In-Depth Notes on Phylogeny and Natural Selection

Learning Objectives

• Describe the types of evidence that can be used to infer an evolutionary relationship, including morphological, molecular, and fossil evidence.

• Explain how a phylogenetic tree and/or cladogram can be used to infer evolutionary relatedness, including the importance of branch points and the interpretation of these diagrams.

Phylogeny

• Definition: Phylogeny refers to the evolutionary history or the hierarchical structure that represents the relationships and lineage connections among all organisms on Earth. It lays foundational knowledge for understanding how life has evolved over millions of years.

• Systematics: This is the scientific method of classifying organisms based on phylogenetic relationships. Systematics combines taxonomy (classification) with phylogenetics (the study of evolutionary relationships).

• Key Concept: Phylogeny is a discovery process aimed at elucidating the factual evolutionary tree, rather than merely positing a theory or conducting a mere activity. It seeks to trace back to the common ancestors of life forms, revealing the complex web of life.

Understanding the Tree of Life

• A phylogenetic tree is depicted as a branching diagram, illustrating the evolutionary relationships among various organisms. It serves as a visual representation of how species have diverged and evolved over time.

• Example: Legless lizards and snakes, while appearing similar and both classified under reptiles, belong to different evolutionary lineages that reflect their distinct adaptations to environments.

Taxonomy

• Taxonomy: The discipline that classifies, names, and categorizes organisms based on shared characteristics. Established by Carolus Linnaeus in the 18th century, taxonomy employs a hierarchical structure to understand biological diversity.

  • Key features: Two-part naming system known as binomial nomenclature, and a hierarchical classification system that organizes life into various ranks based on similarities and differences.

• Binomial Nomenclature: This naming convention includes two parts—first part represents the Genus, and the second part represents the species name.

  • Formatting: The genus name is always capitalized, while the species name is italicized (e.g., Homo sapiens).

Hierarchical Classification

• Organisms are grouped into increasingly inclusive categories which include:

  • Domain

  • Kingdom

  • Phylum

  • Class

  • Order

  • Family

  • Genus

  • Species

• Taxon: A taxonomic unit at any hierarchical level, which can range from broad categories like kingdoms to specific categories like species.

Phylogenetic Trees

• Phylogenetic trees represent hypotheses about evolutionary relationships, offering insights into the evolutionary pathways taken by different species over time.

• Branch Points: These represent the divergence of species; sister taxa are two groups that stem from the same branch point, indicating that they share an immediate common ancestor.

• Rooted Trees: Such trees include a common ancestor for all taxa depicted. The basal taxa, or primitive groups, diverge early in evolutionary history, providing a clear perspective on the tree's overall structure.

• Polytomy: A branch point from which more than two groups emerge, indicating uncertainty in how closely related those groups are due to lack of information about specific evolutionary pathways.

Interpretation of Phylogenetic Trees

• Phylogenetic trees illustrate patterns of descent among species; this is based on evolutionary relationships rather than phenotypic (physical) similarities. Patterns depicted should not be misconstrued as direct representation of degrees of similarity between organisms.

• It is important to note that these diagrams cannot indicate exact times of divergence or the amount of evolutionary change that has occurred.

• Misinterpretation may arise if taxa are assumed to have evolved solely from their immediate neighbors on the tree; rather, they reflect a branching evolutionary lineage.

Molecular and Morphological Evidence

• Morphological and Molecular Homologies:

  • Homologies: These denote phenotypic and genetic similarities that arise due to shared ancestry, indicating common evolutionary paths.

  • It is crucial to distinguish between Homology (shared ancestry) and Analogy (similarity due to convergent evolution, where unrelated species develop similar traits due to similar environmental pressures).

• Example: While bat wings are homologous structures with a common ancestor, bird wings are analogous structures that evolved independently in response to flight demands, illustrating adaptation rather than common ancestry.

Cladistics

• Clades: Defined as groups of organisms that include an ancestor and all of its descendants. Understanding clades is essential for grasping evolutionary relationships and classifications.

• Valid clades are monophyletic, meaning they include a common ancestor and all its descendants. In contrast, paraphyletic and polyphyletic clades do not encapsulate all descendants of a common ancestor, leading to incomplete evolutionary representations.

• Shared Characteristics:

  • Shared ancestral: Traits that originated in ancestors of the taxon under consideration.

  • Shared derived: Traits that are unique to a particular clade, offering insights into evolutionary innovations.

Outgroups and Ingroup Comparisons

• Outgroup: Species that are used for comparison against the ingroup to distinguish between derived traits (those that evolved within the group being studied) and ancestral traits (those inherited from distant ancestors). Outgroups help clarify evolutionary relationships within the ingroup.

Evolutionary Relationships through Genomes

• Genomes not only house an organism's genetic information but also contain invaluable information regarding its evolutionary history. Comparing genomic data enables researchers to trace relationships across taxa and understand evolutionary timelines.

• Analyzing DNA sequences, particularly ribosomal RNA (rRNA) and mitochondrial DNA (mtDNA), provides insights into the timing of divergence and evolutionary relationships among different organisms.

Molecular Clocks

• Molecular clocks facilitate the estimation of evolutionary time by utilizing constant rates of molecular change. When calibrated with fossil records, they help in delineating timelines of species divergence.

• However, challenges such as irregularities that may arise due to natural selection, genetic drift, and environmental influences can complicate the calibration of these clocks.

Three Domains of Life

• The scientific community transitioned from a two-kingdom classification system to recognizing three primary domains of life: Bacteria, Archaea, and Eukarya. This shift was based on advancements in molecular systematics and our understanding of genetic relationships.

• Horizontal Gene Transfer: This phenomenon involves the exchange of genetic material between organisms, which plays a crucial role in influencing phylogeny and driving evolutionary change significantly. It's especially prevalent in prokaryotes and contributes to genetic diversity.