
12.9
2.3
14.4
10.6
2.3
6.1
2.3
4.5
0.8
5.3
0.0
0.0
0.8

0
1
5
0
0
0
2
0
4
0
0
23
1
2
2
7
2
1
0
0
2
4
2
0
1
2
1
0
3
0
8
0
0
4
0
2
4
18
1
22
20
1
11
6
10
1
5
0
1
0
179

0.0
0.6
2.8
0.0
0.0
0.0
1.1
0.0
2.2
0.0
0.0
12.8
0.6
1.1
1.1
3.9
1.1
0.6
0.0
0.0
1.1
2.2
1.1
0.0
0.6
1.1
0.6
0.0
1.7
0.0
4.5
0.0
0.0
2.2
0.0
1.1
2.2
10.1
0.6
12.3
11.2
0.6
6.1
3.4
5.6
0.6
2.8
0.0
0.6
0.0

0
0
7
1
1
1
1
0
5
0
0
14
3
4
1
2
0
0
1
1
1
2
1
0
1
1
0
1
0
0
4
1
0
2
2
3
1
11
1
12
14
1
9
6
6
2
0
0
0
0
124

0.0
0.0
5.6
0.8
0.8
0.8
0.8
0.0
4.0
0.0
0.0
11.3
2.4
3.2
0.8
1.6
0.0
0.0
0.8
0.8
0.8
1.6
0.8
0.0
0.8
0.8
0.0
0.8
0.0
0.0
3.2
0.8
0.0
1.6
1.6
2.4
0.8
8.9
0.8
9.7
11.3
0.8
7.3
4.8
4.8
1.6
0.0
0.0
0.0
0.0

0
0
2
0
1
0
3
0
3
0
0
17
2
0
2
2
0
0
0
0
0
4
0
0
0
1
0
0
0
1
1
0
1
2
0
4
3
6
2
18
11
2
8
3
6
2
2
1
0
0
110

0.0
0.0
1.8
0.0
0.9
0.0
2.7
0.0
2.7
0.0
0.0
15.5
1.8
0.0
1.8
1.8
0.0
0.0
0.0
0.0
0.0
3.6
0.0
0.0
0.0
0.9
0.0
0.0
0.0
0.9
0.9
0.0
0.9
1.8
0.0
3.6
2.7
5.5
1.8
16.4
10.0
1.8
7.3
2.7
5.5
1.8
1.8
0.9
0.0
0.0

0
0
1
0
0
0
1
1
2
0
0
14
0
2
3
6
0
0
0
1
1
1
0
0
0
0
0
0
0
0
3
0
0
1
1
2
0
10
0
11
7
0
6
3
6
0
4
0
0
1
88

0.0
0.0
1.1
0.0
0.0
0.0
1.1
1.1
2.3
0.0
0.0
15.9
0.0
2.3
3.4
6.8
0.0
0.0
0.0
1.1
1.1
1.1
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
3.4
0.0
0.0
1.1
1.1
2.3
0.0
11.4
0.0
12.5
8.0
0.0
6.8
3.4
6.8
0.0
4.5
0.0
0.0
1.1

1
0
1
1
0
0
1
1
3
1
1
6
0
0
0
1
0
0
1
0
0
1
0
1
0
1
0
0
0
1
6
0
0
2
0
2
2
6
3
6
9
0
4
4
5
0
4
0
0
0
75

1.3
0.0
1.3
1.3
0.0
0.0
1.3
1.3
4.0
1.3
1.3
8.0
0.0
0.0
0.0
1.3
0.0
0.0
1.3
0.0
0.0
1.3
0.0
1.3
0.0
1.3
0.0
0.0
0.0
1.3
8.0
0.0
0.0
2.7
0.0
2.7
2.7
8.0
4.0
8.0
12.0
0.0
5.3
5.3
6.7
0.0
5.3
0.0
0.0
0.0

0
0
1
1
0
0
0
0
0
0
0
6
0
0
2
4
0
1
0
0
1
3
0
0
0
0
0
0
0
0
3
0
0
2
0
0
0
1
0
9
9
1
9
2
4
3
2
0
0
1
65

0.0
0.0
1.5
1.5
0.0
0.0
0.0
0.0
0.0
0.0
0.0
9.2
0.0
0.0
3.1
6.2
0.0
1.5
0.0
0.0
1.5
4.6
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
4.6
0.0
0.0
3.1
0.0
0.0
0.0
1.5
0.0
13.8
13.8
1.5
13.8
3.1
6.2
4.6
3.1
0.0
0.0
1.5

