Understanding Phylogenies: The Definition

The definition
Biological evolution, simply put, is descent with modification. This definition encompasses
small-scale evolution (changes in gene — or more precisely and technically, allele —
frequency in a population from one generation to the next) and large-scale evolution (the
descent of different species from a common ancestor over many generations). Evolution
helps us to understand the history of life.
The central idea of biological evolution is that all life on Earth shares a common ancestor, just
as you and your cousins share a common grandmother.
Through the process of descent with modification, the common ancestor of life on Earth gave
rise to the fantastic diversity that we see documented in the fossil record and around us
today. Evolution means that we're all distant cousins: humans and oak trees, hummingbirds
and whales.
Understanding phylogenies
Understanding a phylogeny is a lot like reading a family tree. The root of the tree represents
the ancestral lineage, and the tips of the branches represent the descendants of that
ancestor. As you move from the root to the tips, you are moving forward in time.
When a lineage splits (speciation), it is represented as branching on a phylogeny. When a

speciation event occurs, a single ancestral lineage gives rise to two or more daughter
lineages.
Phylogenies trace patterns of shared ancestry between lineages. Each lineage has a part of
its history that is unique to it alone and parts that are shared with other lineages.
Similarly, each lineage has ancestors that are unique to that lineage and ancestors that are
shared with other lineages — common ancestors.
A clade is a grouping that includes a common ancestor and all the descendants (living and
extinct) of that ancestor. Using a phylogeny, it is easy to tell if a group of lineages forms a
clade. Imagine clipping a single branch off the phylogeny — all of the organisms on that
pruned branch make up a clade.
Trees, not ladders

Several times in the past, biologists have committed themselves to the
erroneous idea that life can be organized on a ladder of lower to higher
organisms. This idea lies at the heart of Aristotle's Great Chain of Being
(see right).
Similarly, it's easy to misinterpret phylogenies as implying that some

organisms are more "advanced" than others; however, phylogenies
don't imply this at all.
In this highly simplified phylogeny, a

speciation event occurred resulting in two
lineages. One led to the mosses of today;
the other led to the fern, pine, and rose.
Since that speciation event, both lineages
have had an equal amount of time to
evolve. So, although mosses branch off Aristotle's vision of a
early on the tree of life and share many Great Chain of
features with the ancestor of all land plants, living moss species are not Being, above. We
ancestral to other land plants. Nor are they more primitive. Mosses are now know that this
idea is incorrect.
the cousins of other land plants.
So when reading a phylogeny, it is important to keep three things in mind:
1. Evolution produces a pattern of relationships among lineages that is tree-like, not

ladder-like.
2. Just because we tend to read phylogenies from left to right, there is no correlation
with level of "advancement."
3. For any speciation event on a phylogeny, the choice of which lineage goes to the right
and which goes to the left is arbitrary. The following phylogenies are equivalent:
Download the three graphics above from the Image library.

Misconceptions about humans
The points described above cause the most problems when it comes to human evolution. The
phylogeny of living species most closely related to us looks like this:
It is important to remember that:
1. Humans did not evolve from chimpanzees. Humans and chimpanzees are evolutionary
cousins and share a recent common ancestor that was neither chimpanzee nor
human.
2. Humans are not "higher" or "more evolved" than other living lineages. Since our
lineages split, humans and chimpanzees have each evolved traits unique to their own
lineages.
3.Homologies and analogies
4. Since a phylogenetic tree is a hypothesis about
evolutionary relationships, we want to use characters
that are reliable indicators of common ancestry to
build that tree. We use homologous characters —
characters in different organisms that are similar
because they were inherited from a common
ancestor that also had that character. An example of
homologous characters is the four limbs
of tetrapods. Birds, bats, mice, and crocodiles all
have four limbs. Sharks and bony fish do not. The
ancestor of tetrapods evolved four limbs, and its
descendents have inherited that feature — so the
presence of four limbs is a homology.
5. Not all characters are homologies. For example,
birds and bats both have wings, while mice and
crocodiles do not. Does that mean that birds and bats are more closely related to one
another than to mice and crocodiles? No. When we examine bird wings and bat wings
closely, we see that there are some major differences.
6.
7. Bat wings consist of flaps of skin stretched between the bones of the fingers and arm.
Bird wings consist of feathers extending all along the arm. These structural
dissimilarities suggest that bird wings and bat wings were not inherited from a
common ancestor with wings. This idea is illustrated by the phylogeny below, which is
based on a large number of other characters.
8. Bird and bat wings are analogous — that is, they

