Genetic audit of farmed abalone

James Cook University - Australia

This genetic audit aimed to accurately establish the relationships and degree of relatedness among farmed abalone using a large number of genome-wide markers (single nucleotide polymorphisms - SNPs).

Map of Jasus lobster distribution.
Discriminant Analysis of Principal Components (DAPC) using the R package “adegenet”. DAPC shows differences between groups (farms A, C, D, E and F) using k-means, a clustering algorithm which finds a given number (say, k) of groups maximizing the variation between groups, B(X) while minimizing variation within clusters. The optimal number of clusters is identified by running k-means sequentially with increasing values of k and comparing different clustering solutions using Bayesian Information Criterion (BIC).
Map of Jasus lobster distribution.
Membership probabilities, inferred from DAPC analysis, of each abalone for the different groups (farms A, C, D, E and F) based on the retained discriminant functions.
Map of Jasus lobster distribution.
Mutual k-nearest neighbour analysis for the different abalone groups (farms A, C, D, E and F) generated using the R package “NetView”, a network-based approach.

References:

Strugnell JM, Silva CNS. Genetic diversity audit of farm held stocks of greenlip and blacklip abalone. Fisheries Research and Development Corporation, FRDC Report No 2016/142.