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

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.