Hello, collegues
I'm analyzing genetic data of a perennial alpine plant. I collected samples from 14 location and genotyped them using ~103 biallelic SNPs. But I am confused that I have got a summary of the H metrics where Ho>He. See the picture attached. Could anyone help me to tell me the reason? Thanks
It means your population is breaking one of the assumptions of your model. So, if you expected level of heterozygosity is based on Hardy-Weinberg genetics (large population, random breeding, no population substructure, etc.) it means that your plants are not following all of these parameters. For example, if you had two isolated populations that were each homozygous for different alleles that just recently starter interbreeding, then you will see higher than expected heterozygosity. Are there any self-incompatible loci in these plants? It's fairly common for plants to avoid self-fertizilation by making self-pollen incompatible with pollen germination.
I am not a plant specialist but this He / Ho difference looks huge to me.... Self-incompatible loci should be an explanation, but I would check also on the genotyping and data processing to unsure that they have not been any mistake...
Regarding of the polymorphism information content values in the table i think that the analyzed sample content probably equal allele frequencies. For any given number of alleles, the expected heterozygosity is highest when the all the allele frequencies are equal.
observed reslts indicate severe effects of small population sizes (population bottlenecks or metapopulation dynamics that severely reduced the level of genetic variation relative to that expected). High heterozygosity means lots of genetic variability. Low heterozygosity means little genetic variability. Often, we will compare the observed level of heterozygosity to what we expect under Hardy-Weinberg equilibrium (HWE). If the observed heterozygosity is lower than expected, we seek to attribute the discrepancy to forces such as inbreeding. If heterozygosity is higher than expected, we might suspect an isolate-breaking effect (the mixing of two previously isolated populations).
Interesting question. I am sure that you studied literature but on every case:
http://www.molecularecologist.com/2015/04/clonal-conundrum-part-deux/
Article Heterozygote excess in a self-incompatible and partially clo...
your calling polyploid variants at a lower ploidy. There is no way you could observe heterozygousity of close to one. I called snp for russian thistle with a diploid caller and got many markers with close to one heterozygousity, switching to freebayes with ploidy set to 4 fixed this.
Use a root squash or flow cytommetry to verify your ploidy.
This discussion also helped me to understand the population I am working. I have got similar higher heterozygosity value compared to the homozygous and also -ve Fst. Thank you.
Katie A S Burnette is absolutely right. The HWE seems not met in this case.
May the content of the analyzed sample have equal allele frequencies. For any given number of alleles, the expected heterozygosity is highest when all the allele frequencies are equal.
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