Multilocus phylogenetics of Pinus subsection Ponderosae using the Hyb-Seq method

Background: Hyb-Seq combines solution hybridization based target enrichment and genome skimming for the study of plant phylogenetics and evolution, including the detection of incomplete lineage sorting and hybridization. Questions: What are the relationships among the principal lineages of Pinus subsection Ponderosae in Mexico? Studied species: Pinus subsection Ponderosae. Study sites and dates: Mexico, Guatemala, and the United States, 2015-2025. Methods: We assembled sequences of low copy nuclear loci and plastomes to compare phylogenetic results between the two genomic compartments. Parsimony and maximum likelihood were used to infer trees for both datasets, and the coalescent method ASTRAL was used for the nuclear sequences. Results: Strict alignment selection criteria, including exclusion of putative paralogs and manual editing of alignments, resulted in less homoplasy and slightly better correspondence to morphology compared to a dataset subject to relaxed filtering. ASTRAL and concatenated analyses recovered the same main clades for the nuclear loci. There were some striking discordances between the nuclear and plastid trees in the placement of specific individuals. Conclusions: The nuclear and plastid trees corroborated previous studies in recovering subsection Ponderosae as monophyletic with high branch support. Branch lengths separating Mexican taxa were relatively short, and support values in the nuclear coalescent trees were low, consistent with rapid speciation. Instances of cytonuclear discordance in the Hyb-Seq data were consistent with plastid capture, but more work is needed to disentangle homoplasy, incomplete lineage sorting, and reticulation.