DOKTORANDUPPSATS ZOOLOGISKA INSTITUTIONEN Stockholms Universitet S-106 91 Stockholm

CONSERVATION GENETIC

MANAGEMENT OF DOMESTIC ANIMALS WITH PARTICULAR FOCUS ON THE

DOG (CANIS FAMILIARIS)

Författare: Maria Jansson Ämne: Populationsgenetik Löpnummer: 2009:3

Arbetets titel:

CONSERVATION GENETIC MANAGEMENT OF DOMESTIC ANIMALS

WITH PARTICULAR FOCUS ON THE DOG (CANIS FAMILIARIS)

Författarens namn: Maria Jansson

Handledare: Linda Laikre

Forskningsämne: Populationsgenetik

Granskningskommitté: Hans Temrin, Bengt Karlsson

Table of contents

1. Introduction ..................................................................................................................... 1

1.1 National and international conservation policy ........................................................ 3

2. Conservation vs. selective breeding ................................................................................ 5

3. Some pioneering work on conservation genetics of domestic animals .......................... 6

4. Conservation genetic management of domestic animals ................................................ 8

4.1 Conservation programs ............................................................................................. 8

4.2 Genetic diversity ..................................................................................................... 10

4.3 Molecular methods .................................................................................................. 10

4.4 Traditional breeds vs. commercial breeds .............................................................. 11

4.5 Breeding programs .................................................................................................. 12

4.6 Inbreeding depression in dog breeds ...................................................................... 12

5. Pedigree analysis for conservation breeding ................................................................ 21

5.1 Pedigree analysis and genetic variation in dogs ..................................................... 22

6. Prioritization for conservation of domestic breeds ....................................................... 23

6.1 Weitzman’s method ................................................................................................ 23

6.2 Eding et al.’s method .............................................................................................. 24

6.3 Holistic view ........................................................................................................... 24

6.4 FAO criteria for prioritization ................................................................................. 25

6.5 Methods for prioritization of dog breeds, conclusion ............................................. 25

7. The domestic dog .......................................................................................................... 27

7.1 Modern dog breeding .............................................................................................. 28

7.2 The effect of selection on behavior ......................................................................... 29

7.2.1 Behavior test on dogs ....................................................................................... 29

8. Concluding remarks ...................................................................................................... 32

9. Literature Cited ............................................................................................................. 34

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1. Introduction

Conservation genetics has been one of the corner stones of conservation biology ever since the field emerged as a science in its own right in the late 1970s (Soulé and Wilcox 1980). With respect to animals, conservation genetics has traditionally focused on conserving genetic variation in wild species that are either maintained in situ (i.e. in their natural habitat) or held in ex situ collections (i.e. in captivity in zoos and wild animal parks; Frankham et al. 2004). During recent years, however, increasing focus has been devoted to conservation genetic on domestic animal populations. This attention includes both scientific efforts and international and national policy work. In this essay I will summarize some of the past and current literature with respect to conservation genetic management of domestic animals. In particular, I will focus on the domestic dog.

Conservation is particularly complicated with respect to small populations (Franklin 1980). Small populations inevitably suffer from inbreeding and loss of genetic variation which may cause inbreeding depression and loss of evolutionary potential (i.e. the ability to adapt to changes in the environment; Gyllensten and Ryman 1985). Virtually all the genetic effects which arise in small populations result from the random sampling of alleles from parents to offspring. This process is known as genetic drift. In a small population, gene frequencies change rapidly from generation to generation because of this random process. A small population size can have genetic effects both over long and short time periods. Inbreeding depression can occur over a short time period. On a longer term, sampling effects that cause fluctuations in gene frequencies have important consequences for future evolution of the species (Crow and Kimura 1970). The necessity of conserving genetic variation in wild animals has been recognized and studied for quite a long time (e.g. Chesser et al. 1982).

The survival of a species in the long run is dependent on retaining enough genetic diversity both within and between populations to accommodate new selection pressures brought about by environmental change (Schonewald-Cox et al. 1983). A variety of parameters, foremost the number of existing gene pools, their heterogeneity, and their effective population sizes affects the probability of survival (Schonewald-Cox et al. 1983). The main threats against, and therefore the main reason for conserving breeding of, threatened wild mammals in Sweden are the chemical or mechanical methods in agriculture and forestry, whereas predators (e.g. the wolf) decrease in numbers primarily due to legal and illegal hunting (WWF 2008).

Regarding conservation of wild populations, a number of issues have been raised by researchers including documenting occurrence and effects of inbreeding in captive populations (Soulé and Wilcox 1980; Ralls and Ballou 1982, Shonewald-Cox et al. 1983), the studies have provided guidlines for captive breeding programs with respect to conservation of genetic diversity (Soulé and Wilcox 1980; Ralls and Ballou 1983; Templeton and Read 1983; Foose 1983; Benirschke 1983), documenting occurrence and effects of inbreeding in the wild (Ryman 1970; Greenwood et al. 1978; Laikre et al. 1997; Liberg et al. 2005), identifying conservation management units (Schwarts et al. 2007), determining degree of genetic isolation among populations (Frankham et al.

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2004), analyzing genetic effects of large scale exploitation of natural populations (Laikre and Ryman 1996; Allendorf et al. 2008), and estimating effective population size of natural populations (Frankham 1995; Jorde and Ryman 1996; Leberg 2005; Wang 2005).

Al though the need for conserving genetic variation within domestic animal breeds and crops was recognized early in the history of conservation genetics (Frankel 1970 1974; Gyllensten et al. 1983), relatively little research attention has been paid to domestic gene pools (but see e.g. Hall 1989; Clarke et al. 1989), particularly with respect to animals. However, the importance of conserving the genetic variability of domestic populations of animals and plants is now becoming increasingly recognized. Genetic conservation of wild populations is assumed to be connected with genetic management of domesticates (Frankel 1983). The common argument is that the wild variant is a genetic resource for the domestic one. Frankel (1983) states that in plants, the domestic variant might also be the most valuable genetic resource for a wild threatened relative. Two concepts are especially important; fitness (impaired by inbreeding) and genetic adaptation (improved by genetic variation).

Several reasons for conserving genetic variation of domestic animal populations have been proposed. These include:

• Economics; Genetic variation is necessary for effective (i.e. economical; Handley et al. 2007; van Marle-Köster et al. 2008) selective breeding (Gyllensten and Ryman 1985). While effectiveness is an economical issue, it also affects politics (Soulé and Wilcox 1980). When domestic gene pools are depleted through strong selective breeding it is difficult to redirect selective pressure to maintain genetic diversity (Gyllensten and Ryman 1985). Genes of old, traditional breeds may prove important for future breeding. Though we never know what might be needed in future we might need a genetic insurance (Bhatia and Arora 2005).

• Research; The gene banks of domestic populations can work as models to understand wild populations (Gyllensten and Ryman 1985; Soulé and Wilcox 1980; Bhatia and Arora 2005; Handley et al. 2007). The domestic populations are easier to control.

• Social history aspects; The domestic animals are a living cultural heritage and a part of important ecological and social considerations (Gyllensten and Ryman 1985; Bhatia and Arora 2005; Handley et al. 2007).

• Practical use; Production of useful components (Bhatia and Arora 2005; van Marle-Köster et al. 2008).

Conservation in general is also motivated on ethical grounds (Franklin 1980; Soulé and Wilcox 1980) and for giving recreation and education (Soulé and Wilcox 1980). Many old, domestic animal breeds which are not used in large scale production are typically small, and many are considered threatened (Lanneck 2007). Because of the potential genetic resources these breeds represent, immediate conservation actions are of great importance.

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1.1 National and international conservation policy

Sweden and the EU are parties to the Convention on Biological Diversity (CBD: www.cbd.org), which explicitly states that domesticated animals and the genetic resources they represent are part of the biological diversity that should be conserved, monitored, and sustainably used. Under Agenda 21 the importance of strengthening the capacity of countries to benefit fully from their biological resources was identified as a priority need (Wilson 1997). In the United Nations environmental conference in Stockholm 1972, an agreement was made that every country would be responsible of domestic breeds with historical origin in that country and pay special attention for the endangered breeds (Swedish Board of Agriculture 2002).

