Building Phylogenetic Trees: Videos & Practice Problems

Phylogenetic trees illustrate evolutionary relationships among organisms, constructed using shared derived characters that indicate common ancestry. The process involves creating a character matrix to differentiate between ingroups and outgroups, identifying shared derived characters, and applying the principle of parsimony, which favors the simplest explanation with the fewest evolutionary changes. This method enhances understanding of evolutionary lineage and relationships, ensuring accurate representation of species connections based on homologous traits rather than analogous ones.

Shared Derived Characters

Building phylogenetic trees involves analyzing traits or characters of organisms to infer their evolutionary relationships. Traits can be morphological features, such as bone structures, or genetic information, like DNA sequences. The key to constructing these trees lies in identifying shared characters, which indicate that organisms are more closely related due to a common ancestor.

Shared characters can be categorized into two main types: shared derived characters and shared ancestral characters. Shared derived characters are traits that evolved after the common ancestor of the organisms in question. For instance, mammals like mice and platypuses share derived traits such as mammary glands and hair, which likely evolved in their common ancestor. This allows us to link these two organisms on the phylogenetic tree.

In contrast, shared ancestral characters are traits that were present in the common ancestor of all organisms in the tree. An example is the presence of bones, which is a trait shared by all the organisms in the tree. While this indicates a common ancestry, it does not provide information about the closer relationships among the organisms, as all share this trait.

It is important to differentiate between homologous and analogous characters when building phylogenetic trees. Homologous characters are inherited from a common ancestor, while analogous characters arise independently, often due to similar environmental pressures. For example, both the platypus and the crocodile have webbed feet, but this trait is analogous and does not indicate a close evolutionary relationship. To avoid misinterpretation, utilizing a larger number of characters increases the likelihood of identifying true homologous traits, thereby enhancing the accuracy of the phylogenetic tree.

In summary, the construction of phylogenetic trees relies on the identification of shared derived characters that suggest evolutionary relationships, while being cautious of shared ancestral characters and analogous traits. The more characters analyzed, the more reliable the inferred relationships among organisms will be.

Building Phylogenetic Trees Example 1

In the study of vertebrate evolution, understanding the distinction between shared derived characters and shared ancestral characters is crucial for interpreting phylogenetic trees. A shared derived character, or synapomorphy, is a trait that is present in a group of organisms but absent in their distant ancestors, indicating a more recent common ancestor. Conversely, a shared ancestral character, or plesiomorphy, is a trait that was present in the common ancestor of a group and remains in its descendants.

For instance, the presence of four limbs is a shared derived character among land vertebrates, as it evolved after the divergence from ancestors like sharks and ray-finned fish, which do not possess this trait. In contrast, the presence of gills is a shared ancestral character, as it was likely present in the common ancestor of all vertebrates, including early fish.

Feathers, however, are a unique trait found only in birds, making them a derived character but not a shared derived character, as they do not appear in other taxa on the tree. Lungs represent another shared derived character, having evolved in a lineage leading to land vertebrates, while laying eggs is a shared ancestral character, as it was present in the common ancestor of most vertebrates.

Terrestrial reproduction is a shared derived trait, as it evolved in specific lineages that adapted to land environments. The ability to produce milk is also derived but not shared among the taxa represented, as it is exclusive to mammals in this context. Lastly, teeth are considered a shared ancestral character, as they were likely present in the common ancestor of vertebrates, with the exception of birds, which have evolved different feeding mechanisms.

Understanding these distinctions helps clarify the evolutionary relationships among vertebrates and the traits that define their adaptations to various environments.

Which of the following statements are true regarding shared derived characters?
I) Shared derived characters are examples of analogies. 
II) Shared derived characters are traits shared by multiple taxa within a tree. 
III) Shared derived characters are used to establish evolutionary relationships.

• A. I & II.
• B. I & III.
• C. II & III.
• D. I, II, & III.

