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Bioinformtica: Inferncia filogentica

WHYDO WE CARE ?

Rita Castilho, rcastil@ualg.pt

What for?

Sistemtica Molecular

Evoluo

Ecologia

Forense

Medicina (evoluo de vrus, vacinas, desenvolvimento de drogas)

Uses of phylogenies: Sistemtica Similar organisms are

grouped together

Clades share common evolutionary history

Phylogenetic classification names clades

Source: Inoue, J.G., Miya, M., Tsukamoto, K., Nishida, M. 2003.

Basal actinopterygian relationships: a mitogenomic perspective on the

phylogeny of the ancient fish. Molecular Phylogenetics and

Evolution, 26: 110-120.

Pryer et al. 2001

Uses of phylogenies: Character evolution

What did the ancestral Darwin's Finch eat?

Example of correlated character evolution

Granivore Insectivore Folivore

MP

Schluter et al. 1997

Uses of phylogenies: Ecology

Study the evolution of ecological interaction and behavior

Why might two related species have a different ecology?

e.g. social vs. solitary, drought tolerant vs. mesophytic, parasitic vs. free living, etc.

What are the causes of these differences? Is the environment causing these differences? Can we infer which condition is ancestral?

Examples of phylogenetic ecology

Evolutionary ecology of mate

choice in swordtail fish (genus Xiphophorus)

Morris et al. 2003

Uses of phylogenies: Co-evolution

Compare divergence patterns in two groups of tightly linked organisms (e.g. hosts and parasites or plants and obligate pollinators)

Look at how similar the two phylogenies are Look at host switching

Evolutionary arms races Traits in one group track traits in another group

e.g. toxin production and resistance in prey/predator or plant/herbivore systems, floral tube and proboscis length in pollination systems

Example of host-parasite phylogeny

Uses of phylogenies: Phylogenetic geography

Sometimes called historical biogeography or phylogeography

Map the phylogeny with geographical ranges of populations or species

Understand geographic origin and spread of species

Look at similarities between unrelated organisms

Understand repeated patterns in distributions e.g. identifying glacial refugia

Example of phylogeographyIndependent sites of pig

domestication

Larson et al. 2005

Example of phylogeography Example of phylogeography

Example of phylogeography

The highly diversified genus Conus includes more then 500 species of venomous marine snails

Example of phylogeographyAll endemic Cape Verde Conus:

are vermivorous (prey on polychaete annelids)

are nonplanktonic lecithotrophic

Example of phylogeography

sm

all

she

lled

spec

ies

large shelled species

Divergence time estimates indicate a double colonization of the archipelago:

the ancestors of large and small shelled species arrived around 16.5

and 4.6 MYA, respectively

Main cladogenetic events in Cape Verde Conus are consistent with geological dates and eustatic sea-level changes

(Haq et al., 1987)

- 80m10.5MYA - 50m

5.5MYA

- 30m3.8MYA

16.5 MYA

4.6 MYA

2,048 bp - mitochondrial genes (12S rRNA, trnaV, 16S rRNA, cob)

ML

Uses of phylogenies: Estimating Divergence Times

Estimate when a group of organisms originated Uses information about phylogeny and rates of

evolutionary change to place timescales on tree

Needs calibration with fossils Combined with mapping characters, correlate

historical events with character evolution

e.g. Radiation of flowering plants in the Cretaceous

Example of timescales on phylogenies

Timing the evolution of sociality in sweat bees to a warm period in geologic history

Brady et al. 2006

Multiple origins of HIV from SIV (Simian Immunodeficiency

Virus)

Uses of phylogenies: Medicine

Learn about the origin of diseases

Look for disease resistance mechanisms in other hosts to identify treatment and therapy in humans

Multiple origins of HIV from SIV (Simian Immunodeficiency Virus)

From: Understanding Evolution. HIV: the ultimate evolver. http://evolution.berkeley.edu/evolibrary/article/0_0_0/medicine_04

Severe acute respiratory syndrome

Example of disease phylogeny

Wendong et al. 2005

Methicillin-resistant Staphylococcus aureus

AsiaEuropaAmrica do Sul

AustralasiaAmrica do Norte

Example of disease phylogeny

Harris et al. 2010

Example of medical forensics

A dentist who was infected with HIV was suspected of infecting some of his patients in the course of treatment

HIV evolves very quickly (10-3 substitutions/year) Possible to trace the history of infections among

individuals by conducting a phylogenetic analysis of HIV sequences

Samples were taken from dentist, patients, and other infected individuals in the community

Study found 5 patients had been infected by the dentistSource: Ou et. al. 1992. Molecular epidemiology of HIV transmission in a dental practice. Science, 256: 1165-1171.

