21

12 11 - tbi.univie.ac.atHs10D,Rn10D Hs10C,Rn10C Hf10D Hf10A 0.1 Rn10A Hs10A Bf10 Fit=71.5 n=178 PmX10 PmW10a PmW10b 99.2 93.5 94.3 79.1 62.2 RnD10 HsA10 RnA10 Bf10 …

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Page 1: 12 11 - tbi.univie.ac.atHs10D,Rn10D Hs10C,Rn10C Hf10D Hf10A 0.1 Rn10A Hs10A Bf10 Fit=71.5 n=178 PmX10 PmW10a PmW10b 99.2 93.5 94.3 79.1 62.2 RnD10 HsA10 RnA10 Bf10 …

� � � � � �� � � � � � � � � � �� �� �� � � � ��

���� � � �� ��� ��� �

� �! �#" $ % & ' ( �!)+* ," - ( � (/. (�0 $ ," $ % & ' ( � )* 1 " �3254 6 0 �#7 8 �#9 * : 0% & ' " ;

< => ?A@ BCED F> GHI J H BK K C

L

Page 2: 12 11 - tbi.univie.ac.atHs10D,Rn10D Hs10C,Rn10C Hf10D Hf10A 0.1 Rn10A Hs10A Bf10 Fit=71.5 n=178 PmX10 PmW10a PmW10b 99.2 93.5 94.3 79.1 62.2 RnD10 HsA10 RnA10 Bf10 …

��� � � � � � � � � � � � � � � � � � � �� � � � �� � � � �� �

1012 11 9 8 7 6 5 4 3 2 1

late

posterior anterior

early

13

� � 9 0 " 0 - 0 " ) � 0 ' $ ' & �� ; $ (% ' " -)% �#7 ( �! " $ ' ) ( % - 7 0% ' ( �" 9

�" '% 0 9 . � ' ( % ; ) ' -) ' � 0

( � 0 ; '% 0 % 9 ' " � 8 0 � �" ) � . - (�0% - '" � ( � 0 % � 0% $ ( � 0 �% 0 �7% 0 -��

- � " & ' () � 0 - � � ( � ( � 0 �% - 0� . 0 " ( � ' � % � 0%

) " - � - ( - $� � 7 '% ' � 9 . - 9 0 " 0 - ( � ' ( '% 0 % 0 � ' (�0 � ( �% . 9 �

9 0 " & 0 � . 7 � �!) ' ( � "

Page 3: 12 11 - tbi.univie.ac.atHs10D,Rn10D Hs10C,Rn10C Hf10D Hf10A 0.1 Rn10A Hs10A Bf10 Fit=71.5 n=178 PmX10 PmW10a PmW10b 99.2 93.5 94.3 79.1 62.2 RnD10 HsA10 RnA10 Bf10 …

� � � �� � � �� � ��� � � � � �� �13 12 11 10 9 8 7 6 5 4 3 2 1

13 12 11 10 9 8 7 6 5 4 3 2 1

Changes in regulatory pattern

Length variation of intergenic regions

Gene loss

Cluster duplication

A

B

D

C

MO

US

E

?

Page 4: 12 11 - tbi.univie.ac.atHs10D,Rn10D Hs10C,Rn10C Hf10D Hf10A 0.1 Rn10A Hs10A Bf10 Fit=71.5 n=178 PmX10 PmW10a PmW10b 99.2 93.5 94.3 79.1 62.2 RnD10 HsA10 RnA10 Bf10 …

� ��� � � � � � � � � �� � � � � �� � �� �� � �� �

Hyperoartia Chondrichtyes SarcopterygiiHyperotretiCephalochordates Actinopterygii

Bichir

Page 5: 12 11 - tbi.univie.ac.atHs10D,Rn10D Hs10C,Rn10C Hf10D Hf10A 0.1 Rn10A Hs10A Bf10 Fit=71.5 n=178 PmX10 PmW10a PmW10b 99.2 93.5 94.3 79.1 62.2 RnD10 HsA10 RnA10 Bf10 …

