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Defining a New Rate Constant for Y-

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The Russian Journal of Genetic Genealogy ( ): 7, 1, 2015
ISSN: 1920-2997 http://ru.rjgg.org RJGG

Defining a New Rate Constant

Dmitry Adamov,
for Y-Chromosome SNPs based Vladimir Guryanov,
Sergey Karzhavin,
on Full Sequencing Data Vladimir Tagankin,
Vadim Urasin

Abstract

Two important advances: 1) the accumulation of BigY and FGC test data, and 2) the publication of Y-chromosome se-
quences for three ancient samples (Anzick-1, Ust-Ishim, and K14), have made it possible to estimate the average rate of base-
substitutions (SNPs). The authors of this study have developed a new method of selecting true mutations in modern and an-
cient samples, and have defined with high accuracy the rate constant of SNP mutations: 0.82 10 per year per bp (95% CI:
(0.70 0.94) 10 ).

Introduction

A single nucleotide polymorphism (SNP) is a nucleotide site of the chromosome, and is the
DNA sequence variation in which a single nucle- rate constant of base-substitutions.
otide (A, T, G or C) in a genome (or another
shared sequence) differs among members of a In practice, many nucleotide sites are
species or between paired chromosomes. The measured simultaneously. Let a total number of
authors use SNP mutation, base- measured base pairs be denoted as B. The
substitution, and mutation interchangeably. average number of SNP mutations ( ) is
determined by the ratio
Substitution of one nucleotide with another
during meiosis occurs at random. The probabil-
ity of SNP mutations is very small: few re-
= , (1)
placements per one hundred million base pairs
(nucleotide sites) occur in the course of a single where is the rate constant of SNP mu-
meiosis. The mutation flow is rare (standard tations. For brevity's sake, we call this the mu-
probability) and subsequent mutations do not tation rate.
depend on previous mutations. These charac-
teristics determine the mutations flow as a Measuring the number of mutations for
Poisson process. The probability of mutations in genealogical purposes became possible a few
the meiosis sequence within T generations is years ago when high-performance Next
estimated using a Poisson distribution: Generation Sequencing (NGS) technologies
capable of large-scale parallel reading of
( ) genomes became available at a reasonable
= , cost.
!

where is the probability of k mutations The commercial NGS testing of Y-

occurring across T generations within the same chromosome samples began in 2013. Table 1
summarizes the data on coverage of Y-
________________________________________________________
chromosome sequences by commercial and
Received: March 18 2015; accepted: March 19 2015: published: March 21
2015.
research laboratories based on NGS technology.
Correspondence: nimissin@mail.ru, gurianov.vm@gmail.com,
karzhavin@inbox.ru, SemarglV@gmail.com, wert22@mail.ru

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The Russian Journal of Genetic Genealogy ( ): 7, 1, 2015
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Table 1. The overall size and reading quality of Y-chromosome segments

Mapping area, Coverage,

Research (Test)
Mbp times
FTDNA BigY up to 11.38 60
FGC Elite 23 60
1000 Genomes Project 23 2-4
Personal Genome Project 23 No data
Poznik et al. (2013) 9.99 3.1
Wei et al. (2013) 8.97 28.4
Francalacci et al. (2013) 8.97 2.16
Yan et al. (2014) 3.90 10
Hallast et al. (2015) 3.72 51

The mapped sequences of the Y- suitable for mapping short reads (about 100 bp)
chromosome supplied by NGS technology were defined. These segments are basically X-
average about 23 Mbp in length. degenerated and, to a lesser extent,
ampliconic. Palindromic segments were
Skaletsky et al. (2003) noted that the excluded.
structure of the Y-chromosome is
heterogeneous. Y-chromosome euchromatin To estimate the age of male genealogical
consists of the nucleotide sequences of the lines using the number of detected derived
following types: variants the ratio (1) is transformed as follows:

