Lecture 10 - Phylogenetics and Macroevolution

Define Taxonomy

The theory and practice of classification & naming (we are interested in giving things names and keeping things organised).

Define Systematics

The study of biodiversity and the evolutionary relationship among organisms.

How are taxonomic names assigned?

They are assigned to align with our present understanding of evolutionary relationships.

Who is the ‘father’ of western taxonomy?

Carolus Linnaeus (he wanted to organise every organism).

What did Carolus Linnaeus come up with?

1. Binomial Nomenclature

2. Hierarchical System of Classification

What is within the hierarchical system of classification?

1. Kingdom (kingdoms)

2. Phylum (phyla)

3. Class (classes)

4. Order (orders)

5. Family (families)

6. Genus (genera)

7. Species (species)

   • King Phillip Came Over For Grape Soda

   • 7 categories in total

What is the definition of binomial nomenclature?

When each species is given a name consisting of two terms of which the first names the genus and the second the species itself.

What is the purpose of biological classification? What good does giving names to things do?

The name gives key information about the organism (so can talk about the species more easily and more quickly).

Why is a stable taxonomic system important for systematics?

The names for one species in the past cannot be different than those used in the present because this creates a big barrier for understanding and confuses people. Hence, slows down progress.

What is the definition of Phylogenies?

The relationships and evolutionary histories of species.

What is a node in a phylogenetic tree?

Nodes correspond to historical speciation events. In simple terms, it shows when a lineage of a species splits into two.

What are branches in a phylogenetic tree?

Branches, or edges, correspond to a single ancestor OR descendant lineage.

• All branches are connected by nodes

• There are 2 types of branches; internal and external

What are external branches in a phylogenetic tree?

External branches, or terminal branches, connect the tip to the node.

What is a tip in a phylogenetic tree?

Tips, or leaves, terminals or OTUs, represent individual organisms or species.

What is the root in a phylogenetic tree?

It is a node but from its earliest time point. It usually looks like an unlabelled branch.

*like the “first” individual or species

What are Sister Taxonomies?

They are the immediate descendants of the same ancestor (ie. sister species, sister branches, sister clades).

What are parent and daughter taxonomies?

• A parent branch gives rise to branches that will be descendant of them.

• Hence, those immediate descendants are called the daughter branches/lineages.

What is an ingroup in a phylogenetic tree?

Those in the ingroup are the species that are being studied.

What is an outgroup in a phylogenetic tree?

An outgroup is a distant relative to the ingroup taxonomy.

• in the example in the picture, Salamanders are the outgroup because they are a SEPARATE group of amphibians that are related to frogs, but still different.

What are the benefits of having an outgroup?

It can help root the phylogeny because it can help determine what character traits are ancestral.

What is the MRCA (Most Recent Common Ancestor)?

It is the youngest node that is ancestral to all lineages in a given group. Hence, it really is just the most recent common ancestor shared between a group of species.

• the MRCA changes depending on the group being looked at.

• For example, the MRCA for taxon 1, 2, 3 and 4 was A.

• However, for taxon 1 and 2, the MRCA would be B.

What is a clade in a phylogenetic tree?

Any piece of a phylogeny which includes an MRCA and all of its descendants. Hence, any piece of a phylogeny that shows monophyly.

• Tip for knowing if a taxonomy is a clade!!!!!

  If you can separate the entire phylogeny with a single snip with ‘scissors.’

What is monophyly?

It describes a group that shows its common ancestor and all of the ancestors’ descendants (aka. monophyletic group or clade).

What is Paraphyly?

Also known as ‘grade.’ It describes a group made up of an ancestor that only shows SOME of the descendants.

• reptiles are a paraphyletic group

What is Polyphyly?

Also known as a ‘polyphyletic group'. It describes a group that DOES NOT show the most recent common ancestor for some descendants.

When is a trait ancestral?

A trait is ancestral when it is inherited in its present form from the MRCA of a clade.

When is a trait derived?

A trait is derived if it originated within the clade (so the trait came from a descendant of the MRCA, not the MRCA itself).

*Look at the blue circle - ignore the red circle.

Can the same trait be ancestral for one species and derived for another?

Yes!

In the picture notice how the clade circled in red had an MRCA which produced all snakes. Indicating that the trait was ancestral since the MRCAs present form (snake form) was passed down to its descendants.

However, for the larger clade in the blue circle, the red mark was no longer an MRCA, but instead one of two descendants. Thus, indicating that the snake trait was derived.

*Hence, the same trait can be ancestral for a clade, but be derived within a larger clade.

What is Synapomorphy?

It is a derived trait that all species in a clade share, and the trait arose from the branch leading to the clade.

Referring to the picture, the snake form is a derived trait in the context of the whole phylogeny, but it is an ancestral trait when looked at from a certain clade.

What is Homology?

Having similar structures within different species due to descent from a common ancestor.

What is Homoplasy?

When different species have similar traits but NOT because of a common ancestor, instead because of convergence.

Define Convergence.

When animals and plants to evolve similar characteristics due to living in similar environmental conditions.

What tells us a lot about the relatedness of organisms?

Homologous species will give us a deeper understanding of the relatedness of organisms, whereas Homoplasy characters will mislead us.

Watch video on how to reconstruct a phylogeny.

How do scientists conduct phylogeny reconstruction?

They use statistical models to make inferences about relationships amongst species.

What are the 2 principles of Macroevolutionary Insights?

1. Paleontology

2. Phylogenetics

What does Paleontology do?

• Provides scientists with a direct record of past evolutionary changes. So we can actually observe evidence of species from the past.

• The best inferences are made on species that fossilise well.

What does Phylogenetics do?

• Provides researchers with an indirect record of past evolutionary change.

• The best inferences are made on species that have living representatives of the species (b/c can use their DNA to make phylogenies)

• Documents explosive diversification that occur in the wake of mass extinctions. Hence, it provides evidence of mass extinction.

Define mass extinction

Extinction of >75% of earth’s species in a geologically short period.

What does the fossil record do for us?

1. Provides evidence for clades that have gone extinct.

2. Documents long term patterns of global biodiversity.

3. Provides really good evidence for catastrophic extinctions throughout history.

What are the features associated with increased diversification?

• herbivory

• species with more sexual selection

• animal pollination in plants

• increased dispersal

• increased range size