Building a Tree of Life

A whale swims in the sea and its body is shaped like a fish’s. Yet it breathes air with lungs, it feeds its young milk, and its closest living relatives are hippos.

At first glance, a whale and a tuna seem to belong together. A hippo spends its days in rivers and walks on four legs. So how did biologists decide that whales and hippos are cousins? Fossil whales with legs, whale embryos and whale DNA each tell part of the story.

Explore: build a tree one trait at a time

In the simulation you start with six animals and a list of traits. You choose a trait, such as a backbone, and the animals that lack it branch off the tree first. Each trait you add splits the group again, until you have a full cladogram. A DNA panel then lets you check your tree against a different kind of evidence.

Try this.

1. Predict which animal will branch off first when you add “backbone”. Then add it and check.
2. Add the traits in a different order. Predict whether the finished tree will change, then test it.
3. Spin two branches around their branch point. Does the tree now say something different about who is related to whom?
4. Open the DNA panel. Predict whether the DNA evidence will agree with the tree you built from body traits.

Explain: the evidence for shared ancestry

Classification is the grouping of organisms by how they are related. Biologists use several kinds of evidence, and they trust a grouping most when the kinds agree.

Homologous structures are body parts built from the same set of parts because they were inherited from a common ancestor. A common ancestor is an earlier population that two or more groups descended from. Look at the forelimb of a human, a bat and a whale. A hand grasps, a wing flies and a flipper steers, yet all three have one upper arm bone, two forearm bones, wrist bones and finger bones.

Embryology is the study of how organisms develop before birth or hatching. Embryos can share parts that the adults lose. Early fish, chick and human embryos all have a tail and a row of folds in the neck called pharyngeal arches, with slits between them sometimes called “gill slits”. In fish, several of these arches go on to support gills. In humans they become parts of the jaw, ear and throat, and the tail shrinks away. Human embryos do not turn into fish first. They share early parts with other vertebrates, then follow their own path. Some old textbook drawings made embryos look more alike than they really are, so biologists now compare photographs of real embryos.

The fossil record is the collection of preserved remains and traces of past life, placed in time order by the rock layers they are found in. Fossils show what bodies looked like long ago, including groups that no longer exist.

DNA and proteins give a fourth line of evidence. The more two species’ sequences match, the more recently they usually shared an ancestor. Deeper still, almost every organism reads its DNA with the same genetic code, the rule that matches each three-letter DNA “word” to an amino acid. The code has a few small exceptions. Most organisms also share the same basic chemical reactions for breaking down sugar. A shared code and shared chemistry are best explained by common ancestry. You can read how the code works in that lesson.

Classification is also a nested list, from broad to specific: domain, kingdom, phylum, class, order, family, genus, species. Each level holds fewer organisms that share more traits. That lesson covers the top levels.

Explain: reading and building a cladogram

A cladogram is a branching diagram that shows the order in which groups split from common ancestors. It is built from a shared derived characteristic, a trait that first appeared in one ancestor and was passed to its descendants. Hair is one: mammals share it, and fish and frogs do not. A trait that every animal in your sample has, such as a backbone in a group of vertebrates, cannot split that group.

A branch point, or node, is where one line splits into two. Each branch point stands for the common ancestor of everything above it. To decide who is most closely related, trace the branches from two tips back to the branch point where they meet. The pair that meets at the most recent branch point is the closest.

Three rules keep you from misreading a tree:

• It branches; it is not a ladder. No tip is the goal, and a tip at the right edge is not “more advanced”.
• Tips side by side are not always closest. You can spin branches around a branch point and the meaning stays the same. Always trace back to the shared branch point.
• Line length depends on the tree. On a plain cladogram, lengths mean nothing. Some trees scale length to the amount of change, and some to millions of years. Read the key before you read lengths.

An analogy: a cladogram is like a family tree that shows only cousins and their shared grandparents. The analogy breaks because the “grandparents” at the branch points are whole populations that lived long ago, not single people, and none of them is alive today.

Elaborate: score six animals and place a whale

This table scores five traits in six animals, using 1 for present and 0 for absent. The lancelet, a small fishlike animal with no backbone, is the outgroup: the animal you compare everyone else to.

These scores are a teaching dataset from a published biology textbook figure (copyright 2005), shown in City Tech (CUNY) course slides for BIO1201 (spring 2019 course website). They are not measurements of individual specimens. The source calls one trait the “amniotic (shelled) egg”. Here it means an embryo that grows inside a protective membrane called the amnion, which is why a leopard scores 1 even though it is born alive.

DNA gives a second check. In 2005 a team compared the genome of one chimpanzee, named Clint, with human DNA. Across about 2.4 billion bases that could be lined up, they found 1.23 mismatches per 100 bases, so about 98.8 percent matched. That figure covers only the aligned parts, not every difference between the two genomes.

1. Which trait separates the lamprey from all the other vertebrates? Which trait groups only the turtle and leopard?
2. The backbone is scored 1 for five animals. Can it tell you whether the turtle is closer to the salamander or to the leopard? Why or why not?
3. Using the chimpanzee numbers, about how many of every 1,000 aligned bases differ between humans and chimps?

Design problem

Plan a study to test whether whales are closer to hippos or to pigs, using inserted pieces of DNA. Say what you would measure and what result would support each answer.

Evaluate: check your thinking

A whale looks like a fish because both swim, but its lungs and milk put it among the mammals. Fossil whales with legs, embryos that start to grow hind limbs, and DNA insertions it shares with hippos all point the same way. A whale’s shape fits where it lives; its relatives are found by tracing shared inherited traits back to a common ancestor.

Science practices you used: reading a data table of scored traits, building a model of relationships and naming its limits, using several lines of evidence to support a claim, and planning a test that could prove a claim wrong.