A critical review of concepts and methods used in classical genome analysis

A short account of the development of classical genome analysis, the analys is of chromosome behaviour in metaphase I of meiosis, primarily in interspe cific hybrids, is given. The application of the concept of homology to desc ribe chromosome pairing between the respective chromosomes of a pair during meiosis is traced, and the relationship between this use of homology and t he concept of homology as common ancestry is discussed at length. To equate the two concepts has led to the erroneous assumption that levels of chromo some pairing is an indication of phylogenetic relationship. Even accepting the fundamental premises, genome analysis is burdened by obs ervational difficulties. Hence, chromosome pairing has been shown to be und er genetic control and is also influenced by environmental conditions. Addi tionally, basic biological observations such as the distribution of meiotic configurations or the identity of the individual chromosomes are frequentl y neglected. Data from chromosome pairing are captured as pair-wise comparisons and are amenable only to phenetic analysis, and hence are not suited for phylogenet ic inferences. As currently perceived, genome analysis may have a role to p lay in plant breeding but it has no place in systematics. With an increased knowledge and understanding of the mechanism behind meiosis, data useful i n a systematic context may eventually be produced.