Unraveling the processes shaping mammalian gut microbiomes over evolutionary time

The effect of host genetics on the gut microbiome

(2016) Marc Jan Bonder et al.   NATURE GENETICS

Cospeciation of gut microbiota with hominids

(2016) A. H. Moeller et al.   SCIENCE

Getting the Hologenome Concept Right: an Eco-Evolutionary Framework for Hosts and Their Microbiomes

(2016) Kevin R. Theis et al.   mSystems

Diet Dominates Host Genotype in Shaping the Murine Gut Microbiota

(2015) Rachel N. Carmody et al.   Cell Host & Microbe

Heritable symbiosis: The advantages and perils of an evolutionary rabbit hole

(2015) Gordon M. Bennett et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microbiomes in light of traits: A phylogenetic perspective

(2015) J. B. H. Martiny et al.   SCIENCE

Baleen whales host a unique gut microbiome with similarities to both carnivores and herbivores

(2015) Jon G. Sanders et al.   Nature Communications

The Hologenome Concept: Helpful or Hollow?

(2015) Nancy A. Moran et al.   PLOS BIOLOGY

Host Biology in Light of the Microbiome: Ten Principles of Holobionts and Hologenomes

(2015) Seth R. Bordenstein et al.   PLOS BIOLOGY

Human Genetics Shape the Gut Microbiome

(2014) Julia K. Goodrich et al.   CELL

EltonTraits 1.0: Species-level foraging attributes of the world's birds and mammals

(2014) Hamish Wilman et al.   ECOLOGY

Convergence of gut microbiomes in myrmecophagous mammals

(2013) Frédéric Delsuc et al.   MOLECULAR ECOLOGY

Stability and phylogenetic correlation in gut microbiota: lessons from ants and apes

(2013) Jon G. Sanders et al.   MOLECULAR ECOLOGY

Cospeciation vs host-shift speciation: methods for testing, evidence from natural associations and relation to coevolution

(2013) D. M. de Vienne et al.   NEW PHYTOLOGIST

Oxygen, ecology, and the Cambrian radiation of animals

(2013) E. A. Sperling et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Hologenomic Basis of Speciation: Gut Bacteria Cause Hybrid Lethality in the Genus Nasonia

(2013) R. M. Brucker et al.   SCIENCE

Lateral Gene Transfer from the Dead

(2013) Gergely J. Szöllősi et al.   SYSTEMATIC BIOLOGY

Efficient Exploration of the Space of Reconciled Gene Trees

(2013) Gergely J. Szöllősi et al.   SYSTEMATIC BIOLOGY

SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes

(2012) Elmar Pruesse et al.   BIOINFORMATICS

Updating the evolutionary history of Carnivora (Mammalia): a new species-level supertree complete with divergence time estimates

(2012) Katrin Nyakatura et al.   BMC BIOLOGY

Gut Immune Maturation Depends on Colonization with a Host-Specific Microbiota

(2012) Hachung Chung et al.   CELL

Shocks to the system: community assembly of the oak savanna in a 40-year fire frequency experiment

(2012) Jeannine Cavender-Bares et al.   ECOLOGY

Non-Invasive Mapping of the Gastrointestinal Microbiota Identifies Children with Inflammatory Bowel Disease

(2012) Eliseo Papa et al.   PLoS One

Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations

(2012) G. J. Szollosi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tempo of trophic evolution and its impact on mammalian diversification

(2012) S. A. Price et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Factors associated with the diversification of the gut microbial communities within chimpanzees from Gombe National Park

(2012) P. H. Degnan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

THE ROLES OF HOST EVOLUTIONARY RELATIONSHIPS (GENUS: NASONIA) AND DEVELOPMENT IN STRUCTURING MICROBIAL COMMUNITIES

(2011) Robert M. Brucker et al.   EVOLUTION

Evolutionary transitions in bacterial symbiosis

(2011) J. L. Sachs et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diet Drives Convergence in Gut Microbiome Functions Across Mammalian Phylogeny and Within Humans

(2011) B. D. Muegge et al.   SCIENCE

Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood

(2010) M. Csuos   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Comparative Metagenomics and Population Dynamics of the Gut Microbiota in Mother and Infant

(2010) Parag A. Vaishampayan et al.   Genome Biology and Evolution

The ecological coherence of high bacterial taxonomic ranks

(2010) Laurent Philippot et al.   NATURE REVIEWS MICROBIOLOGY

Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa

(2010) C. De Filippo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolutionary Relationships of Wild Hominids Recapitulated by Gut Microbial Communities

(2010) Howard Ochman et al.   PLOS BIOLOGY

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

(2009) Nicolas Lartillot et al.   BIOINFORMATICS

Geographical variation in predictors of mammalian extinction risk: big is bad, but only in the tropics

(2009) Susanne A. Fritz et al.   ECOLOGY LETTERS

Diversification of the gut symbiont Lactobacillus reuteri as a result of host-driven evolution

(2009) Phaik Lyn Oh et al.   ISME Journal

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

On the challenge of treating various types of variables: application for improving the measurement of functional diversity

(2009) Sandrine Pavoine et al.   OIKOS

Genomics and Evolution of Heritable Bacterial Symbionts

(2008) Nancy A. Moran et al.   Annual Review of Genetics

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE

Evolution of Mammals and Their Gut Microbes

(2008) R. E. Ley et al.   SCIENCE