Supporting Information Lindqvist et al. 10.1073/pnas.0914266107 Fig. S1. mtDNA sequence coverage per site over the entire mtDNA genome from the 454 shotgun fragment runs of the Poolepynten specimen. Lindqvist et al. www.pnas.org/cgi/content/short/0914266107 1 of 8
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Supporting Information - PNAS...2010/02/19 · Diomede Little Diomede Island 2629 U. maritimus Savoonga St. Lawrence Island Poolepynten coastal cliffs (78 27′N, 11 44′E) Prins
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Supporting InformationLindqvist et al. 10.1073/pnas.0914266107
Fig. S1. mtDNA sequence coverage per site over the entire mtDNA genome from the 454 shotgun fragment runs of the Poolepynten specimen.
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Fig. S3. Molecular phylogeny of the Ursidae based on maximum parsimony (MP) analysis of complete mtDNA genome sequences [excluding the variable-number tandem repeats (VNTR) repeat region of the D loop]. One most-parsimonious tree of 8715 steps resulted from an analysis using a comprehensive MPapproach with a variety of tree space exploration techniques as implemented in TNT (1). Bootstrap support values are shown below branches.
1. Goloboff PA, Farris JS, Nixon KC (2008) TNT, a free program for phylogenetic analysis. Cladistics 24:774–786.
Fig. S4. Molecular phylogeny of the Ursidae based on maximum likelihood (ML) analyses of complete mtDNA genome sequences (excluding the VNTR repeatregion of the D loop). The phylogram with bootstrap support values shown below branches resulted from ML analysis using a rapid bootstrap algorithm asimplemented in RAxML (1). The mtDNA genome sequences (previously published and this study) are identical to the ones shown in Fig. S3. The previouslypublished brown bear sequences represent “eastern” (east) and “western” (west) lineages (2).
1. Stamatakis A, Hoover P, Rougemont J (2008) A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol 75:758–771.2. Bon C, et al. (2008) Deciphering the complete mitochondrial genome and phylogeny of the extinct cave bear in the Paleolithic painted cave of Chauvet. Proc Natl Acad Sci USA 105:
17447–17452.
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Fig. S5. Maximum clade probability tree from a BEAST analysis of short mtDNA control-region sequences. The analysis is based on 197 base-pair sequences fromcarbon-datedbrownbears (inblackbold) (1), theancientPoolepynten specimen(in red),andmodernbrownbearsandpolarbears, including four sequencesofmodernpolar bear from the Barents Sea/Svalbard (in blue). Numbers at nodes indicatemean ages inmillion years. BEAST parameters used: the General Time Reversible (GTR)substitutionmodel, Invariant Sites (I), andGamma4 (Γ4) siteheterogeneitymodelwitha relaxeduncorrelated log-normal clock, a coalescentprior, andaMarkov chainMonte Carlo (MCMC) chain length of 50,000,000. Note that the Svalbard subfossil is considerably older in origin than any modern Svalbard polar bear sampled.
1. Barnes I, Matheus P, Shapiro B, Jensen D, Cooper A (2002) Dynamics of Pleistocene population extinction in Beringian brown bears. Science 295:2267–2270.
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Table S1. Sample information and summary of bear 454 sequencing runs
MID*Sample
IDMSM archive
no.† Species‡ Tissue Location454reads
No. mtreads
Complete(non-VNTR)§ Coverage
GenBankaccessionnumbers
1 503950 NK157104 U. arctos Muscle Alaska (Chilkoot Lake) 83,842 2 No NA NA2 14KB NK157109 U. arctos Muscle Alaska (Baranof Island) 82,790 3,425 Yes 50 GU5734893 12WH NK157111 U. arctos Muscle Alaska (Admiralty Island) 108,532 2,571 Yes 36 GU5734864 A91-05 NK157120 U. arctos Muscle Alaska (Admiralty Island) 10,428 4,866 Yes 70 GU5734875 84688 NK157123 U.arctos Muscle Alaska (Chichagof Island) 44,266 5 No NA NA6 76946 NK157129 U. arctos Muscle Alaska (Kodiak Island) 146 18 No NA NA7 76824 NK157130 U. arctos Muscle Alaska (Kodiak Island) 78,018 891 Yes 12 GU5734918 542 NK157137 U. maritimus Homogenate Alaska (Barrow) 120,195 261 No 3.5 NA9 2495 NK157142 U. maritimus Muscle Alaska (Little Diomede Island) 70,862 4,685 Yes 68 GU57349010 2629 NK157143 U. maritimus Muscle Alaska (St. Lawrence Island) 25,560 1,855 Yes 23 GU573485NA NA NA U. maritimus Tooth Svalbard (Poolepynten) 482,364 1,290 Yes 14 GU573488
*MID, multiplex identifiers (Methods); NA, not applicable.†Aliquots of the modern bear tissues are archived at the Museum of Southwestern Biology (MSM).‡The modern polar bear samples were harvested in 1998 (542), 2001 (2495), and 2002 (2629), that is, before listing of the species in the Endangered Species Act,by the U.S. Fish and Wildlife Marine Region 7 Mammal Management Office.§Four samples provided too low percentages of mitochondrial reads to assemble the mt genome.
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