How to ID clonal thresholds within large database across species

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Kerin Law

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Oct 9, 2023, 6:50:20 PM10/9/23
to poppr
Hi Zhian,

I have a genomic database of thousands of samples across a species. Within the database are a handful of populations of individuals that are clonal cuttings of certain genotypes, some populations that are full siblings to each other and some populations that are half-siblings to each other. The rest (and majority) of the database are considered unrelated random individuals collected from across the species. 

I am trying to identify the clonal threshold in the database to determine if two randomly chosen samples are compared to each other, I can reliably identify them as clonal. 

The input data is a vcf with thousands of SNPs per individual, thousands of individuals. 

I am stumped on the correct approach here based on how poppr functions. I think the approach should be turn the vcf into a genclone object, isolate the clonal populations only into its own genclone object from the rest of the database, and do mlgfilter and then cutoff predictor on the clonal populations to identify the clonal threshold? 

Lastly, is removing the rest of the database when trying to identify a cutoff biasing results in some way? 

Thank you for your time,

Kerin

Zhian Kamvar

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Nov 11, 2023, 3:30:27 PM11/11/23
to Kerin Law, poppr
Hi Kerin,

I think the approach should be turn the vcf into a genclone object, isolate the clonal populations only into its own genclone object from the rest of the database, and do mlgfilter and then cutoff predictor on the clonal populations to identify the clonal threshold? 

Instead of a genclone, you might want to use a snpclone object (if you do want a genclone, be sure you use return.alleles = TRUE when you convert from VCF). 

Beyond that, I'm afraid there's not much I can offer in the way of advice other than to read https://onlinelibrary.wiley.com/doi/full/10.1111/j.1365-294X.2007.03535.x for some information about how to handle clonal organisms. I have been out of this field for several years and I guarantee there is more up-to-date literature on this.

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