These authors have contributed equally.
Version of Record online: 18 MAR 2014
© 2014 John Wiley & Sons Ltd
Volume 23, Issue 7, pages 1780–1798, April 2014
How to Cite
Der Sarkissian, C., Ermini, L., Jónsson, H., Alekseev, A. N., Crubezy, E., Shapiro, B. and Orlando, L. (2014), Shotgun microbial profiling of fossil remains. Molecular Ecology, 23: 1780–1798. doi: 10.1111/mec.12690
- Issue online: 25 MAR 2014
- Version of Record online: 18 MAR 2014
- Accepted manuscript online: 12 FEB 2014 06:52AM EST
- Manuscript Accepted: 2 FEB 2014
- Manuscript Revised: 23 JAN 2014
- Manuscript Received: 22 NOV 2013
- French Archaeological Mission in Oriental Siberia
- Ministry of Foreign and European Affairs, France
- North-Eastern Federal University
- Human Adaptation program of the French Polar Institute Paul Emile Victor
- Danish National Research Foundation. Grant Number: DNRF94
- Marie-Curie Intra-European Fellowship. Grant Number: IEF 302617
- Marie-Curie Career Integration. Grant Number: CIG-293845
- Geological Survey of Denmark and Greenland
- Danish National Research Foundation FNU
Fig. S1 Principal coordinate analysis (A) and hierarchical clustering (B) of microbial genus relative abundance unfiltered for low-abundance taxa from ancient horse shotgun data sets.
Fig. S2 Principal component analysis of microbial genus relative abundance for ancient horse shotgun data sets.
Fig. S3 Principal coordinate analysis of relative abundance for ancient horse shotgun data sets at all taxonomic levels: (A) phylum, (B) class, (C) order, (D) family, (E) genus, Fspecies.
Fig. S4 Principal coordinate analysis of dimensions 3 and 4 for microbial genus relative abundance in ancient horse shotgun data sets.
Fig. S5 Percentages of endogenous (A) and human nonconserved DNA (B) in ancient horse extracts.
Fig. S6 Length distribution of DNA unique to horse in first (grey) and second fraction (black).
Fig. S7 Principal coordinate analysis of microbial genus relative abundance for soil and ancient horse shotgun data sets.
Fig. S8 Principal coordinate analysis of microbial genus relative abundance in subsampled (N = 796 mapped reads) ancient horse shotgun data sets.
Fig. S9 Relative abundance of microbial classes from ancient horse shotgun data sets, as estimated on the basis of shotgun data (metaphlan database) and 16S rDNA (‘_16S’, Greengenes database).
Fig. S10 Principal coordinate analysis of microbial family relative abundance from ancient horse shotgun data sets.
|mec12690-sup-0002-TableS1.xlsx||application/msexcel||33K||Table S1 Relative abundances of micro-organisms in ancient horse extracts.|
|mec12690-sup-0003-TableS2.xlsx||application/msexcel||39K||Table S2 Characteristics of microbial diversity at all taxonomic levels (A-number of identified taxa, B- Shannon diversity index, C-cumulative percentage of low-abundance taxa <1%).|
|mec12690-sup-0004-TableS3.docx||Word document||119K||Table S3 Illumina sequencing of ancient horse DNA extracts and mapping metrics for nonconserved regions.|
|mec12690-sup-0005-TableS4.docx||Word document||77K||Table S4 Mapping coverage obtained for the alignments to microbial genomes used in microbial DNA damage analyses.|
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