J. Anim. Breed. Genet.

116 (1999), 317323 1999 Blackwell Wissenschafts-Verlag, Berlin ISSN 09312668

Ms. received: 10.4.1999

s, Norway Department of Animal Science, Agricultural University of Norway, A

A critical review of the value of genetic distance studies in conservation of animal genetic resources
By J. RUANE

Introduction
There has been a veritable explosion of projects in recent years aiming to calculate genetic distances between domesticated breeds of animals and the number of such projects is still increasing. The extent of this can be appreciated by a glance at the recent proceedings of the 26th International Conference on Animal Genetics (ISAG 1998). All domesticated species are being targeted, using breeds from both developed and developing countries and projects are now almost exclusively based on microsatellite marker loci. Although the goal in a few cases is to provide insights into the history of animal domestication (see, for example, MACHUGH et al. 1997; LAU et al. 1998), the most common justication for genetic distancing projects is their importance for helping the decision-makers to identify genetically unique breeds so that they may be prioritized for breed conservation purposes (e.g. HALL and BRADLEY 1995; MOAZAMI-GUODARZI et al. 1997; CRAWFORD and LITTLEJOHN 1998). On a world-wide basis there are roughly 3000 breeds and breed varieties of the seven major mammalian species cattle, pig, sheep, goat, horse, donkey and buffalo (FAO 1995). Of those with population data, 23% are either endangered or critical (FAO 1995). In addition, in the current century it is estimated that at least 600 breeds have been lost (HALL and RUANE 1993). On the poultry side, the picture is even worse as over half the breeds of the ve major species (chicken, domestic duck, muscovy duck, goose and turkey) are thought to be endangered or critical (FAO 1995). At the same time, there is often a lack of even the most rudimentary information on many of these breeds. Basic phenotypic data, including approximate gures for population sizes, are currently available on only 50% of the worlds animal genetic resources (AGR) (HAMMOND 1998). There is therefore an urgent need to act now to prevent the rapid erosion of AGR. This is especially true for breeds in developing countries, where many will be lost without ever HLER-ROLLEFSON 1997). However, having been adequately characterized or studied (KO resources (both in terms of available manpower and nances) are limited in this area and appropriate use of these resources is therefore of vital importance. Given the large amount of current activity in the area of genetic distancing of domestic breeds, the aim of this article is to critically examine the value that genetic distance projects have for breed conservation. Main areas of activity in the eld of breed conservation Three main areas of breed conservation activities, all of which are important, can be identied. (a) Promotion of the issues involved in AGR, which involves increasing the public awareness about AGR by spreading information and knowledge; promoting its teaching in schools and universities and arranging courses on AGR for people involved in agriculture and research, both nationally and internationally. (b) Documentation of existing genetic resources, which includes the description of the population sizes and phenotypic characteristics of breeds; documentation of their economic
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performance, of any special traits they may have, of their cultural/historical importance, as well as of their genetic uniqueness. (c) Establishment/support of breed conservation programmes directed toward specic breeds, which could include in situ or ex situ programmes for endangered breeds; supporting farmers willing to use breeds of lower productivity in todays economic situation or supporting genetic improvement programmes and managing inbreeding for breeds not currently endangered but which may become so in the near future. The limited resources in the eld of AGR have to be subdivided between these three main areas in some way and this seems to be done in an ad hoc rather than a systematic manner. In the current situation, it is essential that a certain amount be allocated to area (c). A key question then is: which breeds should be chosen for conservation? The question is important because, given the large number of breeds that are currently in danger of extinction, those that are supported are obviously more likely to survive whereas those that are not are more likely to be lost. Criteria for selecting breeds for conservation In attempting to choose specic breeds for conservation programmes, the following seven criteria might be considered (RUANE 1999): (a) degree of endangerment; (b) species of the breed; (c) adaptation to a specic environment; (d) possession of traits of current or future economic importance; (e) possession of unique traits that may be of scientic interest; (f) cultural or historical value ; and (g) genetic uniqueness. Genetic distance results are used to provide information on one of these criteria, the genetic uniqueness of breeds within a species. Note that breeds that are genetically unique can also be identied using documentation on the genetic history of breeds. Since many European breeds are only of fairly recent origin (within the last 200 years) and since many of these were also important for breed development elsewhere (e.g. in the New World), a considerable amount of documentation is available on the history of many breeds. The huge interest in genetic distancing projects today can be attributed to two main reasons. Firstly, many breeds are endangered, resources are scarce and it is not an easy task to prioritize breeds for conservation purposes. The seven potential criteria listed above include some subjective evaluations of breeds and their current and future value to mankind. Genetic distance values have an instinctive appeal because they are objective and, within a species, they numerically quantify some aspect of breed difference. Secondly, the majority of genetic distance studies now rely on DNA-based techniques using microsatellite markers and, as pointed out by PONZONI (1997), some funding agencies seem to show a preference for projects using sophisticated technology, almost regardless of the outcome. This problem is by no means restricted to the eld of AGR, but seems to be common in conservation biology where the message seems to be that traditional research, such as describing the geographical location of species, is boring whereas using molecular biology is fashionable (PIMM and LAWTON 1998). Genetic distance projects The operation of genetic distance projects is normally relatively straightforward. A certain number of animals, considered representative for the breeds of interest, are chosen and typed for a certain number of biochemical or DNA marker loci. Based on the resulting allele frequency data, pairwise genetic distance values between breeds can be estimated and these are then used to construct a phylogenetic tree, which makes it possible to readily identify genetically unique breeds. Any one of roughly 10 different parameters are commonly used to estimate genetic distance values (see, for example, NEI (1987); EDING and LAVAL (1999)). These parameters can have different mathematical and genetic properties and there is still no clear consensus regarding which ones are best for domestic animal

