[집단유전] Arlequin을 이용한 population haplotype 분석

mac osx에서는 안돌아감 / arp, hap 파일 만드는거 귀찮음 / 옵션 다 선택하면 결과 많이 나와 귀찮음

Arlequin은 이탈리아 전통희극 중의 유명한 등장인물인 "Arlecchino"의 프랑스어식 표현으로, 알레치노는 그가 원하는 대로 사물을 바꾸는 능력을 가지고 있었음. 

이러한 다양한 형태로 변화시키는 그의 능력은 그의 알록달록한 의상에서도 나타나며, 이 Arlequin 프로그램의 아이콘 역시 이를 바탕으로 디자인되었음. 

(아마도 nucleotide polymorphism과 연관하여 해당이름을 지은 듯 ;ㅡ;)

The analyses Arlequin can perform on the data fall into two main categories: 

intra-population and inter-population methods. 

In the first category statistical information is extracted independently from each population, 

whereas in the second category(intra-population), samples are compared to each other.

Intra-population methods:	Short description:
Standard indices	Some diversity measures like the number of polymorphic sites, gene diversity.
Molecular diversity	Calculates several diversity indices like nucleotide diversity, different estimators of the population parameter q.
Mismatch distribution	The distribution of the number of pairwise differences between haplotypes, from which parameters of a demographic or spatial population expansion can be estimated
x Haplotype frequency estimation	Estimates the frequency of haplotypes present in the population by maximum likelihood methods.
x Gametic phase estimation	Estimates the most like gametic phase of multi-locus genotypes using a pseudo-Bayesian approach (x ELB algorithm).
x Linkage disequilibrium	Test of non-random association of alleles at different loci.
x Hardy-Weinberg equilibrium	Test of non-random association of alleles within diploid individuals.
Tajima’s neutrality test	Test of the selective neutrality of a random sample of DNA sequences or RFLP haplotypes under the infinite site model.
Fu's FS neutrality test	Test of the selective neutrality of a random sample of DNA sequences or RFLP haplotypes under the infinite site model.
Ewens-Watterson neutrality test	Tests of selective neutrality based on Ewens sampling theory under the infinite alleles model.
Chakraborty’s amalgamation test	A test of selective neutrality and population homogeneity. This test can be used when sample heterogeneity is suspected.
Minimum Spanning Network (MSN)	Computes a Minimum Spanning Tree (MST) and Network (MSN) among haplotypes. This tree can also be computed for all the haplotypes found in different populations if activated under the AMOVA section.

Inter-population methods:	Short description:
Search for shared haplotypes between populations	Comparison of population samples for their haplotypic content. All the results are then summarized in a table.
AMOVA	Different hierarchical Analyses of Molecular Variance to evaluate the amount of population genetic structure.
Pairwise genetic distances	FST based genetic distances for short divergence time.
Exact test of population differentiation	Test of non-random distribution of haplotypes into population samples under the hypothesis of panmixia.
Assignment test of genotypes	Assignment of individual genotypes to particular populations according to estimated allele frequencies.
Mantel test:	Short description:
Correlations or partial correlations between a set of 2 or 3 matrices	Can be used to test for the presence of isolation-by-distance

gametic phase 

in a diploid individual, the gametic phase represents the original allelic combinations that an individual received from its parents. 

it is therefore a particular association of alleles at different loci on the same chromosome. gametic phase is influenced by genetic linkage.

within

theta: population mutation rate 

theta=2Neu, theta=4Neu, Ne=effective pop size, u=mutation rate

theta(s)=based on no. segregating(variable) sites, theta(pi)=based on mean pairwise differences

between 

AMOVA

fixation index, I=individual=inbreeding coefficient, Fst, 0 identical to population, 1 different 

pi=pairwise distance, D unit depend on molecular data

detecting selection, dN/dS, replacement/silent, >1selection, 1>noselection

tajima, polymorphic sites no. and nucleotide differences are correlated, observed average pairwise differences - expected variable sites

(0) neutral 1,23,4,5, (+) balancing bottleneck selection 45,23,1, (-) purifying expansion selection 1,2345

fu's Fs, comparing observed alleles to expectation based on genetic diversity, (+) balancing bottleneck (-) purifying expansion

how can you tell the difference between selection or pop size change?

look multiple genes, if pop size change, same pattern in all genes, if selection, different pattern