Data Scoring and Analysis Practical Lecture Doc. Ruslan Kalendar
Visit Program to Egypt: FCRI-Institute of Field Crops Research, ARC, Egypt; 30.03 - 04.04.2014
Genetic diversity Genetic diversity is refers to the total number of genetic characteristics in the genetic makeup of a species. It is distinguished from genetic variability, which describes the tendency of genetic characteristics to vary.
Dogs of the World.
Genetic diversity of sorghum (left) and millet (right) illustrates the potential of plant breeding.
Schematic representation of a population bottleneck and its effect on a neutral gene and a selected gene
Schematic representation of a population bottleneck and its effect on a neutral gene and a selected gene. In Upper, shaded circles represent genetic diversity. The bottleneck reduces diversity in neutral genes, but selection decreases diversity beyond that caused by the bottleneck alone. Lower illustrates sequence haplotypes of these two hypothetical genes. The neutral gene lost several haplotypes through the domestication bottleneck, but the selected gene is left with only one haplotype containing the selected site.
Polymorphism and information Vest is maximal variation for n samples: đ?‘˝đ?’†đ?’”đ?’• = đ?&#x;?đ?’? − đ?&#x;? n = 4; Vmax = 12
A n = 3; Vmax = 6
A n = 2; Vmax = 2
A
B
B
C
B
C
D
Polymorphism and information Theoretically, estimate: n = 3; Vest = 6
A
B
C
Observed, reality: n = 3; Vobs = 4
A
B
C
I=
đ?‘˝đ?’?đ?’ƒđ?’” đ?‘˝đ?’†đ?’”đ?’•
đ?&#x;? đ?&#x;‘
= = 67%
50% polymorphic bands repeated
Polymorphism and information Theoretically: n = 8; Vest = 254 Observed: Vobs = 32
1 2 3 4 5 6 7 8
I=
đ?‘˝đ?’?đ?’ƒđ?’” đ?‘˝đ?’†đ?’”đ?’•
=
đ?&#x;‘đ?&#x;? đ?&#x;?đ?&#x;“đ?&#x;’
= 12.5%
3% (1/33) polymorphic bands repeated
Consensus tree and population substructure estimated from DNA markers
Genetic and transcriptome diversity
MEGA 6.0 for Phylogeny http://www.megasoftware.net/
MEGA 6.0 for Phylogeny
Converting gel electrophoresis data to digital as text: 1 – is band (1 or “A”) 0 – is no band (0 or “C”)
MEGA 6.0 for Phylogeny Converting gel electrophoresis data to digital as text: 1 – is band (1 or “A”) 0 – is no band (0 or “C”)
MEGA 6.0 for Phylogeny Converting gel electrophoresis data to digital as text: 1 – is band (1 or “A”) 0 – is no band (0 or “C”)
MEGA 6.0 for Phylogeny Converting gel electrophoresis data to digital as text: 1 – is band (1 or “A”) 0 – is no band (0 or “C”)
MEGA 6.0 for Phylogeny Converting gel electrophoresis data to digital as text: 1 – is band (1 or “A”) 0 – is no band (0 or “C”)
MEGA 6.0 for Phylogeny Loading MEGA file to program and apply Phylogeny: Minimum-Evolution Tree, for example:
MEGA 6.0 for Phylogeny MEGA construct Minimum-Evolution Tree: