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decay index (kõduindeks) - kui monofüleetiline klaad esineb kõigis puudes, mis on 5 sammu pikemad kui MP puu, aga mitte kõigis, mis on 6 sammu pikemad, siis selle klaadi kõduindeks on 6. MP puu. 3. 1. 2. 4. ainus informatiivne positsioon. 2. 3. 4. 1. 1 ACACACACACACAC T - PowerPoint PPT Presentation
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decay index (kõduindeks) - kui monofüleetiline klaad esinebkõigis puudes, mis on 5 sammu pikemad kui MP puu,aga mitte kõigis, mis on 6 sammu pikemad, siis selleklaadi kõduindeks on 6
1 ACACACACACACACT2 CACACACACACACAT3 CACACACACACACAC4 TACACACACACACGC
ainus informatiivne positsioon
1
2
3
4
MP puu
2. 143. 15 14. 15 3 2
2 3 4 1
1 ACACACACACACAC-T2 -CACACACACACACAT3 -CACACACACACACAC4 -TACACACACACACGC
viga joondamises või järjestuse lugemises
puude juurimine
puude juurimine
MRCA
puude juurimine
puude juurimine
juure leidmine kaasaegsele inimesele
NJ
MP
networks
consensus trees
network as consenus
võrk väljendab lahendamatust (ambiguity)
kaks andmete poolt võrdselt toetatud puud
network as consenus
66
5570 100
66
66
5570 100
66
66
5570 100
66
33
45
networks
0<s<2n-1
splits
H, C, G, O, B
10 taksoni puhul < 512 juurimata puid >2 miljoni juuritud puid >34 miljoni
networks
H CG
O B
28 posO BG
HC
13 posO BH
GC
12 pos
spectral analysis
spectral analysis
puu:Hadamardtransformation
(Hendy, Penny 1993)
expectedspectrum:
reversible
spectral analysis
networks
parallelisms
A
B
C
D
10 6
1
7
3 9
TL=1+10+6+7+3+9=36
dBC=11 17A
B
C
D
11 4
3
7
16
TL=11+3+4+7+16=41
ghost link
networks
Excoffier, Smouse 1994: minimum spanning trees, networks (MSN)
networks
TC TT
CC CT
TC TT
CC CT
TC TT
CC CT
TC TT
CC CT
TC TT
CC CT
networks
TCC TTC
CCC CTC
TTT
CTT
15 trees
networks
4 x 4 x 4 = 64 trees
networks
Nuu-Chah-Nulth(Ward et al. 1991)
896 MP trees(Bandelt et al. 1995)
Networks and tie trees
A C
B D
F
E
A C
B D
F
E
root
E FDB A CE FDB A C
16
9
10
207
5
73
11
3
2
1
22
2 1
1
1
1
1
4
1
2
1
Estonians, n=53
Russians, n=14
Finns, n=11 (Zerjal et al. 1997)
Yakuts, n=18 (Zerjal et. al 1997)
3
11
DYS 391"283"
DYS 391"291"
DYS 19"202"
DYS 19"186"
DYS 390"219"
DYS 390"207"
Buryats, n=22 (Zerjal et. al 1997)
1
1
Armenians, n=9
1
1
1
1
1
1
2
1
Slovaks, n=2
Turks, n=1
variation in Y-chromosome haplogroup 16 (Tat C): 3 STR loci
networks
median networks
1 21
1
2
3
1
3
2
4
median networks (MN)
1
3
2
4
1
3
2
4data
n dimensionalhypercube
median network mapping all the actual data withconsensus (median) vectors
median networks (MN)
a) 000b) 011c) 101
a
b c
100010
111
a
b c
001
MN includesconsensusvector ofthe triplet‘median vector’
‘inetermediate vector’
median networks (MN)
10000100 0010
0001
101
011
000
110
networks
median vectors
binary (0,1) data quaternary (A,C,G,T) data
AC, GGCG, AA
CC, GA
AC
T
RM networks
split decomposition
expansion
networks
networks
Reduced Median (RM) networks
pre-processing: w (weight)
RM networks
Bandelt et al. 2000
RM networks: reduction
Bandelt et al. 2000 ”Speedy constructions, greedy reductions”
Network20D http://www.fluxus-engineering.com/
RM networks: reduction
Bandelt et al. 2000 ”Speedy constructions, greedy reductions”
RM networks: reduction
Bandelt et al. 2000 ”Speedy constructions, greedy reductions”