A reappraisal of chloroplast genetic SNPs in phylogeny and barcoding of Pteris species (genus Pteris L.): Multispecies coalescence analysis, ancient hybridization, and deep coalescence

The genus Pteris L. (Pteridaceae) is one of the largest fern genera, comprising about 200 to 250 species distributed globally. There is ongoing debate regarding species classification and phylogeny within Pteris, as phylogenetic studies have revealed incongruences between trees constructed from various genetic regions. To address this, we conducted a multispecies coalescence analysis of matK and rbcL sequences using publicly available data, aiming to identify genetic regions suitable for phylogenetic analysis and molecular barcoding of Pteris. We employed methods such as STAR-BEAST and contained gene coalescence analyses for phylogenetic reconstruction, as well as redundancy analysis (RDA) and latent factor mixed model analysis to pinpoint biologically significant SNPs.

Our study highlights phylogenetic relationships among Pteris species based on chloroplast DNA sequences, revealing discordance between matK and rbcL. Findings indicated deep coalescence and incomplete lineage sorting (ILS) within the genus. Both D-statistics and admixture analyses showed evidence of genetic admixture and introgression. Notably, matK sequences demonstrated higher success in species delineation than rbcL, with combined data enhancing taxonomic resolution and indicating the role of SNPs in adaptations to local environments. Additionally, species delineation analyses using the GMYC and ASAP methods revealed congruent results, with most species clustering closely, although a few exceptions were observed. The use of concatenated DNA sequences successfully delineated sections within Pteris, highlighting the taxonomic utility of these markers. Divergence time estimation from the concatenated sequences indicated a deep evolutionary history for P. tremula, with the majority of species diverging more recently within the past 1 to 15 million years, further supporting rapid speciation within the genus.