haploidy, diploidy, polyploidy … not a problem

Investigating pairwise relatedness is fundamental to the characterization of the mating system and inferring genetic structure. If no pedigree exists, then relatedness is estimated from genetic markers (e.g., microsatellite loci) using method-of-moment or maximum-likelihood methods.

However, not all individuals in a population have the same ploidy. In ferns, mosses and some seaweeds, haploid gametophytes alternate with diploid sporophytes. In some insect orders, such as the Hymenoptera, haploid males develop from unfertilized eggs. Thus, individuals may be related, but have differing levels of ploidy. Though many estimators exist for diploid organisms, no estimators exist for organisms with multiple ploidy levels.

Cape honey beesat a feeding station. Photograph by Anthony Vaudo, University of Florida

Cape honey bees at a feeding station. Photograph by Anthony Vaudo, University of Florida

That was until the software package recently published online by Huang et al. in Molecular Ecology Resources. Here, a relatedness coefficient, a maximum-likelihood and three coefficient of coancestry estimators are extended to enable the calculation of relatedness coefficients using co-dominant markers between individuals differing in ploidy.

The simulations and comparisons presented should help with the selection of the appropriate estimator for a given question or application.

Estimating pairwise relatedness between individuals with different ploidies will significantly advance our understanding of mating systems and the structuring of populations of organisms with complex life cycles.

Huang K, Ritland K, Guo S, Dunn DW, Chen D, Ren Y, Qi X, Zhang P, He G and Li B (2014, accepted) Estimating pairwise relatedness between individuals with differing levels of ploidy.  Molecular Ecology Resources DOI: 10.1111/1755-0998.12351

About Stacy Krueger-Hadfield

I am a marine evolutionary ecologist interested in the impacts of seascapes and complex life cycles on marine population dynamics. I use natural history, manipulative field experiments and population genetic and genomic approaches with algal and invertebrate models in temperate rocky shores,estuaries and the open ocean.
This entry was posted in natural history, pedigree, population genetics, software, Uncategorized. Bookmark the permalink.