� � ��� � � � �� � � � � �� � �� � � �Amphioxus

Lamprey

Sharks

Teleosts Tetrapoda

Amphioxus

Lamprey

Sharks

Teleosts Tetrapoda

��� � � � � �� �� � �� ��� � � ��� � ��� � � � � �� �� � �� ��� � � ��� � �

TetrapodaTeleosts

Amphioxus

Lamprey

Sharks

� � � � � �� �� � � ��� � � ��� �

Page 6: 12 11 - tbi.univie.ac.atHs10D,Rn10D Hs10C,Rn10C Hf10D Hf10A 0.1 Rn10A Hs10A Bf10 Fit=71.5 n=178 PmX10 PmW10a PmW10b 99.2 93.5 94.3 79.1 62.2 RnD10 HsA10 RnA10 Bf10 …

� � � �� � � �� � � � �� � � � �� � � � �� � �� � � �

Hs10D,Rn10D

Hs10C,Rn10C

Hf10D

Hf10A

0.1

Rn10A

Hs10A

Bf10

Fit=71.5 n=178

PmX10 PmW10aPmW10b

99.2

93.5

94.3 79.1

62.2

RnD10

HsA10

RnA10

Bf10

Pmw10a

PmW10b

PmX10

HfA10

RnC10

HfD10

HsD10

HsC10

100.0

80.069.0100.0

90.0

96.0

86.0

100.037.0

Hox10

� � ;� 9 0 " 0 ( � ) % 0 � ' ( � " - � �#7 �#" � �!) ' (�0 �" � 0 7 0 " � 0 " ( � . 7 � �!) ' ( �! "

0 2 0 " ( -

Page 7: 12 11 - tbi.univie.ac.atHs10D,Rn10D Hs10C,Rn10C Hf10D Hf10A 0.1 Rn10A Hs10A Bf10 Fit=71.5 n=178 PmX10 PmW10a PmW10b 99.2 93.5 94.3 79.1 62.2 RnD10 HsA10 RnA10 Bf10 …

� �� � � � � � � � � � �� � � � �

1 2 3 M 11109 138

7

6

5

4

3

2

1

Amphioxus Gnathostomes

Lamprey

star

� � � � � ��� � � ��� � �� � �� � �� � �� � � �� � � �� � � � �� � � �� � � �� � �� � �� � � �

� � � � ��� � �� � � � � � � � �� � � � � � � �� �� � � � �� � � � � � ��� � � �

Page 8: 12 11 - tbi.univie.ac.atHs10D,Rn10D Hs10C,Rn10C Hf10D Hf10A 0.1 Rn10A Hs10A Bf10 Fit=71.5 n=178 PmX10 PmW10a PmW10b 99.2 93.5 94.3 79.1 62.2 RnD10 HsA10 RnA10 Bf10 …

� � ;7 ( � 0 - � - $ % ( � 0 � � �� . - (�0% �2 � . ( �! " �#" � '% � ; �0% (�0 �% ' (�0 -

Hyperoartia Chondrichtyes SarcopterygiiHyperotretiCephalochordates Actinopterygii

Bichir

6 ' & 7% 0 ; � � 9 0 " 0 - '% 0 & . ) � & % 0 � 0% �2 0 �

�% � ' �� ; ' � & - ( ) & 7 � 0 (�0 % 0 - � . ( �! " $% 0 � . " � '" ) ; ' $ (�0% �% - (

� . 7 � �!) ' ( �! " �#" 6 ' & 7 % 0 ; -

Page 9: 12 11 - tbi.univie.ac.atHs10D,Rn10D Hs10C,Rn10C Hf10D Hf10A 0.1 Rn10A Hs10A Bf10 Fit=71.5 n=178 PmX10 PmW10a PmW10b 99.2 93.5 94.3 79.1 62.2 RnD10 HsA10 RnA10 Bf10 …

� ��� � � � � � � � � �� � � �� � � � �GTCAGCA CTTTAAAAAAAAAAAAGTTGGGA

ATCAGCA TTTCAGCAGAAA

TTATAGCAGCAAGTCAGCA

AAGAAAGGCGA

ATTAGATGGGT � - � % (

� 9 ' 7 � 0 - -

� � �#9 � � ; ) " - 0% 2 0 �

� & - (� ; ) � . - (�0% 0 �

� � ;� 9 0 " 0 ( �!) � (7 % �" (

� �� �� �� � � �� � � �� ��� � � � � � � � � � � � � � �� � � � � �� � �� � � � �� � �� � � �� � ��

