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Data from: Examination of the efficacy of small genetic panels in genomic conservation of companion animal populations

Citation

Sams, Aaron; Ford, Brett; Gardner, Adam; Boyko, Adam (2020), Data from: Examination of the efficacy of small genetic panels in genomic conservation of companion animal populations, Dryad, Dataset, https://doi.org/10.5061/dryad.k0p2ngf5h

Abstract

In many ways dogs are an ideal model for the study of genetic erosion and population recovery, problems of major concern in the field of conservation genetics. Genetic diversity in many dog breeds has been declining systematically since the beginning of the 1800’s, when modern breeding practices came into fashion. As such, inbreeding in domestic dog breeds is substantial and widespread and has led to an increase in recessive deleterious mutations of high effect as well as general inbreeding depression. Pedigrees can in theory be used to guide breeding decisions, though are often incomplete and do not reflect the full history of inbreeding. Small microsatellite panels are also used in some cases to choose mating pairs to produce litters with low levels of inbreeding. However, the long-term impact of such practices have not been thoroughly evaluated. Here, we use forward simulation on a model of the dog genome to examine the impact of using limited markers panels to guide pairwise mating decisions on genome-wide population level genetic diversity. Our results suggest that in unmanaged populations, where breeding decisions are made at the pairwise- rather than population-level, such panels can lead to accelerated loss of genetic diversity at genome regions unlinked to panel markers, compared to random mating. These results demonstrate the importance of genome-wide genetic panels for managing and conserving genetic diversity in dogs and other companion animals.

Methods

This dataset was generated using SLIM 3 using this template https://github.com/ProjectAussie/embark-research/blob/master/sams_etal_2020_evolutionary_applications/diversity_matechoice_template_for_manuscript.slim.

The specific parameterizations used to generate this dataset are detailed in the following python script, which also details all processing of the simulation data to generate results in the manuscript. https://github.com/ProjectAussie/embark-research/blob/master/sams_etal_2020_evolutionary_applications/analyze_data_and_make_figures_and_tables.py

Usage Notes