The suggested diversity is the first such measure which was designed for the very purpose of studying short term phylogenies, and which is not using genetic drift and mutation, but recombination as the major force creating population differences. Thus it is expected that the method proposed here has a considerable potential to develop a better understanding of short-term phylogenetic structures in farm animal populations. st CHAPTER INTRODUCTION but also the capacity to cope with changing

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... requirements (e.g. other composition fatty acids in animal products) is of high relevance (Simianer, 2005a) . Thus genetic diversity is seen as an insurance against future changes (Smith, 1984) . In livestock populations genetic diversity is expressed on the phenotypic level as variability in production traits, exterior traits, reproduction traits, health traits, and other characters. In comparison with natural populations a wide phenotypic diversity is observed within and between livestock populations Notter, 1999) . These phenotypic differences are the result of genetic diversity and environmental differences . Genetic diversity can be assessed between species, breeds, specific lines and within those groups. A breed is defined by the Food and Agricultural Organization of the United Nations (FAO, 1998) as a group of animals which belong to the same population based on certain characteristics. None of the about 30 livestock species is threatened with extension. But more than a third of the about 6400 documented livestock breeds are under risk of extinction and up to two percent of the breeds go extinct every year (Scherf, 2000). Thus one to two breeds are lost per week. It is estimated that 20% -50% of the total genetic variation within a species exists between breeds . This leads to the assumption that the loss of breeds highly influences the variability within species. However, the small population size of a population at risk causes accelerated erosion of the genetic diversity within this population . Hence, in terms of total However, some aspects remain open. The question arises if the kinship coefficient is powerful enough for the assessment of genetic diversity in short term phylogenies (i.e. 10 -20 generations since fission). Short developing periods might be of interest where cross breeding was applied 10 -20 generations ago (e.q. Fleckvieh) or for recently created breeds with a laboratory use in mind (Goettingen Minipig). Applying marker estimated kinship coefficients a high fraction of identical alleles is due to identity by state. Thus a correction factor is essential. So far, no general applicable rules for the derivation of such a correction factor are given. Further conserved genomic regions spanning over several cM are reported for different