Phylogenies and Taxonomy

Introduction to Phylogenies

• Overview of lecture objectives:

  • Classify over 2,000,000 described species.

  • Represent evolutionary history and relationships using phylogenetic trees.

  • Identify data types for building phylogenies.

  • Explore complexities of evolutionary relationships between organisms.

  • Understand homologous vs. analogous traits and implications of horizontal gene transfer.

• Warm-up question: Estimate the number of species on Earth.

  • Actual number: Approximately 2,000,000 described species.

  • Potential actual number: Estimated between 3,000,000 to 100,000,000 or even billions of undiscovered species.

Taxonomy and Classification

• Importance of taxonomy for organizing biodiversity.

• Taxonomic hierarchy of classification (Example: Dog classification):

  • Domain: Eukarya (eukaryotic cells)

  • Kingdom: Animalia (animals)

  • Phylum: Chordata (vertebrates)

  • Class: Mammalia (mammals)

  • Order: Carnivora (carnivores)

  • Family: Canidae (dogs and relatives)

  • Genus: Canis (dogs, wolves, etc.)

  • Species: Canis lupus (wolf); subspecies: Canis lupus familiaris (domesticated dog).

• Importance of subspecies designation:

  • For differentiating closely related species (dogs vs. wolves).

• Mnemonic for remembering taxonomic hierarchy:

  • "Does King Philip Come Over For Great Soup?"

• Taxonomy reflects evolutionary relationships:

  • More specific categories imply closer relations among organisms.

Phylogenetic Trees

• Definition of a phylogeny:

  • Hypotheses of evolutionary relationships and history of life.

  • Includes both present-day organisms and extinct species (fossils).

• Structure of a phylogenetic tree:

  • Trunk or roots represent ancestral lineages.

  • Tips of branches represent modern organisms.

  • Nodes represent common ancestors.

  • Example phylogeny details:

  • Time markers reveal when major splits occurred in lineage.

• Domains of life illustrated:

  • Bacteria (blue)

  • Archaea (green)

  • Eukarya (red)

• Different types of phylogenetic trees:

  • Rooted: shows common ancestors.

  • Unrooted: focuses on relationships without indicating common ancestry.

The Basics of Reading Phylogenies

• Distinction between ancestors and descendants:

  • Ancestors located at the base of the tree; descendants at the tips.

  • Each branching event represents a speciation event.

• Common ancestors:

  • Found at nodes where lineages diverge.

• Definition of a clade:

  • Group of organisms that includes a common ancestor and all its descendants.

• Finding clades involves:

  • Using a hypothetical cutting method (scissors analogy) to isolate groups.

  • Clades must include all descendants from a common ancestor.

• Example: reptiles and inclusion of birds for accurate clade representation.

Nested Clades and Misconceptions

• Explanation of nested clades:

  • Clades within clades (e.g., Canidae within Mammalia within Animalia).

• Misconceptions about evolutionary trees:

  • Trees are not ladders; no hierarchical advancement.

  • All species have been evolving for the same amount of time.

  • Position on the tree does not reflect advancement or complexity.

  • Importance of understanding branches are interchangeable and do not dictate relationships.

Building Phylogenies

• Types of data for constructing phylogenies:

  • DNA sequences: Closer genetic alignment indicates closer evolutionary relationships.

  • RNA sequences: Similar application as DNA sequencing.

  • Amino acid sequences: Derived from RNA; used for comparisons.

  • Homologous structures: Traits shared due to common ancestry (e.g. vertebrae).

  • Embryology: Similar embryonic development across species.

  • Fossils: Help trace lineage and extinct relatives.

• Step-by-step example with homologous structures:

  • Call out traits shared across different vertebrates (e.g. vertebrae, amniotic egg).

  • Construct phylogeny based on shared characteristics.

Complexities in Evolutionary Relationships

Analogous vs. Homologous Traits

• Analogous traits: Traits that arise independently in various lineages (e.g. wings of bats vs. wings of birds).

  • Not derived from a common ancestor but serve similar functions.

• Homologous traits: Traits that share evolutionary ancestry, even if they serve different functions (e.g. mammal limbs).

• Example visuals:

  • Eyes of cephalopods vs. vertebrates as analogous traits.

  • Adaptation in plant morphology also illustrated with cacti.

Horizontal Gene Transfer

• Definition: Transfer of genes across different species rather than vertically through lineage.

• Examples and implications:

  • Endosymbiosis: Chloroplasts in plants derived from engulfed bacteria.

  • Sea slug obtaining chloroplasts from algae complicates ancestry analysis.

• Importance of recognizing horizontal gene transfer when determining true evolutionary relationships.

Historical Context and Adaptations

• Evolution of classification systems from five kingdoms in 1969 to three domains in 2015.

• Advances in phylogeny building due to genetic sequencing and modern techniques.

• Need for continuous revision of phylogenetic hypotheses based on new data.

Conclusion

• Summary of key learning objectives:

  • Understanding the system of taxonomy.

  • Interpreting and building phylogenetic trees based on diverse data.

  • Navigating complexities introduced by analogous traits and horizontal gene transfer.

• Encouragement to remain open to new evidence and maintain critical thinking in biological classification and evolutionary biology.