Trait&dependent+dispersal+ modelsforphylogenec...
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Traitdependent dispersal models for phylogene4c biogeography, in the R package 'BioGeoBEARS' Nicholas J. Matzke, DECRA Fellow Moritz Lab Group, EEG, Research School of Biology The Australian NaConal University [email protected] phylo.wikidot.com/BioGeoBEARS – June 21, 2016, iEvoBio, 2:12 pm – EvoluCon 2016, AusCn, TX Adolf Meyer (1898), The Birds of Celebes and the neighbouring islands. https:// en.wikipedia.org/wiki/Snoring_rail Snoring rail, Aramidopsis plateni (flightless, Sulawesi)
Transcript of Trait&dependent+dispersal+ modelsforphylogenec...
Trait-‐dependent dispersal models for phylogene4c biogeography, in the R package 'BioGeoBEARS'
Nicholas J. Matzke, DECRA Fellow Moritz Lab Group,
EEG, Research School of Biology The Australian NaConal University
[email protected] phylo.wikidot.com/BioGeoBEARS
–June 21, 2016, iEvoBio, 2:12 pm –EvoluCon 2016, AusCn, TX
Adolf Meyer (1898), The Birds of Celebes and the neighbouring islands. https://
en.wikipedia.org/wiki/Snoring_rail
Snoring rail, Aramidopsis plateni (flightless, Sulawesi)
Figure 1, Matzke 2013, Frontiers of Biogeography
DEC(LAGRANGE)
BioGeoBEARSsupermodelcan produce
various submodels
Addi4onal models in BioGeoBEARS
-‐ ConnecCvity matrices -‐ User-‐specified dispersal probability mulCpliers -‐ Geographic distance matrices -‐ Environmental distance matrices -‐ Any of these can be “Cme-‐straCfied” -‐ Appearing/disappearing areas
h;p://phylo.wikidot.com/BioGeoBEARSAll code online at:
These models leave out traits!• All of the models discussed so far assume the dispersal rate is constant across the tree
• (might be modified by distance or connecCvity, but not by the lineage)
• It’s GOT to be important • Seed dispersal syndromes • Ra]ing & colonizaCon ability • Flying/nonflying, etc.
Case study: Pacific Rails
Data from:
Jeremy J. Kirchman Curator of Birds
New York State Museum
Adolf Meyer (1898), The Birds of Celebes and the neighbouring islands. https://
en.wikipedia.org/wiki/Snoring_rail
Snoring rail, Aramidopsis plateni (flightless, Sulawesi)
“Typical Rails”
Source: Kirchman, Jeremy J. (2012). Speciation of Flightless Rails on Islands: A DNA-Based Phylogeny of the Typical Rails of the Pacific, The Auk, 129(1):56-69.
Living and ex4nct Rail distribu4ons (Kirchman 2012)
Source: Kirchman, Jeremy J. (2012). Speciation of Flightless Rails on Islands: A DNA-Based Phylogeny of the Typical Rails of the Pacific, The Auk, 129(1):56-69.
Living and ex4nct Rail distribu4ons (Kirchman 2012)
Tahi4 Rail: Gallirallus pacificus
https://en.wikipedia.org/wiki/Tahiti_rail
Tahi4 Rail: Gallirallus pacificus
Source: Kirchman, Jeremy J. (2012). Speciation of Flightless Rails on Islands: A DNA-Based Phylogeny of the Typical Rails of the Pacific, The Auk, 129(1):56-69.
https://en.wikipedia.org/wiki/Tahiti_rail
Source: Kirchman, Jeremy J. (2012). Speciation of Flightless Rails on Islands: A DNA-Based Phylogeny of the Typical Rails of the Pacific, The Auk, 129(1):56-69.
Living and ex4nct Rail distribu4ons (Kirchman 2012)
Source: Kirchman, Jeremy J. (2012). Speciation of Flightless Rails on Islands: A DNA-Based Phylogeny of the Typical Rails of the Pacific, The Auk, 129(1):56-69.
Areas (simplified from Kirchman)
Source: Figure 1 of: Kirchman, Jeremy J.; Steadman, David W. (2006). New Species of Rails (Aves: Rallidae) from an Archaeological Site on Huahine, Society Islands. Pacific Science (2006), 60:2, 281–297.