Exemplo 2

Phylogeny and molecular evolution

Rita Castilho, rcastil@ualg.pt

=

Determining the common origin (ancestral)

What are phylogenies for?

Latimeria

Protopterus

What is the most recent common ancestor of tetrapods?

Latimeria

Protopterus

Coelacanth

What is the most recent common ancestor of tetrapods?

Latimeria

Protopterus

Lungfish

What is the most recent common ancestor of tetrapods?

Latimeria

Protopterus

Teleost

What is the most recent common ancestor of tetrapods?

What is the most recent

common ancestor of tetrapods?

What is the most recent

common ancestor of tetrapods?

Tetrapodlimbs

Amnion

Feathers

Lungfishes

Mammals

Amphibians

Lizardsand snakes

Crocodiles

Hawks and other birds

Ostriches

Am

niotesTetrapods

Birds

Common ancestor oflineages to the right

Homologous traitshared by all groupsto the right

2

1

3

4

6

5

Three main assumptions for phylogenetic inference

Three main assumptions for phylogenetic inference

All organisms have a common ancestral

Evolution can be displayed in a bifurcating patternThere are exceptions. Lateral gene transfer

Three main assumptions for phylogenetic inference

Clark and Messer, 2012. Science

Change in characteristics happens through time

Orbit eclipses dorsal midline

Orbit migration

CitharusPsettodesAmphistium/HeteronectesTrachinatus

Migrated orbit

Unmigrated orbit

Three main assumptions for phylogenetic inference

How to build Phylogenetic TreesSelect Sequences

Align Sequences

Choose model and method; Build tree

Evaluate Tree

Interpret Phylogeny

Good

Needs Improvement

Estimating Genetic Differences

0 25 50 750

0.5

1.0

1.5Expected differences

Time

Diff

eren

ces

betw

een

sequ

ence

sEstimating Genetic Differences

If all nucleotides equally likely, observed difference would plateau at 0.75

Simply counting differences underestimates distances.

Fails to count for multiple hits 0 25 50 75

0

0.5

1.0

1.5Expected differences

Observed differences

Time

Diff

eren

ces

betw

een

sequ

ence

s

One substitutions happened - one substitution is visible

G

CG

PAST

G

CA

PAST

Two substitutions happened - only one substitution is visible Two substitutions happened - no visible substitution

GPAST

A A

Estimating Genetic Differences

If all nucleotides equally likely, observed difference would plateau at 0.75

Simply counting differences underestimates distances.

Fails to count for multiple hits 0 25 50 75

0

0.5

1.0

1.5Expected differences

Observed differences

Time

Diff

eren

ces

betw

een

sequ

ence

s

Page RDM, Holmes EC (1998) Molecular Evolution: a phylogenetic approach Blackwell Science, Oxford.

Models of evolution

Models of nucleotide substitution allow for the calculation of probabilities of specific base changes along a branch.

They include different parameters that aim to describe distinct aspects of the process of nucleotide substitution.

Page RDM, Holmes EC (1998) Molecular Evolution: a phylogenetic approach Blackwell Science, Oxford.

Models of evolution Impact of models: 3 sequences

http://artedi.ebc.uu.se/course/X3-2004/Phylogeny/Exercises/nj.html

AGC AAC ACC

Sequences 1 and 2 differs at 1 out of 3 positions = 1/3 Sequences 1 and 3 differs at 1 out of 3 positions = 1/3 Sequences 2 and 3 differs at 1 out of 3 positions = 1/3

1 2 31 -2 0.333 -3 0.333 0.333 -

JC69 model (Jukes-Cantor, 1969)

http://w