Biology 152: Chapter 2 Tree Thinking
Learning Outcomes
2.1 Identify the different parts of a phylogenetic tree: Understand definitions like clade, root, node, branch, and sister taxa.
2.2 Explain geographic isolation: Recognize how it leads to lineage splitting and its relation to nodes in a phylogenetic tree.
2.3 List clades in a tree: Determine if two phylogenetic trees have the same topology based on their clades.
2.4 Degree of evolutionary relationship: Assess the relative relatedness of taxa from various phylogenetic trees.
2.5 Common ancestry and similarity: Predict the similarity of taxa based on shared and unshared ancestry.
Introduction to Phylogenetic Trees
The focus on common ancestry connects all living organisms, depicting relationships through a metaphorical tree of life, as proposed by Darwin.
Key Terminology of Phylogenetic Trees
Root: Base of the tree representing the common ancestor of all taxa.
Branches: Lines that represent population lineages, can be internal (inside the tree) or external (tips).
Tips/Leaves/Taxa: End points of the branches, representing current or ancestral species groups.
Node: Points where lineage splitting occurs; each node represents a common ancestor of two or more lineages.
Clade: A group of all descendants from a single ancestor, identifiable by making a single cut through the tree.
Lineage Splitting and Speciation
Occurs when gene flow between two populations ceases, allowing them to evolve independently, which may eventually lead to the formation of new species (speciation).
Geographic Isolation: A major cause of lineage splitting through:
Fragmentation - Natural barriers (e.g., ravines) split continuous populations, preventing interbreeding.
Dispersal - Events that move part of a population to a distant location, leading to genetic isolation.
Understanding Relatedness in Clades
Relatedness is based on the recency of common ancestors:
Members of the same clade share a more recent ancestor compared to those outside the clade.
Example: Land plants and animals share a more recent ancestor than either does with archaea.
Tree Topology
Refers to the arrangement of clades within a phylogenetic tree:
Different representations (same topology) can still depict the same clade.
Example: Two trees can depict the same relationships but vary in style or arrangement.
Misconceptions about Evolution and Phylogenetic Trees
Common misunderstanding: Trees imply a ‘progress’ or ‘goal’ in evolution, suggesting a hierarchy of organisms (e.g., ‘higher’ vs. ‘lower’ life forms).
Reality: All living organisms have been evolving for the same duration since their respective lineages split. Thus, no species is more evolved than another.
Evolution has no predetermined direction or endpoint; it results in various complexities with many successful simple organisms like bacteria.
Dynamic Nature of Evolution
Evolution is ongoing; species are continuously adapting, and no organism can be considered the pinnacle of evolutionary change.
Glossary of Terms
Branch: Lines in tree diagrams representing population lineages.
Clade: All descendants from a common ancestor.
Lineage Splitting: Splitting of a population without gene flow.
Node: Points indicating lineage splitting.
Phylogenetic Tree: Diagram representing evolutionary relationships.
Pruning: Removing parts of the tree while maintaining topology.
Root: Base of a tree indicating common ancestry.
Speciation: The process leading to new species formed by lineage splitting.
Taxon (plural = taxa): Named group at tips of the tree.
Tree Thinking: Understanding and extracting information from tree diagrams.
Tree Topology: The arrangement of clades within the tree.
Chapter 2: Tree Thinking
Learning outcomes
2.1 Identify the different parts of a phylogenetic tree (clade, root, node, branch, sister taxa)
[Tree terminology]
2.2 Explain how geographic isolation can result in lineage splitting and associate this
phenomenon with nodes in a phylogenetic tree [Lineage splitting]
2.3 List the clades present in a phylogenetic tree and use this to determine if two trees have
the same topology [Tree topology]
2.4 Determine the relative degree of evolutionary relationship from phylogenetic trees of
various types [Relatedness]
2.5 Use the amount of shared (and unshared) common ancestry to predict the similarity of
selected tips or nodes [Non-progressive evolution]
In the last chapter, we learned about the three big ideas of evolution: common ancestry,
evolution, and natural selection. This chapter will focus exclusively on the first of these three big
ideas: common ancestry. When Darwin first identified the notion of common ancestry, he
quickly realized that common ancestry implied the existence of a metaphorical tree of life in
which all living organisms are connected to one another through lines of descent. He wrote, "The
affinities of all beings of the same class have sometimes been represented by a great tree. I
believe this simile largely speaks the truth…The great tree of life covered the Earth with ever
branching and beautiful ramifications." This chapter will expand Darwin’s metaphor of the tree
of life and ask, how can we refine this tree of life model and make it more concrete than just a
loose metaphor?
