I was running a clonal analysis on a rare plant species endemic to Florida.. Initial results showed high levels of clonality within the samples collected for clonal analysis. We wanted to see how common clonality is by extending the study to the other population samples collected.
I got the following error when running the distance matrix...
Error in bitwise.dist(Glight) :
min(ploidy(x)) == max(ploidy(x)) is not TRUE
When I googled this error I found that our data set has individuals with varying ploidies in your data and bitwise.dist().So it means different individuals within the same population have varying ploidy levels? I got this error with many of the populations.
I would like to hear suggestions and any Rcoding SNP data to show ploidy levels in a population.
Thanks.
You could karyotype them in the lab easily without expensive NGS.
V. Negrón‐Ortiz Please, read Margarido, Gabriel RA, and David Heckerman. "ConPADE: genome assembly ploidy estimation from next-generation sequencing data." PLoS computational biology 11.4 (2015): e1004229.
You may have already figured this out, but in case you haven't, one possible option is to use genome-wide estimates of heterozygosity to estimate ploidy. I don't know if allo or auto polyploidy may affect this approach
Take a look at:
Goad et al. (2021) Hybridization, polyploidy and clonality influence geographic patterns of diversity and salt tolerance in the model halophyte seashore paspalum (Paspalum vaginatum), Molecular Ecology, 30
In this paper, they used genome-wide estimates of heterozygosity calculated as the individual inbreeding coefficient (F) using the het function in plink. They did some flow to validate the ploidy estimates
They also cite the following paper, which may be of use:
Gompert, Z., & Mock, K. E. (2017). Detection of individual ploidy levels with genotyping-bysequencing (GBS) analysis. Molecular Ecology Resources, 17(6), 1156–1167. doi: 10.1111/1755-0998.12657
Poppr does not call ploidy level for you (or at least, it shouldn't), so this may just mean your input format is wrong.
Depending on what NGS data you have available, there are many ways to infer ploidy level, including the methods mentioned by Christy Edwards above. Before SNP calling, the two most popular approaches are kmer-based (Smudgeplot or Tetmer) or site-based heterozygosity (with reference genome: nQuire, without reference genome: ploidyfrost).
Smudgeplot: https://github.com/KamilSJaron/smudgeplot
Tetmer: https://github.com/hannesbecher/shiny-k-mers
nQuire: https://github.com/clwgg/nQuire
ploidyfrost: https://doi.org/10.1111/1755-0998.13720
None of these methods are perfect, but they would be able to help you identify if your samples are a single ploidy level vs mixed ploidy level. (We have an improved site-based approach in the works)
If you do have polyploids, you should check out this recently published paper on pop gen analysis in partially clonal and selfed polyploids: doi.org/10.22541/au.166996062.20159219/v1
Thanks so much for various recommendations, Christine and Michelle. Very helpful, indeed.
Hello there. Thank you very much. Of course we will use it! I am proud to work in partnership.
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