Phylogenetic studies of New World species in the plant genus Psychotria (Rubiaceae)

Abstract

This dissertation aimed to investigate genetic variation and modes of speciation in the tropical plant genus Psychotria (Rubiaceae), an extremely diverse group comprising an important component of the neo-tropical understory vegetation. Sequence comparison of P. marginata and Coffea arabica plastomes and available transcriptome data were used to develop non-coding sequence markers and perform multi-locus phylogenetic analyses across 19 species of Psychotria and related taxa (Rudgea, Palicourea and Coffea). In the first study, the complete sequence of the P. marginata chloroplast genome was characterized, and non-coding plastid markers were characterized and assessed for level of polymorphism. The second study investigated the species-level relationships of the 19 species using 5 nuclear (ITS, NL-57800, NL-217, NL-103, NL-A04) and 4 plastid (psbE-petL, trnT-psbD, and trnK-rps16 and trnL-trnF) non-coding sequence markers. Maximum-likelihood gene trees for each locus and coalescent species-tree analyses showed significant improvement of bootstrap support for relationships within Psychotria, although relationships towards the tips of the tree were not well supported, presumably due to rapid radiation of neo-tropical Psychotria species. Subgenus-level relationships, as well as the paraphyly of subgenus Heteropsychotria, were well supported in both the gene trees and the species tree, and were also consistent with previous studies. In addition, polyphyletic patterns of P. pilosa and P. allenii haplotypes on the gene trees indicated incomplete lineage sorting and the possibility of a cryptic species complex as a result of rapid evolution. Thus coalescent simulations were performed in the third study to further assess whether the relationships inferred in the gene tree and species tree analyses could be caused solely through random sorting processes under a regionally sympatric speciation model with gene flow between populations. As expected, random sorting after the speciation event could cause polyphyletic haplotypes on gene trees, which made species delimitation difficult, particularly when effective population sizes are large, gene flow is frequent, and divergence time is short. The simulated data in turn supported the hypothesis that P. pilosa is at a stage in the speciation process where sorting of ancestral lineages is not complete, causing haplotypes from different populations to form paraphyletic groups with its sister species, P. cyanococca, in some of the gene trees.