2.1 The Phylogenetic Tree
Most of the terminology for a phylogenetic tree follows the tree metaphor. We call the point of
the tree where time enters the deepest ancestry of the group the root. The bulk of the tree is
composed of branches, some are internal and some external. We call the tips of the tree tips,
leaves, or taxa. Taxa is the plural of taxon and taxon is a general term for a named biological
group. In practice, we often focus on the living descendants of this branching process, though we
may sometimes also include some tips that correspond to fossils.
The only thing that happens through evolutionary time is reproduction: parents giving rise to
offspring, passing on genetic material. Individual organisms are just temporary repositories of
genes. In sexual populations reproductive relationships are complicated and netlike. Nonetheless,
even for sexual species a tree form is possible when we zoom out from a single population to
look at the relationships between species. This is possible because on an evolutionary tree, the
branches represent population lineages whose component organisms experienced extensive gene
flow.
Where a population lineage splits into two, and gene flow between the two populations stops, we
observe lineage splitting events. These are depicted at the nodes of a tree, where each node
separates two sister lineages. Lineage splitting is a splitting of a population into genetically
separate populations that no longer have gene flow, which allows them to then accumulate
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different traits. If they accumulate differences for long enough, they might be classified as
different species, which is why lineage splitting is sometimes called speciation.
Figure 2-1 The features of a phylogenetic tree are named according to a tree metaphor.
Splitting events usually occur when population lineages are fragmented by geographic isolation.
This can happen in two general ways. First, as shown in Figure 2-2, we can have a continuous
population that somehow gets fragmented into two subpopulations by a geological or climate
change process. The populations on either side of the barrier (a ravine in this case) cease being
able to genetically intermingle. As a result, mutations arising on one side remain restricted to that
side, allowing the lineages to evolve separately and accumulate differences.
Figure 2-2 Speciation caused by geographic isolation.
The second possibility is that we can have a large population on one land mass and a rare event
resulting in dispersal of some propagules to another land mass. If the new landmass is far away,
then the new population can immediately be genetically isolated from the first, allowing it to
begin evolving independently. In this scenario, the unlikeliness of the dispersal event prevents
reintegration of the two populations. In either scenario, we end up with two populations that are
separated from one another, so they stop exchanging genes.
When we split a population at a node, we generate two independent evolutionary trajectories that
can diverge from one another over time. Because they stop exchanging genes, when evolution
happens in one of the populations, those evolved changes are not carried into the other one.
Geographic isolation allows populations to accumulate differences over time until they come to
be different in visible ways. Evolution never stops and so if you isolate two populations and stop
bacteria plants birds marsupials humans
node
root
taxa/tips
external branch
internal branch
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them interbreeding for long enough, they are guaranteed to accumulate differences. If those two
lineages change enough, then they will eventually lose the ability to interbreed which will
prevent them ever fusing back to form a single lineage.
Speciation describes the origin of multiple species from a few ancestral species. Don’t confuse
this process with trait evolution, which we will cover in a later chapter. Trait evolution happens
on evolving lineages (thus, along branches) and is not tied to lineage splitting events.
The key component of a tree is a clade, a grouping of branches and tips that includes all the
descendants of a single ancestral lineage – no more and no less. You can identify a clade by
identifying a chunk of the tree that can be removed from the root with a single cut. Imagine you
had a chainsaw: you could remove both the land plants and red algae lineages off the tree in
Figure 2-3 with one cut. That makes it a clade.
Figure 2-3 All members of a clade share a more recent common ancestor than they share with
any lineage outside of the clade.
Note that archaea and bacteria in Figure 2-3 do NOT make up a clade despite the proximity of
these tips on the tree. Their last common ancestor is shown as the node at the bottom of the
tree, but that ancestor is also an ancestor of land plants, red algae, fungi, and animals. Thus,
archaea and bacteria alone are not a clade.
We sometimes indicate that a set of taxa is a clade by grouping them in parentheses. For
example: (land plants, red algae, fungi, animals) or (land plants, red algae). We can use this
convention to summarize an entire tree in text form. Thus, the tree in Fig. 2-2 can be written:
(bacteria,(archaea,((land plants, red algae),(fungi, animals)))).
2.2 Relatedness
In biology, the same criteria are used to compare the degree of relatedness of taxa as are used to
compare human relationships on a family pedigree. For example, you are more closely related
to your first cousins than your second cousins because you and your first cousins share a more
recent common ancestor, your grandparents, than you and your second cousins do. Your great-
grandparents are the last common ancestor that you and your second cousins share. Due to the
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random chance in heredity and genetic reproduction, it is technically possible to share more
genes in common with a second cousin than with a first cousin. It is also possible to look more
alike and share more personality traits with your second cousin than with your first cousin. But
despite these facts, you are still more closely related to your first cousin than you are to your
second cousin because relatedness is about the recency of common ancestors.