1) X-transposed, which have 99% identical

analogues in the X-chromosome (total length is
approximately 3.7 Mbp),
2) X-degenerated, which are unique and
easily mapped sequences (total length is
approximately 8.6 Mbp),
3) Ampliconic, which are segments 99.9%
similar to the sequences located in other parts
of the Y-chromosome (total length is
approximately 10.2 Mbp, including 8 chromosome of humans and chimpanzees.
palindromic segments of 5.7 Mbp).
In scientific works, research is limited, as a
rule, to the X-degenerated area. Researchers
try to avoid X-transposed and ampliconic
sequences. Wei et al. (2013) wrote:
We identified unique regions within the
male-specific part of the Y chromosome
reference sequence ... where we expected read
mapping and variant detection to escape
complications introduced by repeated
sequences. That was achieved by excluding the
pseudoautosomal, heterochromatic, X-
transposed, and ampliconic segments.
In Poznik D. et al. (2013) 9.99 Mbp
segments of euchromatin which are the most
69
= (2)
The size B of the measured and mapped
area is evaluated using the BED file.
The mean mutation rate is estimated by
using different calibration methods (see Wang,
Gilbert, Jin, Li, 2014).
1. Kuroki et al. (2006) compared the Y-
Assuming that the species division occurred 6
million years ago, the average mutation rate
was estimated at 1.5 10 per year per bp, 95%
CI: (0.767 2.10) 10 .
2. In their well known work, Xue et al.
(2009) used samples with modern genealogies
to calibrate mutation rates. Four mutations
were detected in 13 generations in area with a
total length of 10.15 Mbp. The mutation rate
estimate was 1.0 10 per year per bp, 95% CI:
(0.3 2.5) 10 .
3. The calculations of Mendez et al. (2013),
which were based on the mutation rate in
autosomal chromosomes led to a slower rate at
0.617 10 per year per bp, 95% CI: (0.439
0.707) 10 .
The Russian Journal of Genetic Genealogy ( ): 7, 1, 2015
ISSN: 1920-2997 http://ru.rjgg.org
4. Working from the premise that America
was settled by humans 15,000 years ago,
Poznik et al. (2013) estimated the average
mutation rate at 0.82 10 per year per bp,
95% CI: (0.72 0.92) 10 .
5. Recent progress in the sequencing of
ancient human skeletal remains has made it
possible to perform a direct calibration of the
average mutation rate using the number of
derived alleles accumulated from the time of
ancient humans. Fu et al. (2014) published the
data on the complete genome of an ancient
Ust-Ishim Man who lived about 45 thousand
years ago in Western Siberia. On analyzing a Y-
chromosomal area 1.86 Mbp long, Fu et al.
estimated the rate for SNP mutations at
0.76 10 per year per bp, 95% CI: (0.67 0.86)
10 .
Results
Selection of derived alleles
The variants of derived alleles differing from
the reference sequence are contained in VCF
files. Not all of them reflect actual mutations,
however. Because of the peculiarities of NGS
technology, the imperfections of mapping
methods, the presence of repetitive chains of
nucleotide sequences in the Y-chromosome,
and the coincidence of sequences with
analogues in other chromosomes, some of the
derived variants are not real mutations. The
share of erroneous choices for X-degenerated
segments is not high (between 15% and 25%
of the total). In ampliconic areas, however,
erroneous options can be greater than the
number of real mutations.
The method of selection of real mutations
developed in the present study allows for
elimination of erroneous alternatives from the
analysis. The description of our method is
contained under "Materials and Methods" below.
Our method is based on the selection of X-
degenerated sequences. Our SNP mutation rate
calibration was carried out in what we call the
combBED area (combined BED), which
contains start and end coordinates in the hg19
system of the Y-chromosome segments, in
which we expect our samples to have SNP
70
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variants. Table 1 of the Supplement to this
article shows the location of 857 good regions
of the Y-chromosome (total length of 8,473,821
bp). SNP mutation rate calibration was carried
out for these areas, which will be further
referred to as "combBED area.
Calibration using
the ancient Anzick-1 sample
Rasmussen et al. (2014) wrote about a
sample (Anzick-1) which was obtained from the
bone remains of a boy who lived about 12.6
thousand years ago in the territory of what is
now the State of Montana, USA. The sample
was perfectly preserved, which allowed
Rasmussen et al. (2014) to derive a high-
quality genome sequencing for the boy. The
mutations in the boys Y-chromosome placed
him in haplogroup Q-L54. The age of the
remains was determined with very high
precision by radiocarbon dating. According to
Rasmussen et al. (2014), the boy lived between
12,707 and 12,556 years before the present.
On average, 12632 years BP.
The YFull database has accumulated unique
samples of Q-L54 which we used to construct a
detailed family tree for haplogroup Q-L54. The
tree is shown in Figure 1. Anzick-1 is located
on the same branch (Z780) as a contemporary
sample taken from a present-day Native
American descendant (US1). Twelve thousand
six hundred years ago, US1's ancestor was a
close relative of the Anzick-1 boy.
The structure of the Q-L54 tree required
that the mutation rate be calibrated in two
stages. In the preliminary stage, we computed
the relatively short period between the time the
Anzick-1 boy lived (Z780) and the separation of
L330 and M1107. Our calibrations revealed that
the separation of these branches occurred very
close to the generally accepted time that the
settlement of Anatomically Modern Humans
(AMH) in America (about 15 thousand years
ago). Both branches have sample results with
BigY and FGC in numbers sufficient to achieve
an accurate calibration.
The Russian Journal of Genetic Genealogy ( ): 7, 1, 2015
ISSN: 1920-2997 http://ru.rjgg.org RJGG

Figure 1. The family tree of haplogroup Q-L54 constructed on base-substitutions of 12 private samples
and the ancient Anzick-1 sample

For our pre-calibration, we used the data of
Anzick-1 and the data of US1 who had common
ancestors at level Z780. After Z780, their lines
were distinguished by distinct, differing
mutations. To date, the male line of US1 has
accumulated 78 mutations. In the Anzick-1
sample only one mutation is revealed later
Z780 level. Based on the radiocarbon dating of
the Anzick-1 sample the average rate of base-
substitutions is estimated as 0.831 10 per
year per bp, 95% CI: (0.66 1.04) 10 .
71
We used this evaluation only for calculating
the time interval between the split of the L330
and the M1107 branches and the time that
Anzick-1 lived. According to the number of
mutations detected in the Anzick-1 and US1
samples, the interval is approximately 2,989
years (95% CI: 1,814-4,751 years). The age of
the L330 and the M1107 branches is 15,621
years before the present (95% CI: 14,446-
17,383 years). The dating does not depend on
any model, since the data are based on
The Russian Journal of Genetic Genealogy ( ): 7, 1, 2015
ISSN: 1920-2997 http://ru.rjgg.org
radiocarbon analysis of the Anzick-1 sample
and the molecular clock of the US1 and Anzick-
1 samples.
We secured eleven haplotypes from BigY
and one from FGC which were provided by
contemporary individuals who belong to the
branches under investigation. The samples set
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up four branches: Z780, L330, Y772, L804 (see
Figure 1 above). With a high degree of
accuracy, the branches can be assumed to be
independent. This allows us to reduce the
relative variance in the calibration. The results
of the calibration process are summarized in
Table 2.

