Towards a new classification of Muscidae (Diptera): a comparison of hypotheses based on multiple molecular phylogenetic approaches

Using RAD‐seq for reconstructing phylogenies of highly diverged taxa: a test using the tribe Scandiceae (Apiaceae)

(2020) Marcin Piwczyński et al.   Journal of Systematics and Evolution

The position of the Azeliinae in the Muscidae (Diptera) based on musculature of the male terminalia

(2020) Vera S. Sorokina et al.   ZooKeys

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

Causes and analytical impacts of missing data in RADseq phylogenetics: Insights from an African frog (Afrixalus )

(2019) Marco Crotti et al.   ZOOLOGICA SCRIPTA

Studies on the Australian Muscidae (Diptera). VIII. The genus Lispe Latreille, 1797

(2019) ADRIAN C. PONT   ZOOTAXA

Phylogenomic analysis of Calyptratae: resolving the phylogenetic relationships within a major radiation of Diptera

(2019) Sujatha Narayanan Kutty et al.   CLADISTICS

Anchored hybrid enrichment challenges the traditional classification of flesh flies (Diptera: Sarcophagidae)

(2019) Eliana Buenaventura et al.   SYSTEMATIC ENTOMOLOGY

Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

(2018) Andrew Rambaut et al.   SYSTEMATIC BIOLOGY

New data, same story: phylogenomics does not support Syrphoidea (Diptera: Syrphidae, Pipunculidae)

(2018) THOMAS PAULI et al.   SYSTEMATIC ENTOMOLOGY

Anchored phylogenomics unravels the evolution of spider flies (Diptera, Acroceridae) and reveals discordance between nucleotides and amino acids

(2018) Jessica P. Gillung et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

New systematic position of Itatingamyia Albuquerque (Diptera, Muscidae) based on molecular evidence, and description of the female of I. couriae

(2018) Kirstern Lica F. Haseyama et al.   REVISTA BRASILEIRA DE ENTOMOLOGIA

Assessing the potential of RAD-sequencing to resolve phylogenetic relationships within species radiations: The fly genus Chiastocheta (Diptera: Anthomyiidae) as a case study

(2017) Tomasz Suchan et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Molecular phylogeny of Miltogramminae (Diptera: Sarcophagidae): Implications for classification, systematics and evolution of larval feeding strategies

(2017) Marcin Piwczyński et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Analysis of phylogenetic relationships and genome size evolution of the Amaranthus genus using GBS indicates the ancestors of an ancient crop

(2017) Markus G. Stetter et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

First fossil of an oestroid fly (Diptera: Calyptratae: Oestroidea) and the dating of oestroid divergences

(2017) Pierfilippo Cerretti et al.   PLoS One

To be or not to be a valid genus: the systematic position of Ophyra R.-D. revised (Diptera: Muscidae)

(2017) ANDRZEJ GRZYWACZ et al.   SYSTEMATIC ENTOMOLOGY

RADseq dataset with 90% missing data fully resolves recent radiation of Petalidium (Acanthaceae) in the ultra-arid deserts of Namibia

(2017) Erin A. Tripp et al.   Ecology and Evolution

Anchored enrichment dataset for true flies (order Diptera) reveals insights into the phylogeny of flower flies (family Syrphidae)

(2016) Andrew Donovan Young et al.   BMC EVOLUTIONARY BIOLOGY

Phylogenetic analysis of RAD-seq data: examining the influence of gene genealogy conflict on analysis of concatenated data

(2016) David M. Rivers et al.   CLADISTICS

Phylogenetic inference of calyptrates, with the first mitogenomes for Gasterophilinae (Diptera: Oestridae) and Paramacronychiinae (Diptera: Sarcophagidae)

(2016) Dong Zhang et al.   International Journal of Biological Sciences

Muscidae (Diptera) of forensic importance—an identification key to third instar larvae of the western Palaearctic region and a catalogue of the muscid carrion community

(2016) Andrzej Grzywacz et al.   INTERNATIONAL JOURNAL OF LEGAL MEDICINE

One fly to rule them all—muscid flies are the key pollinators in the Arctic

(2016) Mikko Tiusanen et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Sequence Capture versus Restriction Site Associated DNA Sequencing for Shallow Systematics

(2016) Michael G. Harvey et al.   SYSTEMATIC BIOLOGY

AMAS: a fast tool for alignment manipulation and computing of summary statistics

(2016) Marek L. Borowiec   PeerJ

Advances using molecular data in insect systematics

(2016) Karl Kjer et al.   Current Opinion in Insect Science

A comparative study of SVDquartets and other coalescent-based species tree estimation methods

(2015) Jed Chou et al.   BMC GENOMICS

RAD Capture (Rapture): Flexible and Efficient Sequence-Based Genotyping

(2015) O. A. Ali et al.   GENETICS

Phylogenomics of Phrynosomatid Lizards: Conflicting Signals from Sequence Capture versus Restriction Site Associated DNA Sequencing

(2015) Adam D. Leaché et al.   Genome Biology and Evolution

Identifiability of the unrooted species tree topology under the coalescent model with time-reversible substitution processes, site-specific rate variation, and invariable sites

