Phylogeny and the Tree of Life

Chapter 26

Systematics: Discipline focused on classification of organisms

Taxonomy: naming organisms.

Linnaeus - hierarchy of increasingly inclusive categories.

Taxon: Taxonomic unit at any level of hierarchy

Species

Pantherapardus

PantheraGenus

FamilyFelidae

CarnivoraOrder

MammaliaClass

PhylumChordata

KingdomAnimalia

EukaryaDomain

Binomial nomenclature: genus & specific epithet.

Homo sapiens

Phylogeny: evolutionary history of a group of species.

Phylogenetic tree: evolutionary relationship between species represented in a branching diagram.

Drosophila

Lanc

elet

Fish

Amph

ibia

nBird

Human

Rat

Mou

se

Phylogenetic tree

represents a hypothesis about evolutionary relationships

relationships are represented by a series of dichotomies (branch points)

sister taxa: group of organisms that share an immediate common ancestor (branch point)

branch points within the tree represents the last common ancestor of all taxa in the tree

Polytomy: branch point with more than 2 descendant groups.

Limitations of phylogenetic tree:

Does not tell us when a species arose How much genetic change occurred in each

evolutionary step May not tell us the exact ancestral species

Application of phylogeny:

Agriculture and plant breeding Investigation of poaching Forensic and bioterrorism

Homology: similarities due to shared ancestry

Analogy: similarity due to convergent evolution Homoplasies: Analogous structures; similarities

arose independently

What is the relationship between wings of birds, wings of bats and forelimbs of cats?

Morphological and molecular homologies:

Organisms that share very similar morphologies or similar DNA sequences are likely to be more closely related than organisms with vastly different structures or sequences.

Molecular systematics: Using molecular data to determine evolutionary relationships.

Genes: sequences of thousands of nucleotides.

If genes in two organisms share many portions of their nucleotide sequences, it is highly likely that the genes are homologous.

1

2

1

2

Deletion

Insertion

1

2

1

2

Cladistics: Systematics using common ancestry as the primary criterion.

Clades: groups of species that have been sorted according to common ancestry. Like taxa clades reside within larger clades.

Shared ancestral character: character that originated in an ancestor of the group

Shared derived character: evolutionary novelty unique to a particular group.

Outgroup: species or a group of species from an evolutionary lineage that is known to have diverged before the lineage that is being studied.

Ingroup: species included in the group being studied.

Outgroups and ingroups are determined on the basis of morphology, paleontology, embryonic development, gene sequences

To determine various branch points in a phylogenetic tree we compare members of ingroups to each other and to members of outgroups as well.

Using derived character to infer phylogeny

Hair

Amniotic (shelled) egg

Four walking legs

Hinged jaws

Vertebral column(backbone)

Character table

CH

AR

AC

TE

RS

TAXA

La

nc

ele

t(o

utg

rou

p)

La

mp

rey

Tu

na

Sa

lam

an

de

r

Tu

rtle

Le

op

ard

Turtle Leopard

Hair

Amniotic egg

Four walking legs

Hinged jaws

Vertebral column

Salamander

Tuna

Lamprey

Lancelet (outgroup)

Cladogram

Principle of maximum parsimony: first investigate the simplest explanation that is consistent with the facts Occam’s razor: shaving away unnecessary

complications – minimalist problem solving approach.

Maximum likelihood: the phylogenetic tree that reflects the simplest explanation of DNA change

Gene families and gene duplication:

Gene families: groups of related genes within an organisms genome resulting from repeated duplication.

Orthologous genes: homologous genes found in different species due to speciation.

Paralogous genes: more than one copy of a gene in the same genome

Ancestral gene

Speciation

Orthologous genes

Ancestral gene

Gene duplication

Paralogous genes

Three domain system: All organisms are classified into three domains –

Bacteria: currently known prokaryotes Archaea: very diverse group of prokaryotes,

variety of habitats including extreme ones Eukarya: All organisms that have cells with true

nuclei (single-celled or multicellular)

Eukarya

Characteristics Bacteria Archea Eukarya

Nuclear envelope absent absent present

Membrane bound organelles

absent absent present

Circular chromosomes

present present absent

Peptidoglycans in cell walls

present absent absent

Sensitivity to antibiotics like streptomycin,

chloramphenicol

yes no no

Growth at exterme conditions

(temperature, salt)

nomost species

no

Horizontal gene transfer: genes are transferred through transposable elements, viral infection, plasmids.

According to some scientists – to represent extensive horizontal gene transfer in early organisms, a ring is a better representation than a dichotomous tree

ArchaeaBacteria

Eukarya