(Q34020897)

30 July 2017

title

Experimental design and statistical rigor in phylogenomics of horizontal and endosymbiotic gene transfer (English)

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30 July 2017

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John W Stiller

1

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30 July 2017

publication date

16 September 2011

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30 July 2017

published in

BMC Evolutionary Biology

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30 July 2017

volume

11

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30 July 2017

page(s)

259

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Eukaryote-to-eukaryote gene transfer gives rise to genome mosaicism in euglenids

30 July 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3190393

Plastid origin and evolution: new models provide insights into old problems

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3190393

Red and green algal monophyly and extensive gene sharing found in a rich repertoire of red algal genes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3190393

A Survey of Combinatorial Methods for Phylogenetic Networks

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3190393

Algal genes in the closest relatives of animals

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3190393

A common red algal origin of the apicomplexan, dinoflagellate, and heterokont plastids

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3190393

Large-scale phylogenomic analyses reveal that two enigmatic protist lineages, telonemia and centroheliozoa, are related to photosynthetic chromalveolates

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3190393

Phylogenomic evidence for separate acquisition of plastids in cryptophytes, haptophytes, and stramenopiles

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3190393

Sizing up the genomic footprint of endosymbiosis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3190393

Are algal genes in nonphotosynthetic protists evidence of historical plastid endosymbioses?

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3190393

Phylogenetic positions of Glaucophyta, green plants (Archaeplastida) and Haptophyta (Chromalveolata) as deduced from slowly evolving nuclear genes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3190393

Genomic footprints of a cryptic plastid endosymbiosis in diatoms

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3190393

Chromalveolates and the evolution of plastids by secondary endosymbiosis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3190393

The puzzle of plastid evolution

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3190393

Phylogenetic inference using whole genomes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3190393

Multiple genes of apparent algal origin suggest ciliates may once have been photosynthetic.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3190393

Horizontal gene transfer in eukaryotic evolution

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3190393

Phylogenomics reveals a new 'megagroup' including most photosynthetic eukaryotes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3190393

5 July 2018

The origin of plastids

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3190393

Difficulties in testing for covarion-like properties of sequences under the confounding influence of changing proportions of variable sites

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3190393

The eukaryotic tree of life: endosymbiosis takes its TOL.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3190393

The prokaryotic tree of life: past, present... and future?

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3190393

Chromatophore genome sequence of Paulinella sheds light on acquisition of photosynthesis by eukaryotes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3190393

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3190393

Broadly sampled multigene trees of eukaryotes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3190393

Principles of protein and lipid targeting in secondary symbiogenesis: euglenoid, dinoflagellate, and sporozoan plastid origins and the eukaryote family tree

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3190393

Did an ancient chlamydial endosymbiosis facilitate the establishment of primary plastids?

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3190393

Phytophthora Genome Sequences Uncover Evolutionary Origins and Mechanisms of Pathogenesis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3190393

PhyloGenie: automated phylome generation and analysis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3190393

Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3190393

Dinoflagellate nuclear SSU rRNA phylogeny suggests multiple plastid losses and replacements

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3190393

Long-branch attraction and the rDNA model of early eukaryotic evolution

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3190393

Early-branching or fast-evolving eukaryotes? An answer based on slowly evolving positions

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3190393

Microsporidia are related to Fungi: evidence from the largest subunit of RNA polymerase II and other proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3190393

The origin of red algae: implications for plastid evolution

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3190393

Plastid endosymbiosis, genome evolution and the origin of green plants.

5 July 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-11-259

A HYPOTHESIS FOR PLASTID EVOLUTION IN CHROMALVEOLATES(1).

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-11-259

Cyanobacterial contribution to algal nuclear genomes is primarily limited to plastid functions.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-11-259

PhyloGena--a user-friendly system for automated phylogenetic annotation of unknown sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-11-259

A review of long-branch attraction

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-11-259

Monophyly of primary photosynthetic eukaryotes: green plants, red algae, and glaucophytes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-11-259

Multiple gene phylogenies support the monophyly of cryptomonad and haptophyte host lineages

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-11-259

Heterotachy and tree building: a case study with plastids and eubacteria.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-11-259

Testing congruence in phylogenomic analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-11-259

Signatures of ecological resource availability in the animal and plant proteomes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-11-259

Causes and evolutionary significance of genetic convergence.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-11-259

Heterotachy processes in rhodophyte-derived secondhand plastid genes: Implications for addressing the origin and evolution of dinoflagellate plastids.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-11-259

Mathematical elegance with biochemical realism: the covarion model of molecular evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-11-259

Bayesian estimation of concordance among gene trees.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-11-259

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-11-259

Serial Replacement of Diatom Endosymbionts in Two Freshwater Dinoflagellates, Peridiniopsis spp. (Peridiniales, Dinophyceae)

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-11-259

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-11-259

Phylogeny of Primary Photosynthetic Eukaryotes as Deduced from Slowly Evolving Nuclear Genes

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-11-259

The gene evolution model and computing its associated probabilities

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-11-259

A plastid in the making: evidence for a second primary endosymbiosis

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21923904

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Shopping for plastids

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21923904

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Chromalveolate plastids: direct descent or multiple endosymbioses?

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21923904

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1471-2148-11-259

1 reference

Dimensions Publication ID

30 July 2017

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1 reference

30 July 2017

1 reference