genetics testing (test1)

MtDNA

Haploid, multi-allelic

Microsatellites

Diploid, multi-allelic/locus

SNPs

Diploid, bi-allelic, low per-locus diversity

Strengths of MtDNA

Maternal, historical lineages, 1locus/marker

Strengths of Microsatellites

Polymorphic, fine-scale relatedness, 18markers/loci

Strengths of SNPs

Reproducible, robust/moderate DNA quality, 36 SNPs

Learn from MtDNA

Matriline structure, historical lineages, broad-scale patterns

Learn from Microsatellites

Parentage, Contemporary relatedness, fine-scale relatedness

Learn from SNPs

Long term monitoring, differentiation, strong cross-study baselines

Why is H_e(measure of genetic diversity) not relevant to MtDNA?

MtDNA is haploid (only one allele per locus). Use Haploid diversity instead

Why heterozygosity for Microsatellites is higher than for SNPs

Microsatellites are multi-allelic while SNPs are bi-allelic

Formula for computing H_e(measure of genetic diversity) for 2 allele

H_e =2.718 2pq

Formula for computing H_e(measure of genetic diversity) for 3+ allele

H_e = 1- (p² + p² + p²….)

Why test for excess homozygotes?

Excess of homozygotes (departure from HWE), can signal problems; inbreeding, null alleles, strong selection, etc

Genotype frequency equation

How many observed of given genotype / sample size

When H_o(observed heterozygosity) does not equal H_e(expected heterozygosity)

A HWE assumption has been violated

Allele frequency equation

How many observations of an allele divided by sample size