Supplementary Material for:
Elevated substitution rates estimated from ancient DNA sequences
by Simon Y.W. Ho, Sergios-Orestis Kolokotronis, and Robin G. Allaby
Summary and neutrality statistics
Population genetics summary and neutrality statistics were computed in DnaSP 10.4.9
(Rozas et al. 2003). We calculated the number of segregating (polymorphic) sites (S), the
number of unique haplotypes (h), haplotype diversity (Hd), and the average number of
pairwise nucleotide differences (k). Nucleotide diversity (π), i.e., the average number of
nucleotide differences per site between two sequences, was corrected for multiple
substitutions according to Lynch & Crease (1990). The ratio of segregating sites over
mean pairwise differences S/k – also termed “expansion coefficient” (Peck & Congdon
2004; von Haeseler et al. 1996) – was used as a simple form of evidence of a population
size expansion. Populations with high S/k ratios are expected to have increased in size
over time, while lower ratios should be indicative of a relatively constant long-term
population size (Peck & Congdon 2004). Population size expansion usually leaves traces
in the distribution of haplotypes. An excess of haplotypes is indicative of an expansion, as
well as an excess of singleton mutations. Strobeck’s S statistic (Strobeck 1987) expresses
the probability of observing a sample of sequences with a number of haplotypes equal to
or lower than h. We also used an additional test statistic that draws information from the
polymorphism frequency (R2). R2 contrasts the number of singletons and the mean number
of differences; it approaches low positive values in the case of a recent population growth
event (Ramos-Onsins & Rozas 2002). Statistical significance was assessed with 50,000
coalescent simulations (Hudson 1990) given the total alignment length for each data set
and the total number of sequences, while conditioning on . The full results are given in
Table S2.
Model abbreviations
Model abbreviations follow those used in Modeltest (Posada & Crandall 1998).
Table S1. Sources of data sets analysed in this study
Species
Source
Adélie penguin
Arctic fox
Aurochs
Bison
Boar
Bowhead whale
Brown bear
Cave bear
Cave hyaena
Cave lion
Cow
Horse
Moa
Muskox
Nene
Tuco-tuco
Woolly mammoth
Maize
Chlorobium
Lambert et al. (2002)
Dalen et al. (2007)
Edwards et al. (2007)
Shapiro et al. (2004)
Watanobe et al. (2004; 2001)
Borge et al. (2007)
Barnes et al. (2002)
Loreille et al. (2001), Hofreiter et al. (2002), Orlando et al. (2002)
Rohland et al. (2005)
Barnett et al., unpublished data
Bollongino et al. (2006)
Vila et al. (2001)
Huynen et al. (2003)
MacPhee et al. (2005)
Paxinos et al. (2002)
Chan et al. (2006)
Barnes et al. (2007)
Freitas et al. (2003), Golubinoff et al. (1993)
Coolen and Overmann (2007)
Table S2. Population genetic summary and neutrality statistics. P-values were obtained with 50,000 coalescent simulations. Significant test
statistics at the 5% level are indicated in italics. N, number of individuals; S, number of segregating sites; h, number of haplotypes; Hd, haplotype
diversity; JC, nucleotide diversity using the Jukes-Cantor correction for multiple hits (%); k, average number of nucleotide differences; S/k, ratio
of S over k; SS, Strobeck’s S; R2, Ramos-Onsins & Rozas’s R2. Where three rows per species are shown, they contain ancient, modern, and the
combined sequence data, respectively, while one row per species corresponds to ancient sequence data. Numbers in parentheses denote standard
deviation values. All examined loci are mitochondrial D-loop except for the following: 1cytochrome b, 2tRNA+ATPase subunit 8, 316S rRNA.
