Mephesto
07-27-2015, 02:14 PM
Hi to all of you!
I was wondering if I could get some help regarding my scientific work. Its a simple basic population genetics analysis of a single bi alelic locus in humans via RFLP method in wich one allele doesnt have the required SNP mutations so its the ancestral form and it looks like a single band on gel. The other allele has the mutation so its cut in two unequal halves. So it looks like a piece of cake study for someone who has professional ecudation in this topic. However my background is more health science orientated in wich we didnt cover anything beyond the punnett square and the Hardy-Weinber equlibrium lesson.
My goal is to compare my population with some other populations using the ALFRED data base wich harbours the required populations relative freqeuncys of my gene for populations in diferent parts of the world. The problem is I dont know wich particular statistical or population genetic method should I use? I researched and tryed to master population genetics by msyelf so I conducted a reasearch using the following methods and software packages:
Intrapopulation study
Allele and genotype freqeuncy calculation ( Genalex)
Hardy-Weinberg calculation ( Chi square test, Fixation indeks, ) ( Genalex)
Interpopulation study
Pairwise Fst ( Arlequin)
Genetic distance Nei Ds and Dst (Poptreew2)
AMOVA test for computing the Fst inside population groups for diferent parts of the world ( Africa group, Far east Asia group etc. ) ( Alrequin)
Z two sample score test for to see if my european population differs from the other european populations clustered in one big sample.
Neighbour joining tree using Neis genetic distance matrix ( Mega )
PC principal component using frequencys ( PAST3)
Non metric mulidimensional scaling ( PAST3) using frequencys but I am not sure wich distance should I use I used euclidian distance.
Now I am not sure If I could use more statisitcal methods. I can only work with relative frequencys like ( p alele= 0,54 and q alele=0,46 ) I have only raw data for my population ( I know who is a homozygote or heterozygote for a particular allele) but I dont have raw data for other world wide population whome my population is comparing to. I am wondering If I have choosen the right methods and are there any methods wich I could have also used?
I was wondering if I could get some help regarding my scientific work. Its a simple basic population genetics analysis of a single bi alelic locus in humans via RFLP method in wich one allele doesnt have the required SNP mutations so its the ancestral form and it looks like a single band on gel. The other allele has the mutation so its cut in two unequal halves. So it looks like a piece of cake study for someone who has professional ecudation in this topic. However my background is more health science orientated in wich we didnt cover anything beyond the punnett square and the Hardy-Weinber equlibrium lesson.
My goal is to compare my population with some other populations using the ALFRED data base wich harbours the required populations relative freqeuncys of my gene for populations in diferent parts of the world. The problem is I dont know wich particular statistical or population genetic method should I use? I researched and tryed to master population genetics by msyelf so I conducted a reasearch using the following methods and software packages:
Intrapopulation study
Allele and genotype freqeuncy calculation ( Genalex)
Hardy-Weinberg calculation ( Chi square test, Fixation indeks, ) ( Genalex)
Interpopulation study
Pairwise Fst ( Arlequin)
Genetic distance Nei Ds and Dst (Poptreew2)
AMOVA test for computing the Fst inside population groups for diferent parts of the world ( Africa group, Far east Asia group etc. ) ( Alrequin)
Z two sample score test for to see if my european population differs from the other european populations clustered in one big sample.
Neighbour joining tree using Neis genetic distance matrix ( Mega )
PC principal component using frequencys ( PAST3)
Non metric mulidimensional scaling ( PAST3) using frequencys but I am not sure wich distance should I use I used euclidian distance.
Now I am not sure If I could use more statisitcal methods. I can only work with relative frequencys like ( p alele= 0,54 and q alele=0,46 ) I have only raw data for my population ( I know who is a homozygote or heterozygote for a particular allele) but I dont have raw data for other world wide population whome my population is comparing to. I am wondering If I have choosen the right methods and are there any methods wich I could have also used?