Notes on Evolution and Phylogenetics

Biological Classification and Phylogenetics

• Biological classification and evolutionary relationships are fundamental in understanding life.
• Key Questions:
  • What defines a species?
  • How are phylogenetic trees constructed?
  • What potential pitfalls exist?

Binomial Nomenclature

• Definition: Each biological species has a Latinized name with two components:
  • Genus (first word): Capitalized and italicized (e.g., Musca).
  • Species (second word): Lowercase and italicized (e.g., domestica).
  • In handwritten forms, the genus may be underlined.
• Abbreviations: Genus may be abbreviated in subsequent mentions (e.g., E. coli).

Taxonomy

• Taxonomy refers to the sorting and classification of organisms.
• Phylogenetic trees have expanded beyond taxonomy to encompass all biology fields, emphasizing that all life has interconnected evolutionary histories.
• Tree of Life: Represents the comprehensive evolutionary narrative.

Phylogenetics Definition

• A taxon (plural, taxa) is a named group of species.
• A clade includes all descendants of a common ancestor.
• Sister species are the closest relatives to each other, while sister clades are closest clades.

Defining Species

• The number of living species: estimated to be between 8.7 and 100 million.
• Species Definition: Smallest independently evolving unit not subject to the same evolutionary pressures.
  • Independent evolution occurs through mutations, selections, and genetic drifts.

Biological Species Concept (BSC)

• Proposed by Ernst W. Mayr (1942):
  • Defined as groups of interbreeding natural populations that are reproductively isolated from others.
• Problems with BSC:
  • Fails to apply to asexual species and those that are reproduced in allopatry.
  • The limitations include challenges of reproductive compatibility and geological timelines.

Evolutionary Species Concept

• Defined as a lineage maintaining its identity while possessing its evolutionary history.
• Reproductive isolation is not strictly necessary for defining evolutionary species.

Phylogenetic Species Concept (PSC)

• Uses two-step processes:
  1. Grouping taxa based on shared common ancestry.
  2. Ranking traits to identify diagnosable monophyletic groups.

Tree Construction Methods

Morphological Techniques

• Based on observable characteristics of organisms (e.g., skeletal structure).
• Limitations: Variability due to environmental factors and difficulty in relating distantly related species.

Paleontological Techniques

• Involves studying fossils for historical organism information.
• Limitations: Fragmentary fossil records hinder understanding.

Developmental Methods

• Evaluates similarities in developmental processes.
• Culturally transmitted behaviors complicate phylogenetic classification.

Molecular Techniques

• Utilizes DNA sequences for tree construction:
  • Mitochondrial, chloroplast, nuclear DNA, and gene products (e.g., amino acid sequences).

Homologous vs. Analogous Traits

• Homologous traits indicate shared ancestry, classified into:
  • Plesiomorphy: Ancestral traits (e.g., tetrapod limbs).
  • Synapomorphy: Derived traits indicating common ancestry (e.g., vertebral columns of vertebrates).
• Homoplasy: Similar traits in unrelated groups arise due to convergent evolution.

Using Phylogenetic Trees

• Outgroup Comparison: Helps in determining derived and ancestral traits by contrasting closely related species.
• Synapomorphy Identification: Essential for tree construction, identifying shared derived traits among groups.

Validation and Testing

• Phylogenetic hypotheses tested via experimental simulations and real organism studies.
• Example: Experiment on bacteriophage evolution (Hillis et al. 1992) illustrated lineage diversification under mutation rates.

Group Classification in Phylogenetics

• Monophyletic groups: Consist of an ancestor and all its descendants.
• Polyphyletic groups: Exclude the common ancestor.
• Paraphyletic groups: Exclude some descendants of a common ancestor.

Parsimony Principle

• Emphasizes the simplest explanations or relationships, minimizing assumed evolutionary changes.
• An example involves analyzing character states (bipedalism in birds and humans).

Applications of Phylogenetic Analysis

• Phylogenies inform predictions in systematics: Understanding evolutionary relationships enables insights into traits and adaptations.
• Case Study: The analysis of vision evolution across vertebrates through molecular sequences evidences ancient adaptations for low-light conditions.

Conclusions on Phylogenetic Methodology

• Support for phylogenetic trees using comparative data elucidates complex evolutionary relationships within and among species.
• Contemporary insights, such as those from HIV evolution studies, underscore the significance of phylogenetic understanding in addressing emerging challenges in biology.