(A) Reconstructed karyotype of the Boreoeutheria ancestor (BEA) and its conservation in the chicken genome. The ancestral karyotype is based on comparative chromosome painting data from >80 eutherian species (Richard et al. 2003; Yang et al. 2003; Robinson et al. 2004; Wienberg 2004; Froenicke 2005). Each ancestral chromosome is named according to its orthologous segments in the human genome. The homologies of individual conserved segments to human chromosomes are identified by individual colors and numbers to the right of the ideograms. The degree of synteny conservation of the largest conserved segments in the chicken genome (http://www.ensembl.org) is indicated by gray bars to the left of the ideograms. For the precise homologies of the conserved segments 4a, 4b, 7a, 7b, 12a, 12b, 22a, and 22b see Froenicke (2005). The association of HSA10p to HSA12a is a comparatively weakly supported ancestral chromosome form as indicated by the dotted line, the scissor symbol, and the question mark. (B) Reconstructed karyotype of the ancestral rodent genome (RA). The reconstruction is based on recent comparative squirrel genome maps (Li et al. 2004); the Zoo-FISH data reviewed in Froenicke (2005); and on alignments of mouse, rat, and human genome sequences (http://www.ensembl.org). The association of human chromosomes 3 and 19 has been included according to yet-unpublished studies of representatives of two additional rodent suborders (A.S. Graphodatsky, F. Yang, L. Biltueva, T. Li, S. Romanenko, P. Perelman, N. Serdukova, E. Nevo, E. Ivanitskaya, T.J. Robinson, et al., in prep.). The nomenclature is the same as used in A. The boundaries of orthologous segments of human chromosome 3 are defined as: 3a: 3pter–3p25.1, 3p14.1–p12.3, 3q21.2–21.3; 3b: 3p25.1–3p14.1, 3q21.3–q24; 3c: 3p12.3–3q21.2, 3q24–qter.

Comparisons of chicken, dog, and mouse genome sequence alignments to the human genome (http://www.ensembl.org) and Zoo-FISH data delineate an ancestral Amniota chromosome. Contiguous syntenic associations of human chromosome homologs 3 and 21 (top) are found in the genome sequence data indicated to the left of the human chromosome ideograms as well as in all of species analyzed by reciprocal Zoo-FISH. The vertical bars to the right of the G-banded human chromosome ideogram indicate the extent of the conserved segments displaying the syntenic associations in the selected species and chromosomes listed on top. Homologies to human chromosomes are identified by color: red (HSA3), blue (HSA21). Note that the intersection of homologous segments of human chromosome 3 in chicken, mouse, dog, and the horse (highlighted in yellow) indicate the ancestral fusion point of HSA3 to HSA21 in 3p12.3 (Froenicke 2005). Small genome alignment gaps inside conserved segments have been omitted for the sake of clarity. Similar agreements between chicken/human genome alignments and Zoo-FISH can be presented for the ancestral boreoeutherian associations HSA7/16, 14/15, and 16/19 (Supplemental Fig. 2). All three of these associations are missing in the bioinformatic model (Hillier et al. 2004; Bourque et al 2005).