Phylogeny 
and the Tree of Life.
Phylogeny and Systematics
•	Phylogeny is the evolutionary history of a species or group of related species
•	The discipline of systematics classifies organisms and determines their evolutionary relationships
Phylogenies show evolutionary relationships
•	Taxonomy is the scientific discipline concerned with classifying and naming organisms
•	Binomial Nomenclature
•	In the 18th century, Carolus Linnaeus published a system of taxonomy based on resemblances
•	Two key features of his system remain useful today: two-part names for species and hierarchical classification

Naming Conventions
•	The first part of the name is the genus 
•	The second part, called the specific epithet, is unique for each species within the genus 
•	The first letter of the genus is capitalized, and the entire species name is italicized
•	Both parts together name the species (not the specific epithet alone)
Hierarchical Classification
•	Linnaeus introduced a system for grouping species in increasingly inclusive categories
•	The taxonomic groups from broad to narrow are domain, kingdom, phylum, class, order, family, genus, and species
•	A taxonomic unit at any level of hierarchy is called a taxon

Animation: Classification Schemes
Linking Classification and Phylogeny
•	The evolutionary history of a group of organisms can be represented in a branching phylogenetic tree
•	A phylogenetic tree represents a hypothesis about evolutionary relationships
•	Each branch point represents the divergence of two species
•	Sister taxa are groups that share an immediate common ancestor
•	A rooted tree includes a branch to represent the last common ancestor of all taxa in the tree
•	A basal taxon diverges early in the history of a group and originates near the common ancestor of the group

Applying Phylogenies
•	Phylogeny provides important information about similar characteristics in closely related species
•	Forensic scientists used it to identify the species of whale from which “whale meat” originated

Phylogenies are inferred from morphological and molecular data
•	To infer phylogenies, systematists gather information about morphologies, genes, and biochemistry of living organisms
•	Phenotypic and genetic similarities due to shared ancestry are called homologies
•	Organisms with similar morphologies or DNA sequences are likely to be more closely related than organisms with different structures or sequences
•	When constructing a phylogeny, systematists need to distinguish whether a similarity is the result of homology or analogy
•	Homology is similarity due to shared ancestry
•	Analogy is similarity due to similar enviroments, which leads to convergent evolution.

Convergent evolution 
•	Convergent evolution occurs when similar environmental pressures and natural selection produce similar (analogous) adaptations in organisms from different evolutionary lineages
Shared characters are used to construct phylogenetic trees
•	Once homologous characters have been identified, they can be used to infer a phylogeny
•	Cladistics groups organisms by common descent
•	A clade is a group of species that includes an ancestral species and all its descendants
•	Clades can be nested in larger clades, but not all groupings of organisms qualify as clades
•	A valid clade is monophyletic, signifying that it consists of the ancestor species and all its descendants

•	A paraphyletic grouping consists of an ancestral species and some, but not all, of the descendants
•	A polyphyletic grouping includes distantly related species but does not include their most recent common ancestor
•	Biologists avoid defining polyphyletic groups and instead reclassify organisms if evidence suggests they are polyphyletic

Shared Ancestral and Shared Derived Characters
•	In comparison with its ancestor, an organism has both shared and different characteristics
•	A shared ancestral character is a character that originated in an ancestor of the taxon
•	A shared derived character is an evolutionary novelty unique to a particular clade
•	When inferring evolutionary relationships, it is useful to know in which clade a shared derived character first appeared

•	In other trees, branch length can represent chronological time, and branching points can be determined from the fossil record
Phylogenetic Trees as Hypotheses
•	The best hypotheses for phylogenetic trees fit the most data: morphological, molecular, and fossil
•	Phylogenetic bracketing allows us to predict features of an ancestor from features of its descendants
•	For example, phylogenetic bracketing allows us to infer characteristics of dinosaurs 

•	Birds and crocodiles share several features: four-chambered hearts, song, nest building, and brooding
•	These characteristics likely evolved in a common ancestor and were shared by all of its descendants, including dinosaurs
•	The fossil record supports nest building and brooding in dinosaurs

Animation: The Geologic Record
An organism’s evolutionary history is documented in its genome
•	Comparing nucleic acids or other molecules to infer relatedness is a valuable approach for tracing organisms’ evolutionary history
•	DNA that codes for rRNA changes relatively slowly and is useful for investigating branching points hundreds of millions of years ago
•	mtDNA evolves rapidly and can be used to explore recent evolutionary events
•	Orthologous genes are found in a single copy in the genome and are homologous between species
•	They can diverge only after speciation occurs 

•	Paralogous genes result from gene duplication, so are found in more than one copy in the genome
•	They can diverge within the clade that carries them and often evolve new functions

Molecular clocks help track evolutionary time
•	To extend phylogenies beyond the fossil record, we must make an assumption about how molecular change occurs over time
•	A molecular clock uses constant rates of evolution in some genes to estimate the absolute time of evolutionary change
•	In orthologous genes, nucleotide substitutions are assumed to be proportional to the time since they last shared a common ancestor
•	In paralogous genes, nucleotide substitutions are proportional to the time since the genes became duplicated

Our understanding of the tree of life continues to change based on new data
•	Recently, we have gained insight into the very deepest branches of the tree of life through molecular systematics
•	There have been substantial interchanges of genes between organisms in different domains
•	Horizontal gene transfer is the movement of genes from one genome to another
•	Horizontal gene transfer occurs by exchange of transposable elements and plasmids, viral infection, and fusion of organisms

•	Some biologists argue that horizontal gene transfer was so common that the early history of life should be represented as a tangled network of connected branches