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Figure Legends for Supplementary Figures
Figure SI 1. An early map of the mouse genome. Presented by The Roscoe B. Jackson
Memorial Laboratory at the Tenth International Congress of Genetics, McGill University,
Montreal, Canada, 1958, the map was sparse, but rich in visual impact. This remarkable exhibit
showed the linkage groups of the mouse genome as they were known at the time, with each locus
on the exhibit represented by live mutant mice (in their cages) and corresponding to the known
genetic markers of the day. (Courtesy of The Jackson Laboratory Archives.)
Figure SI 2. Human and mouse c-kit mutations show similar phenotypes. The utility of
mouse as a biomedical model for human disease is enhanced when mutations in orthologous
genes give similar phenotypes in both organisms. In a visually striking example of this, the same
pattern of hypopigmentation is seen in (a) a patient with the piebald trait and (b) a mouse with
dominant spotting, both resulting from heterozygous mutations of the c-kit proto-oncogene. This
figure was reprinted with permission from Dr. Zneimer1.
Figure SI 3. Genetic map versus draft sequence of Chromosome 5. The order of 2,605 genetic
markers in the genetic map and the full assembly was compared. As shown in this example of
Chromosome 5 the agreement between the two maps was very high (only 1.8% disagreed in
chromosomal assignment and 0.7% had conflicts in local order). As was noted for human
chromosomes, the recombination frequency per physical length was often (but not always)
elevated near the telomeres. The relationship was complicated, however, by regions over which
little or no recombination was evident. These regions may reflect rearrangements between the two
strains used in the genetic cross (Ob, the strain where the obese mutation spontaneously occurred
in the C57BL/6J inbred laboratory strain and CAST/Ei an inbred wild-derived M. m. castaneus
strain). Two markers matching another chromosome are seen at the top. Testing of random
examples of such discrepant markers showed that 90% of them resulted from errors in the genetic
map.
Figure SI 4. A schematic representation of the roles of gene clusters known to be involved in
pheromonal and hormonal responses in the mouse. Red text denotes mouse-specific gene
clusters whose definition is included in the text. Additional moderately expanded gene clusters of
interest, which do not fall within our criteria, are shown in black. Blue lines represent neuronal
connections between the highlighted organs. Red arrows represent the proposed pathway of
interactions between expanded genes (intervening steps are not shown). Green arrows represent
the proposed pathway by which metabolism of hormones may influence physiology. It is not
assumed that all of these genes will influence physiology or behaviour at any one time point. The
diagram represents a gender non-specific mouse, where 1 represents the vomeronasal organ, 2 the
accessory olfactory bulb, 3 the hypothalamus and 4 the pituitary gland.
Figure SI 5. The dinucleotide SSR density over 50 equal-sized fractions of each
chromosome, as well as an average over all chromosomes for each relative position. The
density varies considerably for regions in individual chromosomes, but on average it remains
constant until it increases two-fold toward the telomere. Please note that mouse chromosomes are
acrocentric with only one telomere shown to the right.
Figure SI 6. Fraction of repeats lost at family substitution level derived using Jukes-Cantor
in human (a) and mouse (b). For 270 LTR elements in human and 150 LTR elements in mouse,
there is a decent linear correlation between the estimated fraction lost and the substitution level of
each family, giving 1.2 % and 1.5% sequence loss per % substitution, for human (R2 = 0.39) and
mouse (R2 = 0.46) respectively. This would estimate that since the human-mouse split, at least
20% of Mesozoic non-functional DNA has been lost in human and over 50% in mouse.
1.
Fleischman, R. A., Saltman, D. L., Stastny, V. & Zneimer, S. Deletion of the c-kit protooncogene
in the human developmental defect piebald trait. Proc Natl Acad Sci U S A 88, 10885-10889.
(1991).