Areas (simplified from Kirchman)PhillipinesSulawesiMollucasPNG, Australia
New ZealandOkinawaGuam/MarianasNew Britain
Solomon IslandsCook IslandsChatham IslandsLord Howe IslandWake Island
Dated phylogeny of typical Rails (simplified from Kirchman)
Gallirallus_pendiculentusGallirallus_philippensis_melloGallirallus_philippensis_19403Gallirallus_philippensis_42507Gallirallus_ripleyiGallirallus_wakensisTricholimnas_sylvestris_1896Gallirallus_rovianae_28014Gallirallus_rovianae_826433Nesoclopeus_woodfordi_immaculaGallirallus_owstoniHabropteryx_insignisHabropteryx_torquatus_celebensHabropteryx_torquatus_sulcirosHabropteryx_torquatus_torquatuHabropteryx_okinawaeCabalus_modestusEulabeornis_castaneoventrisGallirallus_australis_australiGallirallus_australis_greyiTricholimnas_lafresnayanusHabroptila_wallaciiGallirallus_calayanensisGallirallus_striatusGallirallus_pectoralisAramidopsis_plateni
1 0.8 0.6 0.4 0.2 0Millions of years ago
Not
Not
Not
Not
Not
Not
Not
Not
Not
Not
NotNot
Fly
NotNot
NotNot
NotNot
FlyFly
NotNot
NotFly
NotFlyFlyFlyNotNotNotNotNotNotNotNotFlyFlyFlyNotNotFlyNotNotNotNotNotFlyFlyNot
BioGeoBEARS BAYAREALIKE on traitonly M0_unconstrainedancstates: global optim, 1 areas max. a=1.1954; j=0; LnL=−14.83
Not
NotNot
Not
Not
Not
Not
Not
Not
Not
Not
Not
Fly
NotNot
NotNot
NotNot
FlyFly
NotNot
NotFly
Not
Not
Not
Not
Not
Not
Not
Not
Not
NotNotNot
Fly
NotNot
NotNot
NotNot
FlyFly
NotNot
NotFly
Flying:
Non-‐flying:
Distribu4on of flight in Pacific Rails
Gallirallus_pendiculentusGallirallus_philippensis_melloGallirallus_philippensis_19403Gallirallus_philippensis_42507Gallirallus_ripleyiGallirallus_wakensisTricholimnas_sylvestris_1896Gallirallus_rovianae_28014Gallirallus_rovianae_826433Nesoclopeus_woodfordi_immaculaGallirallus_owstoniHabropteryx_insignisHabropteryx_torquatus_celebensHabropteryx_torquatus_sulcirosHabropteryx_torquatus_torquatuHabropteryx_okinawaeCabalus_modestusEulabeornis_castaneoventrisGallirallus_australis_australiGallirallus_australis_greyiTricholimnas_lafresnayanusHabroptila_wallaciiGallirallus_calayanensisGallirallus_striatusGallirallus_pectoralisAramidopsis_plateni
1 0.8 0.6 0.4 0.2 0Millions of years ago
Not
Not
Not
Not
Not
Not
Not
Not
Not
Not
NotNot
Fly
NotNot
NotNot
NotNot
FlyFly
NotNot
NotFly
NotFlyFlyFlyNotNotNotNotNotNotNotNotFlyFlyFlyNotNotFlyNotNotNotNotNotFlyFlyNot
BioGeoBEARS BAYAREALIKE on traitonly M0_unconstrainedancstates: global optim, 1 areas max. a=1.1954; j=0; LnL=−14.83
Not
NotNot
Not
Not
Not
Not
Not
Not
Not
Not
Not
Fly
NotNot
NotNot
NotNot
FlyFly
NotNot
NotFly
Not
Not
Not
Not
Not
Not
Not
Not
Not
NotNotNot
Fly
NotNot
NotNot
NotNot
FlyFly
NotNot
NotFly
Flying:
Non-‐flying:
Distribu4on of flight in Pacific Rails
(standard trait model)
Gallirallus_pendiculentusGallirallus_philippensis_melloGallirallus_philippensis_19403Gallirallus_philippensis_42507Gallirallus_ripleyiGallirallus_wakensisTricholimnas_sylvestris_1896Gallirallus_rovianae_28014Gallirallus_rovianae_826433Nesoclopeus_woodfordi_immaculaGallirallus_owstoniHabropteryx_insignisHabropteryx_torquatus_celebensHabropteryx_torquatus_sulcirosHabropteryx_torquatus_torquatuHabropteryx_okinawaeCabalus_modestusEulabeornis_castaneoventrisGallirallus_australis_australiGallirallus_australis_greyiTricholimnas_lafresnayanusHabroptila_wallaciiGallirallus_calayanensisGallirallus_striatusGallirallus_pectoralisAramidopsis_plateni