Answer: (C)

The following table shows an inferred ancestral sequence for five DNA nucleotides. Then it shows the sequence for the same five nucleotides in taxa X, Y, & Z. If you wanted to build a phylogenetic tree for taxa X, Y, & Z, which nucleotide would be the most informative?

• A. Nucleotide 1.
• B. Nucleotide 2.
• C. Nucleotide 3.
• D. Nucleotide 4.
• E. Nucleotide 5.

Answer: (C)

Ingroups, Outgroups, & the Character Matrix

Understanding evolutionary relationships among organisms is crucial in biology, and one effective way to visualize these relationships is through a phylogenetic tree. To construct such a tree, we utilize a character matrix, which serves as a table to identify shared derived characters among different taxa. This matrix is essential for distinguishing between ingroups and outgroups, which are fundamental concepts in phylogenetics.

The ingroup consists of the taxa that researchers aim to connect in the phylogenetic tree. For example, if we consider frogs, mice, platypuses, birds, and crocodiles as our ingroup, we seek to understand how these organisms are related. In contrast, the outgroup is a related taxon that is more distantly related to the ingroup. In our example, a fish can serve as an outgroup, providing a reference point to help identify shared derived characters.

A character matrix is structured with taxa listed on one side and various traits or characters across the top. Each cell in the matrix is filled with a '1' if the taxon possesses the character and a '0' if it does not. For instance, traits might include whether the organism lays eggs, has four limbs, possesses an amnion, has mammary glands, or has a gizzard. The more characters included in the matrix, the more robust the resulting phylogenetic tree will be.

To build the tree, the first step is to identify shared derived characters, which are traits present in multiple taxa but absent in the outgroup. This distinction helps in placing the root of the tree accurately. For example, if all ingroup taxa except the fish share a character, that character is considered derived. Next, researchers identify pairs of taxa with the most shared derived characters, known as sister taxa, which are likely to share a recent common ancestor.

After identifying sister taxa, the next step involves connecting these groups based on the number of shared derived characters. For instance, if the bird and crocodile share three derived characters, they can be grouped together. Similarly, if the mouse and platypus also share three derived characters, they form another group. This process continues, linking taxa based on shared characteristics until all ingroup taxa are connected. Finally, the outgroup is added to the base of the tree, establishing the root and completing the phylogenetic tree.

In summary, the concepts of ingroup, outgroup, and character matrix are vital for constructing phylogenetic trees, which illustrate evolutionary relationships. By identifying shared derived characters and systematically linking taxa, researchers can visualize the connections among various organisms, enhancing our understanding of evolutionary biology.

Building Phylogenetic Trees Example 2

In the study of phylogenetics, identifying sister taxa is crucial for understanding evolutionary relationships. Sister taxa are groups of organisms that share a common ancestor and are more closely related to each other than to any other group. To determine sister taxa, researchers analyze a character matrix, which includes various traits or nucleotides across different taxa.

In this scenario, we have three taxa: Q, R, and S, along with an outgroup for comparison. The process begins by examining pairwise comparisons of shared derived characters among the taxa. A shared derived character is a trait that is present in two or more taxa but absent in their outgroup, indicating a closer evolutionary relationship.

To identify sister taxa, we tally the number of shared derived characters between each pair of taxa. For instance, if nucleotide 3 is a shared derived character between taxa Q and R, it receives a tally mark in their comparison. This process continues for each nucleotide, allowing us to quantify the shared traits among the taxa.

After analyzing all nucleotides, we find that taxa Q and R share the most derived characters, indicating a closer evolutionary relationship compared to the other pairs. This conclusion suggests that Q and R are sister taxa, as they likely share a more recent common ancestor than with taxon S.

In summary, the identification of sister taxa relies on the analysis of shared derived characters, which helps construct a phylogenetic tree that reflects evolutionary relationships. The more shared derived characters two taxa have, the more closely related they are, reinforcing the importance of thorough character analysis in phylogenetic studies.

