Download Phylogeny - De Anza College

Phylogeny and the Tree
of Life
Chapter 26

Systematics: Discipline focused on
classification of organisms
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Taxonomy: naming
organisms.
Linnaeus - hierarchy
of increasingly
inclusive categories.
Taxon: Taxonomic
unit at any level of
hierarchy
Panthera
pardus
Species
Panthera
Genus
Felidae
Family
Carnivora
Order
Mammalia
Class
Chordata
Phylum
Animalia
Kingdom
Eukarya
Domain

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.
Phylogenetic tree
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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:

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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:
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Agriculture and plant breeding
Investigation of poaching
Forensic and bioterrorism
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Homology: similarities due to shared ancestry
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Analogy: similarity due to convergent evolution
Homoplasies: Analogous structures; similarities
arose independently

What is the relationship between
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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.
1
2
Deletion
1
2

If genes in two
organisms share
many portions of their
nucleotide sequences,
it is highly likely that
the genes are
homologous.
Insertion
1
2
1
2
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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
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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
CHARACTERS
Hair
Amniotic (shelled) egg
Four walking legs
Hinged jaws
Vertebral column
(backbone)
Character table
Leopard
Turtle
Salamander
Tuna
Lamprey
Lancelet
(outgroup)
TAXA
Turtle
Leopard
Hair
Salamander
Amniotic egg
Tuna
Four walking legs
Lamprey
Hinged jaws
Lancelet (outgroup)
Vertebral column
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 –
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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)
no
most
species
no
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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
Eukarya
Bacteria
Archaea