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For this study, pedigree information was obtained from associated breeders, registries and on-line databases [6, 7] especially in the Netherlands, Belgium, Germany and the United Kingdom (Additional file 1). The database contains 39576 entries among which 4998 Thai (EMS code [8]: THA), 28770 Siamese (EMS code: SIA), 4446 Oriental Shorthairs (EMS code: OSH) and 737 Balinese (EMS code: BAL) cats, excluding unspecified variants of these breeds. The remaining 625 entries are from 25 other breeds, which were used shortly after the Second World War to rebuild the feline livestock and to create new breeds such as the Oriental Shorthair [2]. After 2000, active data collection on non-Thai breeds was stopped, except for animals which were related to the Thai, e.g. in the case of occasional outcrossing with Siamese cats.

The data collection is known to be incomplete for the periods after the Second World War, when the registries had to be rebuilt, and towards the end of the 20th century when the traditional Siamese cats were not accepted anymore for registration or for entering shows, since they did not meet the new breed standards. The percentage of unknown parentage is about 9 %.

The database of the CFA Siamese Breed Council [6] lists 49 animals that were imported from Thailand, Hong Kong or India in the early 20th century and can be regarded as the founders of the European Siamese and Thai population. The most distant founder was traced more than 50 generations back. The average equivalent complete generations of the current Thai cat population is 12.3. After 20 generations, the percentage of pedigree completeness is 21 % (Additional file 2).

Since subsequent generations show a strong overlap and full demographic details are not available, throughout this work we define a population as the parents of the kittens, born in two consecutive years.

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