Another good analogy would be telescopes. Some telescopes are great for focusing in on single galaxies, but there is still a lot of information that we can gather from telescopes that have a large field of view but lower resolution. Different tools have different resolution, and the pictures they gather are used to put the larger collage together. No single paper using a single telescope is going to give us all the answers.
Because I am a science geek, the Large Synpoptic Survey Telescope and the James Webb telescope are the two upcoming telescopes to get excited about. They also fit neatly into the wide field of view v. high resolution analogy.
If my understanding is correct, this is why mitochondrial DNA is so helpful in closely related species. The rate of divergence is much higher which allows for greater resolution over shorter time periods. What you are looking for is DNA that will accumulate a certain number of mutations over the time period you are looking for, not too high and not too low.