The Tree of Life: Understanding Phylogeny

The Tree of Life

Overview

  • This topic discusses how biologists use phylogeny to reconstruct the evolutionary history of life.

Students’ Learning Objectives

  • Phylogenetic Trees:
    • Describe how to build a phylogenetic tree from character states.
    • Explain how homoplasy (convergent evolution & evolutionary reversal) leads to different phylogenetic trees.
    • Understand the concepts of parsimony, consensus tree, and polytomy.
    • Describe some uses of phylogenetic trees, including:
    • Taxonomy (the classification of organisms).
    • Major transitions in evolution.
    • Analysis of traits/features that have changed function over time (Exaptation).
  • Assignments and Exam Dates:
    • Chapter 3 Homework: Due September 17 by 11:59 PM.
    • Quiz 1 (Chapters 1, 2 & 3): September 16.
    • Test 1 (Chapters 1, 2 & 3): September 23 & 24.

Phylogenetic Trees

Building Phylogenetic Trees

  • A phylogenetic tree is a diagram that represents evolutionary relationships among species based on shared ancestry.
    • Example:
    • Lamprey is used as an outgroup to determine the ancestral traits.
    • Characteristics are denoted as follows:
      • 0: Absence of feature
      • +: Presence of feature
    • Start by considering traits with a wide distribution across species (e.g., Jaws).
    • Jaws are considered an older derived trait that evolved early and was inherited by all subsequent descendants.

Possible Phylogenetic Trees

  • Various possible trees can represent relationships among species based on characteristics such as:
    • Fur
    • Feathers
    • Gizzard
    • Lungs
    • Jaws
  • Example of a less parsimonious tree which involves more complex explanations for the data.
  • Parsimony:
    • This is the principle of preferring the simplest explanation that accounts for all observations in the data.

Analysis of Character States

Character States and Their Definitions

  • Character: A heritable aspect of organisms that can be compared across different taxa.
  • Character State Matrices:
    • Used to develop phylogenetic trees with ancestral traits indicated as 0 and derived traits as 1.

Computational Tools

  • Powerful computer programs are utilized to analyze data and generate the most likely phylogenetic trees based on the available character states.

Understanding Phylogenetic Characters

What are Characters?

  • Characters are:
    • Single branches in the tree of life.
    • Species located at the tips of phylogenetic trees.
    • Heritable traits that can be compared across taxa.
    • Nodes in phylogeny that represent ancestral populations or species.

Homoplasy

Definitions and Concepts

  • Homoplasy: Character state similarity that arises not from common descent but through independent evolution.
  • Example:
    • Character 3 (number of lower incisor teeth) increased from 2 to 3 independently on two different branches.

Examples of Homoplasy

  • Convergent Evolution:
    • This refers to the independent evolution of similar traits in separate lineages, such as:
    • Wings of bats and birds.
    • Streamlined body shapes of sharks and dolphins.

Evolutionary Reversal

  • Evolutionary Reversal:
    • Occurs when derived characters revert back to their ancestral character states on some branches of the phylogeny.
    • Identified in characters 2, 4, 7, 9, and 10.

Concepts of Parsimony and Phylogenetic Trees

Key Terms

  • Parsimony:
    • The principle of choosing the phylogenetic tree that explains the observed data with the least number of evolutionary changes.
  • Consensus Tree:
    • A single tree that combines both resolved and unresolved portions of a phylogeny.
  • Polytomy:
    • An internal node in a phylogeny that has more than two branches indicating multiple lineages diverging.

Evolutionary Transitions and Traits

Major Transitions

  • Phylogenetic studies reveal key transitions in the evolution of groups such as:
    • The evolution of tetrapods from lobe-finned fish.
    • Tetrapods: Vertebrates with four limbs, including mammals, birds, reptiles, and amphibians.

Evolution of Tetrapod Traits

  • Traits evolved over time include:
    • Development of forelimbs and hindlimbs, weight-bearing elbows, and digit formation.
  • Overview of fossilized species and their anatomical adaptations over time leading to modern tetrapods.
    • Key fossils mentioned include Tiktaalik, Acanthostega, Ichthyostega, and Tulerpeton.

Changing Functions of Traits

Exaptation

  • Exaptation: The evolutionary process where a trait originally serving one function is co-opted for a new function.
    • Example: Feathers evolved from dinosaurs for purposes other than flight, such as species recognition and insulation.
  • Evidence from fossils demonstrates the nesting behaviors of feathered theropods, indicating social behaviors linked to the evolution of traits.

The Mammalian Ear Example

  • Example of exaptation includes the evolution of the mammalian ear from the jawbone structure of synapsids, showcasing the adaptive reuse of structures.

Application Questions

  • Evidence regarding Feathers of Early Theropods suggests they may have originally assisted in:
    • Swimming
    • Nest construction
    • Avoiding predation
    • Attracting mates or protecting offspring in nests.