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Phylogeny & Systematics:The Tree of Life

An unexpected family tree. What are the evolutionary relationships among a human, a mushroom, and a tulip? Molecular systematics has revealed that—despite appearances—animals, including humans, and fungi, such as mushrooms, are more closely related to each other than either are to plants.

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§ Phylogenetic trees show patterns of descent, not phenotypic similarity

§ Phylogenetic trees do not indicate when species evolved or how much change occurred in a clade

§ Phylogenetic trees do not assumed that a taxon evolved from the taxon next to it, e.g. Dogs did not evolve from wolves and vice versa.

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What We Can and Cannot Learn from Phylogenetic Trees:

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Applying Phylogenies:§ Phylogeny provides important information

about similar characteristics in closely related species

§ A phylogeny was used to identify the species of whale from which �whale meat� originated by analyzing the relatedness of mtDNAsequences from different organisms. Specific whale sp. are protected by the international marine mammal act. It is illegal to harvest them.

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What is the species identity of food being sold as whale meat?Minke(Southern Hemisphere)Unknowns #1a,2, 3, 4, 5, 6, 7, 8Minke(North Atlantic)

Humpback

Blue

Unknown #9

Unknown #1b

Unknowns #10,11, 12, 13Fin

Scientists constructed agene tree, a phylogenetictree that shows patternsof relatedness amongmtDNA sequences rather than among taxa. Only Minke whales canbe legally sold in Japan.Conclusion: This analysis indicatedthat mtDNA sequencesof 6 of the unknown

Samples (in red), weremost closely related to mtDNA sequences ofwhales that are not legal to harvest.

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Phylogenies are inferred from morphological and molecular data:§ To infer phylogenies, systematists gather

information about morphologies, genes, behavior and biochemistry of living organisms

§ Phenotypic and genetic similarities due to shared ancestry are called homologies

§ 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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Sorting Homology from Analogy:§ When constructing a phylogeny, systematists

need to distinguish whether a similarity is the result of homology or analogy

§ Homology is similarity due to shared ancestryeg, bat wing and whale fin§ Analogy is similarity due to convergent evolutioneg, marsupial v. placental mammal Bat and bird wings are homologous as forelimbs, but

analogous as functional wings.Analogous structures or molecular sequences that

evolved independently are also called homoplasieseg. the eye

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Convergent evolution in burrowers:

Australian marsupial “mole”

North American eutherian mole

Convergent evolution occurs when similar environmental pressures and natural selection produce similar (analogous) adaptations in organisms from different evolutionary lineages - it is no indicator of phylogenetic relations!

A long body, large front paws, small eyes, and a pad of thick skin that protects the nose all evolved independently in these species.

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2004-2005

Phylogeny & Systematics:§ Phylogeny

u evolutionary history of a species u based on common ancestries inferred from

§ fossil record§ morphological & biochemical resemblances§ molecular evidence

§ Systematicsu connects classification

system to phylogeny by categorizing & naming organisms

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Fossil record:§ Sedimentary rock are richest source of fossils

u fossil record is a substantial, but incomplete, chronicle of evolutionary history§ incomplete historical documents of biology

u history of life on Earth is punctuated by mass extinctions

u Homology can be distinguished from analogy by comparing fossil evidence and the degree of complexity“Otzi”; 5,300 year old ice mummy found on an Alpine ridge dividing Austria from Italy at 10,500 feet above sea level. 2015; Discovered 19 living relatives in Austria.

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Paleontology:§ Study of fossils

u fossils provide the strongest evidence of change

u links past & current organismsWoolly mammoth tusks

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2004-2005

Fossils:

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Building phylogenies:§ Morphological & molecular homologies

u similarities based on shared ancestries§ bone structure§ DNA sequences

u beware of analogous structures§ convergent evolution

marsupial mole

placental mole

Analogous structures or molecular sequences that evolved independently are also called homoplasies

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2004-2005

Evaluating molecular homologies:§ Aligning DNA

sequencesu more bases in

common = more closely related

u analyzed by software

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Systematics:§ Connecting classification

to phylogenyu hierarchical systemu Carolus Linnaeasu latin binomial

§ genus§ species

2004-2005

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§ Connection between classification & phylogeny

Tracing possible evolutionary relationships between some of the taxa of the order Carnivora, a branch of the class Mammalia.

Building trees:

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§ CladisticsCladograms (CLAY-doe-grams) show:

u Clade - patterns of shared characteristicsu groups organisms by common descentu probable relationships

Classify organisms according to the order in time at which branches arise along a phylogenetic tree

Illustrating phylogeny:

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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 taxoneg. vertebrates§ A shared derived character is an evolutionary

novelty unique to a particular clade, eg. hair in mammalsA derived trait is a trait that the current organism has, but the previous one did

not have. An ancestral trait is a trait that you, and your ancestors had.A vestigial structure is a structure that had some sort of use in your ancestor,

but none in your current body.

