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Dryad

Untying the Gordian Knot of plastid phylogenomic conflict: a case from ferns

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Dec 17, 2021 version files 18.68 MB

Abstract

Phylogenomic studies based on plastid genome have resolved the recalcitrant relationships among various plants, yet the phylogeny of Dennstaedtiaceae at the taxonomic level remains unresolved due to conflicting plastid genes, limited molecular data and incomplete taxon sampling of previous studies. The present study generated 31 new plastid genomes of Dennstaedtiaceae (9 genera, 30 species) and combined 41 publicly available sequences of plastid genome (including 24 families, 26 genera, 41 species) to solve and explore the evolution of Dennstaedtiaceae. In order to minimize the impact of systematic errors on the resolution of phylogenetic inference, we applied six strategies to generate 30 datasets based on CDS, Spacer, and All datasets, and two tree inference methods (maximum-likelihood, ML; and multispecies coalescent, MSC) to comprehensively analyze the plastome-scale data. Besides, the phylogenetic signal among all loci was quantified for the controversial node using the ML framework, and the phylogenetic hypotheses among all datasets were tested. In the species tree based on different data sets and methods, obvious conflicts were detected at the base of the polypod ferns. Meanwhile, the topology of the “CDS-codon-align-rm3” (CDS removed the third codon) matrix was selected as the primary reference or summary tree due to its analysis results are consistent, and similar to the topological structure of the amino-acid matrix. The final phylogenetic tree supported Dennstaedtiaceae as the sister group to eupolypods, and Dennstaedtia (sen. lat.) can divided into smaller genera, which was also supported by geographical distribution and plastid structure. This robust reconstructed phylogenetic backbone established a framework for future studies on Dennstaedtiaceae classification, evolution and diversification. The present study suggests considering plastid phylogenomic conflict when using plastid genomes. From our results, reducing saturated genes or sites can effectively mitigate the tree conflicts of distantly related taxa. Moreover, amino acid sequences may verify the accuracy of nucleotide-based phylogeny.