have separate evolutionary origins, but are superficially
similar because they have both experienced natural
selection that shaped them to play a key role in flight.
Analogies are the result of convergent evolution.
9. Interestingly, though bird and bat wings are
analogous as wings, as forelimbs they are homologous.
Birds and bats did not inherit wings from a common
ancestor with wings, but they did inherit forelimbs from a
common ancestor with forelimbs.
Download the two graphics
abovefrom the Image library.
Using the tree for classification

Biologists use phylogenetic trees for many purposes, including:
 Testing hypotheses about evolution

 Learning about the characteristics of extinct species and ancestral lineages
 Classifying organisms
Using phylogenies as a basis for classification is a relatively new development in biology.
Most of us are accustomed to the Linnaean system of classification that assigns every
organism a kingdom, phylum, class, order, family, genus, and species, which, among other
possibilities, has the handy mnemonic King Philip Came Over For Good Soup. This system
was created long before scientists understood that organisms evolved. Because the Linnaean
system is not based on evolution, most biologists are switching to a classification system that
reflects the organisms' evolutionary history.
This phylogenetic classification system names only clades — groups of organisms that are all
descended from a common ancestor. As an example, we can look more closely at reptiles and
birds
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Adding time to the tree

If you wanted to squeeze the 3.5 billion years of the history of life on
Earth into a single minute, you would have to wait about 50 seconds for
multicellular life to evolve, another four seconds for vertebrates to invade
the land, and another four seconds for flowers to evolve — and only in the
last 0.002 seconds would "modern" humans arise.
Biologists often represent time on phylogenies by drawing the branch

lengths in proportion to the amount of time that has passed since that
lineage arose. If the tree of life were drawn in this way, it would have a
very long trunk indeed before it reached the first plant and animal
branches.
The following phylogeny represents vertebrate evolution — just a small

clade on the tree of life. The lengths of the branches have been adjusted
to show when lineages split and went extinct.
How we know what happened when

Life began 3.8 billion years ago, and insects diversified 290 million years ago, but the human
and chimpanzee lineages diverged only five million years ago. How have scientists figured out
the dates of long past evolutionary events? Here are some of the methods and evidence that
scientists use to put dates on events:
1. Radiometric dating relies on half-life decay of radioactive elements to allow

scientists to date rocks and materials directly.
2. Stratigraphy provides a sequence of events from which relative dates can

be extrapolated.
3. Molecular clocks allow scientists to use the amount of genetic divergence

between organisms to extrapolate backwards to estimate dates.

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The definition

When a lineage splits (speciation), it is represented as branching on a phylogeny. When a

Trees, not ladders

Similarly, it's easy to misinterpret phylogenies as implying that some

In this highly simplified phylogeny, a

So when reading a phylogeny, it is important to keep three things in mind:

1. Evolution produces a pattern of relationships among lineages that is tree-like, not

Download the three graphics above from the Image library.

It is important to remember that:

8. Bird and bat wings are analogous — that is, they

Using the tree for classification

 Testing hypotheses about evolution

Using phylogenies as a basis for classification is a relatively new development in biology.

Adding time to the tree

Biologists often represent time on phylogenies by drawing the branch

The following phylogeny represents vertebrate evolution — just a small

How we know what happened when

1. Radiometric dating relies on half-life decay of radioactive elements to allow

2. Stratigraphy provides a sequence of events from which relative dates can

3. Molecular clocks allow scientists to use the amount of genetic divergence

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