The breeds to be conserved are not only the ones that are commercially important – breeds with a large social history value are also a target for conservation (Swedish Board of Agriculture 2002). Similarly, the National Swedish Environmental Objectives (www.miljomal.nu) recognize the need to conserve both wild and domestic biological diversity. In 2007, the Interlaken Declaration on Animal Genetic Resources was adopted by the international community (FAO 2007), and this declaration explicitly states the need to assure conservation and sustainable use of domestic animal genetic resources. Further, the European Convention for the Protection of Pet Animals states that domestic animals used for breeding should be selected in a way that do not put animal welfare or health at risk due to hereditary disorders or diseases (Council of Europe 1987).With respect to domestic animal populations, the Swedish Board of Agriculture has identified a number of traditional Swedish breeds of particular conservation concern. Regarding dog breeds the Swedish Board of Agriculture propose that Sweden should take conservation responsibility for ten of them (Lanneck, 2007):

• dansk/svensk gårdshund

• drever

• gotlandsstövare

• hamiltonstövare

• jämthund

• norrbottenspets

• schillerstövare

• smålandsstövare

• svensk lapphund

• västgötaspets

The Food and Agriculture Organization of the United Nations (FAO) collects information about existing domestic animal breeds in a database (Lanneck 2007). In Sweden the data collection is done by the Swedish Board of Agriculture. The Swedish Board of

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Agriculture asks for an extensive survey of the breeds that are considered of particular conservation concern for Sweden (Hansson 2008). Data collected for each breed include:

• Number of male and female animals • Sex ratio among sexually mature animals • Number of offspring/year • Genetic status • Population structure • Use today • Pedigree • Breeding planning • Health programs • The breeding clubs documentation

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2. Conservation vs. selective breeding

Domestic populations are traditionally bred through selection. A large amount of genetic variation can be assumed to have been lost in the domestic populations while selection only lets a few animals breed and the others’ genetic variation is lost.

Aims

Selective breeding – getting some characters in a higher proportion by changing the gene pool.

Conservation breeding – to conserve genetic variation (quantity and distribution) to as great extent as possible.

(Laikre and Ryman 1999.)

Selective breeding was practised by humans long before we had any knowledge about genetics or heredity. The conservation breeding approach is only about 30 – 40 years old. People started to realize the importance of conservation genetic management of domestic animals for economic reasons (Handley et al. 2007; van Marle-Köster et al. 2008; Gyllensten and Ryman 1985; Soulé and Wilcox 1980; Bhatia and Arora 2005), for social history aspects (Gyllensten and Ryman 1985; Bhatia and Arora 2005; Handley et al. 2007), for practical use (Bhatia and Arora 2005; van Marle-Köster et al. 2008) and for ethical reasons (Franklin 1980; Soulé and Wilcox 1980). When domestic gene pools are depleted through strong selective breeding it is difficult to redirect selective pressure to maintain genetic diversity (Gyllensten and Ryman 1985). Genes of old, traditional breeds may prove important for future breeding. Though we never know what might be needed in the future we might need a “genetic insurance” (Bhatia and Arora 2005). Modern day dog breeding does not aim at conserving genetic variation within breeds, and the strong focus on external morphology has probably resulted in considerable loss of intra breed genetic diversity, because only very few of the available dogs are used for breeding. The breeding of dogs in Sweden is handled by private persons, most of whom are members of the Swedish Kennel Club (SKK). SKK has only recently recognized the need to modify their breeding strategies to also take the conservation of intra breed genetic variation into consideration. The problem is that breeders want not only to conserve, but also to select for certain characters. This is the same problem that occurs with other domestic animals:

“The aim of animal breeding is to change the genetic makeup of domestic animals so that they better meet our needs.” (Barker, 1999, p.34)

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3. Some pioneering work on conservation genetics of domestic animals

Some of the earliest scientific papers on conservation genetics of domestic animals, were published in 1989 in the journal Conservation Biology (Hall 1989; Clark et al. 1989). In the same year a paper on the application of pedigree analysis in conservation breeding was published in the journal Zoo Biology (Geyer et al. 1989). In this section I will give a brief overview of these pioneering papers which have contributed greatly to the modern field of conservation genetics of domestic animal breeds.

“Breed Structures of Rare Pigs: Implications for Conservation of the Berkshire, Tamworth, Middle White, Large Black, Glouster Old Spot, British Saddleback, and British Lop” (Hall 1989) was the first paper in its field in Conservation Biology. This study showed that pigs (Sus domesticus)whose parents were from different herds were significantly less inbred than those with both parents from the same herd. At that time, in British pedigree pigs, the “bloodline” system of breed subdivision was practiced (according to Hall there was, at that time, not any good definition of the term “bloodline” but it appears to refer to inbreeding based on a founder). In some breeds pigs sharing the same bloodline were more closely related than pigs within the same herd but with different bloodline names. Hall (1989) suggests that the planning of conservation measures should take into account the retention from the founder boars and the most used boars. He comments:

“Indeed the genes of a particular ancestral male can sometimes be concentrated in a present-day female.” (Hall 1989, p. 37)

In the late 1970s the pigs’ registration system had been transferred to a database which made it possible for Hall (1989) to compute inbreeding coefficients, following pedigrees for up to six generations. Further, he investigated mean inbreeding of piglets and classified the piglets by bloodline and herd. He compared kinship for animals to find out whether animals bred in the same herd, of different bloodlines, were more or less closely related than animals bred in different herds. The coefficient of kinship for a pair of animals is defined to equal the inbreeding of potential progeny produced by the pair (Falconer and Mackay 1996). The most important thing is that pedigree information on individual pigs is documented (Hall 1989).

Later in 1989 Conservation Biology published a paper on how pedigree analysis can be combined with molecular methods in order to evaluate the genetic variation of domestic animals. This paper, “Genetic Polymorphisms and Their Relationships with Inbreeding and Breed structure in Rare British Sheep: The Portland, Manx Loghtan, and Hebridean”, use both pedigree and cluster analyzes (Clarke et al. 1989). The pedigree analysis shows that the most unusual alleles could be traced back to particular ancestors, and the cluster analysis showed close relationships (low genetic distance) between the Manx Loghtan and Hebridean breeds of sheep (Ovis aries). Those kind of analyzes were made possible by sampling blood groups and protein polymorphisms (with different phenotypes) of the sheep (Clarke et al. 1989). The purpose of this kind of technique in conservation is to

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check whether genetic variation has been maintained in the population (Clarke et al. 1989).

Clarke et al (1989) suggest that rare variants of alleles traceable to foundation stocks must be seen as part of the genotype of the breeds, and their preservation within the respective breeds would be one of the consequences of successful conservation programs. Pedigree analysis is the appropriate technique to plan mating and aims at the continued representation of foundation animals in the pedigrees of the latest generation (Clarke et al. 1989).

Many domestic breeds have pedigrees, and the papers by Geyer and Thompson (1988) and Geyer et al. (1989) strongly contributed to modern pedigree analysis for conservation purposes, even though they deal with wild animals bred in captivity. The first paper “Gene Survival in the Asian Wild Horse (Equus przewalskii): I. Dependence of Gene Survival in the Calgary Breeding Group Pedigree” (Geyer and Thompson 1988) shows that probabilities of gene survival give a more complete summary of the genetic structure of a set of individuals than is provided by more routine measures such as heterozygosity or founder contribution. The paper shows the feasibility of computing these probabilities for small groups of current individuals descended from few founders in large pedigrees. From these pedigrees the authors were able to calculate the number of surviving founder genes, inbreeding, and kinship (see further chapter 5).

The main feature of the second paper (Geyer et al. 1989); “Gene Survival in the Asian Wild Horse (Equus przewalskii): II. Gene Survival in the Whole Population, in Subgroups, and Through History” is improvements of the computer programs used. In principle, any genetic information might be estimated through gene drop simulations (Geyer et al 1989). Of course the estimated values may be somewhat imprecise so, if possible, one would prefer exact calculations, but in complicated cases it is not doable. Thus, simulations have a great practical importance (Geyer et al. 1989). Thomas (1990) demonstrated that genedrop simulations give very good estimations if run sufficient number or times (e.g. over 1000 runs).

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4. Conservation genetic management of domestic animals

“Biological diversity comprises all species of plants and animals, their genetic material and the ecosystems of which they are part. Farm animal diversity is an important though far too often neglected component of this diversity.” (Wilson 1997, p. 249)

This chapter exemplifies some aspects of the scientific discussion regarding conservation genetic management of domestic animals. Some examples of empirical studies on conservation genetic management of domestic animals are given in Table 1.

The breeds’ future improvement is dependent on genetic variation, both within and between breeds. Each breed is the product of mutation, genetic drift, separate adaptations and evolution to different selection pressures (Barker, 1999).

The interest in conservation genetics and farm animals is currently increasing. In a survey, Baumung et al. (2004) identified 87 farm animal breeds chosen mainly because of their long history of isolation, unique phenotypic qualities or an evolution within a unique environment; and studied them with respect to genetic diversity and conservation.

