hiphop: Parentage Assignment using Bi-Allelic Genetic Markers
Can be used for paternity and maternity assignment and outperforms
conventional methods where closely related individuals occur in the pool of
possible parents. The method compares the genotypes of offspring with any
combination of potentials parents and scores the number of mismatches of these
individuals at bi-allelic genetic markers (e.g. Single Nucleotide Polymorphisms).
It elaborates on a prior exclusion method based on the Homozygous Opposite Test
(HOT; Huisman 2017 <doi:10.1111/1755-0998.12665>) by introducing the
additional exclusion criterion HIPHOP (Homozygous Identical Parents,
Heterozygous Offspring are Precluded; Cockburn et al., in revision). Potential
parents are excluded if they have more mismatches than can
be expected due to genotyping error and mutation, and thereby one can identify the
true genetic parents and detect situations where one (or both) of the true
parents is not sampled. Package 'hiphop' can deal with (a) the case where there
is contextual information about parentage of the mother (i.e. a female has been
seen to be involved in reproductive tasks such as nest building), but paternity
is unknown (e.g. due to promiscuity), (b) where both parents need to be assigned,
because there is no contextual information on which female laid eggs and which
male fertilized them (e.g. polygynandrous mating system where multiple females
and males deposit young in a common nest, or organisms with external fertilisation
that breed in aggregations).
For details: Cockburn, A., Penalba, J.V.,Jaccoud, D.,Kilian, A., Brouwer, L.,
Double, M.C., Margraf, N., Osmond, H.L., van de Pol, M. and Kruuk, L.E.B.
(in revision). HIPHOP: improved paternity assignment among close relatives
using a simple exclusion method for bi-allelic markers.
Molecular Ecology Resources, DOI to be added upon acceptance.
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