Molecular phylogenetic study of Peperomia (Piperaceae) in the Pacific
Citation: Lim, J.Y., Marshall, C.R., Zimmer, E.A. & Wagner, W.L. (in prep) Parallel radiations of peppers (Peperomia, Piperaceae) on the Hawaiian Islands suggest role of ecological release in island biotic assembly.
Step 1: Reference mapping to Piper chloroplast genome (referenceAssembly.sh)
- Adapter trimming using
Trimmomatic - Index the reference genome using
bowtie2(http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#indexing-a-reference-genome) - Mapping to reference genome using
bowtie2 - Evaluating coverage of chloroplast genomes
Step 2: Extract out chloroplast genes using reference annotations
- Multiple sequence alignment using MAFFT, and then BLAT reference sequences of protein-coding genes back to the alignment (
extractAnnotation.py) - Using BLAT annotations, individual locus alignments are parsed out into separate alignment files (
extractLoci.R) - Concatenate and generate a partition file (
concatenateLoci.py)
Step 3: Phylogeny estimation using IQ-TREE
- Step was done in CIPRES (https://www.phylo.org/portal2/)
Step 4: Divergence time estimation of Piperales (fossilBD.rev)
- Bayesian relaxed clock (uncorrelated log-normal) and fossilized birth-death models
- Includes 11 fossil tip constraints
Step 5: Divergence time estimation using non-parametric rate smoothing
- Summarize the maximum a posteriori and maximum clade credibility tree from posterior distribution of trees (
summarizeFossilBD.Rev) - Non-parametric rate smoothing implemented in
TreePL(runTreePL.py) - Randomly samples Peperomia-Piper divergence times from the posterior distribution of fossilized birth death trees (see Step 4)
- Used as a fixed root constraint in
TreePL
plotPhylo.R: Plots phylogeny and maps biogeographic regions onto phylogenyplotPacificMap.R: Recenters worldmap over the Pacific, and reprojects in the Mollweide (equal-area) projection (https://en.wikipedia.org/wiki/Mollweide_projection)