Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX (original) (raw)

• Keane, T.M. et al. Mouse genomic variation and its effect on phenotypes and gene regulation. Nature 477, 289–294 (2011).
  Article CAS Google Scholar
• McVean, G.A. et al. An integrated map of genetic variation from 1,092 human genomes. Nature 491, 56–65 (2012).
  Article CAS Google Scholar
• Nielsen, R., Paul, J.S., Albrechtsen, A. & Song, Y.S. Genotype and SNP calling from next-generation sequencing data. Nat. Rev. Genet. 12, 443–451 (2011).
  Article CAS Google Scholar
• Alkan, C., Coe, B.P. & Eichler, E.E. Genome structural variation discovery and genotyping. Nat. Rev. Genet. 12, 363–376 (2011).
  Article CAS Google Scholar
• Thurman, R.E. et al. The accessible chromatin landscape of the human genome. Nature 489, 75–82 (2012).
  Article CAS Google Scholar
• Ball, M.P. et al. Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nat. Biotechnol. 27, 361–368 (2009).
  Article CAS Google Scholar
• Wheeler, D.A. et al. The complete genome of an individual by massively parallel DNA sequencing. Nature 452, 872–876 (2008).
  Article CAS Google Scholar
• Li, R. et al. The sequence and de novo assembly of the giant panda genome. Nature 463, 311–317 (2010).
  Article CAS Google Scholar
• Overballe-Petersen, S., Orlando, L. & Willerslev, E. Next-generation sequencing offers new insights into DNA degradation. Trends Biotechnol. 30, 364–368 (2012).
  Article CAS Google Scholar
• Margulies, M. et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437, 376–380 (2005).
  Article CAS Google Scholar
• Poinar, H.N. et al. Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA. Science 311, 392–394 (2006).
  Article CAS Google Scholar
• Miller, W. et al. Sequencing the nuclear genome of the extinct woolly mammoth. Nature 456, 387–390 (2008).
  Article CAS Google Scholar
• Rasmussen, M. et al. Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 463, 757–762 (2010).
  Article CAS Google Scholar
• Green, R.E. et al. A draft sequence of the Neandertal genome. Science 328, 710–722 (2010).
  Article CAS Google Scholar
• Krause, J. et al. The complete mitochondrial DNA genome of an unknown hominin from southern Siberia. Nature 464, 894–897 (2010).
  Article CAS Google Scholar
• Reich, D. et al. Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468, 1053–1060 (2010).
  Article CAS Google Scholar
• Rasmussen, M. et al. An Aboriginal Australian genome reveals separate human dispersals into Asia. Science 334, 94–98 (2011).
  Article CAS Google Scholar
• Keller, A. et al. New insights into the Tyrolean Iceman′s origin and phenotype as inferred by whole-genome sequencing. Nat. Commun. 3, 698 (2012).
  Article Google Scholar
• Raghavan, M. et al. Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. Nature 505, 87–91 (2014).
  Article Google Scholar
• Prufer, K. et al. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 505, 43–49 (2014).
  Article Google Scholar
• Meyer, M. et al. A high-coverage genome sequence from an archaic Denisovan individual. Science 338, 222–226 (2012).
  Article CAS Google Scholar
• Orlando, L. et al. Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature 499, 74–78 (2013).
  Article CAS Google Scholar
• Millar, C.D. & Lambert, D.M. Ancient DNA: towards a million-year-old genome. Nature 499, 34–35 (2013).
  Article CAS Google Scholar
• Skoglund, P. et al. Origins and genetic legacy of Neolithic farmers and hunter-gatherers in Europe. Science 336, 466–469 (2012).
  Article CAS Google Scholar
• Lindqvist, C. et al. Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear. Proc. Natl. Acad. Sci. USA 107, 5053–5057 (2010).
  Article CAS Google Scholar
• Miller, W. et al. Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change. Proc. Natl. Acad. Sci. USA 109, E2382–E2390 (2012).
