A chromosome-based model for estimating the number of conserved segments between pairs of species from comparative genetic maps

Comparative genetic maps of two species allow insights into the rearrangeme nts of their genomes since divergence from a common ancestor. When the map details the positions of genes (or any set of orthologous DNA sequences) on chromosomes, syntenic blocks of one or more genes may be identified and us ed, with appropriate models, to estimate the number of chromosomal segments with conserved content conserved between species. We propose a model for t he distribution of the lengths of unobserved segments on each chromosome th at allo cvs for widely differing chromosome lengths. The model uses as data either the counts of genes in a syntenic block or the distance between ext reme members of a block, or both. The parameters of the proposed segment le ngth distribution, estimated by maximum likelihood, give predictions of the number of conserved segments pet chromosome. The model is applied to data from two comparative maps for the chicken, one with human and one with mous e.