Examples of evolution of individual breeds that are adapted to unique environments include the variation of agro-climate conditions of the different regions in India that has led to the development of various breeds/strains of sheep that are well adapted to specific environmental conditions (Bhatia & Arora 2005). In the Balkan region several different types of Pramenka sheep have been developed for different environmental and socio-cultural conditions (Cinkulov et al. 2008a).

4.1 Conservation programs

Nowadays 40 domesticated mammalian and avian species are used to meet our expectations of food (Barker 2001). Within these 40 species there are in total about 5000 (Barker 2001) breeds (3213 according to Hall and Ruane 1993) and the best available information indicates that about 50% of the total genetic variation within a domestic species is variation among breeds. This is why the primary focus in the conservation of domestic animal diversity is on the conservation of breeds (Barker 2001), i.e. the biological unit for conservation in domestic animals is usually the breed (Solis et al. 2005).

About 200 years ago, the situation started to change dramatically, from sustainable use of domestic animals leading to animals well adapted to local conditions, to the rise of the concept of breed (Taberlet et al. 2008). Of the breeds that existed in the beginning of the 19th century, 16% are estimated to have become extinct (Hall and Ruane 1993) and 30% or 1350 breeds of all present day livestock breeds are at risk of extinction (Hall and

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Ruane 1993; Taberlet et al. 2008). Over the past 15 years 300 of the 6000 breeds of farm animals identified by the FAO have become extinct (Taberlet et al. 2008). For example more than 50% of the sheep breeds in India (Bhatia and Arora 2005) and 58% in Europe compared to 32% worldwide (Handley et al. 2007), are currently under threat to extinction.

From a global perspective conservation is not only about endangered breeds but also about those breeds that are not being utilized efficiently (Barker 2001). When making a management program the conservation goals are according to Wilson (1997):

i. identify all genetic resources ii. develop and use the diversity to increase production

iii. monitor resources iv. preserve resources not in current demand

There is only a small proportion of breeds that are involved in planned conservation programs, and those are found mainly in the developed world (Barker 2001).

The stock-holder’s involvement is important for success of a conservation programs (Bhatia and Arora 2005), and cultural, economic, and scientific factors should be considered in management (Solis et al. 2005). The history of the breed may also provide a foundation for conservation (Kantanen et al. 2000), e.g. the Icelandic cattle (Bos Taurus) are known to have experienced isolation for more than 1000 years and are scientifically, historically, and culturally unique (Kantanen et al. 2000). The ex situ conservation might be conducted in a zoological garden. In a survey carried out in Germany, 227 zoological gardens answered a questionnaire regarding whether they kept domestic animals and 178 (78%) of them did (Hermanns et al. 2008).

The data for conservation programs is sometimes collected from databases such as the Global Data Bank for Domestic Livestock of the Food & Agriculture Organization of the United Nations (Hall and Ruane 1993; Baumung et al. 2004). This database has been set up to compare demographic and production information and is of fundamental importance to conservation (Hall and Ruane 1993). It provides an inventory of breeds for each country and the means to identify and monitor endangered populations (Hall and Ruane 1993).

Bhatia and Arora (2005) claim that conservation is often complex and includes several components that have to be combined in a holistic approach;

• Monitoring and describing existing animal genetic resources • Breed characterization at the molecular level • Accessible documentation and informed use of it • Appropriate conservation, in situ and/or ex situ • National watch list

Combining molecular genetic information with physiological, ecological, and ethological data provides the basis for the most informed gene resource management program (Tapio et al. 2005b). Invention is important in most conservation project; one has to find the possibilities for each breed. One example given is livestock breed safari to watch the Indian sheep landrace (Bhatia and Arora 2005).

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4.2 Genetic diversity

Studies of genetic diversity in domestic animals are based on an evaluation of the genetic variation within breeds and the genetic relationships among them, since the breed is the management unit for which factors such as inbreeding are controlled (Tapio et al. 2005b). Research has indicated that domestic species resemble the wild species in the respect that the peripheral or isolated populations/breeds are important contributors to overall genetic variation, especially concerning allelic variation (Tapio et al. 2005a).

According to Tapio et al. (2005b) the methods of choice to evaluate genetic diversity of domestic animal breeds have been:

• Statistical measures derived from Wright’s F-statistics • Bayesian model-based clustering methods which allow for the inference of

population structure and the assignment of individuals to populations • Phylogenetic techniques based on genetic distances estimated from polymorphic

microsatellite markers (described in the next section)

The most commonly used statistic with respect to genetic subdivision is the FST value, which can indicate whether there is a genetic divergence of populations/lines or not (e.g. van Mörle-Köster et al. 2008; Liu et al. 2008; Queney et al. 2002; Rodrigáñez et al. 2008). F-statistics can be used together with clustering methods (e.g. van Mörle-Köster et al. 2008, Li et al. 2007). In this combined approach one can look at the data from two different perspectives; clusters and differences.

Historical evidence is also useful e.g. when investigating separation between breeds (Kantanen et al. 2000). A Nordic study of divergence estimates between Icelandic cattle and Norwegian native breeds based on genetic methods, estimated a separation time of more than 1000 years were found - a finding consistent with historical evidence (Kantanen et al. 2000).

The breeds with the highest genetic diversity are expected to be found close to the domestication centers, which is important information for tracking genetic resources (Taberlet et al. 2008).

4.3 Molecular methods

The contribution of a particular breed to the genetic diversity of a particular domestic species can be estimated using selectively neutral genetic variation, meaning variation that is not affected by neutral or artificial selection (Tapio et al. 2005a). During the past decade a large number of genetic diversity studies in domestic livestock based on microsatellite loci have been carried out all over the world (Baumung et al. 2004). When there are no pedigrees (pedigree-analysis is described in chapter 4) or when there is pedigrees for different populations or breeds and one wants to know how they are connected, genetic markers may be useful. Microsatellites are usually the most

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commonly used molecular genetic marker in this respect (see Table 1). Microsatellites consist of tandem repeats of a short DNA sequence of one to six nucleotides that are repeated along the DNA strand. The number of repeats at a polymorphic locus ranges from approximately five to 100. Methods used to study variation at microsatellite loci include PCR (polymerase chain reaction) to amplify the particular allele, followed by gel electrophoresis to separate the amplified segments according to size (which is determined by the number of repeats). PCR can generate millions of copies of a specific target DNA sequence and the gel electrophoresis makes it possible to determine the genotype of an individual. The main advantage of microsatellites is that they are usually highly polymorphic which results from a high mutation rate (Allendorf and Luikart 2007).

One example of a microsatellite study (Aranguren-Mendez et al. 2001) showed little variation between Spanish donkey breeds, but large differentiation between Spanish breeds and the Moroccan ass (Equus africanus asinus) and also with the horse, used as an outgroup. This kind of information can be used for a conservation plan for maintaining as much genetic variation as possible.

Mitochondrial DNA (mtDNA) has a strictly maternal inheritance and is therefore useful to analyze the evolution of closely related groups (Pérez-Gutiérrez et al. 2008). At last but not least the recent research that made it possible to draft whole genome of different animals (i.e. O´Brien et al. 2008), which shows that there is more to come in this field.

4.4 Traditional breeds vs. commercial breeds

The breeds of the developed world that is included in planned genetic improvement programs have been and are continually selected for performance in high-input production systems. This is in sharp contrast to the developing countries where low to medium input is demanded for the production systems (Barker 2001). In recent years there has been a strong recognition of the need for conservation of the adapted livestock breeds of the developing world both for immediate and for future use (Barker 2001). There are also great problems with the commercial stocks; artificial breeding strategies of cattle are implemented in such a way that it is a genetic contamination to the native gene pools of cattle (Li et al. 2007). In some developing countries (e.g. Nepal; Wilson 1997) the government policy is to upgrade and replace local types with improved stock.

There are threats also to the highly productive breeds (Taberlet et al. 2008):

• Fragmentation of the species into discrete breeds. • Effects of reproductive technologies like artificial insemination (which can have a

huge effect on effective population size.

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4.5 Breeding programs

Conservation of small populations of local breeds faces several threats (Taberlet et al. 2008):

• The socio-economic context; there is a lack of application of methods for estimating real economic value of this breeds.

• Management of small-size populations with respect to inbreeding. • Threats to adaptation by crossbreeding were adaptive traits may be rapidly lost. • Geographical confinement – an infectious disease might wipe out an entire

population.