1 0.8 0.6 0.4 0.2 0Millions of years ago
AB
A
A
A
A
A
J
J
AJ
A
AEH
A
ALO
HJJ
AA
ABAB
FF
BAB
HDEABABLONJJJHIBAAGM
DEFFKCA
ABABB
BioGeoBEARS DEC on Psychotria M0_unconstrainedancstates: global optim, 2 areas max. d=0.7251; e=2.0108; j=0; LnL=−112.84
B
AC
A
D
A
J
J
J
A
A
E
A
NO
HJ
AA
AA
KF
BB
A
A
A
A
A
A
J
J
A
AHH
A
LL
JJ
AA
AB
FF
BB
Rails: Geographic range
PhillipinesSulawesiMollucasPNG, AustraliaNew ZealandOkinawaGuam/MarianasNew Britain
Solomon IslandsCook IslandsChatham IslandsLord Howe IslandWake Island
Rails: Geographic range
PhillipinesSulawesiMollucasPNG, AustraliaNew ZealandOkinawaGuam/MarianasNew Britain
Solomon IslandsCook IslandsChatham IslandsLord Howe IslandWake Island Gallirallus_pendiculentus
Gallirallus_philippensis_melloGallirallus_philippensis_19403Gallirallus_philippensis_42507Gallirallus_ripleyiGallirallus_wakensisTricholimnas_sylvestris_1896Gallirallus_rovianae_28014Gallirallus_rovianae_826433Nesoclopeus_woodfordi_immaculaGallirallus_owstoniHabropteryx_insignisHabropteryx_torquatus_celebensHabropteryx_torquatus_sulcirosHabropteryx_torquatus_torquatuHabropteryx_okinawaeCabalus_modestusEulabeornis_castaneoventrisGallirallus_australis_australiGallirallus_australis_greyiTricholimnas_lafresnayanusHabroptila_wallaciiGallirallus_calayanensisGallirallus_striatusGallirallus_pectoralisAramidopsis_plateni
1 0.8 0.6 0.4 0.2 0Millions of years ago
HDEABABLONJJJHIBAAGM
DEFFKCA
ABABB
BioGeoBEARS DEC+J+t12+t21+jt12+m1 on Pacific Railsancstates: global optim, 2 areas max. d=0.0935; e=0.1565; j=0.3493; t12=9.2439; t21=3.0112; jt12=0.4168; LnL=−97.51
Clearly the group has dispersed …but probably they were flying to do it!
Build a trait-‐based dispersal model
1. Trait flight/flightlessness trait evolves on tree Parameters of model:
Clearly the group has dispersed …but probably they were flying to do it!
Build a trait-‐based dispersal model
1. Trait flight/flightlessness trait evolves on tree Parameters of model: t12 -‐> Rate of flight loss
t21 -‐> Rate of flight gain m2 -‐> MulCplier on dispersal prob. while flightless
Clearly the group has dispersed …but probably they were flying to do it!
Build a trait-‐based dispersal model
1. Trait flight/flightlessness trait evolves on tree Parameters of model: t12 -‐> Rate of flight loss
t21 -‐> Rate of flight gain m2 -‐> MulCplier on dispersal prob. while flightless
FLY NOT
FLY - t12
NOT t21 -
Clearly the group has dispersed …but probably they were flying to do it!
Build a trait-‐based dispersal model
1. Trait flight/flightlessness trait evolves on tree Parameters of model: t12 -‐> Rate of flight loss
t21 -‐> Rate of flight gain m2 -‐> MulCplier on dispersal prob. while flightless
2. Combine trait model with anageneCc dispersal
FLY NOT
FLY - t12
NOT t21 -
Clearly the group has dispersed …but probably they were flying to do it!