Please cite this article in press as: M.H.D. Larmuseau, et al., Increasing phylogenetic resolution still informative for Y chromosomal
studies on West-European populations, Forensic Sci. Int. Genet. (2013), http://dx.doi.org/10.1016/j.fsigen.2013.04.002

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5

Fig. 3. Frequency of the new Y-SNP lineages developed since the latest publication of the Y-chromosome tree by Karafet et al. [6], within (A) sub-haplogroup G-P15, (B) subhaplogroup R-U106, and (C) sub-haplogroup R-P312. The frequencies are those according to the ‘Present Dataset’ (PD).

Fig. 4. Frequency gradients of the two Y-chromosomal sub-haplogroups R-Z381* and R-L48 along the North–South gradient within the genealogical (GD) and present dataset
(PD).

Based on the new Y-SNPs reported since Karafet et al. [6] we
further subdivided the three sub-haplogroups G-P15, R-U106 and
R-P312. G-P15 was further subdivided into four sub-haplogroups
with the highest frequency for G-U8* (80%) (Fig. 3a). R-U106 was
further subdivided into five sub-haplogroups of which two were
frequent, namely R-Z381* (35%) and R-L48 (46%) (Fig. 3b). R-P312
could further be subdivided into seven sub-haplogroups, including
R-SRY2627 and R-U152 which were already defined in Karafet
et al. [6]. The main sub-haplogroups within R-P312 in our current
dataset were R-P312* (32%), R-M529 (23%) and R-L2 (18%) (Fig. 3c).
Finally, based on Karafet et al. [6] there was only one lineage within
haplogroup T found in Flanders. However, based on the – in this
study – new reported Y-SNPs we detected three different lineages
within the five samples belonging to haplogroup T (Table 1).
Based on the GD North–South (N–S) frequency gradients in
Brabant were found for sub-haplogroups R-Z381* and R-L48 (Fig. 4
and Table 1). Next, clear West–East (W–E) gradients in Flanders
were observed for R-L48 and for R-M529 (Fig. 5 and Table 1). Based
on the PD no N–S gradient in Brabant were found for R-Z381* and
for R-L48 (Fig. 4 and Table S1). Clear W–E gradients in Flanders
were still observed for R-L48 and for R-M529 (Fig. 5 and Table S1).
These gradients were not statistically significant (p-value >0.05). A
significant difference was, however, found between the N–S
gradients of R-Z381* based on GD and on PD as the gradient based
on GD was not longer visible based on PD. Next, also a significant
difference was found between the W–E gradients of R-M529 based
on GD and on PD as the gradient based on PD was stronger than the
one based on GD. A strong difference between AFS and FRS was
found for R-Z381* with 9.6% for AFS versus only 1.5% for FRS, and for
R-M529 with 6.5% for AFS versus 13.8% for FRS respectively

Fig. 5. Frequency gradients of the two Y-chromosomal sub-haplogroups R-L48 and
R-M529 along the West–East gradient within the genealogical (GD) and present
dataset (PD). The region Belgian Brabant is the sum of regions ‘Antwerp’ and
‘Vlaams-Waals Brabant’.

Please cite this article in press as: M.H.D. Larmuseau, et al., Increasing phylogenetic resolution still informative for Y chromosomal
studies on West-European populations, Forensic Sci. Int. Genet. (2013), http://dx.doi.org/10.1016/j.fsigen.2013.04.002

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6

Table 2
Frequency of the five most frequent Y-chromosomal sub-haplogroups within the RM269 radiation within the autochthonous Flemish surnames (AFS) and the French/
Roman Surname (FRS) groups. The results of the two sub-haplogroups with a
statistically significant difference in frequency between AFS and FRS are given in
bold.
Sub-haplogroup

AFS

FRS

R1b1b2a1a1b* (R-Z381*)
R1b1b2a1a1b2 (R-L48)
R1b1b2a1a2* (R-P312*)
R1b1b2a1a2e (R-M529)
R1b1b2a1a2g3 (R-L2)
Others

