Chapter 26

Phylogeny & Systematics Fundamentals
Core Definitions
• Phylogeny: The evolutionary history of a species or group of related species
• Systematics: A discipline focused on classifying organisms and determining their evolutionary relationships
• Purpose: Organization system to classify organisms based on common ancestry and evolutionary history, identifying ancestry patterns, convergence, and divergence of different groups
Key Concepts
• Phylogenies help organize living things based on common ancestors, where adaptations appear, and individual taxa of organisms represented on phylogenetic trees
• Example: Glass lizards are legless lizards (not snakes), representing a secondary loss of limbs through evolutionary processes—raising questions about how organisms evolve into seemingly different forms despite shared ancestry
Binomial Nomenclature & Taxonomic Classification
Two-Part Naming System
• Binomial nomenclature: Two-part naming system attributed to Carolus Linnaeus
• Two key features that remain meaningful today:
1. Two-part naming system (genus and specific epithet)
2. Hierarchical classification of organisms in nested hierarchy
• First letter of genus is capitalized; entire species name is italicized or underlined
• Example: Panthera leo (lion), Panthera pardus (leopard)
Hierarchical Classification Levels
Linnaeus introduced a system for grouping species in increasingly inclusive groups, from broadest to most specific:
• Domain (broadest inclusivity)
• Kingdom
• Phylum
• Class
• Order
• Family
• Genus
• Species (most specific—one organism type)
"Did King Philip come over from good Spain?" — Mnemonic device: Did (Domain), King (Kingdom), Philip (Phylum), Come (Class), Over (Order), From (Family), Good (Genus), Spain (Species)
Nested Hierarchy Example
Classification of the Lion (Panthera leo):
• Domain: Eukarya
• Kingdom: Animalia
• Phylum: Chordata
• Class: Mammalia
• Order: Carnivora
• Family: Felidae
• Genus: Panthera
• Species: leo By species level, there is only one Panthera leo, but many species within genus Panthera, many genera in family Felidae, many families in order Carnivora, etc.
Historical Evolution of Classification
• Two kingdoms: Historically, all species classified as plants or animals
• Five kingdoms: By 1960
• Three domains: Recently adopted—Bacteria, Archaea, and Eukaryota
Phylogenetic Trees & Tree Interpretation
Definition & Purpose
• A phylogenetic tree is a branching diagram representing the evolutionary history of a group of organisms
• Represents a hypothesis about evolutionary relationships—not necessarily absolutely accurate, but the most accurate hypothesis of evolutionary relationship available at that point
• Shows patterns of descent, not phenotypic similarity
Key Structural Elements
Branch Points & Divergence
• Each branch point represents the divergence of two evolutionary lineages from a common ancestor
• Evolutionary lineage: A sequence of ancestral organisms leading to a particular descendant taxa
Sister Taxa
• Groups that share a common ancestor that is not shared by any other group
• Example: Chimps and humans are sister taxa; they share an ancestor not shared by other organisms
Rooted Trees
• Include a branch representing the most recent common ancestor of all taxa in the tree
• Allow determination of which taxa are ancestral to which
Basal Taxon
• A lineage that diverges from all other members of the group early in the history of that group
Important Principle
• Should NOT be assumed that a taxon evolved from the taxon next to it in the tree diagram
Characteristics & Homology
Homology vs. Analogy
• Homology: Similarity due to shared ancestry—organisms with similar morphology or DNA sequences are likely more closely related
• Analogy: Similarity due to convergent evolution—unrelated species can evolve superficial similarities through convergent evolution in similar natural conditions/environments
• Example: Australian mole and African golden mole are very similar but not closely related; similarities result from adaptation to similar lifestyles and habitats
Types of Characteristics
Shared Ancestral Characteristics
• A character that originated in an ancestor of the taxon
• Present in broader taxonomic groups
Shared Derived Characteristics
• An evolutionary novelty unique to a particular clade
• Often the core for building cladograms
• Can include loss of features as well as new features
• Example: Loss of limbs in snakes and glass lizards is a shared derived characteristic
• Example: Loss of limbs in whales
Relative Nature of Characteristics
• Whether a character is ancestral or derived depends on what part of the phylogenetic tree is being examined
• Example: Having a backbone is ancestral within vertebrate clade but derived when distinguishing vertebrates from other animals
• Can define both what unites a clade and separates it from other groups
Group Classification in Cladistics
Three Types of Groups
Monophyletic Groups (Clades)
• Group consisting of an ancestor and all of its descendants
• Only groups that include a common ancestor and all descendants are named in modern systematic classification
• "A clade is a group of species that includes an ancestral species and all of its descendants. Clades can be nested within larger clades."
• These are the desired groupings when building cladograms
Paraphyletic Groups
• Consist of an ancestor species and some, but not all, of the descendants
• Unlike polyphyletic groups, the common ancestor to all members is part of the group
• Often initial classifications before full understanding of evolutionary history
Polyphyletic Groups
• Include distantly related species but not their most recent common ancestor
• Essentially a catch-all grouping that may not have a distinct clear common ancestor
• When new evidence indicates a group is polyphyletic, members are typically reclassified
In-groups & Out-groups
• In-group: The group of species being studied
• Out-group: A species or group closely related to but not part of the in-group
• Each in-group species is compared with out-groups to differentiate between shared derived and shared ancestral characteristics
• Characters shared by out-group and in-group are assumed to be ancestral
Character Table Example
Vertebrate classification using characteristics:
• Vertebral column (backbone): All except lancelets
• Jaws: All except lampreys and lancelets
• Forelimbs: All except fish
• Amnion: All except frogs
• Hair: Strictly mammalian, excludes all others
"In each one of those groups, we're using a specific characteristic to separate them out and differentiate them from other groupings of organisms."
Methods for Building Phylogenies
Data Sources
• Morphological data: Physical structure of fossil evidence or extant (living) species
• Molecular data: DNA sequences, genes, biochemistry, and other molecular lines of evidence
• Modern systematics rely increasingly on molecular evidence to supplement or revise morphological classifications
Analytical Principles
Maximum Parsimony
• Assumes the most likely tree is the one requiring the fewest evolutionary events
• Based on principle that simplest explanation is probably most accurate
• For DNA-based phylogenies, most parsimonious tree has fewest base changes
Maximum Likelihood
• Identifies the tree most likely to have produced a given set of DNA data
• Based on probability rules about how DNA changes over time
• Example: May assume all nucleotide substitutions are equally likely
Phylogenetic Bracketing
• Method to predict that features shared by two closely related groups will be present in their ancestor and all descendants
• Used to make predictions about extinct organisms (e.g., dinosaurs)
• Example: Birds and crocodiles both have four-chambered hearts, songs for mating, nest building, and brooding behavior