BIOL 108 - Theme I - Systematics and Phylogeny

Evolutionary Taxonomy

Discipline of naming and classifying things in the context of evolution, using Linnaean classification

Systematics

Focused on classifying organisms based on their evolutionary relationships and history

Phylogenetics

Field of systematics focused on evolutionary relationships among/between organisms

Cladistics

Uses a tree of diverging branches based on shared derived features (similarities). Direct ancestors aren’t specified, but treated as hypothetical.

Challenges of Linnaean In Phylogenetics

1. Number of ranks is limited

   -Not enough ranks to accommodate every taxon

2. Ranks on phylogeny may not be comparable

Phylogenetic Tree

Evolutionary hypothesis of a group of biologically related taxa (such as a species).
It depicts lineages from a common ancestor, and evolutionary patterns.

Assists in classification of organisms.

Parts of a Phylogenetic Tree

Root - Base of phylogeny

Tips - Terminals of the phylogeny

Node - Represents a hypothetical last common ancestor, and divergence

1. External Node - Connected to a node and a tip

2. Internal Node - Connected to two nodes

Branch/Clade - Lines connecting nodes

Ingroup - Taxa under study

Outgroup - Taxa not under study

Sister Taxa - Two closes branches from a node

Basal Taxa - Relatively early divergence

Derived Taxa - Relatively late divergence

Monophyly/Monophyletic Group

A clade that includes the most recent common ancestor and all of its descendants (eg, mammals)

Paraphyletic Group

Group that includes the most recent common ancestor and some of its descendants

Polyphyletic Group

A group that includes some of its descendants without their common ancestor (eg, animals that can fly)

Dichotomy and Polytomy

Dichotomy - Only two branches diverge from a common ancestor (node)

Polytomy - More than two branches diverge from a common ancestor (node)

Soft and Hard Polytomy

Soft Polytomy - Uncertainty about which of the taxa from the node are closely related

1. More data and experiments needed

Hard Polytomy - Hypothesis that more than two taxa arose from a common ancestor

1. Conclusion; Evolutionary event likely has taken place

Morphological Data

Anatomical features;

1. Qualitative (colour, shape, etc)

2. Quantitative (measurements)

Measurements are often rigorous, fossils can assist in this determination

Can be used to build phylogenetics by helping determine common traits

Molecular Data

Genomic (DNA sequence), protein structure, etc.

Can be used to build phylogenetics by helping determine common traits

Homology

Character traits that evolved from a common ancestral structure. These traits are similar due to shared ancestry among taxa.

Analogy

Character traits that independently evolved from convergence evolution

1. Convergence evolution occurs when organisms from separated lineages adapt to similar environements

Analogous traits cannot be used for phylogeny, since it doesn’t demonstrate evolutionary relationships/shared ancestry

Synapomorphy

A derived feature shared by more than two taxa and their last common ancestor

Example; Shell is a synapomorphy of turtles

Autapomorphy

Derived feature found only in one taxa

Example; A species

Symplesiomorphy

Ancestral feature shared by at least some members of a taxonomic group

Example: fur covering most of the body is a symplesiomorphy for mammals

Identification of An Outgroup

1. Typically the sister group of the ingroup is used as an outgroup

2. Character states are coded as numbers, outgroup is set to 0 to represent ancestral traits, or 1 and 2 to represent derived traits

3. Order of change is decided;

   • 0 → 1 = Ancestral to Derived

   • 1 → 0 = Derived to Ancestral

4. Computation performed to determine candidate trees, which are then selected based on their criteria

Maximal Parsimony

In Cladistics, the tree that implies the fewest evolutionary changes is the most likely tree

Methods of Phylogenetic Tree Determination

1. Maximal Parsimony

2. Maximum Likelihood

3. Bayesian Inference

Embryonic Development

A possible remedy in distinguising between ancestral and derived states.

Follows Von Baer’s law, the more general (basal) characters appear earlier in the embryo than the more special (derived) characters.

A trait developed at a relatively early stage across multiple taxa is more likely to be ancestral.

Problems with the Embryonic Development Theory

1. Ancestral traits don’t always appear in embryonic development, example being axolotl grills

2. Metamorphosis can occur, such as in insects or frogs

Fossil Evidence

A possible remedy in distinguising between ancestral and derived states.

Provides indisputable evidence of a taxa, with traits demonstrated by fossil taxa relatively early in Earth’s history likely being ancestral.

Problems with Fossil Evidence Usage

1. Fossil records are incomplete

2. Molecular data is rare in fossils, meaning we’re relying only on morphological data