Phylogeny and the Tree of Life

Overview: Investigating the Tree of Life

• Phylogeny is the evolutionary history of a species or group of related species
• The discipline of systematics classifies organisms and determines their evolutionary relationships
• Systematists use fossil, molecular, and genetic data to infer evolutionary relationships

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Taxonomy

• The science of classifying organisms.
• Tells us about the degree of relation between different organisms

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Taxonomy

• Developed by Swedish biologist Carolus Linnaeus (1707 — 1778).
• Binomial naming system

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Tiger Classification

Domain: Eukarya

Kingdom Animalia

Phylum Chordata

Class Mammalia

Order Carnivora

Family Felidae

Genus Panthera

Species tigris

Dear King Phillip climbed over the fence and got shot

Dude, Keep Plates Clean Or Family Gets Sick

Biological Nomenclature

A species is both defined by its genus name and specific name.

Ex. Panthera tigris

Panthera- genus name

tigris- species name

Biological Species

Organisms that are genetically similar, and have ability to interbreed and produce viable, fertile offspring

Subspecies

Might interbreed if a barrier or other challenge was removed (such as distance).

Hawaiian endemic snails (kahuli)

Offspring is sterile

Panthera leo

Panthera tigris

tigon

Hybrids

Three-domain system

Extremophiles

Prokaryotes

Eukaryotes

Look at how this evolution happened!

Linking Classification and Phylogeny

• Systematists depict evolutionary relationships in branching phylogenetic trees
• Linnaean classification and phylogeny can differ from each other
• Systematists have proposed the PhyloCode, which recognizes only groups that include a common ancestor and all its descendants

Fig. 26-4

Species

Canis

lupus

Pantherapardus

Taxidea

taxus

Lutra lutra

Canis

latrans

Order

Family

Genus

Carnivora

Felidae

Mustelidae

Canidae

Canis

Lutra

Taxidea

Panthera

Fig. 26-5

Sister

taxa

ANCESTRAL

LINEAGE

Taxon A

Polytomy: more than 2 groups emerge

Common ancestor of

taxa A–F

Branch point

(node)

Taxon B

Taxon C

Taxon D

Taxon E

Taxon F

What We Can and Cannot Learn from Phylogenetic Trees

• Phylogenetic trees do show patterns of descent
• Phylogenetic trees do not indicate when species evolved or how much genetic change occurred in a lineage
• It shouldn’t be assumed that a taxon evolved from the taxon next to it
• Applications: whale meat sold illegally in Japan

Phylogenies are inferred from morphological and molecular data

• To infer phylogenies, systematists gather information about morphologies, genes, and biochemistry of living organisms
• Organisms with similar morphologies or DNA sequences are likely to be more closely related than organisms with different structures or sequences

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Compare the bones

Homologous Structures are similarities due to shared ancestry, such as the bones of a whale’s flipper and a tiger’s front limb.

Convergent Evolution

• Convergent Evolution: has taken place when two organisms developed similarities as they adapted to similar environmental challenges-not because they evolved from a common ancestor.
• Example: The streamlined bodies of a tuna and a dolphin show convergent evolution.

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But don’t be fooled by these…

Analogous structures

• look similar on the outside
• Same function
• different structure & development

on the inside

• different origin
• no evolutionary relationship

Solving a similar problem with a similar solution

Analogous structures

Dolphins: aquatic mammal

Fish: aquatic vertebrate

• both adapted to �life in the sea
• not closely related

Evaluating Molecular Homologies

• Systematists use computer programs and mathematical tools when analyzing comparable DNA segments from different organisms

Fig. 26-8

Deletion

Insertion

1

2

3

4

Orange sections no longer align

only with addition of gaps

will they align

Types of mutations that

notmally occur

• It is also important to distinguish homology from analogy in molecular similarities
• Mathematical tools help to identify molecular homoplasies, or coincidences

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• Molecular systematics uses DNA and other molecular data to determine evolutionary relationships

