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Open Access Research article

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

Matthew Parks1*, Richard Cronn2 and Aaron Liston1

Author Affiliations

1 Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331-2902, USA

2 Pacific Northwest Research Station, USDA Forest Service, Corvallis, OR 97331, USA

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BMC Evolutionary Biology 2012, 12:100  doi:10.1186/1471-2148-12-100

Published: 25 June 2012

Additional files

Additional file 1:

Collection and sequencing information for accessions used in this study.

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Additional file 2:

Settings used in AIR-Identifier.

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Additional file 3:

Average per site rate variability of plastome regions for full plastome alignment using tree-dependent methodology. Average per site category ranking for protein-coding exons, introns, rRNA and tRNA genes, and noncoding regions for full plastome alignment of 113 Pinus and Pinaceae species using tree-dependent methodology. Standard deviations are given in parentheses. Mean values with different superscript letters are significantly different at α < 0.05 in Tukey’s HSD test, following one-way ANOVA supporting different means at p < 0.0001.

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Additional file 4:

Phylogenetic relationships within genusPinusas determined from full plastome alignment. a) Cladogram based on ML topology, showing support values below branches as ML bootstrap support / Bayesian posterior probability / parsimony bootstrap support. Support values are shown only for nodes with less than 100% bootstrap support and/or posterior probabilities less than 1.0; single values indicate either ML bootstrap support or Bayesian posterior probability. * indicates branch not supported in Bayesian or parsimony analysis. b) ML Phylogram with branch lengths determined from ML analysis; scale corresponds to probability of change per positions.

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Additional file 5:

Trends in bootstrap support values and topologies for likelihood analyses of alignment partitions (tree-dependent). For tree-dependent site variability 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. Partition metric values shown are 0.1× actual value in order to fit on same scale with branch score values.

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Additional file 6:

Distribution of bootstrap support for phylogenetic position of three clades in genusPinus (tree-dependent). Results for tree-dependent site variability analyses are shown for: a) subsection Krempfianae , b) Pinus merkusii / P. latteri and c) Subsection Contortae . In a), P. krempfii was found sister to subsection Gerardianae for all An partitions. In b), circles correspond to placement of P. merkusii /P. latteri as sister to subsection Pinaster and triangles as sister to subsection Pinus. In c), circles correspond to placement of subsection Contortae as sister to subsection Australes and triangles as basal to both subsections Australes and Contortae; squares represent variable phylogenetic placements not including those represented by circles or triangles. For b) and c), monophyly of P. merkusii/P. latteri and subsection Contortae was supported at 100% bootstrap support for all An partitions.

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Additional file 7:

Trends in corrected vs. uncorrected pairwise distances. All pairwise distance values calculated as uncorrected pairwise distance and with a Jukes-Cantor correction, plotted for: a) all accessions used in study, b) genus Pinus accessions only, c) subgenus Pinus accessions only, d) subgenus Strobus accessions only, e) subsection Quinquefoliae and Pinus monophylla only, f) subsection Pinus and Pinus ponderosa only, and g) subsection Trifoliae and Pinus thunbergii only.

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