Plastome based phylogenetics and younger crown node age in Pelargonium

Sara J van de Kerke; Bikash Shrestha; Tracey A Ruhlman; Mao-Lun Weng; Robert K Jansen; Cynthia S Jones; Carl D Schlichting; Samin Hosseini; Setareh Mohammadin; M Eric Schranz; Freek T Bakker

doi:10.1016/j.ympev.2019.03.021

Plastome based phylogenetics and younger crown node age in Pelargonium

Mol Phylogenet Evol. 2019 Aug:137:33-43. doi: 10.1016/j.ympev.2019.03.021. Epub 2019 Mar 26.

Authors

Affiliations

¹ Biosystematics, Plant Science Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands. Electronic address: sara.vandekerke@wur.nl.
² Department of Integrative Biology, University of Texas at Austin, 205 W. 24th St. Stop C0930, TX 78712, USA.
³ Department of Integrative Biology, University of Texas at Austin, 205 W. 24th St. Stop C0930, TX 78712, USA; Department of Biology, Westfield State University, Westfield, MA 01086, USA.
⁴ Department of Integrative Biology, University of Texas at Austin, 205 W. 24th St. Stop C0930, TX 78712, USA; Department of Biological Sciences, Faculty of Science, King Abdulaziz University, P.O. Box 80141, Jeddah 21589, Saudi Arabia.
⁵ Department of Ecology & Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, Storrs, CT 06269, USA.
⁶ Biosystematics, Plant Science Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands; Department of Plant Protection, College of Agriculture, Vali- e-Asr University of Rafsanjan, Rafsanjan, Iran.
⁷ Biosystematics, Plant Science Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands.
⁸ Biosystematics, Plant Science Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands. Electronic address: freek.bakker@wur.nl.

PMID: 30926482
DOI: 10.1016/j.ympev.2019.03.021

Abstract

The predominantly South-African plant genus Pelargonium L'Hér. (Geraniaceae) displays remarkable morphological diversity, several basic chromosome numbers as well as high levels of organelle genomic rearrangements, and represents the 7th largest Cape Floristic Region clade. In this study, we reconstructed a phylogenetic tree based on 74 plastome exons and nuclear rDNA ITS regions for 120 species, which represents 43% taxon coverage for Pelargonium. We also performed a dating analysis to examine the timing of the major radiations in the genus. Phylogenetic analyses of nucleotide, amino acid, and ITS alignments confirmed the previously-documented subgeneric split into five main clades ((C1,C2),(B(A1,A2))) although clade only A1 received low bootstrap support. Using calibration evidence from a range of sources the Pelargonium crown age was estimated to be 9.7 My old, much younger than previous estimates for the genus but similar to recent studies of other Cape Floristic lineages that are part of both Fynbos and Succulent Karoo biomes.

Keywords: Geraniaceae; Pelargonium; Phylogeny; Plastome; Time-calibrated.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Calibration
Genetic Variation
Genome, Plastid*
Likelihood Functions
Pelargonium / genetics*
Pelargonium / growth & development*
Phylogeny*
Time Factors