How similar are the genomes of the domestic ferret and its relative the black-footed ferret?
This is an evolutionary question. The formula for answering this question is simple but not directly intuitive:
Not every SNP (mutation) identified in each black-footed ferret genome separates the entire black-footed ferret species from the domestic ferret species. The mutations that do separate these two species will have occurred long ago and have accumulated as the species evolved separately. A heterozygous mutation in a single individual is likely a newer mutation – important to population studies, but not to deep time evolution. A mutation that matters to deeper time will have become “fixed” within all black footed ferrets. These fixed differences are thus homozygous mutations possessed by all black-footed ferrets and are different from the domestic ferret. The number of fixed differences can be found on ActiveSite in the following way:
The total number of fixed differences is only part of the equation. To understand how much of the genome between the two species is the same, we need to know some information about the ferret genome. The genome used as the reference for this study is MusPutFur1.0, assembled by the Broad Institute. The info needed can be found on GenBank:
Image from: http://www.ncbi.nlm.nih.gov/assembly/GCA_000215625.1
The total size of the genome is not the number of base pairs being compared in ActiveSite; the number of base pairs being compared in ActiveSite is related to how much of the reference genome has actually been mapped by BFF DNA. By investigating ActiveSite we find that ~90% of the reference genome has been covered.
This means that the number of base pairs compared in ActiveSite is ~2.16 billion base pairs (2,400,000,000 × 0.9 = 2,160,000,000).
Now we can solve:
This number is only an approximation for several reasons:
- not every SNP identified is a single base pair; some are multiple base pairs and some are deleted base pairs, though the vast majority of SNPs do represent a single base pair difference
- only 90% of the full reference genome has been compared, meaning that 90% of the genomes of the two species are 99.6% similar
- four black-footed ferrets have been compared to only one domestic ferret genome, therefore the comparison is not even
These limitations in the data are not significant. With more samples and higher coverage the % similarity will not decrease or increase greatly from 99.6%. We can now begin estimating how long these two species have been evolving separately and investigate these fixed differences to analyze distinctions between the biology of the two unique species.
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