Phylogenetic community ecology of soil biodiversity using mitochondrial metagenomics

Soup to Tree: The Phylogeny of Beetles Inferred by Mitochondrial Metagenomics of a Bornean Rainforest Sample

(2015) Alex Crampton-Platt et al.   MOLECULAR BIOLOGY AND EVOLUTION

What Are Species Pools and When Are They Important?

(2014) Howard V. Cornell et al.   Annual Review of Ecology Evolution and Systematics

Global-scale patterns of assemblage structure of soil nematodes in relation to climate and ecosystem properties

(2014) Uffe N. Nielsen et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Bulk De Novo Mitogenome Assembly from Pooled Total DNA Elucidates the Phylogeny of Weevils (Coleoptera: Curculionoidea)

(2014) Conrad P.D.T. Gillett et al.   MOLECULAR BIOLOGY AND EVOLUTION

Multiplex sequencing of pooled mitochondrial genomes—a crucial step toward biodiversity analysis using mito-metagenomics

(2014) Min Tang et al.   NUCLEIC ACIDS RESEARCH

Beyond classification: gene-family phylogenies from shotgun metagenomic reads enable accurate community analysis

(2013) Samantha J Riesenfeld et al.   BMC GENOMICS

Collembola, the biological species concept and the underestimation of global species richness

(2013) Francesco Cicconardi et al.   MOLECULAR ECOLOGY

Turnover of soil bacterial diversity driven by wide-scale environmental heterogeneity

(2013) L. Ranjard et al.   Nature Communications

The mean and variance of phylogenetic diversity under rarefaction

(2013) David A. Nipperess et al.   Methods in Ecology and Evolution

Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification

(2013) Xin Zhou et al.   GigaScience

Regional factors rather than forest type drive the community structure of soil living oribatid mites (Acari, Oribatida)

(2012) Georgia Erdmann et al.   EXPERIMENTAL AND APPLIED ACAROLOGY

Global biogeography of highly diverse protistan communities in soil

(2012) Scott T Bates et al.   ISME Journal

Landscape geological age explains large scale spatial trends in oribatid mite diversity

(2012) Andrei S. Zaitsev et al.   LANDSCAPE ECOLOGY

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

Optimizing Read Mapping to Reference Genomes to Determine Composition and Species Prevalence in Microbial Communities

(2012) John Martin et al.   PLoS One

Quantifying Phylogenetic Beta Diversity: Distinguishing between ‘True’ Turnover of Lineages and Phylogenetic Diversity Gradients

(2012) Fabien Leprieur et al.   PLoS One

Conveniently Pre-Tagged and Pre-Packaged: Extended Molecular Identification and Metagenomics Using Complete Metazoan Mitochondrial Genomes

(2012) Agnes Dettai et al.   PLoS One

Plant–soil feedbacks mediated by humus forms: A review

(2012) Jean-François Ponge   SOIL BIOLOGY & BIOCHEMISTRY

Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring

(2012) Douglas W. Yu et al.   Methods in Ecology and Evolution

betapart: an R package for the study of beta diversity

(2012) Andrés Baselga et al.   Methods in Ecology and Evolution

Navigating the tip of the genomic iceberg: Next-generation sequencing for plant systematics

(2011) Shannon C. K. Straub et al.   AMERICAN JOURNAL OF BOTANY

Extreme winter warming events more negatively impact small rather than large soil fauna: shift in community composition explained by traits not taxa

(2011) S. Bokhorst et al.   GLOBAL CHANGE BIOLOGY

Relative role of deterministic and stochastic determinants of soil animal community: a spatially explicit analysis of oribatid mites

(2011) Tancredi Caruso et al.   JOURNAL OF ANIMAL ECOLOGY

Phylogeny, phylogeography, phylobetadiversity and the molecular analysis of biological communities

(2011) B. C. Emerson et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Molecular study of worldwide distribution and diversity of soil animals

(2011) T. Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Picante: R tools for integrating phylogenies and ecology

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

Niche conservatism as an emerging principle in ecology and conservation biology

(2010) John J. Wiens et al.   ECOLOGY LETTERS

Soil biodiversity and carbon cycling: a review and synthesis of studies examining diversity-function relationships

(2010) U. N. Nielsen et al.   EUROPEAN JOURNAL OF SOIL SCIENCE

Macroecological patterns in soil communities

(2010) Thibaud Decaëns   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Global patterns in belowground communities

(2009) Noah Fierer et al.   ECOLOGY LETTERS

The Cladistic Basis for the Phylogenetic Diversity (PD) Measure Links Evolutionary Features to Environmental Gradients and Supports Broad Applications of Microbial Ecology’s “Phylogenetic Beta Diversity” Framework

(2009) Daniel Faith et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Deep phylogeographic divisions and long-term persistence of forest invertebrates (Hexapoda: Collembola) in the North-Western Mediterranean basin

(2009) F. CICCONARDI et al.   MOLECULAR ECOLOGY

Phylogenetic structure in tropical hummingbird communities

(2009) C. H. Graham et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenetic beta diversity: linking ecological and evolutionary processes across space in time

(2008) Catherine H. Graham et al.   ECOLOGY LETTERS

Microbes on mountainsides: Contrasting elevational patterns of bacterial and plant diversity

(2008) J. A. Bryant et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nested variation of soil arthropod communities in isolated patches of vegetation on a rocky outcrop

(2008) C. Kounda-Kiki et al.   SOIL BIOLOGY & BIOCHEMISTRY

A Rapid Bootstrap Algorithm for the RAxML Web Servers

(2008) Alexandros Stamatakis et al.   SYSTEMATIC BIOLOGY