Phylogenomics of Lophotrochozoa with Consideration of Systematic Error.
Phylogenomic studies have improved understanding of deep metazoan phylogeny and show promise for resolving incongruences among analyses based on limited numbers of loci. One region of the animal tree that has been especially difficult to resolve, even with phylogenomic approaches, is relationships within Lophotrochozoa (the animal clade that includes molluscs, annelids, and flatworms among others). Lack of resolution in phylogenomic analyses could be due to insufficient phylogenetic signal, limitations in taxon and/or gene sampling, or systematic error. Here, we investigated why lophotrochozoan phylogeny has been such a difficult question to answer by identifying and reducing sources of systematic error. We supplemented existing data with 32 new transcriptomes spanning the diversity of Lophotrochozoa and constructed a new set of Lophotrochozoa-specific core orthologs. Of these, 638 orthologous groups (OGs) passed strict screening for paralogy using a tree-based approach. In order to reduce possible sources of systematic error, we calculated branch-length heterogeneity, evolutionary rate, percent missing data, compositional bias, and saturation for each OG and analyzed increasingly stricter subsets of only the most stringent (best) OGs for these five variables. Principal component analysis of the values for each factor examined for each OG revealed that compositional heterogeneity and average patristic distance contributed most to the variance observed along the first principal component while branch-length heterogeneity and, to a lesser extent, saturation contributed most to the variance observed along the second. Missing data did not strongly contribute to either. Additional sensitivity analyses examined effects of removing taxa with heterogeneous branch lengths, large amounts of missing data, and compositional heterogeneity. Although our analyses do not unambiguously resolve lophotrochozoan phylogeny, we advance the field by reducing the list of viable hypotheses. Moreover, our systematic approach for dissection of phylogenomic data can be applied to explore sources of incongruence and poor support in any phylogenomic data set. [Annelida; Brachiopoda; Bryozoa; Entoprocta; Mollusca; Nemertea; Phoronida; Platyzoa; Polyzoa; Spiralia; Trochozoa.].
Department of Biological Sciences, 101 Rouse Life Sciences, Auburn University, Auburn, AL 36849, USA.|Department of Biological Sciences and Alabama Museum of Natural History, 307 Mary Harmon Bryant Hall, The University of Alabama, Tuscaloosa, AL 35487, USA.
Kevin M
KM
Kocot
Natural History Museum, Department of Research and Collections, University of Oslo, PO Box 1172 Blindern, N-0318 Oslo, Norway.
Torsten H
TH
Struck
Johannes Gutenberg University, Institute of Zoology, 55099 Mainz, Germany.
Julia
J
Merkel
Department of Biological Sciences, 101 Rouse Life Sciences, Auburn University, Auburn, AL 36849, USA.
Damien S
DS
Waits
University Museum of Bergen, The Natural History Collections, University of Bergen, Allégaten 41, 5007 Bergen, Norway.
Christiane
C
Todt
Department of Biological Sciences, 101 Rouse Life Sciences, Auburn University, Auburn, AL 36849, USA.
Pamela M
PM
Brannock
Department of Biological Sciences, 101 Rouse Life Sciences, Auburn University, Auburn, AL 36849, USA.|Department of Biological and Environmental Sciences, Georgia College and State University, Campus Box 81, Milledgeville, GA 31061 USA.
David A
DA
Weese
Department of Biological Sciences, 101 Rouse Life Sciences, Auburn University, Auburn, AL 36849, USA.|Department of Zoology, Naturhistoriska riksmuseet, Box 50007, 104 05 Stockholm, Sweden.
Johanna T
JT
Cannon
The Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd, St Augustine, FL 32080, USA.
Leonid L
LL
Moroz
Johannes Gutenberg University, Institute of Zoology, 55099 Mainz, Germany.
Bernhard
B
Lieb
Department of Biological Sciences, 101 Rouse Life Sciences, Auburn University, Auburn, AL 36849, USA.
Kenneth M
KM
Halanych
D000818:Animals; D002013:Bryozoa / Q000145:classification* / Q000235:genetics*; D002965:Classification / Q000379:methods*; D016678:Genome / Q000235:genetics*; D010802:Phylogeny