Doug RaifordLesson 8

04/22/23 1Phylogenetics

Definition study of evolutionary relatedness

among various groups of organisms

All life evolved from a single-celled organism Cenancestor

Traditional techniques: Relied upon phenotypical

(observable characteristic or trait of an organism) differences

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Understanding of the origins of life Who we are? From whence did we

come? If can understand biological systems

and how they came to be… Perhaps can predict ▪ Reaction to changing environments▪ Reaction to drugs (similar organisms will

probably react similarly) What our future holds

How we will evolve04/22/23 Phylogenetics 3

Why study phylogenetics?

DNA similar in related organisms

How would we go about measuring DNA similarity? Must align first Must use homologous

genes/proteins Just count the

locations where different

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Where do genes and proteins come into the

picture?

Different rates of evolutionary change Organisms: different environmental factors Proteins: under different selective

pressures Regions of proteins: ▪ Interiors, tightly packed,

hydrophobic ▪ External loops, less important for

structural integrity

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Gap of virtually any length could happen in single event

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Buchnera/1-356 MENL----------------DKKKALDRVIMEIEKAYGKGAIMKLG-EMALactobacillus/1-363 MAKD----------------EKKAALDAALKKIEKNFGKGAVMRMG-EKAGeobacter/1-338 MTQ-----------------EREKAIELALSQIEKQFGKGAIMRLGADEAActinobacillus/1-376 MAADNKKAQKNTVTKQIDPEQKEKALAAALAQIEKQFGKGSIMRLG-DTQSalmonella/1-353 MAID---------------ENKQKALAAALGQIEKQFGKGSIMRLG-EDR

DNA material doesn’t stay put

Bacteria reproduce asexually But plasmids…

Also, viruses… Finally, take-up… Not surprising…

Meiosis, mitosis, translocating genes

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Horizontal gene transfer (HGT)More of a bush (especially at the

base)

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Need a gene that is in all organisms (ubiquitous)

The gene should be evolutionarily stable (very similar in all organisms)

Should compare regions of the gene that are highly conserved

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Circular DNA found in organelles outside the nucleus

No crossover: passed down in the egg

Exact copy from female parent

Mitochondria are the powerhouse of the cell Break-down food, release energy

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Dominant molecule in microbial ribosomes (translation)

Ubiquitous, same role in every organism

Highly conserved

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Multiple sequence alignmentsClustalWEasily identify regions that are highly

conserved

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atgccgca-actgccgcaggagatcaggactttcatgaatatcatcatgcgtggga-ttcagacctccatacgtgccccaggagatctggactttcacc---tggatcatgcgaccgtacctact-atgg-t-cgtgccgcaggagatcaggactttca-gt--g-aatcatctgg-cgc--c-aat--tcgt-ac-tgccccaggagatctggactttcaaa---ca-atcatgcgcc-g-tc-tataattccgtacgtgccgcaggagatcaggactttcag-t--a-tatcatctgtc-ggc--tag

Sound familiar? What tools do we already have?

Used 16S to investigate tree of lifeDiscovered three domains (not two)

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Build cladogram or phylogram: A tree diagram used to illustrate phylogenetic

relationships Length of each branch = number of

sequence changes that occurred (except in cladogram where length not used)

The amount of time usually not known

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Sometimes utilize a dendrogram

Each sequence taxon (plural: taxa)Each subtree = clade (long “a”)Tree length

Sum of all the branch lengths

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Sometimes utilize a dendrogram

Assumption of a uniform rate of mutation in the tree branches

Is this reasonable?Allows some conclusions to be drawn

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DistanceMaximum parsimonyMaximum likelihood

Main packages PAUP PHYLIP

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Unweighted pair group method with arithmetic mean (UPGMA) One of the first and

simplest distance methods

Basically hierarchical clustering

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Need all pair-wise distancesHow measure distance?Want to measure the number of

mutations that occurred since the species split

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Organism A Organism B

2 2Distance between

organism A and B is 4

Distance between

organism A and B is 4

Count up the number of columns where there are differences and divide by

the length of the sequences: the

probability of a mutation at a given location

Count up the number of columns where there are differences and divide by

the length of the sequences: the

probability of a mutation at a given location

A B C D

A 0 6 6 6

B 0 4 4

C 0 2

D 0

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All pair-wise distances

11

1

2

1

3

A B C D

Find closestPlace next to each

other in tree

Find average distanceto rest

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A B C D

A 0 6 6 6

B 0 4 4

C 0 2

D 0

11

1

2

1

3

A B C D

A B CD

A 0 6 6

B 0 4

CD

0

Find the next closestPlace next to each

other in tree

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11

1

2

1

3

A B C D

A B CD

A 0 6 6

B 0 4

CD

0

A BCD

A 0 6

BCD

0

A B C D

A 0 6 6 7

B 0 4 5

C 0 3

D 0

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New distance matrix

A B C D

C and D still closest So start tree with these two Find average distance

to rest

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A B C D

A B CD

A 0 6 6.5

B 0 4.5

CD

0

A B C D

A 0 6 6 7

B 0 4 5

C 0 3

D 0

(A,(B,(C,D)))

((A,B),(C,D))

Binary trees04/22/23 Phylogenetics 25

A B C D

A B C D

Find the next closestPlace next to each

other in tree (collapse B with CD)

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A B C D

A BCD

A 0 6.25

BCD

0

A B CD

A 0 6 6.5

B 0 4.5

CD

0

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