9.6
12.4
10.6
6.5
5.5
55.4

1.5
13.8
13.8
13.8
6.2
50.8

(Table 2). These two differences in frequency between AFS and FRS
were statistically significant (p-values <0.05). Pairwise FST-values
between the populations of the GD and between the ones of the PD
are calculated and given in Table S2 (see Supplementary
materials). No significant values were found, although two
pairwise values were significant within the PD.
4. Discussion
Y-SNPs which were not yet known at the time of the latest
published phylogenetic tree of the human Y chromosome by the Y
Chromosome Consortium (YCC; Karafet et al. [6]) are still highly
informative as we show here for a West-European population. The
relevance of these new Y-SNPs in Western Europe is demonstrated
by the possibility to discriminate Y chromosomes better as well as
by the observation of more population differentiation patterns in
Flanders including the Dutch provinces Limburg and NoordBrabant.
The higher level of discrimination among Flemish Y chromosomes is apparent from the number of observed sub-haplogroups.
Following the resolution of the latest published YCC-tree 42 subhaplogroups were found within the PD. However, after applying
the improved phylogenetic resolution by considering the new YSNPs 53 different sub-haplogroups were observed for the same
sample (Table S1). The newly observed lineages belong to three
main haplogroups, namely G, R-M269 and T. More importantly, not
only marginal groups (groups with a low frequency in the
population e.g. haplogroup T and its sub-haplogroups which have
a total frequency of 0.6% in the population) were observed for the
first time in the Flemish population. Eight of the eleven additional
Y-chromosomal lineages strongly add to the observed genetic
variation as they have a frequency of more than 1% in this
population sample. Moreover, the new Y-SNPs could subdivide the
haplogroups R-P312*, R-U106 and R-152 into new lineages,
namely R-L48, R-M529, R-Z381 and R-L2. At the resolution of
Karafet et al. [6] 70% of the Flemish males belonged to one of four
sub-haplogroups with a frequency higher than 10%. However,
according to the new phylogeny only 35% of the Flemish males
belong to sub-haplogroups with a frequency higher than 10%.
Almost all relevant newly described lineages that are observed
within Flanders are part of the Y-chromosomal sub-haplogroup
R1b1b2 (R-M269) which is carried by 110 million European men
and which increases in frequency from east (12% in Eastern Turkey)
to west (85% in Ireland) [8]. Based on the new next-generation
sequencing (NGS) data the phylogenetic tree of R-M269 reveals a
huge polytomy which suggests that in the future still more
relevant lineages will be discovered [9,28].
Evidently, the higher discrimination power based on Y-SNPs
also has consequences for the previously detected population
differentiation within Flanders. The previous detection of a
population structure was based on Y-chromosomal lineages which
are now subdivided into multiple sub-haplogroups (Fig. 3).

Because of the high variability, namely 53 observed subhaplogroups, it is difficult to find significant pairwise FST-values
between populations on a micro-geographical scale as reported in
Table S2 [29]. Nevertheless, due to the observation of subhaplogroup frequency gradients it is still possible to detect
population differentiation as earlier found within Flanders
[10,12]. The previously observed North–South gradient within
Brabant was detected for the sub-haplogroup R-U106 according to
Karafet et al. [6]. Based on the subdivision within this lineage into
several sub-haplogroups (Fig. 3b) we now found a North–South
gradient for two different lineages, namely R-Z381* and R-L48
(Fig. 4 and Table 1). The previously observed North–South gradient
was therefore the sum of two gradients of independent subhaplogroups.
Next to a North–South gradient a West–East gradient was
observed in Flanders for the first time thanks to the higher
resolution of the new Y-chromosomal phylogenetic tree. This
gradient was found for two separate sub-haplogroups, namely a
strong gradient for R-L48 and a much weaker one for R-M529
(Fig. 5 and Table 1). Previously, a West–East gradient was already
found for R-M529 between Ireland and Bretagne (France) by Busby
et al. [30]. As the gradient is still present in Flanders the gradient
observed by Busby et al. is therefore wider than presumed. The
West–East gradient of the frequency of R-L48 is much stronger as
its frequency halves over a distance of only 300 km despite the fact
that there has not yet been any indication for this gradient in the
literature.
The most surprising result of this study was that the West–East
gradients for both R-L48 and R-M529 were still visible when only
the present residence of the autochthonous DNA-donors (PD) was
used (Fig. 5 and Table S1). This is in contrast to the observed North–
South gradients in Brabant which disappeared when switching
from GD to PD (Fig. 4 and Table S1) [12]. Historical demography
explains this contrast: Brabant is the main industrialized region
within Flanders in contrast to the western and eastern parts within
Flanders [31]. As such, many immigrants in Brabant are from the
other parts of Flanders therefore the structure in Brabant
disappeared in the recent past. This is in contrast to the other
regions in Flanders which have been much less affected by
migration.
Finally, another genetic differentiation within Flanders was
found earlier between an autochthonous Flemish surnames group
(AFS) and a French/Roman Surnames group (FRS), the latter being
the remnant of a past gene flow event from Northern France to
Flanders at the end of the 16th century [11]. Based on the extended
Y-SNP data the differences in sub-haplogroup frequencies between
AFS and FRS are statistically significant for two specific subhaplogroups, namely R-Z381* and R-M529 (Table 2). The
frequencies in FRS for these two sub-haplogroups are comparable
with those expected for Northern France based on the observed
gradients in Flanders. However, there are no data (yet) for the
population in Northern France genotyped at such a Y-chromosomal phylogenetic resolution as in this study. Nevertheless, like
the North–South gradient observed in Brabant, the earlier genetic
difference between AFS and FRS turned out to be a combination of
differences of several sub-haplogroups.
5. Conclusion
The results for Flanders suggest that the current update of the
Y-chromosomal tree based on new polymorphisms provides the
opportunity to better discriminate between males based on Y-SNPs
and to study population genetic patterns in more detail even in an
already well-studied region such as Western Europe. Many
(forensic) researchers who deal with Y-chromosomal variation
may have the impression that the phylogenetic tree is a fractal, a