� � � � � ��� � � � � � �� � ��� � � � �� � � � � � � �� �� � � � � � � �� � � � � �� � � � �� � � � � ��

Page 10: 12 11 - tbi.univie.ac.atHs10D,Rn10D Hs10C,Rn10C Hf10D Hf10A 0.1 Rn10A Hs10A Bf10 Fit=71.5 n=178 PmX10 PmW10a PmW10b 99.2 93.5 94.3 79.1 62.2 RnD10 HsA10 RnA10 Bf10 …

� � � ���� �� � � �� � � � � � �

� ��� �% 0 9 . � ' ( % ; -0 � . 0 " ) 0

0 " � '" ) 0% 0 � 0 & 0 " ( -

� � � � � � � �7 � " 9

) " ( ' �" & . � ( �#7 � 0 - � % ( - 0� . 0 " ) 0 � -7 0 ) � �#) � �" � �#" 9 & ( � $ -

$ % (% ' " -)% � 7 ( �! " $ ' ) ( % -

) '% % ; . ( '% 0 9 . � ' ( % ; $. " ) ( �! "

( � ' ( � - ' -. � $. " ) ( �! " $ ' ) & 7 � 0 �% 0 9 . � ' ( % ; 7 ' ( (�0% "

0 �0 ) . (�0 - ( � � - - . � $. " ) ( �! " � � 0 " � �" �0 � ( '% 0 7 % (�0% 9 0 " 0

& ' ; � 0 - 0 7 '% ' (�0 � $% & ( � 0 ( '% 9 0 ( 9 0 " 0 � ; - 0 2 0% ' � � � � � �L�

Page 11: 12 11 - tbi.univie.ac.atHs10D,Rn10D Hs10C,Rn10C Hf10D Hf10A 0.1 Rn10A Hs10A Bf10 Fit=71.5 n=178 PmX10 PmW10a PmW10b 99.2 93.5 94.3 79.1 62.2 RnD10 HsA10 RnA10 Bf10 …

� � � � � � �� � � � �� � � �

A

2−32−3

4−54−56

11’2’3’4’5’5’

BLASTZ

A B

removepoorly conservedregions

remove

regionslow entropy

2−3

C

C1 C2

1’

1

5’4’3’2’

4−5 6

L L

Page 12: 12 11 - tbi.univie.ac.atHs10D,Rn10D Hs10C,Rn10C Hf10D Hf10A 0.1 Rn10A Hs10A Bf10 Fit=71.5 n=178 PmX10 PmW10a PmW10b 99.2 93.5 94.3 79.1 62.2 RnD10 HsA10 RnA10 Bf10 …

�� � � �� � � � ��� � � � � �� � � � �� � � � � � � �� � � � �� �

Nonfunctionalization Neofunctionalization Subfunctionalization

L �

Page 13: 12 11 - tbi.univie.ac.atHs10D,Rn10D Hs10C,Rn10C Hf10D Hf10A 0.1 Rn10A Hs10A Bf10 Fit=71.5 n=178 PmX10 PmW10a PmW10b 99.2 93.5 94.3 79.1 62.2 RnD10 HsA10 RnA10 Bf10 …

� � � ���� �� � � �� � �� � � � � � � � � � � � �� �

�� �� �� � � � �� � � � � � � � � � � � �� � � � � �� � � � �� �� �� � �� � � �

� � �� � � � �� �� � � � � � �� � �� � � �� � � �� ��� � �

� �� � �� � � ��� � �� � �� � � � �� � �� �� � � � �� � �� � � �� �

L �

Page 14: 12 11 - tbi.univie.ac.atHs10D,Rn10D Hs10C,Rn10C Hf10D Hf10A 0.1 Rn10A Hs10A Bf10 Fit=71.5 n=178 PmX10 PmW10a PmW10b 99.2 93.5 94.3 79.1 62.2 RnD10 HsA10 RnA10 Bf10 …

