non independence and convergence mislead morphological phylogenetics of phyllostomids
TRANSCRIPT
Lying through your teeth: non independence and convergence mislead morphological phylogenetics of phyllostomids
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
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
•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
Springer et al. 2007 Syst BiolHermsen & Hendricks 2008 Ann Missouri Bot Gard
Total evidence Conditional combination
•Homology: character changes reflect common descent
•IID: Independent and Identically Distributed
Assumptions of phylogeny
Dávalos, Cirranello et al. 2012 Biol Rev
Morphological Molecular
•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
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
Figure 4
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
47
% Posteriorprobability
1.00
0.13
Phyllostominae
95
59
89
95
97
98
99
90
73
6782
58
71
91
99
96
82
95
91
95
98
91
79
77
91
9986
98
99
47
67
72
95
74
87
79
93
86
99
99
92
95
99
75
99
98
59
99
99
56
0.1 changes/character 0.1 changes/character
0.65
0.62
0.57
0.48
0.91
0.61
0.91
0.89
0.54
0.25
0.99
0.870.82
0.99
0.98
0.88
0.13
0.46
0.64
0.90
0.82
0.930.80
0.77
0.56
0.34
0.98
0.69
0.49
0.63
0.71
0.99
0.38
0.89
0.80
0.62
0.42
0.97
0.52
0.93
0.98
0.91
0.70
0.79
0.96
0.76
0.77
0.99
0.990.77
0.44
0.58
0.99
0.99
0.99
0.78
0.48
0.98
0.97
0.980.95
0.99
0.98
0.510.96
0.63
0.45
0.99
0.85
0.96
0.57
0.98
0.98
0.86
0.74
0.57
0.51
0.99
0.98•>9Kb 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
0
Freq
uenc
y (p
erce
nt)
Morphological
0
5.2
10.4
15.6
Molecular
2.1
4.2
6.3
8.5
Dissimilarity between charactersR
elat
ive
dens
ity b
etw
een
mor
phol
ogic
al c
hara
cter
s0.0 0.2 0.4 0.6 0.8 1.0
0
2
4
6
8
10 A
B
Figure 3
Signal is amplified by repetition
•Measured dissimilarity between pairs of characters
•High dissimilarity among molecular characters•Despite protein-
coding loci•This is not the case for
dental charactersDávalos et al. Accepted Syst Biol
How similarity arises
•Hypotheses:•Occlusion
•Negative selection•Ecological
convergence•Positive selection
•Development•Paths of least
resistance
1!
2!
2!1!
Figure 4
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
47
% Posteriorprobability
1.00
0.13
Phyllostominae
95
59
89
95
97
98
99
90
73
6782
58
71
91
99
96
82
95
91
95
98
91
79
77
91
9986
98
99
47
67
72
95
74
87
79
93
86
99
99
92
95
99
75
99
98
59
99
99
56
0.1 changes/character 0.1 changes/character
0.65
0.62
0.57
0.48
0.91
0.61
0.91
0.89
0.54
0.25
0.99
0.870.82
0.99
0.98
0.88
0.13
0.46
0.64
0.90
0.82
0.930.80
0.77
0.56
0.34
0.98
0.69
0.49
0.63
0.71
0.99
0.38
0.89
0.80
0.62
0.42
0.97
0.52
0.93
0.98
0.91
0.70
0.79
0.96
0.76
0.77
0.99
0.990.77
0.44
0.58
0.99
0.99
0.99
0.78
0.48
0.98
0.97
0.980.95
0.99
0.98
0.510.96
0.63
0.45
0.99
0.85
0.96
0.57
0.98
0.98
0.86
0.74
0.57
0.51
0.99
0.98
Figure 5
Dental characters !
!
MandibularMaxillary
! CanineIncisors
MolarsPremolars
! Significant
B
A
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Supp
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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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!!!
!
!
!!!!!
!
!
!!!!!!!!
!
!
!
!!
!
!
!
!
!
0 100 ���
Character
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!
!
!!
!
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!
!
!
!
Dávalos et al. Accepted Syst Biol
•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
Statistical scaffold
Noconflict
&RQÀLFWLQJcharacters
Dependency
Morphological
Rates
Data matrix
Statistic from
data matrix
Phylogeny
Statistic from
phylogeny
Phylogenetic
analysis
Other
analysis
Comparison
EndpointStarting point
)LJXUH��
Pairwise
dissimilarity Bayesian
Sta
te:s
tep
Simulations
Distribution
morphological
dissimilarity
Bayesian Pairwise
dissimilarity
Distribution
molecular
dissimilarity
Agree?
Yes
No
Null distribution
difference
per-character
likelihoods
Tree with
Tree
without
Backbone
constraints
Ba
ye
sia
n
Bra
nch
le
ng
ths
Ma
xim
um
like
liho
od
Constrained
phylogenies
Molecular
phylogenies
Morphological
phylogenies
Combined
phylogenies
Combined
matrix without
FRQÀLFWLQJcharacters
Variable sites
Relative
distribution
&RQÀLFWLQJnodes
Relative
rates of
evolution
&RQÀLFWLQJnodes
Branch
lengths
&RQÀLFWLQJmorphological
characters
Statisticalscaffold
Alternativecombined
phylogenies
Morphologicalsaturation
plot
Morphological
Combined
Molecular
Analytical innovations
•Statistical scaffolds = condition morphological resolution on molecular posterior
•Morphological parametric bootstraps = uncover significantly conflicting characters
• Funding
• NSF—DEB
• CIDER—SBU
• Speciation & diversification: A. Cirranello, E. Dumont, A. Russell, N. Gerardo, A. Wilson
• Dávalos Lab
• Phylogenetics: B. Baird, S. DelSerra, A. Goldberg, O. Warsi, L. Yohe
Thanks!