I am designing a study to investigate the population genetic structure of an endangered species. We've decided to go the ddRADSeq route, and I have a few questions for anyone who has experience with this sequencing method and/or population genetics.
My species has a large genome (~2Gb), and because I'm assessing change across the entirety of North America over a span of 100 years, I also have a large sample size (n=480).
In order to maintain a higher level of coverage (25x) while also remaining within the current budget, we can only target 0.25% (5 million bases) of the genome.
I was hoping for some insight on this issue. Although low, is 0.25% (and 5 million bases) of the genome per individual enough to answer questions regarding population genetic structure with that many individuals at that level of coverage? Or would it be prudent to reduce the amount of coverage in order to include more of the genome?
Relevant points: 1. No reference genome for this species, but there is one for a closely related species. 2. Very little is known about this species and no population genetics study has been conducted to compare to.
My species has a large genome (~2Gb), and because I'm assessing change across the entirety of North America over a span of 100 years, I also have a large sample size (n=480).
In order to maintain a higher level of coverage (25x) while also remaining within the current budget, we can only target 0.25% (5 million bases) of the genome.
I was hoping for some insight on this issue. Although low, is 0.25% (and 5 million bases) of the genome per individual enough to answer questions regarding population genetic structure with that many individuals at that level of coverage? Or would it be prudent to reduce the amount of coverage in order to include more of the genome?
Relevant points: 1. No reference genome for this species, but there is one for a closely related species. 2. Very little is known about this species and no population genetics study has been conducted to compare to.
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