Study Notes on Phylogeny and the Tree of Life

Lecture Presentations by Nicole Tunbridge and Kathleen Fitzpatrick: Chapter 26 Phylogeny and the Tree of Life

1. Introduction to Phylogeny and Classification

  • Biologists distinguish and categorize millions of species on Earth through shared traits that indicate common ancestry.
  • Common ancestry is critical for classifying organisms within groups that reflect evolutionary history.

1.1 Common Ancestors and Branch Points

  • A branch point in a phylogenetic tree represents the common ancestor of all groups depicted in that section of the tree.
  • Example: All groups such as fishes, frogs, humans, humans' sister group (chimps), and other reptiles trace back to common ancestors.
  • Presence of shared character traits, indicated by hatch marks, such as limbs, defines relationships between groups. For example:
    • The common ancestor of lizards, snakes, and frogs had limbs, which were lost in the lineages of snakes and glass lizards.

2. Concepts in Phylogenic Studies

2.1 Phylogeny

  • Definition: Phylogeny is defined as the evolutionary history of a species or a group of related species.

2.2 Systematics

  • Definition: Systematics is a discipline focused on classifying organisms and determining their evolutionary relationships. It incorporates phylogenetic information to classify species.

3. Taxonomy: Binomial Nomenclature and Hierarchical Classification

3.1 Binomial Nomenclature

  • Developed by Carolus Linnaeus in the 18th century.
  • Key features:
    • Two-part scientific names for species referred to as binomials.
    • The first part indicates the genus, while the second part (specific epithet) is unique for each species within the genus.
    • The genus name starts with a capital letter, and the entire species name is italicized.

3.2 Hierarchical Classification

  • Linnaeus introduced a hierarchical system for grouping species into increasingly inclusive categories:
    • Domain: highest taxonomic rank
    • Kingdom
    • Phylum (plural: phyla)
    • Class
    • Order
    • Family
    • Genus
    • Species
  • A group at any level of hierarchy is termed a taxon.

4. Phylogenetic Trees

4.1 Representation of Evolutionary History

  • Phylogenetic trees represent hypotheses about the evolutionary relationships among different organisms.

4.2 Branch Points in Trees

  • Each branch point signifies the divergence of two evolutionary lineages from a common ancestor, establishing relationships among taxa.
  • Sister taxa are groups that share a common ancestor, which is not shared with any other groups.

4.3 Characteristics of Phylogenetic Trees

  • A rooted tree includes a branch representing the most recent common ancestor of all taxa in the tree.
  • Basal taxa diverge early from the tree's main branches.
  • Phylogenetic trees illustrate patterns of descent rather than mere phenotypic similarity.
  • Importantly, phylogenetic trees do not detail the timing of species evolution or quantify changes in lineages.

5. Data Sources for Inferring Phylogeny

5.1 Morphological and Molecular Data

  • Systematists assess morphological, genetic, and biochemical data to infer phylogeny.
  • Only traits arising from common ancestry—homologies—are informative for determining evolutionary relationships.
5.1.1 Homology vs. Analogy
  • Homology: Similarity due to shared ancestry.
  • Analogy: Similarity due to convergent evolution, where unrelated species evolve similar traits due to similar environmental pressures.

5.2 Evaluating Molecular Homologies

  • DNA sequencing aligns comparable sequences from study species. Closely related species diverge at only a few sites, while distantly related may differ greatly.

6. Cladistics and Clades

6.1 Cladistics Overview

  • Organisms are grouped primarily by common ancestry.
  • Clade: A group of species that includes an ancestral species and all its descendants.

6.2 Types of Clades

  • Monophyletic: Includes an ancestor and all its descendants (true clade).
  • Paraphyletic: Includes an ancestral species and some, but not all, descendants.
  • Polyphyletic: Includes unrelated species but not their most recent common ancestor.

6.3 Shared Characters

  • Shared ancestral characters originate in an ancestor of the taxon.
  • Shared derived characters are evolutionary novelties unique to a particular clade.
    • Example: The loss of limbs in snakes is a derived character.

7. Inferring Phylogenies

7.1 Derived Characters and Outgroups

  • Shared derived characters help in inferring evolutionary relationships.
  • An outgroup is closely related but not part of the studied group (ingroup), helping distinguish between ancestral and derived characters.

7.2 Maximum Parsimony and Maximum Likelihood

  • Employ principles to narrow potential phylogenetic trees based on minimal evolutionary events (max parsimony) and the most probable evolutionary pathways (max likelihood).

8. Molecular Clocks

8.1 Concept and Function

  • Molecular clock: An approach to estimate the absolute time of evolutionary change, linked to the assumption that some genes evolve at a constant rate.
  • Calibration of molecular clocks is conducted by graphing genetic differences against known dates from the fossil record.

8.2 Limitations

  • Molecular clocks face irregularities due to natural selection favoring certain mutations, leading to erratic changes rather than consistent rates over time.

9. The Evolution of Biological Classification

9.1 Historical Context

  • Initially, organisms were classified into two kingdoms (plants and animals).
  • By the 1960s, five kingdoms were recognized: Monera, Protista, Plantae, Fungi, and Animalia.

9.2 The Three-Domain System

  • The modern classification recognizes three domains: Bacteria, Archaea, and Eukarya.
    • Bacteria: Most known prokaryotes.
    • Archaea: Diverse prokaryotes across various environments.
    • Eukarya: Includes both single-celled and multicellular eukaryotes.
9.2.1 Relatedness of Domains
  • Different gene analyses highlight the close evolutionary relationships between eukaryotes and archaea over bacteria, influenced by horizontal gene transfer.
  • Horizontal gene transfer: The movement of genes between genomes, significantly complicating phylogenetic relationships, can occur through various mechanisms.