pebgroup / dypsidinae_species_tree

Reconstructing the species tree of palm subtribe Dypsidinae using the target capture loci of Heyduk et al. 2016 (doi: 10.1111/bij.12551)

Analysis of Dypsidinae target capture data

Wolf Eiserhardt ([email protected])

Overview

This analysis of subtribe Dypsidinae was conducted at two levels:

1. A broad-scale, thinly sampled analysis of tribe Areceae to establish monophyly of subtribe Dypsidinae and identify one or several closely related subtribes/genera to be used as outgroups in the following species-level analysis. This analysis uses the PhyloPalms baits of Loiseau et al. (2019).

A description of the pipeline for this analysis can be found here.

2. A narrower, species-level analysis of subtribe Dypsidinae plus Loxococcus rupicola (Thwaites) H.Wendl. & Drude as an outgroup. This analysis uses the palm baits of Heyduk et al. 2016.

A description of the pipeline for this analysis can be found here.

Disclaimer

The purpose of this repository is documenting the analyses behind the below manuscript. Think extended Materials & Methods. This is neither a pipeline, nor is it supposed to run with other datasets or on other machines. You are welcome to use any of this for your own purposes, but please do not expect it to work without issues, or get any help.

Associated manuscript

Eiserhardt WL, Bellot S, Cowan RS, Dransfield J, Hansen LESF, Heyduk K, Rabarijaona RN, Rakotoarinivo M & Baker WJ (in prep.): Phylogenomics and generic limits of Dypsidinae (Arecaceae), the largest palm radiation in Madagascar.