Universität zu Köln

Di Franco, Arnaud, Baurain, Denis ORCID: 0000-0003-2388-6185, Glockner, Gernot, Melkonian, Michael and Philippe, Herve (2022). Lower Statistical Support with Larger Data Sets: Insights from the Ochrophyta Radiation. Mol. Biol. Evol., 39 (1). OXFORD: OXFORD UNIV PRESS. ISSN 1537-1719

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Abstract

It is commonly assumed that increasing the number of characters has the potential to resolve evolutionary radiations. Here, we studied photosynthetic stramenopiles (Ochrophyta) using alignments of heterogeneous origin mitochondrion, plastid, and nucleus. Surprisingly while statistical support for the relationships between the six major Ochrophyta lineages increases when comparing the mitochondrion (6,762 sites) and plastid (21,692 sites) trees, it decreases in the nuclear (209,105 sites) tree. Statistical support is not simply related to the data set size but also to the quantity of phylogenetic signal available at each position and our ability to extract it. Here, we show that this ability for current phylogenetic methods is limited, because conflicting results were obtained when varying taxon sampling. Even though the use of a better fitting model improved signal extraction and reduced the observed conflicts, the plastid data set provided higher statistical support for the ochrophyte radiation than the larger nucleus data set. We propose that the higher support observed in the plastid tree is due to an acceleration of the evolutionary rate in one short deep internal branch, implying that more phylogenetic signal per position is available to resolve the Ochrophyta radiation in the plastid than in the nuclear data set. Our work therefore suggests that, in order to resolve radiations, beyond the obvious use of data sets with more positions, we need to continue developing models of sequence evolution that better extract the phylogenetic signal and design methods to search for genes/characters that contain more signal specifically for short internal branches.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Di Franco, Arnaud UNSPECIFIED UNSPECIFIED UNSPECIFIED Baurain, Denis UNSPECIFIED orcid.org/0000-0003-2388-6185 UNSPECIFIED Glockner, Gernot UNSPECIFIED UNSPECIFIED UNSPECIFIED Melkonian, Michael UNSPECIFIED UNSPECIFIED UNSPECIFIED Philippe, Herve UNSPECIFIED UNSPECIFIED UNSPECIFIED
URN:	urn:nbn:de:hbz:38-681462
DOI:	10.1093/molbev/msab300
Journal or Publication Title:	Mol. Biol. Evol.
Volume:	39
Number:	1
Date:	2022
Publisher:	OXFORD UNIV PRESS
Place of Publication:	OXFORD
ISSN:	1537-1719
Language:	English
Faculty:	Unspecified
Divisions:	Unspecified
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language PHYLOGENETIC ANALYSIS; CLASSIS-NOVA; GENE TREES; EVOLUTION; MITOCHONDRIAL; PARSIMONY; MODELS; SELECTION; PLASTIDS Multiple languages Biochemistry & Molecular Biology; Evolutionary Biology; Genetics & Heredity Multiple languages
URI:	http://kups.ub.uni-koeln.de/id/eprint/68146