Methods for phylogenetic analysis of microbiome data View Full Text


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Article Info

DATE

2018-05-24

AUTHORS

Alex D. Washburne, James T. Morton, Jon Sanders, Daniel McDonald, Qiyun Zhu, Angela M. Oliverio, Rob Knight

ABSTRACT

How does knowing the evolutionary history of microorganisms affect our analysis of microbiological datasets? Depending on the research question, the common ancestry of microorganisms can be a source of confounding variation, or a scaffolding used for inference. For example, when performing regression on traits, common ancestry is a source of dependence among observations, whereas when searching for clades with correlated abundances, common ancestry is the scaffolding for inference. The common ancestry of microorganisms and their genes are organized in trees—phylogenies—which can and should be incorporated into analyses of microbial datasets. While there has been a recent expansion of phylogenetically informed analytical tools, little guidance exists for which method best answers which biological questions. Here, we review methods for phylogeny-aware analyses of microbiome datasets, considerations for choosing the appropriate method and challenges inherent in these methods. We introduce a conceptual organization of these tools, breaking them down into phylogenetic comparative methods, ancestral state reconstruction and analysis of phylogenetic variables and distances, and provide examples in Supplementary Online Tutorials. Careful consideration of the research question and ecological and evolutionary assumptions will help researchers choose a phylogeny and appropriate methods to produce accurate, biologically informative and previously unreported insights. More... »

PAGES

652-661

References to SciGraph publications

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  • 2008-07-28. PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships in BMC BIOINFORMATICS
  • 2011-04-25. Variance adjusted weighted UniFrac: a powerful beta diversity measure for comparing communities based on phylogeny in BMC BIOINFORMATICS
  • 2012-06-13. Structure, function and diversity of the healthy human microbiome in NATURE
  • 2012-03-28. Molecular phylogenetics: principles and practice in NATURE REVIEWS GENETICS
  • 2000-05. The diversity–stability debate in NATURE
  • 2013-08-14. PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes in NATURE COMMUNICATIONS
  • 2016-04-11. A new view of the tree of life in NATURE MICROBIOLOGY
  • 1986. The Statistical Analysis of Compositional Data in NONE
  • 2013-06-22. Beyond classification: gene-family phylogenies from shotgun metagenomic reads enable accurate community analysis in BMC GENOMICS
  • 2008-07-10. Microbial contributions to climate change through carbon cycle feedbacks in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 1999-10. Inferring the historical patterns of biological evolution in NATURE
  • 2005-08-01. Horizontal gene transfer, genome innovation and evolution in NATURE REVIEWS MICROBIOLOGY
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/s41564-018-0156-0

    DOI

    http://dx.doi.org/10.1038/s41564-018-0156-0

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1104045497

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/29795540


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