Oral Paper

         Phylogenomics

Phylogenetics and species delimitation of the Pinus Oocarpae clade using low copy nuclear genes

Presenting Author
David Gernandt
Description
Pinus is a wind-pollinated, long-lived genus that includes many species long generation times, weak reproductive barriers, and large population sizes. Several North American pine clades have evolved since the Oligocene or Miocene. Consequently, slow coalescence and high interspecific gene flow have been important in shaping their genomes. The Oocarpae clade (Pinus subgenus Pinus, section Trifoliae) comprises 18 taxa classified in 16 species distributed from the southwestern United States to Central America, with its main diversity in Mexico. We inferred phylogenetic relationships for multiple individuals per taxon of the Oocarpae based on >500 low copy nuclear loci recovered using target enrichment. Maximum likelihood and the coalescent method ASTRAL gave results that were largely congruent, although there were important points of discordance with plastid-based trees and a phylogenetic study of Pinus based on transcriptome sequences. We explored the levels of nuclear discordance, evidence for reticulation, and the use of the multispecies coalescent to delimit species.