I want to determine the phylogenetic age of the members of the subfamily Hippotraginae (Bovidae) based on complete mitochondrial genomes, using BEAST software; But I do not have a good indicator. Please what is mutation rate in the mitochondrial genomes of the family Bovidae (0/1 in million years, 0/2, 0/3 etc?
The attached alignment, phylogenetic tree built from that alignment, and paper should get you in the right ballpark.
Ofcourse, I want an exact number. How much is the mitiochondrial variation of the family Bovidae in every one million year?
To get an exact number, you would need some very special fossils precisely dated. Or maybe some other solidly dated evidence for example knowing that one species or population migrated out of Africa into Europe exactly x million years ago,. In practice, we almost never have that tuype of data.
Humans are highly interested in human evolution so we search for fossils and study our closest relatives the chimpanzees and gorillas quite a bit. Even so the date that humans shared a common ancestor with chimpanzees and gorillas is a little fuzzy. The rate of evolution of most mammal mitochondrial DNA is roughly 0.007 subst/pos/Mya. The modern human mitochondrial genome is 91.7% identical (distance 8.3% or 0.083) to chimpanzee mitochondrial genome but the primate mitochondrial DNA evolves a bit differently than most other lineages. If we guess that humans shared a common ancestor with chimpanzees 8 million years ago we get a rate of 0.005 subst/pos/Mya on each lineage so they diverge from each other at a rate of roughly 0.010 subst/pos/Mya. Keep in mind that each lineage diverges from the common ancestor at that rate so the distance between the two increases at a rate of roughly 0.010 subst/pos/Myr.
The point of the transisions vs transversions compared to estimated F84 distance plot above, is that the distance/time relationship is quite linear at low distances but become distorted at higher distances due to multiple changes per site. Mitochondrial genomes are good for the 100,000 year to 20 million year time frame but not so good for 100 million years and beyond. Nuclear DNA is better if you are looking at all vertebrates, or all insects, etc.
Thank you very much my dear brother Dr. Brian Thomas Foley . Thank you for response and your kindness.
The attached paper focused on primates but includes many other mammals. All based on complete mitochondrial genomes.
Thank you very much. Prof. Brian.
You are very kind man I'm proud to be friends with you.
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