Build a trait-‐based dispersal model
3. CladogeneCc parameters of model: jt12 -‐> Chance of “jumping” from flight-‐> flightless during founder-‐event speciaCon
Trait-dependent DEC model
Dispersal-Extinction (on branches)
null A B AB
null -A e - dB e - dAB e e -
ancestorrange
A
A BA B
A A B
A B
d = rate of “dispersal” (range expansion)e = rate of “extinction” (range contraction / local extirpation)
descendant rangeRate matrix:
Traditional:
Trait-dependent DEC model
Dispersal-Extinction (on branches)
null A B AB
null -A e - dB e - dAB e e -
ancestorrange
A
A BA B
A A B
A B
d = rate of “dispersal” (range expansion)e = rate of “extinction” (range contraction / local extirpation)
descendant rangeRate matrix:
Traditional:Rate matrix:
Trait-dependent:
Trait-dependent DEC model
Dispersal-Extinction (on branches)
null A B AB
null -A e - dB e - dAB e e -
ancestorrange
A
A BA B
A A B
A B
d = rate of “dispersal” (range expansion)e = rate of “extinction” (range contraction / local extirpation)
descendant rangeRate matrix:
Traditional:Rate matrix:
Trait-dependent:
FLY NOT
FLY - t12
NOT t21 -
Trait-dependent DEC model
Dispersal-Extinction (on branches)
null A B AB
null -A e - dB e - dAB e e -
ancestorrange
A
A BA B
A A B
A B
d = rate of “dispersal” (range expansion)e = rate of “extinction” (range contraction / local extirpation)
descendant rangeRate matrix:
Traditional:
null A B AB
null -A e - dB e - dAB e e -
ancestorrange
descendant range
Rate matrix:
Trait-dependent:
FLY NOT
FLY - t12
NOT t21 -
null A B AB
null -A e - dB e - dAB e e -
ancestorrange
descendant range
FLY NOT
FLY - t12
NOT t21 -=+
trait matrix dispersal/extinction+
null A B AB
null -A e - dB e - dAB e e -
ancestorrange
descendant range
FLY NOT
FLY - t12
NOT t21 -
t21
=
null A B AB
null -A e - d
B e - d
AB e e -null A B AB
null -A e - md
B e - md
AB e e -
t12
+
Combined anagenetic
matrix
trait matrix dispersal/extinction+
DEC+J model: add trait to jump (Matzke 2014)
Sympatry (narrow)
Sympatry (subset)
Vicariance (narrow)
A
A BA B
A A B
A BCladogenesis(at splits)
Equalper-event
weights
(modified by j in DEC+J)
Jump dispersal (founder events)
Traditional:
DEC+J model: add trait to jump (Matzke 2014)
Sympatry (narrow)
Sympatry (subset)
Vicariance (narrow)
A
A BA B
A A B
A BCladogenesis(at splits)
Equalper-event
weights
(modified by j in DEC+J)
Cladogenesis(at splits)
Jump dispersal (founder events)
Traditional: Trait-dependent:
DEC+J model: add trait to jump (Matzke 2014)
Sympatry (narrow)
Sympatry (subset)
Vicariance (narrow)
A
A BA B
A A B
A BCladogenesis(at splits)
Equalper-event
weights
(modified by j in DEC+J)