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populations (MOAZAMI-GUODARZI et al. 1997). Trees are commonly constructed with one of a handful of methods, which again have varying assumptions and strengths (e.g. BEHARA et al. 1998). Genetic distance studies can provide data of interest. For example, the level of genetic variation, measured at microsatellite loci, has been found in some cases to be as high in small inbred populations as in large commercial breeds of far greater population size (e.g. KANTANEN et al. 1998). They have also been useful for studying the history of animal domestication. For example, it had previously been thought that Bos taurus and Bos indicus originated from a single domestication event about 10 000 years ago. However, MACHUGH et al. (1997), using breeds from Africa, Asia and Europe, found that their estimated time to divergence was 610 000850 000 years, thus providing strong evidence that cattle were domesticated at least twice. However, for the primary purpose of selecting breeds for conservation, there are two major reasons why the ability of genetic distancing projects to identify genetically unique populations may be less than previously imagined. This is due to possible uncertainties about the reliability and relevance of their results. Reliability of genetic distance results Theoretical studies (e.g. NEI and TAKEZAKI 1994; TAKEZAKI and NEI 1996) have shown that the position of breeds on a phylogenetic tree may be inuenced by (i) the number of animals typed per breed (ii) the number of loci used (iii) the parameter used for estimation of genetic distance and (iv) the method used for tree construction. Thus, different combinations of these four factors can lead to different results for exactly the same breeds. Only few published reports using real data consider this aspect. One recent example is the study of genetic relationships between Canadian horse breeds (BEHARA et al. 1998), which showed that different patterns of breed clustering can be got by sampling different numbers of animals per breed or using different parameters to estimate genetic distances. TAKEZAKI and NEI (1996) carried out a detailed simulation study using a phylogeny where a population of size N evolved to split at regular intervals into two separate populations, again of size N, to give a total of eight populations. They presented detailed results using seven different genetic distance parameters and two tree construction methods and showed that the efciencies of obtaining the correct tree topology (Pc) were inuenced by the number of animals and loci sampled and by the genetic distance parameter used. In addition, with the occurrence of bottlenecks (i.e. where the sizes of three of the populations were reduced to N/2 after splitting), Pc was reduced with all genetic distance parameters while the tree construction method that was least efcient in the absence of bottlenecks became the most successful. With domestic breeds, the situation is more complicated than in this simulation study and problems with estimation of genetic uniqueness of breeds are likely to be far greater as, for example, large uctuations in population sizes over time and some degree of gene ow between breeds after divergence are also quite common. No simulation studies have yet considered how the genetic distance parameters commonly used for domestic breeds, which were mostly dened with species in mind, can cope with these situations. TAKEZAKI and NEI (1996) used two different models for simulating microsatellite loci information because their pattern of mutation is quite complicated (see, for e.g. TTERER 1998). For genetic distance projects involving domesticated breeds, it is SCHLO however, likely that genetic drift will still be a far more important factor than mutation since domestication occurred, relatively speaking, quite recently. Nevertheless, for studies of breeds from species with short generation intervals, such as poultry, the mutation pattern of microsatellites may be an additional complicating factor. Since the number of animals and loci sampled is known to inuence genetic distance results, an FAO working group (BARKER et al. 1993) published guidelines for genetic

