Are single nucleotide polymorphisms (SNPs) robust indicators of evolutionary relatedness in single-celled green algae?

Question

SNPs are very abundant in genomes and are not necessary mutations but variations of specific alleles at specific locus where the high majority of them do not alter protein structure or gene expression. They have been reported to actually account for 90% of variations between unrelated humans. As such, SNPs or SNP groups have been used to understand evolutionary relationships because they are so highly abundant in the genome (1 every 1kb in humans), found in non-coding regions, making then excellent markers for evolutionary studies because relatively stable and also highly variable.

My question is this. Because the offer a robust mechanism to elucidate evolutionary relations, is it possible that for instance if one is doing a study of certain genus and family of single celled green algae, and alignment of a large nucleotide sequence gene is used to build Phylogenetic trees to see species and genus relatedness, would the SNPs THAT ARE NOT USED IN THE ALIGNMENT AND TREE CONTSRUCTION possibly have some effect on the test data SNP where the SNP used in the study may be somehow affected by neighboring SNPs not used in the study. Further, would this putatively unreported mechanisms be any different if the SNP not being used in the study is upstream or downstream of the SNP that affects evolutionary relatedness?

Answer 1

Hey there!

I hope your question is still relevant after a couple of weeks.

You're absolutely right that SNPs are useful in human genomics (it's what services like 23andMe are examining!)... but they're not necessarily the preferred method for undertaking an evolutionary study that might need to involve multiple species. Going from INTRAspecific variation (differences among one species, humans, here) to INTERspecific variation (a whole family, potentially comprised of dozens of specie) is quite a leap.

Much of our molecular data that informs phylogeny is taken from more conserved aspects of an organism, those parts of a genome that are not subject to high variability (such as you understand is the case among different humans, and all our respective SNPs).While you COULD determine phylogeny to some degree of accuracy with SNPs alone, it would likely be better to examine something like this:

https://www.zo.utexas.edu/faculty/antisense/downloadfilestol.html

While SNP data can be good for studying intraspecific variation, other things are better for studying interspecific relationships.

That said,

If you're going about such a thing in the manner you've described, I would not generally imagine that unanalyzed SNPs would have a significant influence on your test strands. They would only potentially affect your proposed study if they were involved in the same pathways as the studied ones, but then again, nto to the effect of your study. I think you have a slight gap between your understanding of how cellular processes work and how genetic analyses might be performed. Let me know if I can clarify anything further.