Abstract
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.
Highlights
Chloroplast data have been the most prominent source of information for plant phylogenetics, largely due to the ease with which chloroplast genes can be sequenced, assembled, and analyzed (Palmer, 1985; Taberlet et al, 1991)
Because it is possible that apparent relationships between alignment length and concordance may reflect signal from gene information content per alignment site, we modeled gene performance as a function of length and tree length, to assess the relationship between alignment length and gene performance after controlling for variation associated with rate
We find notable levels of gene-tree conflict within the plastome, at all levels of angiosperm phylogeny, highlighting the necessity of future research into the causes of plastome conflict: do some genes share different evolutionary histories, or is systematic error the source of the observed conflict? With rare exceptions, most genes are largely uninformative and, when analyzed as a whole, are unlikely to mislead researchers
Summary
Chloroplast data have been the most prominent source of information for plant phylogenetics, largely due to the ease with which chloroplast genes can be sequenced, assembled, and analyzed (Palmer, 1985; Taberlet et al, 1991). The majority of broadscale phylogenetic studies on plants have used chloroplast genes (e.g., Chase et al, 1993; Soltis et al, 2000; Soltis et al, 2011), and the resulting phylogenies have been used for countless comparative studies examining ancestral states, historical biogeography, and other evolutionary patterns. RbcL and matK, recent advances in DNA sequencing have drastically increased the ease and affordability of whole-chloroplast genome (i.e., plastome) sequencing (Moore et al, 2006; Cronn et al, 2008; Cronn et al, 2012; Stull et al, 2013; Uribe-Convers et al, 2014), increasing the number of studies employing plastome-scale data for phylogenetic and comparative analyses (e.g., Jansen et al, 2007; Moore et al, 2007; Moore et al, 2010; Ruhfel et al, 2014; Stull et al, 2015; Gitzendanner et al, 2018; Li et al, 2019). The utility of plastid genes, as well as the entire plastome, is determined by the extent to which they reflect ‘true’ evolutionary relationships (i.e., the ‘species tree’) of the lineages in question (Doyle, 1992)
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