Casey Luskin wrote a wonderful article called “A Primer on the Tree of Life” that will help you to consider whether universal common ancestry is true.

Excerpt:

Evolutionists often claim that universal common ancestry and the “tree of life” are established facts. One recent opinion article argued, “The evidence that all life, plants and animals, humans and fruit flies, evolved from a common ancestor by mutation and natural selection is beyond theory. It is a fact. Anyone who takes the time to read the evidence with an open mind will join scientists and the well-educated.”¹ The take-home message is that if you doubt Darwin’s tree of life, you’re ignorant. No one wants to be ridiculed, so it’s a lot easier to buy the rhetoric and “join scientists and the well-educated.”

But what is the evidence for their claim, and how much of it is based upon assumptions? The truth is that common ancestry is merely an assumption that governs interpretation of the data, not an undeniable conclusion, and whenever data contradicts expectations of common descent, evolutionists resort to a variety of different ad hoc rationalizations to save common descent from being falsified.

Here are two of the four evidences he looks at:

Molecular phylogenies

…the cover story of the journal New Scientist… titled, “Why Darwin was wrong about the tree of life.” …reported that “The problem was that different genes told contradictory evolutionary stories.” The article observed that with the sequencing of the genes and proteins of various living organisms, the tree of life fell apart…

You get completely different molecular phylogenies depending on which gene or protein you analyze from the organism. If UCA were true, all the genes and proteins would have to give similar molecular phylogenies. Casey also addresses horizontal gene transfer.

Convergent evolution

One data-point that might suggest common design rather than common descent is the gene “pax-6.” Pax-6 is one of those pesky instances where extreme genetic similarity popped up in a place totally unexpected and unpredicted by evolutionary biology. In short, scientists have discovered that organisms as diverse as jellyfish, arthropods, mollusks, and vertebrates all use pax-6 to control development of their very distinct types of eyes. Because their eye-types are so different, it previously hadn’t been thought that these organisms even shared a common ancestor with an eye.

Here, you have the same gene being used for the same function in different organisms that do not share a common ancestor.

Homologies and Morphological phylogenies

Casey goes on to look at the evidence from homologies and the disparities between molecular phylogenies and morphological phylogenies, (e.g. – Cytochrome B). Casey’s article is worth looking at, especially if you have never considered the case against universal common ancestry.