昆虫体系学8 - 北海道大学lab.agr.hokudai.ac.jp/.../systent.slide8.pdf画び ょうが...
TRANSCRIPT
昆虫体系学8 系統推定の方法論 系統樹の評価
吉澤和徳
ACGTACGTAGACACACTCTCCTACGTTGACGTACGT-GA-A-AC-CT-C-ACGTTG
or
ACGTACGTAGACACACTCTCCTACGTTGACGTACGTGAA-A----C-CTCACGTTG
ACGTACGTAGACACACTCTCCTACGTTGACGTACGTGAAACCTCACGTTG
１２
１２
１２
better?
Stem Loop
Better :-)
Worse :-(
ACGTAG
TGCATC
||
||
||
ACGTGA
TGCACT
||
||
||
１２
１２
StemStemLoopLoopStemStemACGTACGTAGACACACTCTCCTACGTTGACGTACGT-GA-A-AC-CT-C-ACGTTG
or
ACGTACGTAGACACACTCTCCTACGTTGACGTACGTGAA-A----C-CTCACGTTG
Jukes-Cantor モデル
木村の２パラメータ
長谷川-岸野ー矢野モデル
AAC
AC
C→A: 確率 α, C→C: 確率 1-α A→C: 確率 β, A→A: 確率 1-β
C→A: 確率 α, C→C: 確率 1-α A→C: 確率 β, A→A: 確率 1-β
α×(1-α)×(1-β)^2
AAC
AC
C→C
C→AA→AA→A
←確率の積「尤度」
AAC
A
C→A: 確率 α, C→C: 確率 1-α A→C: 確率 β, A→A: 確率 1-β
CC→C
C→CC→AC→A
α^2×(1-α)^2α×(1-α)×(1-β)^2
AAC
C→A: 確率 α, C→C: 確率 1-α A→C: 確率 β, A→A: 確率 1-β
＜もし
ならば，下を採用
AC
C→C
C→CC→AC→AA
CC→C
C→AA→AA→A
α^2×(1-α)^2α×(1-α)×(1-β)^2
以下のデータセットを仮定する one AAAAACCCCGGGGTTTTtwo CACGTACGTACGTACGTthree AAAAAAAAAAAAAAAAAfour CAAAAAAAAAAAAAAAA
Cha. 7, 12, 17 Cha. 1
子供 乳 嘴 毛
魚 卵 × なし なし
鳥 卵 × あり なし
カモノハシ 卵 ○ あり あり
哺乳類 仔 ○ なし あり
祖先形質 派生形質
外 群
トカゲ
哺乳類カモノハシ鳥
哺乳類カモノハシ鳥
鱗→毛 x 2 餌→乳 x 2
口→嘴
口→嘴 x 2
鱗→毛 餌→乳
Total 4 steps
Total 5 steps
トカゲ
O E D C B A
Hemipsocus sp.228Hemipsocus sp.196
Psilopsocus malayanusLichenomima sp.
Myopsocus sp.
Kaindipsocus sp.Amphi. jezoensis
Amphigerontia sp.Blaste sp.
Blaste quietaBlastopsocus lithinis
Blastopsocus sp.Camelopsocus monticola
Loensia variegataLoensia moesta
Loensia conspersaOreopsocus buholzei
Genus sp.Ptycta sp.
Copostigma sp.Ptycta johnsoni
Atlantopsocus personatusSymbiopsocus hastatus
Steleops sp.Psocomesites sp.
Steleops elegansPsocidus sp.
Indiopsocus bisignatusIndiopsocus sp.
Trichadenotecnum circularoidesTrichadenotecnum sp.
Trichadenotecnum quaesitumTrichadenotecnum desolatum
Hyalopsocus morioAtropsocus atratus
Hyalopsocus floridensisHyalopsocus sp.
Psocus bipunctatusPsocus crosbyi
Atricha. quadripunctatusAtrichadenotecnum sp.
Sigmatoneura kolbeiPodopterocus sp.
Metylophorus purusMetylophorus novaescotiae
Thyrsophorus sp.Cerastipsocus trifasciatus
Longivalvus nubilusPsococerastis sp.
Clematiscena sp.
0.05 substitutions/site
"Ptyctini"
Psocini
Atrichadenotecnini
Sigmatoneurini
Metylophorini
Thyrsophorini
Blastini
Amphigerontini
Kaindipsocini
Ptyctini
Psocini
Cerastipsocini
Metylophorini
THYRSOPHORINAE
Cerastipsocini
AM
PH
IGE
RO
NT
INA
EP
SO
CIN
AE
Lienhard & Smithers (2002)Present study
AM
PH
IGE
RO
NT
INA
EP
SO
CIN
AE
100/100/100
100/100/99
100/100/100
100/100/100
100/100/94
100/100/100
100/100/98
100/</<
100/100/100
100/55/60
100/100/100
100/97/55
100/100/100
100/91/89
100/97/98
100/</<
100/</<
100/100/100
100/100/100
100/100/97
100/100/100
100/99/84
100/99/82 100/100/100
99/</<
99/57/<
100/100/100
99/85/89
98/93/61
96/</<
95/</<
90/</<
94/51/58
92/</74
80/56/85
63/70/<
85/62/<
71/</63
Hemipsocus sp.228Hemipsocus sp.196
Psilopsocus malayanusLichenomima sp.