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distance projects, recommending that at least 25 animals per breed should be used and that 25 to 30 microsatellite marker loci, with four to 10 alleles each, should be typed. Nevertheless, these guidelines are often ignored and results are often published based on much lower requirements with, for example, eight microsatellite marker loci used to examine sheep (BUCHANAN et al. 1994) and pig breeds (PASZEK et al. 1998). Results from a study by MOAZAMI-GUODARZI et al. (1997) show clearly the importance of loci number. Using 17 microsatellite and 13 biochemical markers they failed to nd genetic distance values that were signicantly different from zero for nine French cattle breeds. They indicated, however, that by analysing data sets based on a small, random subsample of microsatellite loci, signicant results were found which later disappeared when all microsatellite loci were used. A key problem with estimation of genetic distances for real populations is that the true values are unknown and so it is very difcult to validate the results. Paradoxically, this may only be done when good documentation of breed history and development is available and, in these cases, since some information about the genetic uniqueness of the breeds is already known, genetic distance projects have least value for breed conservation. In these cases, genetic distance results can only be used to conrm existing historical documentation or to contradict it. In the latter case, where results based on marker and historical documentation differ, it will generally be difcult to say which information source is incorrect since both the genetic distance results as well as historical documentation may be subject to uncertainty. Relevance of genetic distance results Microsatellite markers used for estimating genetic distances are assumed to represent neutral loci. However, both natural and articial selection, in a range of different environments, have been crucial forces in the formation and evolution of breeds of the main animal species since their domestication 600010 000 years ago (DIAMOND 1997). Since neutral loci are used, differences between populations at loci that are, or have been, under selection are not measurable by genetic distance studies. Populations may thus be seen to have diverged very little if neutral loci are considered whereas they could also differ at a small but important set of selected loci. In addition, it is known that important phenotypic differences between breeds may be due to differences in only a few loci. Results from other elds of research underline this point. Studies in plant breeding have shown that genetic distances based on neutral markers are poorly correlated with phenotypic distances (BURSTIN and CHARCOSSET 1997) while MILLIGAN et al. (1994), reviewing studies in conservation biology, concluded that the relationship between variation at neutral marker loci and adaptation or individual tness is still somewhat unclear. PONZONI (1997) has therefore summarized the situation as follows: genetic distance measures can be used to demonstrate that populations that look and perform similarly are actually different, but cannot be used as evidence that populations that look and perform differently are the same genetically. In the future, when a battery of loci affecting tness, adaptation and production traits have been identied for domesticated animal populations, it should be possible to construct phylogenetic trees based on these loci and there is no guarantee that the tree topology will resemble that from neutral loci. Nevertheless it is these protein-coding loci and not those representing neutral noncoding DNA segments that are most relevant for breed conservation and for the ability of the surviving AGR to produce efciently in the future production environment.

Discussion
Genetic uniqueness of breeds is an important criterion that can be used when breeds are selected for conservation action. Mankind has domesticated only a handful of animal species

