Reconstruction of family-level phylogenetic relationships within Demospongiae (Porifera) using nuclear encoded housekeeping genes (Q28709570)

Elizabeth Danka

12

0 references

Bernard Picton

Bernard Picton

20

0 references

Gisele Lôbo-Hajdu

Gisele Lobo-Hajdu

16

0 references

Ana Riesgo

Ana Riesgo

26

0 references

Jose V. Lopez

Jose Lopez

3

0 references

Allen G. Collins

Allen G Collins

33

0 references

Nicole Boury-Esnault

9

Nicole Boury-Esnault

0 references

Eduardo Hajdu

15

Eduardo Hajdu

0 references

Shirley A. Pomponi

5

Shirley Pomponi

0 references

Niamh E. Redmond

23

Niamh E Redmond

0 references

Andia Chaves Fonnegra

11

Andia Chaves-Fonnegra

0 references

Erik A Sperling

30

Erik A Sperling

0 references

Jignasa Patel

19

Jignasa Patel

0 references

Ewelina Rubin

27

Ewelina Rubin

0 references

Malcolm Hill

1

Malcolm S Hill

0 references

April L Hill

2

April L Hill

0 references

Klaus Rützler

29

Klaus Rützler

0 references

Maria Cristina Díaz

6

Maria C Diaz

0 references

Christine Morrow

Christine C Morrow

18

0 references

author name string

Kevin J Peterson

4

0 references

Robert W Thacker

7

0 references

Maja Adamska

8

0 references

Paco Cárdenas

10

0 references

Bre-Onna De Laine

13

0 references

Dawn Formica

14

0 references

Sarah Klontz

17

0 references

Deborah Pohlmann

22

0 references

John Reed

24

0 references

Stacy Richey

25

0 references

Zach Russell

28

0 references

Michael di Stefano

31

0 references

James E Tarver

Creative Commons CC0 License

32

0 references

language of work or name

English

0 references

publication date

2013

0 references

published in

PLOS One

0 references

volume

8

0 references

issue

1

0 references

page(s)

e50437

0 references

copyright license

start time

23 January 2013

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted, dedicated to the public domain by copyright holder

0 references

cites work

Horny sponges and their affairs: on the phylogenetic relationships of keratose sponges

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3553142

The Cambrian conundrum: early divergence and later ecological success in the early history of animals

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3553142

Molecular phylogeny of the Astrophorida (Porifera, Demospongiae(p)) reveals an unexpected high level of spicule homoplasy

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3553142

Resolving difficult phylogenetic questions: why more sequences are not enough

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3553142

The Amphimedon queenslandica genome and the evolution of animal complexity

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3553142

Where's the glass? Biomarkers, molecular clocks, and microRNAs suggest a 200-Myr missing Precambrian fossil record of siliceous sponge spicules

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3553142

Phylogenomics revives traditional views on deep animal relationships

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3553142

Fossil steroids record the appearance of Demospongiae during the Cryogenian period

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3553142

RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3553142

Origin of the Eumetazoa: testing ecological predictions of molecular clocks against the Proterozoic fossil record

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3553142

ProtTest: selection of best-fit models of protein evolution

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3553142

Estimating metazoan divergence times with a molecular clock

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3553142

MUSCLE: multiple sequence alignment with high accuracy and high throughput

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3553142

TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3553142

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3553142

Likelihood-mapping: a simple method to visualize phylogenetic content of a sequence alignment

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3553142

SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3553142

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3553142

An improved general amino acid replacement matrix

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3553142

A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3553142

Phylogenetic relationships of the marine Haplosclerida (Phylum Porifera) employing ribosomal (28S rRNA) and mitochondrial (cox1, nad1) gene sequence data

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3553142

Spongivory on Caribbean reefs releases corals from competition with sponges

9 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3553142

Genome-wide analysis of the sox family in the calcareous sponge Sycon ciliatum: multiple genes with unique expression patterns

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3553142

Sponge systematics facing new challenges

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3553142

Deep phylogeny and evolution of sponges (phylum Porifera).

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3553142

Optimization of preservation and storage time of sponge tissues to obtain quality mRNA for next-generation sequencing.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3553142

Congruence between nuclear and mitochondrial genes in Demospongiae: a new hypothesis for relationships within the G4 clade (Porifera: Demospongiae).

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3553142

A method for inferring the rate of evolution of homologous characters that can potentially improve phylogenetic inference, resolve deep divergence and correct systematic biases

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3553142

Marine sponges and their microbial symbionts: love and other relationships

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3553142

Reconstructing ordinal relationships in the Demospongiae using mitochondrial genomic data

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3553142

Cryptic diversity of the symbiotic cyanobacterium Synechococcus spongiarum among sponge hosts

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3553142

Reassessment of the classification of the Order Haplosclerida (Class Demospongiae, Phylum Porifera) using 18S rRNA gene sequence data.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3553142

An evaluation of support for order-level monophyly and interrelationships within the class Demospongiae using partial data from the large subunit rDNA and cytochrome oxidase subunit I.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3553142

Clann: investigating phylogenetic information through supertree analyses

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3553142

Molecular phylogeny of Demospongiae: implications for classification and scenarios of character evolution

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3553142

Evaluating multiple alternative hypotheses for the origin of Bilateria: An analysis of 18S rRNA molecular evidence

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3553142

Phylogeny and classification of lithistid sponges (porifera: Demospongiae): a preliminary assessment using ribosomal DNA sequence comparisons.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3553142

The use of marine sponge, Haliclona tenuiramosa as bioindicator to monitor heavy metal pollution in the coasts of Gulf of Mannar, India.

3 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0050437

Phylogenetic-signal dissection of nuclear housekeeping genes supports the paraphyly of sponges and the monophyly of Eumetazoa.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0050437

Morphology and molecules on opposite sides of the diversity gradient: four cryptic species of the Cliona celata (Porifera, Demospongiae) complex in South America revealed by mitochondrial and nuclear markers.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0050437

Biodiversity, molecular ecology and phylogeography of marine sponges: patterns, implications and outlooks

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0050437

Polyphyly of the genus Axinella and of the family Axinellidae (Porifera: Demospongiaep).

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0050437

Phylogeny and evolution of glass sponges (porifera, hexactinellida).

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0050437

Phylogeny and evolution of calcareous sponges: monophyly of calcinea and calcaronea, high level of morphological homoplasy, and the primitive nature of axial symmetry.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0050437

Non-monophyly of most supraspecific taxa of calcareous sponges (Porifera, Calcarea) revealed by increased taxon sampling and partitioned Bayesian analysis of ribosomal DNA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0050437

TOPD/FMTS: a new software to compare phylogenetic trees.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0050437

An analysis of partial 28S ribosomal RNA sequences suggests early radiations of sponges

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0050437

Phylogenetic relationships of the family Axinellidae (Porifera: Demospongiae) using morphological and molecular data

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0050437

The Chemical Ecology of Sponges on Caribbean Reefs: Natural Products Shape Natural Systems

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0050437

Molecular phylogenetic position of hexactinellid sponges in relation to the Protista and Demospongiae

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23372644

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Matrix representation with parsimony, taxonomic congruence, and total evidence

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23372644

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Poriferan mtDNA and Animal Phylogeny Based on Mitochondrial Gene Arrangements

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23372644