Chapter 22.2 - Building a Phylogenetic Tree

Question 1

How is the evolutionary history of organisms determined?

Answer 1

Evolutionary history is determined by building phylogenetic trees based on organism characteristics.

Question 2

Why are similarities among organisms important in this process?

Answer 2

Similarities among organisms suggest shared ancestry, aiding in the construction of phylogenetic trees.

Question 3

What caution should be exercised when using shared characteristics for building phylogenetic trees?

Answer 3

Not all shared characteristics are informative; some can be misleading, so careful consideration is necessary.

Question 4

What are characters in the context of constructing phylogenetic trees?

Answer 4

Characters are the morphological, physiological, or molecular features of organisms used to build phylogenetic trees.

Question 5

What are character states, and how do they relate to characters?

Answer 5

Character states are the different observed conditions of characters. For example, the presence or absence of a character like lungs or the different arrangements of petals in flowers.

Question 6

Why can character states in different species be similar?

Answer 6

Character states in different species can be similar either due to common ancestry (homologous) or independent adaptation to similar environments (analogous or convergent evolution).

Question 7

What is the difference between homologous and analogous character states?

Answer 7

Homologous character states are similar because they originate from a common ancestor, while analogous character states are similar due to independent adaptation to similar selective pressures.

Question 7

Can you provide an example of homologous character states?

Answer 7

Amniotic eggs in mammals and sauropsids (birds and reptiles) are homologous character states because they originate from a common ancestor.

Question 8

What is an example of analogous character states?

Answer 8

Wings in birds and bats are analogous character states because they evolved independently in response to similar selective pressures for flight.

Question 9

How can we determine whether character states are homologous or analogous?

Answer 9

To determine if character states are homologous or analogous, we consider evidence from phylogenetic trees, anatomical or genetic details, and the placement of species on the tree. Homologous character states should have common ancestry, while analogous character states should result from independent evolution.

Question 10

Why are the details of anatomy and genetic construction important in distinguishing homologous from analogous character states?

Answer 10

The details of anatomy and genetic construction help differentiate between homologous and analogous character states. For example, the anatomy of wings in birds and bats differs, suggesting independent evolution.

Question 11

What is the difference between homologous and analogous characters, and which is useful for constructing phylogenetic trees?

Answer 11

Homologous characters result from shared ancestry and are useful for constructing phylogenetic trees. Analogous characters arise independently due to similar adaptations and are not used in tree construction.

Question 12

What is the significance of unique character states in phylogenetic tree construction?

Answer 12

Character states unique to a species or monophyletic group cannot help determine its sister group relationship because they evolved after divergence. They characterize a group but don’t relate it to others.

Question 12

What are synapomorphies, and why are they important in building phylogenetic trees?

Answer 12

Synapomorphies are shared derived character states that reveal common ancestry among species within a group. They are essential for constructing phylogenetic trees as they help identify sister group relationships.

Question 13

What is cladistics, and how does it use synapomorphies?

Answer 13

Cladistics is an approach to building phylogenetic trees based on synapomorphies. It seeks to identify shared derived character states to determine evolutionary relationships.

Question 14

How does the principle of parsimony apply to phylogenetic reconstruction?

Answer 14

Parsimony in phylogenetic reconstruction involves finding the tree with the fewest character state changes to explain the data. It aims to minimize the number of independent mutations needed to account for trait diversity.

Question 15

What is the role of statistical methods in evaluating phylogenetic hypotheses?

Answer 15

Statistical methods are used to assess the strength of support for a given phylogenetic hypothesis. They help determine the level of confidence in the proposed tree structure based on available character data.

Question 16

How do biologists handle unresolved branching patterns in phylogenetic trees?

Answer 16

When support for a specific branching pattern is weak, biologists depict unresolved branches, indicating that multiple hypotheses of relationship are possible due to limited data. These patterns represent opportunities for future research.

Question 17

How are phylogenetic trees constructed using molecular data?