(2015) Julia Chifman et al.   JOURNAL OF THEORETICAL BIOLOGY

Morphology successfully separates third instar larvae ofMuscina

(2015) A. GRZYWACZ et al.   MEDICAL AND VETERINARY ENTOMOLOGY

When do species-tree and concatenated estimates disagree? An empirical analysis with higher-level scincid lizard phylogeny

(2015) Shea M. Lambert et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Say goodbye to tribes in the new house fly classification: A new molecular phylogenetic analysis and an updated biogeographical narrative for the Muscidae (Diptera)

(2015) Kirstern L.F. Haseyama et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Coalescence vs. concatenation: Sophisticated analyses vs. first principles applied to rooting the angiosperms

(2015) Mark P. Simmons et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing

(2015) Richard O. Prum et al.   NATURE

Larval morphology of Atherigona orientalis (Schiner) (Diptera: Muscidae) —A species of sanitary and forensic importance

(2014) Andrzej Grzywacz et al.   ACTA TROPICA

Quartet Inference from SNP Data Under the Coalescent Model

(2014) Julia Chifman et al.   BIOINFORMATICS

PyRAD: assembly of de novo RADseq loci for phylogenetic analyses

(2014) Deren A. R. Eaton   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Hydrotaea similis Meade (Diptera: Muscidae) newly reported from a human cadaver: A case report and larval morphology

(2014) Andrzej Grzywacz et al.   FORENSIC SCIENCE INTERNATIONAL

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

(2014) Patrick Kück et al.   Frontiers in Zoology

Empirical Assessment of RAD Sequencing for Interspecific Phylogeny

(2014) Astrid Cruaud et al.   MOLECULAR BIOLOGY AND EVOLUTION

ExaBayes: Massively Parallel Bayesian Tree Inference for the Whole-Genome Era

(2014) Andre J. Aberer et al.   MOLECULAR BIOLOGY AND EVOLUTION

Complete tribal sampling reveals basal split in Muscidae (Diptera), confirms saprophagy as ancestral feeding mode, and reveals an evolutionary correlation between instar numbers and carnivory

(2014) Sujatha Narayanan Kutty et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Rates of genomic divergence in humans, chimpanzees and their lice

(2014) K. P. Johnson et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Phylogenomics resolves the timing and pattern of insect evolution

(2014) B. Misof et al.   SCIENCE

Whole-genome analyses resolve early branches in the tree of life of modern birds

(2014) E. D. Jarvis et al.   SCIENCE

Unforeseen Consequences of Excluding Missing Data from Next-Generation Sequences: Simulation Study of RAD Sequences

(2014) Huateng Huang et al.   SYSTEMATIC BIOLOGY

A large-scale molecular phylogeny of flesh flies (Diptera: Sarcophagidae)

(2014) MARCIN PIWCZYŃSKI et al.   SYSTEMATIC ENTOMOLOGY

Morphology of immature stages ofAtherigona reversura(Diptera: Muscidae), with notes on the recent invasion of North America

(2013) Andrzej Grzywacz et al.   JOURNAL OF NATURAL HISTORY

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

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

Is RAD-seq suitable for phylogenetic inference? An in silico assessment and optimization

(2013) Marie Cariou et al.   Ecology and Evolution

ape 3.0: New tools for distance-based phylogenetics and evolutionary analysis in R

(2012) Andrei-Alin Popescu et al.   BIOINFORMATICS

Larval morphology, development and forensic importance of Synthesiomyia nudiseta (Diptera: Muscidae) in Europe: a rare species or just overlooked?

(2012) Y. Velásquez et al.   BULLETIN OF ENTOMOLOGICAL RESEARCH

PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses

(2012) R. Lanfear et al.   MOLECULAR BIOLOGY AND EVOLUTION

Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics

(2012) Alan R. Lemmon et al.   SYSTEMATIC BIOLOGY

Applications of next-generation sequencing to phylogeography and phylogenetics

(2011) John E. McCormack et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Review of Coenosia attenuata Stein and its first record as a predator of important greenhouse pests in Turkey

(2011) Daniel Pohl et al.   PHYTOPARASITICA

Episodic radiations in the fly tree of life

(2011) B. M. Wiegmann 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

Parametric and non-parametric masking of randomness in sequence alignments can be improved and leads to better resolved trees

(2010) Patrick Kück et al.   Frontiers in Zoology

Comprehensive gene and taxon coverage elucidates radiation patterns in moths and butterflies

(2010) M. Mutanen et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Molecular phylogeny of the Calyptratae (Diptera: Cyclorrhapha) with an emphasis on the superfamily Oestroidea and the position of Mystacinobiidae and McAlpine's fly

(2010) SUJATHA NARAYANAN KUTTY et al.   SYSTEMATIC ENTOMOLOGY

A Monte Carlo Approach Successfully Identifies Randomness in Multiple Sequence Alignments : A More Objective Means of Data Exclusion

(2009) Bernhard Misof et al.   SYSTEMATIC BIOLOGY

Conflict, Convergent Evolution, and the Relative Importance of Immature and Adult Characters in Endopterygote Phylogenetics

(2008) Rudolf Meier et al.   Annual Review of Entomology

The Muscoidea (Diptera: Calyptratae) are paraphyletic: Evidence from four mitochondrial and four nuclear genes

(2008) Sujatha Narayanan Kutty et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION