SUPPLEMENTARY INFORMATION
Interpolation of map: Minimum curvature interpolation was applied separately for each ordination
axis, which resulted from the three interpolated grid layers of ordination axis scores. Minimum
Curvature interpolation using TNT Mips v.6.9 was applied as follows: first, a grid with pixel size 20
x 20 km was constructed from sampling point values (axis scores in our case) using the inverse
distance, weighting power of 2, search distance of 100 cells and coarse grid ratio of two. In other
words, the algorithm calculated values for every second grid intersection as a weighted mean of the
sampling points located within the distance of 100 grid cells. Secondly, the initial grid was
smoothed using 100 iterations, a matching tolerance (the difference between new values and
original values in an iteration run) of 0.1, and no variation between original values and iterative
results in sampling points.
Interpretation of the map: The produced map may be interpreted with the help of a RGB color
cube (Supplementary Figure S1), where three axes of the colour cube (red, green and blue)
correspond to the three ordination axes in such a way that scores from axis 1 are shown in red,
scores from axis 2 in green and scores from axis 3 in blue. Intensities of the colours increase when
axis scores become higher. Blending of the main colours corresponds to the three-dimensional value
of axis scores (Supplementary Figure S2). For instance the red areas in the map have high values in
axis 1 (breed FFR in Fig. S2), correspondingly green areas have high values in axis 2 (breed RDM
in Fig. S2) and blue areas have high values in axis 3 (breed SLB in Fig. S2). The areas having
magenta (purple) colour in the map have high axis scores values in axis 1 and 3 but not in axis 2,
and yellow areas in turn have high values in axis 1 and 2 but not in axis 3. The light areas have
higher axis values in general than darker areas (breeds ESN and REG in Fig. S2), and the black
colour occurs when all axes values are close to zero, and the white colour when axes score values
are close to the maximum value of 255. The most similar breeds in terms of genetic data are shown
in similar colours, whereas the genetically most distinct breeds are shown in colours located in the
opposite corners or sides of the colour cube.
SUPPLEMENTARY FIGURE S1
Figure S1. RGB color cube for help of map interpretation. Scores from PCO axis 1 are shown in
red, scores from PCO axis 2 in green and scores from PCO axis 3 in blue. The sampling points,
with the population acronyms, are shown as for map 4A in the main text.
SUPPLEMENTARY FIGURE S2
Figure S2. Illustration of blending of shades in RGB map for help of map interpretation. Legend in
the separate box tells that each figure tells separately the scores of PCA axis 1, axis 2 and 3 and the
colours corresponding to the scores for selected breeds. The circle in the middle shows the colour in
RGB map 4A corresponding to three axes scores and abbreviation of the breed. Note that ranges of
the axes scores varied; range of axis 1 [-0.217, 0.119], axis 2 [-0.112, 0.228] and axis 3 [-0.103,
0.155].
SUPPLEMENTARY FIGURE S3
Figure S3. A neighbor-joining tree of mtDNA haplotypes. Only the most common T3 haplotypes
(frequency ≥ 5) were included in the analysis (see also the Figures 1 and 2). The numbers above the
branches indicate bootstrap proportions (only values > 50% shown) in 1,000 replications.
SUPPLEMENTARY FIGURE S4
12000
Frequency
10000
8000
6000
4000
2000
31
29
27
25
23
21
19
17
15
13
11
9
7
5
3
1
0
Pairwise differences
Figure S4. The mismatch distribution of mtDNA sequences in 235 animals analysed. A bimodal
distribution indicates the deep genetic divergence between the taurine and zebu sequences.
Unweighted mean pairwise difference between the sequences was 2.641.
SUPPLEMENTARY FIGURE S5
Frequency
The entire data set of 405 chromosomes
20000
18000
16000
14000
12000
10000
8000
6000
4000
2000
0
0
1
2
3
4
5
6
7
8
9 10 11 12 13 14 15 16
Sum of size differences
Figure S5. The mismatch distribution of the entire Y-data set.
SUPPLEMENTARY TABLE S1
Table S1. Y-chromosomal and mtDNA diversity estimates for the breeds and their geographic origins.