Cladogenesis(at splits)
Jump dispersal (founder events)
Traditional: Trait-dependent:
DEC+J model: add trait to jump (Matzke 2014)
Sympatry (narrow)
Sympatry (subset)
Vicariance (narrow)
A
A BA B
A A B
A BCladogenesis(at splits)
Equalper-event
weights
(modified by j in DEC+J)
Cladogenesis(at splits)
Jump dispersal (founder events)
Trait model:
Traditional: Trait-dependent:
DEC+J model: add trait to jump (Matzke 2014)
Sympatry (narrow)
Sympatry (subset)
Vicariance (narrow)
A
A BA B
A A B
A BCladogenesis(at splits)
Equalper-event
weights
(modified by j in DEC+J)
Cladogenesis(at splits)
Jump dispersal (founder events)
m2 xTrait model:
Traditional: Trait-dependent:
Cladogenetic range-change model: DEC
Cladogenetic range-change events:
Sympatry (narrow)
Sympatry (subset)
Vicariance (narrow)
ending&rangeleft: A A A A A A A B B B B B B B C C C C C C C AB AB AB AB AB AB AB BC BC BC BC BC BC BC AC AC AC AC AC AC AC ABCABCABCABCABCABCABCright: A B C AB BC AC ABC A B C AB BC AC ABC A B C AB BC AC ABC A B C AB BC AC ABC A B C AB BC AC ABC A B C AB BC AC ABC A B C AB BC AC ABC countA sym 1B sym 1
starting C sym 1range AB vic sub vic sub sub sub 6
BC vic sub vic sub sub sub 6AC vic sub vic sub sub sub 6ABC vic sub vic sub vic sub vic vic vic sub sub sub 12
jjjj
jjj
jj j
jj j
j
jj j
j
Cladogenetic transition matrix:
ending&rangeleft: A A A A A A A B B B B B B B C C C C C C C AB AB AB AB AB AB AB BC BC BC BC BC BC BC AC AC AC AC AC AC AC ABCABCABCABCABCABCABCright: A B C AB BC AC ABC A B C AB BC AC ABC A B C AB BC AC ABC A B C AB BC AC ABC A B C AB BC AC ABC A B C AB BC AC ABC A B C AB BC AC ABC countA sym 1B sym 1
starting C sym 1range AB vic sub vic sub sub sub 6
BC vic sub vic sub sub sub 6AC vic sub vic sub sub sub 6ABC vic sub vic sub vic sub vic vic vic sub sub sub 12
jjjj
jjj
jj j
jj j
5 5 5 8 8 8 12
j
jj j
j
Cladogenetic transition matrix:
Cladogenetic range-change events:
Sympatry (narrow)
Sympatry (subset)
Vicariance (narrow)
Founder-event speciation
Cladogenetic range-change model: DEC+J
ending&rangeleft: A A A A A A A B B B B B B B C C C C C C C AB AB AB AB AB AB AB BC BC BC BC BC BC BC AC AC AC AC AC AC AC ABCABCABCABCABCABCABCright: A B C AB BC AC ABC A B C AB BC AC ABC A B C AB BC AC ABC A B C AB BC AC ABC A B C AB BC AC ABC A B C AB BC AC ABC A B C AB BC AC ABC countA sym 1B sym 1
starting C sym 1range AB vic sub vic sub sub sub 6
BC vic sub vic sub sub sub 6AC vic sub vic sub sub sub 6ABC vic sub vic sub vic sub vic vic vic sub sub sub 12
jjjj
jjj
jj j
jj j
5 5 5 8 8 8 12
j
jj j
j
Cladogenetic transition matrix while flying:
Cladogenetic range-change events:
Sympatry (narrow)
