A time and a place for everything: phylogenetic history and geography as joint predictors of oak plastome phylogeny.

Journal Article

Owing to high rates of introgressive hybridization, the plastid genome is poorly suited to fine-scale DNA barcoding and phylogenetic studies of the oak genus (Quercus, Fagaceae). At the tips of the oak plastome phylogeny, recent gene migration and reticulation generally cause topology to reflect geographic structure, while deeper branches reflect lineage divergence. In this study, we quantify the simple and partial effects of geographic proximity and nucleome-inferred phylogenetic history on oak plastome phylogeny at different evolutionary scales. Our study compares pairwise phylogenetic distances based on complete plastome sequences, pairwise phylogenetic distances from nuclear restriction site-associated DNA sequences (RADseq), and pairwise geographic distances for 34 individuals of the white oak clade representing 24 North American and Eurasian species. Within the North American white oak clade alone, phylogenetic history has essentially no effect on plastome variation, while geography explains 11%-21% of plastome phylogenetic variance. However, across multiple continents and clades, phylogeny predicts 30%-41% of plastome variation, geography 3%-41%. Tipwise attenuation of phylogenetic informativeness in the plastome means that in practical terms, plastome data has little use in solving phylogenetic questions, but can still be a useful barcoding or phylogenetic marker for resolving questions among major clades.

Full Text

Duke Authors

Cited Authors

  • Pham, KK; Hipp, AL; Manos, PS; Cronn, RC

Published Date

  • September 2017

Published In

Volume / Issue

  • 60 / 9

Start / End Page

  • 720 - 732

PubMed ID

  • 28445658

Electronic International Standard Serial Number (EISSN)

  • 1480-3321

International Standard Serial Number (ISSN)

  • 0831-2796

Digital Object Identifier (DOI)

  • 10.1139/gen-2016-0191

Language

  • eng