Course code: ZOO560

Week 3a) Phylogenetics &

b) Dynamic genomes Advanced molecular biology (ZOO560) by Rania M. H. Baleela is licensed under a

Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License.

This week content

• Molecular phylogenetics• Transposable Elements (TEs)• Retroviruses

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Molecular phylogenetics

Study evolutionary relationships between organisms or genes by a combination of

molecular biology & statistical techniques.

relationships among a group of organisms are illustrated in:a bifurcating phylogeny tree,in a phylogeny network. 3

Ancestral population/root

2 descendant populations, each with unique derived traits

4 descendant populations, each with unique derived traits

To read/understand it

Direction

recent

past

nodes represent the taxonomic units

descendantsrecent

past

Tree terminology

• Each branch in the tree = clade.

• Monophyletic = a taxon that is derived from a single

ancestral species. only legitimate cladogram type!

• Polyphyletic = a taxon whose members were derived

from 2 or >2 ancestors not common to all members.

• Paraphyletic = a taxon that excludes some members

that share a common ancestor with members included

in the taxon.

Branches & clades

• A clade is a group of organisms that are all descendents from a common ancestor=>

a clade= an ancestor + all descendents of that ancestor.

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Tree building methods

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Mathematical basis of molecular

phylogenetic reconstruction

Tree building methods

• Can be classified into 4 types: 1. distance based methods, 2. maximum parsimony methods (Nucleotides are

used directly), 3. maximum likelihood methods (Searches for the

maximum-likelihood (ML) value for the character state configurations between the sequences),

4. Bayesian methods (Incorporates other (a priori) information to infer phylogenies & the Bayes‘ theorem).

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e.g. Distance based methods

• Involves:

1. computing the evolutionary distances for all

pairs of taxa,

2. constructing a tree using a clustering

algorithm based on some functional

relationships among the distance values.

(Fast & produce a single tree making it widely used)

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e.g. of distance based methods:

1. The unweighted pair-group method with arithmetic mean (UPGMA) (the simplest),

2. Neighbor-Joining (NJ) method.

• A drawback of using UPGMA is that because of the construction of all branches having identical rates of evolution, some fast or slow evolving branches or lineages may cause errors in branching order.

• In NJ method, if some distances are large or if the evolutionary rate varies greatly among sites, then accurate estimation of distances become difficult (Li, 1997) although it is generally very robust (Page and Holmes, 2000).

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What do phylogeny shapes tell us?

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What do phylogeny shapes tell us?

NeutralPopulationgrowth(star-like phylogeny)

(Kaessman and Paabo 2002 J. Int. Medicine)

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Human mtDNA phylogeny(Cavalli-Sforza &

Feldman 2003 N

at. Genetics Suppl.)

Mitochondrial Eve was African (~200,000 years ago)

The tree is fairly star-like (short internal branches and long external branches)

Human Y chromosome tree

(Cavalli-Sforza & Feldm

an 2003 Nat. G

enetics Suppl.)

Is also fairly star-like, what does a star-like tree mean?

Gene trees within species

Genetic diversity in humans is substantially reduced compared to apes

(Kaessman and Paabo 2002 J. In

t. Medicin

e)

Aver

age

hete

rozy

gosi

ty

Timescale:how deep are the trees for sequences sampled within species?

(Garr

igan

& H

am

mer

2006 N

at.

R

ev.

Gen

et.

)

MRCA

MRCA

MRCA=> most recent common ancestor (the limit [“horizon”] for population genetics studies)

The coalescent

D

Sequences

C B A

MRCA

The most recent common ancestor

coalescent

coalescent

Time of coalescence

for n lineages

Time isrunning

backwards

n(n-1)Tn=

4Ne

Tn =

2Ne

It takes almost half of the time for the last two lineages to coalesce

b) TEs

“Without transposable elements we

would not be here & the living world

would probably look very different

from the one we know.”Labrador & Corces (2002)

What are TEs?