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Inferring Phylogenies Using Derived Characters:

Phylogenies showing the terminology used to describe different patterns of

ancestral and derived character or trait

§ When inferring evolutionary relationships, it is useful to know in which clade a shared derived character first appeared

A shared derived character is shared by the ancestral species and a single group: it is the only reliable guide to inferring phylogeny.

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Lancelet(outgroup)

Lamprey

Bass

Frog

Turtle

LeopardHair

Amnion

(b) Phylogenetic tree

Four walking legs

Hinged jaws

Vertebralcolumn

Leo

par

d

Turt

le

Fro

g

Bas

s

Lam

pre

y

Lan

cele

t(o

utg

rou

p)

TAXA

Vertebralcolumn

(backbone)Hinged jaws

Four walkinglegs

Amnion

Hair

CH

AR

AC

TE

RS

(a) Character table

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

Constructing a phylogenetic tree using shared derived characters: �

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§ In some trees, the length of a branch can reflect the number of genetic changes that have taken place in a particular DNA sequence (homologous genes) involved in development. The lengths are proportional to the amount of genetic change in each lineage; the change has evolved at different rates.

Question: Which lineage shows the greatest genetic change since they diverged?Drosophila

Lancelet

Zebrafish

Frog

Chicken

Human

Mouse

Phylogenetic Trees with Proportional Branch Lengths:

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Drosophila

Lancelet

Zebrafish

Frog

Chicken

Human

Mouse

PALEOZOIC MESOZOIC

542 251 65.5 PresentMillions of years ago

CENO-ZOIC

§ In other trees, branch length can represent chronological time, and branching points can be determined from the fossil record. (This tree is based on the same molecular data as the previous slide). The lengths are proportional to time. Each lineage has the same total length from the base of the tree to the branch tip, indicating that all the lineages have diverged from the common ancestor for equal amounts of time.

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2004-2005

Molecular Systematics:§ Hypothesizing phylogenies using molecular data

u apply principle of parsimony§ simplest explanation based on statistics§ fewest evolutionary events that explain data

hypothetical bird species

3 possible phylogenies

(there are more)

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Maximum Parsimony and Maximum Likelihood:§ Systematists can never be sure of finding the best

tree in a large data set§ They narrow possibilities by applying the principles of

maximum parsimony and maximum likelihood

“the shortest possible tree that explains the data is considered best”

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§ Maximum parsimony assumes that the tree that requires the fewest evolutionary events (appearances of shared derived characters) is the most likely model

§ The principle of maximum likelihood states that, given certain rules about how DNA changes over time, a tree can be found that reflects the most likely sequence of evolutionary events

§ In modern cladistics, advances in computer programs and molecular genetics are used to search for trees that are parsimonious and likely

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Figure 26.15Technique

Species I Species II Species III

Three phylogenetic hypotheses:I

II

III

III

II

I III

II

I

I

III

II

3/A2/T

3/A 4/C

I

III

II

I

III

II

I

III

II

Results

1/C

1/C

1/CI

III

II

I

III

II1/C

1/CI

III

II

4/C3/A

2/T

3/A2/T

2/T3/A

4/C

4/C2/T

4/C

I

III

II

6 events 7 events 7 events

Species I

Species II

Species IIIAncestralsequence

C

C

A

A G

G

T

T

T

T

T T

CA

C

A1 2 43

Site

1

2

4

3

I

III

II

Research method: Determine all the base change events and byapplying parsimony to a problem in molecular systematics

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§ Choose the “tree” that explains the data invoking the fewest number of evolutionary events

“the shortest possible tree that explains the data is considered best”

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Parsimony:

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Phylogenetic trees are hypothesesWhich is the most parsimonious tree?

Parsimony:

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Modern Systematics:§ Shaking up some trees!

Crocodiles are now thought to be closer to birds than other reptiles

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Phylogenetic Trees as Hypotheses:§ The best hypotheses for phylogenetic trees fit the

most data: morphological, molecular, and fossil§ Phylogenetic bracketing allows us to predict features of an ancestor

from features of its descendantsu For example, phylogenetic bracketing allows

us to infer characteristics of dinosaurs Lizardsand snakes

Crocodilians

Ornithischiandinosaurs

Saurischiandinosaurs

Birds

Commonancestor ofcrocodilians,dinosaurs,and birds

§ Birds and crocodiles share several features: four-chambered hearts, song, nest building, and brooding

§ These characteristics likely evolved in a common ancestor and were shared by all of its descendants, including dinosaurs

§ The fossil record supports nest building and brooding in dinosaurs

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§ Evolving genomes: An organism�s evolutionary history is documented in its genome

§ Comparing nucleic acids or other molecules to infer relatedness is a valuable approach

§ 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

§ now that we can compare the entire genomes of different organisms, we find…

Of Mice and Men… good book

humans & mice have 99% of their genes in common (orthologous)• 50% of human genes have a close match with those of yeast!

