-------------------------------------------
PAUP*/MacCladeを用いた崩壊指数の同時計算
-------------------------------------------
先に送った「■PAUP統計(3)」の中で，クレードの強度を数値化する崩壊指数（decay index）について説明した．MacCladeを用いると，ある分岐図に含まれるすべてのクレードの崩壊指数を一挙に計算するPAUP*コマンドファイルを出力できるので，以下ではその手順を説明する．
テストデータとして下記の「Primate mtDNA Small」を利用する．
#NEXUS
BEGIN DATA;
DIMENSIONS NTAX=7 NCHAR=898;
FORMAT DATATYPE=DNA MISSING=? GAP=- MATCHCHAR=. INTERLEAVE ;
MATRIX
Homo_sapiens AAGCTTCACCGGCGCAGTCATTCTCATAATCGCCCACGGGCTTACATCCTCATTACTATTCTGCCTAGCAAACTCAAACTACGAACGCACTCACAGTCGC [100]
Pan ................A.T..C.................A...............T......................T..T........C......... [100]
Gorilla ..................TG....T.....T........A........A......T...............................A..C.....C... [100]
Pongo ................AC..CC.....G..T.....T..A..C........CC....G.............................A..C.....C... [100]
Hylobates ......T..A..T...AC.G.C.................A..A..C..T..CC.G...........T....................A........C... [100]
Macaca_fuscata ......TT........AC...C..T..G.....T.....A..C..C..T..CA..TAT...........C..T........T.............AC..T [100]
Lemur_catta ........TA..A...AC......A........A..T..C........A..CA..T.......T.....C.....T...........A.TC..T..C..T [100]
＜中略＞
END;
手順
●１）PAUP*を起動し，上記データファイルを実行する．最節約分岐図を計算し，ツリーファイル（Primate mtDNA Small.tre）に格納する．このツリーファイルは２個の最節約分岐図を含む．
Branch-and-bound search completed:
Score of best tree found = 697
Number of trees retained = 2
Time used = 0.02 sec
ここで得られた樹長はクレードに関する制約なしの最短樹長であり，同時に最節約分岐図に含まれるクレードｃをもつと制約付けたときの最短樹長[with-ｃ]に等しい．
●２）いま一方の分岐図「tree PAUP_1 = [&U] (1,(2,(3,(4,(5,(6,7))))));」を選択したとする．
Tree number 1 (rooted using default outgroup)
/-------------------------------------------------------------------------- Homo sapiens
|
+-------------------------------------------------------------------------- Pan
|
| /----------------------------------------------------------- Gorilla
| |
\--------------+ /-------------------------------------------- Pongo
| |
\--------------+ /------------------------------ Hylobates
| |
\-------------+ /--------------- Macaca fuscata
\--------------+
\--------------- Lemur catta
この分岐図は無根（unrooted）なので，ツリーエディターを用いて外群（Lemur＝7）での根付け（rooting）を行なう．
Outgroup status changed:
1 taxon transferred to outgroup
Total number of taxa now in outgroup = 1
Number of ingroup taxa = 6
2 trees converted from unrooted to rooted.
Tree number 1 (rooted using user-specified outgroup)
/----------- Homo sapiens
/---------+
| \----------- Pan
/----------+
| \--------------------- Gorilla
/---------+
| \-------------------------------- Pongo
/----------+
| \------------------------------------------ Hylobates
/---------+
| \----------------------------------------------------- Macaca fuscata
-----------+
\--------------------------------------------------------------- Lemur catta
●３）MacCladeを起動し，同じデータファイルをオープンし，ツリーウィンドウに移る．「Trees」メニューから「Open Tree File」を選び，上で保存した「Primate mtDNA Small.tre」を開く．そして，上の最節約分岐図を選択して，ツリー表示させる．
●４）「Σ」メニューから「Decay Index PAUP File...」を選択すると，崩壊指数計算のための系統推定オプションウィンドウが現れる．必要であればオプション設定して，実行すると「Primate mtDNA small Decay Commands」というコマンドファイルが生成される．その中身は下記の通り：
#NEXUS
begin paup;
set autoclose nowarnreset nowarntree;
[!============= clade 1, node number 13 =============]
constraint clade1.13 = (Lemur_catta,Macaca_fuscata,Hylobates,Pongo,Gorilla,(Homo_sapiens,Pan));
showconstr clade1.13;
HSearch enforce converse constraint=clade1.13;
filter best permdel;
savetrees file=clade1.13.tree;
pscore 1/scorefile='scores' append;
[!============= clade 2, node number 12 =============]
constraint clade2.12 = (Lemur_catta,Macaca_fuscata,Hylobates,Pongo,(Gorilla,Homo_sapiens,Pan));
showconstr clade2.12;
HSearch enforce converse constraint=clade2.12;
filter best permdel;
savetrees file=clade2.12.tree;
pscore 1/scorefile='scores' append;
[!============= clade 3, node number 11 =============]
constraint clade3.11 = (Lemur_catta,Macaca_fuscata,Hylobates,(Pongo,Gorilla,Homo_sapiens,Pan));
showconstr clade3.11;
HSearch enforce converse constraint=clade3.11;
filter best permdel;
savetrees file=clade3.11.tree;
pscore 1/scorefile='scores' append;
[!============= clade 4, node number 10 =============]
constraint clade4.10 = (Lemur_catta,Macaca_fuscata,(Hylobates,Pongo,Gorilla,Homo_sapiens,Pan));
showconstr clade4.10;
HSearch enforce converse constraint=clade4.10;
filter best permdel;
savetrees file=clade4.10.tree;
pscore 1/scorefile='scores' append;
end;
各コマンドは，PAUP*において指定されたクレードをもたない（converse）という樹形制約のもとで最節約分岐図を計算させる．
●５）PAUP*に戻り，上のコマンドファイル「Primate mtDNA small Decay Commands」を実行すると，各クレードごとに制約つきの最節約分岐図を計算し，結果を「Primate mtDNA Small.log」というファイルに出力する．その内容は下記の通り：
P A U P *
Version 4.0b10 for Macintosh (PPC)
This copy registered to: MINAKA Nobuhiro
NIAES, Tsukuba
(serial number = B412214)
============= clade 1, node number 13 =============