Transposable elements (TEs) are fragments of

DNA that can insert into new chromosomal

locations & often make duplicate copies of

themselves in the process.

Discovered in corn (Zea mays) by Barbra McClintock (1940s)

TEs (jumping genes)

• Causes mutations (e.g. corn kernel colour),

• Increases (or decreases) the DNA content,

• Associated with antibiotic resistance of

bacteria,

• Causes sterility of the Drosophila sp. Offspring

(P element),

I. TEs classes = 2 (based on mechanism of movement)

II. Transposition=movement: is a nonhomologous recombination

III. TEs can cause genetic changes

TEs

Class I: RNA (only in

eukaryotes)

Class II: DNA (in

prokaryotes &

eukaryotes)

I. Classes

Class I: Retrotransposons

• 2 groups:

A. Long terminal repeat retrotransposons

(LTRs).

B. Non-LTR retrotransposons.

“LTRs resemble retroviruses in

both their structure &

mechanism”

LTRs Gag & Pol

• Gag encodes structural proteins important

for the packaging of retrotransposon RNA,

• The pol gene encodes the enzymatic

activities needed for the retrotransposon life

cycle.

A. LTRs

• Have long terminal repeats (LTRs) (~100bp-5kb).

• Are divided into 2 groups (based on the enzymatic

activity differences):

Ty1-copia,

Ty3-gypsy.

~8% of human genome and 10% of mouse genome.

Peter J. Russell, iGenetics: Copyright © Pearson Education, Inc., publishing as Benjamin Cummings.

The Ty transposable element of yeast

1. Ty1-copia

Are abundant in species ranging from single-cell algae to bryophyte, gymnosperms & angiosperm.

gymnosperms

Magnolia (angiosperm)

Liverwort (bryophyte)

2. Ty3-gypsy

• Are widely distributed:

In plants (gymnosperms and angiosperms);

Lampreys,

Bony fishes,

Amphibians,

Reptiles,

Mammals.

“non-LTR retrotransposons

are the dominant element

type in mammalian

genomes, where they

appear to account for most

of the species-specific

differences”

B. Non-LTRs

• Are divided into 2 groups:1. Long interspersed nuclear elements (LINEs)

(e.g. L1).2. Short interspersed nuclear elements (SINEs)

(e.g. Alu).

LINEs and SINEs terminate by a simple sequence repeat, usually poly(A).

Encode 2 ORFs, which are transcribed as:

1. RNA binding protein (ORF1),

2. Endonuclease & RT activities (ORF2).

1. LINEs

2. SINEs

• Are characterized by an internal RNA pol III promoter.

• Heterogeneous group of TEs (length from 90-300bp).

• Do not have any coding capacity.• Use LINE-specified functions to transpose.

Species-specific TEs TEs varies from species to species in 2 important ways

1. By the classes of TEs present and their fractional representation in the genome,

2. By the level of TE activity.

Type of TE Human Rat Rice Arabidopsis

Chicken

Caenorhabditis

Drosophila

LINE/SINE 33.4 30.2 1.2 0.5 6.5 0.4 0.7

LTR 8.1 9.0 14.8 4.8 1.3 0.0 1.5Class II 2.8 0.8 13.0 5.1 0.8 5.3 0.7

Total (+other TEs) 44.4 40.3 35.0 10.5 8.6 6.5 3.1

Alu sequence (SINE)

Karyotype from a ♀lymphocyteChromosomes were hybridized with a probe for Alu sequences (green) and counterstained with TOPRO-3 (red).

Alu insertions & disease

Alu insertions are sometimes disruptive & can

result in inherited disorders.

Most Alu insertions act as markers that

segregate with the disease.

Disesase linked with Alu insertion include:

Breast CA, hypercholesterolemia, haemophilia

A & B, diabetes mellitus type II, …etc.

