Phylogeny

Phylogeny

• Study of evolutionary history of species or related groups, examining how species evolve and diverge over time, and providing insights into the common ancestry of diverse organisms.

Key Concepts

• Phylogeny vs Phenotype: Phylogeny refers to the evolutionary family tree illustrating the historical relationships between organisms, while phenotype pertains to the observable physical and biological traits of an organism resulting from the interaction of its genotype with the environment.

• Systematics: This field classifies organisms based on evolutionary relationships, employing a variety of tools including morphological studies, fossil records, and molecular and genetic data to construct a more accurate representation of how species are related through evolution.

Taxonomy Basics

• Linnaean System: Established by Carl Linnaeus, this classification method introduced the two-part naming system known as binomial nomenclature (e.g., Homo sapiens) and organized life into hierarchical categories: Domain, Kingdom, Phylum, Class, Order, Family, Genus, and Species.

• Taxon: A term used to denote a group or unit at any taxonomic level, which helps in identifying and categorizing organisms efficiently.

• Species: Refers to the basic unit of classification, signifying a group of individuals capable of interbreeding and producing fertile offspring. It is important to distinguish between species and specimen, which refers to an individual organism sampled for study.

Phylogenetic Trees

• Branching trees: These diagrams represent hypotheses regarding evolutionary relationships among species, with each branch point indicating a point of divergence from a common ancestor.

  • Sister taxa refer to groups that share an immediate common ancestor, highlighting their close evolutionary relationship.

  • Rooted trees incorporate a branch representing the last common ancestor of all included taxa, providing a clearer ancestral context.

  • Basal taxon: This term describes a lineage that diverges early in the evolutionary history of a group, often serving as a reference point for evolutionary studies.

  • Polytomy: A situation in a phylogenetic tree where a single branch splits into multiple branches, indicating that the relationships among the resulting taxa are not well resolved.

Homology vs Analogy

• Homology: Refers to similarities in characteristics resulting from shared ancestry among species. For instance, the forelimbs of bats and birds exhibit homologous structures derived from a common ancestor, though they may serve different functions (flight in birds and manipulation in bats).

• Analogy: This term describes similarities in features due to convergent evolution, where organisms from different lineages develop similar traits or adaptations in response to similar environmental pressures, such as the wings of bats and insects.

Cladistics

• Cladistics is a methodology that groups organisms based on common descent, highlighting evolutionary lineages.

• Clade: A group that includes an ancestor and all of its descendants, providing a clear view of evolutionary relationships.

• Valid clades are characterized as monophyletic, meaning they contain all descendants of a common ancestor, and are distinguished from paraphyletic (excluding some descendants) and polyphyletic (including unrelated lineages) groups.

Shared Characters

• Shared ancestral traits: Traits that originated from a common ancestor and were preserved over time, such as the vertebral column in mammals.

• Shared derived traits: New evolutionary features that are unique to a particular clade, exemplified by hair in mammals, which distinguishes them from other vertebrates.

Outgroup vs Ingroup

• Outgroup: A species or group known to be closely related to the ingroup (the primary focus of study) but diverged before it, allowing researchers to identify which traits are ancestral versus derived.

Interpreting Phylogenetic Trees

• Cladogram: A type of tree where the order of taxa is irrelevant, focusing instead on the branch points that indicate relationships.

• Phylogram: This representation uses branch lengths to convey quantitative information such as genetic changes or evolutionary time, enhancing the understanding of relationships among species.

Classification of Life

• Life was traditionally classified into two kingdoms (Plant and Animal), evolving through further discoveries to encompass five kingdoms (Monera, Protista, Fungi, Plantae, and Animalia), and is currently grouped into three domains: Bacteria, Archaea, and Eukarya, reflecting our understanding of molecular genetics and evolutionary biology.

Applications

• Phylogenetic bracketing is a method that allows scientists to infer ancestral traits and reactions to environmental pressures by analyzing extant species related through shared evolutionary history, thereby providing insights into the potential characteristics of extinct organisms.