lying through your teeth: saturation and non independence in morphological data, and what to do...
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Lying through your teeth: saturation and non independence in morphological data, and what to do about it
Liliana M. Dávalos —Stony Brook UniversityPaul M. Velazco —American Museum of Natural HistoryOmar M. Warsi —Stony Brook UniversityPeter D. Smits —University of ChicagoNancy B. Simmons —American Museum of Natural History
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Diphylla Diaemus Desmodus Brachyphylla Erophylla Phyllonycteris Platalina Lonchophylla Lionycteris Monophyllus Glossophaga Leptonycteris Anoura Hylonycteris Lichonycteris Scleronycteris Choeroniscus Musonycteris Choeronycteris Phylloderma Phyllostomus Macrophyllum Lonchorhina Mimon crenulatum Mimon bennettii Trachops Tonatia Chrotopterus Vampyrum Trinycteris Glyphonycteris Lampronycteris Macrotus Micronycteris minutaMicronycteris hirsutaMicronycteris megalotisRhinophylla Carollia Sturnira Enchisthenes hartiiArtibeus concolorArtibeus jamaicensisArtibeus cinereusUroderma Platyrrhinus Vampyrodes Chiroderma Vampyressa bidensVampyressa nymphaeaVampyressa pusillaEctophylla Mesophylla Ametrida Centurio Sphaeronycteris Pygoderma Phyllops Stenoderma Ariteus Ardops
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MP bootstrap
Macrotus
Lampronycteris
Micronycteris minuta
Micronycteris schmidtorum
Micronycteris hirsuta
Microncyteris megalotis
Diphylla
Diaemus
Desmodus
Lonchorhina
Macrophyllum
Trachops
Chrotopterus
Vampyrum
Lophostoma
Tonatia
Phylloderma
Phyllostomus
Mimon
Anoura
Hylonycteris
Choeroniscus
Musonycteris
Choeronycteris
Erophylla
Brachyphylla
Monophyllus
Glossophaga
Leptonycteris
Lonchophylla
Lionycteris
Carollia
Trinycteris
Glyphonycteris daviesi
Glyphonycteris sylvestris
Rhinophylla
Sturnira
Mesophylla
Vampyressa
Platyrrhinus
Vampyrodes
Uroderma
Vampyressa bidens
Vampyressa brocki
Chiroderma
Enchisthenes
Ectophylla
Artibeus
Dermanura
Ariteus
Ardops
Stenoderma
Centurio
Pygoderma
Ametrida
Sphaeronycteris
< 0.97������
BYS posterior probability
Baker et al. 2003 Occas Pap Mus TTUDatzmann et al. 2010 BMC Evol Biol
Wetterer et al. 2000 B Am Mus Nat Hist
Mor
phol
ogica
l
Mol
ecula
r
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•Majority of species are extinct•Fossils are all that
remain•Phylogenies must use
morphology•How?
Genome not always available
Morgan & Czaplewski 2012 Evolutionary History of Bats
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Springer et al. 2007 Syst BiolHermsen & Hendricks 2008 Ann Missouri Bot Gard
Total evidence Conditional combination
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•Homology: character changes reflect common descent
•IID: Independent and Identically Distributed
Assumptions of phylogeny
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Dávalos, Cirranello et al. 2012 Biol Rev
Morphological Molecular
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•If rates of evolution are high, then signal erased over time•Results in
unresolved phylogeny
•Other signal must emerge to resolve phylogeny
Saturation is not everything
Dávalos & Perkins 2008 Genomics
• First position• Second positiono Third position
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Pteronotus
Monophyllus
Glossophaga
Anoura
Lonchorhina
Chrotopterus
Noctilio
Lampronycteris
Phylloderma
Lonchophylla
Micronycteris
Erophylla
Enchisthenes
†Palynephyllum
Trachops
Glyphonycteris
Macrophyllum
Artibeus
Phyllostomus
Hylonycteris
Vampyrum
Brachyphylla
Choeroniscus
LonchophyllaLionycteris
Thyroptera
Pygoderma
Uroderma
TrinycterisNeonycteris
DiphyllaPlatalina
Micronycteris
Vampyrodes
Sturnira
Mimon
Xeronycteris
Macrotus
Phyllonycteris
Diaemus
Tonatia
Platyrrhinus
Carollia
†Notonycteris
Lichonycteris
Leptonycteris
Rhinophylla
Musonycteris
Desmodus
Mormoops
Lophostoma
39
54
14
59
2526
74
28
2
2
58
0
48
44
59
970
3
8
13
0
24
48
4
14
35
33
99
123
9
61
99
0
21
