Phylogenetics, Taxonomy, and Animal Form & Function: Study Notes

Phylogenetics and Systematics

Introduction to Phylogenetic Trees

Phylogenetic trees are branching diagrams that represent hypotheses about the evolutionary relationships among various biological species or entities based upon similarities and differences in their physical or genetic characteristics.

• Phylogeny: The evolutionary history of a species or group of related species.

• Clade: A group of organisms believed to comprise all the evolutionary descendants of a common ancestor.

• Sister Groups: Two descendants that split from the same node in a phylogenetic tree.

Reading and Interpreting Phylogenetic Trees

• Branches represent evolutionary lineages.

• Nodes (branch points) represent common ancestors.

• Rooted trees indicate a common ancestor for all taxa in the tree.

• Unrooted trees show relationships but not evolutionary paths.

Types of Groups in Phylogenetics

• Monophyletic group: Includes a common ancestor and all its descendants.

• Paraphyletic group: Includes a common ancestor and some, but not all, of its descendants.

• Polyphyletic group: Does not include the most recent common ancestor of all members of the group.

Applications and Examples

• Determining sister groups (e.g., microsporidians as a sister group to ascomycetes).

• Identifying closest relationships (e.g., zygomycetes and chytrids).

• Recognizing monophyletic, paraphyletic, and polyphyletic groups in trees.

Table: Types of Taxonomic Groups

Group Type	Definition	Example
Monophyletic	Common ancestor and all descendants	Mammals
Paraphyletic	Common ancestor and some descendants	Reptiles (excluding birds)
Polyphyletic	Does not include most recent common ancestor	Marine mammals (whales, seals, etc.)

Taxonomy and Classification

Taxonomy is the science of naming, defining, and classifying organisms into groups based on shared characteristics. The hierarchical classification system includes levels such as domain, kingdom, phylum, class, order, family, genus, and species.

• Carolus Linnaeus: Developed the binomial nomenclature and hierarchical classification system.

• Taxonomic levels differ in their inclusiveness (e.g., domain is more inclusive than species).

Cladistics and Outgroups

• Cladistics: A method of classification based on common ancestry.

• Outgroup: A species or group that is closely related to but not part of the group of species being studied; used to root the tree and infer ancestral traits.

Molecular Clocks

Molecular clocks use the rate of genetic mutations to estimate the time of evolutionary divergence between species.

• Most reliable when significant proportions of mutations are not acted upon by natural selection.

• Useful for dating evolutionary events when the fossil record is incomplete.

Animal Form and Function

Adaptations and Evolutionary Convergence

Animals have evolved various adaptations to survive in their environments. Convergent evolution occurs when unrelated species develop similar traits due to similar environmental pressures.

• Example: Penguins, seals, and tuna have streamlined bodies for efficient swimming, an example of convergent evolution.

• Large body size in animals is associated with adaptations such as increased thickness, decreased surface area to volume ratio, and improved heat retention.

Animal Tissues and Exchange Surfaces

• Most exchange surfaces in animals are lined with epithelial tissue.

• Types of muscle tissue: smooth, cardiac, skeletal.

• Basal surface of epithelial cells faces the underlying tissue; apical surface faces the lumen or outside.

Homeostasis and Thermoregulation

Homeostasis is the maintenance of a stable internal environment. Thermoregulation is the process by which animals maintain their body temperature within certain boundaries.

• Endotherms: Regulate body temperature internally (e.g., mammals, birds).

• Ectotherms: Rely on external sources for body heat (e.g., reptiles, amphibians).

• Adaptations for thermoregulation include insulation, circulatory adjustments, and behavioral changes.

Table: Endotherms vs. Ectotherms

Characteristic	Endotherms	Ectotherms
Heat Source	Internal (metabolic)	External (environmental)
Examples	Mammals, birds	Reptiles, amphibians, fish
Energy Use	High	Low
Temperature Stability	Stable	Variable

Regulation and Control Systems

• The endocrine system and nervous system both transmit information, but the nervous system is faster and more specific.

• The hypothalamus is the temperature-regulating center in vertebrates.

Behavioral and Physiological Adaptations

• Animals may change behavior or physiology in response to environmental changes (e.g., hibernation, migration, basking).

• Adaptations can be advantageous or disadvantageous depending on the environment (e.g., endotherms in variable food environments).

Examples and Applications

• Antlers in beetles and deer are an example of convergent evolution due to similar selective pressures.

• Snake behavior in Wisconsin changes with the seasons due to temperature and food availability.

Summary Table: Key Terms and Concepts

Term	Definition
Phylogeny	Evolutionary history of a species or group
Clade	Group of organisms with a common ancestor
Monophyletic	Group with ancestor and all descendants
Paraphyletic	Group with ancestor and some descendants
Polyphyletic	Group without most recent common ancestor
Homeostasis	Maintenance of stable internal environment
Endotherm	Organism that generates heat internally
Ectotherm	Organism that relies on external heat
Convergent Evolution	Independent evolution of similar traits

Key Equations

• Surface Area to Volume Ratio:

$\text{Surface Area to Volume Ratio} = \frac{\text{Surface Area}}{\text{Volume}}$

• Molecular Clock Equation:

$\text{Divergence Time} = \frac{\text{Genetic Distance}}{\text{Rate of Mutation}}$

Additional info:

• Some context and explanations have been expanded for clarity and completeness.

• Tables have been recreated and summarized for study purposes.