HIest (version 2.0)

HIC3: Closed form maximum-likelihood estimates of ancestry and heterozygosity for diagnostic markers in a three-way hybrid zone

Description

For hybrids with up to three parental lineages with diagnostic molecular markers (one allele fixed in each parental lineage). The function computes genomic proportions and ancestry indices using closed form estimators.

Usage

HIC3(G, P)

Arguments

G

A matrix or data frame of diploid genotypes. Each individual occupies two consecutive rows (one for each allele). Each marker is a column. For heterozygotes, it does not matter which allele is entered first.

P

A matrix or data frame identifying which alleles are fixed in each parental lineage. The first column stores locus identifiers and the second allele identifiers (one per parental lineage). The value of the third column is 1 for each allele fixed in the first parental lineage, and 0 otherwise. The value of the fourth column is 1 for each allele fixed in the second parental lineage, and 0 otherwise. The value of the fifth column is 1 for each allele fixed in the third parental lineage, and 0 otherwise.

Value

A matrix with 10 named columns for each individual

p11

Proportion of markers homozygous for lineage 1 alleles

p22

Proportion of markers homozygous for lineage 2 alleles

p33

Proportion of markers homozygous for lineage 3 alleles

p12

Proportion of markers heterozygous for lineage 1 and 2 alleles

p13

Proportion of markers heterozygous for lineage 1 and 3 alleles

p23

Proportion of markers heterozygous for lineage 2 and 3 alleles

S1

Lineage 1 ancestry index: proportion of alleles derived from parental lineage 1

S2

Lineage 2 ancestry index: proportion of alleles derived from parental lineage 2

S3

Lineage 3 ancestry index: proportion of alleles derived from parental lineage 3

logLik

log-likelihood of the genomic proportions given the individual marker data

References

Fitzpatrick, B. M. 2012. Estimating ancestry and heterozygosity of hybrids using molecular markers. BMC Evolutionary Biology 12:131. http://www.biomedcentral.com/1471-2148/12/131

See Also

threeway finds maximum likelihood estimates for non-diagnostic marker data. thirdclass and HItest3 evaluate simple classification of three-way hybrids into parental, F1, F2, and backcross categories. For conventional two-way hybrid zone analyses, see HIC, HIest,link{HIclass},link{HItest}.

Examples

	## all possible 2-way crosses after 2 generations
G <- rbind(
rep(1,12),rep(1,12),               # parental 1
rep(2,12),rep(2,12),               # parental 2
rep(3,12),rep(3,12),               # parental 3
rep(1,12),rep(2,12),               # 1 x 2 F1
rep(1:2,each=6),rep(1:2,6),        # 1 x 2 F2
rep(1,12),rep(1:2,6),              # 1 x 1 x 2 BC
rep(2,12),rep(1:2,6),              # 1 x 2 x 2 BC
rep(1,12),rep(3,12),               # 1 x 3 F1
rep(c(1,3),each=6),rep(c(1,3),6),  # 1 x 3 F2
rep(1,12),rep(c(1,3),6),           # 1 x 1 x 3 BC
rep(3,12),rep(c(1,3),6),           # 1 x 3 x 3 BC
rep(2,12),rep(3,12),               # 2 x 3 F1
rep(2:3,each=6),rep(2:3,6),        # 2 x 3 F2
rep(3,12),rep(2:3,6),              # 2 x 3 x 3 BC
rep(2,12),rep(2:3,6)               # 2 x 2 x 3 BC
)

P <- data.frame(Locus=rep(1:12,each=3),allele=rep(1:3,12),P1=rep(c(1,0,0),12),
	P2=rep(c(0,1,0),12),P3=rep(c(0,0,1),12))

HIC3(G,P)