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Ultraconserved elements help resolve the phylogeny of an ancient radiation of venomous flies (Diptera: Asilidae)

https://doi.org/10.1101/2020.11.09.375196

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Outgoing claims: the papers this work cites, builds on, or argues with.

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Phylogenetic Bias in the Likelihood Method Caused by Missing Data Coupled with Among-Site Rate Variation: An Analytical Approach

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ASTRAL-III: Increased Scalability and Impacts of Contracting Low Support Branches

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A phylogenetic hypothesis for Asilidae based on a total evidence analysis of morphological and DNA sequence data (Insecta: Diptera: Brachycera: Asiloidea)

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BaCoCa – A heuristic software tool for the parallel assessment of sequence biases in hundreds of gene and taxon partitions

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Should genes with missing data be excluded from phylogenetic analyses?

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A confounding effect of missing data on character conflict in maximum likelihood and Bayesian MCMC phylogenetic analyses

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Genome-wide ultraconserved elements exhibit higher phylogenetic informativeness than traditional gene markers in percomorph fishes

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Combining transcriptomes and ultraconserved elements to illuminate the phylogeny of Apidae

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Effects of missing data and data type on phylotranscriptomic analysis of stony corals (Cnidaria: Anthozoa: Scleractinia)

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Larger, unfiltered datasets are more effective at resolving phylogenetic conflict: Introns, exons, and UCEs resolve ambiguities in Golden-backed frogs (Anura: Ranidae; genus Hylarana)

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A phylogeny of robber flies (Diptera: Asilidae) at the subfamilial level: molecular evidence

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

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Model selection may not be a mandatory step for phylogeny reconstruction

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Episodic radiations in the fly tree of life

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Increased Taxon Sampling Greatly Reduces Phylogenetic Error

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Missing Data, Incomplete Taxa, and Phylogenetic Accuracy

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Taxonomic Sampling, Phylogenetic Accuracy, and Investigator Bias

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On the importance of homology in the age of phylogenomics

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trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

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Understanding UCEs: A Comprehensive Primer on Using Ultraconserved Elements for Arthropod Phylogenomics

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New Methods to Calculate Concordance Factors for Phylogenomic Datasets

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Phylogenomics of Eukaryotes: Impact of Missing Data on Large Alignments

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Impact of Missing Data on Phylogenies Inferred from Empirical Phylogenomic Data Sets

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

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The Impact of Missing Data on Species Tree Estimation

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Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes)

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Fragmentary Gene Sequences Negatively Impact Gene Tree and Species Tree Reconstruction

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Estimating Improved Partitioning Schemes for Ultraconserved Elements

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The Effect of Ambiguous Data on Phylogenetic Estimates Obtained by Maximum Likelihood and Bayesian Inference

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Missing Data in Phylogenetic Analysis: Reconciling Results from Simulations and Empirical Data

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Can Deliberately Incomplete Gene Sample Augmentation Improve a Phylogeny Estimate for the Advanced Moths and Butterflies (Hexapoda: Lepidoptera)?

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Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

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

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How Should Genes and Taxa be Sampled for Phylogenomic Analyses with Missing Data? An Empirical Study in Iguanian Lizards

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Comparison of Target-Capture and Restriction-Site Associated DNA Sequencing for Phylogenomics: A Test in Cardinalid Tanagers (Aves, Genus:Piranga)

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Sequence Capture versus Restriction Site Associated DNA Sequencing for Shallow Systematics

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Phylogenomics Uncovers Confidence and Conflict in the Rapid Radiation of Australo-Papuan Rodents

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

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High phylogenetic utility of an ultraconserved element probe set designed for Arachnida

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Enriching the ant tree of life: enhanced UCE bait set for genome‐scale phylogenetics of ants and other Hymenoptera

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Identifying conserved genomic elements and designing universal bait sets to enrich them

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Phylogenomics of A nnelida revisited: a cladistic approach using genome‐wide expressed sequence tag data mining and examining the effects of missing data

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Misleading results of likelihood‐based phylogenetic analyses in the presence of missing data

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Ultraconserved elements show utility in phylogenetic inference of A dephaga ( C oleoptera) and suggest paraphyly of ‘Hydradephaga’

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Taxon sampling to address an ancient rapid radiation: a supermatrix phylogeny of early brachyceran flies (Diptera)

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

inferredcites →https://doi.org/10.1126/science.1102036openalex-snapshot

Prospects for Building the Tree of Life from Large Sequence Databases

inferredcites →https://doi.org/10.1126/science.1206357openalex-snapshot

Terraces in Phylogenetic Tree Space

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Studies of Asilidae (Diptera) systematics and evolution: I. A preliminary classification in subfamilies

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Review of the genus Ceraturgus Wiedemann (Diptera: Asilidae) in North America north of Mexico

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Phylogenomics with incomplete taxon coverage: the limits to inference

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Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment?

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Phylogenomic methods outperform traditional multi-locus approaches in resolving deep evolutionary history: a case study of formicine ants

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Phylogeny of Asilidae Inferred from Morphological Characters of Imagines (Insecta: Diptera: Brachycera: Asiloidea)

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The Impact of Outgroup Choice and Missing Data on Major Seed Plant Phylogenetics Using Genome-Wide EST Data

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Inferring Phylogenies from RAD Sequence Data

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Highly Incomplete Taxa Can Rescue Phylogenetic Analyses from the Negative Impacts of Limited Taxon Sampling

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

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

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Incomplete taxa, incomplete characters, and phylogenetic accuracy: is there a missing data problem?

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Spruceup: fast and flexible identification, visualization, and removal of outliers from large multiple sequence alignments

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Vergleichend-morphologische Untersuchungen der männlichen Kopulationsorgane bei Asiliden (Diptera).

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The phylogeny of Empis and Rhamphomyia (Diptera, Empididae) investigated using UCEs including an over 150 years old museum specimen

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A Review of Australian Species of Laphria (Asilidae, Diptera), with Descriptions of Three New Species from Lord Howe Island

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Three new species of Questopogon Dakin and Fordham (Diptera: Asilidae) from Australia

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Illumiprocessor - software for Illumina read quality filtering

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Genomic and transcriptomic resources for assassin flies including the complete genome sequence ofProctacanthus coquilletti(Insecta: Diptera: Asilidae) and 16 representative transcriptomes

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

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Adapterama I: universal stubs and primers for 384 unique dual-indexed or 147,456 combinatorially-indexed Illumina libraries (iTru & iNext)

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