Table 2. Number of mutations in 12 contemporary samples selected to calibrate

the average rate of SNP mutations at the time of separation of the L330 and the M1107 branches

Average
Number of Average Lower Upper
combBED number
mutations combBED 95% 95%
Branch Sample area size, of
later than area size, confidence confidence
Mbp mutations
L54 level Mbp interval interval
per branch
Z780 US1 92 7.335 7.335 92.00 74.19 112.83
L330 US7 102 7.527 7.639 104.50 85.46 126.56
L330 RUS1 107 7.751
Y772 US2 93 8.129 7.741 88.00 70.60 108.42
Y772 US3 90 7.856
Y772 US4 85 7.365
Y772 US5 88 7.693
Y772 US6 84 7.660
L804 US8 105 7.895 7.937 107.50 88.17 129.85
L804 SCO1 100 7.900
L804 SWE2 115 8.072
L804 NOR1 110 7.882
Total: 30.65 392.00 354.26 432.83

Based on the average number of mutations
(392 out of 30.65 million b.p.), and the age of
the L330 and the M1107 branches (15,621
years), we arrive at a final calibration rate of
SNP mutations
= 0.819 10 per year per bp.
.
95% CI: (0.704 0.935) 10 . exact number of generations in which private
To recalculate an average rate per one gen-
eration, we take an average interval of one
generation of men equal to 31.5 years (Fenner,
2005):
number of generations to the most recent
common ancestor in the samples varied from 1
to 23. We used the property that the sum of
random numbers distributed according to the
Poisson is a random number itself distributed
according to the Poisson. In our case, it is the
sum of the accumulated mutations.
The advantage of this calibration is that the
mutations occurred is known. The result of the
calibration based on modern genealogies is:
2.56 10 per generation per bp,
95% CI: (2.03 3.16) 10 .

0.819 10 31.5 = 2.58 10 per generation This is in agreement with the calibration on
per bp. the dating of Anzick-1 calculated for the
average interval of one generation of 31.5
years.
Calibration with modern genealogies
The average interval between generations in
Some of the samples in the YFull database the chosen genealogies is 32.1 years. There-
belong to relatives with paternal lines which can fore, the absolute calibration for one year cor-
be proved by documentation. We chose 41 responds to 0.798 10 per year per bp.
samples representing 14 genealogies. The
72
The Russian Journal of Genetic Genealogy ( ): 7, 1, 2015
ISSN: 1920-2997 http://ru.rjgg.org RJGG
Calibration using the Ust-Ishim sample mutation (M2308/Z4842). Studying the BAM
file, we identified 11 mutations (including
According to radiocarbon dating reported by M2308), which emerged after M526 in the
Fu et al. (2014), Ust-Ishim Man (UIM) lived combBED area (total length of 8.463 Mbp). This
about 45 thousand years ago. On the family number was used to calculate the average
tree below, he is at the beginning of branch K- mutation rate.
M2335 (see Fig. 2). Fu et al. (2014) studied the
full genome of the ancient sample. The
presence of a mutation at M526 placed UIM at
the beginning of haplogroup K(xLT). Detailed
examination of derived options revealed a later

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The Russian Journal of Genetic Genealogy ( ): 7, 1, 2015
ISSN: 1920-2997 http://ru.rjgg.org RJGG

Figure 2. Haplogroup K(xLT) family tree constructed on base-substitutions

of 38 private samples and the ancient sample of Ust-Ishim Man (UIM).

74
The Russian Journal of Genetic Genealogy ( ): 7, 1, 2015
ISSN: 1920-2997 http://ru.rjgg.org
For the calibration, haplogroups N, O, Q
and R are appropriate.
In order to reduce possible errors to a
minimum, we selected from the YFull database
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35 samples with at least one fairly close relative
and three samples (of haplogroup O) who were
not close relatives (see Fig. 2). Table 3 shows
the number of identified mutations in these
samples downstream of K(xLT).

Table 3. The number of actual mutations in 38 samples collected to calibrate

an average rate of SNP mutations at Ust-Ishim Mans dating

combBED area size,

within haplogroup

within haplogroup
of mutations later
than K(xLT) level

Average number

Average number
within branch

Mutation rate
Of mutations

Of mutations
per 1 Mbp,

per 1 Mbp,

estimate,
Number
Branch

bp
ID

1 S01 N-Y7310 7452832 260 34.44 34.14 0.732
2 S02 N-Y7310 7415734 252
3 S03 N-Y5743 7480204 253 33.74
4 S04 N-Y5743 7517710 253
5 S05 N-Y4374 7500387 258 34.25
6 S06 N-Y4374 7769783 265
7 US2 Q-Y6131 8129326 293 35.09 36.58 0.786
8 US4 Q-Y6131 7364970 258
9 US5 Q-Y6131 7693497 269
10 US6 Q-Y6131 7659810 264
11 S32 Q-Y6131 7650626 267
12 AJ2 Q-Y2780 8455137 324 38.30
13 AJ5 Q-Y2780 8230718 315
14 S07 Q-Y4929 8419169 311 36.34
15 S08 Q-Y4929 7649280 279
16 S09 Q-Y4929 7461979 270
17 S10 Q-Y4929 7510483 268
18 S11 R1a-YP430 7232725 276 38.15 37.95 0.816
19 S12 R1a-YP430 7418179 283
20 S13 R1a-YP615 7181725 282 39.22
21 S14 R1a-YP615 7632739 299
22 S15 R1a-YP1041 6795545 242 36.47
23 S16 R1a-YP1041 7902430 294
24 S17 R1b-Y5626 7650748 270 34.46 35.19 0.755
25 S18 R1b-Y5626 7235989 243
26 S19 R1b-Y7729 7515672 265 34.89
27 S20 R1b-Y7729 7446027 257
28 S21 R1b-Y7369 7855639 287 36.23
29 S22 R1b-Y7369 7462871 268
30 S23 R-L1069 7412514 290 39.00 39.00 0.840
31 S24 R-L1069 7640179 298
32 S25 R-L1069 7777760 302
33 S26 R-L1069 7826576 304
34 S27 R-L1069 7476862 287
35 S28 R-L1069 8070902 321
36 S29 O-F270 7527844 271 36.00 35.31 0.758
37 S30 O-Y7114 7157490 237 33.11
38 S31 O-Y8387 7658568 282 36.82
average 7611596 36.03 36.36 0.781

