ctivity 10 Homework: Phylogenetic inference (1 point each) Briefly describe the steps involved in conducting phylogenetic inference using parsimony Why is using parsimony with morphological data problematic? (Hint: imagine character – ‘wings’ of bats, humans, mice and butterflies. Based on parsimony, bats and butterfly will be put together. How is that a problem?)

QUESTION

Activity 10 Homework: Phylogenetic inference (1 point each)

1. Briefly describe the steps involved in conducting phylogenetic inference using parsimony

2. Why is using parsimony with morphological data problematic? (Hint: imagine character – ‘wings’ of bats, humans, mice and butterflies. Based on parsimony, bats and butterfly will be put together. How is that a problem?)

3. The eyes of an octopus and human look very similar but they do not share a common ancestor. This is an example of a(n)
4. Homoplasy
5. Homology
6. Synapomorphy
7. Plesiomorphy
8. Apomorphy

4. What does it mean for a trait to have an appropriate amount of variation for a use in a phylogenetic analysis? Use examples
5. Which statement(s) is/are true about Bayesian method?

1. Bayesian searches for trees with highest posterior probability
2. It is based on Bayes theorem
3. Does not use models for tree inference
4. Utilizes prior information/probability
5. Same principle as maximum parsimony

ANSWER

Conducting Phylogenetic Inference Using Parsimony: Unveiling Evolutionary Relationships

Introduction

Phylogenetic inference is a fundamental tool in evolutionary biology that aims to uncover the evolutionary relationships among organisms. One popular method used in this process is parsimony, which seeks to reconstruct a phylogenetic tree by minimizing the number of evolutionary changes required to explain the observed data. In this essay, we will explore the steps involved in conducting phylogenetic inference using parsimony and the challenges posed by using this method with morphological data.

Steps in Conducting Phylogenetic Inference Using Parsimony

Character Selection: The first step is to carefully select the characters to be included in the analysis. These characters should be informative and relevant to the evolutionary relationships being studied. They can encompass morphological traits, anatomical features, or even molecular sequences.

Character Coding: Once the characters have been chosen, discrete character states or values are assigned to each taxon under study. These states represent the different variations or presence/absence of traits observed in the organisms. For example, in the case of the character “wings,” bats and butterflies would be coded as having wings, while humans and mice would be coded as lacking wings.

Character Matrix Construction: A character matrix is then constructed, which serves as the input data for the phylogenetic analysis. This matrix represents the presence or absence of characters for each taxon. Each row corresponds to a specific character, and each column represents a particular taxon. The matrix provides a comprehensive overview of the character distribution across the organisms being analyzed.

Character Optimization: The core principle of parsimony is to infer the most parsimonious evolutionary tree by minimizing the number of evolutionary changes required to explain the observed character distribution. The analysis involves searching for the tree that requires the fewest number of character state changes to reconcile the observed data. This is accomplished through algorithms such as tree branch swapping or heuristic searches.

Challenges of Using Parsimony with Morphological Data

While parsimony is a valuable tool, its application to morphological data can pose challenges. One such challenge is the presence of homoplastic characters, which are traits that have evolved independently in different lineages (Neumann et al., 2020). This can lead to misleading results, as parsimony may group organisms together solely based on the shared presence or absence of a trait, without considering the underlying evolutionary history (Cuthill, 2015).

For instance, consider the example of “wings” in bats, humans, mice, and butterflies. Based on parsimony alone, bats and butterflies would be grouped together due to their shared possession of wings, despite having different evolutionary origins (Schäffer et al., 2010). This problem arises because parsimony cannot differentiate between convergent evolution (where similar traits evolve independently) and shared ancestry. Hence, relying solely on morphological characters for phylogenetic inference may yield erroneous conclusions.

Conclusion

Phylogenetic inference using parsimony is a valuable method for uncovering evolutionary relationships among organisms. By carefully selecting informative characters, coding them, constructing a character matrix, and optimizing tree topologies, researchers can gain insights into the evolutionary history of diverse taxa. However, caution must be exercised when using parsimony with morphological data, as the presence of homoplastic characters can lead to erroneous grouping of organisms. To overcome this limitation, combining multiple lines of evidence, such as molecular data, can enhance the accuracy and reliability of phylogenetic inferences.

References

Cuthill, J. F. H. (2015). The morphological state space revisited: what do phylogenetic patterns in homoplasy tell us about the number of possible character states? Interface Focus, 5(6), 20150049. https://doi.org/10.1098/rsfs.2015.0049 

Neumann, J. T., DeSalle, R., Narechania, A., Schierwater, B., & Tessler, M. (2020). Morphological Characters Can Strongly Influence Early Animal Relationships Inferred from Phylogenomic Data Sets. Systematic Biology, 70(2), 360–375. https://doi.org/10.1093/sysbio/syaa038 

Schäffer, S., Koblmüller, S., Pfingstl, T., Sturmbauer, C., & Krisper, G. (2010). Ancestral state reconstruction reveals multiple independent evolution of diagnostic morphological characters in the “Higher Oribatida” (Acari), conflicting with current classification schemes. BMC Evolutionary Biology, 10(1), 246. https://doi.org/10.1186/1471-2148-10-246