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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #306156

Title: Disentangling methodological and biological sources of gene tree discordance on oryza (poaceae) chromosome 3

item ZWICKL, DERRICK - University Of Arizona
item STEIN, JOSHUA - Cold Spring Harbor Laboratory
item WING, ROD - University Of Arizona
item Ware, Doreen
item SANDERSON, MICHAEL - University Of Arizona

Submitted to: Systematic Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/18/2014
Publication Date: 4/9/2014
Citation: Zwickl, D.J., Stein, J.C., Wing, R.A., Ware, D., Sanderson, M.J. 2014. Disentangling methodological and biological sources of gene tree discordance on oryza (poaceae) chromosome 3. Systematic Biology. DOI: 10.1093/sysbio/syu027.

Interpretive Summary: Phylogenetic gene tree analysis is used to infer evolutionary relationships between species by inter-comparison of molecular gene sequences. Many methods have been developed for constructing and interpreting gene trees, but few have been directly compared in a systematic fashion. This study examines 20 distinct analysis pipelines to understand the effects of methodology on outcomes. It uses a large data set consisting of annotated genes along the short arm of chromosome 3 in a set of species in the Oryza (rice) genus. Methods were compared for patterns of tree discordance, that is, cases in which the resulting tree failed to match expectations. It distinguished cases of tree discordance caused by methodological bias versus those caused by true evolutionary process, such as gene introgression between species. Conclusions from this study are expected to by generalizable to phylogenetic analysis in different systems.

Technical Abstract: We describe new methods for characterizing gene tree discordance in phylogenomic datasets, which screen for deviations from neutral expectations, summarize variation in statistical support among gene trees, and allow comparison of the patterns of discordance induced by various analysis choices. Using an exceptionally complete set of genome sequences for the short arm of chromosome 3 in Oryza (rice) species, we applied these methods to identify the causes and consequences of differing patterns of discordance in the sets of gene trees inferred using a panel of 20 distinct analysis pipelines. We found that discordance patterns were strongly affected by aspects of data selection, alignment, and alignment masking. Unusual patterns of discordance evident when using certain pipelines were reduced or eliminated by using alternative pipelines, suggesting that they were the product of methodological biases rather than evolutionary processes. In some cases, once such biases were eliminated, evolutionary processes such as introgression could be implicated. Additionally, patterns of gene tree discordance had significant downstream impacts on species tree inference. For example, inference from supermatrices was positively misleading when pipelines that led to biased gene trees were used. Several results may generalize to other data sets: we found that gene tree and species tree inference gave more reasonable results when intron sequence was included during sequence alignment and/or tree inference, the alignment software PRANK was used, and/or detectable "block-shift" alignment artifacts were removed. We discuss our findings in the context of well-established relationships in Oryza and continuing controversies regarding the domestication history of O. sativa.