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(DIAMOND 1997), so variation within these species is important. However, it must be kept in mind that it is only one of several key criteria. The degree of endangerment of breeds is probably the most important factor (RUANE 1999). Breeds of large, stable population size, regardless of whether they are genetically unique or not, should not be prioritized for conservation action. Adaptation to a specic environment, especially one that is itself of interest, is an important criterion while breeds possessing traits of current or future economic importance or unique traits of scientic value would obviously be worthy of conservation. In addition, the historical/cultural value of breeds is considered to be one of their most important features. Genetic distance projects are however, quite expensive. For example, FAOs working group estimated in 1993 that a budget of roughly US$ 1 million would be needed to estimate genetic distances between 50 breeds of a given species, using 25 animals per breed and 25 microsatellite loci (BARKER et al. 1993). Genetic distancing has often been described as a means of gathering essential initial information on breeds as part of an overall conservation programme (e.g. BARKER et al. 1993). However, because of the large costs and the fact that nancial resources are so limited in the area of AGR, there may be little left over for documentation of the other criteria or, indeed, for the nal goal, the establishment or support of concrete conservation programmes. By comparison, collection of basic data on production characteristics or population sizes can be relatively easy and cheap to organize (RUANE 1993). In the current situation, where so many breeds are in danger of extinction, it is essential that the limited resources (personnel and nancial) available be best used to ensure that as much valuable genetic diversity as possible survives into the future. Since many of the threatened breeds, especially in developing countries, have not even been properly characterized, the strategy should be to quickly and cost-effectively document these genetic resources and to prevent their extinction. In this critical situation, there seems currently to be an over-emphasis on genetic distancing. The expensive nature of these studies, as well as possible uncertainties concerning the reliability and relevance of their results, seem to suggest therefore that their current value for breed conservation is relatively limited. Acknowledgements
The author thanks the Nordic Council of Ministers for nancial support and Drs P. MURPHY and H. KLUNGLAND for reading the manuscript. Summary In recent years, a large and increasing number of genetic distancing projects have been established for domestic animal populations. The most common justication given for these projects is that they can help to identify genetically unique breeds that can then be conserved. There are, nevertheless, several other criteria that can and should be used when deciding which breeds to conserve. In addition, genetic distancing projects are relatively expensive and there is possible uncertainty about the reliability and relevance of their results. In the current situation, where large numbers of the worlds breeds are in danger of extinction and where basic documentation of these resources is often totally or partially lacking, it is concluded that the relative value of genetic distance studies for breed conservation is limited. sume Re es dernie ` res, un nombre e leve (et qui augmente toujours) de projets ont e te etabli pour le Dans les anne ne tiques entre des races animales domestiques. Le raisonnement le plus souvent calcul des distances ge pour ces projets est quils peuvent nous aider didentier des races qui sont ge ne tiquement donne anmoins, plusieurs crite ` res quon peut et doit utiliser uniques, que on peut ensuite sauvegarder. Il y a ne lection des races pour la conservation. En plus, les projets pour le calcul des distances pour la se ne tiques cou tent assez chers et il y a lincertitude potentielle en ce qui ce concerne la abilite et ge sultats. Dans la situation actuelle, ou ` beaucoup de races du monde sont menace es et limportance des re ` il manque souvent linformation de base (totale ou partielle) sur ces ressources ge ne tiques, la valeur ou

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relative des projets pour le calcul des distances ge ne tiques est assez limite e pour la conservation des races.

Zusammenfassung
bersicht u Eine kritische U ber den Wert von Studien zur genetischen Distanz im Zusammenhang mit der Konservierung von genetischen Ressourcen In den letzten Jahren wurden zunehmend Projekte etabliert, um die genetische Distanz zwischen Nutztierpopulationen zu ermitteln. Die gebra uchlichste Rechtfertigung fu r die Durchfu hrung solcher Projekte liegt darin, da mit Hilfe solcher Untersuchungen Rassen identiziert werden ko nnen, die ber die Untersuchung von aufgrund ihrer genetischen Einzigartigkeit konserviert werden sollten. U genetischen Distanzen hinaus existieren aber noch einige weitere Kriterien, die bei der Entscheidung bezu glich der Konservierung einer Rasse beachtet werden ko nnen und sollen. Weiterhin sind Untersuchungen von genetischen Distanzen relativ teuer, und es existiert eine gewisse Unsicherheit u ber die Zuverla ssigkeit und die Relevanz der Ergebnisse. In der momentanen Situation sind weltweit viele Nutztierrassen vom Aussterben bedroht und eine grundlegende Dokumentation dieser Ressourcen fehlt oft teilweise oder ganz, daher ist der relative Nutzen aus Studien u ber genetische Distanzen in Bezug auf die Rassenkonservierung begrenzt.

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Authors address: JOHN RUANE, Department of Animal Science, Agricultural University of Norway, s, Norway PO Box 5025, N-1432 A