Phylogenetic trees contain all the information needed to ascertain the degree of relatedness of
taxa. All taxa in a clade are more closely related to one another than they are to any taxon outside
of the clade. Also, members of a clade are equally related to any species outside of that
clade. For example, in Figure 2-3, land plants and animals are more closely related to each other
than they are to archaea. Furthermore, land plants and animals are equally related to archaea as
shown by the fact that they trace to the same common ancestor.
A tree topology is a representation of relationships between the clades in a tree, and it gives us
information about relationships. You can take the same topology and draw it in different
ways. The two trees in Figure 2-4 are the same topology because they both contain the same
clade, the (B,C) clade.
Figure 2-4 The same tree drawn two different ways.
The trees in Figure 2-5 are not the same topology because they contain different sets of clades.
The tree on the left has a (B,C) clade while the tree on the right has a (A,C) clade.
Figure 2-5 These trees contain different clades, and thus have different topologies.
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You can also draw a tree in different styles while retaining the same topology. In Figure 2-6 you
can see a diagonal format, a rectangular format, and an angled format that all depict the same
tree. You can confirm that they depict the same topology by observing that they contain the same
two clades: (C,D) and (B,C,D).
Figure 2-6 The same tree can be drawn in different styles.
2.3 Telling Evolutionary Stories
While tree diagrams are commonly seen, evidence shows that they are also commonly
misinterpreted. It is, therefore, important to help you develop good tree thinking skills, which
refers to the ability to extract accurate information from tree diagrams and to use trees effectively
to convey evolutionary history.
A common misinterpretation of phylogenetic trees is to view them as telling a story of
progress. It may be tempting to view a tree as a directional transition from early unicellular life
to the endpoint of humans today. But in fact, all the living tips of a phylogenetic tree have been
evolving for the same amount of time and have all been vetted to the same degree by natural
selection. Therefore, every living species is equally evolved and equally advanced.
The lineages leading to a living amoeba and a living human have both been evolving since the
moment when their lineages split from their common ancestor. Even if the common ancestor of
an amoeba and a human would have looked more like an amoeba than like a human, both have
evolved extensively, and neither is more evolved than the other. There's no basis for describing
some organisms as “higher” or “lower” or “advanced” or “primitive.” So, anytime you hear
somebody talk about the “higher animals” or the “advanced fishes” “primitive organisms,” or
“basal lineages,” be alert to the fact that they are inaccurately summarizing or oversimplifying
how evolution works.
There is a human tendency to think of ourselves as the pinnacle or goal of evolution. But
evolution is an idiosyncratic process in which many chance events happened on the way. Every
living species is equally a result of that process. Evolution doesn't have a direction or
purpose. When life emerged some 4 billion years ago it started with simple forms, because life
had to start simple. While complexity has accumulated, there is no evidence of any intrinsic
drive to complexity. In fact, many of the most diverse and successful species alive today are
simple. Bacteria are, numerically, vastly more successful than animals are (there are many more
bacteria in one human’s gut than there are humans on the planet).
Tree Thinking Worksheet
Learning Outcomes
Identify the Different Parts of a Phylogenetic Tree
a. Define the following terms (in your own words):Clade
Root
Node
Branch
Sister Taxa
Explain Geographic Isolation
a. Describe how geographic isolation can lead to lineage splitting.
b. Discuss how this phenomenon is represented in phylogenetic trees, particularly at the nodes.List Clades Present in a Tree
a. Examine a provided phylogenetic tree (attach tree here, if available) and list three clades visible in the diagram.
b. Explain how you would compare two different phylogenetic trees to determine if they have the same topology.Degree of Evolutionary Relationship
a. Using two hypothetical taxa from a phylogenetic tree, explain how to assess their evolutionary relationship based on recency of their common ancestors.Common Ancestry and Similarity
a. Describe how to use shared and unshared ancestry to predict the similarity of two taxa.
Activities
Labeling Exercise
Draw a simple phylogenetic tree (or use one provided) and label the following: root, branches, nodes, tips, and any identified clades.
Case Study on Geographic Isolation
Describe a natural event (e.g., geological, climate change) that could lead to geographic isolation of a population. Explain how this isolation can result in speciation.
Comparative Analysis of Topology
Review two different representations of a phylogenetic tree. Identify their clades and compare their topologies. Discuss any differences or similarities in the representations.
Discussion:
In pairs or small groups, discuss the misconception that evolution is a process with a specific direction. Provide examples to support your arguments and clarify why this perspective is scientifically inaccurate.