Untying the Gordian knot of plastid phylogenomic conflict: A case from ferns

Ting Wang; Ting-Zhang Li; Si-Si Chen; Tuo Yang; Jiang-Ping Shu; Yu-Nong Mu; Kang-Lin Wang; Jian-Bing Chen; Jian-Ying Xiang; Yue-Hong Yan

doi:10.3389/fpls.2022.918155

Untying the Gordian knot of plastid phylogenomic conflict: A case from ferns

Front Plant Sci. 2022 Nov 24:13:918155. doi: 10.3389/fpls.2022.918155. eCollection 2022.

Authors

Ting Wang^{1

2}, Ting-Zhang Li^{1

2}, Si-Si Chen¹, Tuo Yang¹, Jiang-Ping Shu¹, Yu-Nong Mu³, Kang-Lin Wang⁴, Jian-Bing Chen¹, Jian-Ying Xiang⁵, Yue-Hong Yan^{1

3}

Affiliations

¹ Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China.
² College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China.
³ Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China.
⁴ Green Development Institute, Southwest Forestry University, Kunming, China.
⁵ Yunnan Academy of Biodiversity, Southwest Forestry University, Kunming, China.

Abstract

Phylogenomic studies based on plastid genome have resolved recalcitrant relationships among various plants, yet the phylogeny of Dennstaedtiaceae at the level of family and genera remains unresolved due to conflicting plastid genes, limited molecular data and incomplete taxon sampling of previous studies. The present study generated 30 new plastid genomes of Dennstaedtiaceae (9 genera, 29 species), which were combined with 42 publicly available plastid genomes (including 24 families, 27 genera, 42 species) to 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, intergenic spacers, and whole plastome, 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 controversial nodes using ML framework, and different topologies hypotheses among all datasets were tested. The species trees based on different datasets and methods revealed obvious conflicts at the base of the polypody ferns. The topology of the "CDS-codon-align-rm3" (CDS with the removal of the third codon) matrix was selected as the primary reference or summary tree. The final phylogenetic tree supported Dennstaedtiaceae as the sister group to eupolypods, and Dennstaedtioideae was divided into four clades with full support. This robust reconstructed phylogenetic backbone establishes 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 tree conflicts for distantly related taxa. Moreover, phylogenetic trees based on amino acid sequences can be used as a comparison to verify the confidence of nucleotide-based trees.

Keywords: Pteridineae; gene tree conflict; phylogeny; plastome; slowly evolving genes.