Biodiversity & Evolution: Reconstructing the Phylogeny

  • Monophyletic Group:

    • A group that includes a common ancestor and all of its descendants.

    • Can be removed from a tree with a single cut.

  • Paraphyletic Group:

    • Includes the common ancestor and some, but not all, of the descendants.

    • Exemplified by a group represented in green box notation in diagrams.

  • Polyphyletic Group:

    • Does not include the common ancestor of the group.

    • Represented in orange box notation in diagrams.

RECONSTRUCTION OF AN EVOLUTIONARY TREE

  • Tree Construction: Cladistics

    • Based on the analysis of homologous morphological or molecular features (‘characters’).

    • The state of these characters is compared across different taxonomic groups.

    • Similarities and differences recorded to identify informative changes.

  • Data Processing:

    • Data is input into tree algorithms.

    • Distance Methods:

    • Compute a distance matrix and then find a minimal distance tree, e.g., using the Neighbour Joining method.

    • Character Methods:

    • Evaluate multiple trees to determine the most likely or most parsimonious (i.e., least number of evolutionary changes) tree. Examples include Maximum Likelihood and PhyML for maximum likelihood checks.

TERMINOLOGY IN CLADISTICS / PHYLOGENETICS

  • Plesiomorphy:

    • An ancestral character state.

  • Symplesiomorphy:

    • A character state shared by multiple groups but inherited from ancestors older than their last common ancestor.

  • Apomorphy:

    • A derived character state.

  • Autapomorphy:

    • Apomorphy unique to a single group.

  • Synapomorphy:

    • Apomorphy shared by two or more groups, originating in their last common ancestor.

  • Importance:

    • Only synapomorphies (shared derived character states) are informative for constructing phylogenetic trees.

COMPLICATIONS IN TREE RECONSTRUCTION

  • Hybridization:

    • Interspecies crossing resulting in exchange of genetic material between closely related but distinct species.

  • Different Rates of Evolution:

    • Evolution rate for a character may differ across clades in a tree.

    • Potentially caused by adaptive radiation.

  • Homoplasies:

    • Similar character states that evolved independently, termed as parallel evolution or convergence.

    • Examples include:

    • Legs in arthropods vs. tetrapods adapting to terrestrial life.

    • Similar shape of fins and flippers in various species adapting to aquatic life.

    • Thermal homeostasis observed in birds and mammals.

ANALOGOUS TRAITS / HOMOPLASIES

  • Examples of analogous traits leading to homoplasies:

    • Bat and bird wings

    • Butterfly and bird wings

    • Shark and dolphin body shapes

CONVERGENT EVOLUTION EXAMPLE

  • Marsupials in Australia:

    • Resemble placental mammals that occupy similar ecological niches despite evolutionary distance.

PHYLOGENETIC TREE CONSTRUCTION MECHANICS

  • Character Matrix Example:

    • Traits analyzed include absence/presence of jaws, lungs, amniotic membranes, etc. for different organisms. Example organisms evaluated:

    • Lamprey

    • Shark

    • Salamander

    • Lizard

    • Tiger

    • Gorilla

    • Human

DISTANCE MATRIX DERIVATION

  • Utilizing the character matrix to develop a distance matrix:

    • Example showing numbers of differences between species:

    • Lamprey vs. Shark = 1; Shark vs. Salamander = 1; and so forth.

    • This matrix records numbers of differences whereby closely related species show fewer differences.

TREE RESULTS FROM DISTANCE MATRIX

  • Transition from distance matrix to a resulting tree of relationships:

    • Estimated phylogeny or cladogram showing the emergence of derived character states.

MAXIMUM PARSIMONY METHOD

  • Tree construction reliant on correct character state interpretation (ancestral vs derived).

  • Example Context:

    • The loss of a tail in frogs vs. apes: if interpreted as a synapomorphy, results in five character changes; interpreted as homoplasy, results in only four.

TREE CONSTRUCTION USING DNA SEQUENCES

  • Example sequences to compare:

    • Sequences A, B, C, D to analyze informative vs non-informative characters such as plesiomorphies, autapomorphies, and synapomorphies.

SEQUENCE ALIGNMENT IMPORTANCE

  • Sequence methods compare homologous positions which may include mutations (insertions and deletions).

  • Process recognizes how sequences must be aligned to identify evolutionary relationships.

HOMOPLASIES IN SEQUENCE EVIDENCE

  • Explanation of how DNA sequences can exhibit homoplasies:

    • Limited character states (4) lead to rapid saturation over time.

    • Issues with parsimony methods in determining accurate trees (e.g., problems arising with long branch attraction).

LONG BRANCH ATTRACTION

  • Issue arising with fast-evolving lineages leading to multiple substitutions at identical sites, causing false similarities across some branches within the phylogenetic tree.

MAXIMUM LIKELIHOOD METHOD

  • Method used to identify the tree which makes the observed data most probable under a specific model of evolution.

    • Example: Transition probabilities favor A<->G and C<->T.

  • Strengths:

    • Statistically rigorous and generally achieves higher accuracy compared to maximum parsimony.

    • Accommodates varying rates of evolution across sites and lineages.

  • Weaknesses:

    • Computationally intensive, especially with large datasets.