Most conservation genetic studies on domestic animals result in some sort of suggestions for breeding programs and/or strategies for conservation. For instance, the results of a study of genetic diversity and population structure of six local chicken (Gallus domesticus) lines in South Africa showed that some lines were clearly defined and this information should be taken into consideration in conservation strategies (van Mörle-Köster et al. 2008). Sadly, many developing countries lack breeding programs for native breeds. Nepal, which is a scientifically documented example, lacks conservation programs except for one type of goat (Carpra hircus; Wilson 1997).

Breeding programs are usually designed to minimize inbreeding. Sometimes inbreeding seems not to accumulate deleterious alleles but to purge those (Visscher et al. 2001). As an example there is a viable, feral herd of genetically uniform cattle in northern England that is thought to have experienced no immigration for at least 300 year, but the homozygosity of the Chillingham herd might help the genetics of disease resistance (Visscher et al. 2001).

4.6 Inbreeding depression in dog breeds

Because of the closed gene pools, founder-effects are responsible for several breed related diseases (Ubbink et al. 1998). Such diseases constitute a huge problem in many dog populations and are probably threatening their survival (Ubbink et al. 1998). A population of Dutch Labrador retrievers (with elbow dysplasia) showed estimates of relatedness to seven related ancestors when modeling the most likely pattern in passage of genetic risk down the generations (Ubbink et al. 1998). A similar approach was used on English keeshounds that have problems with canine epilepsy. By calculating inbreeding and identifying common ancestors under the hypothesis that both parents of an epileptic pup were themselves carriers, it could be assumed that the predisposition of the epilepsy in keeshounds was determined by a single autosomal recessive gene (Hall & Wallace 1996).

Another approach, using molecular markers is suggested by Zajc et al. (1997). The markers should be as polymorphic as possible, for the investigator to stand a good chance

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of finding markers linked to inherited diseases in highly inbred dog breeds (Zajc et al. 1997).

Another case of inbreeding depression is found in the Icelandic sheepdog. A significant relationship between inbreeding and the occurrence of hip dysplasia was found (Ólafsdóttir & Kristjánsson 2008).

P G C Bedford, at the Royal Veterinary College in UK, states in an editorial comment in Animal Welfare 1999 that:

“Within the world of the pedigree dog, competition is extreme – and breeding policy based on dedication to breed type has resulted in the appearance of some 300 inherited diseases among canine species worldwide.”

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Tabel 1. Empirical studies on conservation genetic management of domestic animals.

Species Objective/main observations/conclusions Method No of populations

No of individuals Reference

Artic fox (Alopex lagopus), Bee (Apis mellifera), Cat (Felis catus), Cattle (Bos taurus), Chicken (Gallus domesticus), Dog (Canis familiaris), Goat (Capra hircus), Goose (Anser anser), Horse (Equus caballus), Mink (Mustela vison), Pig (Sus domesticus), Rabbit (Oryctolagus cuniculus), Red fox (Vulpes vulpes), Reindeer (Rengifer tarandus), Salmon (Salmo salar), Sheep (Ovis aries), Turkey (Meleagris gallopavo)

Comparing and scoring 45 breeds from 17 domestic animal species, to facilitate decision making for conservation. Identified Norwegian breeds of high priority for conservation (e.g. Lundehund)

literature study 45 - Ruane (2000)

Ass (Equus africanus asinus), Buffalo, Cattle (Bos taurus), Chicken (Gallus gallus domesticus), Dromedary (Camelus dromedarius), Goat (Capra aegagrus hircus), Horse (Equus caballus), Pig (Sus scrofa), Sheep (Ovis), Yak (Bos grunniens)

1. Evaluation of recommend microsattelite loci for different species. 2. Assessment of genetic diversity in different species; The cattle were found to be most genetically diverse and the chicken exhibited the lowest level of variation.

microsattelite 86 95 % of projects sampled at least 25 animals per breed (varied between 10 and 2500 animals).

Baumung et al. (2004)

Ass (Equus africanus asinus), Cattle (Bos taurus), Goat (Capra aegagrus hircus), Horse (Equus caballus), Pig (Sus scrofa), Sheep (Ovis)

Stresses that characterization of breeds for genetic uniqueness is presently the most urgent task in conservation.

overview 1029 - Simon (1999)

Ass (Equus africanus asinus), Cattle (Bos taurus), Goat (Capra aegagrus hircus), Horse (Equus caballus), Pig (Sus scrofa), Sheep (Ovis), Water buffalo (Bubalus bubalis)

The richest countries have lost the highest proportions of their breeds, implying that agricultural development is hostile to animal genetic resources.

overview 618 extinct, 475 rare, 2738 common

- Hall & Ruane (1993)

Ave, Bovidae, Cattle (Bos taurus and Bos indicus), Chicken (Gallus gallus domesticus), Duck (Anas platyhuncos), Elephant (Loxodonta africana), Goat (Capra hircus), Horse (Equus caballus), Pig (Sus scrofa), Pigeon (Columba livia), Rabbit (Oryctolagus cuniculus), Sheep (Ovis aries), Water buffalo (Bubalus bubalis)

Identifying and listing conservation needs for livestock in Nepal.

literature study 17 species, several populations

- Wilson (1997)

Buffalo (Bubalus) The population of South Kanara buffaloes showed departure from Hardy-Weinberg equilibrium at all of the 10 loci tested. Considerably inbreeding was found. The breed has not encountered a genetic bottleneck in the recent past.

microsattelite 1 48 Kathiravan et al. (2008)

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Buffalo (Bubalus) Lack of heterozygotes in the population. FIS = 0.181 microsattelite 1 397 Mishra et al. (2009)

Buffalo (Syncerus caffer) The degree of differentiation between Italian and Greek buffalo was moderate.

microsattelite 2 38 and 32 Moioli et al. (2001)

Camel (Camelus dromedarius) FST of 3.1 % between Majoreo camels and African camels. FIS were almost three times higher in the African camel.

microsattelite 2 10 Majorero and 37 African

Schulz et al. (2005)

Camel (Camelus dromedarius) Description of genetic differentiation within and between three different camel breeds. The least genetic variability was found in the Jaisalmeri breed.

PCR on random oligonucleotide primers

3 29 Bikaneri, 30 Jaisalmeri, 18 Kachchhi

Mehta et al. (2006)

Cattle (Bos taurus) The expected loss of diversity in the set of breeds is between 1 and 3 percent of the actual diversity within 20 to 50 years.

micorosatellite and simulation

44 - Bennewitz et al. (2006)

Cattle (Bos taurus) Grouping of European cattle breeds into four major breed groups. Separation time estimated to more than 1000 years between Icelandic cattle and Norwegian native cattle breeds.

microsatellite 15 743 in total Kantanen et al. (2000)

Cattle (Bos taurus) Insight into the historical patterns of cattle breeding in the former Soviet Union identifying some neighboring regions as areas of genetic endemism were populations should be given priority.

microsatellite 21 772 in total Li et al. (2007)

Cattle (Bos taurus) Both Weitzman's and Eding's methods recognize the importance of local populations as a valuable resource of genetic variation.

microsatellite 35 1246 in total (11-49 per breed)

Tapio et al. (2006)

Cattle (Bos taurus) The six north Ethiopian cattle breeds can be sufficiently maintained.

microsatellite 6 41-19 per breed Zerabruk et al. (2007)

Cattle (Bos taurus) Provides a framework for classification and identification of threatened and extinct breeds.

questionnaires, field visits, information gartering, literature review

145 - Rege (1999)

Cattle (Bos taurus) The female founder alleles of Danish Shorthorn are at greater risk of being lost than the male founder alleles.

simulation by gene dropping

1 varied between simulation; 8 or 16

Trinderup et al. (1999a.)

Cattle (Bos taurus) 23 % of alleles in the Danish Shorthorn population of 1997 originated from the "Old type".

simulation by gene dropping

1 482 Trinderup et al. (1999b.)

