(Q21283857)

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Can comprehensive background knowledge be incorporated into substitution models to improve phylogenetic analyses? A case study on major arthropod relationships

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Can comprehensive background knowledge be incorporated into substitution models to improve phylogenetic analyses? A case study on major arthropod relationships (English)

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Johann Wolfgang Wägele

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Johann Wolfgang Wägele

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Johann Wolfgang

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Wägele

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18 August 2022

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Bernhard Misof

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Bernhard

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Misof

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18 August 2022

Emiliano Dell'Ampio

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Emiliano Dell'Ampio

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Emiliano

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Dell'Ampio

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18 August 2022

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Heike Hadrys

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Heike

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Hadrys

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18 August 2022

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Günther Pass

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Günther

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Pass

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18 August 2022

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Björn M von Reumont

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Björn M

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von Reumont

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18 August 2022

Karen Meusemann

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Karen

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Meusemann

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18 August 2022

Nikolaus U Szucsich

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Nikolaus U

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Szucsich

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18 August 2022

Vivek Gowri-Shankar

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Vivek

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Gowri-Shankar

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18 August 2022

Daniela Bartel

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Daniela

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Bartel

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18 August 2022

Sabrina Simon

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Sabrina

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Simon

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18 August 2022

Harald O Letsch

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Harald O

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Letsch

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18 August 2022

Roman R Stocsits

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Roman R

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Stocsits

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18 August 2022

Yun-xia Luan

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Yun-xia

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Luan

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18 August 2022

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2009

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BMC Evolutionary Biology

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9

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119

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1

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https://scigraph.springernature.com/pub.10.1186/1471-2148-9-119

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Phylogenetic analysis of mitochondrial protein coding genes confirms the reciprocal paraphyly of Hexapoda and Crustacea

1 reference

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6 April 2017

Mitochondrial genomes suggest that hexapods and crustaceans are mutually paraphyletic

1 reference

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19 March 2017

Pancrustacean phylogeny: hexapods are terrestrial crustaceans and maxillopods are not monophyletic

1 reference

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19 March 2017

MUSCLE: a multiple sequence alignment method with reduced time and space complexity

1 reference

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19 March 2017

MUSCLE: multiple sequence alignment with high accuracy and high throughput

1 reference

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19 March 2017

The colonization of land by animals: molecular phylogeny and divergence times among arthropods

1 reference

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The European ribosomal RNA database

1 reference

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19 March 2017

Phylogenetic analysis of arthropods using two nuclear protein-encoding genes supports a crustacean + hexapod clade

1 reference

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19 March 2017

Broad phylogenomic sampling improves resolution of the animal tree of life

1 reference

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The complete atomic structure of the large ribosomal subunit at 2.4 A resolution

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Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis

1 reference

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Application of phylogenetic networks in evolutionary studies

1 reference

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19 March 2017

Hexapod origins: monophyletic or paraphyletic?

1 reference

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1 reference

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19 March 2017

Visualizing differences in phylogenetic information content of alignments and distinction of three classes of long-branch effects

1 reference

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19 March 2017

The brain of the Remipedia (Crustacea) and an alternative hypothesis on their phylogenetic relationships

1 reference

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19 March 2017

Were the first springtails semi-aquatic? A phylogenetic approach by means of 28S rDNA and optimization alignment

1 reference

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Bayesian phylogenetic analysis of combined data

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7 April 2017

BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences

1 reference

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Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods

1 reference

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Among-site rate variation and its impact on phylogenetic analyses

1 reference

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Neighbor-net: an agglomerative method for the construction of phylogenetic networks

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A Monte Carlo approach successfully identifies randomness in multiple sequence alignments: a more objective means of data exclusion

1 reference

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12 September 2017

EST sequencing of Onychophora and phylogenomic analysis of Metazoa

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12 September 2017

An epipodite-bearing crown-group crustacean from the Lower Cambrian

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12 September 2017

Ancient rapid radiations of insects: challenges for phylogenetic analysis

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The importance of data partitioning and the utility of Bayes factors in Bayesian phylogenetics.

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12 September 2017

Myriapod monophyly and relationships among myriapod classes based on nearly complete 28S and 18S rDNA sequences

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12 September 2017

Characteristics of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) rRNA genes of Apis mellifera (Insecta: Hymenoptera): structure, organization, and retrotransposable elements

1 reference

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Model use in phylogenetics: nine key questions.

1 reference

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12 September 2017

Further use of nearly complete 28S and 18S rRNA genes to classify Ecdysozoa: 37 more arthropods and a kinorhynch

1 reference

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12 September 2017

Phylogeny of Arthropoda inferred from mitochondrial sequences: strategies for limiting the misleading effects of multiple changes in pattern and rates of substitution

1 reference

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12 September 2017

A hexapod nuclear SSU rRNA secondary-structure model and catalog of taxon-specific structural variation

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12 September 2017

RNA structure: reading the ribosome

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Evolution of early development of the nervous system: a comparison between arthropods

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Evidence for multiple reversals of asymmetric mutational constraints during the evolution of the mitochondrial genome of metazoa, and consequences for phylogenetic inferences

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12 September 2017

From variable to constant cell numbers: cellular characteristics of the arthropod nervous system argue against a sister-group relationship of Chelicerata and "Myriapoda" but favour the Mandibulata concept.

