Characterizing gene tree conflict in plastome-inferred phylogenies

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.

Complete chloroplast genomes of Liliaceae (s.l.) species: comparative genomic and phylogenetic analyses

“…Interestingly, it has been suggested that Hosta and Yucca have a relatively closer affinity in the Liliaceae, although Hosta was previously considered to belong to the Liliaceae (Hutchinson 1959, Cronquist 1981 or Funkiaceae (Dahlgren et al 1985). Previous studies have suggested different topologies for the Liliaceae family, plausibly because of actual conflicting signals from methods or models (Hutchinson 1959, Cronquist 1981, Dahlgren et al 1985, Walker et al 2019. In summary, we obtained consistent results in our phylogenetic analyses based on the complete cp genomes and protein-coding sequences, which makes our conclusions more reliable and convincing.…”

“…wabuensis with 100% bootstrap support, as also previously indicated (Lan et al 2018). Previous studies have suggested different topologies for the Liliaceae family, plausibly because of actual conflicting signals from methods or models (Hutchinson 1959, Cronquist 1981, Dahlgren et al 1985, Walker et al 2019. 6, Supplementary material Appendix 1 Fig.…”

Insights into chloroplast genome variation across Opuntioideae (Cactaceae)

“…Eight of the top 10 markers are more than 900 bp, indicating that longer genes are superior for phylogeny reconstruction, as previous suggested by Walker et al (2019), although they may require internal primer designing for complete Sanger's sequencing. A list of the top 10 markers with less than 900 bp is reported (Table S5), and primer pair design for the top five is provided in Table 4.…”

“…Gonçalves et al (2019) emphasized the importance of considering variation in phylogenetic signal across plastid genes and the exploration of plastome data to increase accuracy of estimating relationships; they also revealed that phylogenies inferred with multispecies coalescent (MSC) methods are accurate with plastome matrices and should be considered in future phylogenomic investigations. Walker et al (2019) highlighted that most genes are largely uninformative and are unlikely to misguide plant systematics. However, the concatenating of plastid genes without some level of scrutiny can mislead branch length estimation .…”

“…The main explanations include systematic errors (e.g. poor modeling, stochastic events) or more biologically meaningful processes, such as heteroplasmic recombination that have been invoked to explain discordance in disparate plant clades (Huang et al 2001;Marshall et al 2001;Bouillé et al 2011;Walker et al 2019).…”