97
93
18
13
1
1
36
99
90
59
31
1
58
94
70
49
9
63
28
0
0
90
92
7785
17
6
53
1
7
5
4530
57
6
3937
13
11
1
5
14
10
68
54
0
46
86
11
67
6
8
19
0
7
65
91
78
6
39
0
12
94
66
4
21
39
78
†Notonycteris
Choeronycteris
†Palynephyllum
Platalina
Uroderma
Pteronotus
Artibeus
Glossophaga
Erophylla
HylonycterisLichonycteris
Mimon
Neonycteris
Choeroniscus
Platyrrhinus
Phyllonycteris
Chrotopterus
Brachyphylla
Glyphonycteris
Musonycteris
Lonchorhina
Xeronycteris
Vampyrodes
Pygoderma
Anoura
Micronycteris
Diaemus
Trachops
Lionycteris
RhinophyllaCarollia
Desmodus
Sturnira
Lophostoma
Phylloderma
Phyllostomus
Vampyrum
Monophyllus
MormoopsThyroptera
Macrophyllum
Tonatia
Enchisthenes
Macrotus
Lonchophylla
Noctilio
Lampronycteris
Diphylla
Leptonycteris
Trinycteris35
79
20
30
50
51
30
95
94
22
48
1310
44
65
18
91
25
31
60
31
15
7170
52
31
82
55
34
8939
87
53
19
11
99
67
59
44
80
15
92
35
83
28
14
59
77
78
24
30
41
97
19
27
86
0
70
80
74
45
40
23
73
24
87
41
25
26
25
45
88
51
24
63
80
91
36
14
95
82
75
18
94
22
40
31
31
43
13
36
53
83
66
14
35
47
4895
40
60
93
30
60
47
17
Phyllonycteris
Mormoops
Platyrrhinus
Monophyllus
Anoura
Choeroniscus
Hylonycteris
Brachyphylla
Neonycteris
Lonchophylla
Leptonycteris
Thyroptera tricolor
Diphylla
Vampyrum
Glyphonycteris
Macrophyllum
Pteronotus
Trachops
Diaemus
Macrotus
ChoeroniscusChoeronycteris
Platalina
Lophostoma
Erophylla
Lonchophylla
Lonchorhina
Vampyrodes
Lionycteris
Phylloderma
Carollia
Chrotopterus
Enchisthenes
Tonatia
Micronycteris
Trinycteris
Sturnira
†Notonycteris
Lichonycteris
Phyllostomus
Noctilio
Lampronycteris
Artibeus
Musonycteris
Desmodus
Micronycteris
Rhinophylla
†Palynephyllum
Glossophaga
Xeronycteris
Pygoderma
Uroderma
Mimon
54
36
99
99
92
38
30
54
51
85
52
79
57
57
49
8078
55
87
42
39
47
31
55
46
94
73
88
91
53
95
26
22
57
85
57
7
82
93
85
77
96
70
48
9095
92
52
16
71
46
80
98
96
56
95
85
67
92
87
42
87
99
89
62
49
68
39
98
96
98
53
93
97
94
32
83
87
6563
93
60
6071
86
86
96
41
62
83
82
99
43
98
95
63
79
68
Bootstrapsupport
100
0
0.5 changes/character
Bootstrapsupport
100
0
0.1 changes/character
% Posteriorprobability
100
7
Supplementary Figure 4
BA C
Dávalos et al. Accepted Syst BiolDental characters highly
convergent
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Figure 3
BA
Micronycteris
Mimon
†Notonycteris
Trachops
Tonatia
Mimon crenulatum Phylloderma
Phyllostomus
Lonchorhina
Lonchophylla
Carollia
Glyphonycteris
Rhinophylla
Vampyrodes
Artibeus
Anoura
Choeroniscus
Macrotus
Pygoderma
†Palynephyllum
PlatyrrhinusSturnira
Choeronycteris
Neonycteris
Lichonycteris
Thyroptera
Musonycteris
Macrophyllum
Mormoops
Hylonycteris
Desmodus
Enchisthenes
Chrotopterus
Noctilio
Platalina
Lampronycteris
Diphylla
Uroderma
XeronycterisLionycteris
Pteronotus
Trinycteris
Vampyrum
Diaemus
Brachyphylla
Glossophaga
Leptonycteris
Monophyllus
Phyllonycteris Erophylla
Lophostoma
Trinycteris
Pygoderma
Desmodus
Macrophyllum
LichonycterisHylonycteris
Uroderma
LionycterisPlatalina
Mormoops
Diaemus
Chrotopterus
Sturnira
Xeronycteris
Vampyrum
Enchisthenes
Pteronotus
Thyroptera
Platyrrhinus
Diphylla
Choeronycteris
Lampronycteris
†Palynephyllum
Noctilio
Neonycteris
Musonycteris
Macrotus
Micronycteris
Mimon crenulatum
†Notonycteris
Trachops
Tonatia
Lophostoma
Phylloderma
Phyllostomus
Lonchorhina
Carollia
Glyphonycteris Rhinophylla
Vampyrodes
Artibeus
Lonchophylla
Anoura
Choeroniscus
Brachyphylla Erophylla
Phyllonycteris
Monophyllus
Leptonycteris
Glossophaga
Micronycteris
Mimon
Plant-visiting
Support
100
40
% Posteriorprobability
100
26
Phyllostominae
99
87
98
83
68
63
79
94
71
56
40
66
94
81
66
94
99
87
57
9464
99
48
58
90
82
94
94
81
83
86
0.05 changes/character 1
1
54
94
78
99
56
57
95
92
52
92
59
99
98
99
67
55
57
90
44
94
84
91
44
49
9499
95
89
52
99
76
99
93
66
33
98
81
91
93
54
99
62
63
57
99
54
81
9593
71
63
89
28
95
99
99
95
96
26
99
99
63
57
97
66
0.05 changes/character
•>10Kb from 7 chromosomes & mt + <300 dental traits
•= signal from dental traits
•What makes this signal so strong?