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The Russian Journal of Genetic Genealogy ( ): 7, 1, 2015
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The average number of mutations occurred
later K(xLT) level is 36.36 mut./Mbp.
The correction for UIM mutations is:
= 1.30 mut./Mbp.
. limit of the mutation rate. Still, in the K14
The estimate of the mutation rate is:
. .
= 0.781 10 per year per bp.
95% CI: (0.709 0.853) 10 .
Calibration using the K14 sample
Seguin-Orlando et al. (2014) studied a
genetic sample (K14) secured from a male
bones found in Kostenki, Russia. According to
radiocarbon dating, the sample is 37 thousand
Table 4. The number of actual mutations in 4 samples collected to calibrate an average rate
of SNP mutations at K14 dating
RJGG
years old. The quality of the K14 genetic
sample is not as good as either the Ust-Ishim
sample or the Anzick-1 sample.
Published accounts of the sequencing reveal
that it is only possible to estimate the upper
sample we can confidently read two derived
alleles at K29 and CTS6773 (combBED area
length of 1.381 Mbp). According to YFull, this is
the beginning of haplogroup C1. Unfortunately,
the other 15 candidates identified in the sample
have poor coverage, mainly 3X-5X and cannot
be used for calibration. Still, with the confirmed
SNPs, we were able to calculate an upper limit
for the mutation rate.
In the YFull database there are four samples
from branch C1-K29; details are given in Table
4.

Number of mutations later than combBED area size, Average number

Sample
1-K29 level Mbp of mutations per 1 Mbp
S33 326 8.042 40.5
S34 303 7.866 38.5
S35 329 8.022 41.0
S36 339 8.244 41.1
Total: 1297 32.174 average 40.3

