Separating the wheat from the chaff: mitigating the effects of noise in a plastome phylogenomic data set from Pinus L. PinaceaeReport as inadecuate




Separating the wheat from the chaff: mitigating the effects of noise in a plastome phylogenomic data set from Pinus L. Pinaceae - Download this document for free, or read online. Document in PDF available to download.

BMC Evolutionary Biology

, 12:100

First Online: 25 June 2012Received: 19 January 2012Accepted: 14 June 2012DOI: 10.1186-1471-2148-12-100

Cite this article as: Parks, M., Cronn, R.
& Liston, A.
BMC Evol Biol 2012 12: 100.
doi:10.1186-1471-2148-12-100

Abstract

BackgroundThrough next-generation sequencing, the amount of sequence data potentially available for phylogenetic analyses has increased exponentially in recent years.
Simultaneously, the risk of incorporating ‘noisy’ data with misleading phylogenetic signal has also increased, and may disproportionately influence the topology of weakly supported nodes and lineages featuring rapid radiations and-or elevated rates of evolution.

ResultsWe investigated the influence of phylogenetic noise in large data sets by applying two fundamental strategies, variable site removal and long-branch exclusion, to the phylogenetic analysis of a full plastome alignment of 107 species of Pinus and six Pinaceae outgroups.
While high overall phylogenetic resolution resulted from inclusion of all data, three historically recalcitrant nodes remained conflicted with previous analyses.
Close investigation of these nodes revealed dramatically different responses to data removal.
Whereas topological resolution and bootstrap support for two clades peaked with removal of highly variable sites, the third clade resolved most strongly when all sites were included.
Similar trends were observed using long-branch exclusion, but patterns were neither as strong nor as clear.
When compared to previous phylogenetic analyses of nuclear loci and morphological data, the most highly supported topologies seen in Pinus plastome analysis are congruent for the two clades gaining support from variable site removal and long-branch exclusion, but in conflict for the clade with highest support from the full data set.

ConclusionsThese results suggest that removal of misleading signal in phylogenomic datasets can result not only in increased resolution for poorly supported nodes, but may serve as a tool for identifying erroneous yet highly supported topologies.
For Pinus chloroplast genomes, removal of variable sites appears to be more effective than long-branch exclusion for clarifying phylogenetic hypotheses.

KeywordsPhylogenetic noise Plastome Pinus Chloroplast Electronic supplementary materialThe online version of this article doi:10.1186-1471-2148-12-100 contains supplementary material, which is available to authorized users.

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Author: Matthew Parks - Richard Cronn - Aaron Liston

Source: https://link.springer.com/



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