� � � � � � �� � � � � � � �� � � � � � � �� � � �� �

7 0% ) 0 " ( ' 9 0 - $ 7% (�0 �" - 0� . 0 " ) 0 � � 0 " ( � ( � 0 -

� � � � �� ��� �� �� � � �� � �

� � � �� � �

� � � � � � � �

� � � � � �� � � � �

� � � � � � � � � � � � �

7 � ;� 9 0 " 0 ( � ) $ (7% �" ( ) � �� . 0 -

L �

Page 15: 12 11 - tbi.univie.ac.atHs10D,Rn10D Hs10C,Rn10C Hf10D Hf10A 0.1 Rn10A Hs10A Bf10 Fit=71.5 n=178 PmX10 PmW10a PmW10b 99.2 93.5 94.3 79.1 62.2 RnD10 HsA10 RnA10 Bf10 …

� � � � � � �� � � � � � � �� � � � � � � �� � � �� �

�� �� �� �� � �� �� � � �� �

� �� � � �� � � �� � � �� � � � � � � � � � � �� � � �� �

� �� � �� � �

� � � � � � �� � � � � � � �� � � ��

� �� � �� �� �� � �� � � � �� � � � � � � � � � � � �� � �

10

HfN

HsD

HsB HsC

100

100

100

100 100

99.9

77 99.1

100

100HsA

HfM

0.01 RnC

HfM HfN

RnDRnA

RnB

100

100

100

100

100100

95.8

78.4100100

99.9

100

��� � � �� � �� !#" $" % &' $ ( ��� � � �) � ' !* $" % &' $ (

+, & ' -, � � - &' � . �� � ) � * * %/10 2� � & $ 3 �/ � &54�

687 9 : $ - � '% � � - & - ( ) � -0 � ;% 0 � ' (�0 � ( & ' & & ' � � '" 6 7 9 ;L �

Page 16: 12 11 - tbi.univie.ac.atHs10D,Rn10D Hs10C,Rn10C Hf10D Hf10A 0.1 Rn10A Hs10A Bf10 Fit=71.5 n=178 PmX10 PmW10a PmW10b 99.2 93.5 94.3 79.1 62.2 RnD10 HsA10 RnA10 Bf10 …

� � � �� � � �� � � � � �� � � � � � � � � � � �13 12 11 10 9 8 7 6 5 4 3 2 1

13 12 11 10 9 8 7 6 5 4 3 2 1

13 12 11 10 9 8 7 6 5 4 3 2 1

13 12 11 10 9 8 7 6 5 4 3 2 1

13 12 11 10 9 8 7 6 5 4 3 2 1

loss of 9 genesloss of one cluster?

tetrapods

loss of 4 genesloss of 3 genesDuplication

Ancient

fish

Hypotheticalancestor

Zebrafish

ray−finned

Hypotheticalteleost ancestor

loss of 3 genesloss of 2 genes

AaAbBa

AaAb

DCbCaBbBa

DCa

Bb

Pufferfish

L �

Page 17: 12 11 - tbi.univie.ac.atHs10D,Rn10D Hs10C,Rn10C Hf10D Hf10A 0.1 Rn10A Hs10A Bf10 Fit=71.5 n=178 PmX10 PmW10a PmW10b 99.2 93.5 94.3 79.1 62.2 RnD10 HsA10 RnA10 Bf10 …

� � � � � ��� � � � � � �� �

+ , & ' -, � � - & ' � 2�� ��� 2� & � > � J =D

L �

Page 18: 12 11 - tbi.univie.ac.atHs10D,Rn10D Hs10C,Rn10C Hf10D Hf10A 0.1 Rn10A Hs10A Bf10 Fit=71.5 n=178 PmX10 PmW10a PmW10b 99.2 93.5 94.3 79.1 62.2 RnD10 HsA10 RnA10 Bf10 …

� � �� � � � � � � � � �� � � � � �� �� � � � � �� � �� � � � �� �

Shark Human

Bichir

Teleost fishes

10

1610

21

1719

1616

9

15

11

48

1

2

1

1

ntax=7 nchar=188 const=6 nonparsi=55 −psplits

HfMHsA

PsA

DrAa

FuAa

FuAb

DrAb

� �#9 � 0% (�0 � 0 - ( - . " � 0% �

�0 " ( ' " ' � � � ( �! " ' � � �

) � . - (�0% � . 7 � �!) ' ( �! "

