Mammalian chromosomal evolution: From ancestral states to evolutionary regions

Chromosome painting by fluorescence in situ hybridization (FISH) has allowed the detection of regions of orthology in most orders of mammals permitting the formulation of ancestral mammalian karyotypes at higher taxonomic levels. We show (1) how the availability of genome sequence data from outgroup species has facilitated the identification of chromosomes and chromosomal segments that define eutherian monophyly, and (2) that FISH together with in silico analysis of genomic sequences point to a nonrandom distribution of evolutionary breakpoints that are rich in repeat elements and segmental duplications. These regions may mediate rearrangement by nonallelic homologous recombination between misaligned copies of duplicated regions and lead to breakpoint reuse. Characters that have arisen convergently (i.e., homoplasy), pose a significant challenge in systematics, as does lineage sorting of genetic polymorphisms across successive speciation nodes (hemiplasy). We show how hemiplasy, a theoretically plausible evolutionary phenomenon, can materially affect data sets and explore the distinction between homoplasy and hemiplasy based on persistence times of phylogenetic markers. © 2010 Springer-Verlag Berlin Heidelberg.