Hi I am using both ND2 and Cyt b as two genetic markers to study pop.genetics and phylogeny of a seabird subspecies complex. the samples were collected from 1: Libya, 2: Red Sea, 3:Bahrain with only one consensus sequence from GenBank belonging to Australian subspecies.
I need to calculate genetic distances, I did that using MEGA, but in my report, shall I include both tables and trees from the two markers?
My dataset is not complete (i.e. some samples were amplified for ND2 but not for Cyt b), shall I include all contigs in the ananlysis or I only include samples amplified by both markers? I lose this way many haplotypes identified by using all contigs.
How to calculate allele frequency and how to evaluate genetic evidence for population size changes
Hope to hear from you soon
A hmz
Your question is a little difficult to address since you have multiple components -- what have you tried so far?
I personally don't trust MEGA, so I would (at least) use two different platforms (methods also) to calculate your genetic differences. Whether you show both trees and tables are constrained on how you are communicating your data. For example you can show trees in the paper and tables in the supplemental materials section of your report. This depends on lots of factors.
Again, if your data set is not complete it can be difficult to assess how to communicate your data -- this should be something you discuss with your collaborators.
What attempts have you made to calculate allele frequency or evaluate population size changes?
Please consider editing your question to clarify and help us address your research problems. Thanks!
I have aligned my contigs, then selected samples that were amplified for both genes, ended up with about 5-10 contigs for each population. Then I run DNAsp to check for haplotype diversity and types at each population (no. of haplotypes is greater using all samples, i.e. without excluding samples that have no similar amplification in the second gene. Then I have used MEGA to build trees using 1000 bootstrap and default conditions, resulting two trees per gene, ML and NJ.
My question originally is simple, is the current subspecies classification is valid or the species can be considered as one, especially as the morphological features differs each population are almost not exist. from trees it appears that there is no pattern in clustering of individuals based on population geopgraphic location, except in few individuals that merely having similar sequences then clustered toghther.
I want to know how to determine if my birds belongs to one or several populations. Distance table interpretation is a bit hard to understand for me, as I am new on these issues.
thanks for any advise
My complete guess, but Fst could be a good measure in this case. (Negative Fst values indicate that intra population variation is more than inter population variation). Secondly you can check the software dadi (https://bitbucket.org/gutenkunstlab/dadi ) which infers demographic history and gene flow between populations. Also DNAsp also seems to do tests for "Gene Flow and Genetic Differentiation".