Myopsocus sp.
Kaindipsocus sp.Amphi. jezoensis
Amphigerontia sp.Blaste sp.
Blaste quietaBlastopsocus lithinis
Blastopsocus sp.Camelopsocus monticola
Loensia variegataLoensia moesta
Loensia conspersaOreopsocus buholzei
Genus sp.Ptycta sp.
Copostigma sp.Ptycta johnsoni
Atlantopsocus personatusSymbiopsocus hastatus
Steleops sp.Psocomesites sp.
Steleops elegansPsocidus sp.
Indiopsocus bisignatusIndiopsocus sp.
Trichadenotecnum circularoidesTrichadenotecnum sp.
Trichadenotecnum quaesitumTrichadenotecnum desolatum
Hyalopsocus morioAtropsocus atratus
Hyalopsocus floridensisHyalopsocus sp.
Psocus bipunctatusPsocus crosbyi
Atricha. quadripunctatusAtrichadenotecnum sp.
Sigmatoneura kolbeiPodopterocus sp.
Metylophorus purusMetylophorus novaescotiae
Thyrsophorus sp.Cerastipsocus trifasciatus
Longivalvus nubilusPsococerastis sp.
Clematiscena sp.
0.05 substitutions/site
"Ptyctini"
Psocini
Atrichadenotecnini
Sigmatoneurini
Metylophorini
Thyrsophorini
Blastini
Amphigerontini
Kaindipsocini
Ptyctini
Psocini
Cerastipsocini
Metylophorini
THYRSOPHORINAE
Cerastipsocini
AM
PH
IGE
RO
NT
INA
EP
SO
CIN
AE
Lienhard & Smithers (2002)Present study
AM
PH
IGE
RO
NT
INA
EP
SO
CIN
AE
100/100/100
100/100/99
100/100/100
100/100/100
100/100/94
100/100/100
100/100/98
100/</<
100/100/100
100/55/60
100/100/100
100/97/55
100/100/100
100/91/89
100/97/98
100/</<
100/</<
100/100/100
100/100/100
100/100/97
100/100/100
100/99/84
100/99/82 100/100/100
99/</<
99/57/<
100/100/100
99/85/89
98/93/61
96/</<
95/</<
90/</<
94/51/58
92/</74
80/56/85
63/70/<
85/62/<
71/</63
統計的推測 簡単な例
画びょうを１００回なげて落とし，表を向くか，裏を向くか？
1 2 3 4 5 6 7 8 9 10表 裏 表 裏 裏 表 裏 裏 裏 表
11 12 13 14 15 16 17 18 19 20裏 裏 裏 表 表 表 裏 裏 裏 表
91 92 93 94 95 96 97 98 99 100裏 表 表 表 裏 表 裏 裏 表 裏
結果： 表=43回，裏=57回
表を向いた頻度 =43
100= 0.43
4
画びょうが表を向く頻度を１０回毎に区切ってみる1-10 11-20 21-30 31-40 41-50 51-60 61-70 71-80 81-90 91-100 1-100
表 4 4 4 3 6 3 3 5 6 5 43裏 6 6 6 7 4 7 7 5 4 5 57
表の割合 0.4 0.4 0.4 0.3 0.6 0.3 0.3 0.5 0.6 0.5 0.43
• 標本 ＝ 有限 ⇒ 頻度のバラツキ
• 母集団 ＝ 実験回数が非常に多い(無限)のとき頻度の極限 ⇒ 画びょうが表を向く確率
実際には有限回しか実験は行えない．同じ条件で実験を多数繰り返すのは大変難しい⇒ 確率というのは抽象的な概念 ⇒ モデル
5
(ノンパラメトリック)ブートストラップ
T T T T TT T TT T T T T T T T TT T TT T T T T T T T TT T T T T T T T T T TT T T T T T TT T T T T T TT T TT T T T TT T T T T T TT T TT T T T TT T TT T T TT TT T T TT T TT T TT T T TT TT T T TT T TT T T TTTT T T T T TTTT T TT T T TTTT T T T T TTTT T TT T T T T T T TT T T T TT T T T T T T TT T T T TT TT TT T T T TT T T T T T T T TT TT TT T T T TT T T T T T T T
G G G GG G G G GG G G G G G G G G G G G G GG G G GG G G G G G G G G G G G G G G G G G G G G
AA A A A A AA AA AA A A A A AA AA A AA A A A A AA AA A A AA A A A A AA AA A A AA A A A AA A AA A A AA A A A AA A AA A A AA A AA A AA A A A A A AA A AA A AA A A A A A AA A A AA A A A A A A AA A A AA A A A A A A AA A AA A A AA A A A AA A AA A A AA A A A AA A AA A A A A A A A A AA A AA A A A A A A A
