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Assessing inbreeding and loss of genetic variation in canids, domestic dog (Canis familiaris) and wolf (Canis lupus), using pedigree data
Stockholm University, Faculty of Science, Department of Zoology.
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: urn:nbn:se:su:diva-100371ISBN: 978-91-7447-858-7 (print)OAI: oai:DiVA.org:su-100371DiVA: diva2:692880
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
List of papers
1. mPed: a computer program for converting pedigree data to a format used by the PMx-software for conservation genetic analysis
Open this publication in new window or tab >>mPed: a computer program for converting pedigree data to a format used by the PMx-software for conservation genetic analysis
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

Keyword
PMx, Pedigree analysis, Conservation, genetic management, Inbreeding, Genetic variation, Founder statistics
National Category
Zoology
Research subject
Population Genetics
Identifiers
urn:nbn:se:su:diva-88127 (URN)10.1007/s12686-013-9874-z (DOI)000322619900013 ()
Available from: 2013-03-06 Created: 2013-03-06 Last updated: 2017-12-06Bibliographically approved
2. Recent breeding history of dog breeds in Sweden: modest ratesof inbreeding, extensive loss of genetic diversity and lack ofcorrelation between inbreeding and health
Open this publication in new window or tab >>Recent breeding history of dog breeds in Sweden: modest ratesof inbreeding, extensive loss of genetic diversity and lack ofcorrelation between inbreeding and health
2014 (English)In: Journal of Animal Breeding and Genetics, ISSN 0931-2668, E-ISSN 1439-0388, Vol. 131, no 2, 153-162 p.Article in journal (Refereed) Published
Abstract [en]

One problem in modern dogs is a high occurrence of physical diseases,defects and disorders. Many breeds exhibit physical problems that affectindividual dogs throughout life. A potential cause of these problems isinbreeding that is known to reduce the viability of individuals. We investigatedthe possible correlation between recent inbreeding and health problemsin dogs and used studbook data from 26 breeds provided by theSwedish Kennel Club for this purpose. The pedigrees date back to themid-20th century and comprise 5–10 generations and 1 000–50 000 individualsper pedigree over our study period of 1980–2010. We comparedlevels of inbreeding and loss of genetic variation measured in relation tothe number of founding animals during this period in the investigated dogbreeds that we classified as ‘healthy’ (11 breeds) or ‘unhealthy’ (15) basedon statistics on the extent of veterinary care obtained from Sweden’sfour largest insurance companies for pets. We found extensive loss ofgenetic variation and moderate levels of recent inbreeding in all breedsexamined, but no strong indication of a difference in these parametersbetween healthy versus unhealthy breeds over this period. Thus, recentbreeding history with respect to rate of inbreeding does not appear to be amain cause of poor health in the investigated dog breeds in Sweden. Weidentified both strengths and weaknesses of the dog pedigree data importantto consider in future work of monitoring and conserving geneticdiversity of dog breeds.

Keyword
animal genetic resources, conservation genetics, domestic gene pools, pedigree analysis
National Category
Genetics
Identifiers
urn:nbn:se:su:diva-100600 (URN)10.1111/jbg.12060 (DOI)000332780900009 ()
Available from: 2014-02-07 Created: 2014-02-07 Last updated: 2017-12-06Bibliographically approved
3. Hunting Effects on Favourable Conservation Status of Highly Inbred Swedish Wolves
Open this publication in new window or tab >>Hunting Effects on Favourable Conservation Status of Highly Inbred Swedish Wolves
Show others...
2013 (English)In: Conservation Biology, ISSN 0888-8892, E-ISSN 1523-1739, Vol. 27, no 2, 248-253 p.Article in journal (Refereed) Published
Abstract [en]

The wolf (Canis lupus) is classified as endangered in Sweden by the Swedish Species Information Centre, which is the official authority for threat classification. The present population, which was founded in the early 1980s, descends from 5 individuals. It is isolated and highly inbred, and on average individuals are more related than siblings. Hunts have been used by Swedish authorities during 2010 and 2011 to reduce the population size to its upper tolerable level of 210 wolves. European Union (EU) biodiversity legislation requires all member states to promote a concept called “favourable conservation status” (FCS) for a series of species including the wolf. Swedish national policy stipulates maintenance of viable populations with sufficient levels of genetic variation of all naturally occurring species. Hunting to reduce wolf numbers in Sweden is currently not in line with national and EU policy agreements and will make genetically based FCS criteria less achievable for this species. We suggest that to reach FCS for the wolf in Sweden the following criteria need to be met: (1) a well-connected, large, subdivided wolf population over Scandinavia, Finland, and the Russian Karelia-Kola region should be reestablished, (2) genetically effective size (Ne) of this population is in the minimum range of Ne = 500–1000, (3) Sweden harbors a part of this total population that substantially contributes to the total Ne and that is large enough to not be classified as threatened genetically or according to IUCN criteria, and (4) average inbreeding levels in the Swedish population are <0.1.