  Article CAS Google Scholar
• Gilbert, M.T. et al. Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes. Proc. Natl. Acad. Sci. USA 105, 8327–8332 (2008).
  Article CAS Google Scholar
• Gilbert, M.T. et al. Paleo-Eskimo mtDNA genome reveals matrilineal discontinuity in Greenland. Science 320, 1787–1789 (2008).
  Article CAS Google Scholar
• Bon, C. et al. Coprolites as a source of information on the genome and diet of the cave hyena. Proc. Biol. Sci. 279, 2825–2830 (2012).
  Article CAS Google Scholar
• Dabney, J. et al. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proc. Natl. Acad. Sci. USA 110, 15758–15763 (2013).
  Article CAS Google Scholar
• Fu, Q. et al. DNA analysis of an early modern human from Tianyuan Cave, China. Proc. Natl. Acad. Sci. USA 110, 2223–2227 (2013).
  Article CAS Google Scholar
• Lari, M. et al. The complete mitochondrial genome of an 11,450-year-old aurochsen (Bos primigenius) from Central Italy. BMC Evol. Biol. 11, 32 (2011).
  Article CAS Google Scholar
• Vilstrup, J.T. et al. Mitochondrial phylogenomics of modern and ancient equids. PLoS ONE 8, e55950 (2013).
  Article CAS Google Scholar
• Haus, T. et al. Mitochondrial diversity and distribution of African green monkeys (Chlorocebus Gray, 1870). Am. J. Primatol. 75, 350–360 (2013).
  Article CAS Google Scholar
• Meyer, M. et al. A mitochondrial genome sequence of a hominin from Sima de los Huesos. Nature 505, 403–406 (2014).
  Article CAS Google Scholar
• Burbano, H.A. et al. Targeted investigation of the Neandertal genome by array-based sequence capture. Science 328, 723–725 (2010).
  Article CAS Google Scholar
• Bos, K.I. et al. A draft genome of Yersinia pestis from victims of the Black Death. Nature 478, 506–510 (2011).
  Article CAS Google Scholar
• Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
  Article CAS Google Scholar
• Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
  Article Google Scholar
• McKenna, A. et al. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297–1303 (2010).
  Article CAS Google Scholar
• Wang, K., Li, M. & Hakonarson, H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 38, e164 (2010).
  Article Google Scholar
• Schubert, M. et al. Improving ancient DNA read mapping against modern reference genomes. BMC Genomics 13, 178 (2012).
  Article CAS Google Scholar
• Krause, J. et al. A complete mtDNA genome of an early modern human from Kostenki, Russia. Curr. Biol. 20, 231–236 (2010).
  Article CAS Google Scholar
• Ginolhac, A., Rasmussen, M., Gilbert, M.T., Willerslev, E. & Orlando, L. mapDamage: testing for damage patterns in ancient DNA sequences. Bioinformatics 27, 2153–2155 (2011).
  Article CAS Google Scholar
• Jonsson, H., Ginolhac, A., Schubert, M., Johnson, P.L. & Orlando, L. mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics 29, 1682–1684 (2013).
  Article CAS Google Scholar
• Martin, M.D. et al. Reconstructing genome evolution in historic samples of the Irish potato famine pathogen. Nat. Commun. 4, 2172 (2013).
  Article Google Scholar
• Yoshida, K. et al. The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine. Elife 2, e00731 (2013).
  Article Google Scholar
• Kircher, M. Analysis of high-throughput ancient DNA sequencing data. Methods Mol. Biol. 840, 197–228 (2012).
  Article CAS Google Scholar
• Goecks, J., Nekrutenko, A. & Taylor, J. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 11, R86 (2010).
  Article Google Scholar
• Lindgreen, S. AdapterRemoval: easy cleaning of next-generation sequencing reads. BMC Res. Notes 5, 337 (2012).
  Article Google Scholar
• Briggs, A.W. et al. Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA. Nucleic Acids Res. 38, e87 (2010).