CC CC CC C CC C CCC C C C CC CC CC C CC C CCC C C C CC CC CC C CC C CCC CC C C CC CC CC C CC C CCC CC C C C C C C CCC C CC C CC C C C C CCC C CC C CC C C C CCC CC CC C C C CCC CC CC C C CC CC CC C CC C C CC CC CC C CC CC C C CC C CCCC C C CC CC C C CC C CCCC C C CC C CCC CC CC C C CCC CC CC C
有限長の配列データからのリサンプリング29
ブートストラップ確率 T T T T TT T TT T T T T T T T TT T TT T T T T T T T TT T T T T T T T T T TT T T T T T TT T T T T T TT T TT T T T TT T T T T T TT T TT T T T TT T TT T T TT TT T T TT T TT T TT T T TT TT T T TT T TT T T TTTT T T T T TTTT T TT T T TTTT T T T T TTTT T TT T T T T T T TT T T T TT T T T T T T TT T T T TT TT TT T T T TT T T T T T T T TT TT TT T T T TT T T T T T T T
G G G GG G G G GG G G G G G G G G G G G G GG G G GG G G G G G G G G G G G G G G G G G G G G
AA A A A A AA AA AA A A A A AA AA A AA A A A A AA AA A A AA A A A A AA AA A A AA A A A AA A AA A A AA A A A AA A AA A A AA A AA A AA A A A A A AA A AA A AA A A A A A AA A A AA A A A A A A AA A A AA A A A A A A AA A AA A A AA A A A AA A AA A A AA A A A AA A AA A A A A A A A A AA A AA A A A A A A A
CC CC CC C CC C CCC C C C CC CC CC C CC C CCC C C C CC CC CC C CC C CCC CC C C CC CC CC C CC C CCC CC C C C C C C CCC C CC C CC C C C C CCC C CC C CC C C C CCC CC CC C C C CCC CC CC C C CC CC CC C CC C C CC CC CC C CC CC C C CC C CCCC C C CC CC C C CC C CCCC C C CC C CCC CC CC C C CCC CC CC C
1 2 3 4 5
1 2 3 4 5
1 2 3 4 5
1 23 4 5
1 2 3 4 5
30
Hemipsocus sp.228Hemipsocus sp.196
Psilopsocus malayanusLichenomima sp.
Myopsocus sp.
Kaindipsocus sp.Amphi. jezoensis
Amphigerontia sp.Blaste sp.
Blaste quietaBlastopsocus lithinis
Blastopsocus sp.Camelopsocus monticola
Loensia variegataLoensia moesta
Loensia conspersaOreopsocus buholzei
Genus sp.Ptycta sp.
Copostigma sp.Ptycta johnsoni
Atlantopsocus personatusSymbiopsocus hastatus
Steleops sp.Psocomesites sp.
Steleops elegansPsocidus sp.
Indiopsocus bisignatusIndiopsocus sp.
Trichadenotecnum circularoidesTrichadenotecnum sp.
Trichadenotecnum quaesitumTrichadenotecnum desolatum
Hyalopsocus morioAtropsocus atratus
Hyalopsocus floridensisHyalopsocus sp.
Psocus bipunctatusPsocus crosbyi
Atricha. quadripunctatusAtrichadenotecnum sp.
Sigmatoneura kolbeiPodopterocus sp.
Metylophorus purusMetylophorus novaescotiae
Thyrsophorus sp.Cerastipsocus trifasciatus
Longivalvus nubilusPsococerastis sp.
Clematiscena sp.
0.05 substitutions/site
"Ptyctini"
Psocini
Atrichadenotecnini
Sigmatoneurini
Metylophorini
Thyrsophorini
Blastini
Amphigerontini
Kaindipsocini
Ptyctini
Psocini
Cerastipsocini
Metylophorini
THYRSOPHORINAE
Cerastipsocini
AM
PH
IGE
RO
NT
INA
EP
SO
CIN
AE
Lienhard & Smithers (2002)Present study
AM
PH
IGE
RO
NT
INA
EP
SO
CIN
AE
100/100/100
100/100/99
100/100/100
100/100/100
100/100/94
100/100/100
100/100/98
100/</<
100/100/100
100/55/60
100/100/100
100/97/55
100/100/100
100/91/89
100/97/98
100/</<
100/</<
100/100/100
100/100/100
100/100/97
100/100/100
100/99/84
100/99/82 100/100/100
99/</<
99/57/<
100/100/100
99/85/89
98/93/61
96/</<
95/</<
90/</<
94/51/58
92/</74
80/56/85
63/70/<
85/62/<
71/</63