Phylogenetics Notes

BIOL 2200 Lecture 9: Intro to Phylogenetics

Learning Objectives

Review the terminology of classification and phylogenetics.
Understand the structure of a phylogenetic tree and the basic rules for tree building.
Consider how analogous traits affect tree building.
Compare different groups of species in a phylogeny.
Mention of a phylogeny of dragons by R. Colautti.

Tree Thinking

Phylogeny: A visual hypothesis of the evolutionary history of a group of species, populations, or genes.

Applied Phylogenetics: Conservation

Identify species at risk using phylogenetic relationships.
Example: Phylogenetic relationships of coral species at risk (red) vs. coral species of least concern (blue) in Australia (Huang and Roy, 2015).
Complex species have less calcification than robust species.

Applied Phylogenetics: Agriculture

Targeted breeding using phylogenetic insights.
Example: Phylogeny of $Brassica rapa$ L. demonstrating morphological variation across subspecies.
Selecting lines for increasing genetic variation (Bird et al. 2017).

Applied Phylogenetics: Food Science

Tracking food identity using phylogeny.
Example: Phylogeny mapping seafood sequenced from restaurants in Washington, D.C. (Stern et al. 2017).
Mislabelling: Chilean Seabass and Tuna species were mislabeled.

Applied Phylogenetics: Medicine

Using phylogenetics to understand infectious diseases.
Molecular phylogeny of SARS-CoV-2 supports the hypothesis that the virus originated from bats (Boni et al. 2020).
Branch tips color-coded:
- Grey = bat
- Green = pangolin
- Blue = SARS-CoV
- Red = SARS-CoV2

Applied Phylogenetics: Tracking SARS-CoV-2 Spread

Using molecular phylogenetics to track the early spread of SARS-CoV-2 (Worobey et al. 2020).

Classic Classification: Binomial Nomenclature

Taxonomic ranks:
- Domain: Eukarya
- Kingdom: Animalia
- Phylum: Chordata
- Class: Mammalia
- Order: Carnivora
- Family: Canidae
- Genus: Vulpes
- Species: Vulpes vulpes
Example: Red fox ( $Vulpes vulpes$ )

Connecting Classification & Phylogeny

Phylogenetic tree illustrating the relationships between different groups of Carnivora.
- Feliformia:
  - Nimravidaet
  - Stenoplesictidaet
  - Percrocutidaet
  - Nandinidae (African palm civet)
  - Feloidea
    - Prionodontidae (linsangs)
    - Barbourofelidaet
    - Felidae (cats, lynxes, etc.)
- Viveroidea
  - Viverridae (civets, genets, etc.)
  - Hyaenidae (hyenas)
- Herpestoidea
  - Herpestidae (meerkats, mongooses, etc.)
  - Eupleridae (fossa, fanaloka, etc.)
- Caniformia
  - Arctoidea
    - Amphicyonidaet
    - Canidae (dogs, wolves, foxes, etc.)
    - Hemicyonidaet
    - Ursidae (bears)
    - Pinnipedia
      - Enaliarctidaet
      - Phocidae (seals)
      - Otariidae (sea lions, fur seals, etc.)
    - Musteloidea
      - Odobenidae (walrus)
      - Alluridae (red panda)
      - Mephitidae (skunks, stink badgers, etc.)
      - Procyonidae (raccoons, coatis, etc.)
      - Mustelidae (weasels, otters, badgers, etc.)

Phylogenetic Trees Show Relatedness

Illustrative example of relatedness: You, Sister, Cousin, Cousin, Mom, Aunt, Grandma.
Evolutionary context: Early tetrapod, Early bony fish, Ray-finned fish.

Parts of the Phylogenetic Tree

Key components:
- Node
- Root
- Ancestral
- Derived
- Branch
- Clades
- Sister taxa
- Polytomy

Relationships Are Not Linear

Diagrammatic representation of non-linear relationships in a phylogenetic tree.

