Chapter 20: Phylogeny – Investigating the Evolutionary History of Life

Phylogeny: Investigating the Evolutionary History of Life

Introduction to Phylogeny and Systematics

Phylogeny is the study of the evolutionary history and relationships among species or groups of related species. Systematics is the scientific discipline that classifies organisms and determines their evolutionary relationships, providing a framework for understanding biological diversity.

• Phylogeny: The evolutionary history of a species or group of related species.

• Systematics: The discipline that classifies organisms and determines their evolutionary relationships.

• Example: Legless lizards and snakes appear similar but evolved independently from different lineages, demonstrating convergent evolution.

Convergent Evolution and Homology

Convergent evolution occurs when unrelated organisms independently evolve similar traits due to adaptation to similar environments. Homology refers to similarities due to shared ancestry, while analogy refers to similarities due to convergent evolution.

• Homology: Similarity due to shared ancestry.

• Analogy: Similarity due to convergent evolution.

• Example: European glass lizard and snakes both lack limbs, but this trait evolved independently in each lineage.

Taxonomy and Binomial Nomenclature

Taxonomy is the ordered division and naming of organisms. The binomial nomenclature system, developed by Carolus Linnaeus, assigns each species a two-part scientific name: the genus and the specific epithet.

• Genus: The first part of the species name, capitalized.

• Specific epithet: The second part, unique for each species, not capitalized.

• Scientific name format: Genus species (italicized).

• Example: Panthera pardus (leopard).

Hierarchical Classification

Linnaeus introduced a hierarchical system for grouping species into increasingly broad categories. Each level is called a taxon (plural: taxa).

• Taxonomic hierarchy (least to most inclusive): species, genus, family, order, class, phylum, kingdom, domain.

• Example: Panthera pardus is classified as follows: Species: Panthera pardus Genus: Panthera Family: Felidae Order: Carnivora Class: Mammalia Phylum: Chordata Kingdom: Animalia Domain: Eukarya

Linking Classification and Phylogeny

Evolutionary relationships are often represented in branching diagrams called phylogenetic trees. These trees illustrate how taxonomists classify groups of organisms nested within more inclusive groups.

• Phylogenetic tree: A diagram representing evolutionary relationships.

• Branch point: Represents the divergence of two evolutionary lineages from a common ancestor.

• Sister taxa: Groups sharing an immediate common ancestor not shared by other groups.

Interpreting Phylogenetic Trees

Phylogenetic trees are hypotheses about evolutionary relationships. The arrangement of taxa at the tips does not indicate the sequence of evolution, and trees can be rotated around branch points without changing relationships.

• Rooted tree: Includes a branch representing the most recent common ancestor of all taxa in the tree.

• Basal taxon: A lineage that diverges early in the history of a group.

• Important note: Phylogenetic trees show patterns of descent, not phenotypic similarity or the amount of evolutionary change.

Applying Phylogenies

Phylogenies provide information about similar characteristics in closely related species and can be used to infer species identities, such as identifying the source of whale meat using DNA sequences.

Inferring Phylogenies from Morphological and Molecular Data

Phylogenies are inferred from similarities in morphology, genetics, and biochemistry. Only similarities resulting from common ancestry (homologies) are used to infer evolutionary relationships.

• Molecular homologies: Based on the degree of similarity in nucleotide sequences among taxa.

• Computer programs: Used to align DNA sequences and identify genetic matches.

Cladistics and Clade Types

Cladistics classifies organisms by common descent. A clade is a group of species that includes an ancestral species and all its descendants.

Group Type	Description
Monophyletic	Includes ancestor and all descendants (a clade)
Paraphyletic	Includes ancestor and some, but not all, descendants
Polyphyletic	Includes distantly related species but not their most recent common ancestor

Shared Ancestral and Shared Derived Characters

Characters can be ancestral (originated in an ancestor) or derived (evolutionary novelty unique to a clade). The context determines whether a character is ancestral or derived.

• Shared ancestral character: Present in ancestor and descendants.

• Shared derived character: Unique to a particular clade.

• Example: The backbone is a shared derived character for vertebrates, but an ancestral character for mammals.

Inferring Phylogenies Using Derived Characters

Determining the clade in which shared derived characters first appeared helps infer evolutionary relationships. The ingroup is the group of species being studied, while the outgroup is closely related but not part of the ingroup.

Phylogenetic Trees with Proportional Branch Lengths

Branch lengths in phylogenetic trees can represent the number of genetic changes or chronological time, as determined from the fossil record.

Maximum Parsimony

The principle of maximum parsimony states that the best phylogenetic tree is the one that requires the fewest evolutionary events. Computer programs are used to search for the most parsimonious trees.

Phylogenetic Trees as Hypotheses

All phylogenetic trees are hypotheses that are modified as new evidence arises. Phylogenetic bracketing is used to predict features of ancestors and extinct descendants based on features of closely related living organisms.

Molecular Clocks

Molecular clocks use the constant rate of evolution in some genes to estimate the absolute time of evolutionary change. The number of nucleotide substitutions is assumed to be proportional to the time since two species last shared a common ancestor.

• Equation: $\text{Number of substitutions} \propto \text{Time since divergence}$

• Calibration: Molecular clocks are calibrated using fossil record data.

• Limitations: Not all genes evolve at a constant rate; some mutations are neutral, while others are subject to selection.

Revising the Tree of Life: Domains and Horizontal Gene Transfer

The classification of life has evolved from two kingdoms (plants and animals) to three domains: Bacteria, Archaea, and Eukarya. Horizontal gene transfer, the movement of genes between species, has played a significant role in the evolution of life.

Domain	Characteristics
Bacteria	Single-celled prokaryotes
Archaea	Single-celled prokaryotes, distinct from bacteria
Eukarya	Includes multicellular kingdoms: Plantae, Fungi, Animalia

• Horizontal gene transfer: The transfer of genes between different species, often via plasmids, viruses, or fusion of organisms.

• Impact: Horizontal gene transfer complicates the reconstruction of evolutionary relationships and may be better represented as a web rather than a tree.

Additional info: These notes expand on the provided slides with definitions, examples, and context to ensure a comprehensive understanding of phylogeny and its role in modern biology.