Morphology has a strong signal
Dávalos et al. Accepted Syst Biol
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0
9.5
19
0
1.3
2.6
3.9
Molecular
Morphological
Freq
uenc
y (p
erce
nt)
Figure 2
B
A
Pairwise dissimilarity between characters
Rel
ativ
e de
nsity
bet
wee
n m
orph
olog
ical
cha
ract
ers
0.0 0.2 0.4 0.6 0.8 1.0
0.0
0.5
1.0
1.5
2.0
2.5
Signal is amplified by repetition
•Measured dissimilarity between pairs of characters
•25% sequence characters are completely dissimilar•Despite protein-
coding loci•This is not the case for
dental charactersDávalos et al. Accepted Syst Biol
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Figure 3
BA
Micronycteris
Mimon
†Notonycteris
Trachops
Tonatia
Mimon crenulatum Phylloderma
Phyllostomus
Lonchorhina
Lonchophylla
Carollia
Glyphonycteris
Rhinophylla
Vampyrodes
Artibeus
Anoura
Choeroniscus
Macrotus
Pygoderma
†Palynephyllum
PlatyrrhinusSturnira
Choeronycteris
Neonycteris
Lichonycteris
Thyroptera
Musonycteris
Macrophyllum
Mormoops
Hylonycteris
Desmodus
Enchisthenes
Chrotopterus
Noctilio
Platalina
Lampronycteris
Diphylla
Uroderma
XeronycterisLionycteris
Pteronotus
Trinycteris
Vampyrum
Diaemus
Brachyphylla
Glossophaga
Leptonycteris
Monophyllus
Phyllonycteris Erophylla
Lophostoma
Trinycteris
Pygoderma
Desmodus
Macrophyllum
LichonycterisHylonycteris
Uroderma
LionycterisPlatalina
Mormoops
Diaemus
Chrotopterus
Sturnira
Xeronycteris
Vampyrum
Enchisthenes
Pteronotus
Thyroptera
Platyrrhinus
Diphylla
Choeronycteris
Lampronycteris
†Palynephyllum
Noctilio
Neonycteris
Musonycteris
Macrotus
Micronycteris
Mimon crenulatum
†Notonycteris
Trachops
Tonatia
Lophostoma
Phylloderma
Phyllostomus
Lonchorhina
Carollia
Glyphonycteris Rhinophylla
Vampyrodes
Artibeus
Lonchophylla
Anoura
Choeroniscus
Brachyphylla Erophylla
Phyllonycteris
Monophyllus
Leptonycteris
Glossophaga
Micronycteris
Mimon
Plant-visiting
Support
100
40
% Posteriorprobability
100
26
Phyllostominae
99
87
98
83
68
63
79
94
71
56
40
66
94
81
66
94
99
87
57
9464
99
48
58
90
82
94
94
81
83
86
0.05 changes/character 1
1
54
94
78
99
56
57
95
92
52
92
59
99
98
99
67
55
57
90
44
94
84
91
44
49
9499
95
89
52
99
76
99
93
66
33
98
81
91
93
54
99
62
63
57
99
54
81
9593
71
63
89
28
95
99
99
95
96
26
99
99
63
57
97
66
0.05 changes/character
Figure 5
Dental characters !
!
MandibularMaxillary
! CanineIncisors
MolarsPremolars
! Significant
B
A
ï�
ï�
0
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Supp
ort f
or Neonycteris
in Micronycteris
C
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0
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Supp
ort fRU�QHFWDUï
feed
ing
clad
e
!
!
!
!
!
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!!
!
!
!
!
!
!
!
!
!
!
!
!!
!
!
!
!!
!
!
!
Supp
ort f
or Lonchorhina
sits
ter t
o Ph
yllo
stom
inae
ï�
0
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!!!
!
!
!!!!!
!
!
!!!!!!!!
!
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0 100 ���
Character
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Dávalos et al. Accepted Syst Biol
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•Less is more when collecting certain kinds of characters
•Dental data violate key assumptions of phylogenetic models
•Saturation, convergence, and non-independence•= model failure
•New data & models needed
Data & models don’t match
Czaplewski et al. 2003 Caldasia
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Analytical innovations
•Statistical scaffolds = condition morphological resolution on molecular posterior
•Morphological parametric bootstraps = uncover significantly conflicting characters
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• Funding
• NSF—DEB
• CIDER—SBU
• Speciation & diversification: A. Cirranello, E. Dumont, A. Russell, N. Simmons, P. Velazco
• N. Gerardo, A. Wilson
• Dávalos Lab
• Phylogenetics: B. Baird, S. DelSerra, A. Goldberg, O. Warsi, L. Yohe
Thanks!