The upper limit of SNP mutation rate is
estimated as:
= 1.08 10 per year per bp.
.
This result agrees with other calibrations,
but is not of practical importance.
Coefficients for age estimate
It is convenient to estimate genealogical age
directly from the actual number of mutations.
The formula for calculation of the coefficient is
derived from equation (2). It is:
= (3)
It is essential for researchers to know the
value B of the measured area length. For BigY,
the confidence regions length averaged over
individual bed files is 10.31 Mbp (BigY White
76
Paper, 2014). For FGC Elite, the length is 23
Mbp. At the average mutation rate 0.82 10
the coefficient (formula 3) is 118 years for BigY,
and 53 years for FGC.
If the size of the measured area changes, it
is necessary to recalculate the coefficient. For
example, if the measured area of BigY were not
10.31 Mbp but 11.0 Mbp, then the coefficient
would be
.
= 118 = 111 years per base-
substitution.
For a more effective selection of actual
mutations, we recommend that any research
area be within the boundaries of the combBED
area. The size of the combBED area in
individual BigY samples varies and the average
is about 7.6 Mbp. The appropriate conversion
factor, therefore, is 160 years per base-
substitution.
The Russian Journal of Genetic Genealogy ( ): 7, 1, 2015
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Discussion
We used four methods of calibrating the rate
of SNP mutations. The four methods are within
measurement accuracy, and are consistent.
The values of the rate constant obtained by
the dating of the ancient Anzick-1 sample and
of contemporary genealogies are in agreement.
These are the most accurate calibrations.
The difference between the results of the
calibrations between Anzick-1 and UIM is only
5%. However, we should note two things about
the sequencing UIM calibrations:
1) Radiocarbon dating estimates the age of
UIM as approximately 45,000, which is quite
close to the reliability limit of radiocarbon
dating (50,000 years).
Calibrating UIM with the Anzick-1 sample
(using the rate 0.819 10 ) we estimate Ust-
Ishim Mans age to be 42,800 years (95% CI:
49,800-37,500). Fu et al. (2014) estimate the
age of UIM at between 46,880-43,210 years,
with a 95.4% confidence level. Although our
value (42,800 years) falls slightly outside the
radiocarbon calibration, the lower estimate falls
within measurement accuracy.
2) We cannot be sure of the average interval
of generations for men who lived thousands of
years ago.
The rate constant of base-substitutions per
calendar year ( ) is associated with a constant
per one generation ( ) using the ratio
=
,
where is average interval of one generation
(fathers average age).
Kong et al. (2012) made an analysis of the
complete genomes of 78 parent-offspring trios
(i.e. father-mother-offspring). The study strictly
confirmed the fact that the number of
mutations per meiosis increases with the age of
the father. For the purposes of our study, we
represented the increase of base-substitutions
in a fathers gametes versus his age t as a
power-law
~ .
77
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According to genomes of five parent-
offspring trios (Kong et al., 2012) 1.02.
If we assume that the number of mutations
in the Y-chromosome of the son increases in
proportion to the age of the father ( = 1), the
average rate of SNP mutations based on a
calendar year will not depend on the average
interval of one male generation.
In general, the mutation rate per year will
be described by a ratio:
~ . (4)
This ratio is useful for understanding the
relationship between the change in the average
age of a father and the corresponding change in
the mutation rate for one year. Suppose we
observe a decrease in the rate constant of
mutations in one calendar year during the
transition from one calibration to another.
When > 1, this reduction corresponds to the
decrease in the fathers average age. If < 1,
the decrease in the rate of mutations indicates,
on the contrary, an increase in the father's
generation interval.
Our understanding of the lives of humans
during the Paleolithic (12,600-45,000 years BP)
makes us think that the average interval of one
male generation was less than 31 or 32 years.
The average mutation rate calibrations of
Anzick-1 and Ust-Ishim do not show any
significant difference. This suggests a linear
relation of the mutation rate per generation
with the age of the father. In any event, the
mutation rate per one calendar year slightly
depend on the male generation interval.
In general, our results are consistent with
recent data available, including Poznik et al.
(2013) 0.82 10 , Fu et al. (2014) 0.76 10 .
However, our rates are more accurate.
According to Poznik et al (2013), their
method of mutation rate evaluation depends on
the age of separation between the lines
represented by Maya samples HGDP00856 and
HGDP00877. HGDP00856 enters the Q-Y772
branch and HGDP00877 enters the Q-Z780
branch. Poznik et al. supposed this time to be
15,000 years BP (the first settlement of
America). In our work, we don't use an
arbitrary parameter to estimate the date at
which these two genetic lines split, instead, we
The Russian Journal of Genetic Genealogy ( ): 7, 1, 2015
ISSN: 1920-2997 http://ru.rjgg.org
base our calculations using the Anzick-sample.
Replacement of the age parameter (15,621
instead of 15,000) reduces the mutation rate in
Poznik et al. (2013) to 0.79 10 .
The base of mutation rate evaluation in Fu
et al. (2014) paper is 45000 1.86 = 83,700
Mbpyear. Our evaluation base, using the
Anzick-1 sample, is much larger: 15621 7.7 =
120,000 Mbpyear. A 7.7 Mbp length is
calculated by averaging over 12 modern
samples bed files (see Table 2). The quality of
the data in the Anzick-1 sample is higher than
the quality of the data collected from the Ust-
Ishim sample.
Kuroki et al. (2006) estimates the mutation
rate (1.5 10 ), since the ancestors of humans
and chimpanzees separated. This estimate is
80% higher than our.
The pioneering work of Xue et al. (2009)
established the rate 1.0 10 per year per bp
which contributed greatly to the development of
genealogical research on the Y-chromosome.
Our research, however, has shown that the
calibration Xue et al. obtained in four derived
alleles is outdated.
The rate 0.617 10 from the work of Mendez
et al. (2013) seems to us to be underestimated.
The criticism of Mendez et al.'s mutation rate
conversion method from data on autosomal
chromosomes is contained in Sayres (2013).
Overall, the results of our research on the
rate constant of base-substitutions
consistent with the conclusions of Wang,
Gilbert, Jin, Li (2014) in their paper, Evaluating
the Y chromosomal timescale in human
demographic and lineage dating.
The probable time America was first settled
is revealed by the structure of the branches of
Q-M1107 (see Figure 1, above). Currently, two
branches are known to extend from M1107:
branch Z780 and branch M930. Z780 occurs
exclusively in the male lines of Native
Americans (Indians). The L804 sub-branch of
M930 is classed as European (the members of
L804 seem to have remained in Eurasia) while
those with the Y772 sister-mutation appear to
have migrated to America. There are only four
mutations at the same level as M930 in
combBED area. There are five samples of sub-
branch Y772 and four samples of sub-branch
L804. The age separation of M930 is estimated
RJGG
at about 14,800 years. We believe this is
closest to the time of the settlement of
America. Our estimate agrees with the results
of the those who study the settlement of
America specifically: they assert that humans
appeared in the America no later than 14
thousand years ago (Barnosky et al., 2014). We
note that the first male immigrants to America
do not belong to only one haplogroup: they
belong not only to M930 but also to Z780 like
the ancestors of Anzick-1.
Hallast et al. (2015) published research on
two samples of the aboriginal population of
Australia. Mutations F3393 and K35 (measuring
3.7 Mbp) indicated that the samples belong to
haplogroup C1 (see YFull tree at
http://www.yfull.com/tree/C/). We found that
129 SNPs (of Hallast et al., 2015) in the
Australian samples are distinct from the C1a
and C1b branches in the Y Full data base. To
determine the date of the first settlement of
Australian Aborigines, we sought to calibrate
the time of the separation of haplogroup C1
from its subclades C1a and C1b. Using four
modern samples C-V20 (see Table 4 above) we
arrived at 49,200 years (95% CI: 43,900-
54,600). This result is in agreement with the
estimates archaeologists O'Connell and Allen
(2004) and Hiscock (2013) give for the peopling
of Sahul: approximately 50 thousand years ago.
On the basis of probability theory we
obtained from formula (2) an estimate of the
root-mean-square (r.m.s.) error:
are ( ) ( ) ( )
= + (5)
With the large number of independent
measurements, the average mutation rate can
be evaluated with high relative accuracy:
( ) ( )
(6)
In this case, the age estimation accuracy
would be determined only by the number of
mutations:
( ) ( )
= = = (7)
Equation (7) allows us to calculate the
theoretical limit of accuracy of the SNP branch
age estimation. Table 5 shows the relative
confidence intervals for the 95% probability
78
The Russian Journal of Genetic Genealogy ( ): 7, 1, 2015
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(i.e. 1.96/T) for the next parameters:
= 0.82 10 ( ) , = 8 10 bp.
Table 5. The theoretical limit of accuracy of the age estimation versus the SNP branch age
Branch age, years
1000
2000
5000
10000
We could double the accuracy of the limits
specified in Table 5 if we selected actual
mutations among ampliconic segments (+10
Mbp added to the combBED area), and take
into account second SNP branches (+N
substitutions).
Materials and methods
In order to calibrate the average rate of
mutations, we used private Y-chromosome NGS
data from two commercial laboratories, FTDNA
and Full Genome Corporation. The private
samples were provided by the YFull team in
compliance with the confidentiality
requirements for personal data. All the persons
had given individual permits for the use of their
data for research.
The data on the ancient Y-chromosome
samples were taken from scientific articles:
Anzick-1 from Rasmussen et al. (2014), Ust-
Ishim Man from Fu et al. (2014), and K14 from
Seguin-Orlando et al. (2014).
We developed a selection method which
effectively excluded from consideration false
options with derived alleles (false positives).
We used the following filtration criteria:
1. Reg criterion. There are derived
variants (i.e. alleles different from the reference
sequence) revealed in the BAM files. The
nucleotide sequences under investigation had a
total length between 13-15 Mbp for BigY, and
about 23 Mbp for FGC. Single base read
coverage varied from 1X to 8000X. The average
coverage of commercial samples is about 60X.
From this set of variants, we selected only
those coordinates that fell into the combBED
regions. As it was mentioned above, the
combBED area was designed by the authors to
select X-degenerate segments. The combBED
area borders were formed by mutual
79
RJGG
1.96/T
76%
54%
34%
24%
overlapping BED file taken from the work of
Poznik et al. (2013) (total length of 10.45 Mbp)
and by the generalized BigY BED file (11.38
Mbp long), published in the BigY White Paper
(2014). The result was 857 continuous
segments of the Y-chromosome with a total
length of 8,473,821 bp. The coordinates of the
beginning and the end of these regions are
contained in Table 1 of Supplement.
2. Indel criterion. We excluded insertions
and deletions (indels), as well as multiple
nucleotide polymorphism (more than one base
position in derived alleles, MNP) variants.
3. Locs criterion. We excluded variants
which were detected in more than five different
localizations. (Note: localization is defined as
a group of samples from the YFull database
[2,900 samples at February, 2015] belonging to
the same subclade and having derived allele
nomination that have been studied). In some
cases, the same derived variants were revealed
in samples from different subclades or
haplogroups. One of the reasons consists of the
fact that standard reference sequence is based
on haplogroup R1b data and also to a lesser
extent on haplogroup G data. Thus, some
variants in some haplogroups are ancestral
allele, not derived. Another reason is mapping
errors. We found limit of five localization
empirically. This criterion is soft but effective.
4. Reads criterion. We excluded from
consideration any one or two read variants.
5. Qual criterion. We excluded variants
with a read quality less than 90%. Quality is
defined as weighted average of the quality
index where correct values are taken with the
positive and error values, with the negative.
6. Post mortem criterion. Its applied only
to the ancient samples. Postmortem damages
of DNA, lead to the replacement of these base
The Russian Journal of Genetic Genealogy ( ): 7, 1, 2015
ISSN: 1920-2997 http://ru.rjgg.org
pairs: CT and GA (Briggs et al., 2007) were
excluded.
7. Single SNP criterion. We excluded
variants with Double Nucleotide Polymorphisms
(DNP). Our program interpreted DNP as a
base-substitution in two adjacent positions and
therefore were not excluded by our Indel
criterion. This secondary criterion allowed us to
reject both options.
8. Trash criterion. We excluded suspicious
variants which have alignment error or reading
error. In general, these are variants in
palindromic segments and segments with
repetitive copies at other Y-chromosome
segments.
Variants that pass our criteria are actually
base-substitutions. Criteria 2-8 collectively
eliminated up to one-third of entered variants,
an average of 20%.
The individual combBED area includes all
nucleotide positions with three or more reads.
RJGG
The modern samples selected for study ranged
from 7.2 to 8.45 Mbp in length (depending on
the quality of the sequencing and reflected in
the BAM file [see the tables 2 and 3]). The
length of the combBED area in the ancient
samples varied: Anzick-1 - 6.355 Mbp, Ust-
Ishim Man - 8.463 Mbp, K14 - 1.381 Mbp.
There is no single formula for calculating the
mutation rate because of the difference in the
calibration methods. In all calculations ratio (1)
= was used.
An evaluation of 95% confidence intervals
was performed in each case individually based
on the properties of the Poisson distribution.
Figure 3 shows the distribution of the mutation
rate estimate at a two-step calibration based on
Anzick-1 dating. The distribution was obtained
by computer simulation of 5 10 random
events. It is clear that the curve is very close to
a normal distribution.