� � . 7 � �!) ' ( �! " �#" � �!) � �%

� �#9 " � � ) '" ( (�0 � 0 - (�

-7 0 ) � � ) $ (7% �" ( -

' �% 0 ' � ; 0 � � - ( �" ( � 0

� � ) � �%

L �

Page 19: 12 11 - tbi.univie.ac.atHs10D,Rn10D Hs10C,Rn10C Hf10D Hf10A 0.1 Rn10A Hs10A Bf10 Fit=71.5 n=178 PmX10 PmW10a PmW10b 99.2 93.5 94.3 79.1 62.2 RnD10 HsA10 RnA10 Bf10 …

� �� � �� � � � � � �� �� � � �� � � � � � � �� � � � �� � � � �� � �

�� � 0 � � % � (7% �" ( �2 � . ( �! "�

�� � $ (7 % �#" ( - '% 0 � - ( � � ( � ( � 0 �% ' - - ) � ' (�0 � 9 0 " 0

�� � - ( ) � ' - ( �!) % 0 - � . ( �! " - $ % % 0 ( ' �" 0 � � . 7 � �!) ' (�0 -

� � � $ (7 % �#" ( - '% 0 � - ( � $% 0 9 . � ' ( �" 9 9 0 " 0 � - � - (

�� � " " � - (% . ) (/.% ' � ) " (% � � . ( �! " -

� � �� � �� � �� �� � �� ��

� � � � �� � � � � �

�� ��� �

� �� � � � � �� ��� �� �� � � � �� �� � �

� !� (� � � �/ ' / ' & , �� ' / , � � / / $ & �,! � $! % � $' / �"$# � � �

� �� ! ' &, , � � / / $ - &' � L $' , �* / � "� �� % , � $%� � �

� �� ! ' &, , � /& ' & ! ' � / / $ & / ' & �/ / ' -, � �'� � �

� �� ! ' &, , � � / / $ � �, � -� &! � � � / / & $ �/ � � %� ' / * !� , & ! � $/( '*) L (

+ � 0 7 '% ' & 0 (�0% � & 0 ' -.% 0 - , �.- / �.-0 � �132 154 6- 77 2 6 ' " �98 /8 : 1 �7 2

2 ;2 �1 �4

L

Page 20: 12 11 - tbi.univie.ac.atHs10D,Rn10D Hs10C,Rn10C Hf10D Hf10A 0.1 Rn10A Hs10A Bf10 Fit=71.5 n=178 PmX10 PmW10a PmW10b 99.2 93.5 94.3 79.1 62.2 RnD10 HsA10 RnA10 Bf10 …

� � � � � � � � � � �� � � � � � ��� � � �� � � �� �

�� . - (�0% �9 0 " 0 - � �� � � � � � � �� � � : � �� ' ( ' - (% . ) (/.% ' �

; 6 6 7 9 �8 � �4 � � �4 � � �4 � � �4 � �

; 6 6 7 9 � , � �4 � � �4 �� �4 �� �4 � �

; 6 6 7 9 � � � �4 � � �4 � � �4 � � �4 � �

� 6 687 9 �8 � �4 � � �4 � � �4 � � �4 � �

� 6 687 9 � , � � 4 � � �4 � � �4 � � �4 � �

� 6 687 9 � � � �4 �� �4 � � �4 �� �4 � �

," )% 0 ' - 0 � ' � ' 7 ( �2 0 0 2 � . ( �! " �" ( � 0 �. 9 . � � � � ) � . - (�0% ��

Page 21: 12 11 - tbi.univie.ac.atHs10D,Rn10D Hs10C,Rn10C Hf10D Hf10A 0.1 Rn10A Hs10A Bf10 Fit=71.5 n=178 PmX10 PmW10a PmW10b 99.2 93.5 94.3 79.1 62.2 RnD10 HsA10 RnA10 Bf10 …

� � � � � � �

Hyperoartia Chondrichtyes SarcopterygiiHyperotretiCephalochordates Actinopterygii

Bichir

� L