mPed: a computer program for converting pedigree data to a format used by the PMx-software for conservation genetic anal
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TECHNICAL NOTE
mPed: a computer program for converting pedigree data to a format used by the PMx-software for conservation genetic analysis Mija Jansson • Ingvar Sta˚hl • Linda Laikre
Received: 15 September 2012 / Accepted: 28 January 2013 / Published online: 19 February 2013 Ó The Author(s) 2013. This article is published with open access at Springerlink.com
Abstract There is a growing need for conservation genetic management of animal populations when individual relatedness data (pedigrees) are available. Such data can be used to monitor rates of inbreeding and loss of genetic diversity. Traditionally, pedigree analysis for conservation management has focused on zoo populations of threatened wild animals; available software has been developed in that context. Population Management x (PMx) is a free software for estimating genetic parameters including inbreeding, kinship, founder allele contribution and survival. PMx is an accessory program to the zoo studbook platform Single Population Analysis and Records Keeping System (SPARKS) and is not easily applied outside this platform, but such use is of interest for various domestic breeds or wild populations. We developed a converter program (mPed) for making pedigrees of any studbook format fitting the input requirements of PMx. mPed can be downloaded free at www.popgen.su.se/mped.php. Keywords PMx Pedigree analysis Conservation genetic management Inbreeding Genetic variation Founder statistics
Conservation genetic management of populations with known individual relatedness (pedigrees) has traditionally focused on populations of wild animals bred in zoos (Ballou et al. 1995). For such populations, maintenance of
M. Jansson (&) L. Laikre Division of Population Genetics, Department of Zoology, Stockholm University, 106 91 Stockholm, Sweden e-mail: [email protected] I. Sta˚hl Ingvar Sta˚hl IT, Jenny Linds gata 26, 129 52 Ha¨gersten, Sweden
genetic variation is typically the main goal, and pedigree data can be used to monitor rates of inbreeding and loss of genetic variation measured in relation to alleles contributed by separate founding animals of the population (Lacy 1989). Computer programs have been developed within the zoo community to aid in genetic management by handling studbook data and performing statistical pedigree analyses. There is an increasing need for methods, including software, developed for zoo populations to be applied to populations kept outside the zoo community. With current worldwide awareness of the need for conserving biological diversity, genetic monitoring is becoming topical for many populations in addition to those of threatened species in zoos. International policy agreements explicitly state that genetic variation of domestic animal breeds should be conserved and used sustainably (FAO 2007). For instance, within the framework of the United Nations Convention on Biological Diversity conservation targets to be reached during the period 2011–2020 were recently adopted, and one of these target focuses on the genetic d
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