0,018

0,016

0,014

0,012
Probability

0,01

0,008

0,006

0,004

0,002

0
6E-10 7E-10 8E-10 9E-10 1E-09 1,1E-09
Mutation Rate Estimation
Figure 3. Distribution of the mutation rate estimate based on the ancient Anzick-1 sample dating.
The full brown line represents a normal distribution

The variance calculation method for simple

one-step calibration is given in Poznik et al.
(2013).

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The Russian Journal of Genetic Genealogy ( ): 7, 1, 2015
ISSN: 1920-2997 http://ru.rjgg.org
Conclusion
Our method of base-substitution variants
filtration allowed us effectively select actual
mutations and exclude false positives in
individual samples.
Using four independent calibrations and
ranking them in order of validity and reliability
yielded independent but similar rates constant
for SNP mutations (0.82 10 per year per bp,
95% CI: (0.70 0.94) 10 ).
81
RJGG
Our analysis of the BigY and FGC data
collected in the YFull database allowed us to
fine tune the probable date of the arrival of
humans in the Western Hemisphere (14,800
b.p.), and the arrival of humans in Australia
(49,200 b.p.).
We express gratitude to Roman Sychev for
the help and discussion.
We thank Judith Remy Leder for help with
translation and discussion.
We thank Olga Vassilieva for help with
translation.
The Russian Journal of Genetic Genealogy ( ): 7, 1, 2015
ISSN: 1920-2997 http://ru.rjgg.org
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Supplement

Table 1. List of 857 Y-chromosome start and end positions (hg 19 coordinates)
of target sequences (combBED area).
The start position is not included in the target sequence,
the end position is included in the target sequence

