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DNA variation in Ecology and Evolution

I- Organization of the genome

Maria Eugenia D’Amato

BCB 703:Scientific Methodology

Aim of the course

Understanding the underlying principles and forces that

mold genetic variation in organisms

1. DNA. Organization of the genetic information.

2. Methodological approaches to the study of genetic variation. Application of molecular markers.

3. Patterns of genetic variation and inference of underlying processes in natural populations

wild

Early Neolithic

Bronze AgePresent day

Ovis orientalis Maize

Domestication: an early understanding of transmission of characters.

Discovery of the mechanisms of inheritance

Gregor Mendel (1822- 1884)

Cross-pollination

experiments with peas

Mendelian laws of inheritance

1. Independent assortment

2. Independent segregation

3. Dominant-recessive

Parental genotype

GgWw

Parental genotype

GgWw

Meiosis

Homologous chromosomes

segregate

Sister chromatides

segregate

2 haploid cells with

duplicated genetic material

4 haploid cells

4c

2c

c

2c

2c

Mitosis

2N - Homologous chromosomes

Homologous chromosomes

duplicate information

Sister chromatides separate

2N chromosomes

2C

2C

4C

Organization of the genetic information

Plant cell Animal cell

Nuclear genetic information

Human karyotype

Condensation of chromatin

Molecular structure of DNA

5’

5’

3’

3’

Purines Pyrimidines

H-bond

Discovery of DNA molecular structure

James Watson Francis Crick

(1928- ) 1916-2004

Nobel Price 1962Rosalind Franklin

1920-1958Maurice Wilkins

1916-2004

Nobel Price 1962

Nuclear DNA: coding and non-coding sequences

• Coding DNA Genes.

Ribosomal and transfer RNA.

• Non-coding DNA

Satellite DNA

Introns

Microsatellites

Transposon-like elements

Regulatory regions

Interspersed repetitive DNA

Genes: the coding DNA

The role of the three types of gene products: mRNA, tRNA, rRNA

tRNA

Yeast 18S and 5.8 S rRNA

Genes: organization of rRNA and tRNA

Ribosomal genes

Nucleolus-organizing region in wheat

rDNA repeat unit

tRNA and rRNA genes are organized in clusters of repeats

Genes: organization of single copy DNA

Proteins and gene families

Gene families: conceptsHomologs

time

Paralogs

Identity by descent

Identity by descent

Similar function

Orthologs

Identity by descent

different function

Non-coding DNA1. Satellite DNA

ATTCATTCGATATAAAAAAACGTATATTA….

• Repeats = 100s -1000s

base pairs

• centromeric- telomeric position

Non-coding DNA2. Minisatellites and the origin of DNA fingerprinting

Locus 1 (GATTTAA)9

(GATTTAA)7

• VNTR, 10-100 bp repeats

• Mostly subtelomeric position

• Individual identification

Sir Alec Jeffreys

Non-coding DNA3. Microsatellites

(AC)n, (ACT)n, (AGTA)n, etc(AC)n, (ACT)n, (AGTA)n, etc

• STR, STR, simple sequence repeats stretches of 2-6 bpsimple sequence repeats stretches of 2-6 bp

•Allelic number is high, mutation rate highAllelic number is high, mutation rate high..

• Accurate individual identificationAccurate individual identification..

•Use in genome mapping, forensics, population studies, Use in genome mapping, forensics, population studies,

pedigree reconstruction, pedigree reconstruction, etcetc..

Mobile elements.The origin of interspersed repetitive DNA

Barbara McClintock, 1902-1992.

Nobel Price 1983

• Fragments of DNA that self-propagate within cell genome

• Cause mutations

• Challenge the central dogma

of molecular biology

Mobile elements: Retrotransposons

•RNA is copied into DNA and inserted elsewhere in the genome

•40% of human genome is composed of retroelements

•Propagation similar to retroviral infections (HIV, HTLV, etc)

•LINES

•SINES (Alu elements)

LTRs

RNA

cDNA

Target DNA

insertion

The other genome: mitochondrial DNA

• Coding for 13 proteins, 22 tRNA, 2rRNA

• Maternally inherited

• Higher evolutionary rate than nuclear DNA

• Utilized in the study of

microevolutionary processes, phylogenetics,

phylogeography, etc

The genetic code• Information coding for aminoacids is carried by codons in DNA and recognized by the anticodons in the tRNA

• The genetic code is redundant

• Different code for mtDNA, nuclear DNA, clDNA and taxonomic levels.

