Development and testing of a genetic marker-based pedigree reconstruction system 'PR-genie' incorporating size-class data

Cope, Robert C., Lanyon, Janet M., Seddon, Jennifer M. and Pollett, Philip K. (2014) Development and testing of a genetic marker-based pedigree reconstruction system 'PR-genie' incorporating size-class data. Molecular Ecology Resources, 14 4: 857-870. doi:10.1111/1755-0998.12219


Author Cope, Robert C.
Lanyon, Janet M.
Seddon, Jennifer M.
Pollett, Philip K.
Title Development and testing of a genetic marker-based pedigree reconstruction system 'PR-genie' incorporating size-class data
Journal name Molecular Ecology Resources   Check publisher's open access policy
ISSN 1755-0998
1755-098X
Publication date 2014-07
Year available 2014
Sub-type Article (original research)
DOI 10.1111/1755-0998.12219
Open Access Status
Volume 14
Issue 4
Start page 857
End page 870
Total pages 14
Place of publication Oxford, United Kingdom
Publisher Wiley-Blackwell Publishing
Collection year 2015
Language eng
Abstract For wildlife populations, it is often difficult to determine biological parameters that indicate breeding patterns and population mixing, but knowledge of these parameters is essential for effective management. A pedigree encodes the relationship between individuals and can provide insight into the dynamics of a population over its recent history. Here, we present a method for the reconstruction of pedigrees for wild populations of animals that live long enough to breed multiple times over their lifetime and that have complex or unknown generational structures. Reconstruction was based on microsatellite genotype data along with ancillary biological information: sex and observed body size class as an indicator of relative age of individuals within the population. Using body size-class data to infer relative age has not been considered previously in wildlife genealogy and provides a marked improvement in accuracy of pedigree reconstruction. Body size-class data are particularly useful for wild populations because it is much easier to collect noninvasively than absolute age data. This new pedigree reconstruction system, PR-genie, performs reconstruction using maximum likelihood with optimization driven by the cross-entropy method. We demonstrated pedigree reconstruction performance on simulated populations (comparing reconstructed pedigrees to known true pedigrees) over a wide range of population parameters and under assortative and intergenerational mating schema. Reconstruction accuracy increased with the presence of size-class data and as the amount and quality of genetic data increased. We provide recommendations as to the amount and quality of data necessary to provide insight into detailed familial relationships in a wildlife population using this pedigree reconstruction technique.
Keyword Cross-entropy method
Genealogy
Microsatellite DNA
Wildlife
Population
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

 
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