Start End Start End Start End

position position position position position position
1 2655000 2669950 301 14550565 14552625 601 18925326 18928386
2 2680900 2683020 302 14553005 14554575 602 18928656 18930246
3 2683240 2684220 303 14554965 14556545 603 18930486 18932006
4 2684440 2688930 304 14558425 14559405 604 18932496 18967146
5 2689390 2697630 305 14560525 14561505 605 18971806 18974736
6 2699410 2708370 306 14561635 14563015 606 18976366 18987126
7 2708470 2744910 307 14566345 14567325 607 18990886 19000276
8 2745730 2768038 308 14569565 14574215 608 19000986 19012836
9 2773800 2775090 309 14575685 14584745 609 19020046 19025106
10 2775160 2786260 310 14585995 14589065 610 19031226 19040646
11 2787070 2788503 311 14589631 14605385 611 19044366 19055712
12 2792920 2856720 312 14607965 14612985 612 19056046 19062366
13 2858890 2865900 313 14620755 14623105 613 19065886 19071226
14 2866444 2895330 314 14623338 14624786 614 19073190 19075336
15 2900860 2913000 315 14625805 14630585 615 19075446 19081416
16 6619420 6621660 316 14635455 14648875 616 19085906 19097296
17 6626650 6637410 317 14649415 14660649 617 19102526 19137766
18 6642670 6645650 318 14661328 14668038 618 19138606 19145846
19 6646720 6648240 319 14691439 14695028 619 19146376 19155236
20 6648460 6654290 320 14695728 14700888 620 19155886 19163999
21 6654780 6663699 321 14701388 14703908 621 19188000 19210016
22 6666100 6682350 322 14704168 14712048 622 19211430 19213536
23 6688450 6690090 323 14712768 14714948 623 19213666 19235416
24 6694660 6709320 324 14720208 14724708 624 19235446 19244866
25 6714900 6720570 325 14726988 14736348 625 19245916 19248366
26 6731140 6747310 326 14743708 14755791 626 19249996 19251626
27 6747820 6748950 327 14761211 14764571 627 19254286 19297066
28 6752380 6756090 328 14764971 14785111 628 19304486 19310346
29 6756940 6765700 329 14785371 14788111 629 19310816 19324396
30 6765780 6770070 330 14788631 14792961 630 19331486 19340266

31 6773890 6790340 331 14798441 14815451 631 19340276 19351706

32 6791590 6798940 332 14815751 14823811 632 19356176 19375935
33 6799060 6807020 333 14823911 14908514 633 19375986 19381999
34 6807070 6819200 334 14909394 14959764 634 19391000 19415546
35 6822371 6825510 335 14965116 14990530 635 19416576 19417556
36 6825940 6826920 336 14991036 14992636 636 19418076 19423986
37 6830520 6832150 337 14992740 15011876 637 19429306 19433456
38 6833100 6881370 338 15012546 15044416 638 19435536 19437136

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39 6882280 6892160 339 15045356 15066106 639 19438236 19459406
40 6892325 6901280 340 15066236 15073366 640 19460556 19461896
41 6903490 6916230 341 15073506 15080836 641 19464756 19479336
42 6917610 6922680 342 15084476 15098256 642 19479686 19483000
43 6922900 6925890 343 15103476 15109436 643 19493000 19510016
44 6930914 6976140 344 15109616 15113756 644 19510036 19517496
45 6977380 6983940 345 15113886 15115016 645 19517667 19539936
46 6984550 6998220 346 15115446 15116825 646 19542106 19544266
47 7008550 7015440 347 15122106 15126466 647 19544346 19551000
48 7034000 7039350 348 15126996 15141206 648 21049052 21054562
49 7045470 7048310 349 15143436 15146636 649 21061442 21072462
50 7048410 7053960 350 15151086 15168206 650 21073142 21077202
51 7054090 7058460 351 15171349 15177686 651 21078782 21095972
52 7063690 7080930 352 15180126 15183916 652 21097042 21107022
53 7081600 7085500 353 15189426 15201666 653 21109782 21118722
54 7086630 7088090 354 15202316 15210976 654 21125482 21139562
55 7088270 7090830 355 15210996 15212756 655 21139802 21150000
56 7091170 7093350 356 15253000 15279106 656 21158000 21162572
57 7093530 7094510 357 15279216 15281806 657 21162842 21170662
58 7094970 7097626 358 15303000 15333702 658 21171792 21187522
59 7099090 7100070 359 15334726 15364826 659 21187712 21196762
60 7102350 7107360 360 15365096 15366076 660 21200022 21201442

61 7107400 7108500 361 15370776 15376186 661 21202342 21207062

62 7109300 7110660 362 15381116 15394606 662 21208772 21211442
63 7111710 7114000 363 15401138 15402618 663 21211602 21219992
64 7127000 7127530 364 15402688 15423078 664 21221062 21241992
65 7128100 7132440 365 15424539 15429698 665 21243882 21245042
66 7132660 7134270 366 15429988 15431938 666 21248492 21268172
67 7135230 7138390 367 15432780 15442518 667 21281852 21296802
68 7138930 7140000 368 15445363 15497118 668 21297642 21320262
69 7144000 7148410 369 15497278 15532610 669 21325602 21334802
70 7150510 7154790 370 15533460 15541916 670 21340082 21346562
71 7156811 7160640 371 15541920 15570440 671 21353092 21362102
72 7160710 7162470 372 15570609 15595310 672 21362892 21371282
73 7162860 7165620 373 15599840 15619262 673 21371432 21375802
74 7167490 7170050 374 15619652 15626771 674 21383222 21386602
75 7170590 7174530 375 15631852 15636000 675 21387062 21392552
76 7175710 7182000 376 15643000 15643192 676 21394662 21408122
77 7182020 7183850 377 15647762 15653162 677 21409942 21416802
78 7185370 7186409 378 15653402 15655252 678 21421982 21427292
79 7186570 7199580 379 15655362 15662452 679 21427542 21448022
80 7202040 7210120 380 15662552 15666000 680 21450492 21455602
81 7211160 7217550 381 15682000 15682622 681 21455902 21457419
82 7218075 7221478 382 15686556 15687892 682 21459702 21473922

