22 - Phylogenetics

What is Systematics?

The study of diversity of organisms and evolutionary relationships

What are the two parts to systematics?

- Taxonomy

- Phylogeny

What is taxonomy?

- Describing, naming, and classifying

- Binomial nomenclature for naming species (unique 2-part name)

- Many names are still used today

Who developed the binomial nomenclature for naming species?

Carolus Linnaeus

How does the unique two-part name work?

Genus + Specific epithet

Homo + sapiens = Homo sapiens

How many species of plants and animals did Carolus Linnaeus name?

~11,000 spp of plants and animals

What are the rules for the naming system?

- Latin/latinized

- Genus name upper case, specific epithet is not

- Both italicized or underlined

- Genus can be abbreviated, specific epithet can NOT

- Genus is unique and can specify all species within a genus

- Specific epithet isn't necessarily unique

Examples of the rules

- Both italicized or underlined

Escherichia coli

- Genus can be abbreviated, specific epithet can NOT

E. Coli

- Genus is unique and can specify all species within a genus

Genus Escherichia

- Specific epithet isn't necessarily unique

Can NOT say "Species coli"

What is hierarchical classification?

Levels:

Domain -> Kingdom -> Phylum -> Class -> Order -> Family -> Genus -> Species

Species = smallest unit of classification

What is a taxon?

- It is the grouping of organisms at any one of the levels above

- Plural: Taxa

Moving from species to domain, what happens?

- Each level is more inclusive

What happens at each level?

All species on a certain level share characteristics of that group

Example of species sharing characteristics at each level

Class: Mammalia

- Hair and milk production

Order: Carnivora

- Above AND teeth modified for sharing meat

Family: Carnivora

- ALL above AND anatomy of a middle ear

Genus: Canis

- ALL above AND long limbs relative to head and body length, elongated snouts, well-developed canines

What is Phylogeny?

- The study of evolutionary history and relationship among organisms

- Based on shared ancestry, not phenotypic similarity

What is a Phylogenetic Tree?

- A branching diagram that shows patterns of descent from a common ancestor

- Hypothesis may change with more data

How to read an Unrooted Tree

Shows relationship, but does not show the ancestral root

How to read a Rooted Tree

One branch point represents most recent common ancestor of all taxa on the tree

What do the branchpoints represent?

They are nodes

What are Dichotomies on a tree?

- The divergence of 2 lineages from a common ancestor

- Branches can rotate without changing relationships

What are Extant Species?

They are currently living and exist at the tip of the branches

What is a Basal Taxon?

1st lineage to diverge from a common ancestor of a group

What is a Sister Taxa?

Organisms that share an immediate common ancestor, they are each others closest relatives

What is Polytomy?

A branch point with more than 2 descendent groups, meaning evolutionary relationships are not clear (Not Good!)

What is a Character?

An attribute of a species

What are States?

Alternate forms of a character

What is an example of a state?

Four legs: Present vs. Absent

Body Covering: Hair vs. Feathers vs. Scales

Compare characters and states

- They more closely 2 species are related, the more characters they share

- Must result from common ancestry

Where do homologous traits come from?

They are inherited from a common ancestor

What is an example of a homologous trait?

- Look at function of wings in birds and bats

- Underlying structure is the same because it was inherited from a common ancestor

What can be connected to homologous traits?

Darwinian evolution

What traits are a result of Convergent Evolution?

Analogous

What are Analogous traits?

- Independently acquired

- Similar adaptations in organisms from different evolutionary lineages

- Similar environment can cause this (similar selection pressure, similar character although they do not share a CA)

What is an example of an analogous trait?

- Birds and Honeybees do not share a common ancestor with the same wing structure

- Bird wings are different from insect wings

Why do birds and honeybees both have wings even though they don't have a common ancestor?

Aerodynamic pressure, they converged on structures for flight

What is an example of choosing a character?

Anatomical/Morphological features (developmental and life history traits)

How do we get Molecular Data?

- Compare DNA sequences

- Genes are sequences of 100's of nucleotides

- Compare RNA seqs

- Compare aa seqs of proteins

- If a gene in 2 organisms shares many nucleotides, then possibly homologous

An example of molecular data

12 nucleotides --> 12 characteristics

- A, C, G, or T at each site -> States

What are Cladistics?

- It is a widely used method of systematics

- Uses homologous to classify organisms based on common ancestry

What is a Clade?

A group which includes ancestral species and all of its descendants

What are the three possible groups of clades?

- Monophyletic clade

- Paraphyletic clade

- Polyphyletic clade

What is a monophyletic clade?

Common ancestry and ALL descendants

What is paraphyletic clade?

Common ancestor and SOME of its descendants

What is a polyphyletic clade?

Distantly related species and it does NOT include the most recent common ancestor

What is an example of a monophyletic group?

Vertebrates

What is an example of a paraphyletic group?

Fish

What is an example of a polyphyletic group?

Mammalian fins

What are shared ancestral characters?

- Not unique to clade

- Originated in ancestor

- Point 1

What are shared derived characters?

- Unique to clade

- Point 2

An example of Shared Characteristics

Shared Ancestral Character = Vertebral Column

Shared Derived Character = Hair