Is anyone aware of a rarefaction approach (to account for unequal sample sizes) similar to that implemented for allelic richness in ADZE that can be used for haplotype and nucleotide diversity?
Dear Peter,
We have recently used a rarefaction analysis. We focused on 2 levels: 1) rarefaction curves based on individuals per population (individual based) and 2) population-based species accumulation curves (Gotelli and Colwell 2001, Ecol. Lett. 4:379-391). For rarefaction curves based on individuals the procedure of Chao and Jost (2012) was used as implemented in the R “iNEXT” package (Hsieh et al. 2016; http://chao.stat.nthu.edu.tw/wordpress/software_download/inext-online/). Analyses are performed with X randomizations and extrapolating to X individuals that represented a little more than the total number of individuals sampled in this study. For population-based rarefaction curves, computations were performed in EstimateS version 9.0 (Colwell 2013; Available from: http://purl.oclc.org/estimates) using X replications and extrapolating to X populations that represent the all of the localities sampled in this study.
Does this make sense?
Best
Juan Francisco Ornelas
Hi Peter,
I used the "rarefy" function in the R package "vegan". Each column was a population (or sample site) and in the rows I replace species by haplotypes. However, this rarefaction curve represents the haplotype richness and not haplotype diversity.
I plot the results using the "ggplot2" and the "multiplot" function (http://www.cookbook-r.com/Graphs/Multiple_graphs_on_one_page_(ggplot2)/). I have attached a plot (from Seixas et al. 2018) and its script.
Best,
Victor
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