Ancestral vs. Derived Characters

Ancestral: Trait originated from the ancestor of the taxon.
Derived: Trait is an evolutionary novelty to the clade.
Synapomorphy: Trait shared by all clade members.
Example: bones and limbs in Early tetrapod, Early bony fish, and Ray-finned fish.

Key Points About Phylogenies

Show pattern of descent, NOT similarity.
Order of branching indicates relative age.
Proximity of two taxa does not imply direct origination.
Trees are hypotheses that can be revised with new data.
Some phylogenetic trees estimate time since divergence.

Phylogenies Are Built on Homologies

Homology: Similarity due to common ancestry.
Evidence of evolutionary relatedness through molecular and morphological homology.

Analogy or Homoplasy (Convergence)

Similar environmental pressure leads to similar adaptation in different organisms.
Distinguishing homology from analogy.
Molecular and morphological analogy.

Cladistics

Using clades to build a phylogenetic tree.
Grouping taxa based on shared ancestry.
Smaller clades are nested in larger clades.
Example: Early tetrapod, Early bony fish, Ray-finned fish.

Different Groups of Species

Monophyletic: An ancestor and ALL of its descendants.
Polyphyletic: Group does not include the most recent common ancestor.
Paraphyletic: An ancestor but only some of its descendants.
Illustration using Hawk and Raven.

Different Groups of Species: Homology and Homoplasy

Similarity due to homology leads to accurate trees.
Lack of similarity (missing homology) can lead to inaccurate trees.
Similarity due to homoplasy leads to inaccurate trees.

Today, we will consolidate our understanding of evolution, focusing on how we can create testable hypotheses using phylogenetics. This will mark the beginning of a broader discussion, with two lectures leading up to our first midterm. Throughout the semester, you will continue to build on these skills, learning the language of phylogenetics essential for our studies.

Announcements

Reminder about P.2 L. sessions currently taking place; these facilitated group study times have shown increased attendance and success among students.
Regular student hours this week: Monday, Tuesday, Wednesday, with optional Zoom hours on Thursday for Q&A and exam prep practice.
Practice exam questions will be posted by tomorrow; the formal exam will be available on Wednesday.
Friday's class will be a Q&A session with no new content.

Phylogenetics Basics

Phylogeny is a visual hypothesis of the evolutionary history of species, populations, or genes.
Different representations of phylogenetic trees exist (lateral, vertical, circular), with an emphasis on firm branches for clarity.

Importance of Phylogenetics

Understanding phylogenetics is crucial for addressing contemporary biological challenges:

Conservation: Identifying at-risk species (e.g., coral species phenotypes).
Agriculture: Targeting breeding strategies (e.g., phylogenetic insights on $Brassica rapa$ lines).
Food Science: Tracking food identity and addressing mislabeled products.
Medicine: Understanding the origins of infectious diseases, especially evidenced during the SARS-CoV-2 pandemic.
Evolutionary Relationships: Building trees to understand common ancestry and evolutionary patterns.

Building Phylogenetic Trees

Key components include nodes (points of divergence), branches (lineage connections), and the root (the most ancestral point).
Cladistics is the method used to group taxa based on shared ancestry, creating nested patterns of relatedness on trees.
Distinguish between:
- Monophyletic: Ancestor and all descendants.
- Paraphyletic: Ancestor and some descendants (e.g., excluding certain lineages).
- Polyphyletic: Grouping organisms that do not share a common ancestor.
The presence of homologies (similar traits from a common ancestor) supports accurate trees, while homoplasies (similar traits due to convergent evolution) can complicate interpretations.

Application in Class

In class, we delved into vocabulary and terminology surrounding tree reading and building, including:

Ancestral vs. Derived Traits: Identifying traits that define groups on a tree.
Synapomorphy: A shared derived trait useful for building trees.
Trees serve as hypotheses, not definitive answers, and can be revised with new data.