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Chapter 26: Phylogeny and the Tree of Life

Introduction

• Overview of phylogeny as the evolutionary history of species/groups of related species.

• Example: Legless lizards vs. snakes evolved from different legged lizard lineages.

• Systematics: Discipline classifying organisms and determining evolutionary relationships.

Learning Objectives

1. Define phylogeny and its usage.

2. Explain how phylogenetic trees are inferred.

3. Differentiate between derived and ancestral characters and their role in trees.

4. Describe genomic evidence for evolutionary history.

5. Explain molecular clocks and their use.

6. Describe the structure of the tree of all life.

7. Engage in online cladogram construction.

8. Complete practice exercises and crossword puzzles for terminology.

Investigating the Tree of Life

• Phylogeny depicts the evolutionary history.

• Importance of understanding the links between organisms through systematics.

Binomial Nomenclature

• Introduced by Carolus Linnaeus in the 18th century.

• Key Features:

  • Two-part names for species (genus + specific epithet).

  • Hierarchical classification from broad to narrow.

• Example: Humans: Homo sapiens.

Hierarchical Classification

• Categories from broad to narrow: domain, kingdom, phylum, class, order, family, genus, species.

• A taxon is a taxonomic unit at any hierarchical level.

Linking Classification and Phylogeny

• Phylogenetic trees represent evolutionary history.

• Tips of branches represent taxa.

• Tree structure illustrates divergence of lineages.

What We Can and Cannot Learn from Phylogenetic Trees

• Phylogenetic trees hypothesize evolutionary relationships.

• Branch points indicate divergence of lineages.

• Important notes:

  • Trees can be oriented differently without change in relationships.

  • Phylogenetic trees do not indicate actual timing of species evolution or the extent of change.

Inferring Phylogenies from Data

• Systematists analyze morphologies, genes, and biochemistry for phylogenetic inference.

• Homologies are similarities due to shared ancestry, while analogies are due to convergent evolution.

• Example: Human legs (homologous) vs. insect legs (analogous).

Shared Characters in Phylogenetic Trees

• Homologies used to construct phylogenies.

• Cladistics: organisms grouped by common ancestry into clades.

• Valid clades must be monophyletic, meaning they include all descendants of a common ancestor.

Types of Phylogenetic Groupings

• Monophyletic: Ancestor and all descendants.

• Paraphyletic: Ancestor and some descendants.

• Polyphyletic: Grouping with distantly related species without the common ancestor.

Shared Ancestral vs. Shared Derived Characters

• Shared ancestral characters originate in an ancestor.

• Shared derived characters are unique to specific clades.

• Context determines if a character is ancestral or derived.

Outgroups and Ingroups

• Outgroup: species/group closely related, diverged before ingroup (species under study).

• Useful for distinguishing shared derived vs. shared ancestral characters.

Tree Building Activity

• Hands-on activity for constructing a cladogram based on characters exhibited by organisms.

Phylogenetic Trees with Proportional Branch Lengths

• Longer branches can indicate more genetic changes.

• Branch length may also represent geological time and can be corroborated with fossil records.

Maximum Parsimony and Maximum Likelihood

• Methods for optimizing phylogenetic tree construction:

  • Maximum Parsimony: Simplest tree with the least events.

  • Maximum Likelihood: Based on probability and evolutionary patterns.

Phylogenetic Hypotheses

• Best phylogenetic tree reflects morphological, molecular, and fossil data.

• Phylogenetic bracketing helps predict features of ancestors from descendants.

Molecular Clocks

• Utilize constant rates of molecular change to date evolutionary shifts.

• Distinguish between orthologous (common ancestor across species) and paralogous (gene duplications within a species) genes.

Gene Variations and Evolution

• Gene duplications lead to increased opportunities for evolutionary changes.

• Complexity of organisms not directly linked to gene number.

• Example: Humans vs. yeasts.

Importance of New Data in Understanding Phylogeny

• Evolutionary insight via molecular systematics reshapes understanding of the tree of life.

• Three-domain system: Bacteria, Archaea, Eukarya reflects modern understandings.

Horizontal Gene Transfer

• Significant in the evolution of prokaryotes and eukaryotes; complicates the tree of life.

• Gene transfer events lead to complex relationships among organisms.