Genetic code: examples

Aminoacid codekrill species F G A W A G M V G T S L S L I I R A E L G H P G S

E.brevis TTC GGA GCT TGA GCT GGG ATA GTA GGT ACC TCT TTA AGT TTA ATT ATT CGA GCT GAA TTA GGA CAC CCT GGG AGAE. crystallorophias TTC GGT GCG TGA GCT GGG ATA GTG GGA ACT TCA TTA AGA CTG ATT ATC CGA GCT GAG TTA GGA CAA CCA GGA AGTE.distinguens TTT GGT GCG TGA GCA GGA ATA GTG GGT ACC TCG TTA AGA TTA ATC ATT CGA GCT GAA TTA GGG CAC CCG GGT AGAE.gibboides TTT TGT GCA TGA GCT GGG ATG GTA GGC ACC TCA TTA AGA TTA ATT ATT CGA GCT GAG CTA GGC CAC CCA GGT AGAE.hemigibba TTT GGT GCC TGA GCA GGA ATA GTG GGT ACA TCT TTA AGA CTA ATT ATT CGA GCA GAG CTA GGT CAA CCC GGT AGTE.krohni TTC GGG GCT TGA GCT GGT ATA GTA GGT ACC TCA TTA AGT TTA ATT ATT CGA GCC GAA TTA GGA CAC CCA GGA AGAElamellige TTT GGT GCT GGA GCA GGA ATA GTA GGT ACT TCA CTG AGA TTG ATT ATT CGA GCT GAG TTA GGC CAA CCC GGT AGAE.mutica TTC GGG GCT TGA GCT GGT ATA GTA GGT ACT TCA TTA AGT TTA ATT ATT CGA GCT GAT TTA GGG CAC ACC CGG AAAE.pacifica TTT GGT GCA TGA TCC GGG ATA GTT GGT ACT TCT TTA AGA TTA ATT ATT CGA GCT GAA CTA GGA CAA CCA GGT AGGE.superba TTC GGT GCA TGA GCT GGA ATA GTA GGT ACT TCA CTA AGA TTG ATT ATT CGA GCT GAG TTA GGA CAA CCA GGT AGTE.tenera TTC GGG GCT TGA GCT GGA ATA GTA GGT ACT TCA CTC AGA CTG ATT ATT CGA GCT GAA CTA GGA CAA CCT GGT AGAE.tricantha TTT GGT GCT TGA GCT GGG ATA GTA GGT ACT TCA TTA AGA TTA ATT ATC CGT GCC GAG TTA GGT CAG CCA GGT AGT

Serine is coded by

6 different codons

Alanine

4-fold degeneracy

Hystidine.

Transversion in 3rd position changes to Glutamine

2-fold degeneracy

QGlycine changes to Cysteine

Change in 1st position

0-fold degeneracy

Krill COI

The origin of genetic variation: MUTATIONS

Change in the heritable material Raw material of evolution Source of variation to be affected by

evolutionary processes

Point mutations

Gene duplication

Chromosomal rearrangements

Polyploidization

Types

Types of mutations

Synonymous

Non-synonymous

Intronic regions

Within lociWithin lociNumber of repeats in

microsatellites

Protein coding genes

Changes in RNA genes

• Single point

• Insertions

• Deletions

Point mutations

A T

C G

TransversionsTransversions

Transitions

Purine- Purine

Pyrimidine- Pyrimidine

Insertions and deletions

AAT CGA TTA TCT AGG

AAT ACG ATT ATC TAG G..

• Reading frame changes in protein-coding regions.

Asn Arg Leu Ser Arg

Asn Thr Ile Ile STOP

Single point insertion

New reading frame

Insertions and deletionsKrill ITS-1

CCCCCATCA

CCCCC-TCA

Chromosomal rearrangements

AA

BB

CC

D D

EE

F F

AA

BB

EE

D D

CC

F F

Inversion

AA

BB

CC

D D

EE

F F

GG

HH

II

JJ

KK

AA

BB

CC

D D

JJKK

GG

HH

II

D D

EEFF

Translocation

Fusion

+

Changes at the ploidy level

Ploidy: number of single sets of chromosomes in a cell or organism

Polyploidy is a common speciation processes in plants

•Tetraploids: maize, cotton, leek

•Hexaploids: wheat, oat.

•Octaploids: strawberries, sugar cane.

How often do mutations occur?Mutation rate :

the number of mutation events per gene per unit of time

Mutation rates per generation

Per base pair ~10-8 - 10-9

nuclear coding Per gene ~10-6 - 10-5

Per genome ~0.02 - 1

Microsatellites per loci 10-3 - 10-4

HVR human mtDNA 4.3 10-3

Molecular clocksCBA

• Constant mutation rate

• Inference of divergence timetime