Pattern pluralism and the Tree of Life hypothesis (Q22066333)

PubMed publication ID

7 February 2023

Eric Bapteste

Eric

Bapteste

1 reference

PubMed publication ID

17261804

Proceedings of the National Academy of Sciences of the United States of America

7 February 2023

language of work or name

English

0 references

publication date

13 February 2007

0 references

published in

0 references

volume

104

0 references

issue

0 references

page(s)

2043-9

0 references

cites work

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Prokaryotic evolution in light of gene transfer

7 April 2017

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Genome phylogeny based on gene content

7 April 2017

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7 April 2017

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Maximum likelihood of phylogenetic networks

12 September 2017

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12 September 2017

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12 September 2017

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12 September 2017

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12 September 2017

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12 September 2017

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12 September 2017

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12 September 2017

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12 September 2017

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Genomic insights that advance the species definition for prokaryotes

12 September 2017

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Phylogeny determined by protein domain content

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1892968

Computing prokaryotic gene ubiquity: rescuing the core from extinction

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1892968

Phylogenetic reconstruction and lateral gene transfer.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1892968

From a phylogenetic tree to a reticulated network

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1892968

On the conceptual difficulties in rooting the tree of life

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1892968

Phylogenetics and the cohesion of bacterial genomes

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1892968

Horizontal gene transfer: a critical view

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1892968

Lateral gene transfer and the evolution of plastid-targeted proteins in the secondary plastid-containing alga Bigelowiella natans

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1892968

Recycled plastids: a 'green movement' in eukaryotic evolution

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1892968

Genome trees and the tree of life

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1892968

Inferring genome trees by using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1892968

Recombination and the population structures of bacterial pathogens

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1892968

Universal trees based on large combined protein sequence data sets.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1892968

Early evolution and the origin of eukaryotes

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1892968

Origins of Prokaryotes, Eukaryotes, Mitochondria, and Chloroplasts

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1892968

Whole-genome trees based on the occurrence of folds and orthologs: implications for comparing genomes on different levels

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1892968

Whole genome-based phylogenetic analysis of free-living microorganisms

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1892968

Problems in the development of an explicit hypothetical phylogeny of the lower eukaryotes

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1892968

Reconstructing an ultrametric galled phylogenetic network from a distance matrix.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1892968

Visualizing and assessing phylogenetic congruence of core gene sets: a case study of the gamma-proteobacteria

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1892968

Genomics. Are there bugs in our genome?

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1892968

Does a tree-like phylogeny only exist at the tips in the prokaryotes?

30 May 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0610699104

Rooting the tree of life by transition analyses

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0610699104

Representations of the Natural System in the Nineteenth century

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0610699104

Species, rules and meaning: the politics of language and the ends of definitions in 19th century natural history.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0610699104

The tree of life is a tree (more or less)

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0610699104

Fuzzy species among recombinogenic bacteria

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0610699104

Evolutionary genetics and biogeographic structure of Rhizobium gallicum sensu lato, a widely distributed bacterial symbiont of diverse legumes

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0610699104

Ancient gene duplications and the root(s) of the tree of life.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0610699104

Eubacterial phylogeny based on translational apparatus proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0610699104

The consistent phylogenetic signal in genome trees revealed by reducing the impact of noise

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0610699104

Using homolog groups to create a whole-genomic tree of free-living organisms: an update.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0610699104

Reconstructing reticulate evolution in species-theory and practice.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0610699104

Phylogenetic networks from multi-labelled trees.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0610699104

Genomics and the bacterial species problem

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1892968

A comparison of the nucleotide sequences of the adk and recA genes of pathogenic and commensal Neisseria species: evidence for extensive interspecies recombination within adk.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1892968

Genome phylogenetic analysis based on extended gene contents

29 November 2018

1 reference

https://pubmed.ncbi.nlm.nih.gov/17261804

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Frequent recombination in a saltern population of Halorubrum

1 reference

https://pubmed.ncbi.nlm.nih.gov/17261804

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

1 reference

18 October 2022

https://opencitations.net/index/coci/api/v1/citations/10.1128/MR.51.2.221-271.1987

Identifiers

DOI

10.1073/PNAS.0610699104

1 reference

ADS bibcode

2007PNAS..104.2043D

0 references

1 reference

1 reference

PubMed publication ID

17261804

1 reference