12 11 - tbi.univie.ac.aths10d,rn10d hs10c,rn10c hf10d hf10a 0.1 rn10a hs10a bf10 fit=71.5 n=178...
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< => ?A@ BCED F> GHI J H BK K C
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1012 11 9 8 7 6 5 4 3 2 1
late
posterior anterior
early
13
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( � 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 � �!) ' ( � "
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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
?
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Hyperoartia Chondrichtyes SarcopterygiiHyperotretiCephalochordates Actinopterygii
Bichir
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� � ��� � � � �� � � � � �� � �� � � �Amphioxus
Lamprey
Sharks
Teleosts Tetrapoda
Amphioxus
Lamprey
Sharks
Teleosts Tetrapoda
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TetrapodaTeleosts
Amphioxus
Lamprey
Sharks
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� � � �� � � �� � � � �� � � � �� � � � �� � �� � � �
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
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0 2 0 " ( -
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1 2 3 M 11109 138
7
6
5
4
3
2
1
Amphioxus Gnathostomes
Lamprey
star
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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 ; -
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� ��� � � � � � � � � �� � � �� � � � �GTCAGCA CTTTAAAAAAAAAAAAGTTGGGA
ATCAGCA TTTCAGCAGAAA
TTATAGCAGCAAGTCAGCA
AAGAAAGGCGA
ATTAGATGGGT � - � % (
� 9 ' 7 � 0 - -
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� & - (� ; ) � . - (�0% 0 �
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$ % (% ' " -)% � 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�
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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
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Nonfunctionalization Neofunctionalization Subfunctionalization
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7 � ;� 9 0 " 0 ( � ) $ (7% �" ( ) � �� . 0 -
L �
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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
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+, & ' -, � � - &' � . �� � ) � * * %/10 2� � & $ 3 �/ � &54�
687 9 : $ - � '% � � - & - ( ) � -0 � ;% 0 � ' (�0 � ( & ' & & ' � � '" 6 7 9 ;L �
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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 �
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+ , & ' -, � � - & ' � 2�� ��� 2� & � > � J =D
L �
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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
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; 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 � �
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Hyperoartia Chondrichtyes SarcopterygiiHyperotretiCephalochordates Actinopterygii
Bichir
� L
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