NOTES: Chapter 26 Phylogeny and the Tree of Life

Phylogeny: the evolutionary history of a species or group of species ● Systematics: discipline focused on classifying organisms and determining their evolutionary relationships ● The fossil record: the ordered array of fossils, within layers, or strata, of sedimentary rock ● Paleontologists: collect and interpret fossils

a “family tree”… Figure 26.2 An unexpected family tree.

Linnaeus convinced us to use a hierarchical classification system Darwin provided us with the mechanism by which evolution results in descent with modification ● Taxonomy – naming & classifying organisms ● Systematics – naming & classifying organisms according to their evolutionary relationships These two contributions (from Linnaeus and Darwin) combine in the modern branches of biology known as taxonomy, systematics, phylogenetics, and systematic phylogenetics. Systematics Phylogenetics ● Phylogenetics – reconstructing the evolutionary relationships among 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 Aptenodytes forsteri

Binomial Nomenclature ● The two-part scientific name of a species is called a binomial ● The first part of the name is the genus ● The second part 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 Chelonia mydas

Hierarchical Classification ● 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

Species: Panthera pardus Genus: Panthera Family: Felidae Order: Carnivora Class: Mammalia Phylum: Chordata Figure 26.3 Linnaean classification. Kingdom: Animalia Domain: Bacteria Domain: Archaea Domain: Eukarya

5 Kingdom classification system in use through the late 1900s

5 Kingdom classification system in use through the late 1900s gave way to Woese’s 3 Domains

5 Kingdom classification system in use through the late 1900s gave way to Woese’s 3 Domains and multiple Kingdoms

“Did King Philip Come Over From Great Spain?” Each taxonomic level is more inclusive or comprehensive than the previous one (moving from species toward domains).

The Major Lineages of Life: the 5 Kingdom System Living organisms (now PLUS 3 domains!)   Prokaryotic Eukaryotic Simple/unicells Multicellular Autotrophic Heterotrophic Absorptive Ingestive nutrition nutrition (Monera) (Protista) (Plantae) (Animalia) (Fungi)

Linking Classification and Phylogeny ● Systematists depict evolutionary relationships in branching phylogenetic trees

Order Family Genus Species Panthera pardus (leopard) Felidae Panthera Taxidea taxus (American badger) Taxidea Carnivora Mustelidae Lutra lutra (European otter) Lutra Figure 26.4 The connection between classification and phylogeny. Canis latrans (coyote) Canidae Canis Canis lupus (gray wolf)

Macroevolution & Phylogeny ● Phylogenetic tree - – hypothesized genealogy traced back to the last common ancestor (i.e., the most recent) through hierarchical, dichotomous branching Note that this is a highly pruned tree!

Phylogenetic Trees ● 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

Phylogenetic Trees ● 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 ● A polytomy is a branch from which more than two groups emerge

where lineages diverge Taxon A Branch point: where lineages diverge Taxon A Taxon B Sister taxa Taxon C Taxon D Taxon E ANCESTRAL LINEAGE Taxon F Figure 26.5 How to read a phylogenetic tree. Basal taxon Taxon G This branch point represents the common ancestor of taxa A–G. This branch point forms a polytomy: an unresolved pattern of divergence.

Macroevolution & Phylogeny Phylogenetic tree, phylogeny, or cladogram ● Node – branch point, speciation event Note that this is a highly pruned tree!

Constructing Phylogenetic Trees ● Sorting homology vs. analogy... ● Homology: likenesses attributed to common or shared ancestry ● Analogy: likenesses attributed to similar ecological roles and natural selection ● Convergent evolution: species from different evolutionary branches that resemble one another due to similar ecological roles

Phylogenies – HOMOLOGY HOMOLOGIES: Similar characters (e.g., morphological, behavioral, molecular, etc. traits or features) suggest relatedness… Wasps [Hymenoptera]

Phylogenies – HOMOLOGY ● Homologous characters share common ancestry **Lack of similarity among taxa results from DIVERGENCE

Phylogenies – HOMOLOGY ● As a general rule, the more homologous characters shared by two species, the more closely they are related ● Sequences of DNA & RNA (nucleotides) and proteins (amino acids) are used as characters; as a general rule, the more recently two species shared a common ancestor, the more similar their sequences

But, not all similarity derives from common ancestry! Phylogenies - ANALOGY But, not all similarity derives from common ancestry! CONVERGENT EVOLUTION: can produce superficially similar traits that lack homology with one another

**Similarity among taxa results from CONVERGENCE Phylogenies - ANALOGY ● Analogous characters do not share common ancestry **Similarity among taxa results from CONVERGENCE

Figure 26.7 Convergent evolution of analogous burrowing characteristics.

Evaluating Molecular Homologies: ● Systematists use computer programs and mathematical tools when analyzing comparable DNA segments from different organisms ● Molecular systematics uses DNA and other molecular data (i.e. amino acid sequences) to determine evolutionary relationships

1 1 2 Deletion 2 1 2 Insertion 3 1 Figure 26.8 Aligning segments of DNA. 2 4 1 2

Each nucleotide can be treated as a character Cladistic Analysis Each nucleotide can be treated as a character Character changes (mutations) from the ancestral to the derived state include: Substitutions …AGCTCTAGG… …AGCTATAGG… Insertions A = adenine; C = cytosine; G = guanine; T = thymine …AGCTCTAGG… Mutations …AGCTGATCTAGG… Deletions …AGCTCTAGG… …AGCTCTAGG…

Figure 26.9 A molecular homoplasy.

