Chapter 20: Phylogeny – Understanding Evolutionary Relationships

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, often using data from morphology, genetics, and biochemistry.

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

• Systematics: The scientific study of the diversity and relationships among organisms.

• Example: Limbless lizards and snakes appear similar but evolved independently from different lineages of lizards with legs. This is an example of convergent evolution, where similar traits evolve in unrelated groups due to adaptation to similar environments.

Taxonomy and Classification

Binomial Nomenclature

Taxonomy is the ordered division and naming of organisms. The system of binomial nomenclature, developed by Carolus Linnaeus, provides each species with a two-part scientific name.

• Genus: The first part of the scientific name; always capitalized and italicized (e.g., Homo).

• Specific epithet: The second part; unique for each species within the genus and italicized (e.g., sapiens).

• Species name: Both parts together (e.g., Homo sapiens).

Hierarchical Classification

Linnaeus also introduced a hierarchical system for grouping species into increasingly broad categories.

• From least to most inclusive: Species, Genus, Family, Order, Class, Phylum (plural: phyla), Kingdom, Domain.

• Each named taxonomic unit at any level is called a taxon (plural: taxa).

• Larger categories are not always comparable between lineages (e.g., an order of snails vs. an order of mammals).

Phylogenetic Trees

Structure and Interpretation

Phylogenetic trees are branching diagrams that represent hypotheses about evolutionary relationships. Each branch point (node) represents the divergence of two lineages from a common ancestor.

• Sister taxa: Groups that share an immediate common ancestor.

• Phylogenetic trees can be drawn in various orientations (horizontal, vertical, diagonal) without changing the relationships.

• The order of taxa at the tips does not indicate the sequence of evolution.

• Branches can be rotated around nodes without altering 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.

• Phylogenetic trees show patterns of descent, not phenotypic similarity or the age of lineages.

Applications of Phylogenies

• Phylogenies can help identify species, such as using DNA sequences to determine the origin of whale meat in markets.

Inferring Phylogenies: Morphological and Molecular Data

Homology vs. Analogy

Phylogenies are inferred from similarities in morphology, genetics, and biochemistry. It is crucial to distinguish between homology (similarity due to shared ancestry) and analogy (similarity due to convergent evolution).

• Homology: Similarity due to shared ancestry (e.g., forelimbs of mammals).

• Analogy: Similarity due to convergent evolution (e.g., wings of bats and insects).

• Complex structures are more likely to be homologous if they are similar.

• Genetic homology is inferred from high similarity in DNA sequences.

Evaluating Molecular Homologies

• Molecular homologies are based on the degree of similarity in nucleotide sequences.

• Insertions or deletions can cause mismatches; computer programs help align sequences.

• Statistical tools distinguish between coincidental matches and true homologies.

Cladistics and Phylogenetic Groupings

Clades and Group Types

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

• Monophyletic group: Consists of an ancestor and all its descendants (a clade).

• Paraphyletic group: Includes an ancestor and some, but not all, descendants.

• Polyphyletic group: Includes distantly related species but not their most recent common ancestor.

Group Type	Definition
Monophyletic	Ancestor and all descendants
Paraphyletic	Ancestor and some descendants
Polyphyletic	Distantly related species, not including common ancestor

Shared Ancestral vs. Shared Derived Characters

• Shared ancestral character: Originated in an ancestor of the taxon.

• Shared derived character: Evolutionary novelty unique to a particular clade (e.g., loss of limbs in snakes).

• A character can be ancestral or derived depending on the context.

Outgroup and Ingroup Analysis

• Ingroup: The group of species being studied.

• Outgroup: A species or group closely related to but not part of the ingroup; used to infer ancestral characters.

Phylogenetic Trees: Branch Lengths and Parsimony

Branch Lengths

• Branch lengths can represent the number of genetic changes or chronological time (from fossil record).

Maximum Parsimony

• The most parsimonious tree requires the fewest evolutionary events (e.g., base changes in DNA).

• Computer programs are used to search for the most parsimonious trees.

Phylogenetic Trees as Hypotheses

• Phylogenetic trees are hypotheses that are revised as new data become available.

• Phylogenetic bracketing: Used to predict features of ancestors and extinct descendants based on living relatives (e.g., inferring dinosaur nesting behavior from birds and crocodiles).

Molecular Clocks and Evolutionary Time

Molecular Clocks

A molecular clock uses 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 divergence.

• Clocks are calibrated using fossil record data.

• Not all genes evolve at the same rate; some are more clocklike than others.

• Neutral mutations (with little effect on fitness) tend to accumulate at a regular rate.

• Critical genes evolve slowly; less critical genes evolve more quickly.

• Molecular clocks can be used to date events such as the origin of HIV in humans.

Revising the Tree of Life: Domains and Horizontal Gene Transfer

From Two Kingdoms to Three Domains

• Early classification: Plants and animals.

• Later: Five kingdoms (Monera, Protista, Plantae, Fungi, Animalia).

• Current: Three domains—Bacteria, Archaea, and Eukarya.

• Bacteria and Archaea are single-celled prokaryotes; Eukarya includes multicellular kingdoms (Plantae, Fungi, Animalia).

• Kingdom Monera is obsolete (would span two domains); Kingdom Protista is obsolete (members more closely related to other kingdoms).

Horizontal Gene Transfer

• Horizontal gene transfer is the movement of genes between different species, often via plasmids, viruses, or fusion of organisms.

• This process was likely common in early life and complicates the tree of life, making it more like a web.

• Evidence suggests that a large proportion of prokaryotic genes have moved between species.

Summary Table: Three Domains of Life

Domain	Cell Type	Representative Groups
Bacteria	Prokaryotic	Cyanobacteria, Proteobacteria
Archaea	Prokaryotic	Halophiles, Thermophiles
Eukarya	Eukaryotic	Plants, Fungi, Animals, Protists

Additional info: The study of phylogeny is fundamental to understanding the diversity of life, evolutionary processes, and the classification of organisms. Modern systematics integrates molecular data, fossil evidence, and morphological traits to construct robust evolutionary trees.