close
Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2012 Jun 25:12:100.
doi: 10.1186/1471-2148-12-100.

Separating the wheat from the chaff: mitigating the effects of noise in a plastome phylogenomic data set from Pinus L. (Pinaceae)

Matthew Parks  1 , Richard Cronn, Aaron Liston
Affiliations

Separating the wheat from the chaff: mitigating the effects of noise in a plastome phylogenomic data set from Pinus L. (Pinaceae)

Matthew Parks et al. BMC Evol Biol. .

Abstract

Background: Through 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.

Results: We 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.

Conclusions: These 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.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Phylogenetic hypotheses for genus Pinus . Alternate placements (indicated by dashed lines) of subsections Contortae and Krempfianae, as well as the clade consisting of Pinus merkusii and P. latteri are shown. The most common plastid-based resolution of these groups is indicated by gray shading. Tree topology and relative branch lengths reflective of data from Gernandt et al. [42], Parks et al. [31] and this study.
Figure 2
Figure 2
Distribution of OV for variable plastome alignment positions. Schematic of the Pinus chloroplast genome with annotated protein-coding exons (blue), rRNA loci (yellow), tRNA loci (orange) and noncoding regions (green). The coding loci ycf1 and ycf2 are highlighted in light blue. The distribution of OV values > 0 is indicated by the internal histogram, as follows: red – most variable 4.6 kbp (A142165 to A136665 ); yellow – most variable sites from 4.6 to 8.3 kbp (A136565 to A133065 ); green – remaining sites with OV > 0.
Figure 3
Figure 3
Trends in bootstrap support values and topologies for likelihood analyses of alignment partitions. For OV-based analyses, the following are shown: a) Distributions of bootstrap support values for all nodes. Circles represent median bootstrap support for each An partition size. b) Distribution of branch score metric (triangles) and partition metric (circles) values for tests of topological congruence between An and corresponding Bn data partitions. Filled data points correspond to An partitions sizes falling between final decrease of branch score metric values and start of decreases in overall bootstrap support values for An partitions. Partition metric values shown are 0.1× actual value in order to fit on same scale with branch score metric values.
Figure 4
Figure 4
Distribution of bootstrap support values for phylogenetic position of three clades in genus Pinus . a) Bootstrap support values for placement of subsection Krempfianae . Circles correspond to placement of P. krempfii sister to subsection Gerardianae . b) Bootstrap support values for placement of Pinus merkusii / P. latteri . Circles correspond to placement of P. merkusii/P. latteri as sister to subsection Pinaster and triangles as sister to subsection Pinus. c) Bootstrap support values for placement of subsection Contortae. Circles correspond to placement of subsection Contortae as sister to subsection Australes and triangles as basal to both subsections Australes and Contortae. For all charts, filled data points correspond to An partition sizes falling between final decrease of branch score metric values and start of decrease in overall bootstrap support values for An partitions, as shown in Figure  3. Squares represent variable phylogenetic placements not including those represented by circles or triangles. Arrows in b) and c) indicate partition size at which bootstrap support for monophyly of clade falls below 100%.
See this image and copyright information in PMC

References

    1. Fitch WM. Cautionary remarks on using gene expression events in parsimony procedures. Systematic Zool. 1979;28:375–379. doi: 10.2307/2412591. - DOI
    1. Fitch WM. In: Cladistics: Perspectives on the Reconstruction of Evolutionary History. Duncan T, Stuessy TF, editor. New York: Columbia University Press; 1984. Cladistic and other methods: problems, pitfalls, and potentials; pp. 221–252.
    1. Felsenstein J. Cases in which parsimony or compatibility methods will be positively misleading. Syst Zool. 1978;27:401–410. doi: 10.2307/2412923. - DOI
    1. Hendy MD, Penny D. A framework for the quantitative study of evolutionary trees. Syst Biol. 1989;38:297–309.
    1. Huelsenbeck JP. Tree-length distribution skewness: an indicator of phylogenetic information. Syst Biol. 1991;40:257–270.

Publication types

LinkOut - more resources