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mPed: a computer program for converting pedigree data to a format used by the PMx-software for conservation genetic analysis
Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.ORCID iD: 0000-0001-9286-3361
2013 (English)In: Conservation Genetics Resources, ISSN 1877-7252, E-ISSN 1877-7260, Vol. 5, no 3, 651-653 p.Article in journal (Refereed) Published
Abstract [en]

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 conservationmanagement 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

Place, publisher, year, edition, pages
2013. Vol. 5, no 3, 651-653 p.
Keyword [en]
PMx, Pedigree analysis, Conservation, genetic management, Inbreeding, Genetic variation, Founder statistics
National Category
Zoology
Research subject
Population Genetics
Identifiers
URN: urn:nbn:se:su:diva-88127DOI: 10.1007/s12686-013-9874-zISI: 000322619900013OAI: oai:DiVA.org:su-88127DiVA: diva2:609691
Available from: 2013-03-06 Created: 2013-03-06 Last updated: 2017-12-06Bibliographically approved
In thesis
1. Assessing inbreeding and loss of genetic variation in canids, domestic dog (Canis familiaris) and wolf (Canis lupus), using pedigree data
Open this publication in new window or tab >>Assessing inbreeding and loss of genetic variation in canids, domestic dog (Canis familiaris) and wolf (Canis lupus), using pedigree data
2014 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Genetic variation is necessary to maintain the ability of wild and domestic populations to genetically adapt to changed selective pressures. When relationships among individuals are known, conservation genetic management can be based on statistical pedigree analysis. Such approaches have traditionally focused on wild animal conservation breeding in captivity. In this thesis, I apply pedigree-based techniques to domestic and wild animal populations, focusing on two canids – the domestic dog and the wild wolf.

Main objectives include to 1) develop a means for making any pedigree fit the input requirements of the software Population Management x (PMx) and to use this program to 2) investigate rate of inbreeding and loss of genetic variation in dog breeds, including possible correlations between recent inbreeding and health problems, 3) estimate effects on inbreeding of the 2010 hunt of the endangered Swedish wolf population, and to 4) evaluate the potential to genetically support this wolf population through cross-fostering releases of zoo bred pups from a conservation breeding program.

Results include successfully developing the converter program mPed (Paper I) and applying both mPed and PMx to dog and wolf pedigrees. I found extensive loss of genetic variation and moderate rates of recent inbreeding in 26 dog breeds, but no major difference in these parameters between breeds classified as “healthy” vs. “unhealthy“ (Paper II). I found average inbreeding coefficients to more than double (from F=0.03 to 0.07) and founder genetic variation to decrease by c. 30 percent over the past few decades in traditional Swedish dog breeds identified as being of conservation concern (Paper IV). Hunting will make it less likely to reach genetically based Favourable Conservation Status criteria for the Swedish wild wolf population (Paper III), but release of zoo bred wolves through cross-fostering may potentially almost double founder genetic variation of this population (Paper V).

Place, publisher, year, edition, pages
Stockholm: Department of Zoology, Stockholm University, 2014. 72 p.
National Category
Zoology
Research subject
Population Genetics
Identifiers
urn:nbn:se:su:diva-100371 (URN)978-91-7447-858-7 (ISBN)
Public defence
2014-03-07, Nordenskiöldsalen, Geovetenskapens hus, Svante Arrhenius väg 12, Stockholm, 13:00 (English)
Opponent
Supervisors
Note

At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Epub ahead of print. Paper 4: Manuscript. Paper 5: Manuscript.

Available from: 2014-02-13 Created: 2014-02-03 Last updated: 2014-10-13Bibliographically approved

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