Dimensionality of genomic information and performance of the Algorithm for Proven and Young for different livestock species

International audienceAbstractBackgroundA genomic relationship matrix (GRM) can be inverted efficiently with the Algorithm for Proven and Young (APY) through recursion on a small number of core animals. The number of core animals is theoretically linked to effective population size (Ne). In a simulation study, the optimal number of core animals was equal to the number of largest eigenvalues of GRM that explained 98% of its variation. The purpose of this study was to find the optimal number of core animals and estimate Ne for different species.MethodsDatasets included phenotypes, pedigrees, and genotypes for populations of Holstein, Jersey, and Angus cattle, pigs, and broiler chickens. The number of genotyped animals varied from 15,000 for broiler chickens to 77,000 for Holsteins, and the number of single-nucleotide polymorphisms used for genomic prediction varied from 37,000 to 61,000. Eigenvalue decomposition of the GRM for each population determined numbers of largest eigenvalues corresponding to 90, 95, 98, and 99% of variation.ResultsThe number of eigenvalues corresponding to 90% (98%) of variation was 4527 (14,026) for Holstein, 3325 (11,500) for Jersey, 3654 (10,605) for Angus, 1239 (4103) for pig, and 1655 (4171) for broiler chicken. Each trait in each species was analyzed using the APY inverse of the GRM with randomly selected core animals, and their number was equal to the number of largest eigenvalues. Realized accuracies peaked with the number of core animals corresponding to 98% of variation for Holstein and Jersey and closer to 99% for other breed/species. Ne was estimated based on comparisons of eigenvalue decomposition in a simulation study. Assuming a genome length of 30 Morgan, Ne was equal to 149 for Holsteins, 101 for Jerseys, 113 for Angus, 32 for pigs, and 44 for broilers.ConclusionsEigenvalue profiles of GRM for common species are similar to those in simulation studies although they are affected by number of genotyped animals and genotyping quality. For all investigated species, the APY required less than 15,000 core animals. Realized accuracies were equal or greater with the APY inverse than with regular inversion. Eigenvalue analysis of GRM can provide a realistic estimate of Ne

Data from: Staying close to home? Genetic differentiation of rough-toothed dolphins near oceanic islands in the central Pacific Ocean

Rough-toothed dolphins have a worldwide tropical and subtropical distribution, yet little is known about the population structure and social organization of this typically open-ocean species. Although it has been assumed that pelagic dolphins range widely due to the lack of apparent barriers and unpredictable prey distribution, recent evidence suggests rough-toothed dolphins exhibit fidelity to some oceanic islands. Using the most comprehensively extensive dataset for this species to date, we assess the isolation and interchange of rough-toothed dolphins at the regional and oceanic scale within the central Pacific Ocean. Using mtDNA and microsatellite genotyping (nDNA), we analyzed samples of insular communities from the main Hawaiian (Kaua‘i n = 93, O‘ahu n = 9, Hawai‘i n = 57), French Polynesian (n = 70) and Samoan (n = 16) archipelagos, and pelagic samples off the Northwestern Hawaiian Islands (n = 18). An overall AMOVA indicated strong genetic differentiation among islands (mtDNA FST = 0.265; p < 0.001; nDNA FST = 0.038; p < 0.001), as well as among archipelagos (mtDNA FST = 0.299; p < 0.001; nDNA FST = 0.055; p < 0.001). Shared haplotypes (n = 4) between the archipelagos may be a product of a relatively recent divergence and/or periodic exchange from poorly understood pelagic populations. Analyses using STRUCTURE and GENELAND identified four separate management units among archipelagos and within the Hawaiian Islands. These results confirm the presence of multiple insular populations within the Pacific and island-specific genetic isolation among populations attached to islands in each archipelago. Insular populations seem most prevalent where oceanographic conditions indicate high local productivity or a discontinuity with surrounding oligotrophic areas. Our findings have important implications for a little studied species that faces increasing anthropogenic threats around oceanic islands