Characterizing gene tree conflict in plastome-inferred phylogenies

PeerJ

article

Joseph F. Walker¹  Nathanael Walker-Hale²  Oscar M. Vargas³  Drew A. Larson⁴  Gregory W. Stull⁵ 

[1] Sainsbury Laboratory ,(SLCU), University of Cambridge;Department of Plant Sciences, University of Cambridge;University of California;University of Michigan—Ann Arbor;Department of Botany, Smithsonian Institution

关键词: Angiosperms;    Chloroplast;    Gene tree conflict;    rpoC2;    Phylogenomics;    Plastome;    matK;    rbcL;   

DOI  :  10.7717/peerj.7747

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

Evolutionary relationships among plants have been inferred primarily using chloroplast data. To date, no study has comprehensively examined the plastome for gene tree conflict. Using a broad sampling of angiosperm plastomes, we characterize gene tree conflict among plastid genes at various time scales and explore correlates to conflict (e.g., evolutionary rate, gene length, molecule type). We uncover notable gene tree conflict against a backdrop of largely uninformative genes. We find alignment length and tree length are strong predictors of concordance, and that nucleotides outperform amino acids. Of the most commonly used markers, matK, greatly outperforms rbcL; however, the rarely used gene rpoC2 is the top-performing gene in every analysis. We find that rpoC2 reconstructs angiosperm phylogeny as well as the entire concatenated set of protein-coding chloroplast genes. Our results suggest that longer genes are superior for phylogeny reconstruction. The alleviation of some conflict through the use of nucleotides suggests that stochastic and systematic error is likely the root of most of the observed conflict, but further research on biological conflict within plastome is warranted given documented cases of heteroplasmic recombination. We suggest that researchers should filter genes for topological concordance when performing downstream comparative analyses on phylogenetic data, even when using chloroplast genomes.

【 授权许可】

CC BY