Please cite this article in press as: M.H.D. Larmuseau, et al., Increasing phylogenetic resolution still informative for Y chromosomal
studies on West-European populations, Forensic Sci. Int. Genet. (2013), http://dx.doi.org/10.1016/j.fsigen.2013.04.002

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FSIGEN-982; No. of Pages 7
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never-ending extension of new lineages. However, as long as
newly discovered Y-SNPs are significantly polymorphic in the
population (frequency >1%), it seems useful to genotype them to
increase the discrimination power and to study the population
structure. However, the validation status of many potential
polymorphic Y-SNPs is often unclear but this is being resolved
through the sharing of genomic data among genetic genealogists
who are interested to find new Y-SNPs to resolve their particular
paternal ancestry [32] as well as by pioneer studies such as the
present one, providing insights into the frequency levels in
particular geographic regions. For example, some of the new YSNPs used in this study were discovered in samples of the 1000
Genomes project [7] and were validated by amateur genetic
genealogists [9]. Therefore, this is an area in which closer
collaborations between amateurs and (forensic) academics could
prove particularly useful.
Next, based on the present results it appears that there is a
larger intra- and intercontinental differentiation than previously
observed based on the sub-haplogroups R-U106 and U152 [33].
Frequency distribution maps for markers such as L48 and Z381, for
which we observed already strong spatial differentiation within
Flanders, are therefore relevant. In contrast to earlier reports which
state that regional differentiation is something exceptional [34]
we expect many micro-geographical structures based on these
Y-chromosomal sub-haplogroup frequency maps within Europe.
Acknowledgments
We thank all the volunteers who donated DNA samples. We
acknowledge the Flemish society for genealogical research
‘Familiekunde Vlaanderen’, Marc Van den Cloot and Marc Gabrie¨ls,
who were involved in the collection of the samples. We want to
thank Peter de Knijff, Luc De Meester, Jean-Jacques Cassiman, Lucie
Larno, Tine Brouns, Joost Vanoverbeke, Karolien Vanaenroyde, Tom
Havenith, Hendrik Larmuseau and Lucrece Lernout for useful
assistance and discussions. Maarten H.D. Larmuseau is postdoctoral fellow of the FWO-Vlaanderen (Research FoundationFlanders). This work was supported in part by the Netherlands
Forensic Institute (NFI), the Netherlands Genomics Initiative (NGI)/
Netherlands Organization for Scientific Research (NWO) within the
framework of the Forensic Genomics Consortium Netherlands
(FGCN), the Flemish Society for Genealogical Research ‘Familiekunde Vlaanderen’ (Antwerp), the Flanders Ministry of Culture
and the KULeuven BOF-Centre of Excellence Financing on ‘Eco- and
socio-evolutionary dynamics’ (Project number PF/2010/07).
Appendix A. Supplementary data
Supplementary data associated with this article can be found, in
the online version, at http://dx.doi.org/10.1016/j.fsigen.2013.04.002.
References
[1] M.A. Jobling, M.E. Hurles, C. Tyler-Smith, Human Evolutionary Genetics: Origins,
Peoples and Disease, Garland Science Publishing, London/New York, 2004 p.
523.
[2] P.A. Underhill, T. Kivisild, Use of Y chromosome and mitochondrial DNA population structure in tracing human migrations, Annu. Rev. Genet. 41 (2007) 539–564.
[3] M.A. Jobling, C. Tyler-Smith, The human Y chromosome: an evolutionary marker
comes of age, Nat. Rev. Genet. 4 (2003) 598–612.
[4] J.M. Butler, Y-chromosomal DNA testing, in: J.M. Butler (Ed.), Advanced Topics in
Forensic DNA Typing: Methodology, Academic Press, London, 2011, pp. 371–403
(Chapter 13).
[5] J. Chiaroni, P.A. Underhill, L.L. Cavalli-Sforza, Y chromosome diversity, human
expansion, drift, and cultural evolution, Proc. Natl. Acad. Sci. U.S.A. 106 (2009)
20174–20179.

