Detailed Study Notes on Phylogenetic Systematics and Homology

Rudimentary Tree of Life

  • Chloroplast: More evolved and more complicated structure.

  • Every ancestor we have survived.

Homology

  1. Definition of Homology: Similarity resulting from inheritance from a common ancestor.
       * Positional Homology: Similar arrangement of similar parts.
       * Developmental Homology: Developed in a similar manner from an embryo.
       * Genetic Homology: Development controlled by the same gene.
       * Phylogenetic Homology: Inherited from a common ancestor.
       * Identification and analysis of homology is central to phylogenetic systematics.

  • Example: Are the eyes of a mosquito and a fish homologous?
       * Positional = NO
       * Developmental = NO
       * Genetic = YES
       * Phylogenetically: sort of. Only takes one to deem structure homologous.

  • Creation of trees shows ancestral relationships between living organisms.

  • Naming of organisms involves understanding these relationships.

Phylogenetic Systematics

  • Uses homology as evidence of common ancestry.

  • Diagram Representation: These diagrams portray relationships based upon recency of common ancestry.
       * Monophyletic Groups (Clades): Groups that contain species which are more closely related to each other than to any other group.
       * Phylogeny: A branching diagram showing the relationship between species (or higher taxa) based on shared, common ancestors.

Components of Phylogenetic Trees

  • Species: Represented as tips or leaves, corresponding to nouns.

  • Nodes: Points on the tree where speciation occurs, representing common ancestors (considered verbs).

  • Time: Represented along branches indicating lineage divergence.

  • Gene flow must stop between populations through processes like drift, selection, and mutation.
       * Example: A & B are closely related because they share a common ancestor more recently than A & C.
       * C is more closely related to A & B than to D.
       * All relationships are relevant to the nodes of time.

Phylogeny + Classification

  1. Types of Clades:
       * Monophyletic: An ancestor and all its descendants (also known as clades).
       * Paraphyletic: An ancestor and some of its descendants.
       * Polyphyletic: Groups of organisms that do not include their common ancestor, formed by convergent evolution.

  2. Hierarchy of Classification:
       * Genus
       * Family
       * Order
       * Class
       * The classification must maintain monophyletic integrity.

  3. Mistakes in Classification:
       * Monophyletic vs. Paraphyletic vs. Polyphyletic must be correctly understood to avoid significant mistakes in classification.
       * Example: Canids are monophyletic, including all descendants from a common ancestor without including unrelated descendent groups.
       * Groups in canid phylogeny showcasing monophyletic lineage: Puppet's fox, red fox, short-eared dog, etc.

  4. Example of Paraphyletic Groups:
       * Lizards (Sauria) are paraphyletic with respect to snakes (Serpentes).
       * Monophyletic Clade: Snakes form a monophyletic clade within lizards.
       * The group Squamata (lizards + snakes) is a monophyletic clade sister to Sphenodontida.

Molecular and Morphological Characters

  • Molecular Characters: Used for constructing phylogenies from DNA sequences.

  • Morphological Characters: Physical traits used for classification, e.g., skull structure in cetaceans.

Methodology for Analysis:

  1. Extract Sample: Obtain tissue samples from species.

  2. Sequence: Determine the nucleotide sequences.

  3. Align: Arrange sequences for comparison.

  • Synapomorphies: Shared derived conditions that provide evidence for monophyletic clades and define monophyletic groups.

  • Invariable: Traits with no change across a lineage.

  • Importance of identifying outgroups, which are the most closely related ancestral lineage separate from the group being studied, to establish phylogenetic relationships.

  • Example of Character Analysis:
       * Analysis of mutations must involve closely related species to understand lineage divergence.
       * Derived traits (synapomorphies) must be utilized to support classification within a phylogenetic framework.