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”… Linnaeus Darwin provided us convinced us to with the mechanism by use a hierarchical which evolution results classification in descent with system modification ● Taxonomy – naming & classifying organisms ● Systematics – naming & classifying organisms according to their evolutionary relationships Systematics ● Phylogenetics – reconstructing the Phylogenetics 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 Domain: Kingdom: Bacteria Animalia 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?” The Major Lineages of Life: the 5 Kingdom System Living organisms (now PLUS 3 domains!) Prokaryotic Eukaryotic (Monera) Simple/unicells Multicellular (Protista) Autotrophic Heterotrophic (Plantae) Absorptive Ingestive nutrition nutrition (Fungi) (Animalia) Linking Classification and Phylogeny ● Systematists depict evolutionary relationships in branching phylogenetic trees Order Family Genus Species Panthera Felidae Panthera pardus (leopard) Taxidea Carnivora Mustelidae Taxidea taxus (American badger) Lutra Lutra lutra (European otter) Canis Canidae Canis latrans (coyote) 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 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 Branch point: where lineages diverge Taxon A Taxon B Sister taxa Taxon C Taxon D Taxon E ANCESTRAL LINEAGE Taxon F Basal Taxon G taxon This branch point This branch point forms a represents the polytomy: an unresolved common ancestor of pattern of divergence. taxa A–G. Macroevolution & Phylogeny Phylogenetic tree, phylogeny, or cladogram ● Node – branch point, speciation event 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 Phylogenies - ANALOGY But, not all similarity derives from common ancestry! CONVERGENT EVOLUTION: can produce superficially similar traits that lack homology with one another Phylogenies - ANALOGY ● Analogous characters do not share common ancestry **Similarity among taxa results from CONVERGENCE 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 2 4 1 2 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 …AGCTCTAGG… Mutations …AGCTGATCTAGG… Deletions …AGCTCTAGG… …AGCTCTAGG… 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) A B Group C D E F G CLADISTICS: ● A paraphyletic grouping consists of an ancestral species and some, but not all, of the descendants (b) Paraphyletic group A B C D E Group F G CLADISTICS: ● A polyphyletic grouping consists of various species with different ancestors (c) Polyphyletic group A B Group C D 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 G G G Macroevolution & Phylogeny Phylogenetic tree, phylogeny, or cladogram A clade is a monophyletic group, i.e., an ancestral species and all of its descendents Macroevolution & Phylogeny 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) Lamprey Bass Turtle Lancelet (outgroup) Lamprey Frog Leopard Vertebral column 0 1 1 1 1 1 Bass (backbone) Vertebral Hinged jaws 0 0 1 1 1 1 column Frog Four walking Hinged jaws 0 0 0 1 1 1 legs Turtle Four walking legs Amnion 0 0 0 0 1 1 CHARACTERS Amnion Hair 0 0 0 0 0 1 Leopard Hair (a) Character table (b) Phylogenetic tree TAXA Bass Lancelet (outgroup) Lamprey Frog Leopard Turtle Vertebral column 0 1 1 1 1 1 (backbone) Hinged jaws 0 0 1 1 1 1 Four walking 0 0 0 1 1 1 legs Amnion 0 0 0 0 1 1 CHARACTERS Hair 0 0 0 0 0 1 (a) Character table Lancelet (outgroup) Lamprey Bass Vertebral column Frog Hinged jaws Turtle Four walking legs Amnion Leopard Hair (b) Phylogenetic tree Cladistic Analysis Shared Analogies All Primitive similar Characters characters (ancestral) Homologies Shared Derived Characters (unique to a clade) **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 ● 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