Organism
Adélie penguin
Arctic fox
Aurochs
Bison
Boar
Species
Pygoscelis adeliae
Alopes lagopus
Bos primigenius
Bison bison
Sus scrofa
N
S
h
Hd
96
60
60
380
105
227
476
91
214
8
3
3
41
16
22
49
9
11
41
24
13
160
115
120
22
16
11
182
110
124
81
39
32
0.972
(0.008)
0.986
(0.002)
0.967
(0.004)
0.464
(0.200)
0.945
(0.021)
0.616
(0.078)
0.765
(0.063)
0.976
(0.008)
0.909
(0.037)
0.965
(0.010)
0.920
(0.015)
JC
k
S/k
2.678
6.944
8.64
1.0
0.0554
3.150
8.138 12.90
1.0
0.0382
1.933
4.599 12.79
1.0
0.0248
0.834
0.929
3.23
0.8
0.2318
1.131
2.610
6.13
1.0
0.0749
0.993
1.107
8.13
1.0
0.0646
1.114
2.115 11.35 0.998
0.0823
SS
R2
3.032 11.966
9.61
1.0
0.0493
0.718
3.662
4.37
0.973
0.1036
3.639 11.915
9.23
1.0
0.0518
1.105
6.23
1.0
0.0760
6.262
Bowhead whale
Balaena mysticetus
7
15
7
88
47
39
99
50
58
68
58
68
167
72
113
Brown bear
Ursus arctos
30
66
82
Cave bear
Ursus spelaeus
26
21
16
Cave hyaena
Crocuta soelaea
10
27
5
Cave lion
Panthera leo spelaea
23
12
8
36
10
8
91
62
67
127
59
71
12
41
11
33
55
32
45
70
42
14
20
10
Cow
Horse
Moa
Bos taurus
Equus caballus
Pachyornis mappini
1.000
(0.076)
0.932
(0.001)
0.935
(0.020)
1.000
(0.003)
0.974
(0.008)
0.994
(0.004)
0.963
(0.018)
0.800
(0.100)
0.581
(0.120)
0.438
(0.102)
0.977
(0.009)
0.902
(0.024)
0.985
(0.040)
0.998
(0.008)
0.997
(0.005)
0.923
(0.060)
1.279
7.238
2.07
1.0
0.2182
1.182
6.693
7.02
1.0
0.0676
1.348
6.029
8.29
1.0
0.0579
1.872
8.357
6.94
1.0
0.0685
1.569
7.010 10.27
1.0
0.0472
6.687 11.824
5.58
1.0
0.0861
3.219
6.000
3.5
0.996
0.1388
2.256
8.022
3.37
0.175
0.1883
0.808
1.636
7.33
0.977
0.0702
0.228
0.805 12.42 0.998
0.0563
1.131
4.595 13.49
1.0
0.0331
0.905
3.176 18.58
1.0
0.0244
3.618 12.152
3.37
0.986
0.1123
2.929
9.945
5.53
1.0
0.0795
3.526 11.839
5.91
1.0
0.0768
3.171
2.71
0.916
0.1659
7.374
Muskox
1
Nene2
Tuco-tuco1
Woolly
mammoth
Chlorobium3
Maize
Ovibos moschatus
Branta sandvicensis
Ctenomys sociabilis
Mammuthus
primigenius
Chlorobium limicola
Zea mays
11
3
4
6
0
1
17
3
4
4
4
3
45
11
8
1
-
-
46
11
8
32
42
24
4
6
2
12
34
11
16
35
12
16
14
10
15
12
6
31
19
14
0.691
(0.128)
0.0
0.500
(0.135)
0.833
(0.222)
0.705
(0.041)
0.699
(0.048)
0.962
(0.024)
0.500
(0.265)
0.985
(0.040)
0.917
(0.064)
0.867
(0.079)
0.762
(0.081)
0.813
(0.058)
1.488
1.055
-
-
1.100
0.779
1.130
2.84
0.873
0.1742
-
-
3.85
0.879
0.1353
2.167
1.85
0.851
0.3353
1.435
3.501
3.14
0.321
0.1544
-
-
-
-
1.429
3.487
3.15
0.315
0.1539
0.966
7.077
5.93
1.0
0.0791
0.636
3.000
2.00
0.325
0.4330
3.044 14.106
2.41
0.977
0.1944
2.961 13.708
2.55
0.821
0.1811
2.018
3.308
4.23
0.991
0.0962
2.406
3.943
3.04
0.484
0.1438
1.882
3.049
6.23
0.998
0.0691
-
-
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