1. Chromosome-level Mutation
A B C D E F
G H I J K L M
A B C D E F G
D E F G H I J K L M
I H G J K L M
A B C
inversion
translocation

2. Processes of Gene Rearrangement
A B C D C D E
duplication
A B C D
B A C D E
terminal deletion
pericentric inversion
A B C D E
Eliminate
A D C B E
paracentric inversion
A B C E
A B C D E
interstitial deletion
breakage

3. Exchange of Genetic Information
A B C D E F
W X Y Z
Translocation
Centric fusion
A B C X Y Z
Z Y X C D E F
W D E F

4. Terms for Comparing Gene Order
Synteny : Occurence of two or more genes on a
chromosome.
Conserved Synteny : Synteny of orthologous genes
between species.

5. Ambystoma Linkage Map
5251 cM (~93%)

6. Salamander Genome….BIG!
Human
Salamander
Reptile

7. Genome-wide recombination is not proportional
to chromosome # in Ambystoma
genome Chom. Chrom obligatory proportion
size (Gbp) # Arms Map (cM) cM / Mb (A# * 50cM) obligatory cM/arm
Mouse
Rat
Human
Chicken
Ambystoma

8. Chromosomal Distribution of Orthologous Genes
Salamander
Salamander
MOUSE
HUMAN
N = 338
Refseq database
size = 16,800
N = 402
Refseq database
size = 21,098
CHICKEN
RAT
N = 338
Refseq database
size = 11,348
N = 236
Refseq database
size = 12,427

9. Number of Conserved Syntenies
Comparison #a #b
Human
Mouse
Chicken
Rat
#a based on 2 or more orthologues
#b based on 4 or more orthologues

10. Spatial Distribution of Orthologous Loci : Segmental Homology
(1-23)
Lg1
Lg2
Lg3
Lg14
white
met
melanoid
Salamander Genome

11. Conserved Synteny based upon 3 or more genesH I K E N G O M
(1-23)
Lg1
Lg2
Lg3
Lg14
white
met
melanoid
Salamander Genome

12. Candidate Genes
sex
Cross-Referencing
melanoid
white
met

13. Addition (duplication) (tandom duplications)
Primary Mechanism of Duplication : Unequal Crossing Over
Crossing over
Between Daughter
Strands
Addition (duplication)
Deletion
(tandom duplications)
Crossing over
Between Daughter
Strands
Addition
Deletion

14. Members of a gene family evolve in concert.
Concerted Evolution
Members of a gene family evolve in concert.
Mutations are transferred among members of the family (homogenization)
Mutations are spread to all individuals in the population (fixation).

15. Fate of Duplicated Loci
Both copies retain original function
e.g. rRNA genes
(2) Gain new function through mutation and selection
e.g. globin genes
(3) Become functionless pseudogenes
e.g globin genes

16. a and b are said to be paralogous genes
Duplication TD a b
Speciation TS a b a b
Species 1
Species 2
a and b are said to be paralogous genes
aspecies1 and aspecies2 are said to be orthologous genes

17. Time of duplication may be estimated by observing the
phylogenetic distribution of genes
All vertebrates but jawless fish have a and b
H1: Two independent gene losses
H2: Duplication

18. Creation of a processed pseudogene.

19. Fate of a Processed Pseudogene
Functional
Jingwei (see your book, p. 464)
Human phosphoglycerate kinase (PGK)
Preproinsulin in some mammals
Nonfunctional
Examples are known for all gene types

20. Polyploidization : complete genome duplication