The SITE-100 Project: Site-Based Biodiversity Genomics for Species Discovery, Community Ecology, and a Global Tree-of-Life

Connecting high‐throughput biodiversity inventories – opportunities for a site‐based genomic framework for global integration and synthesis

(2021) Paula Arribas et al.   MOLECULAR ECOLOGY

High‐throughput methods for efficiently building massive phylogenies from natural history collections

(2021) Ryan A. Folk et al.   Applications in Plant Sciences

Coming of age for COI metabarcoding of whole organism community DNA: towards bioinformatic harmonisation

(2021) T.J. Creedy et al.   Molecular Ecology Resources

Molecular systematics, higher‐rank classification and Gondwanan origins of Cryptocephalinae leaf beetles

(2021) Jesús Gómez‐Zurita et al.   ZOOLOGICA SCRIPTA

Assessing the impact of incomplete species sampling on estimates of speciation and extinction rates

(2020) Rachel C. M. Warnock et al.   PALEOBIOLOGY

Rethink the expansion of access and benefit sharing

(2020) Sarah Laird et al.   SCIENCE

The omission of critical data in the pursuit of ‘revolutionary’ methods to accelerate the description of species

(2020) Alireza Zamani et al.   SYSTEMATIC ENTOMOLOGY

Rapid alignment-free phylogenetic identification of metagenomic sequences

(2019) Benjamin Linard et al.   BIOINFORMATICS

A validated workflow for rapid taxonomic assignment and monitoring of a national fauna of bees (Apiformes) using high throughput DNA barcoding

(2019) Thomas J. Creedy et al.   Molecular Ecology Resources

Review and Interpretation of Trends in DNA Barcoding

(2019) Rob DeSalle et al.   Frontiers in Ecology and Evolution

The evolution and genomic basis of beetle diversity

(2019) Duane D. McKenna et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees

(2018) Chao Zhang et al.   BMC BIOINFORMATICS

Earth BioGenome Project: Sequencing life for the future of life

(2018) Harris A. Lewin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics

(2017) Robert M Waterhouse et al.   MOLECULAR BIOLOGY AND EVOLUTION

Shotgun mitogenomics across body size classes in a local assemblage of tropical Diptera: Phylogeny, species diversity and mitochondrial abundance spectrum

(2017) Le Qin Choo et al.   MOLECULAR ECOLOGY

Inordinate Fondness Multiplied and Redistributed: the Number of Species on Earth and the New Pie of Life

(2017) Brendan B. Larsen et al.   QUARTERLY REVIEW OF BIOLOGY

Modeling Site Heterogeneity with Posterior Mean Site Frequency Profiles Accelerates Accurate Phylogenomic Estimation

(2017) Huai-Chun Wang et al.   SYSTEMATIC BIOLOGY

Capturing the Phylogeny of Holometabola with Mitochondrial Genome Data and Bayesian Site-Heterogeneous Mixture Models

(2016) Fan Song et al.   Genome Biology and Evolution

Phylogenetics and biogeography of the dung beetle genus Onthophagus inferred from mitochondrial genomes

(2016) Thijmen Breeschoten et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The discovery of Iberobaeniidae (Coleoptera: Elateroidea): a new family of beetles from Spain, with immatures detected by environmental DNA sequencing

(2016) L. Bocak et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Construction of a Species-Level Tree of Life for the Insects and Utility in Taxonomic Profiling

(2016) Douglas Chesters   SYSTEMATIC BIOLOGY

Intraspecific genetic variation in complex assemblages from mitochondrial metagenomics: comparison with DNA barcodes

(2016) Carola Gómez-Rodríguez et al.   Methods in Ecology and Evolution

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Mitochondrial metagenomics: letting the genes out of the bottle

(2016) Alex Crampton-Platt et al.   GigaScience

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Family-Level Sampling of Mitochondrial Genomes in Coleoptera: Compositional Heterogeneity and Phylogenetics

(2015) Martijn J. T. N. Timmermans et al.   Genome Biology and Evolution

Metagenome skimming for phylogenetic community ecology: a new era in biodiversity research

(2015) Anna Papadopoulou et al.   MOLECULAR ECOLOGY

Synthesis of phylogeny and taxonomy into a comprehensive tree of life

(2015) Cody E. Hinchliff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inselect: Automating the Digitization of Natural History Collections

(2015) Lawrence N. Hudson et al.   PLoS One

The founding charter of the Genomic Observatories Network

(2014) Neil Davies et al.   GigaScience

Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding

(2013) Yinqiu Ji et al.   ECOLOGY LETTERS

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

(2013) Xin Zhou et al.   GigaScience

21 years of shelf life between discovery and description of new species

(2012) Benoît Fontaine et al.   CURRENT BIOLOGY

Utility of the DNA barcoding gene fragment for parasitic wasp phylogeny (Hymenoptera: Ichneumonoidea): data release and new measure of taxonomic congruence

(2012) DONALD L. J. QUICKE et al.   Molecular Ecology Resources

Creating a Buzz About Insect Genomes

(2011) G. E. Robinson et al.   SCIENCE

How Many Species Are There on Earth and in the Ocean?

(2011) Camilo Mora et al.   PLOS BIOLOGY

Nucleotide substitution rates for the full set of mitochondrial protein-coding genes in Coleoptera

(2010) Joan Pons et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The merging of community ecology and phylogenetic biology

(2009) Jeannine Cavender-Bares et al.   ECOLOGY LETTERS