You are constructing a phylogenetic tree of all species in the family Bovidae, which includes all cattle, sheep, goats, antelope, bison, and buffalo. What do you think would be a good outgroup?

• A. A moose.
• B. A domestic cow.
• C. A fish.
• D. An oak tree.

Answer: (A)

You are constructing a phylogenetic tree of the oak trees, and you include one species of chestnut tree as an outgroup. Why would you include the chestnut species?

• A. To test if oak trees are a monophyletic group or if some may be more closely related to chestnut.
• B. Adding the chestnut will help establish branch lengths for the oak species.
• C. The chestnut will help establish which derived characters are homologous and which are analogous.
• D. The chestnut species will help add the correct root to the tree as it helps to establish ancestral traits.

Answer: (D)

Based on the following character matrix, which of the following organisms would you predict to be sister taxa?

• A. New and Old World monkeys.
• B. New World monkeys and apes.
• C. Lemurs and New World monkeys.
• D. Old World monkeys and apes.

Answer: (D)

Parsimony

Phylogenetic trees are essential tools in understanding evolutionary relationships among organisms, and they are constructed using the principle of parsimony. Parsimony, often associated with Occam's razor, posits that the simplest explanation is usually the correct one. In the context of phylogenetics, a maximum parsimony approach suggests that the tree with the fewest evolutionary changes is the most likely representation of the true relationships among species.

To illustrate this concept, consider two phylogenetic trees that include a fish, a frog, a mouse, a platypus, a pigeon, and a crocodile. The left tree suggests that the mouse and the platypus are closely related, while the right tree proposes a closer relationship between the platypus and the bird/crocodile lineage. By mapping character state changes—such as the ability to lay eggs, the presence of four limbs, the amnion, the gizzard, and mammary glands—on these trees, we can evaluate the number of evolutionary changes required for each hypothesis.

For instance, laying eggs is an ancestral trait, so it does not require mapping. However, since mice do not lay eggs, a character state change is noted on the lineage leading to the mouse. Similar mappings are done for other traits, leading to a total count of evolutionary changes for each tree. The left tree, with five changes, is deemed more parsimonious than the right tree, which has six changes, thus making it the more likely correct representation.

While parsimony is a foundational concept in phylogenetics, modern biology employs more sophisticated statistical methods, such as maximum likelihood. This approach acknowledges that not all evolutionary changes are equally probable; some mutations occur more frequently due to the underlying chemistry of DNA. For example, a mutation from cytosine (C) to thymine (T) is more likely than a mutation from cytosine to guanine (G). By integrating these probabilities into phylogenetic models, researchers can refine their understanding of evolutionary relationships beyond mere counts of changes.

In summary, the principle of parsimony serves as a guiding framework in constructing phylogenetic trees, emphasizing the importance of simplicity in explaining evolutionary relationships while also accommodating the complexities of biological data through advanced statistical methods.

Building Phylogenetic Trees Example 3

In the study of evolutionary biology, understanding the concept of parsimony is crucial when analyzing phylogenetic trees. In the context of bird evolution, we can examine the character of flight, which has two states: flighted and flightless. The tinamous, a group of birds native to South America, are the only birds in a specific tree that retain the ability to fly, while all other birds depicted are flightless.

To determine the most parsimonious ancestral state for flight, we consider the likelihood of evolutionary changes. If we assume that the ancestor of this tree was flightless, then the only evolutionary change would be the tinamous gaining the ability to fly. This scenario results in just one transition in the character state of flight.

However, if we consider the possibility that the tinamous are the only birds that retained the ancestral flighted state, we must analyze the evolutionary transitions differently. In this case, we trace the lineage of each bird back to their common ancestors. For instance, if we follow the lineage of the ostrich, rhea, kiwi, cassowary, and emu, we find that each of these birds has ancestors that could fly. This leads to four distinct evolutionary changes where flight was lost independently in these lineages.