Answer 17

Molecular data, such as DNA or protein sequences, are used to build phylogenetic trees by comparing shared derived characters (synapomorphies) among species or by assessing overall similarity, indicating their evolutionary relationships.

Question 18

What is the advantage of using molecular data in phylogenetics?

Answer 18

Molecular data provide more characters for phylogenetic analysis compared to morphological data, allowing for finer resolution of evolutionary relationships, especially in organisms with limited morphological information.

Question 19

What is the assumption underlying distance-based methods in molecular phylogenetics, and why is it less likely to be violated compared to morphological data?

Answer 19

Distance-based methods assume a constant or nearly constant rate of evolution. This assumption is less likely to be violated in molecular data because of the molecular clock hypothesis, which suggests a relatively constant rate of genetic divergence over time.

Question 19

How do distance-based methods work in molecular phylogenetics?

Answer 19

Distance-based methods in molecular phylogenetics involve counting differences in DNA or protein sequences between species pairs. Fewer differences suggest closer relatedness, while more differences indicate greater evolutionary distance.

Question 20

How are molecular data and morphological data often used together in phylogenetic analyses?

Answer 20

Molecular and morphological data are frequently combined in phylogenetic analyses, and each can serve as independent assessments of the other. Results from both types of data are usually compatible, especially for organisms rich in morphological characters.

Question 21

Where can researchers access a substantial repository of molecular data for taxonomic and phylogenetic studies?

Answer 21

GenBank, hosted by the National Institutes of Health, is a major repository of molecular data, providing access to over 100 billion observations (mostly nucleotides) collected under more than 710,000 taxonomic names.

Question 22

What additional resources are available for researchers interested in phylogenetic studies and taxonomic information?

Answer 22

The Encyclopedia of Life gathers biological information about species, including ecology, geographic distributions, photographs, and sounds. The Tree of Life provides information on phylogenetic trees for various groups of organisms.

Question 23

What information do phylogenetic trees document about evolutionary changes?

Answer 23

Phylogenetic trees document the sequence of changes from a tree’s root to its tips, revealing the evolutionary changes that have occurred over time.

Question 24

How do phylogenetic trees help in understanding the relationships among groups of organisms?

Answer 24

Phylogenetic trees show the relationships among groups of organisms, helping us understand how they are related to one another.

Question 25

Provide examples of practical applications of phylogenetics.

Answer 25

Phylogenetics has practical applications, such as identifying the true nature of microorganisms like oomycetes, tracking invasive species like the lime swallowtail butterfly, and tracing the spread of diseases like HIV, influenza, and COVID-19. It is also used for tracking biological material and identifying endangered species.

Question 26

How did phylogenetic analysis help identify the source population of an invasive butterfly species in the Dominican Republic?

Answer 26

Phylogenetic analysis of DNA sequences identified the Malaysian parent population of the invasive lime swallowtail butterfly in the Dominican Republic, aiding in pinpointing sources for seeking natural enemies of this pest.

Question 27

How does phylogenetic evidence assist in tracking biological material?

Answer 27

Phylogenetic evidence is used as a kind of fingerprint or barcode to track biological material, allowing quick identification of samples like endangered species or emerging diseases.

Question 28

Despite having many traits in common with fish, including a streamlined body and fins, dolphins are mammals, not fish. Are these similar traits homologous or analogous?

Answer 28

The traits are analogous, the result of convergent evolution. Both animals are adapted for swimming in water and converged independently on similar traits, including a streamlined body and fins. However, they are only distantly related, as one is a fish and the other is a mammal.

Question 29

Which type of homology is useful in building phylogenetic trees? Why is this kind of homology, and not others, useful?

Answer 29

Synapomorphies, or shared derived characters between some members of a group, are useful in building phylogenetic trees because the homologies are shared by some, but not all, of the members of the group. If an entire group shared the same homologous trait, we would not be able to construct a meaningful phylogenetic tree.

Question 30

Why is parsimony commonly favoured in evaluating phylogenetic trees?

Answer 30

Parsimony is commonly favored in evaluating phylogenetic trees because the tree that requires the fewest changes in character state is the simplest explanation available.