Constraint-tree "clade1.13":
/------------------------------------- Homo sapiens
/------------------------------------+
| \------------------------------------- Pan
|
+-------------------------------------------------------------------------- Gorilla
|
+-------------------------------------------------------------------------- Pongo
|
+-------------------------------------------------------------------------- Hylobates
|
+-------------------------------------------------------------------------- Macaca fuscata
|
\-------------------------------------------------------------------------- Lemur catta
Heuristic search settings:
Optimality criterion = parsimony
Character-status summary:
Of 898 total characters:
All characters are of type 'unord'
All characters have equal weight
469 characters are constant
223 variable characters are parsimony-uninformative
Number of parsimony-informative characters = 206
Gaps are treated as "missing"
Starting tree(s) obtained via stepwise addition
Addition sequence: simple (reference taxon = Homo sapiens)
Number of trees held at each step during stepwise addition = 1
Branch-swapping algorithm: tree-bisection-reconnection (TBR)
Steepest descent option not in effect
Initial 'MaxTrees' setting = 100
Branches collapsed (creating polytomies) if maximum branch length is zero
'MulTrees' option in effect
Keeping only trees NOT compatible with constraint-tree "clade1.13"
Trees are unrooted
Heuristic search completed
Total number of rearrangements tried = 62
Score of best tree(s) found = 697
Number of trees retained = 1
Time used = 0.02 sec
Tree filter retaining trees that satisfy all of the following criteria:
Best score according to current optimality criterion
Results:
Number of trees originally in memory = 1
Number of trees retained by filter = 1
Trees not retained by filter have been permanently deleted.
All trees satisfied the filtering criteria.
1 tree saved to file "clade1.13.tree"
Tree lengths written to file "scores"
Tree # 1
Length 697
============= clade 2, node number 12 =============
Constraint-tree "clade2.12":
/------------------------------------- Homo sapiens
|
/------------------------------------+------------------------------------- Pan
| |
| \------------------------------------- Gorilla
|
+-------------------------------------------------------------------------- Pongo
|
+-------------------------------------------------------------------------- Hylobates
|
+-------------------------------------------------------------------------- Macaca fuscata
|
\-------------------------------------------------------------------------- Lemur catta
Heuristic search settings:
Keeping only trees NOT compatible with constraint-tree "clade2.12"
Heuristic search completed
Total number of rearrangements tried = 56
Score of best tree(s) found = 715
Number of trees retained = 1
Time used = 0.02 sec
============= clade 3, node number 11 =============
Constraint-tree "clade3.11":
/------------------------------------- Homo sapiens
|
+------------------------------------- Pan
/------------------------------------+
| +------------------------------------- Gorilla
| |
| \------------------------------------- Pongo
|
+-------------------------------------------------------------------------- Hylobates
|
+-------------------------------------------------------------------------- Macaca fuscata
|
\-------------------------------------------------------------------------- Lemur catta
Heuristic search settings:
Keeping only trees NOT compatible with constraint-tree "clade3.11"
Heuristic search completed
Total number of rearrangements tried = 69
Score of best tree(s) found = 706
Number of trees retained = 1
Time used = 0.02 sec
============= clade 4, node number 10 =============
Constraint-tree "clade4.10":
/------------------------------------- Homo sapiens
|
+------------------------------------- Pan
|
/------------------------------------+------------------------------------- Gorilla
| |
| +------------------------------------- Pongo
| |
| \------------------------------------- Hylobates
|
+-------------------------------------------------------------------------- Macaca fuscata
|
\-------------------------------------------------------------------------- Lemur catta
Heuristic search settings:
Keeping only trees NOT compatible with constraint-tree "clade4.10"
Heuristic search completed
Total number of rearrangements tried = 69
Score of best tree(s) found = 723
Number of trees retained = 1
Time used = 0.02 sec
また上の出力ファイルと同時に，得られた分岐図は「clade***.tree」，スコア（最短樹長[without-ｃ]）は「scores」に格納される．
●６）各クレードｃの崩壊指数（最短樹長[without-ｃ]−最短樹長[with-ｃ]）は次のように計算できる：
制約clade1.13 697−697＝0
制約clade2.12 715−697＝18
制約clade3.11 706−697＝9
制約clade4.10 723−697＝26
崩壊指数の値が大きいほど，当該クレードの強度は高いと判定される．