Abstract [es]

El lobo (Canis lupus) está clasificado como en peligro en Suecia por el Centro Sueco de Información de Especies, que es la autoridad oficial para la clasificación de amenazas. La población actual, que fue fundada a principio de la década de 1980, desciende de 5 individuos. Esta aislada y tiene altos niveles de endogamia, y en promedio los individuos están más relacionados que los hermanos. Durante 2010 y 2011, las autoridades suecas han usado la cacería para reducir el tamaño de la población hasta su nivel superior tolerable de 210 lobos. La legislación de biodiversidad en la Unión Europea (UE) requiere que todos los países miembros promuevan un concepto denominado “estatus de conservación favorable” (ECF) para una serie de especies incluyendo al lobo. La política nacional sueca establece el mantenimiento de poblaciones viables, con niveles suficientes de variación genética, de todas las especies que ocurren naturalmente. La cacería para reducir el número de lobos en Suecia no se alinea con los acuerdos políticos nacionales y de la UE y es una limitante para que se cumplan los criterios para un ECF basado genéticamente. Sugerimos que para alcanzar el ECF para el lobo en Suecia se requiere cumplir con los siguientes criterios: (1) el restablecimiento de una población grande, subdividida y bien conectada en Escandinavia, Finlandia y la región Karelia-Kola de Rusia, (2) tamaño efectivo genéticamente (Ne) de esta población en el rango mínimo de Ne = 500–1000. (3) Suecia tiene una parte de esta población total que contribuye sustancialmente al Ne total, y que es lo suficientemente grande para no ser clasificada como amenazada genéticamente o de acuerdo con los criterios de la UICN, y (4) los niveles promedio de endogamia en la población sueca son <0.1.

Keyword
Canis lupus, conservation genetics, conservation policy, convention on biological diversity, FCS, genetic management, habitats directive, pedigree analysis, Análisis de pedigrí, Canis lupus, Convención de Diversidad Biológica, Directiva de Hábitat, genética de la conservación, manejo genético, políticas de conservación
National Category
Zoology
Identifiers
urn:nbn:se:su:diva-88499 (URN)10.1111/j.1523-1739.2012.01965.x (DOI)000316694600003 ()
Available from: 2013-03-17 Created: 2013-03-17 Last updated: 2017-12-06Bibliographically approved
4. Monitoring rate of inbreeding and loss of genetic variation in traditional Swedish dog breeds of conservation concern using pedigree data
Open this publication in new window or tab >>Monitoring rate of inbreeding and loss of genetic variation in traditional Swedish dog breeds of conservation concern using pedigree data
(English)Manuscript (preprint) (Other academic)
Abstract [en]

Increasing conservation genetic focus is directed towards domestic animal populations because: 1) domestic animals are of direct socio-economic importance to humans, and 2) strong selective breeding for a single or a few traits are considered to rapidly deplete the genetic variability of many domestic animal populations. International policy work within the Convention on Biological Diversity identifies strategies for minimizing genetic erosion of domesticated animals as one of the key biodiversity targets for 2010-2020. We investigated recent rate of inbreeding and loss of genetic variation in 12 traditional Swedish dog breeds, 10 of which have been identified as of conservation concern by the Swedish Board of Agriculture. We used studbook data provided by the Swedish Kennel Club with pedigrees dating back to the mid 20th century and comprising 5-10 generations with 350-60,000 individuals per pedigree. We assessed levels of inbreeding and loss of genetic variation measured in relation to the number of founding animals (founder alleles) among live animals at five points in time (1980, 1990, 2000, 2006, and 2012). We found average inbreeding coefficients among breeds to double over our period of monitoring, from an average of 0.03 over breeds in 1980 to 0.07 in 2012. This is in spite of the majority of breeds being large with pedigrees comprising thousands of individuals. The loss of genetic variation is extensive with an average of 70 percent loss of founder alleles over the study period, and the proportion of founder genome equivalents in relation to the number of founders is on average only 0.09. This is comparable to previously published rates of genetic variability loss in dog breeds, indicating that the explicit conservation goals for these traditional Swedish breeds is not yet reflected in conservation genetic status. One of the breeds is particularly threatened - the Gotland hound with less than 150 living individuals, but this breed also shows comparably larger retention of genetic variation.

Keyword
animal genetic resources; conservation genetics; pedigree analysis; domestic dog, Canis familiaris, Convention on Biological Diversity, Aichi Target 13, genetic biodiversity
National Category
Genetics
Identifiers
urn:nbn:se:su:diva-100601 (URN)
Available from: 2014-02-07 Created: 2014-02-07 Last updated: 2014-10-13Bibliographically approved
5. Supportive release from a zoo population by cross-fostering can significantly increase genetic variation in the highly inbred wild Swedish wolf population
Open this publication in new window or tab >>Supportive release from a zoo population by cross-fostering can significantly increase genetic variation in the highly inbred wild Swedish wolf population
(English)Manuscript (preprint) (Other academic)
Abstract [en]

The wild wolf population (Canis lupus) in Sweden is classified as Endangered and descends from only five individuals. The population is isolated and highly inbred; individuals are on average more related to each other than siblings. Inbreeding depression expressed as reduced litter size and a high frequency of spinal disorders have been reported. Management goals include reducing levels of inbreeding, and one suggestion to achieve this is through crossfostering release of pups from a zoo conservation breeding program into wild dens. We used pedigree data of the wild and zoo populations, respectively, to evaluate to what extent the zoo population can support the wild one with respect to increased genetic variation and reduction of inbreeding. The results show a potential to almost double genetic variation measured as founder alleles from 11.2 to 21.1, despite the fact that the two populations have three common founders. Potentially, the number of founder genome equivalents can be increased from present 1.8 to around 3.2. However, to achieve maximum genetic support, almost 50 percent of the wild population gene pool must consist of genes from the zoo population. Average kinship in the joint population of zoo and wild wolves is 0.15, thus release of zoo wolves cannot in itself be expected to reduce average inbreeding below the management target of 0.1. We conclude that releases from the zoo can support but not resolve the genetically precarious situation of the wild Swedish wolf population.

Keyword
captive breeding, pedigree analysis, Swedish wolves, conservation policy, genetic rescue
National Category
Genetics
Research subject
Population Genetics
Identifiers
urn:nbn:se:su:diva-100602 (URN)
Available from: 2014-02-07 Created: 2014-02-07 Last updated: 2014-10-13Bibliographically approved

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