Evolution of multigene families
• Orthologs - homologs by speciation
• Paralogs - homologs by gene duplication
Gene duplication and multigene families
Phylogenetic consequences of duplication, speciation, and gene conversion in gene families
Identify the evolutionary events indicated by circles
Gene duplication and polyploidization in plants
Poplar
Papaya
Arabidopsis
Retroposon-mediated duplication of IQD12 gene and morphological evolution in tomatoes
Using age distribution of gene duplication events to infer whole-genome duplications
Recent and ancient duplications in the soybean genome
Origin of new gene regulatory functions
Evidence for adaptive evolution in ribonuclease
genes of primates
Evidence for localized gene conversion & concerted evolution in primate globin gene family
Immunoglobulin Vh gene family in vertebrates
The vertebrate major histocompatibility complex (Mhc)
Human
Mouse
Chicken
Frog
DPDNDM DO DQ DRB C X E J H G F
BA BA A AB B BA BA B ABB
K FM OA E D Q T M
II
B A BB BBA B BA
B-G
B BA
B-G
B
rDNA
B B
A BBB
complementHSP70
complementHSP70
complementHSP70
TAPLMP
TAPLMP
LMP
TAP
Class II Class III Class I
I II III I
II I II I II
II I
I
A
Concerted evolution of avian Mhc genes revealed by Genetree analysis
A, species tree B, gene tree
Agph-DAB1Agph-DAB2
Agph1.1Agph1.2Agph1.3
Came.11Came1.2
Came2.1Apco1.1Apco1.2Apco1.3Apco2.1
Apco3.6Apco3.4Apco3.3Apco3.2
Apco2.3Apco2.4
Apco3.5Apco3.1Apco2.2
BLBIBLBIICHKBLBETA
BLBIIIBLBIV
BLBVXHLA-DRB1HLA-DRB7
HLA-DRB2Mus-E
HLA-DOBMaru-DAB1
HLA-DPBMus-A
HLA-DQBXela-DAB
Pore-DXB0.10 substitutions/site
88
88
96
95100
100100
81
96
XenopusPoecilia
mammals
chicken
Scrub Jay
House Finch
Red-winged Blackbird
100
birdsmammals
Phylogeny of bird and mammal Mhc class II B genes (exon3)
The DDC model of subfunctionalization, as illustrated by Hox genes
Complementary expression patterns in duplicated zebrafish engrailed genes
High rate of gene duplication(Lynch)
Using gene order to estimate times of gene duplication in yeast
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Age estimates based on Ks and orthology do not match
Paralogs clustering by species - a telltale sign of concerted evolution