7

[6] T.M. Karafet, F.L. Mendez, M.B. Meilerman, P.A. Underhill, S.L. Zegura, M.F.
Hammer, New binary polymorphisms reshape and increase resolution of the
human Y chromosomal haplogroup tree, Genome Res. 18 (2008) 830–838.
[7] D.L. Altshuler, R.M. Durbin, G.R. Abecasis, D.R. Bentley, A. Chakravarti, A.G. Clark, F.S.
Collins, F.M. De la Vega, P. Donnelly, M. Egholm, et al., A map of human genome
variation from population-scale sequencing, Nature 467 (2010) 1061–1073.
[8] N.M. Myres, S. Rootsi, A.A. Lin, M. Jarve, R.J. King, I. Kutuev, V.M. Cabrera, E.K.
Khusnutdinova, A. Pshenichnov, B. Yunusbayev, et al., A major Y-chromosome
haplogroup R1b Holocene era founder effect in Central and Western Europe, Eur. J.
Hum. Genet. 19 (2011) 95–101.
[9] R.A. Rocca, G. Magoon, D.F. Reynolds, T. Krahn, V.O. Tilroe, P.M.O. Boots, A.J.
Grierson, Discovery of Western European R1b1a2 Y chromosome variants in 1000
Genomes project data: an online community approach, PLoS ONE 7 (2012)
e41634.
[10] M.H.D. Larmuseau, N. Vanderheyden, M. Jacobs, M. Coomans, L. Larno, R. Decorte,
Micro-geographic distribution of Y-chromosomal variation in the central-western European region Brabant, Forensic Sci Int Genet 5 (2011) 95–99.
[11] M.H.D. Larmuseau, J. Vanoverbeke, G. Gielis, N. Vanderheyden, H.F.M. Larmuseau,
R. Decorte, In the name of the migrant father – analysis of surname origin
identifies historic admixture events undetectable from genealogical records,
Heredity 109 (2012) 90–95.
[12] M.H.D. Larmuseau, C. Ottoni, J.A.M. Raeymaekers, N. Vanderheyden, H.F.M.
Larmuseau, R. Decorte, Temporal differentiation across a West-European Ychromosomal cline – genealogy as a tool in human population genetics, Eur. J.
Hum. Genet. 20 (2012) 434–440.
[13] M. Van den Cloot, DNA Brabant – DNA-project 2009 oud-hertogdom Brabant,
Familiekunde Vlaanderen, Antwerpen, 2010p. 352.
[14] M. Van den Cloot, DNA Belgie¨ – DNA-project 2010 Belgie¨, exclusief oud-hertogdom Brabant, Familiekunde Vlaanderen, Antwerpen, 2011p. 328.
[15] M.H.D. Larmuseau, A. Van Geystelen, M. van Oven, R. Decorte, Genetic genealogy
comes of age – perspectives on the use of deep-rooted pedigrees in human
population genetics, Am. J. Phys. Anthropol. 150 (2013) 505–511.
[16] F. Debrabandere, Woordenboek van de familienamen in Belgie¨ en NoordFrankrijk, L.J. Veen/Het Taalfonds, Amsterdam/Antwerpen, 2003.
[17] W.T. Athey, Haplogroup prediction from Y-STR values using a Bayesian-allelefrequency approach, J. Genet. Geneal. 2 (2006) 34–39.
[18] L.M. Sims, D. Garvey, J. Ballantyne, Improved resolution haplogroup G phylogeny
in the Y-chromosome, revealed by a set of newly characterized SNPs, PLoS ONE 4
(2009) e5792.
[19] F.L. Mendez, T.M. Karafet, T. Krahn, H. Ostrer, H. Soodyall, M.F. Hammer, Increased
resolution of Y chromosome haplogroup T defines relationships among populations of the Near East, Europe, and Africa, Hum. Biol. 83 (2011) 39–53.
[20] A. Van Geystelen, R. Decorte, M.H.D. Larmuseau, AMY-tree: an algorithm to use