Shared characters are used to construct phylogenetic trees

• Cladistics groups organisms by common descent
• A clade is a group of species that includes an ancestral species and all its descendants
• A valid clade is monophyletic, signifying that it consists of the ancestor species and all its descendants
• A paraphyletic grouping consists of an ancestral species and some, but not all, of the descendants
• A polyphyletic grouping consists of various species that lack a common ancestor

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Fig. 26-10

A

A

A

B

B

B

C

C

C

D

D

D

E

E

E

F

F

F

G

G

G

Group III

Group II

Group I

(a) Monophyletic group (clade)

(b) Paraphyletic group

(c) Polyphyletic group

Includes all descendants

Shared Ancestral and Shared Derived Characters

• In comparison with its ancestor, an organism has both shared and different characteristics
• A shared ancestral character is a character that originated in an ancestor of the taxon (vertebrae in mammals)
• A shared derived character is an evolutionary novelty unique to a particular clade (hair in mammals)
• A character can be both ancestral and derived, depending on the context, it is useful to know in which clade a shared derived character first appeared

Fig. 26-11

TAXA

Lancelet

(outgroup)

Lamprey

Salamander

Leopard

Turtle

Tuna

Vertebral column

(backbone)

Hinged jaws

Four walking legs

Amniotic (shelled) egg

CHARACTERS

Hair

(a) Character table

Hair

Hinged jaws

Vertebral

column

Four walking legs

Amniotic egg

(b) Phylogenetic tree

Salamander

Leopard

Turtle

Lamprey

Tuna

Lancelet

(outgroup)

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

An organism’s evolutionary history is documented in its genome

• Comparing nucleic acids or other molecules to infer relatedness is a valuable tool for tracing organisms’ evolutionary history
• DNA that codes for rRNA changes relatively slowly and is useful for investigating branching points hundreds of millions of years ago
• mtDNA evolves rapidly and can be used to explore recent evolutionary events

Gene Duplications and Gene Families

• Gene duplication increases the number of genes in the genome, providing more opportunities for evolutionary changes
• Like homologous genes, duplicated genes can be traced to a common ancestor
• Orthologous genes are found in a single copy in the genome and are homologous between species
• They can diverge only after speciation occurs

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• Paralogous genes result from gene duplication, so are found in more than one copy in the genome
• They can diverge within the clade that carries them and often evolve new functions

Molecular Clocks

• They are methods used to measure the absolute time of evolutionary change based on the observation that some genes and other regions of the genome appear to evolve at constant rates.
• The underlying assumption for molecular clocks is that the number of nucleotide substitutions in related genes is proportional to the time that has elapsed since the genes branched from their common ancestor.

New information continues to revise our understanding of the tree of life

• Recently, we have gained insight into the very deepest branches of the tree of life through molecular systematics

Biological Kingdoms

Fig. 26-21

Fungi

EUKARYA

Trypanosomes

Green algae

Land plants

Red algae

Forams

Ciliates

Dinoflagellates

Diatoms

Animals

Amoebas

Cellular slime molds

Leishmania

Euglena

Green nonsulfur bacteria

Thermophiles

Halophiles

Methanobacterium

Sulfolobus

ARCHAEA

COMMON

ANCESTOR

OF ALL

LIFE

BACTERIA

(Plastids, including

chloroplasts)

Green

sulfur bacteria

(Mitochondrion)

Cyanobacteria

Chlamydia

Spirochetes

A Simple Tree of All Life

• The tree of life suggests that eukaryotes and archaea are more closely related to each other than to bacteria
• The tree of life is based largely on rRNA genes, as these have evolved slowly

• Some researchers suggest that eukaryotes arose as an endosymbiosis between a bacterium and archaean
• If so, early evolutionary relationships might be better depicted by a ring of life instead of a tree of life

Is the Tree of Life Really a Ring?

Fig. 26-23

Archaea

Bacteria

Eukarya