Whole genome resequencing sample size for population genetics?

Question

[Dylan]

Hi everyone,

I'm a master's student, and I'm currently considering using whole genome resequencing to obtain SNP data for an endangered species for population genetics analysis. However, I'm unsure about the minimum sample size I should choose, and no one in my research group has experience with this approach. Below is a brief summary of the analyses I want to conduct:

1. Genetic diversity
2. Genetic structure
3. Current and historical effective population size (Ne)
4. Isolation by distance (IBD) and EEMS (Estimated Effective Migration Surfaces)

Could anyone provide guidance on what sample size or strategy would be appropriate for these analyses? Any advice would be greatly appreciated.

Thank you!

Answer 1

[dthorbur]

More samples and is always nice, as is sequencing to a good depth, but there are a lot of other factors to consider.

Just off the top of my head, here are some other considerations that will need to be discussed before you can decide on number of samples:

1. Do you have an idea of the genome size/complexity?
2. How many populations are you aiming on sampling?
3. What sequencing method/platform is available to you?
4. Are you outsourcing or doing the library prep yourself?
5. What genomic resources are available for this species?
6. What is your budget?

I'm sure there are a few more considerations I'm missing too. We once sequenced 10 population pairs with only 6 individuals in each at a reasonable depth, and it was a nice dataset, but only having 6 individuals in each population limited the analyses we ended up publishing because reviewers disagreed we had the necessary power to report some findings.

Ultimately, you should be discussing this with the PI. They are meant to be there to support you.