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Data from: implications of methodologies for integrating empirical kinships into ex situ population management using PMx: a case study of Baer’s Pochard (Aythya baeri) in North America

Abstract

In this study, we aimed to understand the implications of integrating empirical kinships into the genetic management of an ex situ population of the endangered waterfowl, Baer’s pochard (Aythya baeri), in North America. Single nucleotide polymorphism data were generated for 141 Baer’s pochard using double digest restriction site-associated DNA sequencing and empirical kinships were derived and integrated into the population management software PMx. We compared three different scenarios for appying empirical kinships within PMx: 1) no empirical kinships applied, 2) empirical kinships applied for pedigree terminals, 3) empirical kinships applied for the entire populations of pedigree terminals and descendants. We determined that most genetic summary statistics were impacted through the calculation of the population’s mean kinship, which increased signficantly after empirical kinships were integrated into our analyses. Our results also revealed the importance of understanding how molecular kinships derived from a particular estimator are scaled, if the scale differs significantly from pedigree-based kinships. We describe the theory behind the genetic metrics impacted and provide general guidance on incorporating empirical kinships into ex situ population management as well as provide suggestions for sampling strategies to minimize the biases inherent in merging two types of kinship estimators.