Week 2: Phylogenetics

Lab #2 Goals

  • What is phylogenetics?

    • Phylogenetics is the study of evolutionary relationships among biological entities - often species, individuals, or genes.

  • How do you interpret one?

    • Understanding the relationships depicted in a phylogenetic tree can inform us about the history of evolution and genetic traits.

  • How do you build one?

    • Class experiment: Maximum Parsimony: This method emphasizes the tree with the fewest evolutionary changes.

Comparative Methods

  • What are comparative methods?

    • These methods enable comparisons between species or populations using phylogenetic trees.

  • Class experiment: Tracking an outbreak:

    • Contact Tracing: A technique used to monitor the spread of diseases.

    • Phylogeny Reconstruction: Using genetic information to construct a phylogenetic tree that reflects the relationships and evolutionary history of samples.

    • Example in R:

    • Simulating trees and reconstructing traits: This involves creating artificial phylogenetic trees and mapping traits onto them in programming language R.

  • Microscopy:

    • Creating slides: Preparing specimens for microscopic examination.

    • Measuring Diversity: Assessing the variety and abundance of species in a given area.

    • Set up Group Experiment: Arrange collaborative tasks for practical investigations.

Observed Phenotype in P. cinereus

  • Red-back (dominant): 78 individuals observed.

  • Lead-back (recessive): 22 individuals observed.

    • Proportions calculated based on phenotype samples.

  • Allele Frequencies Calculations:

    • Let |p| be the frequency of dominant allele A and |q| = 1 - |p| be the recessive allele.

    • Use Hardy-Weinberg principle equations:

    • p+q=1p + q = 1

    • q2=racextnumberofrecessivephenotypesexttotalphenotypesq^2 = rac{ ext{number of recessive phenotypes}}{ ext{total phenotypes}}

    • 2pq=extheterozygotes2pq = ext{heterozygotes} = 0.531.

Genetic Structure and Morph Frequency

  • Study Reference: Hantak et al. 2019.

  • Questions Addressed by Genetic Structure:

    • How are these populations related?

    • Did the lead-back morph evolve once or multiple times?

    • Evolution timing and initial locations of morph appearance.

Population and Evolution Basics

  • Evolution works on populations

    • Species evolve through changes in allele frequencies across generations in populations.

  • Shepherd's Purse (Capsella bursa-pastoris):

    • Multiple generations contribute to population evolution.

    • Generational breakdown:

    • G1: Parents

    • G2: Offspring

    • Continuing to G5.

Phylogenetics Overview

  • Life Classification:

    • Branching of evolutionary trees showing relationships among major groups: Eukaryotes, Archaea, Bacteria, and various extinct species.

  • Phylogenetic Systematics Definition:

    • The field concerned with discovering and understanding the evolutionary relationships in extant and extinct species.

    • Similarity among species derives from common descent.

    • Phylogenies can assess relationships across diverse scales of biological organization.

Example Phylogenetic Structures

  • Illustrating taxonomic hierarchies including individual species to family classifications.

    • Include frogs and toads as case studies with detailed hierarchical classification.

Phylogenetic Trees and Their Significance

  • Utilization of Phylogenies:

    • They answer and raise questions about the relationships among species.

    • They help ascertain evolutionary questions like common descent and divergence.

Concepts in Phylogenetics

  • Maximum Parsimony:

    • An optimality criterion choosing the tree that minimizes the total number of character-state changes among organisms.

    • Challenges might include biases and oversimplifications in representing evolutionary relationships.

  • Simulating Processes:

    • Use of simulations to illustrate evolutionary processes and phylogenetic developments, emphasizing slow changes over substantial periods.

Practical Applications in Phylogenetics

  • Utilizing genetic data for contact tracing and outbreak tracking.

    • Phylogenetic trees are essential for understanding how diseases spread and evolve in populations.

    • Understanding the branching of evolutionary trees serves practical investigations into disease management and biological classification.

Data Illustrations

  • Examples of class exercises involving phylogenetic trees, species classification, and genetic data representation.

  • Utilizing tools such as R for visualizing simulations and data collection processes.

  • Cladogram:

    • Just shows relationships, no meaning to length of the branches, illustrating how closely related different species are based on shared characteristics.

  • Phylogram:

    • Shows relationships and phylogenetic change. The longer the branch, the more change

  • Chronogram:

    • Displays relationships over time, where branch lengths represent the time since divergence, allowing us to understand the chronological order of species evolution.

Ethics and Considerations in Biology

  • Discussing implications of phylogenetics in comprehension of biodiversity; understanding of evolutionary trees can add depth to discussions on environmental changes and conservation efforts.

Conclusion: Phylogenetics as a Tool

  • Phylogenetics acts not just as a classification system but as a framework facilitating questions about life’s diversity, evolution, and emerging relationships across species.