Chapter 20: Phylogenies and the History of Life

Chapter 20: Phylogenies and the History of Life

Be Able To…

  • Summarize the classification system of life: Understand how classifying organisms is foundational to understanding phylogenies and systematics.

  • Interpret phylogenetic trees: Gain the ability to read and understand representations of evolutionary relationships among species.

  • Describe cladistics methods: Learn the techniques used to construct clades and interpret cladograms.

  • Describe the phylogenetic relationships of the major groups of life: Identify how different life forms are related across the tree of life.

  • Describe horizontal gene transfer: Understand the phenomenon of genetic material transfer between species that are not parent and offspring.

  • Describe the three types of phylogenetic models: Learn about various frameworks used in constructing phylogenetic trees.

Chapter 20 Topics

  1. Organizing Life on Earth

    • Introduction

    • Diversity of life on Earth

    • Classification and why it matters

    • Taxonomy

    • Phylogeny

    • Building phylogenetic trees

    • Determining evolutionary relationships

  2. Phylogenetic Modeling Concepts

    • Limitations to the classic model

    • Horizontal gene transfer

    • Endosymbiotic theory

    • Different models of evolution

Diversity of Life on Earth

Introduction

  • Estimates for diversity of life:

    • Species Cataloged: 1.5 - 2.3 million

    • Total Estimated Species: 5 (±3) million

    • Total Individuals: 100 billion – 1 trillion (inclusive of all prokaryotes)

  • Characteristics of all organisms:

    • Composed of one or more cells

    • Carry out metabolism

    • Transfer energy with ATP

    • Encode hereditary information in DNA

Classification: Bringing Order to Diversity

Introduction

  • Biologists group organisms based on shared characteristics, including:

    • Fossil records

    • Morphology

    • Physiology

    • Behavior

    • Embryological development

    • DNA/RNA sequences

  • Systematics: Field that organizes and classifies organisms based on evolutionary relationships.

Common Names

  • Common names can vary:

    • Example: Corpse flower, Corpse plant, Titan arum

Organizing Life on Earth

Taxonomy

  • Taxonomy: The science of classifying organisms into taxa (groups).

  • Phylogeny: Hypothesis about relationships among taxonomic groups depicted as phylogenetic trees or cladograms (akin to a family tree).

Classification Levels

  • Traditional Linnaean System: Uses a nested hierarchical system, moving from broad to specific classifications.

  • Mnemonic to remember levels: Dashing King Phillip Came Over For Good Soup.

Binomial Nomenclature

  • Species Name: Composed of genus + species epithet.

  • Format: Genus is capitalized; full species name is italicized (e.g., Homo sapiens, Canis lupus familiaris).

  • Capitalization of higher taxonomic names, e.g., Hominidae, Primates, Mammalia.

Importance of Phylogenies

  • Understanding evolutionary processes aids in:

    • Research on related species for insights into human health and medical issues.

    • Tracking evolution of parasites and viruses.

    • Utilizing biotechnology for productive crops and domesticated animals.

    • Producing effective drugs (e.g., human insulin).

    • Enhancing conservation efforts for threatened and endangered species.

  • Phylogenetics enriches understanding of gene, genome, and species evolution.

Phylogeny

  • Definition: The evolutionary history and relationship among organisms.

  • Types of Phylogenetic Trees:

    • Rooted Trees: Show a single lineage at the base representing a common ancestor.

    • Unrooted Trees: Show relationships without indicating a common ancestor.

Rooted Phylogenetic Trees

  • Concepts:

    • Root: Represents ancestral lineage that gave rise to all organisms in the tree.

    • Branch Point (Node): Represents divergence of a single lineage into two clades.

    • Most Recent Common Ancestor (MCRA): For taxa sharing a node, indicating they originate from a common ancestor.

Taxa and Clades

  • Definitions:

    • Taxon (taxa, pl): Groups of organisms (species, family, domain).

    • Basal Taxon: The initial lineage that diverged.

    • Sister Taxon: Closely related taxa.

    • Clade: A lineage representing a monophyletic group that includes an ancestor and all its descendants.

    • Polytomy: A branch with more than two lineages.

  • Difference between Clades and Taxa: Clades are monophyletic, meaning they include the common ancestor and all descendants.

Monophyly, Paraphyly & Polyphyly

  • Monophyletic Taxon: Includes an ancestor and all descendants (a clade).

  • Paraphyletic Taxon: Excludes a common descendant.

  • Polyphyletic Taxon: Includes species with different ancestors.

Identifying Taxon Types

  • Terms:

    • “Paraphyletic”, “Polyphyletic”, “Monophyletic” refer to how taxa are structured based on common ancestry.

Building Phylogenetic Trees

Cladistics

  • Cladistics: The process to arrange taxa by homologous characters into clades (branches) and construct cladograms.

  • Goal: Produce cladograms where all clades are monophyletic.

Shared Characteristics

  • Types of shared characteristics:

    • Shared Ancestral Character: Found in common ancestor of taxa, shared by all members; for example, vertebrae for Vertebrata.

    • Shared Derived Character (Synapomorphy): Arose within the larger clade, distinguishes members, and provides information about relatedness.

Determining Evolutionary Relationships

  • Systematists' Approach:

    • Utilize a variety of evidence (morphologic, physiologic, behavioral, genetic) to determine relationships among organisms and higher taxa.

Choosing Relationships: Maximum Parsimony

  • Maximum Parsimony: If two potential cladograms exist, choose the simplest one that requires the fewest evolutionary steps. This approach minimizes excessive evolutionary changes.

Evolutionary Confusion

  • Convergent Evolution: Structures evolve due to similar environmental pressures, not from a common ancestor (e.g., bird and insect wings).

  • Evolutionary Reversal: Loss of ancestral traits in the descendants of a lineage (e.g., loss of legs in snakes).

Structural Similarities

  • Homologous Structures: Similar due to shared evolutionary origin (same ancestral source), reflecting genetic and developmental origins.

  • Analogous Structures: Similar due to functional or ecological pressures despite evolutionary divergence.

Limitations to the Classic Model of Inheritance

Phylogenetic Modeling

  • Origin of Phylogenetic Trees: Charles Darwin sketched the first tree in 1837, visualizing common ancestry.

  • The classic model: assumes vertical gene transfer from parent to offspring; however, this does not encompass all evolutionary scenarios in organisms.

Horizontal Gene Transfer (HGT)

  • Definition: Transfer of genetic material between unrelated species, especially prevalent in prokaryotes.

  • Types of HGT in Prokaryotes:

    • Transformation: Uptake of naked DNA.

    • Transduction: Transfer of genes by viruses.

    • Conjugation: Transfer of genes through direct contact between bacteria via a pilus.

HGT in Eukaryotes

  • Rare compared to prokaryotes due to complex genetic systems; however, there are examples like the carotenoid enzyme from fungi to aphids.

The Endosymbiotic Theory: Eukaryote Evolution

  • Endosymbiont: A cell living within another cell mutually benefiting both.

  • Theory components:

    • Mitochondria and chloroplasts: Originated from engulfment of prokaryotic cells by protoeukaryotic cells.

    • Genome fusion may explain some gene transfers between endosymbionts.

Web and Network Models

  • Alternative Evolution Models:

    • Web of Life: Proposes early prokaryotes evolved through extensive HGT, leading to a model that accounts for species swapping genes rather than purely vertical inheritance.

    • Ring of Life: Suggests all domains evolved from a pool of prokaryotes exchanging genes through HGT, explaining gene resemblance in eukaryotes to both bacteria and archaea.

  • Future Research Needed: Continued research is essential to clarify evolutionary models and mechanisms of gene transfer.