Cattle (Bos taurus) Telling about conservation of Sahiwal cattle by keeping herds on state farms and individual ranches. There is also a semen bank.

overview 1 - Muhuyi et al. (1999)

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Cattle (Bos taurus) Farmers’ opinions of a native cattle breed in Norway. The result showed that native cattle breeds were significantly different from the predominant breed regarding traits that may be considered important for extensive production systems.

questionnaire 2 - Saether & Vangen (2001)

Cattle (Bos taurus) Inbreeding was not found to be a major problem in any of the populations examined, however more and more breeders demand proven sires to increase milk production from fewer cows which may result in future increase of inbreeding.

pedigree analysis 4 - Hansen et al. (2003)

Cattle (Bos taurus) The average inbreeding from all cows in the breeding population was between zero and 55%. The top 26% most inbred cows had inbreeding coefficients of at least 13.8%.

pedigree analysis 1 17936 Olori & Wickham (2004)

Cattle (Bos taurus) The population of Uruguayan Creole cattle is not at risk due to its genetic diversity and demographic structure however all the individuals are concentrated in only one place.

population viability analysis with VORTEX

1 575 Armstrong et al. (2006)

Cattle (Bos taurus) The Creole breeds and the Zebu Brahmna were predominantly of European origin.

microsattelite 7 80 Barrera et al. (2006)

Cattle (Bos taurus) The level of inter- and intra-population variability has been determined and described in Spanish.

microsattelite, mtDNA

1 300 Luque et al. (2006)

Cattle (Bos taurus) Presences of Bos indicus genes in the three Cuban populations of cattle.

proteins analyzed by PCR-RFLP

3 - Uffo et al. (2006)

Cattle (Bos taurus) Description of how the Randall cattle was rescued from extinction. A man had an isolated strain for nearly 80 years and left 13 animals (representing 12 different founders) when he died.

field visits 1 300 Sponenberg et al. (2007)

Cattle (Bos taurus) All four populations of cattle breeds (in India) were outbreed and Kasargod and Iduki animals should be considered as one population even though these are reared for different purposes.

microsattelite 4 102 Tantia et al. (2008)

Cattle (Bos taurus) Introgression from Bos indicus was examined in five populations of cattle in Nigeria. The results showed different levels of introgression in the populations.

microsattelite 5 200 Koudandé et al. (2009)

Cattle (Bos taurus) The results show that the two breeds Arab and Mbororo are not genetically different. Possible reasons are population admixture and sample collection.

microsattelite 2 131 Arab, 74 Mbororo

Flury et al. (2009)

Cattle (Bos taurus), Chicken (Gallus gallus domesticus)

Conservation priorities should not only be decided based on genetic marker data, one should also consider uses and performance of animals in relation to their natural environment and farming system.

field visits 3 - Verrier et al. (2005)

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Cattle (Bos taurus), Dog (Canis familiaris), Goat (Capra aegagrus hircus), Horse (Equus caballus), Sheep (Ovis)

Review of Spanish publications on microsatellite variation of domestic animals.

microsatellite review

- - Delgago et al. (2001)

Cattle (Bos taurus), Goat (Capra aegagrus hircus), Pig (Sus scrofa), Sheep (Ovis)

Utilization values for South African landrace breeds. overview 8 - Ramsay et al. (2000)

Cattle (Bos taurus), Goat (Capra aegagrus hircus),Sheep (Ovis)

Although cattle, sheep, and goats cannot be considered as endangered species according to the number of individuals, it is clear that many breeds are highly endangered.

overview Cattle, sheep and Goat worldwide

- Taberlet et al. (2008)

Chicken (Gallus gallus domesticus) Six South African chicken lines were grouped into six clusters. Although some individual birds tend to share more than one cluster.

microsatellite 6 100-150 per group

van Marle-Köster et al. (2008)

Chicken (Gallus gallus domesticus) The population of Punjab Brown chicken has not undergone any recent bottleneck.

microsattelite 1 532 Vij et al. (2006)

Dog (Canis familiaris) Extremely inbred dogs in 9/10 breeds, effective population size between 40 and 80 for 8/10 breeds and >90% of diversity loss over six generation in 7/10 breeds.

pedigree analysis 10 Pedigree size 1060 - 474078 individuals.

Calboli et al. (2008)

Dog (Canis familiaris) Polish hound: High imbalance of founder contributions with dominant contribution of four founders. Inbreeding coefficient ranged from 0.077 to 0.370.

pedigree analysis 1 247 litters from 105 kennels (1177 dogs)

Glazewska (2008)

Dog (Canis familiaris) The predisposition of keeshounds to idiopathic epilepsy appears to be determined by a single autosomal recessive gene.

pedigree analysis 1 49 litters Hall & Wallace (1996)

Dog (Canis familiaris) In the Icelandic sheepdog, a recently bottlenecked population, there is a significant relationship between inbreeding (f) and occurrence of hip dysplasia.

pedigree analysis, microsatellite

1 Pedigree size 1878, 409 with HD scores.

Olafsdottir & Kristjansson (2008)

Dog (Canis familiaris) 33 dog breeds indicated that the majority of the markers complied with HWE expectations. The entire cohort of dogs showed a significant deviation from HWE for all SNPs tested.

single-nucleotide polymorphisms (SNPs)

33 894 in total Short et al. (2007)

Dog (Canis familiaris) Estimates showed relatedness to seven ancestors were for the Labrador retrievers with elbow arthrosis.

pedigree analysis 1 Puppies born between January 1, 1988 and January 1, 1992.

Ubbink et al. (1998)

Dog (Canis familiaris) The intraspecies variation of dogs is lower than in humans, mouse, or rat, but similar to that in domestic animals. None of the three dog breeds (greyhound, Labrador, German shepherd) correspond to HWE.

microsatellite 3 50 per breed Zajc et al. (1997)

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Donkey (Equus asinus) Little differentiation between Spanish breeds, but great differentiation between them and the Moroccan ass and also with the horse.

microsatellite 5 74 - 140 (9, 24) Araguren-Mendez et al. (2001)

Duck (Anas platyrhychos) FST value for all breeds of the studied Chinese duck breeds were 0.155, showing medium differentiation, short domestication history and admixture of breeds after domestication.

microsatellite 26 31 per breed, 806 in total

Liu et al. (2008)

Fowl / Chicken (Gallus gallus) Life in captivity affect animals an animals behavior and capacity in a reintroduction situation. While there are morphological differences due to genetic variation found, there might be behavior differences as well.

behavioral studies 1 12 Håkansson & Jensen (2005)

General, livestock Inbreeding must be controlled efficiently to maintain sustainable livestock production in the future. Animal breeding, evolutionary biology and conservation genetics can contribute with knowledge.

literature study - - Kristensen & Sorensen (2005)

Horse (Equus caballus) The Hispano-Breton heavy horse breed exhibits high allelic richness but a certain degree of inbreeding is observed using microsatellite analysis.

microsatellite and mitochondrial DNA

1 53 (compared to 40 pure breed Spanish horses)

Perez-Gutierrez et al. (2008)

Horse (Equus caballus) In the phylogenetic tree, the Java Navarra breed was similar to the Pottoka, but appeared to stand in an intermediate position between this and the meat breeds.

microsatellite 4 417 in total Solis et al. (2005)

Horse (Equus caballus) Three native Danish horse breeds FST values and population assignment confirm population differentiation into tree different breeds.

microsatellite 3 30, 33 and 34 /population

Thirstrup et al. (2008)

Horse (Equus caballus) The group of Iberian ponies is morphologically very similar, in contrast to that which occurs with the groups of the riding and carriage horses.

morphological distance

17 - Jordana & Parés (1999)

Pig (Sus scrofa) Pigs with parents from different herds were significantly less inbred than those with both parents from the same herd. In some breeds pigs with the same bloodline name were more closely related.

pedigree analysis 7 445 - 1807 Hall (1989)

Pig (Sus scrofa) The rank of Spanish wild and domestic pig populations according to their contribution to the diversity will be different depending on the criteria utilized.

microsatellite 5 68 wild and 234 domestic pigs

Rodrigañez et al. (2008)

Pig (Sus scrofa) Introgression from other breeds has occurred in many pedigrees pig populations and there is an interest to develop methods to detect introgression.

DNA markers 3 - Alderson & Plastow (2004)

Rabbit (Oryctolagus cuniculus) European domestic rabbit has a good conservation of diversity. microsatellite and 4 34-129 Queney et

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Selected strains (artificial selection for a performance trait such as fur) keep higher level of diversity compared to other breeds.

mitochondrial DNA

al. (2002)

Rabbit (Oryctolagus cuniculus) Conservation actions; constitution of a bank of frozen embryos, in situ preservation by breeding selected populations in farms.

A number of different markers (e.g. mtDNA, microsatellite, proteins)

100 - Bolet et al. (1999)

Sheep (Ovis)

The ovine diversity in India is rapidly decreasing and over 50 percent of breeds are under threat, conservation programs are needed.

overview

40-43

-

Bhatia & Arora (2005)

Sheep (Ovis) The West Balkan Pramenka sheep types have their origin in two different maternal lineages and represent a valuable resource of genetic diversity in sheep.

microsatellite and mitochondrial DNA

7 178 in total Cinkulov et al. (2008a.)

