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KinshipMoments.jl

PopGen.jl/src/Kinship/KinshipMoments.jl​

📦 not exported🔵 exported by PopGen.jl

🔵 Blouin​

Blouin(ind1::GenoArray, ind2::GenoArray)::Float64

Allele sharing index described by Blouin (1996)

  • Single Locus Equation: The number of alleles shared between individuals over ploidy.
    • If both allele positions are shared (e.g. AA x AA or AB x AB) then 1
    • If one allele position is shared (e.g. AB x AC) then 0.5
    • If neither allele position is shared (e.g. AB x CD) then 0
  • How to combine multiple loci: Single locus estimates are simply averaged together
  • Assumes no inbreeding

Blouin, M. S., Parsons, M., Lacaille, V., & Lotz, S. (1996). Use of microsatellite loci to classify individuals by relatedness. Molecular ecology, 5(3), 393-401.

📦 _blouin​

_blouin(geno1::NTuple{2,T}, geno2::NTuple{2,T})::Float64 where T<:Union{Int16, Int8}

🔵 LiHorvitz​

LiHorvitz(ind1::GenoArray, ind2::GenoArray, locus_names::Vector{Symbol}; alleles::NamedTuple)

Allele sharing index described by Li and Horvitz (1953)

  • Single Locus Equation: If all alleles are the same between individuals (eg. AA x AA) then 1.
    • If two alleles are shared between individuals (eg. AA x AB or AB x AB) then 0.5.
    • If only one allele is shared between individuals (eg. AB x AC) then 0.25.
    • If no alleles are shared (eg. AB x CD) then 0.
  • How to combine multiple loci: Single locus estimates are simply averaged together
  • Assumes no inbreeding

Li, C. C., & Horvitz, D. G. (1953). Some methods of estimating the inbreeding coefficient. American journal of human genetics, 5(2), 107.

📦 _lihorvitz​

_lihorvitz(geno1::NTuple{2,T}, geno2::NTuple{2,T})::Float64 where T<:Union{Int16, Int8}

🔵 Loiselle​

Loiselle(ind1::GenoArray, ind2::GenoArray, allelefrq::U; kwargs...) where U <: Tuple

Calculates the moments based estimator of pairwise relatedness using the estimator propsed by Loiselle et al (1995) and modified to individual dyads by Heuertz et al. (2003).

  • Multiple Locus Equation:
  • Assumes no inbreeding

See equations 22 in: Wang(2017) for variant of estimator used

Loiselle, B. A., Sork, V. L., Nason, J., & Graham, C. (1995). Spatial genetic structure of a tropical understory shrub, Psychotria officinalis (Rubiaceae). American journal of botany, 82(11), 1420-1425.

Heuertz, M., Vekemans, X., Hausman, J. F., Palada, M., & Hardy, O. J. (2003). Estimating seed vs. pollen dispersal from spatial genetic structure in the common ash. Molecular Ecology, 12(9), 2483-2495.

Wang, J. (2017). Estimating pairwise relatedness in a small sample of individuals. Heredity, 119(5), 302-313.

📦 _loiselle_num​

_loiselle_num(geno1::NTuple{2,T}, geno2::NTuple{2,T}, frqdict::Dict{T, Float64})::Float64 where T<:Union{Int16, Int8}

📦 _loiselle_denom​

_loiselle_denom(freqs)::Float64

📦 _lynch​

_lynch(geno1::NTuple{2,T}, geno2::NTuple{2,T})::Float64 where T<:Union{Int16, Int8}

🔵 Lynch​

Lynch(ind1::GenoArray, ind2::GenoArray)::Float64

Allele sharing index described by Lynch (1988)

  • Single Locus Equation: If all alleles are the same between individuals (eg. AA x AA) then 1.
    • If both individuals are heterozygous with the same alleles or one is homozygous for the shared allele (eg. AB x AB or AA x AB) then 0.75.
    • If only one allele is shared between individuals (eg. AB x AC) then 0.5.
    • If no alleles are shared (eg. AB x CD) then 0.
  • How to combine multiple loci: Single locus estimates are simply averaged together
  • Assumes no inbreeding

Lynch, M. (1988). Estimation of relatedness by DNA fingerprinting. Molecular biology and evolution, 5(5), 584-599.

🔵 LynchLi​

LynchLi(ind1::T, ind2::T, alleles::U; kwargs...) where T <: GenoArray where U <: Tuple

Calculates the moments based estimator of pairwise relatedness by Lynch (1988) & improved by Li et al. (1993).