Y-chromosomal haplotypes
Population
EUROPEAN BREEDS
Byelorussian Red
Danish Red
Danish Jersey
Jutland breed (Denmark)
Estonian Red
Estonian Holstein-Friesian
Estonian Native
Faroe Islands Cattle
Finnish Ayrshire
Finnish Holstein-Friesian
Eastern Finncattle
Northern Finncattle
Western Finncattle
German Simmental
Icelandic Cattle
Latvian Brown
Latvian Danish Red
Latvian Blue
Lithuanian Red
Lithuanian Black-and-White
Lithuanian Light Grey
Sample
size
22
15
12
6
10
NA
10
3
14
11
11
3
9
3
11
8
10
9
9
10
10
Number of
haplotypes
MtDNA
Haplotypic
diversity
Total
Private
7
3
3
3
3
0
0
0
0
0
0.909
0.378
0.682
0.733
0.378
3
3
3
4
4
2
3
3
3
2
5
2
7
4
4
0
0
0
0
2
0
0
0
1
0
1
0
1
0
0
0.378
0.385
0.709
0.600
0.556
0.655
0.250
0.800
0.556
0.909
0.733
0.733
Sample
size
8
9
NA
9
5
1
4
14
7
7
18
8
7
NA
NA
NA
NA
NA
NA
NA
NA
Number of
haplotypes
Haplotypic
diversity
Mean
number of
differences
between
haplotypes
Nucleotide
diversity x
10-3
Total
Private
5
2
2
0
0.786
0.500
1.250
0.500
4.92
1.97
6
4
1
1
3
3
2
2
5
4
2
1
1
0
1
1
1
0
0
1
0.833
0.900
1.500
2.800
5.94
11.02
0.000
0.385
0.524
0.476
0.209
0.786
0.810
0.000
0.956
1.714
0.952
0.418
1.179
1.905
0.00
3.76
6.75
3.75
1.65
4.64
7.50
Lithuanian White Backed
Norwegian Red Cattle (NRF)
Western Red Polled (Norway)
Eastern Red Polled (Norway)
Doela Cattle (Norway)
Troender Cattle (Norway)
Telemark (Norway)
Western Fjord Cattle (Norway)
Polish Holstein-Friesian
Suksun (Russia)
Istoben (Russia)
Pechora type (Russia)
Kholmogory (Russia)
Yaroslavl (Russia)
Red Gorbatov (Russia)
Yurino (Russia)
Yakutian Cattle (Russia)
Busa (Serbia)
Podolian (Serbia)
Swedish Holstein-Friesian
Swedish Red-and-White
Vane Cattle (Sweden)
Ringamala Cattle (Sweden)
Swedish Red Polled
Swedish Mountain Cattle
Bohus Poll (Sweden)
Fjall Cattle (Sweden)
Ukrainian Whitehead
Ukrainian Grey
10
12
4
6
4
7
2
6
10
5
9
7
8
4
2
6
17
5
4
NA
NA
NA
NA
5
9
NA
4
11
7
3
3
2
3
2
2
1
4
4
2
3
2
3
4
1
1
3
2
2
0
0
0
1
1
0
0
0
0
0
0
0
0
2
0
0
0
0
0
0.644
0.621
3
2
0
0
0.800
0.286
2
7
4
0
3
4
0.909
0.810
CENTRAL ASIAN BREEDS
Ala-Tau (Kazakshtan)
Bushuev (Uzbekistan)
6
4
3
3
0
1
0.600
0.286
0.867
0.533
0.400
0.667
0.571
0.607
0.600
0.600
0.600
NA
NA
NA
NA
NA
NA
NA
NA
NA
10
9
9
14
10
2
4
24
8
11
5
5
5
7
5
4
6
6
10
8
8
6
3
4
2
2
3
7
2
4
3
2
2
2
3
3
1
5
7
1
4
3
1
2
1
1
0
5
1
3
1
0
2
0
0
2
0
4
4
0
0.956
0.833
0.556
0.626
0.356
2.622
1.944
0.833
0.868
0.711
10.32
7.66
3.28
3.42
2.80
0.645
0.536
0.709
0.800
0.600
0.400
0.286
0.700
0.833
0.000
0.933
0.933
0.000
1.630
1.071
1.091
2.400
1.200
2.000
0.571
0.800
1.000
0.000
2.200
10.911
0.000
6.42
4.22
4.29
9.45
4.72
7.87
2.25
3.15
3.94
0.00
8.66
42.96
0.00
5
4
3
3
2
0
0.800
0.814
14.800
1.613
58.27
6.36
NEAR-EASTERN BREEDS
Anatolian Black (Turkey)
East Anaolian Red (Turkey)
South Anatolian Red (Turkey)
Turkish Grey
Damascus (Syria)
Middle Iraqi
North Iraqi
South Iraqi
6
4
4
4
5
5
3
4
6
4
4
4
5
5
3
4
4
0
1
1
2
0
3
2
1.000
1.000
1.000
NA
NA
NA
NA
NA
NA
NA
NA
NA= Not analysed in this study
The frequencies of mtDNA and Y-chromosomal haplotypes in each breed can be obtained on request from the corresponding author.
SUPPLEMENTARY TABLE S2
Table S2. Allele frequencies of the Y-chromosomal microsatellites in the present cattle data set.
Locus
INRA124
Allele size (bp)
130
132
Frequency
0.025
0.975
INRA189
82
88
90
98
100
102
104
106
0.015
0.022
0.017
0.672
0.027
0.104
0.119
0.025
BM861
156
158
160
0.020
0.978
0.002
DYZ1
360
362
364
366
0.133
0.170
0.002
0.694
BYM-1
252
254
256
258
0.010
0.035
0.178
0.778