  Article Google Scholar
• Langmead, B. & Salzberg, S.L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
  Article CAS Google Scholar
• Briggs, A.W. et al. Patterns of damage in genomic DNA sequences from a Neandertal. Proc. Natl. Acad. Sci. USA 104, 14616–14621 (2007).
  Article CAS Google Scholar
• McLaren, W. et al. Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics 26, 2069–2070 (2010).
  Article CAS Google Scholar
• Katoh, K. & Standley, D.M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013).
  Article CAS Google Scholar
• de Queiroz, A. & Gatesy, J. The supermatrix approach to systematics. Trends Ecol. Evol. 22, 34–41 (2007).
  Article Google Scholar
• Stamatakis, A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22, 2688–2690 (2006).
  Article CAS Google Scholar
• Fierer, N. et al. Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Proc. Natl. Acad. Sci. USA 109, 21390–21395 (2012).
  Article CAS Google Scholar
• Cotillard, A. et al. Dietary intervention impact on gut microbial gene richness. Nature 500, 585–588 (2013).
  Article CAS Google Scholar
• Schloissnig, S. et al. Genomic variation landscape of the human gut microbiome. Nature 493, 45–50 (2013).
  Article Google Scholar
• Segata, N. et al. Metagenomic microbial community profiling using unique clade-specific marker genes. Nat. Methods 9, 811–814 (2012).
  Article CAS Google Scholar
• Altschul, S.F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402 (1997).
  Article CAS Google Scholar
• Huson, D.H., Richter, D.C., Mitra, S., Auch, A.F. & Schuster, S.C. Methods for comparative metagenomics. BMC Bioinformatics 10 (suppl. 1), S12 (2009).
  Article Google Scholar
• Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature 486, 207–214 (2012).
• Der Sarkissian, C., Ermini, L., Jónsson, H., Alekseev, A.N., Crubezy, E., Shapiro, B. & Orlando, L. Shotgun microbial profiling of fossil remains. Mol. Ecol. 10.1111/mec.12690 (2014).
• Ondov, B.D., Bergman, N.H. & Phillippy, A.M. Interactive metagenomic visualization in a Web browser. BMC Bioinformatics 12, 385 (2011).
  Article Google Scholar
• R Development Core Team. R: A Language and Environment for Statistical Computing, http://www.r-project.org/ (2013).
• Suzuki, R. & Shimodaira, H. Pvclust: an R package for assessing the uncertainty in hierarchical clustering. Bioinformatics 22, 1540–1542 (2006).
  Article CAS Google Scholar
• Quinlan, A.R. & Hall, I.M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).
  Article CAS Google Scholar
• Daley, T. & Smith, A.D. Predicting the molecular complexity of sequencing libraries. Nat. Methods 10, 325–327 (2013).
  Article CAS Google Scholar
• Li, H. Tabix: fast retrieval of sequence features from generic TAB-delimited files. Bioinformatics 27, 718–719 (2011).
  Article Google Scholar
• Venables, W.N. & Ripley,, B.D. Modern Applied Statistics with S (Springer, 2002).
• Paradis, E., Claude, J. & Strimmer, K. APE: Analyses of Phylogenetics and Evolution in R language. Bioinformatics 20, 289–290 (2004).
  Article CAS Google Scholar
• Wickham, H. ggplot2: Elegant Graphics for Data Analysis (Springer, 2009).
• Haas, B.J. et al. Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans. Nature 461, 393–398 (2009).
  Article CAS Google Scholar
• Avila-Adame, C. et al. Mitochondrial genome sequences and molecular evolution of the Irish potato famine pathogen, Phytophthora infestans. Curr. Genet. 49, 39–46 (2006).
  Article CAS Google Scholar
• Cock, P.J., Fields, C.J., Goto, N., Heuer, M.L. & Rice, P.M. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res. 38, 1767–1771 (2010).
  Article CAS Google Scholar