Is phylogenetic diversity any better than richness or Shannon diversity? (CC210)
Channel: Riffomonas Project
Date: 2022-05-05

Phylogenetic diversity is an approach to quantifying alpha diversity based on a phylogenetic tree generated from sequences. But is it much different from traditional alpha diversity metrics like richness or Shannon diversity? In this Code Club, Pat will use R to quantify the difference between these metrics using the same tools. He'll answer the question using data generated with mothur and R functions from vegan, dplyr, and ggplot2.

You can find my blog post for this episode at https://www.riffomonas.org/code_club/2022-05-05-phylogenetic-diversity. The data were generated in our Kozich et al. 2013 paper (http://doi.org/10.1128/AEM.01043-13) using samples from the Schloss et al. 2012 paper (http://doi.org/10.4161/gmic.21008).

#microbiome #tidyverse #vegan #R #Rstudio #Rstats #ggplot2

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Microbial ecology data: https://www.riffomonas.org/minimalR/
General data: https://www.riffomonas.org/generalR/

0:00 Introduction
2:36 Getting rarefied phylogenetic diversity
5:03 Generating rarefied richness
7:58 Generating rarefied Shannon diversity
11:33 Comparing alpha diversity metrics
14:32 Measuring correlation between metrics