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