Classification and Taxonomy

• Topic 1 covers Phylogenetics and Cladistics, based on Chapter 26.1-26.3.

Housekeeping Notes

• Access the textbook without the Mastering option via the UM Learn Page for BIOL 1030 A03.
• Go to "Content," then "Textbook Information," and click "Access eText without Mastering."

Investigating the Tree of Life

• The northern pygmy owl is more related to dinosaurs than crocodiles.
• Birds and dinosaurs share a more recent common ancestor than to crocodiles.
• Morphological characteristics are compared using the fossil record to show transitional stages.
• Molecular characteristics are compared by looking at specific DNA or protein sequences that identify key nucleotide differences.
• Phylogenetic trees are constructed as hypotheses of the evolutionary history between species (phylogeny).
• Systematics, a discipline focussed on classifying organisms, is used.

26.1 Phylogenies Show Evolutionary Relationships

• Organisms share characteristics due to common ancestry.
• Taxonomy is the scientific discipline of naming and classifying organisms.
• Common names can cause confusion.
• Latin scientific names are used based on the Linnaean system.
• Binomial nomenclature is the full species name.
• The genus is the first part of the name (e.g., Castor).
• The specific epithet is second part of the name (e.g., canadensis).
• Castor canadensis is the North American beaver.
• Genus names are always capitalized.
• Specific epithets are always lowercase.
• Binomial names are always italicized (or underlined when handwritten).

26.1 Hierarchical Classification

• Carl Linnaeus grouped organisms into taxa using the Linnaean classification system.
• Related species are placed into genera.
• Related genera are placed into families.
• Related families are placed into orders.
• Related orders are placed into classes.
• Related classes are placed into phyla.
• Related phyla are placed into kingdoms.
• Related kingdoms are placed into domains.
• Species are the narrowest classification.
• Domains are the broadest.

26.1 Linking Classification and Phylogeny

• A phylogenetic tree represents the evolutionary relationship of a group of organisms.
• Branching patterns can reflect how taxonomists classify organisms
• Phylogenetic trees can be a hypothesis.
• Characteristics can change, leading to reclassification.
• DNA evidence can resolve discrepancies between taxonomy and phylogeny.
• Linnaean classification is based on shared characteristics.
• Evolutionary relationships are not always considered in Linnean classification.

26.1 Visualizing Phylogenetic Relationships

• Phylogenetic trees depict a series of dichotomies.
• Each branch point (internal node) represents a common ancestry.
• Sister taxa are groups sharing an immediate common ancestor not shared by others.
• A rooted tree has a branch point representing the most recent common ancestor of all taxa.
• A basal taxon is a lineage that diverges early on from other members of its group.
• Phylogenetic trees can be drawn horizontally, vertically, or diagonally.
• Rotating branches around a branch point does not change the information within the tree.

26.1 Phylogenies (Limitations)

• Phylogenies do not indicate phenotypic similarity.
• Phylogenies show patterns of descent.
• Crocodiles are more related to birds than lizards, despite looking different.
• Phylogenies do not indicate the ages of taxa or branch points.
• Phylogenies do not tell when chimpanzees diverged from humans, just that they share an ancestor.
• Phylogenies do not reveal when a common ancestor lived.
• Phylogenies can only provide an age if the branch lengths have a defined meaning.
• Phylogenies do not determine "who" evolved from "whom."
• It cannot be assumed a taxon evolved from the one next to it on the tree.
• Phylogenies suggest lineages leading to species and their sister taxa evolved from the same ancestor.

26.2 Phylogenies Inferred from Data

• Phylogenies are inferred from morphological and molecular data, not just certain features.
• The most complete data gives the best hypothesis.
• Phylogenetic trees analyze multiple homologies.
• Homologies are shared traits due to descent from a common ancestor.
• Analogous structures share form and function due to the environment.
• Moles look similar but have different internal systems.
• Analogous structures are not inherited from a common ancestor.
• Morphological data can include bones in limbs.
• Molecular data can include shared gene sequences.
• Convergent evolution can confuse phylogenetic.

26.2 Evaluating Molecular Homologies

• To compare DNA sequences, comparable sequences must be aligned.
• Similar species have more conserved regions.
• Different species have more nucleotide changes and varying lengths of DNA.
• Mutations (insertions and deletions) change DAN sequences over time.
• Molecular systematics uses computer programs to align DNA sequences.
• Similar sequences along their lengths are likely homologies.
• Homoplasies are DNA sequences coincidentally similar in unrelated organisms, i.e., DNA analogies.

26.3 Common Ancestry in Classification

• Cladistics is a branch of systematics based on common ancestry.
• Species are placed into clades that consist of an ancestral species and all its descendants.
• Clades can be nested into larger clades.
• Monophyletic clades contain an ancestral species and all descendants.
• Paraphyletic clades contain an ancestral species and some, but not all, of its descendants.
• Polyphyletic clades include distantly related species based on molecular data.

26.3 Cladistic classification of groups

• Diagram 1 represents a monophyletic group.
• Diagram 2 represents a paraphyletic group.
• Diagram 3 represents a polyphyletic group.

26.3 Ancestral Shared Characteristics

• Darwin observed descent with modification on the HMS Beagle, which is explained by natural selection.
• Shared ancestral characteristics are shared by clade members and originated in a non-member ancestor like the backbone for vertebrates.
• Shared derived characteristics are evolutionary novelties unique to a clade, such as hair in mammals.
• The loss of features is also a derived characteristic, like the loss of legs in snakes or whales.

26.3 Phylogenies Using Derived Characters

• Shared derived characters are unique.
• An outgroup is a species or group of species from an evolutionary lineage before the ingroup of interest.
• Organisms sharing the same level of complexity/adaptations are called a grade.
• Ancestral characters exist in the ingroup and outgroup.
• Derived characters occur in the ingroup only.
• Derived characters connect species into a phylogenetic tree.

26.3 Constructing Phylogenies

• DNA sequences can build phylogenies like those from derived morphologies.
• Phylogenies remain hypotheses, meaning statistics are used to produce the most likely guesses.
• Maximum Parsimony: the simplest explanation is the most likely (Occam’s Razor).
• Requires fewest evolutionary events, or for DNA, fewest base changes.
• Maximum Likelihood: identifies the most likely tree given DNA data, assuming equal probabilities.

26.3 Types of Phylogenetic Trees

• In a Cladogram, branch lengths and terminal taxa order depict only branching patterns.
• Only relationship based on shared derived characters is conveyed, not when species diverged.
• In a Phylogram, branch lengths are proportional to evolutionary change.
• Phylograms for DNA data depict the number of changes; longer branches mean more nucleotide changes.

Applications of Phylogenies

• DNA forensics can track down illegal poaching.
• DNA from meat can match samples from wild game populations.
• Universal Species Identification can occur by comparing DNA to a database.
• Gene flow within populations can be inferred.
• New species can be characterized and named by knowing where it fits in the Tree of Life.

Explore binomial nomenclature, Linnaean classification, and phylogenetic trees, examining their roles in understanding organismal relationships. Analyzing the classification system and its hierarchical structure. Discussion on determining evolutionary relationships.