What is one disadvantage to using molecular evidence to compare species?

A major disadvantage with molecular phylogeny is the difficulty in making assumptions in a species with variations in their phylogenies yet they have the same genotype. The emergence of horizontal gene transfer has also complicated molecular phylogenetics. Making inferences on positional homology in different organisms is also difficult and complicated.

you are certainly talking about this picture:

a: is the label of the white square, it is showing the  replication fork, formed by helicase (d) ==> so it is the site of dna separation and replication 

b: is a new dna brand that is following directly the replication fork, so it is continuous ==> built continuously from 5' to 3

c: dna polymerase cannot replicate dna on its own, it needs the of their proteins, and one of them plays the role of a clamp which fixes  the dna with the dna template and increases  the processivity of the enzyme. ==>   stops polymerase from falling off the  template.

d: is the enzyme responsible for forming the replication fork (helicase) ==> unwinds and separates dna into two strands

e: is the delayed strand, it is built  in the opposite sense of the helicase, so dna will be built in fragments ==> built  fragments from 5' to 3 joins

and finally f: is the enzyme that builds  the new dna strand (dna polymerase) ==>   adds nucleotides to make a new dna helix.

credit: gradman555p98x9p

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