Thus, the most parsimonious explanation suggests that the tinamous retained their ability to fly, while flight was lost independently four times among the other birds. This understanding challenges previous assumptions and highlights the complexity of evolutionary traits, emphasizing that the loss of flight is more common than the gain of flight in this group of birds.

What does it mean to apply the concept of parsimony to an evolutionary tree?

• A. A tree should consider both the number of evolutionary steps and the likelihood of each step.
• B. A tree should clearly display which evolutionary changes occurred within each lineage.
• C. A tree that has the fewest evolutionary changes is usually the correct interpretation.
• D. A tree should have as few branch points (nodes) as possible.

Answer: (C)

Here’s what students ask on this topic:

What are shared derived characters and how are they used in building phylogenetic trees?

Shared derived characters, also known as synapomorphies, are traits that are present in two or more taxa and have evolved from a common ancestor. These characters are crucial in constructing phylogenetic trees because they indicate evolutionary relationships among organisms. When building a phylogenetic tree, scientists look for these shared derived characters to determine which organisms are more closely related. By identifying these traits, researchers can infer the branching patterns of the tree, linking organisms that share a common ancestor. This method helps in distinguishing between homologous traits, which are inherited from a common ancestor, and analogous traits, which are not. Thus, shared derived characters provide a framework for understanding evolutionary lineage and relationships among species.

How does the concept of parsimony apply to phylogenetic trees?

The concept of parsimony, often referred to as Occam's razor, is applied in phylogenetic tree construction to favor the simplest explanation with the fewest evolutionary changes. In the context of phylogenetic trees, maximum parsimony suggests that the tree with the least number of character state changes is the most likely representation of evolutionary relationships. This approach helps in minimizing assumptions and complexities, ensuring that the tree reflects the most straightforward evolutionary path. By using parsimony, scientists can avoid overcomplicating the tree with unnecessary evolutionary events, leading to a more accurate depiction of species connections. However, modern methods also incorporate statistical models like maximum likelihood to account for the probability of certain changes occurring more frequently than others.

What is a character matrix and how is it used in phylogenetic analysis?

A character matrix is a table used in phylogenetic analysis to organize and compare traits or characters across different taxa. It lists organisms (taxa) along one axis and characters or traits along the other. Each cell in the matrix is filled with a binary value (1 or 0) indicating the presence or absence of a character in a taxon. This matrix helps identify shared derived characters, which are essential for constructing phylogenetic trees. By comparing these characters, scientists can determine evolutionary relationships and group organisms into ingroups and outgroups. The character matrix serves as a foundational tool in phylogenetic analysis, allowing researchers to systematically evaluate traits and build accurate evolutionary trees.

What is the difference between homologous and analogous traits in phylogenetic trees?

In phylogenetic trees, homologous traits are those inherited from a common ancestor, indicating evolutionary relationships among organisms. These traits are crucial for constructing accurate phylogenetic trees as they reflect true evolutionary lineage. In contrast, analogous traits arise independently in different lineages due to similar environmental pressures or convergent evolution, not from a common ancestor. While analogous traits may appear similar, they do not provide reliable information about evolutionary relationships. Distinguishing between homologous and analogous traits is essential in phylogenetic analysis to ensure that the tree accurately represents the evolutionary history of the organisms. By focusing on homologous traits, scientists can build trees that reflect genuine ancestral connections.

How do ingroups and outgroups help in constructing phylogenetic trees?

In phylogenetic tree construction, ingroups and outgroups are used to determine evolutionary relationships among organisms. The ingroup consists of taxa that are the primary focus of the study, while the outgroup is a related taxon known to be more distantly related to the ingroup. By comparing the ingroup to the outgroup, scientists can identify shared derived characters that are unique to the ingroup. This comparison helps differentiate between ancestral and derived traits, allowing researchers to accurately place the root of the tree. The outgroup serves as a reference point, providing context for the evolutionary changes within the ingroup, and ensuring that the phylogenetic tree accurately reflects the evolutionary history of the organisms.