gl.report.heterozygosity number of individuals with decimal numbers

[Audrey Wong]

Hello team,

This is my first time using dartR and everything has been great! I am currently working on some fish data, and I just have a small question on the number of indivuals (n.Ind) in the output of gl.report.heterozygosity.

So to start with, after filtering, I confirmed I have 116 individuals under Western Tasmania here:

> table(pop(glhet3h3)) Eastern Bass Strait Eastern Tasmania Western Tasmania 43 14 116

I then run gl.report.heteroygosity and below is my output:

> gl.report.heterozygosity(glhet3h3) #0.300 Starting gl.report.heterozygosity Processing genlight object with SNP data Calculating Observed Heterozygosities, averaged across loci, for each population Calculating Expected Heterozygosities pop n.Ind n.Loc n.Loc.adj polyLoc monoLoc Eastern Bass Strait Eastern Bass Strait 42.52474 6104 1 5940 164 Eastern Tasmania Eastern Tasmania 13.85747 6104 1 5029 1075 Western Tasmania Western Tasmania 114.81520 6104 1 6103 1 all_NALoc Ho HoSD HoSE HoLCI HoHCI Ho.adj Ho.adjSD Eastern Bass Strait 0 0.189252 0.148828 0.001905 NA NA 0.189252 0.148828 Eastern Tasmania 0 0.190525 0.171060 0.002189 NA NA 0.190525 0.171060 Western Tasmania 0 0.196284 0.147378 0.001886 NA NA 0.196284 0.147378 Ho.adjSE Ho.adjLCI Ho.adjHCI He HeSD HeSE HeLCI Eastern Bass Strait 0.001905 NA NA 0.223062 0.164145 0.002101 NA Eastern Tasmania 0.002189 NA NA 0.217260 0.169943 0.002175 NA Western Tasmania 0.001886 NA NA 0.226854 0.160605 0.002056 NA HeHCI uHe uHeSD uHeSE uHeLCI uHeHCI He.adj He.adjSD Eastern Bass Strait NA 0.225716 0.166098 0.002126 NA NA 0.223062 0.164145 Eastern Tasmania NA 0.225392 0.176304 0.002257 NA NA 0.217260 0.169943 Western Tasmania NA 0.227847 0.161308 0.002065 NA NA 0.226854 0.160605 He.adjSE He.adjLCI He.adjHCI FIS FISSD FISSE FISLCI Eastern Bass Strait 0.002101 NA NA 0.143427 0.239253 0.003062 NA Eastern Tasmania 0.002175 NA NA 0.132162 0.308331 0.003946 NA Western Tasmania 0.002056 NA NA 0.141854 0.183965 0.002355 NA FISHCI Eastern Bass Strait NA Eastern Tasmania NA Western Tasmania NA

I have also attached the graph output.

I am confused as to why the number of individuals would come out in decimal numbers and also one individual was missing from the Western Tasmania group? Thank you!

Best regards,

Audrey Wong

[Jose Luis Mijangos]

Hi Audrey,

Thank you for your question, and welcome to dartR.

The n.Ind column is not the total number of individuals in each population. Instead, it shows the average number of individuals successfully genotyped per locus within that population.

For example, if an individual has missing data at a particular locus, that individual is not counted for that locus. Because the number of successfully genotyped individuals can vary slightly among loci, the average across all loci may be slightly lower than the total sample size and may therefore include decimals.

So, your Western Tasmania group still contains all 116 individuals, but on average 114.8 individuals have genotype data at any given locus. This average is used as the denominator when calculating heterozygosity.

We realised this was not explained clearly enough in the function documentation, so we have now updated it. Thanks for bringing it to our attention.

Cheers,
Luis

[Audrey Wong]

Hi Luis,

Thank you for your reply! That makes a lot of sense and does clear up the confusion. All the best to the team!

Cheers,

Audrey

[Renee Catullo]

Hi Audrey,

Just noticing that you have both variable and large sample sizes, which strongly affect the comparability of heterozygosity estimates. You’ll need to call SNPs on similar numbers and then do heterozygosity estimates for them to be solid.

Cheers,

Renee

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[Audrey Wong]

Hi Renee,

Thanks for the comment! Unfortunately that's all I have to work on, I will take a note of that.

Cheers,

Audrey