Sympatry (subset)
Vicariance (narrow)
Founder-event speciation
Trait-based cladogenetic model: DEC+J
ending&rangeleft: A A A A A A A B B B B B B B C C C C C C C AB AB AB AB AB AB AB BC BC BC BC BC BC BC AC AC AC AC AC AC AC ABCABCABCABCABCABCABCright: A B C AB BC AC ABC A B C AB BC AC ABC A B C AB BC AC ABC A B C AB BC AC ABC A B C AB BC AC ABC A B C AB BC AC ABC A B C AB BC AC ABC countA sym 1B sym 1
starting C sym 1range AB vic sub vic sub sub sub 6
BC vic sub vic sub sub sub 6AC vic sub vic sub sub sub 6ABC vic sub vic sub vic sub vic vic vic sub sub sub 12
mjj 5
5 5 8 8 8 12
j
Cladogenetic transition matrix while non-flying: j = m x j
mj mj
mj
mj
mj mjmj
mj
mj
mjmjmj
mj mjmj
Results: Model choice
Base%model rate%of%ran
ge%%%%expan
sion
rate%of%ran
ge%loss
weight%o
f%fou
nder5event%
speciatio
n
rate%of%flight%5>
%flightlessne
ss
rate%of%flightlessne
ss%5>
%flight
dispersal%m
ultip
lier%w
hen%
trait=1%(flight)
dispersal%m
ultip
lier%w
hen%
trait=2%(flightless)
rate%of%switch%to%flightlessne
ss%
durin
g%foun
der%e
vent
rate%of%switch%to%flight%during%
foun
der%e
vent
numbe
r%of%free%pa
rameters
log5likelihoo
d
delta
%AICc
mod
el%weight
d e j t12 t21 m1 m2 jt12 jt21 np LnL dAICc mw
DEC 3.84 1.94 0 3.31 0.94 1 0 0 0 4 +119.6 37.6 0.0%DEC 0.18 0.00 0.28 5.18 1.65 1 0 0 0 5 +103.9 9.4 0.9%DEC 3.81 2.01 0 2.58 0 1 0 0 0 3 +120.3 36.2 0.0%DEC 0.15 0.00 0.16 2.84 0 1 0 0 0 4 +107.5 13.5 0.1%DEC 2.50 1.69 0 3.60 1.28 1 0 1.00 0 5 +119.4 40.3 0.0%DEC 0.18 0.00 0.82 4.37 1.12 1 0 0.75 0 6 +104.2 13.3 0.1%DEC 3.31 1.98 0 2.57 0 1 0 1.00 0 4 +120.2 38.9 0.0%DEC 0.15 1E+12 0.16 2.84 0 1 0 0.00 0 5 +107.5 16.6 0.0%
DIVALIKE 1.99 0.82 0 5.16 1.48 1 0 0 0 4 +115.2 28.9 0.0%DIVALIKE 0.24 0.00 0.22 5.73 1.71 1 0 0 0 5 +104.1 9.8 0.7%DIVALIKE 2.68 1.50 0 2.60 0 1 0 0 0 3 +117.7 31.0 0.0%DIVALIKE 0.16 0.00 0.10 2.61 0 1 0 0 0 4 +109.3 17.1 0.0%DIVALIKE 2.35 0.90 0 4.38 1.11 1 0 0.91 0 5 +115.3 32.2 0.0%DIVALIKE 0.24 0.00 0.49 5.49 1.49 1 0 0.62 0 6 +104.1 13.2 0.1%DIVALIKE 2.56 1.45 0 2.70 0 1 0 0.58 0 4 +117.7 33.8 0.0%DIVALIKE 0.17 1E+12 0.64 2.81 0 1 0 0.87 0 5 +109.3 20.1 0.0%
BAYAREALIKE 6.40 3.70 0 4.13 2.37 1 0 0 0 4 +129.7 57.8 0.0%BAYAREALIKE 5.34 3.70 0.95 4.14 2.38 1 0 0 0 5 +122.3 46.2 0.0%BAYAREALIKE 3.32 3.91 0 2.67 0 1 0 0 0 3 +130.8 57.2 0.0%BAYAREALIKE 3.34 3.91 0.78 2.67 0 1 0 0 0 4 +123.0 44.4 0.0%BAYAREALIKE 4.36 3.46 0 5.66 2.45 1 0 0.98 0 5 +129.9 61.4 0.0%BAYAREALIKE 0.09 0.16 0.35 9.24 3.01 1 0 0.42 0 6 +97.51 0.0 96.5%BAYAREALIKE 3.36 2.66 0 2.61 0 1 0 0.00 0 4 +132.5 63.5 0.0%BAYAREALIKE 0.07 1E+12 0.14 2.59 0 1 0 0.14 0 5 +103.4 8.4 1.5%
Black:>free>parameter>that>is>estimated.>Gray:>fixed>parameter.