whole genome SNP calling for Y chromosomal phylogenetic applications, BMC
Genom. 14 (2013) 101.
[21] S. Caratti, S. Gino, C. Torre, C. Robino, Subtyping of Y-chromosomal haplogroup EM78 (E1b1b1a) by SNP assay and its forensic application, Int. J. Legal Med. 123
(2009) 357–360.
[22] M. van Oven, A. Ralf, M. Kayser, An efficient multiplex genotyping approach for
detecting the major worldwide human Y-chromosome haplogroups, Int. J. Legal
Med. 125 (2011) 879–885.
[23] L. Excoffier, G. Laval, S. Schneider, ARLEQUIN ver.3.0: an integrated software
package for population genetics data analysis, Evol. Bioinform. Online 1 (2005)
47–50.
[24] W.R. Rice, Analyzing tables of statistical tests, Evolution 43 (1989) 223–225.
[25] T. Hothorn, K. Hornik, M.A.V. van de Wiel, A. Zeileis, Implementing a class of
permutation tests: the coin Package, J. Stat. Softw. 28 (2008) 1–23.
[26] R. Scozzari, A. Massaia, E. D’Atanasio, N.M. Myres, U.A. Perego, B. Trombetta, F.
Cruciani, Molecular dissection of the basal clades in the human Y chromosome
phylogenetic tree, PLoS ONE 7 (2012) e49170.
[27] H. Skaletsky, T. Kuroda-Kawaguchi, P.J. Minx, H.S. Cordum, L. Hillier, L.G. Brown,
S. Repping, T. Pyntikova, J. Ali, T. Bieri, et al., The male-specific region of the
human Y chromosome is a mosaic of discrete sequence classes, Nature 423
(2003) 825–837.
[28] W. Wei, Q. Ayub, Y. Chen, S. McCarthy, Y. Hou, I. Carbone, Y. Xue, C. Tyler-Smith, A
calibrated human Y-chromosomal phylogeny based on resequencing, Genome
Res. 23 (2013) 388–395.
[29] D.L. Hartl, A.G. Clark, Principles of Population Genetics, 4th ed., Sinauer
Associates Inc., Sunderland, USA, 2006p. 545.
[30] G.B.J. Busby, F. Brisighelli, P. Sa´nchez-Diz, E. Ramos-Luis, C. Martinez-Cadenas,
M.G. Thomas, D.G. Bradley, L. Gusmao, B. Winney, W. Bodmer, et al., The peopling
of Europe and the cautionary tale of Y chromosome lineage R-M269, Proc. Roy.
Soc. B 279 (2012) 884–892.
[31] M. Cloet, C. Vandenbroeke, Tien bijdragen tot de lokale en regionale demografie in
Vlaanderen, Gemeentekrediet, Brussel, 1989p. 291.
[32] T.E. King, M.A. Jobling, What’s in a name? Y chromosomes, surnames and the
genetic genealogy revolution, Trends Genet. 25 (2009) 351–360.
[33] F. Cruciani, B. Trombetta, C. Antonelli, R. Pascone, G. Valesini, V. Scalzi, G. Vona, B.
Melegh, B. Zagradisnik, G. Assum, et al., Strong intra- and inter-continental
differentiation revealed by Y chromosome SNPs M269, U106 and U152, Forensic
Sci. Int. Genet. 5 (2011) E49–E52.
[34] M. Brion, B. Quintans, M. Zarrabeitia, A. Gonzalez-Neira, A. Salas, V. Lareu, C. TylerSmith, A. Carracedo, Micro-geographical differentiation in Northern Iberia
revealed by Y-chromosomal DNA analysis, Gene 329 (2004) 17–25.

Please cite this article in press as: M.H.D. Larmuseau, et al., Increasing phylogenetic resolution still informative for Y chromosomal
studies on West-European populations, Forensic Sci. Int. Genet. (2013), http://dx.doi.org/10.1016/j.fsigen.2013.04.002


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