Class II: Transposons

• Most elements transpose by a ‘cut and paste’ mechanism mediated by a transposase that recognize their short terminal inverted repeated sequences (TIRs)

• Transposons structure is simple:

1. A short terminal inverted repeat (TIR) (~10–40 bp to ~200 bp).

2. A single gene encoding the transposase.

Class II elements

• Plasmid-borne transposons are responsible for the rapid evolution of drug resistance in disease causing bacteria.

Examples:1. Insertion sequences (IS) elements of E. coli,2. Ac & Ds elements of corn.3. P elements of Drosophila melanogaster.

Miniature inverted-repeat TEs (MITEs)

• MITEs are a special class of class II elements

(found in genomes at very high copy number).

• MITEs are short (< 500 bp).

• Are the most common TEs in plant genes (also

abundant in insects & fish).

“Most MITEs insert within a TA or a

TAA sequence (seem to target

very high AT-rich regions for

integration)”

mPing MITE: a case study

• Rice (Oryza sativa) genome size= ~430Mb.• Maize genome size= ~2500Mb & barley

5000Mb.• O. s. japonica is one of the 3 rice

domesticated subspecies.• mPing (a 429bp MITE) is active in japonica

rice varieties.

mPing• Temperate japonicas contain the highest number of

mPing elements (> 1000 elements!).

• Tropical japonicas contain the least (many have only

a single element).

Temperate & tropical cultivars diverged from a

common ancestor since domestication: 5000-7000

yrs ago.

mPing copy number

The dramatic difference is significant

• The 2 varietal groups are adapted to radically

different temperature & water regimes:

a) Tropical cultivars flourish in tropical & subtropical

environments,

b) Temperate cultivars were selected for productivity

in cool zones with very short growing seasons.

Justification

1. Stress activation of mPing elements during the domestication of temperate japonicas,

2. mPing preferential insertion into genic regions,

1 & 2 might have diversified these cultivars & hastened their domestication by creating new allelic combinations that might be favored by human selection.

Impact

• The impact of the bursts of mPing insertions on

genome evolution is unclear.

• 1000s of new insertions, presumably into gene

rich regions of the genome, will be the focus of

detailed analyses to determine which, if any,

contributed to adaptation and/or domestication.

Restructuring genomes!

3 ways to restructure the host genome

1. TE-mediated chromosome breakage &

rejoining (i.e. nonhomologus recombination),

2. TEs as insertional mutagens,

3. TEs and epigenetic regulation.

TEs as insertional mutagens

I. Purpurea TEs (Tip100 element is a Ac/Ds)

Variegated kernel colour in corn due to interaction between the TEs Ac & Ds

• Kernels contain 2 copies of Ds (chromosome 9 proximal to the locus of Cl)

• Cl is responsible for the purple anthocyanin pigment.

• The homologous chromosome carries an inactive mutant allele cl.

• The element Ac is present elsewhere in the genome.

• When Ac breaks chromosome 9 at the position of either Ds element, the tip ofchromosome 9 containing the dominant Cl allele is lost, and the portion of the kernel that develops from such a cell is colourless.

• The colourless patches are large or small depending on whether the breakageoccurred early or late in development.

(Weil & Wessler, 1993. The Plant Cell 5:515.]

Non-mendelian

Peter J. Russell, iGenetics: Copyright © Pearson Education, Inc., publishing as Benjamin Cummings.

Kernel color in corn & transposon effects

TEs as insertional mutagens

Defending against the spread of TEs

1. Purifying selection (i.e. negative selection,

elimination by natural selection).

2. DNA methylation (add methyl group –

CH3).

Positive impacts of TEs

• Transposition events can create advantageous mutations by mixing & matching fragments of genes and producing novel combinations that benefit the organism.

• The immunoglobulin enzyme genes (RAG1 & RAG2) originated in a transposition event several hundred million yrs ago.

• Telomerase “domestication” within eukaryotes.

What do you know about retroviruses? Revisit ZOO405