Predicting microbial traits with phylogenies

Inferring ancestral states without assuming neutrality or gradualism using a stable model of continuous character evolution

(2014) Michael G Elliot et al.   BMC EVOLUTIONARY BIOLOGY

Abiotic stress tolerance and competition-related traits underlie phylogenetic clustering in soil bacterial communities

(2014) Marta Goberna et al.   ECOLOGY LETTERS

Why are some microbes more ubiquitous than others? Predicting the habitat breadth of soil bacteria

(2014) Albert Barberán et al.   ECOLOGY LETTERS

How much of the world is woody?

(2014) Richard G. FitzJohn et al.   JOURNAL OF ECOLOGY

A trait based perspective on the biogeography of common and abundant marine bacterioplankton clades

(2014) Mark V. Brown et al.   Marine Genomics

Molecular Phylogenetics and Temporal Diversification in the Genus Aeromonas Based on the Sequences of Five Housekeeping Genes

(2014) J. Gaspar Lorén et al.   PLoS One

Seeing the forest for the genes: using metagenomics to infer the aggregated traits of microbial communities

(2014) Noah Fierer et al.   Frontiers in Microbiology

Hidden state prediction: a modification of classic ancestral state reconstruction algorithms helps unravel complex symbioses

(2014) Jesse R. R. Zaneveld et al.   Frontiers in Microbiology

CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction

(2014) Florent E Angly et al.   Microbiome

ANCESTRAL CHARACTER ESTIMATION UNDER THE THRESHOLD MODEL FROM QUANTITATIVE GENETICS

(2013) Liam J. Revell   EVOLUTION

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

(2013) Morgan G I Langille et al.   NATURE BIOTECHNOLOGY

Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing

(2013) P. M. Shih et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenetic prediction of the maximum per capita rate of population growth

(2013) W. F. Fagan et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Phylogenetic eigenvector maps: a framework to model and predict species traits

(2013) Guillaume Guénard et al.   Methods in Ecology and Evolution

Phylogenetic conservatism of functional traits in microorganisms

(2012) Adam C Martiny et al.   ISME Journal

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance

(2012) Steven W. Kembel et al.   PLoS Computational Biology

Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data

(2011) J. Raes et al.   Molecular Systems Biology

Bacterial community assembly based on functional genes rather than species

(2011) C. Burke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

phytools: an R package for phylogenetic comparative biology (and other things)

(2011) Liam J. Revell   Methods in Ecology and Evolution

Picante: R tools for integrating phylogenies and ecology

(2010) S. W. Kembel et al.   BIOINFORMATICS

Selectivity in Mammalian Extinction Risk and Threat Types: a New Measure of Phylogenetic Signal Strength in Binary Traits

(2010) SUSANNE A. FRITZ et al.   CONSERVATION BIOLOGY

Quantitative Traits and Diversification

(2010) Richard G. FitzJohn   SYSTEMATIC BIOLOGY

The Systemic Imprint of Growth and Its Uses in Ecological (Meta)Genomics

(2010) Sara Vieira-Silva et al.   PLoS Genetics

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

(2009) Dongying Wu et al.   NATURE

The genomic basis of trophic strategy in marine bacteria

(2009) F. M. Lauro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution

(2008) T. Dagan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microbial Biogeography: From Taxonomy to Traits

(2008) J. L. Green et al.   SCIENCE

Phylogenetic Signal, Evolutionary Process, and Rate

(2008) Liam J. Revell et al.   SYSTEMATIC BIOLOGY