clone-correction question
Chiara Pedrazzini
Dear Zhian,
I am sorry to bother you, and maybe my question is naive and I should read the literature better, in which case sorry. However, I am a bit confused regarding clone-correction.
I have 2 datasets for 2 species of ascomycota fungus (239 isolates of B. brongniartii and 397 isolates of B. pseudobassiana), haploid and with asexual (hence clonal) reproduction. SNPs were obtained by ddRADseq and Illumina sequencing. I have 87 and 1092 SNPs in the 2 species, respectively.
The aim of my research is to explore if there is genetic structure in the populations and if this is influenced by the geographical component (we collected samples from different areas in Europe). What I thought I would do was to try the analyses with clone-corrected data (based on mlg.filter) and without correction, for index of association, AMOVA and genotypic diversity.
Here comes my question, I'm a bit confused about clone-correction:
1. Why is clone-correction necessary?
2. I was thinking of indicating in the paper that the analyses were carried out with clone and not clone corrected date. is it advisable to show all the results? For Ia and AMOVA it doesn't change anything...
3. Regarding genotypic diversity, eveness and richness; do you recommend to present the data with clone-correction or not? Because here I have quite different values..
Sorry for all the questions!
Have a nice day and best,
Chiara