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Available at http://planet.uwc.ac.za/nisl
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