A pairwise relatedness estimator for polyploids

Huang, Kang; Ritland, Kermit; Guo, Songtao; Shattuck, Milena R.; Li, Baoguo

doi:10.1111/1755-0998.12217

Cited by 31 publications

(43 citation statements)

References 34 publications

(40 reference statements)

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“…Polyploid method-of-moment estimator Huang et al (2014) developed a method-of-moment estimator for polyploids, which models the probability of each similarity index conditioned on the reference genotype (see also Lynch and Ritland, 1999). The similarity index is defined by the number of alleles that are identical in state between two individuals.…”

Section: Parameter Spacementioning

confidence: 99%

“…The estimate across all loci is the weighted average of each estimate of each locus, with both individuals being used for reference; the final r^is the arithmetic mean of the two estimates. Huang et al (2014) also developed a solution to address ambiguous genotypes using this estimator: the matrices E and M are weighted by the probability of each reference genotype, and P is weighted by the probability of each proband-reference genotype pair.…”

Section: Parameter Spacementioning

confidence: 99%

“…These included the maximum-likelihood estimator (ML) described in this paper, the method of moment for polyploids (MOM; Huang et al, 2014) and a coefficient of coancestry estimator (RI; Ritland, 1996), applied when genotypes are known and when genotypes are ambiguous, the latter of which are denoted ML*, MOM* and RI*. All estimators were truncated to the range of 0-1 for ease of comparison.…”

Section: Statistical Behaviour Of Estimators Of Relatednessmentioning

confidence: 99%

“…The MOM estimator may encounter a singular matrix problem when the number of alleles is too small (Huang et al, 2014). Singularity or near singularity can result from zero or near-zero coefficients in the set of equations, making Equation (7) unsolvable.…”

Section: Statistical Behaviourmentioning

confidence: 99%

“…For example, for biallelic loci with uniformly distributed allele frequency, the Lynch and Ritland (1999) estimator has a sampling variance of infinity. Unfortunately, this scenario is more frequent for polyploids, but the probability of a singular matrix is reduced when the number of alleles is greater or equal to the level of ploidy (Huang et al, 2014). However, this does not guarantee that singularity is avoided, because some combinations of allele frequencies can also result in a singular matrix.…”

Section: Statistical Behaviourmentioning

confidence: 99%

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A maximum-likelihood estimation of pairwise relatedness for autopolyploids

et al. 2014

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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.

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Section: Parameter Spacementioning

confidence: 99%

Section: Parameter Spacementioning

confidence: 99%

Section: Statistical Behaviour Of Estimators Of Relatednessmentioning

confidence: 99%

Section: Statistical Behaviourmentioning

confidence: 99%

Section: Statistical Behaviourmentioning

confidence: 99%

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A maximum-likelihood estimation of pairwise relatedness for autopolyploids

et al. 2014

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The role of kinship in the formation of a primate multilevel society

Guo

Huang

et al. 2014

American J Phys Anthropol

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A small number of mammalian species live in a modular or multilevel society in which several individual social/reproductive units called one-male units (OMUs) are embedded within a large cohesive band. Factors that affect band composition and stability are poorly understood. In this study we examined the role of kinship in the formation and maintenance of a multilevel society in an endangered population of golden snub-nosed monkeys (Rhinopithecus roxellana). From 2005 to 2011, we obtained genetic samples from 86 individuals (including 88.9% of leader males and 80.5% of adult females) living in a band of 8-10 OMUs. We used microsatellite genotyping to identify patterns of relatedness and individual transfer. We found that adult females residing in the same OMU were more closely related to each other than to a random set of females drawn from the band and that females tended to disperse into OMUs that contained female relatives. In addition, adult females who transferred were not more closely related to their previous leader male than to the leader male of their new OMU. These results support the contention that kin bonds contribute importantly to the formation and stability of this primate multilevel society by influencing a female's decision to remain in her current OMU, or during transfer, which new OMU to enter.

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Development of simple sequence repeat markers for Chamerion angustifolium (Onagraceae)

Wang

Dunn

et al. 2019

Appl Plant Sci

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Premise Rosebay willowherb, or fireweed (Chamerion angustifolium: Onagraceae), has diploid, tetraploid, and hexaploid cytotypes. There are known physiological and ecological differences among the three cytotypes, but genetic differences remain undetermined. We developed simple sequence repeat (SSR) markers for this species. Methods and Results Leaf samples were collected from three hexaploid C. angustifolium populations. We successfully amplified 16 SSR loci, which were found to be highly polymorphic. The number of alleles, the observed heterozygosity levels, and the expected heterozygosity levels ranged from four to 13, 0.286–0.899, and 0.372–0.871, respectively. Most primers could also be amplified successfully in C. conspersum and the closely related species Epilobium palustre. Conclusions The 16 polymorphic SSR markers developed here will be useful for genetic studies in C. angustifolium and related species.

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A pairwise relatedness estimator for polyploids

Cited by 31 publications

References 34 publications

A maximum-likelihood estimation of pairwise relatedness for autopolyploids

A maximum-likelihood estimation of pairwise relatedness for autopolyploids

The role of kinship in the formation of a primate multilevel society

Development of simple sequence repeat markers for Chamerion angustifolium (Onagraceae)

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