The scientific name for rock pocket mice is Chaetodipus intermedius. These mice are typically light and gray in appearance with the exception of melanic coloration near lava areas. They are small mices, typically three to four inches in length. These mice prefer a rocky area in the desert in which to inhabit (4). One study found that the mouse's diet consists primarily of seeds but is supplemented by insects (5).
Figure one shows the number and type of mice caught in each of four sites. Mice caught at Avra Valley and Portal were all light. At the locations with lava beds, Armendaris and Pinacate, both light and dark mice were found. In Pinacate, twenty nine mice were captured. Of those caught, eighteen were dark and eleven were light. Nine percent of mice caught off the dark substrate were dark while eleven percent of those caught on the dark substrate were light.
The basis of melanism in the Pinacate rock pocket mice (Chaetodipus intermedius) was found to be four polymorphisms in the gene encoding for the melanocortin-1-receptor (Mc1r). Table 1 "Mc1r polymorphisms in light and dark C. intermedius from the Pinacate population" illustrates the changes in nucleotide bases in the Mc1r gene.
The table is set up to show differences in the nucleotide sequence of the Mc1r gene. The top is labeled to show the nucleotide position at which the change occurs and the bottom row is the corresponding amino acid positions. The consensus sequence at the top is the basis for comparison for all other sequences. This is the expected sequence for light mice. Each position that receives a period is in agreement at that position with the consensus sequence.
The genetic code of each Mc1r allele is given for twenty-nine rock pocket mice (twelve light and seventeen dark) and two related species (Chaetodipus penicillatus and Chaetodipus baileyi). All dark mice exhibit at least one allele that has the four necessary changes in nucleotide bases to create melanism. The polymorphisms are a change from cytosine to thiamine at position 52, from cytosine to thiamine at position 325, from cytosine to thiamine at 478, and from adenine to cytosine at 699. There is also a change from thiamine to cytosine at position 633 but as we can see in the amino acid and nucleotide sequences in figure three, this is a silent mutation. The codon CTT is changed to CTC, but these codons both specify the amino acid Leucine. So this polymorphism is probably arbitrary and does not affect melanism. No other mutations occur in all mice exhibiting melanism.
Other polymorphisms occur in the sequences of some light mice. However, there are no uniform changes and apparently no connections to mouse color.
Specimens 1372, 1379, 1382, 1384, 1412, and 1416 of table 1 only have one allele with the changes necessary to incur melanism but they are still dark. This shows that melanism is the dominant trait. The allele in which the polymorphisms necessary for melanism occur receives the name D while the allele without these polymorphisms is d. Thus the six aforementioned specimens have the genotype Dd.
In Table 2, the exact genotypes of all twenty-nine specimens caught in Pinacate. Eleven mice were homozygous dominant (Dd), exhibiting dark coloration. Also showing the melanic phenotype, six mice had the heterozygous dominant allele pair (Dd). Appearing light, twelve mice were homozygous recessive (dd).
Figure 2 shows the phylogenetic tree exhibiting the evolution of two sequences in DNA in rock pocket mice and also in two other species, C. penicillatus and C. baileyi, which act as outgroups. Light mice are shown by colorless circles and dark mice are shown by filled in circles. By showing that mice exhibiting melanism and those that do not could have the same mitochondrial DNA, Dr. Nachman's group showed that the mutation was based in the Mc1r gene sequences and not other genetic differences in the species.
Figure 3 illustrates the entire Mc1r genetic sequence of 954 nucleotides and the 317 amino acids they encode. A comparison is made between light mice, dark mice, and two other species: C. penicillatus and C. baileyi. The top four rows represent amino acids and the bottom four rows are nucleotides. Any space with a period indicates no difference from the light mouse sequence. The four changes necessary for melanism are boxed. The polymorphism at nucleotide location 52 changes the amino acid from arginine to cysteine. The polymorphism at nucleotide location 325 changes arginine to tryptophan. The change at nucleotide location 478 also changes arginine to tryptophan. Lastly, the polymorphism at nucleotide location 699 changes the amino acid glutamine to histidine.
2 = 4.89, P = 0.087), consistent with disruptive selection
across the two habitats.