Using ultraconserved elements to reconstruct the termite tree of life

Phylogeny, biogeography and classification of Teletisoptera (Blattaria: Isoptera)

(2022) Menglin Wang et al.   SYSTEMATIC ENTOMOLOGY

Phylogenomic conflict coincides with rapid morphological innovation

(2021) Caroline Parins-Fukuchi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Blattodea Karyotype Database

(2021) Marek JANKÁSEK et al.   EUROPEAN JOURNAL OF ENTOMOLOGY

Revising dating estimates and the antiquity of eusociality in termites using the fossilized birth–death process

(2021) Corentin Jouault et al.   SYSTEMATIC ENTOMOLOGY

Draft genome sequence of the termite, Coptotermes formosanus: Genetic insights into the pyruvate dehydrogenase complex of the termite

(2020) Shuji Itakura et al.   JOURNAL OF ASIA-PACIFIC ENTOMOLOGY

MitoFinder: Efficient automated large‐scale extraction of mitogenomic data in target enrichment phylogenomics

(2020) Rémi Allio et al.   Molecular Ecology Resources

Protein‐encoding ultraconserved elements provide a new phylogenomic perspective of Oestroidea flies (Diptera: Calyptratae)

(2020) Eliana Buenaventura et al.   SYSTEMATIC ENTOMOLOGY

Genomic Characterization and Curation of UCEs Improves Species Tree Reconstruction

(2020) Matthew H Van Dam et al.   SYSTEMATIC BIOLOGY

An integrative phylogenomic approach illuminates the evolutionary history of cockroaches and termites (Blattodea)

(2019) Dominic A. Evangelista et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Termite Taxonomy, Challenges and Prospects: West Africa, A Case Example

(2019) Judith Korb et al.   Insects

Phylogenomic analysis and revised classification of atypoid mygalomorph spiders (Araneae, Mygalomorphae), with notes on arachnid ultraconserved element loci

(2019) Marshal Hedin et al.   PeerJ

The oldest known mastotermitids (Blattodea: Termitoidae) and phylogeny of basal termites

(2019) Zhipeng Zhao et al.   SYSTEMATIC ENTOMOLOGY

Sequence capture phylogenomics of historical ethanol‐preserved museum specimens: Unlocking the rest of the vault

(2019) Shahan Derkarabetian et al.   Molecular Ecology Resources

Evolution of Termite Symbiosis Informed by Transcriptome-Based Phylogenies

(2019) Ales Bucek et al.   CURRENT BIOLOGY

Extracting phylogenetic signal from phylogenomic data: Higher-level relationships of the nightbirds (Strisores)

(2019) Noor D. White et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

OUP accepted manuscript

(2018)   BIOINFORMATICS

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

(2018) Chao Zhang et al.   BMC BIOINFORMATICS

Hemimetabolous genomes reveal molecular basis of termite eusociality

(2018) Mark C. Harrison et al.   Nature Ecology & Evolution

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

UFBoot2: Improving the Ultrafast Bootstrap Approximation

(2017) Diep Thi Hoang et al.   MOLECULAR BIOLOGY AND EVOLUTION

On the independent gene trees assumption in phylogenomic studies

(2017) W. Bryan Jennings   MOLECULAR ECOLOGY

Universal target-enrichment baits for anthozoan (Cnidaria) phylogenomics: New approaches to long-standing problems

(2017) Andrea M. Quattrini et al.   Molecular Ecology Resources

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Ultraconserved elements (UCEs) resolve the phylogeny of Australasian smurf-weevils

(2017) Matthew H. Van Dam et al.   PLoS One

Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies

(2016) Erfan Sayyari et al.   MOLECULAR BIOLOGY AND EVOLUTION

Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices

(2016) Olga Chernomor et al.   SYSTEMATIC BIOLOGY

Sequence Capture and Phylogenetic Utility of Genomic Ultraconserved Elements Obtained from Pinned Insect Specimens

(2016) Bonnie B. Blaimer et al.   PLoS One

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

PHYLUCE is a software package for the analysis of conserved genomic loci

(2015) Brant C. Faircloth   BIOINFORMATICS

Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants

(2015) Stephen A Smith et al.   BMC EVOLUTIONARY BIOLOGY

Phylogeny of Dictyoptera: Dating the Origin of Cockroaches, Praying Mantises and Termites with Molecular Data and Controlled Fossil Evidence

(2015) Frédéric Legendre et al.   PLoS One

FASconCAT-G: extensive functions for multiple sequence alignment preparations concerning phylogenetic studies

(2014) Patrick Kück et al.   Frontiers in Zoology

The Evolutionary History of Termites as Inferred from 66 Mitochondrial Genomes

(2014) Thomas Bourguignon et al.   MOLECULAR BIOLOGY AND EVOLUTION

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera

(2014) Brant C. Faircloth et al.   Molecular Ecology Resources

Complementary symbiont contributions to plant decomposition in a fungus-farming termite

(2014) Michael Poulsen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Inference of Gene Trees with Species Trees

(2014) Gergely J. Szöllősi et al.   SYSTEMATIC BIOLOGY

Molecular traces of alternative social organization in a termite genome

(2014) Nicolas Terrapon et al.   Nature Communications

Insect Mitochondrial Genomics: Implications for Evolution and Phylogeny

(2013) Stephen L. Cameron   Annual Review of Entomology

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Target Capture and Massively Parallel Sequencing of Ultraconserved Elements for Comparative Studies at Shallow Evolutionary Time Scales

(2013) Brian Tilston Smith et al.   SYSTEMATIC BIOLOGY

The evolution of ultraconserved elements with different phylogenetic origins

(2012) Taewoo Ryu et al.   BMC EVOLUTIONARY BIOLOGY

A mitochondrial genome phylogeny of termites (Blattodea: Termitoidae): Robust support for interfamilial relationships and molecular synapomorphies define major clades

(2012) Stephen L. Cameron et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

(2012) Brant C. Faircloth et al.   SYSTEMATIC BIOLOGY

ART: a next-generation sequencing read simulator

(2011) Weichun Huang et al.   BIOINFORMATICS

The termites of Early Eocene Cambay amber, with the earliest record of the Termitidae (Isoptera)

(2011) Michael Engel et al.   ZooKeys

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads

(2010) G. Lunter et al.   GENOME RESEARCH

The effects of fossil placement and calibration on divergence times and rates: An example from the termites (Insecta: Isoptera)

(2009) Jessica L. Ware et al.   ARTHROPOD STRUCTURE & DEVELOPMENT

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Gene tree discordance, phylogenetic inference and the multispecies coalescent

(2009) James H. Degnan et al.   TRENDS IN ECOLOGY & EVOLUTION

The phylogeny of termites (Dictyoptera: Isoptera) based on mitochondrial and nuclear markers: Implications for the evolution of the worker and pseudergate castes, and foraging behaviors

(2008) Frédéric Legendre et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Genome size of termites (Insecta, Dictyoptera, Isoptera) and wood roaches (Insecta, Dictyoptera, Cryptocercidae)

(2008) Shigeyuki Koshikawa et al.   NATURWISSENSCHAFTEN