  • Single Locus Equation:
  • How to combine multiple loci: Sum the difference between observed and expected similarity across all loci and then divide by the sum of 1 - the expected similarity
  • Assumes no inbreeding

See equations 13 - 16 in Wang (2017) for variant of estimator used

Li, C. C., Weeks, D. E., & Chakravarti, A. (1993). Similarity of DNA fingerprints due to chance and relatedness. Human heredity, 43(1), 45-52.

Wang, J. (2017). Estimating pairwise relatedness in a small sample of individuals. Heredity, 119(5), 302-313.

📦 _lynchli​

_lynchli(geno1::NTuple{2,T}, geno2::NTuple{2,T})::Float64 where T<:Union{Int16, Int8}

📦 _lynchS0​

_lynchliS0(alleles)::Float64

🔵 LynchRitland​

LynchRitland(ind1::GenoArray, ind2::GenoArray, locus_names::Vector{Symbol}; alleles::NamedTuple)

Calculates the moments based estimator of pairwise relatedness by Lynch and Ritland (1999).

  • Single Locus Equation:
  • How to combine multiple loci: Weighted average of each term seperately weighted by the sample variance (assuming zero relatedness) and subsequently divided by the average sampling variance
  • Assumes no inbreeding

See equation 10 in Wang (2017) for variant of estimator used

Lynch, M., & Ritland, K. (1999). Estimation of pairwise relatedness with molecular markers. Genetics, 152(4), 1753-1766.

Wang, J. (2017). Estimating pairwise relatedness in a small sample of individuals. Heredity, 119(5), 302-313.

📦 _lynchritland​

_lynchritland(geno1::NTuple{2,T}, geno2::NTuple{2,T}, frqdict::Dict{T, Float64}) where T<:Union{Int16, Int8}

🔵 Moran​

Moran(ind1::GenoArray, ind2::GenoArray, locus_names::Vector{Symbol}; alleles::NamedTuple)

Reinterpretation of Moran's I (commonly used for spatial autocorrelation) to estimate genetic relatedness by Hardy and Vekemans (1999)

  • Multiple Locus Equation:
  • Assumes no inbreeding

Hardy, O. J., & Vekemans, X. (1999). Isolation by distance in a continuous population: reconciliation between spatial autocorrelation analysis and population genetics models. Heredity, 83(2), 145-154.

📦 _moran​

_moran(geno1::NTuple{2,T}, geno2::NTuple{2,T}, frqdict::Dict{T, Float64}) where T<:Union{Int16, Int8}

🔵 QuellerGoodnight​

QuellerGoodnight(ind1::GenoArray, ind2::GenoArray, locus_names::Vector{Symbol}; alleles::NamedTuple)

Calculates the moments based estimator of pairwise relatedness developed by Queller & Goodnight (1989).

  • Single Locus Equation:
  • How to combine multiple loci:
    • Multiple loci are combined by independently summing the two numerator and two denominator terms before performing the final division and averaging the two components.
  • Assumes no inbreeding

See equation 3 in Wang (2017) for variant of estimator used.

Queller, D. C., & Goodnight, K. F. (1989). Estimating relatedness using genetic markers. Evolution, 43(2), 258-275.

Wang, J. (2017). Estimating pairwise relatedness in a small sample of individuals. Heredity, 119(5), 302-313.

📦 _quellergoodnight​

_quellergoodnight(geno1::NTuple{2,T}, geno2::NTuple{2,T}, frqdict::Dict{T, Float64}) where T<:Union{Int16, Int8}

🔵 Ritland​

Ritland(ind1::GenoArray, ind2::GenoArray, locus_names::Vector{Symbol}; alleles::NamedTuple)

Calculates the moments based estimator of pairwise relatedness proposed by Li and Horvitz (1953) and implemented/made popular by Ritland (1996).

  • Single Locus Equation:
  • How to combine multiple loci: A weighted average of individual locus specific estimates weighted by sampling variance
  • Assumes no inbreeding

See equation 7 in: Wang (2017) for variant of estimator used

Ritland, K. (1996). Estimators for pairwise relatedness and individual inbreeding coefficients. Genetics Research, 67(2), 175-185.

Wang, J. (2017). Estimating pairwise relatedness in a small sample of individuals. Heredity, 119(5), 302-313.

📦 _ritland​

_ritland(geno1::NTuple{2,T}, geno2::NTuple{2,T}, frqdict::Dict{T, Float64}) where T<:Union{Int16, Int8}