Sheep (Ovis) The Serbian Tsigai sheep has been polluted by exotic genetic material. Linkage disequilibrium was below expected and Hardy-Weinberg disequilibrium was found.

microsatellite 1 100 Cinkulov et al. (2008b.)

Sheep (Ovis) Most rare or unusual alleles could be traced back to particular ancestors. Highly inbred animals showed the predicted lack of heterozygosity.

blood groups, protein polymorphism and pedigree analysis

3 320 in total for the molecular studies

Clarke et al. (1989)

Sheep (Ovis) Importance of isolation for genetic differentiation through genetic drift. Isolated northern European sheep breeds show the greatest divergence.

microsatellite 29 820 in total Handley (2007)

Sheep (Ovis) Three native and four modern Baltic sheep breeds were studied and clustered, showing that one breed (Estonian Saaremaa sheep) was found to be inconsistent with a distinct genetic population.

microsatellite 7 195 in total Tapio et al. (2005b.)

Sheep (Ovis) Many old, small populations made a positive contribution to total molecular variation.

microsatellite 32 924 in total Tapio et al. (2005a.)

Sheep (Ovis) Imported and native Romanov breed populations’ diversity parameters are marked similar.

microsatellite 13 336 in total Tapio et al. (2007)

Sheep (Ovis) The Sambucana sheep was saved from the threat of crossbreeding by monitoring and mating only of their own breed. With rotation between farms to avoid inbreeding.

individuals are appraised genetically by examing their descendants

1 3200 Luparia (2000)

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Sheep (Ovis) The Wool-Less Canary Sheep’s relationship with the present breeds in America.

review - - Delgago et al. (2000)

Sheep (Ovis) The leading instinct that has evolved within the short-tailed native breed of Iceland sheep are genetically based and should be conserved.

overview 1 1000 Dýrmundsson (2002)

Sheep (Ovis) Four Nigerian breeds were found to have an evolutionary history that makes them distinct genetic management entities.

microsattelite 4 - Olufunmilayo et al. (2004)

Sheep (Ovis)

Over use of some individuals was detected while analyzing the herdbook.

pedigree analysis

1

-

Álvarez Sevilla et al. (2004)

Sheep (Ovis) Genetic origin and geographic distribution of Creole, Moro, Hampshire, Cheviot, Romney, Blackface, Merina and Corriedale

pedigree analysis, morphometric characterization analysis

8 - Rodrigo & Rodrigo (2005)

Turkey (Meleagris gallopavo) Non-industrial strains of turkeys in the USA have dangerously low population sizes.

review - 15627 females Sponenberg et al. (2000)

Water buffalo (Bubalus bubalis) Phylogenetic diversity, based on microsatellite loci, should be used as an initial guide in making conservation decisions for livestock breeds.

polymorphic protein coding loci, microsatellite

11 - Barker (1999)

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5. Pedigree analysis for conservation breeding

When the relationships among individuals in a population are known, statistical pedigree analysis can be used to address several issues of importance in conservation genetics. Such issues include the estimations of rate of inbreeding and inbreeding coefficients of individual animals, rate of loss of genetic variation, identification of genetically important individuals for founder allele retention, etc. (Thomas 1990). Because pedigrees of threatened populations are often complex, computation of exact probabilities are often difficult even when using computers. Thus, computer simulation methods have been of great value (MacCluer et al. 1986). One widely used simulation procedure is called “gene dropping”. This method implies that two hypothetical, unique, alleles are assigned to each population founder, and genotypes of descendant individuals are created by Mendelian segregation of parental alleles (MacCluer et al. 1986; Thomas 1990) using Monte Carlo randomizations. Gene dropping can be used to estimate inbreeding coefficients, assessing the extent of existing genetic variability, and predicting the risk of future loss of genetic variation (MacCluer et al. 1986). The results from gene dropping include founder representation in the present population and the loss of genetic variability over the same period (MacCluer et al. 1986).

The exact computational technique of doing this is called “peeling”. Peeling gives the likelihoods for the genotypes of the founders given data on the current individuals (Thomas 1990) e.g. P(both genes are extinct). The major restriction in peeling is the large amount of storage required to keep intermediate results, this increasing exponentially with the complexity of the pedigree; a good deal of computational time is also required (Thomas 1990). But the perhaps most important point when comparing gene dropping and peeling is that gene dropping yields a very good approximation (Thomas 1990).

The measurement of inbreeding is the probability of alleles that are identical by descent (IBD), meaning that they are copies of the same ancestral gene received via repeated segregations from some common ancestor within the defined pedigree. In the coupling of two individuals the IBD genes meets again (Thompson 1988). Usually IBD is calculated for one locus but IBD for multi-locus is also possible to calculate and compute (Thompson 1998). Descent probabilities can provide evidence for the ancestry of rare alleles in complex pedigrees (Thompson and Morgan 1989).

Another useful measurement is the concept of founder equivalents and founder genome equivalents. The founder equivalents of a population are the number of equally contributing founders that would be expected to produce the same genetic diversity as in the population under study (Lacy 1989). The number of founder genome equivalents of a population is the number of equally contributing founders with no random loss of founder alleles in descendants that would be expected to produce the same genetic diversity as in the population under study (Lacy 1989).

A related use for pedigree studies is for monitoring genetic change. In a selection experiments (Fredeen 1986) of cattle, pigs and poultry, pedigrees was used as the baseline data.

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5.1 Pedigree analysis and genetic variation in dogs

Just as inbreeding can be studied either via homozygosity in genotype or by pedigree analysis, population structure can be studied without genotyping (Calboli et al. 2008). Recently a “pedigree structure index” was introduced (Calboli et al. 2008). is analogous to FST and is a measurement for populations structure when analyzing pedigrees. The measurement has been tested on ten dog breeds and showed that each of the ten breeds hade a moderate to strong level of clustering of current-generation dogs with their founder, meaning that the breeds actually were breeds (Calboli et al. 2008).

Pedigrees exist for most of modern dog breeds and the studbooks often go many generations back. For example the Swedish Kennel Club was founded in 1889; by studbooks, dog shows and competitions the purpose was to conserve and refine the breeds’ specific characters (www.skk.se).

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6. Prioritization for conservation of domestic breeds

Although the need to conserve the genetic diversity of domestic animal breeds is now politically accepted, strategies for such conservation has only to a limited degree been developed. An important issue in this context is how to use available resources in the most efficient way to retain domestic gene pools (Ruane 2000). In this context, methods for prioritizing among breeds with respect to “conservation genetic value” are of importance, and the approaches of Weitzman (1992) and Eding et al. (2002) have been suggested as valuable tools for domestic animal breeds (Bennewitz et al. 2006; Tapio et al. 2006). The methods of Weitzman (1992) and Eding et al. (2002) are based on economics and mathematics and none of them are particularly straightforward – only very brief descriptions are given below.

6.1 Weitzman’s method

Weitzman’s method (Weitzman 1992) is based on economics complex mathematics aimed at quantifying the amount of diversity at various biological levels, and has been applied at the biological intraspecific level to quantify diversity among groups of breeds (Bennewitz et al. 2006). The method is founded in fundamental information about the dissimilarity-distance between any pair of objects in the set (taxonomy; Weitzman 1992). The loss of genetic variation is estimated from the genetic distance between populations (Thirstrup et al. 2008).

For example, in a phylogenetic tree, it is natural to define the distance between any two species as the time when they diverged from a common ancestor (Weitzman 1992). The genetic distance and variation could be calculated from the length of the branches of the phylogenetic tree according to the theorems of Weitzman (1992).

The loss of genetic variation is estimated from the genetic distance between populations (Thirstrup et al. 2008). This implies that the more genetically diverse a population is from other populations the more it contributes to the overall variation according to Weitzman´s method, which results in a greater conservation value.

Several authors have criticized Weitzman’s method because it ignores within-population diversity (Eding et al. 2002; Thirstrup et al. 2008). Empirical data indicates that about 50% of the total genetic variation within a domestic species usually is represented by within breed variation (Barker 2001). This level of variation is not considered using Weitzman´s measure, however. It focuses exclusively on between breed variation, and the degree of genetic uniqueness of a breed in relation to other breeds determines the conservation value of the breed regardless of the level of within breed variation.

