Phylogeny, Taxonomy, and the Tree of Life

• Phylogeny studies the evolutionary history of organisms and their relationships and is represented by the tree of life.
• Taxonomy is the science of describing, naming, and classifying organisms.

Taxonomic Hierarchy

• Organisms are classified into progressively smaller groups (taxa) based on shared characteristics.
• This classification ranges from most exclusive (species) to most inclusive (domain).

The Tree of Life

• Illustrates the evolutionary relationships between all living organisms.
• Different species are related through common ancestors in this model.

Domains of Life

• Bacteria, Archaea, and Eukarya
• Bacteria: prokaryotic organisms
• Archaea: prokaryotic organisms
• Eukarya: eukaryotic organisms (protists, fungi, plants, and animals)

Linnaean Taxonomy

• Carl Linnaeus is the "Father of modern taxonomy."
• He established the system of binomial nomenclature.
• Binomial nomenclature involves giving each organism a unique two-part scientific name.
• The scientific name consists of genus and specific epithet (species).
• Ex: Quercus alba for white oak.

Systematics

• Involves studying the diversity of life and its evolutionary relationships.
• Systematics informs taxonomy by classifying organisms based on evolutionary relationships.

Phylogeny and Phylogenetic Trees

• Phylogeny is the evolutionary history of a group of organisms.
• A phylogenetic tree is a visual representation of phylogeny.
• Phylogenetic tree's hypothesize relationships among groups of organisms.

Components of a Phylogenetic Tree

• Root: The oldest point in the tree, representing the common ancestor of all species.
• Lines: Represent lineages (e.g., species, families).
• Implied time scale indicates changes in genetic makeup and appearance of new characters.
• Node: The last common ancestor of the branches above.
• Represents a point when an ancestral group splits into descendant groups.

Systematics and Taxonomy

• In traditional taxonomy, organisms are grouped based on common features.
• However, sharing a feature does not always imply close evolutionary relatedness.
• Systematics classifies organisms to reflect evolutionary history.

Evolutionary Classifications

• Phylogenetic trees are converted into classifications by identifying monophyletic groups (clades).
• Monophyletic group includes a common ancestor and all of its descendants.

Non-Monophyletic Groups

• Sometimes groups are named for convenience or due to missing data, and do not reflect evolutionary history.
• Polyphyletic group: Collection of organisms where the most recent common ancestor is not included in the group.
• Ancestor is excluded because it lacks the characteristics of the group.
• Ex: Warm-blooded Animals
• Paraphyletic group: Common ancestor and some, but not all, of the descendants.
• Ex: Old classification of reptilia.

Estimating Phylogenies

• Species' morphological and/or genetic characteristics are analyzed.
• Morphological differences reflect genetic differences.
• Traits must be heritable
• Closely related species share more characteristics.
• Closely related species are typically located closer together on the phylogenetic tree.

Sources of Data

• Homologous characters: Molecular or morphological traits resulting from shared ancestry.

Homoplasy (A Problem)

• Organisms may look similar, but aren't closely related resulting in Homoplasy.
• Ex: Cetaceans and seals
• Convergent evolution results from independent evolution.

Convergent Evolution

• Similar adaptations evolve arise in organisms that do not share the same evolutionary lineage.
• Similar solutions are favored for similar problems.
• Resulting is analogous structures.
• Analogous structures are biological structure/characteristic that 2(+) different species have in common that was not inherited from a common ancestor.
• Evolved Independently
• May have different developmental paths

Homology vs. Homoplasy

• Homology: Similarity due to shared ancestry, similar anatomical configuration, and position.
• Result: Homologous structures
• Homoplasy: Results from convergent evolution.
• There is similar function, but not developmental path
• Result can be Analogous structures.

DNA Revolution

• Starting in the 1960s, The DNA revolution revolutionized study of the relations between different organisms.
• Polymerase Chain Reaction (PCR) allowed for many copies of DNA from very little material to be made.
• Molecular systematics utilizes DNA and RNA to infer relationships between organisms.

Advantages of Molecular Data

• Abundant Data
• Interpretation is easier and less subjective
• Can compare distantly related or very similar looking species that don't look similar.
• Environmentally-caused morphological variations are factored out when molecular data is used.

Cladistics

• A method of producing phylogenetic hypotheses.
• Character states of a specific character are examined.
• Evolutionary processes change character state.
• Considers the ancestral or derived character state.
• Uses shared derived character states which appear in a group, but not outside that group.
• The end result is a Cladogram.

Determining Ancestral vs. Derived Characters

1. Examine fossils (organisms that lived before)
2. Outgroup comparison.