(Phylo)genetic Relationships

(Phylo)genetic Relationships
2
1
3
2
1
3
The principle of parsimony
2
34
A
5
1
B
C
A
B
C
D
E
1
+
+
+
-
2
+
+
-
3
+
-
4
+
-
D
5
+
-
E
Dermatonotus muelleri
Kassina maculata
Rhacophorus
reinwardtii
Laliostoma labrosum
Kaloula pulchra
Leptopelis natalensis
Breviceps fuscus
Boophis
luteus
(use B.
doulioti)
Dyscophus atongilii
Searching with topological
constraints
•
Topological constraints are user-defined
phylogenetic hypotheses
•
Can be used to find optimal trees that either:
1. include a specified clade or set of
relationships
2. exclude a specified clade or set of
relationships (reverse constraint)
Searching with topological constraints
A
B
C
D
E
F
G
CONSTRAINT TREE
((A,B,C,D)(E,F,G))
EFG
ABCD
A
A
B
C
D
E
F
B
C
E
D
F
G
G
EFG
ABCD
Incompatible with constraint tree
Compatible with constraint tree
Incompatible with reverse constraint tree
Searching with topological
constraints
backbone constraints
l
Backbone constraints specify relationships among a subset of the
taxa
A
B
D
E
BACKBONE CONSTRAINT
((A,B)(D,E))
relationships of taxon C are not specified
A
B
D
E
A
possible positions of taxon C
Compatible with backbone constraint
Incompatible with reverse constraint
D
•
E
Incompatible with backbone constraint
Compatible with reverse constraint
Support
•
B
Bootstrapping
Bremer support (Decay index)
Bootstrapping
Sp1
Sp2
Sp3
Sp4
AGGCTCCAAA
AGGTTCGAAA
AGCCCCGAAA
ATTTCCGAAC
1
2
3
4
Re1 0120301201
Re2 1000222003
Sp1
Sp2
Sp3
Sp4
GGGTTTCAAA
GGGTTTGAAA
GCCCCCGAAA
TTTCCCGAAC
1
2
3
4
Sp1
Sp2
Sp3
Sp4
1
2
3
4
ATTCCCCAAA
ATTCCGGAAA
ACCCCGGAAA
ACCCCGGCCC
Bootstrapping
Sp1
Sp2
Sp3
Sp4
AGGCTCCAAA
AGGTTCGAAA
AGCCCCGAAA
ATTTCCGAAC
1
2
3
4
Re3 1120301101
Sp1
Sp2
Sp3
Sp4
AGGGTTTCAA
AGGGTTTGAA
AGCCCCCGAA
ATTTCCCGAC
1
2
3
4
100
100
66
1
2
3
4
Bremer support (Decay index)
Sp1
Sp2
Sp3
Sp4
AGGCT...CCAAA
AGGTT...CGAAA
AGCCC...CGAAA
ATTTC...CGAAC
1
2
3
4
4
3
1
1
1
1
1
2
3
2
3
2
3
2
3
3
2
4
4
4
4
4
TL=250
TL=251
TL=252
TL=253
TL=254
Question: How can we calculate this (without calculating all these trees)?
Origin and early diversification of frogs
GYMNOPHIONA
a) Neobatrachia monophyletic
CAUDATA
Hynobius
Eurycea
Ascaphus montanus
100-100
(ASCAPHIDAE)
Ascaphus truei
100-100
Leiopelma hochstetteri
100-100
(LEIOPELMATIDAE)
Leiopelma archeyi
b) sister relationship of
Ascaphidiae and
Leiopelmatidae
Bombina variegata
(BOMBINATORIDAE)
Bombina orientalis
Alytes
100(DISCOGLOSSIDAE)
96
Discoglossus
Rhinophrynus
(RHINOPHRYNIDAE)
100Crown-group
Pipa
96 100-100
frogs 100- /
Hymenochirus
(PIPIDAE)
Xenopus
100- / 100-100
Silurana
Scaphiopus
100-100
100-100
c) a basal position for
Amphicoela
c
(SCAPHIOPODIDAE)
Spea
Pelodytes (PELODYTIDAE)
Pelobates
(PELOBATIDAE)
Leptobrachium
100-99
100-100
100-79
100-99
100-100
100- /
100-100
100-100
e
(MEGOPHRYIDAE)
(MYOBATRACHIDAE)
93-83
0.05 subst./site
Leptolalax
Brachytarsophrys
97-88
100-100
100-65 100-100
(HYLIDAE)
(CERATOPHRYINAE)
(RHINADERMATIDAE)
(MICROHYLIDAE)
(RANIDAE)
(LEPTOPELINAE)
(ASTYLOSTERNIDAE)
NEOBATRACHIA
d
PELOBATOIDEA
PIPOIDEA
a 100-100 100-97
DISCOGLOSSOIDEA
b
Which value is support for:
AMPHICOELA
Geotrypetes
Gegeneophis
Typhlonectes
Pleurodeles
Questions
95
99
100
Homo sapiens
Pan paniscus
Which value is support
for:
Gorilla gorilla
a) a (homo, Pan) sister
relationship
Pongo pygmaeus
b) a basal position for
Pongo
Hylobates
OUTGROUP