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

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

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

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

Ambystoma Linkage Map 5251 cM (~93%)

Salamander Genome….BIG! Human Salamander Reptile

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 2.7 20 20 1361 0.5 1000 0.73 68.1 Rat 2.6 21 33 1749 0.7 1050 0.94 53.0 Human 3.0 23 46 3615 1.2 1150 0.64 78.6 Chicken 1.2 38 44 3800 3.2 1900 0.58 86.4 Ambystoma 30.0 14 28 5152 0.2 700 0.27 184.0

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

Number of Conserved Syntenies Comparison #a #b Human 69 28 Mouse 82 24 Chicken 52 17 Rat 58 14 #a based on 2 or more orthologues #b based on 4 or more orthologues

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

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

Candidate Genes sex Cross-Referencing melanoid white met

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

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).

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

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

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

Creation of a processed pseudogene.

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

Polyploidization : complete genome duplication