7.2.4 Cladistics

Linnaean Classification System

• Organisms are grouped into hierarchies

• Still used today but w less emphasis

• Kings Play Cards On Fat Green Stools

Binomial Nomenclature

• Scientific names for species

• always italicized or underlined

• 2 parts

  • Genus → can NOT be reused

  • species epithet → can be reused for other genuses

1. we don’t have enough taxonomic levels to show ALL relationships

2. or over-generalize by placing all organisms into one group → eliminates relationships

BPQ

What are some of the problems w the Linnaean Classification system?

Taxonomy

process of naming and classifying organisms

based on phylogeny

loosely fit into Linnaean classification

Monophyletic Group

• consists of 1 common ancestor and all the descendants

• good taxonomic names are ones that are monophyletic

Paraphyletic group

Consists of 1 common ancestor but is missing some descendants

Polyphyletic group

consists of distantly related organisms

Paraphyletic

BPQ

Think about what you consider a fish

Are fish monophyletic, paraphyletic, or polyphyletic?

Cladistics

a sound method for developing hypothesis of evolutionary relationships

• ALL phylogeny are hypotheses

Cladistics is NOT just based on organisms looking similar

Cladistics requirements

1. Informative characters (traits)

2. Parsimony

Characters

1. Synapomorphies

2. Plesiomorphies

3. Autapomorphies

Synapomorphies

• shared derived (new) characters

• Informative

Plesiomorphies

• shared ancestral (old) characters

• Uninformative

Autapomorphies

• unshared derived (new) characters

• uninformative

Outgroup

distantly related group that is used to distinguish synapomorphies from plesiomorphies

without an outgroup, we dont know which traits are synapomorphies and which are plesiomorphies

• presence (1) or absence (0) of a trait are arbitrary

If outgroup has the trait, it is considered a Plesiomorphy

• evolved before the ingroup did

Looking like a lizard is a plesiomorphy (uninformative) bc all amniotes looked like lizards

BPQ

how can we explain how crocs can be more closely related to birds even tho they look more like lizards?

AP way to make a phylogeny

group by similarities

Parsimony Analysis

assumption = evolutionary change

• phylogeny w least number of evolutionary changes is probably the correct one

Character Matrix

columns: characters/traits

rows: organisms/taxa

1: presence of trait

0: absence of trait

Ingroup: Organisms/taxa being studied

Outgroup: distant relative

• used to determine synapomorphy/plesiomorphy

• not shown in picture

• all the traits listed on the slide are not informative

• human’s traits are autapomorphies

• chimps, gorillas, orangutan traits are plesiomorphies

BPQ

how is it possible chimps are more closely related to humans?

Homoplasy

shared characters NOT due to common ancestry

Goal of cladistics

• maximize homology

• minimize homoplasy

  • homoplasies require extra evolutionary steps

Competing Hypotheses

• different sets of data can create multiple phylogenies

• many problems in phylogenetics are still unresolved

• All phylogenies are hypotheses

  • phylogenies are often reassessed as new data comes in

each tree is arranged differently, but have the SAME relationships

BPQ What is the difference in relationships between the following phylogenies?

Tree Topology

• nodes on a tree can rotate without changing relationships

• Polytomy

Polytomy

an unresolved tree - when there is more than one most parsimonious solution, so a node splits into 3+ branches

• Hard Polytomy - Results from actual evolutionary processes that happened (real)

• Soft Polytomy - Results from bad data/not enough data (not real)

Taxonomic Definitions

3 ways to define a taxonomic group (clade)

• Apomorphy-based Clade

• Node-based Clade

• Stem-based Clade

Apomorphy-based clade

the first ancestor to evolve a synapomorphy and all of its descendants

Node-based clade

the most recent common ancestor of two taxa and all of its descendants

• when both taxa are extant, it is called a crown clade

Stem-based Clade

all organisms more closely related to one taxa than to another

Character Optimization

• placing characters on phylogenies in a way to yield the most parsimonious evolution

• Process

  1. If the outgroup is 1, place that character at the root

  2. Add characters to the tree use the least number of steps

  3. Use (-) in front of a character to show loss of the character

DELTRAN optimization

• delayed optimization

• prioritizes convergent evolution

• in phylogeny, draw the trait evolving twice

• only equally parsimonious to ACCTRAN during polytomy

ACCTRAN optimization

• accelerated optimization

• prioritizes losses or reversals

• in phylogeny, draw trait evolving and then being lost

• only equally parsimonious to DELTRAN during polytomy