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6.2 Eding et al.’s method

Eding et al. (2002) developed a method that is based on relative breed contribution in order to maximize genetic diversity of a common gene pool; the method gives a ranking of breeds according to their contribution to the overall level of genetic diversity. In this approach, diversity of a set of populations is defined as the genetic variance that can be found in offspring that are obtained from interbreeding, in a randomly mating population, of those breeds that contribute to the gene pool (Eding et al. 2002). In other words it is based on average kinships between- and within-populations estimated from genetic marker data (Zerabruk et al. 2007). This implies that Eding et al.´s method considers both within and between breed genetic variation.

6.3 Holistic view

Choosing a method for prioritization conservation value of breeds’ implies choosing between methods that address the problem using different mathematical, biological, and computational properties (Zerabruk et al. 2007). Table 2 shows that the ranking is not the same in the most commonly used methods. Tapio et al. (2006) used the methods of Eding et al. (2002) and Weitzman (1992) to prioritize between northern European cattle breeds for conservation. They found that the two methods provided different results with respect to which breeds that were of particular conservation importance (Table 2). However, Tapio et al. (2006) conclude that their results indicate that both methods recognize the importance of local populations as a valuable resource of genetic variation.

Table 2. There is not a big difference between the methods. The table shows contribution to diversity according to the Weitzman and Eding et al. method from Tapio et al. (2006). The table includes only the cattle breeds in Tapio et al. (2006) that has a Swedish origin. Safe breed is a breed that is currently not at risk of extinction (Tapio et al. 2006). The ranking is due to each methods results regarding contribution to the overall diversity for each method.

Weitzman Eding et al.

Breed Type Safe breed Ranking Safe breed Ranking

Bohus Poll native no 2 no 5

Fjällnära cattle native no 4 no 2

Ringamala cattle native no 3 no 4

Swedish Friesian modern yes 8 yes 7

Swedish Mountain cattle native no 6 no 1

Swedish Red Polled native no 5 no 6

Swedish Red-and-White modern yes 7 yes 8

Väne cattle native no 1 no 3

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However, when deciding conservation priorities, several additional factors that are not included in either the Weitman or the Eding et al. approach should be taken into account. Such factors include adaptation to specific environments or diseases, possession of special traits of cultural, historical, scientific or future economic value, and degree of endangerment and particular landscape value (Ruane 2000).

The relative cost of the conserving action should also be considered (Ruane 2000). Big animals like cattle are more expensive to conserve than small animals like rabbits and dogs that hobby farmers can keep (Ruane 2000).

6.4 FAO criteria for prioritization

FAO (Food and Agriculture Organization of the United Nations) has a view that is easier for a biologist to understand. The FAO use three criteria for prioritization (Alderson, 2003):

• Distinctiveness (in genetic distance, performance, or type). • Local adaptation (e.g. the North Ronaldsay sheep which can exist on an exclusive

diet of seaweed is an example of strong local adaptation). • Numerical scarcity, measured by the number of annual female registration (not

the number of breeding females). This system is uncomplicated for the grassroots and flexible at the analytical stage (Alderson, 2003), however, it may not result in the most efficient way of conserving animal genetic resources.

6.5 Methods for prioritization of dog breeds, conclusion

Some dog breeds are not very old, others have no obvious use. The economic value is minor and one might think that we could live with or without them.

But the FAO approach, as described in the previous chapter, tells us why we need to conserve dog breeds or at least which dog breeds we need to conserve. The distinct one needs to be conserved. The genetic distinct breeds are an obvious resource for genetic variation and the morphological or behavioral distinct breeds might represent a character we need. One such character might be a local adaptation.

The methods of Weitzman (1992) and Eding et al. (2002) attempts to rank genetic distinctiveness. Weitzmans (1992) estimates the loss of genetic variation from the genetic distance between populations whilst Edings (2002) method is based on relative breed contribution in order to maximize genetic diversity of a common gene pool.

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There has been no discussion about this regarding dog breeds. Therefore it would be interesting to test different approach (like table 2) on dog breeds.

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7. The domestic dog

The domestic dog originates from East Asia, according to a study by Savolainen (et al. 2002; Savolainen 2007) showing that over 95% of all sequences examined belong to three phylogenetic groups suggesting a single gene pool origin for all dog populations, with a larger variation in East Asia. The first domestic dog appears 9000-14000 B.C. according to archeological records and according to mtDNA 15000-40000 B.C., concluding (Savolainen et al. 2002; Savolainen 2007) around 15000 years ago.

There are associations of dog haplotypes with wolf lineages which indicate mixture between wolves and dogs (Vilà et al. 2003). A repeated exchange can have been an important source of variation. Dog sequences cluster with different groups of wolf haplotypes, therefore, after the origin of dogs from a wolf ancestor, the gene flow might have continued. A recent finding of a wolf-dog hybrid in the endangered Scandinavian wolf population confirms that inter-specific hybridization between wolves and dogs can occur in natural wolf populations (Vilà et al. 2003). However, the question of the number of domestication times remains unsolved (Vilà & Leonard, 2007).

In hard times for domestic animals (and plants) wild progenitors can enrich the gene pool trough periodic interbreeding (Vilà et al. 1997). Consequently, the preservation of wild progenitors (such as the wolf) may be a critical issue in the continued evolution of domestic animals (such as the domestic dog; Vilà et al. 1997).

Some North Scandinavian/Finnish dog breeds were recently proven to have a different origin than the dog population worldwide. These breeds are the results of wolf-dog crossings a few hundred to a few thousand years ago rather than from one domestic event (Klütsch et al. 2009).

In the origin of most dog breeds there are strong indications that a smaller number of males than females were involved in the formation of the breed (Sundqvist et al. 2006). Within dog breeds fewer Y chromosome haplotypes than mtDNA haplotypes were found in opposite to that found in natural wolf populations (Sundqvist et al. 2006). In a natural gray wolf population about as many females as males contribute to reproduction in a single year (Sundqvist et al. 2006).

The unequal sex-ratio has resulted from the existence of “popular sires” of which some has produced over 100 litters during there lifetime (Sundqvist et al. 2006). A bias towards males may be common to all large domestic animals, but in the dog it represents a more extreme deviation from the ancestral social behavior than common (Sundqvist et al. 2006).

Modern domestic dog breeds have a recent origin, probably less than 200 years ago (Sundqvist et al. 2006). One special “dog breed” is the Australian dingo that descends from domesticated dogs. A small population of dogs were introduced from East Asia, and have since lived isolated (Savolainen et al. 2004).

The domestication of the dog caused a dramatic change in the way of the dogs’ life compared with that of their ancestor, the gray wolf (Björnerfeldt et al. 2006). This created

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a selective force that made the changes of the mitochondrial genes appear at a faster rate than common in the wolf, and this diversity may have worked as raw material for artificial selection (Björnerfeldt et al. 2006).

Dog breeds are, according to phylogenetic studies, organized into a distinct evolutionary hierarchy with the following primary groups (Wayne & Ostrander 2007; Vilà & Leonard 2007):

• “Herding” • “Mastiff” (including i.e. some terriers) • “Modern European” (from the 1800) • “Mountain” (including i.e. German Shepard and some spaniels)

Dog breeds show high but varied levels of linkage disequilibrium (i.e. the non-random association of genes at different loci; Wayne & Ostrander 2007). Dog breeds also show significant deviations from Hardy-Weinberg expectations (Short et al. 2007; Zajc et al. 1997) and there are at least 2.5 million specific genetic differences across dog breeds. The dogs genome is well known and a high-quality genome sequence has been published (Lindblad-Toh et al. 2005).

7.1 Modern dog breeding

Today’s modern breeds are closed gene pools (99 % of 414 dogs from 85 breeds were correctly assigned to their breed in a cluster analysis) resulting in reduced population size and an overall increase in genetic drift among domestic dogs (Wayne & Ostrander 2007). The latter results in loss of genetic diversity within breeds and greater divergence among them. In some breeds genetic variation has been further reduced by catastrophic events such as the Second World War (Wayne & Ostrander 2007). A single gene mutation occurred early in the history of the domestic dog and is common to all small breeds. It may have been the gateway to a change that led to an increased selection (Wayne & Ostrander 2007).

In the past 150 years, breeding clubs and canine associations have flourished, and in these clubs dogs for breeding have been selected mainly on appearance relative to a “breed standard” (Beilharz 2007). As breed standards displaced working behavior as the main target for selection, working abilities appear to have been reduced (Svartberg, 2006; Beilharz, 2007; Calboli et al., 2008). Modern dog breeding have had effects both on the way the dogs behave (Svartberg, 2006), the way they look, and on their health (Companion Animal Welfare Council, 2006) and genetic variation (Sampson, 2005).

