Or these both terms are synonym to each other? if yes, then haplotype diversity, calculated using DnaSP, can be an alternative for genetic diversity calculated by arlequin?
Hi!
Check the following your doubt will be cleared so that yourself can answer the question.
Haplotype or haploid is considered set of genes that inherited together from a single parent. Haplo group is a group of same or almost identical haplotypes that share/part a common ancestor with SNP (single-nucleotide polymorphism mutation)
Where as genotype is referred to a single or multiple traits that inherited together from a parent. Genotype is combination of genes at particular locus.
Haplotypes versus genotypes on pedigrees
(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3102622/pdf/1748-7188-6-10.pdf)
Hi Faaras
Jetty's answer is Ok, but probably far too specialized.
A simpler answer could be that haplotype diversity is usually measured by (H), the number of haplotypes.
Genetic diversity is usually measured by Ho and He (observed and expected heterozygosity, which Nei called gene diversity). Nonetheless, another measure of genetic diversity could be the number of alleles (or the rarefacted allelic richness), in multiallelic markers, such as SSRs.
If you are working with DNA sequences, H keeps being the number of haplotypes, but genetic diversity is usually measured by nucleotide diversity (Pi), or by the number of segregant sites. This will give you two different measures of Theta, that can be used for further analyses (i.e., Tajima's test, etc)
Hope this helps
Pablo
Thank you for your valuable answers. I am working with full mtDNA sequences generated by illumina Hi-seq, and I wanted to calculate the genetic diversity from these sequences of a specific population. I tried to calculate genetic diversity using Arlequin ver 3, but couldn't be successful in doing so. Then, I simply calculated haplotype diversity in place of genetic diversity, using DnaSP. The question is, would haplotype diversity suffice the need of genetic diversity while studying the population diversity? Or else, could you people can help me in running .arp file on Arlequin (its giving errors like "phenotypes have different number of loci"). I would be much grateful.
Hi Faaras
You can calculate a lot of diversity statistics with DnaSP. Check out the manual. but indeed you can calculate Pi, S, ....
Pablo
Thank you Pablo for your kind words. I'll keep in touch with you. Thanks once again.
I was just about to ask the same question. am working on DNA sequences. I have DNASp, can I now say haplotype diversity is similar to genetic diversity. Or they are completely different.
Thank you in advance
Hi Nellia
No, you can't compare both. Comparisons should be kept among parameters measuring the same statistic (for example, between Pi and S, as both measure nucleotide diversity). Haplotype diversity is different to nucleotide diversity and they can't be compared. But just as Pi and S can be used for the Tajima test (which tries to measure neutrality), haplotype diversity can be also used to test neutrality.(for example, Ewens-Watterson and derived tests, if I recall correctly).
Hope this helps
Pablo
Great, thank you so much Pablo....really appreciate your response.