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How can phylogenetic relationship estimates differ when using mitochondrial DNA and nuclear DNA? What are some...

How can phylogenetic relationship estimates differ when using mitochondrial DNA and nuclear DNA? What are some of the main drivers causing these differences?

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Answer #1

The difference in phylogenetic relationship estimates mainly arise because nuclear DNA of an organism is inherited from all ancestors while mitochondrial DNA is inherited from a single lineage (i.e., maternal inheritance).

Main drivers:

(i) Recombination: mitochondrial DNA is passed from mother only so has no recombination while nuclear DNA undergoes recombination in every generation.

(ii) Mutation rate: mitochondrial DNA has a very high rate of mutation due to the generation of reactive oxygen species in mitochondria, while mutation rate is low in nuclear DNA because of efficient DNA repair systems.

(iii) Lineage: mitochondria DNA is inherited from a single lineage while nuclear DNA is inherited from all the ancestors.

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