Phylogeny - Lecture 1

Taxonomy

Discipline of categorizing organisms through names

• based on shared traits, not phylogenies

Shared Traits Taxonomy bases naming on

• Morphology

• Molecular Data (Biochemistry)

• Genetics (DNA Sequences)

How to use the Binomal Naming System

Genus species

• Capitalization matters!

Order of Taxonomic Levels (small → big)

Species, Genus, Family, Order, Class, Phylum, Kingdom, Domain

• ex of Phylum: Chordata (Vertebrates!)

Phylogeny

The evolutionary history of a species or a group of species

• never definite

Most confident means of measuring Phylogeny

DNA sequencing based on the # of deletions, insertions, and substitutions in one’s genome

Systematics

The classification of evolutionary relationships, not just naming

How Systematists Classify evolutionary relationships

• Morphological Data

• Genetics

• Biochemical Data

EX: Myoglobin (RBC) Protein Sequence

• The more similar the myoglobin (RBC) sequence, the more related two organisms are.

Branch Points

The divergence of a common ancestor into two unique species, essentially a site of speciation

• can be rotated

Sister Taxa

Groups sharing an immediate taxa, said to be the most related to each other because of their close common ancestor

Outgroup

A relative term used for a species that is relatively related and similar to the ingroup, but lacks a distinct trait

“Rooted” Trees

Phylogenic Trees that have a common ancestor at the beginning that relates to the ENTIRETY of the tree!

Polytomy

A phenomenon on a phylogenic tree where a branch point leads to MORE THAN TWO organisms rather than just two

• preferably, we have only 2

Rules of Constructing Phylogenies

• Use morphological and molecular data

• Use homologies and not analogies

Homologies

Traits of species’ that have the same structure and different function, signifying there was a common ancestor and an evolutionary relationship

Analogies

Structures with the same function, but not a common ancestor

Cladistics

The grouping of organisms into clades

Clade

A monophyletic group that includes all ancestral species plus ALL of its descendants

Paraphyletic group

Like a monophyletic group, it has a common ancestor, but not ALL of its descendants: only some

Polyphyletic

A group of species with no common ancestor (ex: Thinking whales and seals are related, so we group them, but their common ancestor is long ways away)

Shared Derived Character

A characteristic that is not in the ancestor, but in all of its descendants

• more informative and definite about relationships

Shared Ancestral Character

A characteristic found in an ancestor and all of its descendants

How a character can both be Shared Derived and Shared Ancestral

Ex: Hair on Mammals

• It depends on where you look on the tree

Three ways of Inferring Evolutionary Relationships

• DNA, Mitochondrial DNA, or rRNA relationships

• Asking live organisms about their insights

• DNA Barcoding Project (stocking the entire genome of an organism!)

Why use rRNA or mitochondrial DNA over regular DNA?

There are multiple copies of rRNA and multiple mitochondria in a cell, thus there is easier isolation and more abundance to isolate