Results: Model choice
Base%model rate%of%ran
ge%%%%expan
sion
rate%of%ran
ge%loss
weight%o
f%fou
nder5event%
speciatio
n
rate%of%flight%5>
%flightlessne
ss
rate%of%flightlessne
ss%5>
%flight
dispersal%m
ultip
lier%w
hen%
trait=1%(flight)
dispersal%m
ultip
lier%w
hen%
trait=2%(flightless)
rate%of%switch%to%flightlessne
ss%
durin
g%foun
der%e
vent
rate%of%switch%to%flight%during%
foun
der%e
vent
numbe
r%of%free%pa
rameters
log5likelihoo
d
delta
%AICc
mod
el%weight
d e j t12 t21 m1 m2 jt12 jt21 np LnL dAICc mw
DEC 3.84 1.94 0 3.31 0.94 1 0 0 0 4 +119.6 37.6 0.0%DEC 0.18 0.00 0.28 5.18 1.65 1 0 0 0 5 +103.9 9.4 0.9%DEC 3.81 2.01 0 2.58 0 1 0 0 0 3 +120.3 36.2 0.0%DEC 0.15 0.00 0.16 2.84 0 1 0 0 0 4 +107.5 13.5 0.1%DEC 2.50 1.69 0 3.60 1.28 1 0 1.00 0 5 +119.4 40.3 0.0%DEC 0.18 0.00 0.82 4.37 1.12 1 0 0.75 0 6 +104.2 13.3 0.1%DEC 3.31 1.98 0 2.57 0 1 0 1.00 0 4 +120.2 38.9 0.0%DEC 0.15 1E+12 0.16 2.84 0 1 0 0.00 0 5 +107.5 16.6 0.0%
DIVALIKE 1.99 0.82 0 5.16 1.48 1 0 0 0 4 +115.2 28.9 0.0%DIVALIKE 0.24 0.00 0.22 5.73 1.71 1 0 0 0 5 +104.1 9.8 0.7%DIVALIKE 2.68 1.50 0 2.60 0 1 0 0 0 3 +117.7 31.0 0.0%DIVALIKE 0.16 0.00 0.10 2.61 0 1 0 0 0 4 +109.3 17.1 0.0%DIVALIKE 2.35 0.90 0 4.38 1.11 1 0 0.91 0 5 +115.3 32.2 0.0%DIVALIKE 0.24 0.00 0.49 5.49 1.49 1 0 0.62 0 6 +104.1 13.2 0.1%DIVALIKE 2.56 1.45 0 2.70 0 1 0 0.58 0 4 +117.7 33.8 0.0%DIVALIKE 0.17 1E+12 0.64 2.81 0 1 0 0.87 0 5 +109.3 20.1 0.0%
BAYAREALIKE 6.40 3.70 0 4.13 2.37 1 0 0 0 4 +129.7 57.8 0.0%BAYAREALIKE 5.34 3.70 0.95 4.14 2.38 1 0 0 0 5 +122.3 46.2 0.0%BAYAREALIKE 3.32 3.91 0 2.67 0 1 0 0 0 3 +130.8 57.2 0.0%BAYAREALIKE 3.34 3.91 0.78 2.67 0 1 0 0 0 4 +123.0 44.4 0.0%BAYAREALIKE 4.36 3.46 0 5.66 2.45 1 0 0.98 0 5 +129.9 61.4 0.0%BAYAREALIKE 0.09 0.16 0.35 9.24 3.01 1 0 0.42 0 6 +97.51 0.0 96.5%BAYAREALIKE 3.36 2.66 0 2.61 0 1 0 0.00 0 4 +132.5 63.5 0.0%BAYAREALIKE 0.07 1E+12 0.14 2.59 0 1 0 0.14 0 5 +103.4 8.4 1.5%
Black:>free>parameter>that>is>estimated.>Gray:>fixed>parameter.
Base%model rate%of%ran
ge%%%%expan
sion
rate%of%ran
ge%loss
weight%o
f%fou
nder5event%
speciatio
n
rate%of%flight%5>
%flightlessne
ss
rate%of%flightlessne
ss%5>
%flight
dispersal%m
ultip
lier%w
hen%
trait=1%(flight)
dispersal%m
ultip
lier%w
hen%
trait=2%(flightless)
rate%of%switch%to%flightlessne
ss%
durin
g%foun
der%e
vent
rate%of%switch%to%flight%during%
foun
der%e
vent
numbe
r%of%free%pa
rameters
log5likelihoo
d
delta
%AICc
mod
el%weight
d e j t12 t21 m1 m2 jt12 jt21 np LnL dAICc mw
