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Dissecting phylogenetic signal and accounting for bias in whole-genome data sets: a case study of the Metazoa

Marek L. Borowiec, Ernest K. Lee, Joanna C. Chiu, David C. Plachetzki
doi: https://doi.org/10.1101/013946
Marek L. Borowiec
1Department of Entomology and Nematology, University of California, Davis, USA
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  • For correspondence: mlborowiec@ucdavis.edu david.plachetzki@unh.edu
Ernest K. Lee
2Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, USA
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Joanna C. Chiu
1Department of Entomology and Nematology, University of California, Davis, USA
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David C. Plachetzki
3Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, USA
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  • For correspondence: mlborowiec@ucdavis.edu david.plachetzki@unh.edu
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Abstract

Transcriptome-enabled phylogenetic analyses have dramatically improved our understanding of metazoan phylogeny in recent years, although several important questions remain. The branching order near the base of the tree is one such outstanding issue. To address this question we assemble a novel data set comprised of 1,080 orthologous loci derived from 36 publicly available genomes and dissect the phylogenetic signal present in each individual partition. The size of this data set allows for a closer look at the potential biases and sources of non-phylogenetic signal. We assessed a range of measures for each data partition including information content, saturation, rate of evolution, long-branch score, and taxon occupancy and explored how each of these characteristics impacts phylogeny estimation. We then used these data to prepare a reduced set of partitions that fit an optimal set of criteria and are amenable to the most appropriate and computationally intensive analyses using site-heterogeneous models of sequence evolution. We also employed several strategies to examine the potential for long-branch attraction to bias our inferences. All of our analyses support Ctenophora as the sister lineage to other Metazoa, although support for this relationship varies among analyses. We find no support for the traditional view uniting the ctenophores and Cnidaria (jellies, anemones, corals, and kin). We also examine phylogenetic placement of myriapods (centipedes and millipedes) and find it more sensitive to the type of analysis and data used. Our study provides a workflow for minimizing systematic bias in whole genome-based phylogenetic analyses.

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Posted January 20, 2015.
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Dissecting phylogenetic signal and accounting for bias in whole-genome data sets: a case study of the Metazoa
Marek L. Borowiec, Ernest K. Lee, Joanna C. Chiu, David C. Plachetzki
bioRxiv 013946; doi: https://doi.org/10.1101/013946
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Dissecting phylogenetic signal and accounting for bias in whole-genome data sets: a case study of the Metazoa
Marek L. Borowiec, Ernest K. Lee, Joanna C. Chiu, David C. Plachetzki
bioRxiv 013946; doi: https://doi.org/10.1101/013946

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