1. Evolution of multigene families

2. Orthologs - homologs by speciation
Gene duplication and multigene families
Orthologs - homologs by speciation
Paralogs - homologs by gene duplication

3. Phylogenetic consequences of duplication, speciation, and gene conversion in gene families
C:\Figures\Chapter19\high-res\Evolution-Fig jpg

4. Identify the evolutionary events indicated by circles

5. Gene duplication and polyploidization in plants
Poplar
Papaya
Arabidopsis

6. Retroposon-mediated duplication of IQD12 gene
and morphological evolution in tomatoes

7. Using age distribution of gene duplication events to infer whole-genome duplications
C:\Figures\Chapter19\high-res\Evolution-Fig jpg

8. Recent and ancient duplications in the soybean genome

9. Origin of new gene regulatory functions

10. Evidence for adaptive evolution in ribonuclease genes of primates

11. Evidence for localized gene conversion & concerted evolution in primate globin gene family
C:\Figures\Chapter19\high-res\Evolution-Fig jpg

12. Immunoglobulin Vh gene family in vertebrates

13. The vertebrate major histocompatibility complex (Mhc)
Class II
Class III
Class I
LMP
TAP DP DN DM DO DQ DR
complement
HSP70 B C X E J A H G F
Human B A A B A A B B B A B A B B B A I II
III I K
TAP O
complement D Q T M F M
LMP A E
Mouse
HSP70 B A B B B B A B B A II II I II I II
B-G
TAP
B-G
rDNA
Chicken A B B B B B II I
HSP70
LMP
complement
Frog A B B B I

14. Concerted evolution of avian Mhc genes revealed by Genetree analysis
A, species tree
B, gene tree

15. Phylogeny of bird and mammal Mhc class II B genes (exon3)88
Agph-DAB1
Agph-DAB2
Red-winged
Blackbird
Agph1.1 96
Agph1.2
Agph1.3 88
Came.11
Came1.2
House Finch
Came2.1
100
Apco1.1
Apco1.2
Apco1.3
Apco2.1
Apco3.6
birds
Apco3.4
Apco3.3
Scrub Jay
mammals
100 95
Apco3.2
Apco2.3
Apco2.4
Apco3.5
Apco3.1
Apco2.2
BLBI
100
BLBII
100
CHKBLBETA
chicken
BLBIII
BLBIV
BLBVX
HLA-DRB1
HLA-DRB7 96
HLA-DRB2
Mus-Eb
HLA-DOB
mammals 81
Maru-DAB1
HLA-DPB
Mus-Ab
HLA-DQB
Xela-DAB
Xenopus
Pore-DXB
Poecilia
0.10 substitutions/site

16. The DDC model of subfunctionalization, as illustrated by Hox genes
C:\Figures\Chapter19\high-res\Evolution-Fig jpg

17. Complementary expression patterns in duplicated zebrafish engrailed genes

18. High rate of gene duplication (Lynch)

19. Using gene order to estimate times of gene duplication in yeast} }

20. Age estimates based on Ks and orthology do not match

21. Paralogs clustering by species - a telltale sign of concerted evolution