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83 7223340 7228583 383 15688262 15698782 683 21476211 21495722
84 7228910 7231270 384 15700842 15728984 684 21498672 21500462
85 7231300 7236630 385 15728994 15730674 685 21503102 21511422
86 7238080 7239060 386 15731124 15732384 686 21512092 21522342
87 7243540 7248250 387 15732724 15733704 687 21526732 21534982
88 7248340 7253930 388 15734144 15739614 688 21540742 21543302
89 7258910 7263970 389 15743967 15745734 689 21545122 21551659
90 7264590 7275260 390 15746725 15748215 690 21554532 21574142
91 7277390 7281990 391 15749134 15758724 691 21589342 21597182
92 7282150 7285290 392 15764024 15769224 692 21602592 21624472
93 7285330 7296080 393 15769234 15770364 693 21624522 21629742
94 7301410 7303410 394 15770514 15773634 694 21635092 21668982
95 7304410 7307970 395 15776044 15788244 695 21672022 21677152
96 7308090 7309390 396 15791044 15792984 696 21681502 21697442
97 7309780 7310760 397 15798024 15803664 697 21698082 21708502
98 7310800 7313280 398 15808764 15834286 698 21708992 21742857
99 7313440 7318820 399 15839516 15852986 699 21748082 21770262
100 7320250 7337140 400 15858156 15882866 700 21771372 21786272
101 7338700 7339970 401 15894386 15918718 701 21796422 21802982
102 7340175 7341155 402 15923958 15931558 702 21806982 21819032
103 7347580 7348710 403 15932168 15936958 703 21821322 21823312
104 7349160 7353236 404 15937088 15943138 704 21824612 21828000
105 7353400 7360470 405 15944110 15958048 705 21843000 21846842
106 7360650 7362430 406 15963638 15985778 706 21852402 21861782
107 7363760 7369110 407 15986408 15987518 707 21861952 21863242
108 7374758 7378680 408 15987978 15995368 708 21863682 21886022
109 7381600 7383890 409 15995388 16000034 709 21888108 21909862
110 7385730 7390230 410 16005908 16006888 710 21911092 21912582
111 7390480 7392050 411 16018142 16020969 711 21915602 21919582
112 7394950 7422490 412 16032166 16033596 712 21920482 21939862
113 7424980 7431000 413 16035496 16044416 713 21945122 21949222
114 7519000 7536150 414 16048786 16052356 714 21949842 21954692
115 7536220 7573010 415 16053996 16054976 715 21959042 21963982
116 7578850 7579830 416 16057036 16059036 716 21969092 21975022
117 7579880 7621400 417 16060496 16062316 717 21975092 21991122
118 7621760 7630079 418 16187000 16206076 718 21991282 21996818
119 7632950 7664410 419 16210886 16214076 719 22001662 22011502
120 7664560 7704855 420 16216536 16240916 720 22017812 22048822
121 7705405 7709085 421 16241566 16245156 721 22052452 22056432
122 7713085 7723805 422 16246016 16266296 722 22060202 22064102
123 7724305 7753305 423 16267086 16270586 723 22065102 22076062
124 7755025 7756425 424 16270896 16272226 724 22076072 22080692
125 7757065 7758405 425 16274036 16275596 725 22080822 22084962
126 7759061 7774395 426 16275896 16277926 726 22085702 22090152

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127 7774795 7829185 427 16279226 16295976 727 22091102 22113762
128 7829455 7860310 428 16297036 16316986 728 22114532 22128862
129 7861980 7866190 429 16323846 16336286 729 22129902 22132642
130 7866390 7885670 430 16336676 16344756 730 22132762 22134565
131 7886040 7894850 431 16344766 16351764 731 22135372 22150132
132 7898600 7917190 432 16357006 16379272 732 22155442 22168162
133 7918330 7923930 433 16384482 16394522 733 22173412 22182102
134 7925080 7964800 434 16399712 16410422 734 22182942 22193222
135 7970140 7984600 435 16411092 16421322 735 22198642 22203932
136 7986460 7990350 436 16430792 16462602 736 22205382 22209212
137 7991230 7996200 437 16463222 16464662 737 22541000 22541302
138 7996720 8002710 438 16471432 16474872 738 22548182 22591072
139 8007999 8043405 439 16475052 16480092 739 22591292 22592272
140 8044435 8052155 440 16480852 16490152 740 22594292 22613992
141 8052345 8056482 441 16491152 16492672 741 22615222 22619542
142 8058285 8061975 442 16492862 16498252 742 22624822 22628000
143 8067185 8072565 443 16503552 16522642 743 22645000 22651132
144 8075995 8076975 444 16522792 16539932 744 22651222 22666132
145 8079355 8080335 445 16540902 16572988 745 22668650 22690122
146 8080405 8091105 446 16574948 16602828 746 22696192 22713202
147 8091945 8110845 447 16603068 16605228 747 22714862 22756792
148 8112295 8135835 448 16605368 16617188 748 22757312 22765822
149 8137825 8159145 449 16625656 16636088 749 22766492 22767622
150 8159395 8166915 450 16636668 16652158 750 22767897 22777162
151 8167675 8174025 451 16654528 16656988 751 22782782 22788952
152 8178685 8235869 452 16658818 16662658 752 22790822 22797867
153 8237190 8276420 453 16665958 16673288 753 22801532 22809082
154 8279710 8293410 454 16678438 16682888 754 22811792 22836892
155 8293570 8295690 455 16688148 16700398 755 22842092 22851582
156 8296570 8321860 456 16710188 16719728 756 22857442 22871662
157 8326150 8344122 457 16729108 16738308 757 22874162 22876642
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170 8712910 8720310 470 16931933 16941763 770 23039392 23047792

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ISSN: 1920-2997 http://ru.rjgg.org RJGG
171 8720380 8723900 471 16941943 16944863 771 23049242 23050542
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The Russian Journal of Genetic Genealogy ( ): 7, 1, 2015
ISSN: 1920-2997 http://ru.rjgg.org RJGG
215 13946030 13947010 515 17486080 17499110 815 24389742 24402162
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258 14279666 14283626 558 18080336 18085696

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The Russian Journal of Genetic Genealogy ( ): 7, 1, 2015
ISSN: 1920-2997 http://ru.rjgg.org RJGG
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