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There are indications that the genetic homogeneity in some dog breeds is much higher than in humans and also higher than in pure-bred cats due to the intensive artificial selection and inbreeding, (Zajc et al. 1997). Inbreeding is associated with reduced fitness both in the dog and its ancestor the wolf (Laikre 1996). Inbreeding is generally also associated with increased occurrences of hereditary disorders caused by autosomal, recessive alleles (Laikre and Ryman 1999), and such disorders are common in many dog breeds (Wallin 1994).

7.2 The effect of selection on behavior

“Domestication, the process whereby an animal is transformed from a life in the wild to a life under some control of humans, is one of the most dramatic evolutionary processes accessible to scientific investigation.” (Jensen, 2002, p. 26.)

The traditional view is that domestication began with human agriculture (Jensen, 2002). But more than 50000 years ago the wolves that were to become dogs were separated from other wolves and the “dogs” found a niche with the new species Homo sapiens (Jensen, 2002). The domestication process of the dog is still in progress (Svartberg 2006). For example the social structure of feral dogs is an aggregation of monogamous breeding pairs and their pups, which is substantially different from the strict hierarchy of a wolf pack (Boitani et al. 2007).

The cultural changes during the last century have moved the focus for selection and it is now the dogs’ practical functions that are put to side (Svartberg 2006). In a recent study correlations between breed scores in mental tests and current use of the breeding stocks were found which suggests that selection in the recent past has affected breed-typical behavior (Svartberg 2006).

7.2.1 Behavior test on dogs

Behavior tests on dogs are a possible way of evaluate whether selection affects behavior. Test of behavior in working dogs has a long tradition in Sweden. The L-test (“Lämplighetstest”) is a test of the dogs’ mental characters and was designed for selection of dogs for different military and working tasks (Reuterwall & Ryman 1973). The L-test has been generally accepted, and is used to this date to evaluate individual working dogs ability (Reuterwall & Ryman 1973; Sjöström/Rikspolisstyrelsen, 2009). According to the designers there are possibilities to shorten the selection substantially (Swedish army 1970). The test was developed during discussion with people with great experience of dog training and they were certain that there are hereditary characters of certain kind that are possible to test when they are triggered by certain situations (Swedish army 1970). An empirical test showed low heritability and the authors (Reuterwall & Ryman 1973) suggest that this is due to previous selection which has left

30

little additive genetic variance in the population (the result showed a low degree of genetic variance).

Another type of quite common behavior test that has been empirically studied is behavior tests for puppies. The puppy tests show that no more than a few characteristics are needed in order to describe the differences between dogs (Wilsson & Sundgren, 1997a,b). Heritability calculated for characteristics evaluated in behavioral tests can be used as a tool to select different kinds of service dogs (Wilsson & Sundgren, 1997a,b). Examples of patterns that in different studies have been shown to have high heritability and are possible to study at an early age are the ability to be a “successful” guide dog, fearfulness, and a military dog’s suitability for protection and tracking (Wilsson & Sundgren 1997a,b).

Of course, at juvenile age, the maternal effects are large and the puppies are greatly affected by the degree of maturation (Wilsson & Sundgren 1997a) which must be taken into consideration. Maternal effects that are seen when comparing estimates of heritability based on sire and dam may arise from common litter environmental factors (Wilsson & Sundgren 1997a). Heritability for behavior characteristics such as vocalization when isolated, contact with people, retrieving, tug of war, and the results of the arena test (puppies put in unfamiliar building) was medium or high (Wilsson & Sundgren 1997b). The major conclusion, however, is that breeding programs aimed of improving behavior in dogs should not be based on information collected on tests performed as early as eight weeks of age as the adult behavior not can be predicted from that even though there is heritability involved in the behavior the puppies show (Wilsson & Sundgren 1997b, 1998).

A test widely used by the Swedish Working Dog Association, mainly as a tool for dog breeding, is the Dog Mentality Assessment (“MH” in Swedish). In the test, dogs are exposed to several different novel situations and their reactions are described (Svartberg 2002). The test can be used in applications like selection of service dogs and breeding animals (Svartberg & Forkman 2002). The test is also useful to describe components of a dog’s personality that are expressed in every day life (Svartberg 2005).

Some outcomes from studies using the MH-test as a method of testing personality of dogs are:

• Breeds used in dog shows are associated with high playfulness, low curiosity/fearfulness, low sociability, and low aggressiveness (Svartberg 2006).

• Breeds used in working dog trials were positively correlated with playfulness and aggressiveness in sires (Svartberg 2006). Successful working dogs seem to have higher boldness (playfulness, curiosity/fearlessness and sociability) compared to less successful dogs (Svartberg 2006). Selection for dogs scoring high in the trait playfulness might be analogous with selection for trainability (Svartberg 2006), but the trait aggressiveness seems to have no influence on success on working dog trials (Svartberg, unpublished data). There is no difference in boldness score between dogs succeeding in different types of working dog trials, suggesting boldness being good for training in general (Svartberg 2002).

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• Popular breeds have higher sociability and playfulness scores than less popular breeds, suggesting that a positive attitude towards strangers is an important character for a pet dog (Svartberg 2006).

• There are differences between breeds (Svartberg 2002), but breed specific behavior has decreased with the change in purpose of the selection for breeding in various dog breeds (Svartbert 2006).

A similar test situation used by the Swedish Dog Training Center has shown similar results: dogs with a high “willingness to please” seem to be more fearful, less aggressive, less defensive, less competitive, and more nervous (van der Waaij et al. 2008)

Breeds generally seem to be used very differently today compared to what function they had in the origin (Svartberg 2005). Characteristics such as playfulness, sociality, exploration, avoidance, and aggressiveness are stable personality traits in the individual. These characteristics have a moderate to high heritability and seem to have been important during the evolution of the domestic dog because of their possible fitness consequences (Svartberg et al. 2005).

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8. Concluding remarks

With respect to animals, conservation genetics has traditionally focused on conserving genetic variation in wild species that are either maintained in situ (i.e. in their natural habitat) or held in ex situ collections (i.e. in captivity in zoos and wild animal parks; Frankham et al. 2004). During recent years, however, increasing conservation genetic focus has been devoted to domestic animal populations. This attention includes both scientific efforts and international and national policy work. Domestic populations are traditionally bred through relatively strong selection. Selection inevitably results in loss of genetic variation and conservation breeding thus focus on reducing selective pressures. Loss of genetic variation has been demonstrated to be considerable in domestic breeds. This is due to the strong selection which implies that only a few animals are used in breeding.

The needs for conservation genetic management of domestic animals are well documented (Table 1). I found 72 empirical studies during my ten weeks work on this project, the majority of these concern the conservation of landrace cattle breeds. Only seven of the studies concern dog breeds, and only four of these concern conservation of genetic variation while the other three mainly concern single disorders and their possible association to inbreeding.

Typically, conservation efforts for domestic animals focus on food producing breeds. However, the Swedish Board of Agriculture has identified 10 traditional dog breeds of Swedish origin that are considered to be of conservation concern. Similarly, the Swedish Kennel Club (2008), Sweden’s leading dog breeding association, is increasingly stressing the need for conserving genetic variation in dog breeds.

A series of actions are needed to increase the conservation genetic management of dog breeds. These actions include:

i. More information, guidance and teaching in conservation genetic management to breeders, breeding advisers and others involved in dog breeding. Even though there are tools (such as inbreeding coefficients and founder representation), they are barely used.

ii. Thorough genetic analyses and discussion of the problems that many dog breeds have with health and/or genetic variation. These discussions should include the need for conservation genetic thinking in contrast to pure selective breeding.

Presently, the conservation genetic status of most dog breeds is unclear, although the necessity of such analyses is underlined in the national an action plan for animal genetic resources (National Board of Agriculture and Swedish Biodiversity Center, in preparation). To date a series of degree projects carried out at the Department of Zoology, Division of Population Genetics, Stockholm university appear to be the only studies that have provided such analyses (Håkansson 2002; Gåvsten 2005; Lindberg 2005; Winkler 2007; Jansson 2008). Some aspects concerning population genetics are

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also included in some degree projects carried out at Swedish University of Agricultural Sciences (Ferm 2002; Skarp 2003; Eriksson 2004; Svensson 2004).

Conservation genetic research needs regarding dog breeding include:

i. Evaluation of the effect of selection on conservation genetic status of dog breeds, including comparisons between different types of breeds.

ii. Effects of loss of genetic variation including possible association between inbreeding and health and behavioral problems.

iii. Strategies for combining conservation and selective breeding, while one want to select for some characters but still want to avoid unnecessary loss of genetic variation.

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