Phylogeny

Phylogenetics is the study of evolutionary relationships among species or other groups. These relationships are represented using diagrams - particularly phylogenetic trees and cladograms, which show how groups are related through common ancestry.

These trees help us understand how organisms evolved and where they share a most recent common ancestor. Importantly, phylogenetic trees are hypotheses - scientists build them using the best available evidence, such as DNA sequences or physical traits, but they can change with new data. Molecular data typically provides more accurate and reliable evidence, and many trees have been adjusted as more and more genetic sequencing has been done.

What's the difference between a phylogenetic tree and a cladogram?

When we want to figure out how different species are related to each other, we use diagrams that show patterns of shared ancestry. Two of the most common diagrams are phylogenetic trees and cladograms. These terms sometimes get used interchangeably, but they aren’t exactly the same thing. A cladogram shows relationships between organisms based only on shared characteristics. It tells you who is related to who, but not necessarily how much time passed or how different they are. It’s kind of like a family tree that just shows the branches without any birthdays or timelines.

A phylogenetic tree, on the other hand, includes that extra information. It tries to estimate how long ago species split from a common ancestor and how different they are genetically. This is shown by the lengths of the branches. In a phylogenetic tree, longer branches usually mean more time has passed or more evolutionary change has occurred. So if one species has a really long branch and another has a shorter one, that might suggest one has been evolving separately for longer. Some trees even have a timeline along the bottom so you can actually estimate the number of millions of years between events. In other words, a phylogenetic tree has branches that aren’t just about who is related, but also about how far apart they are on the evolutionary timeline. The timeline of divergence can be estimated by using molecular clocks - this is done using the amount of molecular differences and working under the idea that mutations occur at roughly a constant rate.

Parts of a Tree

Understanding how to read a tree means recognizing the parts:

Branches - Independently evolving lineages.

Tips – The ends of the branches represent the species, genes, or groups being compared.

Nodes – Points where branches split. These represent a common ancestor shared by the lineages branching from that point.

MRCA – The most recent common ancestor of two or more groups is found at the node that joins them.

Clade – A group that includes a common ancestor and all of its descendants.

Root – The base of the tree, representing the most ancient ancestor of all organisms in the tree.

Outgroup – The least related group to the others - usually on the tree as a point of reference/comparison.

What matters when determining relationships is the branching structure of the tree. You can rotate branches around a node without changing its meaning. To determine relatedness, trace back through the tree to see how recently two species shared a common ancestor. The more closely they share a common ancestor, the more related they are. All members of a clade are equally-distantly related to those outside the clade.

Click here to learn about ways to classify organisms.

When classifying organisms based on evolutionary history, scientists group them according to shared common ancestry.

A monophyletic group includes a common ancestor and all of its descendants - it's a clade. These groups accurately represent evolutionary relationships.

All mammals form a monophyletic group. They share a single common ancestor, and the group includes all of its descendants.

A paraphyletic group includes a common ancestor and some, but not all, of its descendants. This kind of group leaves out one or more lineages that also came from that ancestor.

Reptiles, when defined without birds, are paraphyletic. Birds evolved from within the reptile lineage but are sometimes excluded from the group, which makes it incomplete.

A polyphyletic group includes organisms that do not share a recent common ancestor but appear similar because of convergent evolution—when different lineages evolve similar traits independently.

Warm-blooded animals, such as birds and mammals, form a polyphyletic group if you classify them together just because they regulate their body temperature internally. Birds and mammals evolved this trait independently.

The Principle of Parsimony

A phylogenetic tree is a proposed explanation about the evolutionary relationships between organisms, based on the evidence we currently have. Scientists build these trees using data such as physical traits, DNA sequences, protein structures, and fossil records.

To figure out which organisms are most closely related, scientists look for shared derived characters - traits that evolved in a common ancestor and were passed on to its descendants. These traits are considered "derived" because they are new evolutionary features, not present in more distant ancestors. For example, the presence of feathers is a derived character that links birds and their closest dinosaur relatives, but not reptiles more broadly. If multiple species share a derived character that no other group has, it suggests they inherited it from a more recent common ancestor.

However, we only see living organisms and cannot look into the past to see exactly how populations diverged, so it's often possible to build multiple trees that all fit the evidence in slightly different ways. This means that for any group of organisms, there may be more than one plausible tree. Did three organisms evolve the same trait independently? Did their one ancestor evolve it and pass it on to three, but the fourth lost it?

The challenge is to decide which possible tree is most likely to represent how those species actually evolved.

To choose between possible phylogenetic trees, scientists often use the principle of parsimony. This principle states that the best explanation is usually the one that requires the fewest evolutionary changes. For example, if two possible trees explain the same trait distribution, but one of them requires a trait to evolve three times and the other only once, the simpler version (with one evolutionary event) is considered more likely.

Parsimony helps scientists avoid overcomplicating things. Instead of assuming traits were gained, lost, and regained multiple times, it favors the tree that explains the data with the least number of changes. While not always correct, parsimony is a useful tool for guiding tree construction when multiple options are possible.

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