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The use of approximate Bayesian computation in conservation genetics and its application in a case study on yellow-eyed penguins

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Abstract

The inference of demographic parameters from genetic data has become an integral part of conservation studies. A group of Bayesian methods developed originally in population genetics, known as approximate Bayesian computation (ABC), has been shown to be particularly useful for the estimation of such parameters. These methods do not need to evaluate likelihood functions analytically and can therefore be used even while assuming complex models. In this paper we describe the ABC approach and identify specific parts of its algorithm that are being the subject of intensive studies in order to further expand its usability. Furthermore, we discuss applications of this Bayesian algorithm in conservation studies, providing insights on the potentialities of these tools. Finally, we present a case study in which we use a simple Isolation-Migration model to estimate a number of demographic parameters of two populations of yellow-eyed penguins (Megadyptes antipodes) in New Zealand. The resulting estimates confirm our current understanding of M. antipodes dynamic, demographic history and provide new insights into the expansion this species has undergone during the last centuries.

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Abbreviations

ABC:

Approximate Bayesian computation

MCMC:

Markov chain Monte Carlo

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Acknowledgements

We would like to thank the organizers of the Trondheim ConGen meeting, Kuke Bijlsma, Volker Loeschcke and Joop Ouborg, for creating such scientific environment that allowed for the creation of this collaborative paper. We are especially grateful to Mark Beaumont, whose insightful comments helped to improve the previous version of the paper considerably. We would also like to thank two anonymous reviewers that helped increase the quality of the manuscript. J.L. is funded by EPSRC grant EP/C533550/1, by Fundacao Ciencia e Tecnologia grant SFRH/BD/43588/2008 and by the “ESF Science Networking Programme ConGen”. The University of Otago supported S.B. and provided funding for the genetic analyses of yellow-eyed penguins.

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Lopes, J.S., Boessenkool, S. The use of approximate Bayesian computation in conservation genetics and its application in a case study on yellow-eyed penguins. Conserv Genet 11, 421–433 (2010). https://doi.org/10.1007/s10592-009-0032-9

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