How do we know what today's lifeforms were like when they first evolved? For years, biologists could make inferences about how recent species shared common ancestors based on an approach called cladistics, which quantified how many similar features they shared. This approach worked with fossils as well as living species, allowing us to group them in the sort of branching hierarchies produced by common descent. But these days, rather than things like bone shape and tooth number, we have DNA.

So how do you build a tree out of that? As it turns out, the general approach of cladistics also works with genetic information.

Cladistics

Let's say you want to understand the origin of mammals. To do that, it helps to have a separate but closely related group—for mammals, reptiles would work well. Reptiles and mammals share a number of features, such as having four limbs (they're all tetrapods—even snakes and whales, which can have vestigial limbs). Others are distinct to mammals, like fur or the presence of specific bones in the inner ear. You can also have some features that are partly shared (like the egg laying of a platypus) or present in only a subset of mammals (like flight in the bats).

Using these traits, you can start to see how things group together. Even though bats and whales are very distinctive, neither of them lay eggs, so they're probably more closely related than monotremes. And since monotremes share egg-laying with reptiles, they probably branched off from the rest of the mammalian lineage quite early.

Sometimes, you do have odd features that seem to cause trouble for a nice tree, such as the fact that both snakes and whales only have vestigial legs even though they don't seem very related otherwise. It's possible to solve issues like this by looking at enough features. The number of things that make whales distinct within mammals is smaller than the number of features they share with other mammals. You can see an example of the sort of groupings of traits in the chart below.

The logic of this sort of analysis is very simple: the most closely related groups have the fewest differences. Thus, humans clearly group among the primates rather than the rodents because we share more traits (or fewer differences) with other primates.

Cladistics can also help us understand what the past looked like. Since both reptiles and monotremes lay eggs like the platypus, we can infer that all mammalian lineages laid eggs at the time the monotremes branched off. By applying this sort of logic, we can identify where specific features first appeared on now-extinct mammals and sort out the relative order of branching of various lineages.

It's important to note that this sort of reasoning isn't always perfect. For example, we now know that whales and hippos are relatively closely related. Both are aquatic, so it would make sense to reason that their last common ancestor was also aquatic. Fossil data, however, tells us that's not so; the two represent separate branches from a lineage that has largely been living on land.

Cladistics goes genetic

Conveniently, the exact same logic can apply to DNA. Cladistics is based on the idea that organisms with the lowest number of different features are likely to be the most closely related. With DNA, almost every base pair can be changed by mutation (with the exception of parts of some essential genes). Therefore, every base has the potential to act as a distinct feature. A small number of changes requires the fewest mutations to create, and therefore this probably represents the smallest separation between two DNA sequences.

Look at the short sequences below, where base differences relative to the first sequence are highlighted in red. There are only two differences between the first and second sequences, while there are four between the first and third. Therefore, the first two sequences are more closely related.

But is sequence one or two more closely related to the third? To figure that out, let's repeat the highlighting, this time looking at changes in respect to the third sequence.

Now, you can see that both sequence one and two have the same number of differences with sequence four. It's impossible to tell which is more closely related. If you were building a tree based on this, it would look like this:

Researchers tend to rely on a lot more than a dozen base pairs to figure out the relative relatedness of two organisms, but the basic process is pretty similar. Put the DNA sequences on a possible tree, then see how many changes each branch on the tree would need. Shuffle the tree and repeat the analysis. It becomes a simple matter of finding the tree that requires the minimum number of changes.

Well, sort of simple. Part of the challenge is identifying sequences that really are equivalent in order to compare. Many genes in vertebrates belong to large gene families. For example, humans have 22 different members of the FGF gene family. If you were comparing them to mice, you'd want to make sure you compare human FGF-14 with the mouse version of FGF-14 and not some other member of the family. Some of these genes can get lost or experience a duplication, in which case there might be two FGF-14-like genes in a species or none at all.

These events—duplications and deletions of sequences—occur regularly outside of genes, too. When you're comparing two different sequences like the ones above, you also have to be aware that some bases, rather than being changed, might be missing entirely. Other sequences might have a spot where bases have been inserted, and these have to be taken into account as well. But given enough DNA and a cautious analysis, it's possible to reconstruct evolutionary trees just as we can with features.

However, we can also reconstruct the past. Let's look at same three differences with a different highlighting.

Now, the base that's in red represents the odd one out—the one base that's different out of the three. If we have evidence that these three sequences are related by common descent, then it's most likely that each of these differences represents a single mutation at some point in the past. If that's the case, we can make inferences about the ancestral sequence; it's the one that involves the fewest changes to produce its descendants. Thus, where the three sequences have G's and one A as the first base, the probability is that the ancestral DNA had a G there.

This analysis has its limitations. There's no way to tell whether a base has changed more than once in its history, which can be a problem when you try to work further back in time. But still, the technique is a success. We've used it to reconstruct ancient proteins, many of which are functional when placed in a modern context. In many cases, they have distinct properties—like tolerance to high temperatures—that can tell us something about the environment the organism inhabited.

It's also possible to use this information to figure out when this ancestral protein, or the species that used it, existed. For most lineages, we can count the number of new mutations that typically appear each generation. That number can be compared with the total number of mutations present to tell us how many generations it probably took for the sequence to reach its present state. Combine that with a measure of the average time between generation and you can estimate how long it took for the DNA to reach its present state. There are large uncertainties involved, but the approach can still be valuable.

It's a bit of a cliché to say "the past is gone." But the past obviously leaves its mark upon the present. By reading that mark, we can create a vivid and informative picture of the past, even if we don't yet have a time machine that will allow us to visit it.