Ch. 26 - Phylogeny & the Tree of Life PDF

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Know what can be learned from the Phylogenetic Tree and what all the different points on the tree are.
Professor Brinton...

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Ch. 26 - Phylogeny & the Tree of Life Investigation Tools Taxonomy is the scientific discipline concerned with classifying and naming organisms ● In the 18th century, Carolus Linnaeus published a system of taxonomy based on resemblance between organisms ● Two key features of his system remain useful today ○ Binomial nomenclature: Two-part names for species ○ Hierarchical classification: Nested groups Phylogeny is the evolutionary history of a species or group of related species Systematics: classification of organisms and determination of their evolutionary relationship

Binomial Nomenclature & 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

Binomial nomenclature: The genus (plural: genera) and species (plural & singular) for an organism A taxonomic unit at any level is called a taxon ● A clade is a monophyletic taxon ● Diversity varies between taxa of the same level

Linking Classification and Phylogeny Evolutionary history of a group of organisms can be represented in a branching phylogenetic tree Linnaean classification vs. Systemic phylogenetics ● Classification groups organisms based on their observable characteristics, regardless of their origin ● Systematists propose a classification system that would ONLY recognize groups that include a common ancestor and all its descendant

Tree Terminology Each branch point represents the divergence of two species ● Tree branches can be rotated around a branch point without changing the evolutionary relationships Sister taxa are groups that share an immediate common ancestor ● Would sister taxa be closely related? ● The taxon level influences how far back the common ancestor will be A rooted tree includes a branch to represent the last common ancestor of all taxa in the tree ● (nearly all the trees you see in this course will be rooted) A basal taxon diverges early in the history of a group and originates near the common ancestor of the group of taxa A polytomy is a branch from which more than two groups emerge

What We Can and Cannot Learn from Phylogenetic Trees Phylogenetic trees show patterns of descent, not phenotypic similarity Phylogenetic trees do not indicate how much change occurred in a lineage It should not be assumed that a taxon is most closely related to the taxon next to it

Applying Phylogenies Phylogeny provides important information about similar characteristics in closely related species A phylogeny can be used to identify the species of whale from which “whale meat” originated

Sorting Homology from Analogy 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

● Homologous: If Trait X is seen in one taxon, other taxa with this same trait will be connected via a common ancestor. Analogy is similarity due to convergent evolution ● Analogous: If Trait X is seen on several taxa that are not connected via a common ancestor Convergent evolution occurs when similar environmental pressures and natural selection produce similar (analogous) adaptations in organisms from different evolutionary lineages

Evaluating Molecular Homologies Computer programs and mathematical tools ● Analyze comparable DNA segments from different organisms ● Identifying mutations, similarities ● Look for coincidence

Real similarities? It is also important to distinguish homology from analogy in molecular similarities Mathematical tools help to identify molecular homoplasies, or coincidences

Once real homologous characters have been identified, they can be used to infer a phylogeny and create a phylogenetic tree

Cladistics Cladistics groups organisms by common descent A clade is a group of species that includes an ancestral species and all its descendants ● Only monophyletic clades are valid: consists of the ancestral species and ALL of its descendants ● Clades can be nested in larger clades, but not all groupings of organisms qualify as clades Polyphyletic and paraphyletic groups also exist, but are not considered valid clades ● Paraphyletic group: an ancestral species and SOME BUT NOT ALL, of the descendants ● Polyphyletic group: several species of varying relatedness but NOT their most recent common ancestor

Shared Ancestral and Shared Derived Characters In comparison with its ancestor, an organism has both shared and derived 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 A character can be both ancestral and derived, depending on the context When inferring evolutionary relationships, it is useful to know in which clade a shared derived character first appeared

Inferring Phylogenies Using Derived Characters To infer an evolutionary relationship, it is useful to know in which clade a shared derived character appeared ● Examine which groups have common characteristics ● And which characteristics are not commonly shared

Outgroup vs. Ingroup Taxa An outgroup is a species or group of species that is closely related to the various ingroup species being studied ● The outgroup is a group that diverged before the ingroup species ● The outgroup and ingroup still share a common ancestor Systematists compare each ingroup species with the outgroup to differentiate between shared derived and shared ancestral characteristic

Phylogenetic Trees CAN have Proportional Branch Lengths Length = number of genetic changes that have taken place in a particular DNA sequence Length = chronological time, with branching points determined from the fossil record

Finding Trees in a Forest of Data: Analysis Systematists can never be sure of finding the best tree in a large data set ● Maximum parsimony assumes that the tree that requires the fewest evolutionary events (appearances of shared derived characters) is the most likely ● The principle of maximum likelihood states that, given certain rules about how DNA changes over time, a tree can be found that reflects the most likely sequence of evolutionary events Computer programs are used to search for trees that are both parsimonious and likely

Phylogenetic Trees as Hypotheses The best hypotheses fit the most data: morphological, molecular, and fossil Predict features of an ancestor from features of its descendants via phylogenetic trees ● Recall: Principle of Uniformity 1. Birds and crocodiles share several features: four-chambered hearts, song, nest building, and brooding 2. These characteristics likely evolved in a common ancestor: homologs shared by all of its descendants 3. Morphology: Dinosaurs are part of a monophyletic clade that includes birds and crocodiles 4. Fossil evidence: supports nest building and brooding in dinosaurs

5. Supported Hypothesis: Dinosaurs built nests and brooded their eggs...