title: A maximum-likelihood estimation of pairwise relatedness for autopolyploids.
abstract: Relatedness between individuals is central to ecological genetics. Multiple methods are available to quantify relatedness from molecular data, including method-of-moment and maximum-likelihood estimators. We describe a maximum-likelihood estimator for autopolyploids, and quantify its statistical performance under a range of biologically relevant conditions. The statistical performances of five additional polyploid estimators of relatedness were also quantified under identical conditions. When comparing truncated estimators, the maximum-likelihood estimator exhibited lower root mean square error under some conditions and was more biased for non-relatives, especially when the number of alleles per loci was low. However, even under these conditions, this bias was reduced to be statistically insignificant with more robust genetic sampling. We also considered ambiguity in polyploid heterozygote genotyping and developed a weighting methodology for candidate genotypes. The statistical performances of three polyploid estimators under both ideal and actual conditions (including inbreeding and double reduction) were compared. The software package POLYRELATEDNESS is available to perform this estimation and supports a maximum ploidy of eight.
authors.affiliation: Key Laboratory of Resource Biology and Biotechnology in Western China of Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China.
authors.forename: K
authors.initials: K
authors.lastname: Huang
authors.affiliation: Key Laboratory of Resource Biology and Biotechnology in Western China of Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China.
authors.forename: S T
authors.initials: ST
authors.lastname: Guo
authors.affiliation: Center of Human Origins, Department of Anthropology, New York University, New York, NY, USA.
authors.forename: M R
authors.initials: MR
authors.lastname: Shattuck
authors.affiliation: Key Laboratory of Resource Biology and Biotechnology in Western China of Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China.
authors.forename: S T
authors.initials: ST
authors.lastname: Chen
authors.affiliation: Key Laboratory of Resource Biology and Biotechnology in Western China of Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China.
authors.forename: X G
authors.initials: XG
authors.lastname: Qi
authors.affiliation: Key Laboratory of Resource Biology and Biotechnology in Western China of Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China.
authors.forename: P
authors.initials: P
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Resource Biology and Biotechnology in Western China of Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China.
authors.forename: B G
authors.initials: BG
authors.lastname: Li
mesh_terms: D005838:Genotype; D006579:Heterozygote; D007178:Inbreeding; D040582:Inheritance Patterns; D016013:Likelihood Functions; D008957:Models, Genetic; D015233:Models, Statistical; D011123:Polyploidy; D012984:Software