Supplementary Material For s1

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 q. 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 / Lambert et al. (2002)
Arctic fox / Dalen et al. (2007)
Aurochs / Edwards et al. (2007)
Bison / Shapiro et al. (2004)
Boar / Watanobe et al. (2004; 2001)
Bowhead whale / Borge et al. (2007)
Brown bear / Barnes et al. (2002)
Cave bear / Loreille et al. (2001), Hofreiter et al. (2002), Orlando et al. (2002)
Cave hyaena / Rohland et al. (2005)
Cave lion / Barnett et al., unpublished data
Cow / Bollongino et al. (2006)
Horse / Vila et al. (2001)
Moa / Huynen et al. (2003)
Muskox / MacPhee et al. (2005)
Nene / Paxinos et al. (2002)
Tuco-tuco / Chan et al. (2006)
Woolly mammoth / Barnes et al. (2007)
Maize / Freitas et al. (2003), Golubinoff et al. (1993)
Chlorobium / 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; pJC, 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 / Species / N / S / h / Hd / pJC / k / S/k / SS / R2
Adélie penguin / Pygoscelis adeliae / 96 / 60 / 60 / 0.972
(0.008) / 2.678 / 6.944 / 8.64 / 1.0 / 0.0554
380 / 105 / 227 / 0.986
(0.002) / 3.150 / 8.138 / 12.90 / 1.0 / 0.0382
476 / 91 / 214 / 0.967
(0.004) / 1.933 / 4.599 / 12.79 / 1.0 / 0.0248
Arctic fox / Alopes lagopus / 8 / 3 / 3 / 0.464
(0.200) / 0.834 / 0.929 / 3.23 / 0.8 / 0.2318
41 / 16 / 22 / 0.945
(0.021) / 1.131 / 2.610 / 6.13 / 1.0 / 0.0749
49 / 9 / 11 / 0.616
(0.078) / 0.993 / 1.107 / 8.13 / 1.0 / 0.0646
Aurochs / Bos primigenius / 41 / 24 / 13 / 0.765
(0.063) / 1.114 / 2.115 / 11.35 / 0.998 / 0.0823
Bison / Bison bison / 160 / 115 / 120 / 0.976
(0.008) / 3.032 / 11.966 / 9.61 / 1.0 / 0.0493
22 / 16 / 11 / 0.909
(0.037) / 0.718 / 3.662 / 4.37 / 0.973 / 0.1036
182 / 110 / 124 / 0.965
(0.010) / 3.639 / 11.915 / 9.23 / 1.0 / 0.0518
Boar / Sus scrofa / 81 / 39 / 32 / 0.920
(0.015) / 1.105 / 6.262 / 6.23 / 1.0 / 0.0760
7 / 15 / 7 / 1.000
(0.076) / 1.279 / 7.238 / 2.07 / 1.0 / 0.2182
88 / 47 / 39 / 0.932
(0.001) / 1.182 / 6.693 / 7.02 / 1.0 / 0.0676
Bowhead whale / Balaena mysticetus / 99 / 50 / 58 / 0.935
(0.020) / 1.348 / 6.029 / 8.29 / 1.0 / 0.0579
68 / 58 / 68 / 1.000
(0.003) / 1.872 / 8.357 / 6.94 / 1.0 / 0.0685
167 / 72 / 113 / 0.974
(0.008) / 1.569 / 7.010 / 10.27 / 1.0 / 0.0472
Brown bear / Ursus arctos / 30 / 66 / 82 / 0.994
(0.004) / 6.687 / 11.824 / 5.58 / 1.0 / 0.0861
Cave bear / Ursus spelaeus / 26 / 21 / 16 / 0.963
(0.018) / 3.219 / 6.000 / 3.5 / 0.996 / 0.1388
Cave hyaena / Crocuta soelaea / 10 / 27 / 5 / 0.800
(0.100) / 2.256 / 8.022 / 3.37 / 0.175 / 0.1883
Cave lion / Panthera leo spelaea / 23 / 12 / 8 / 0.581
(0.120) / 0.808 / 1.636 / 7.33 / 0.977 / 0.0702
Cow / Bos taurus / 36 / 10 / 8 / 0.438
(0.102) / 0.228 / 0.805 / 12.42 / 0.998 / 0.0563
91 / 62 / 67 / 0.977
(0.009) / 1.131 / 4.595 / 13.49 / 1.0 / 0.0331
127 / 59 / 71 / 0.902
(0.024) / 0.905 / 3.176 / 18.58 / 1.0 / 0.0244
Horse / Equus caballus / 12 / 41 / 11 / 0.985
(0.040) / 3.618 / 12.152 / 3.37 / 0.986 / 0.1123
33 / 55 / 32 / 0.998
(0.008) / 2.929 / 9.945 / 5.53 / 1.0 / 0.0795
45 / 70 / 42 / 0.997
(0.005) / 3.526 / 11.839 / 5.91 / 1.0 / 0.0768
Moa / Pachyornis mappini / 14 / 20 / 10 / 0.923
(0.060) / 3.171 / 7.374 / 2.71 / 0.916 / 0.1659
Muskox1 / Ovibos moschatus / 11 / 3 / 4 / 0.691
(0.128) / 1.488 / 1.055 / 2.84 / 0.873 / 0.1742
6 / 0 / 1 / 0.0 / - / - / - / - / -
17 / 3 / 4 / 0.500
(0.135) / 1.100 / 0.779 / 3.85 / 0.879 / 0.1353
Nene2 / Branta sandvicensis / 4 / 4 / 3 / 0.833
(0.222) / 1.130 / 2.167 / 1.85 / 0.851 / 0.3353
Tuco-tuco1 / Ctenomys sociabilis / 45 / 11 / 8 / 0.705
(0.041) / 1.435 / 3.501 / 3.14 / 0.321 / 0.1544
1 / - / - / - / - / - / - / - / -
46 / 11 / 8 / 0.699
(0.048) / 1.429 / 3.487 / 3.15 / 0.315 / 0.1539
Woolly mammoth / Mammuthus primigenius / 32 / 42 / 24 / 0.962
(0.024) / 0.966 / 7.077 / 5.93 / 1.0 / 0.0791
Chlorobium3 / Chlorobium limicola / 4 / 6 / 2 / 0.500
(0.265) / 0.636 / 3.000 / 2.00 / 0.325 / 0.4330
12 / 34 / 11 / 0.985
(0.040) / 3.044 / 14.106 / 2.41 / 0.977 / 0.1944
16 / 35 / 12 / 0.917
(0.064) / 2.961 / 13.708 / 2.55 / 0.821 / 0.1811
16 / 14 / 10 / 0.867
(0.079) / 2.018 / 3.308 / 4.23 / 0.991 / 0.0962
Maize / Zea mays / 15 / 12 / 6 / 0.762
(0.081) / 2.406 / 3.943 / 3.04 / 0.484 / 0.1438
31 / 19 / 14 / 0.813
(0.058) / 1.882 / 3.049 / 6.23 / 0.998 / 0.0691

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