Shared characters are used to construct phylogenetic trees ● Once homologous characters have been identified, they can be used to infer a phylogeny

CLADISTICS: ● 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) Monophyletic group (clade) B Group  C D Figure 26.10 Monophyletic, paraphyletic, and polyphyletic groups. E F G

CLADISTICS: ● A paraphyletic grouping consists of an ancestral species and some, but not all, of the descendants

(b) Paraphyletic group D Figure 26.10 Monophyletic, paraphyletic, and polyphyletic groups. E Group  F G

CLADISTICS: ● A polyphyletic grouping consists of various species with different ancestors

(c) Polyphyletic group A B Group  C D Figure 26.10 Monophyletic, paraphyletic, and polyphyletic groups. E F G

(a) Monophyletic group (clade) (b) Paraphyletic group (c) Polyphyletic group A A A B Group  B B Group  C C C D D D E E Group  E F F F Figure 26.10 Monophyletic, paraphyletic, and polyphyletic groups. G G G

Macroevolution & Phylogeny Phylogenetic tree, phylogeny, or cladogram Note that this is a highly pruned tree! A clade is a monophyletic group, i.e., an ancestral species and all of its descendents

Macroevolution & Phylogeny Note that this is a highly pruned tree! Taxonomic groups often reflect true clades…

Shared Ancestral and Shared Derived Characters ● In comparison with its ancestor, an organism has both shared and different characteristics

Ancestral vs. Derived Characters ● A shared ancestral character is a character that originated in an ancestor of the taxon ● A shared derived character is an evolutionary novelty unique (“new”) to a particular clade ● A character can be both ancestral and derived, depending on the context

Inferring Phylogenies Using Derived Characters ● When inferring evolutionary relationships, it is useful to know in which clade a shared derived character first appeared

TAXA Lancelet (outgroup) (outgroup) Lancelet Lamprey Lamprey Leopard Bass Frog Turtle Vertebral column (backbone) 1 1 1 1 1 Bass Vertebral column Hinged jaws 1 1 1 1 Frog Hinged jaws Four walking legs CHARACTERS 1 1 1 Turtle Four walking legs Amnion 1 1 Figure 26.11 Constructing a phylogenetic tree. Amnion Hair 1 Leopard Hair (a) Character table (b) Phylogenetic tree

TAXA (outgroup) Lancelet Lamprey Leopard Bass Frog Turtle Vertebral column (backbone) 1 1 1 1 1 Hinged jaws 1 1 1 1 Four walking legs CHARACTERS 1 1 1 Figure 26.11 Constructing a phylogenetic tree. Amnion 1 1 Hair 1 (a) Character table

Lancelet (outgroup) Lamprey Bass Vertebral column Frog Hinged jaws Turtle Four walking legs Figure 26.11 Constructing a phylogenetic tree. Amnion Leopard Hair (b) Phylogenetic tree

All similar characters Cladistic Analysis Shared Primitive Characters (ancestral) Analogies All similar characters Homologies Shared Derived Characters(unique to a clade) This flowchart summarizes types of similarities among species… **The sequence of branching in a cladogram then represents the sequence in which evolutionary novelties (shared derived characters) evolved

Ingroup vs. Outgroup ● An OUTGROUP is a species or group of species that is closely related to the INGROUP, the various species being studied ● The outgroup is a group that has diverged before the ingroup ● Systematists compare each ingroup species with the outgroup to differentiate between shared derived and shared ancestral characteristics

● Characters shared by the outgroup and ingroup are ancestral characters that predate the divergence of both groups from a common ancestor

Cladistic Analysis Ingroup vs. Outgroup An outgroup helps identify shared ancestral and shared DERIVED CHARACTERS (unique to a clade)

Phylogenetic Trees with Proportional Branch Lengths ● In some trees, the length of a branch can reflect the number of genetic changes that have taken place in a particular DNA sequence in that lineage

Drosophila Lancelet Zebrafish Frog Chicken Human Mouse Figure 26.12 Branch lengths can represent genetic change. Human Mouse

● In other trees, branch length can represent chronological time, and branching points can be determined from the fossil record Drosophila Lancelet Zebrafish Frog Chicken Human Mouse PALEOZOIC MESOZOIC CENOZOIC 542 251 65.5 Present Millions of years ago

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

Lizards and snakes Crocodilians Ornithischian dinosaurs Common ancestor of crocodilians, dinosaurs, and birds Saurischian dinosaurs Figure 26.16 A phylogenetic tree of birds and their close relatives. Birds

Phylogenetic Trees as Hypotheses ● 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

(b) Artist’s reconstruction of the dinosaur’s Front limb Hind limb Figure 26.17 Fossil support for a phylogenetic prediction: Dinosaurs built nests and brooded their eggs. Eggs (a) Fossil remains of Oviraptor and eggs (b) Artist’s reconstruction of the dinosaur’s posture based on the fossil findings

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 (i.e. human ancestral groups)

Molecular clocks help track evolutionary time ● To extend molecular phylogenies beyond the fossil record, we must make an assumption about how change occurs over time

Molecular Clocks

Molecular Clocks ● A molecular clock uses constant rates of evolution in some genes to estimate the absolute time of evolutionary change ● In orthologous genes (genes found in different species; e.g. cytochrome c for E.T.C.), nucleotide substitutions are proportional to the time since they last shared a common ancestor ● In paralogous genes (similar genes found within one species; e.g. olfactory receptor genes in humans), nucleotide substitutions are proportional to the time since the genes became duplicated

Molecular Clocks ● Molecular clocks are calibrated against branches whose dates are known from the fossil record ● Individual genes vary in how clocklike they are

Divergence time (millions of years) 90 60 Number of mutations 30 Figure 26.19 A molecular clock for mammals. 30 60 90 120 Divergence time (millions of years)