Phylogenies & the History of Life Flashcards

Phylogenies & the History of Life

Phylogeny

• The evolutionary history and relationships of an organism to other organisms.
• Shares information about how organisms are related.
• Does not share information about how organisms are similar or different.
• Can be used to study entire groups of organisms.

Rooted Phylogenetic Tree

• Single lineage.
• Based on representing a common ancestor.
• Branching indicates evolutionary relationships.

Phylogenetic Tree Branch Points

• Where a split occurs represents an evolutionary divergence.
• Evolution can occur early from the root.
• Two lineages stemming from the same branch indicate a close relationship.
• A branch with two or more lineages represents a polytomy, indicating uncertainty in evolutionary relationships.

Unrooted Phylogenetic Tree

• Does not represent common ancestry.
• Shows relationships among species.
• Example:
  • Animals, Fungi, Slime molds, Plants, Algae, Protozoa, Gram-positives, Chlamydiae, Crenarchaeota, Nanoarchaeota, Euryarchaeota, Green nonsulfur bacteria, Actinobacteria, Planctomycetes, Spirochaetes, Fusobacteria, Cyanobacteria (blue-green algae), Thermophilic sulfate-reducers, Acidobacteria, Proteobacteria.

Systematics

• The branch of science that organizes organisms based on their evolutionary relationships.
• Evidence used:
  • Fossils.
  • Similar form & body structures.
  • Molecules an organism uses.
  • DNA.
• A branch of biology that is continuously changing!

Technology Improves

• As technology continues to improve so does our knowledge of evolutionary relationships.

Limitations of Phylogenetic Trees

• Closely “related” groups may not appear similar.
• Branches do not account for length of time.
• Each tree is part of a larger whole as there are many other branches.
• Distant groups could be phenotypically similar due to similar environments.
• An organism can lack a vertebral column and still be related, branching can put organisms with different characters in different groups based on shared characteristics.

Taxonomy

• The science of classifying organisms to construct internationally shared classification systems with each organism placed into increasingly more inclusive groupings.
• Taxonomic classification system uses a hierarchical model to organize living organisms into increasingly specific categories.
• Binomial nomenclature is used.
• Taxon.
• Example:
  • The common dog, Canis lupus familiaris, is a subspecies of Canis lupus, which also includes the wolf and dingo.

Taxonomy: Evidence

• What evidence do we use?
  • Morphology (form and function).
  • Genetics.

Morphological Homology

• Organisms that share similar physical features and genomes are more closely related than those who do not.
• The more complex the shared feature the more likely there is a close evolutionary relationship.
• Bat and bird wings are homologous structures, indicating that bats and birds share a common evolutionary past.

Looks Can Be Deceiving!

• Analogy or homoplasy.
  • Similar traits due to similar environmental pressures.
• Analogous traits = similar function.
• Homologous traits = similar embryonic origin.

Molecular Comparisons

• Molecular systematics uses DNA information.
  • Taxonomic information.
  • Biogeographical information.
• Uncover missed relationships & correct incorrect assumptions.

Building Phylogenetic Trees

• Sort out homologous and analogous traits.
• Organize homologous traits into cladistics.
  • Groups of organisms that descend from a common ancestor (clade or monophyletic group).

Cladistics

• Analyze shared characteristics.
• Descent with modification.
  • Shared ancestral character - vertebrae.
  • Share derived character - amniotic egg.
  • Relative to the part of the phylogenetic tree you are looking at

Making Sense of Phylogenies

• Taxonomy is a subjective field of study because many species have more than one connection to each other.
• Taxonomists aim to use the simplest line of events to help describe phylogenies.

Perspectives on the Phylogenetic Tree

• The Classic Model
• The concept of the “tree of life” dates to an 1837 Charles Darwin sketch.
• Like an oak tree, the “tree of life” has a single trunk and many branches.

Limitations to the Classic Model

• Vertical transfer of genetic information leads to linear evolution.
  • Eukaryotes vs. Prokaryotes.
  • Random mutation?
• Gene transfer between unrelated species?
  • Horizontal gene transfer - antibiotic resistance.
  • More prevalent in prokaryotes.
  • Could be a significant source of genetic variation.

Web & Network Models

• Phylogenetic model arose from a community of ancestral cells and has multiple trunks.
• There are connections between branches where horizontal gene transfer has occurred.
• Visually, this concept is better represented by the multi-trunked Ficus than by an oak's single trunk.

Horizontal Gene Transfer in Prokaryotes

• Transformation: bacteria takes up naked DNA.
• Transduction: a virus transfers the genes.
• Conjugation: a hollow tube, or pilus transfers genes between organisms.
• Small, virus-like particles, or gene transfer agents (GTAs) transfer random genomic segments from one prokaryote species to another.

Genome Fusion & Eukaryotic Evolution

• When two symbiotic organisms become endosymbiotic - one takes the other into itself.
  • Endosymbiont Theory
    • Mitochondria and chloroplasts

Ring of Life Models

• Pool of primitive prokaryotes with three domains stemming outwards (Archaea, Bacteria, Eukarya).
• Many scientists are skeptical of this model!

Testing Models

• Each model is testable!