A well supported multi gene phylogeny of 52 dictyostelia.
Ancestral state reconstruction
Dictyostelia
Dictyostelium caveatum
Phylogenetic marker genes
Phylogenomics
Polysphondylium multicystogenum
Journal
Molecular phylogenetics and evolution
ISSN: 1095-9513
Titre abrégé: Mol Phylogenet Evol
Pays: United States
ID NLM: 9304400
Informations de publication
Date de publication:
05 2019
05 2019
Historique:
received:
11
10
2018
revised:
09
01
2019
accepted:
21
01
2019
pubmed:
4
2
2019
medline:
14
6
2019
entrez:
4
2
2019
Statut:
ppublish
Résumé
The Dictyostelid social amoebas are a popular model system for cell- and developmental biology and for evolution of sociality. Small subunit (SSU) ribosomal DNA-based phylogenies subdivide the known 150 species into four major and some minor groups, but lack resolution within groups, particularly group 4, and, as shown by genome-based phylogenies of 11 species, showed errors in the position of the root and nodes separating major clades. We are interested in the evolution of cell-type specialization, which particularly expanded in group 4. To construct a more robust phylogeny, we first included 7 recently sequenced genomes in the genome-based phylogeny of 47 functionally divergent proteins and next selected 6 proteins (Agl, AmdA, PurD, PurL, RpaA, SmdA) that independently or in sets of two fully reproduced the core-phylogeny. We amplified their coding regions from 34 Dictyostelium species and combined their concatenated sequences with those identified in the 18 genomes to generate a fully resolved phylogeny. The new AAPPRS based phylogeny (after the acronym of the 6 proteins) subdivides group 4 into 2 branches. These branches further resolve into 5 clades, rather than the progressively nested group 4 topology of the SSU rDNA tree, and also re-orders taxa in the other major groups. Ancestral state reconstruction of 25 phenotypic traits returned higher "goodness of fit" metrics for evolution of 19 of those traits over the AAPPRS tree, than over the SSU rDNA tree. The novel tree provides a solid framework for studying the evolution of cell-type specialization, signalling and other cellular processes in particularly group 4, which contains the model Dictyostelid D. discoideum.
Identifiants
pubmed: 30711536
pii: S1055-7903(18)30654-7
doi: 10.1016/j.ympev.2019.01.017
pmc: PMC6430600
pii:
doi:
Substances chimiques
Protozoan Proteins
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
66-73Subventions
Organisme : Wellcome Trust
ID : 100293/Z/12/Z
Pays : United Kingdom
Informations de copyright
Copyright © 2019 The Authors. Published by Elsevier Inc. All rights reserved.
Références
Nature. 2005 May 5;435(7038):43-57
pubmed: 15875012
Eukaryot Cell. 2007 Jan;6(1):110-6
pubmed: 17056743
Science. 2006 Oct 27;314(5799):661-3
pubmed: 17068267
Genome Res. 2008 May;18(5):821-9
pubmed: 18349386
Mycologia. 2008 Mar-Apr;100(2):347-51
pubmed: 18592909
PLoS One. 2009 Dec 22;4(12):e8407
pubmed: 20027311
Genome Biol. 2011;12(2):R20
pubmed: 21356102
BMC Evol Biol. 2011 Mar 31;11:84
pubmed: 21453486
Genome Res. 2011 Nov;21(11):1882-91
pubmed: 21757610
J Bacteriol. 2012 May;194(9):2373-4
pubmed: 22493190
Evolution. 2012 Sep;66(9):2697-707
pubmed: 22946797
Syst Biol. 2013 Jul;62(4):611-5
pubmed: 23564032
Proc Biol Sci. 2013 Jun 19;280(1764):20130976
pubmed: 23782883
Methods Mol Biol. 2014;1079:105-16
pubmed: 24170397
Evodevo. 2014 Oct 01;5:34
pubmed: 25904998
Mol Phylogenet Evol. 2015 Nov;92:53-62
pubmed: 26048704
Nat Commun. 2016 Jun 30;7:12085
pubmed: 27357338
BMC Evol Biol. 2016 Nov 17;16(1):251
pubmed: 27855631
Genome Res. 2017 May;27(5):722-736
pubmed: 28298431
Protist. 2018 Feb;169(1):1-28
pubmed: 29367151
Genome Biol Evol. 2018 Feb 1;10(2):591-606
pubmed: 29378020
Gene. 1988 Nov 30;71(2):491-9
pubmed: 3224833
Genetics. 1995 Dec;141(4):1641-50
pubmed: 8601501