I wonder if it is possible to infer the origin of invasive lineages based on genetic data for many native and invasive populations. I first planned to use DIYABC v2.1.0, but I am not used to Genepop file format and information on input formatting of DNA sequence is scarce. Does it work with >300bp loci? Is triploidy a problem? Is there an easy way to convert FASTA data into genepop data? (Knowing that widgetcon does not handle DNA data for genepop format) Is DIYABC still used (last release in 2015) or are there better options for now? Thanks for any answer.
Are the structure signals between the lineages clear?
- DIY-ABC is a very feasible option, still used - One option may be using the pipeline "snp-sites" to extract variable loci, obtain a .vcf file and then (with PGDSpider software) transform it to Genepop format. Article SNP-sites: rapid efficient extraction of SNPs from multi-FAS...
- Check out the PGDSpider manual. Maybe there is a way to transform from your multi-FASTA alignment to Genepop directly.
*triploidy may be an issue.
Good luck!
Thank you for this answer!
I did not run a Structure analysis; to my knowledge, this software is also designed for microsatellite data only. Am I wrong, is it doable with DNA sequence data? I quickly checked the manual again, and found nothing about this.
I have checked the PGDSpider manual (thanks for the advice), it seems it can handle both FASTA and Genepop format but the Genepop format is not suitable with DNA data (if I well understand the table pages 24-25, this is thus the same problem than with widgetcon). Direct conversion really seems an issue.
I will definitely try this SNP extraction with SNP-sites, thanks again for the tip! I hope triploidy would not be a major issue, and I also hope the SNP format ouput PGDSpider would be close to the required input in DIYABC, as this format also seems like an "non-original extended and adapted format".
I can keep you posted of the result if interested.
Have a nice day.
Great, I hope everything goes well with snp-sites.
If you can obtain the .vcf file, take a look in both these resources, they may help you to analyze your data in terms of structure: https://grunwaldlab.github.io/Population_Genetics_in_R/TOC.html https://popgen.nescent.org/index.html
From my experiences, after having a .vcf, and with the help of PGDSpider, you can go for many different analyzes.
Good luck and sure, tell me how everything is going.
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