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Modeling compositional heterogeneity

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The accuracy of ribosomal RNA comparative structure models

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Exploring among-site rate variation models in a maximum likelihood framework using empirical data: effects of model assumptions on estimates of topology, branch lengths, and bootstrap support

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Arthropod phylogeny based on eight molecular loci and morphology

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Comparative analysis of more than 3000 sequences reveals the existence of two pseudoknots in area V4 of eukaryotic small subunit ribosomal RNA.

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Molecular phylogeny of the major arthropod groups indicates polyphyly of crustaceans and a new hypothesis for the origin of hexapods

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12 September 2017

The rate of compensatory evolution

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12 September 2017

Use of rRNA secondary structure in phylogenetic studies to identify homologous positions: an example of alignment and data presentation from the frogs

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Ribosomal DNA phylogeny of the major extant arthropod classes and the evolution of myriapods

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12 September 2017

Inferring phylogenies from DNA sequences of unequal base compositions

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Structure of mottse rRNA precursors.Complete sequence and potential folding of the spacer regions between 18S and 28S rRNA

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27 September 2017

The complete mitochondrial genome of Pollicipes mitella (Crustacea, Maxillopoda, Cirripedia): non-monophylies of maxillopoda and crustacea.

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A Bayesian compound stochastic process for modeling nonstationary and nonhomogeneous sequence evolution

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30 May 2018

Neurogenesis in the chilopod Lithobius forficatus suggests more similarities to chelicerates than to insects

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30 May 2018

Hadamard conjugations and modeling sequence evolution with unequal rates across sites.

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30 May 2018

Evolution of the secondary structures and compensatory mutations of the ribosomal RNAs of Drosophila melanogaster.

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30 May 2018

Neurogenesis in myriapods and chelicerates and its importance for understanding arthropod relationships.

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29 November 2018

Neurophylogeny: Architecture of the nervous system and a fresh view on arthropod phyologeny.

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29 November 2018

Ribosomal DNA gene and phylogenetic relationships of Diplura and lower hexapods.

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29 November 2018

Filling the gap between identified neuroblasts and neurons in crustaceans adds new support for Tetraconata.

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29 November 2018

Towards an 18S phylogeny of hexapods: accounting for group-specific character covariance in optimized mixed nucleotide/doublet models.

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29 November 2018

The complete mitochondrial genome of Scutigerella causeyae (Myriapoda: Symphyla) and the phylogenetic position of Symphyla

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29 November 2018

A reversible jump method for Bayesian phylogenetic inference with a nonhomogeneous substitution model.

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29 November 2018

Evolution. The origin of insects.

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29 November 2018

Searching for convergence in phylogenetic Markov chain Monte Carlo

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29 November 2018

On the Correlation Between Composition and Site-Specific Evolutionary Rate: Implications for Phylogenetic Inference

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29 November 2018

Biases in phylogenetic estimation can be caused by random sequence segments.

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29 November 2018

The phylogenetic positions of three Basal-hexapod groups (protura, diplura, and collembola) based on ribosomal RNA gene sequences

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29 November 2018

A secondary structural model of the 28S rRNA expansion segments D2 and D3 for Chalcidoid wasps (Hymenoptera: Chalcidoidea).

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29 November 2018

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29 November 2018

Consideration of RNA secondary structure significantly improves likelihood-based estimates of phylogeny: examples from the bilateria.

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29 November 2018

Aligned 18S and insect phylogeny.

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29 November 2018

Ecdysozoan phylogeny and Bayesian inference: first use of nearly complete 28S and 18S rRNA gene sequences to classify the arthropods and their kin.

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29 November 2018

Sampling properties of the bootstrap support in molecular phylogeny: influence of nonindependence among sites.

1 reference

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29 November 2018

Bayesian phylogenetics using an RNA substitution model applied to early mammalian evolution.

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29 November 2018

Invariable sites models and their use in phylogeny reconstruction.

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29 November 2018

Mitochondrial protein phylogeny joins myriapods with chelicerates.

1 reference

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29 November 2018

Shared nucleotide composition biases among species and their impact on phylogenetic reconstructions of the Drosophilidae

1 reference

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29 November 2018

Elongation factor-2: a useful gene for arthropod phylogenetics

1 reference

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29 November 2018

The complete sequence of the mitochondrial genome of the crustacean Penaeus monodon: are malacostracan crustaceans more closely related to insects than to branchiopods?

1 reference

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29 November 2018

The performance of several multiple-sequence alignment programs in relation to secondary-structure features for an rRNA sequence.

1 reference

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29 November 2018

An episodic change of rDNA nucleotide substitution rate has occurred during the emergence of the insect order Diptera.

1 reference

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29 November 2018

A Stochastic Model for the Evolution of Autocorrelated DNA Sequences

1 reference

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29 November 2018

A multi criterion approach for the selection of optimal outgroups in phylogeny: recovering some support for Mandibulata over Myriochelata using mitogenomics

1 reference

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The Biasing Effect of Compositional Heterogeneity on Phylogenetic Estimates May be Underestimated

1 reference

https://pubmed.ncbi.nlm.nih.gov/19473484

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The architecture of 5S rRNA and its relation to function

1 reference

https://pubmed.ncbi.nlm.nih.gov/19473484

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Detecting and Overcoming Systematic Errors in Genome-Scale Phylogenies

1 reference

https://pubmed.ncbi.nlm.nih.gov/19473484

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Should we use model-based methods for phylogenetic inference when we know that assumptions about among-site rate variation and nucleotide substitution pattern are violated?

1 reference

https://pubmed.ncbi.nlm.nih.gov/19473484

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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10.1186/1471-2148-9-119

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