• the simplest eukaryote

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Molecular clocks:Trace variations in genomes to date evolutionary changes

Rate of change is calculated and then extrapolate back

What does this assume?

Celldivision

error

0.20

Inde

x of

bas

e ch

ange

s be

twee

nH

IV g

ene

sequ

ence

s 0.15

0.10

0.05

01900 1920 1940 1960 1980 2000

Year

Range

HIV

Adjusted best-fit line(accounts for uncertaindates of HIV sequences)

HIV-1M samples were collected from patients between early 1980s & late 1990s. The gene evolved at a relatively constant rate. Concluded that HIV-1M strain first infected humans in 1930s.

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Model Organisms and DNA’s “Molecular Clock”

The Rate of Evolution: the genetic differences between these “model organism” and humans is approximately proportional to the amount of time that has elapsed since our “Last Common Ancestor” (LCA). These DNA differences have been combined with the fossil record to build the phylogenetic “Tree of Life” such as that pictured above. On average, different types of DNA evolve at different rates and can be utilized to best define different branch points of this tree: 1) Non-coding DNA: changes the fastest and can be used to date LCA’s from ~1-100 million years ago. 2) Protein DNA: changes ~10x slower than non-coding DNA and can be used to date LCA’s for most (but not all) of evolutionary history.3) ribosomal RNA DNA: change ~100x slower than non-coding DNA can be used to date the most ancient LCA all the way back to near the origin of life.

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https://theconversation.com/dna-dating-how-molecular-clocks-are-refining-human-evolutions-timeline-65606

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Potential Problems with Molecular Clocks:§ The molecular clock does not run as smoothly as

expected if mutations were neutral§ Irregularities result from natural selection in which

some DNA changes are favored over others§ The use of multiple genes or genes that evolved in

different taxa may improve estimates

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2004-2005

Universal Tree of Life…. Says who?

§ 3 Domainsu Bacteriau Eukaryau Archaea

This branch point formsa polytomy: an

unresolved pattern ofmore than two

divergence.�

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From Two Kingdoms to Three Domains:§ Early taxonomists classified all species as either

plants or animals§ Later, five kingdoms were recognized: Monera

(prokaryotes), Protista, Plantae, Fungi, and Animalia

§ Most recent, the three-domain system has been adopted: Bacteria (the largest), Archaea, and Eukarya

§ The three-domain system is supported by data from many sequenced genomes

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Cell

division

error

Euglenozoans

Forams

Diatoms

Ciliates

Red algae

Green algae

Land plants

Fungi

Animals

Amoebas

Nanoarchaeotes

Methanogens

Thermophiles

Proteobacteria

(Mitochondria)*

Chlamydias

Spirochetes

Gram-positive

bacteria

Cyanobacteria

(Chloroplasts)*

Do

main

Bacte

riaD

om

ain

Arc

haea

Do

main

Eu

kary

a

COMMON

ANCESTOR

OF ALL LIFE

The three domains

of life:

This branch point forms

a polytomy

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§ 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;

however, some

other genes reveal

different

relationships

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Ancestral cellpopulations

Proteobacteria

Cyanobacteria

Thermophiles

MethanogensD

omain Eukarya

Dom

ainA

rchaeaD

omain B

actera

A tangled web of life:§ There have been

substantial interchanges of genes between organisms in different domains

§ Horizontal gene transfer is the movement of genes from one genome to another

§ Horizontal gene transfer occurs by exchange of transposable elements and plasmids, viral infection, and fusion of organisms

§ Some biologists argue that horizontal gene transfer was so common that the early history of life should be represented as a tangled network of connected branches

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The new tree of life that researchers published. It

shows that much of Earth’s biodiversity is bacteria, top,

half of which includes “candidate phyla radiation” that are still waiting to be

discovered. Humans are in the bottom branch of

eukaryotes.

CreditJill Banfield/UC Berkeley, Laura

Hug/University of Waterloo

Scientists Unveil New ‘Tree of Life’By CARL ZIMMER APRIL 11, 2016

�we are

here

§ Disparities between gene trees can be explained by the occurrence of horizontal gene transfer

§ Horizontal gene transfer has played a key role in the evolution of both prokaryotes and eukaryotes

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Hominid Phylogeny�

�

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1

2

3

4

5

Branch point:

where lineages diverge

ANCESTRAL

LINEAGE

This branch point

represents the

common ancestor of

taxa A–G.

This branch point forms

a polytomy:

more than two groups emerge

An unresolved pattern of

divergence.

Taxon A

Taxon B

Taxon C

Taxon D

Taxon E

Taxon F

Taxon G

Sister

taxa

Basal

taxon

How to read a phylogenetic tree:

�

�

�

�

Common

ancestor

to A-C

�

Sister taxa-share an

Immediate common

ancestor to B-C

�

Basal taxa - lineage

that diverges early

in the history of the

group, and

originates near

the common

ancestor of the group

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��

A rooted tree - a branch

to represent

the last common

ancestor of all taxa