Phylogenomics provides a robust topology of the major cnidarian lineages and insights on the origins of key organismal traits. (Q55019249)

http://europepmc.org/abstract/PMC/5932825

15 June 2018

title

Phylogenomics provides a robust topology of the major cnidarian lineages and insights on the origins of key organismal traits. (English)

1 reference

http://europepmc.org/abstract/PMC/5932825

15 June 2018

1 reference

1 reference

1 reference

6

David C. Plachetzki

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC5932825&resulttype=core&format=json

14 May 2020

Monica Medina

5

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Ehsan Kayal

object named as

Ehsan Kayal

1

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Allen G. Collins

object named as

Allen G. Collins

7

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author name string

Bastian Bentlage

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC5932825&resulttype=core&format=json

14 May 2020

M. Sabrina Pankey

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC5932825&resulttype=core&format=json

14 May 2020

Aki H. Ohdera

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC5932825&resulttype=core&format=json

14 May 2020

Joseph F. Ryan

8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC5932825&resulttype=core&format=json

14 May 2020

publication date

13 April 2018

1 reference

http://europepmc.org/abstract/PMC/5932825

15 June 2018

published in

BMC Evolutionary Biology

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC5932825&resulttype=core&format=json

14 May 2020

volume

18

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC5932825&resulttype=core&format=json

Three Cambrian fossils assembled into an extinct body plan of cnidarian affinity

14 May 2020

cites work

1 reference

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A Large and Consistent Phylogenomic Dataset Supports Sponges as the Sister Group to All Other Animals

16 June 2018

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Phylogenomic analysis of Copepoda (Arthropoda, Crustacea) reveals unexpected similarities with earlier proposed morphological phylogenies

16 June 2018

1 reference

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Comparative internal anatomy of Staurozoa (Cnidaria), with functional and evolutionary inferences

16 June 2018

1 reference

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The Transcriptome of the Zoanthid Protopalythoa variabilis (Cnidaria, Anthozoa) Predicts a Basal Repertoire of Toxin-like and Venom-Auxiliary Polypeptides

16 June 2018

1 reference

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Systematics of stalked jellyfishes (Cnidaria: Staurozoa)

16 June 2018

1 reference

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Inferring Orthologs: Open Questions and Perspectives

16 June 2018

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Genomic insights into the evolutionary origin of Myxozoa within Cnidaria

16 June 2018

1 reference

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Extracting phylogenetic signal and accounting for bias in whole-genome data sets supports the Ctenophora as sister to remaining Metazoa

16 June 2018

1 reference

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Phylogenomic Analyses Support Traditional Relationships within Cnidaria

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5932825

OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy

16 June 2018

1 reference

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Evaluation of BLAST-based edge-weighting metrics used for homology inference with the Markov Clustering algorithm.

16 June 2018

1 reference

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The Road To Cnidaria: History of Phylogeny of the Myxozoa

16 June 2018

1 reference

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Predictable transcriptome evolution in the convergent and complex bioluminescent organs of squid

16 June 2018

1 reference

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The engine of the reef: photobiology of the coral-algal symbiosis

16 June 2018

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Hidden among sea anemones: the first comprehensive phylogenetic reconstruction of the order Actiniaria (Cnidaria, Anthozoa, Hexacorallia) reveals a novel group of hexacorals

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5932825

Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads.

16 June 2018

1 reference

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Trimmomatic: a flexible trimmer for Illumina sequence data

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5932825

Fast-evolving mitochondrial DNA in Ceriantharia: a reflection of hexacorallia paraphyly?

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5932825

InterProScan 5: genome-scale protein function classification

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5932825

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

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5932825

Agalma: an automated phylogenomics workflow

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5932825

PhyloTreePruner: A Phylogenetic Tree-Based Approach for Selection of Orthologous Sequences for Phylogenomics

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5932825

Internal anatomy of Haliclystus antarcticus (Cnidaria, Staurozoa) with a discussion on histological features used in Staurozoan taxonomy

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5932825

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5932825

Identifying hidden rate changes in the evolution of a binary morphological character: the evolution of plant habit in campanulid angiosperms

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5932825

Cnidarian phylogenetic relationships as revealed by mitogenomics

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5932825

Insights into bilaterian evolution from three spiralian genomes

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5932825

Development and myogenesis of the vermiform Buddenbrockia (Myxozoa) and implications for cnidarian body plan evolution

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5932825

Estimation of divergence times in cnidarian evolution based on mitochondrial protein-coding genes and the fossil record.

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5932825

The ancient evolutionary origins of Scleractinia revealed by azooxanthellate corals

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5932825

Phylogenomics reveals deep molluscan relationships

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5932825

REVIGO summarizes and visualizes long lists of gene ontology terms

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5932825

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

16 June 2018

1 reference

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Repeated loss of coloniality and symbiosis in scleractinian corals

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5932825

Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic "supergroups"

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5932825

Phylogenetic placement of the enigmatic parasite, Polypodium hydriforme, within the Phylum Cnidaria

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5932825

Broad phylogenomic sampling improves resolution of the animal tree of life

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5932825

Phyutility: a phyloinformatics tool for trees, alignments and molecular data

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5932825

Exceptionally preserved jellyfishes from the Middle Cambrian

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5932825

Sea Anemone Genome Reveals Ancestral Eumetazoan Gene Repertoire and Genomic Organization

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5932825

The deepest divergences in land plants inferred from phylogenomic evidence

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5932825

Medusozoan phylogeny and character evolution clarified by new large and small subunit rDNA data and an assessment of the utility of phylogenetic mixture models

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5932825

SIMMAP: stochastic character mapping of discrete traits on phylogenies

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5932825

Origins of bilateral symmetry: Hox and dpp expression in a sea anemone

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5932825

OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5932825

DNA sequence variation of mitochondrial large-subunit rRNA provides support for a two-subclass organization of the Anthozoa (Cnidaria).

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5932825

The demise of a phylum of protists: phylogeny of Myxozoa and other parasitic cnidaria.

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5932825

Systematic relationships within the Anthozoa (Cnidaria: Anthozoa) using the 5'-end of the 28S rDNA.

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5932825

Basic local alignment search tool

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5932825

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

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5932825

Contentious relationships in phylogenomic studies can be driven by a handful of genes.

13 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5932825

PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses

13 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5932825

PhyloBayes MPI: phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment

13 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5932825

Character evolution in Hydrozoa (phylum Cnidaria).

13 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5932825

Molecular phylogenetic insights into the evolution of Octocorallia: a review

13 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5932825

Molecular phylogenetics of Thecata (Hydrozoa, Cnidaria) reveals long-term maintenance of life history traits despite high frequency of recent character changes

13 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5932825

13 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5932825

Using native and syntenically mapped cDNA alignments to improve de novo gene finding.

13 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5932825

Phylogenetic relationships within the class Anthozoa (phylum Cnidaria) based on nuclear 18S rDNA sequences

13 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5932825

Origin and evolution of a myxozoan worm

13 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5932825

10.1186/S12862-018-1142-0

30 November 2018

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC5932825&resulttype=core&format=json

14 May 2020

1 reference