DEC 3.84 1.94 0 3.31 0.94 1 0 0 0 4 +119.6 37.6 0.0%DEC 0.18 0.00 0.28 5.18 1.65 1 0 0 0 5 +103.9 9.4 0.9%DEC 3.81 2.01 0 2.58 0 1 0 0 0 3 +120.3 36.2 0.0%DEC 0.15 0.00 0.16 2.84 0 1 0 0 0 4 +107.5 13.5 0.1%DEC 2.50 1.69 0 3.60 1.28 1 0 1.00 0 5 +119.4 40.3 0.0%DEC 0.18 0.00 0.82 4.37 1.12 1 0 0.75 0 6 +104.2 13.3 0.1%DEC 3.31 1.98 0 2.57 0 1 0 1.00 0 4 +120.2 38.9 0.0%DEC 0.15 1E+12 0.16 2.84 0 1 0 0.00 0 5 +107.5 16.6 0.0%
DIVALIKE 1.99 0.82 0 5.16 1.48 1 0 0 0 4 +115.2 28.9 0.0%DIVALIKE 0.24 0.00 0.22 5.73 1.71 1 0 0 0 5 +104.1 9.8 0.7%DIVALIKE 2.68 1.50 0 2.60 0 1 0 0 0 3 +117.7 31.0 0.0%DIVALIKE 0.16 0.00 0.10 2.61 0 1 0 0 0 4 +109.3 17.1 0.0%DIVALIKE 2.35 0.90 0 4.38 1.11 1 0 0.91 0 5 +115.3 32.2 0.0%DIVALIKE 0.24 0.00 0.49 5.49 1.49 1 0 0.62 0 6 +104.1 13.2 0.1%DIVALIKE 2.56 1.45 0 2.70 0 1 0 0.58 0 4 +117.7 33.8 0.0%DIVALIKE 0.17 1E+12 0.64 2.81 0 1 0 0.87 0 5 +109.3 20.1 0.0%
BAYAREALIKE 6.40 3.70 0 4.13 2.37 1 0 0 0 4 +129.7 57.8 0.0%BAYAREALIKE 5.34 3.70 0.95 4.14 2.38 1 0 0 0 5 +122.3 46.2 0.0%BAYAREALIKE 3.32 3.91 0 2.67 0 1 0 0 0 3 +130.8 57.2 0.0%BAYAREALIKE 3.34 3.91 0.78 2.67 0 1 0 0 0 4 +123.0 44.4 0.0%BAYAREALIKE 4.36 3.46 0 5.66 2.45 1 0 0.98 0 5 +129.9 61.4 0.0%BAYAREALIKE 0.09 0.16 0.35 9.24 3.01 1 0 0.42 0 6 +97.51 0.0 96.5%BAYAREALIKE 3.36 2.66 0 2.61 0 1 0 0.00 0 4 +132.5 63.5 0.0%BAYAREALIKE 0.07 1E+12 0.14 2.59 0 1 0 0.14 0 5 +103.4 8.4 1.5%
Black:>free>parameter>that>is>estimated.>Gray:>fixed>parameter.
Base%model rate%of%ran
ge%%%%expan
sion
rate%of%ran
ge%loss
weight%o
f%fou
nder5event%
speciatio
n
rate%of%flight%5>
%flightlessne
ss
rate%of%flightlessne
ss%5>
%flight
dispersal%m
ultip
lier%w
hen%
trait=1%(flight)
dispersal%m
ultip
lier%w
hen%
trait=2%(flightless)
rate%of%switch%to%flightlessne
ss%
durin
g%foun
der%e
vent
rate%of%switch%to%flight%during%
foun
der%e
vent
numbe
r%of%free%pa
rameters
log5likelihoo
d
delta
%AICc
mod
el%weight
d e j t12 t21 m1 m2 jt12 jt21 np LnL dAICc mw
DEC 3.84 1.94 0 3.31 0.94 1 0 0 0 4 +119.6 37.6 0.0%DEC 0.18 0.00 0.28 5.18 1.65 1 0 0 0 5 +103.9 9.4 0.9%DEC 3.81 2.01 0 2.58 0 1 0 0 0 3 +120.3 36.2 0.0%DEC 0.15 0.00 0.16 2.84 0 1 0 0 0 4 +107.5 13.5 0.1%DEC 2.50 1.69 0 3.60 1.28 1 0 1.00 0 5 +119.4 40.3 0.0%DEC 0.18 0.00 0.82 4.37 1.12 1 0 0.75 0 6 +104.2 13.3 0.1%DEC 3.31 1.98 0 2.57 0 1 0 1.00 0 4 +120.2 38.9 0.0%DEC 0.15 1E+12 0.16 2.84 0 1 0 0.00 0 5 +107.5 16.6 0.0%
DIVALIKE 1.99 0.82 0 5.16 1.48 1 0 0 0 4 +115.2 28.9 0.0%DIVALIKE 0.24 0.00 0.22 5.73 1.71 1 0 0 0 5 +104.1 9.8 0.7%DIVALIKE 2.68 1.50 0 2.60 0 1 0 0 0 3 +117.7 31.0 0.0%DIVALIKE 0.16 0.00 0.10 2.61 0 1 0 0 0 4 +109.3 17.1 0.0%DIVALIKE 2.35 0.90 0 4.38 1.11 1 0 0.91 0 5 +115.3 32.2 0.0%DIVALIKE 0.24 0.00 0.49 5.49 1.49 1 0 0.62 0 6 +104.1 13.2 0.1%DIVALIKE 2.56 1.45 0 2.70 0 1 0 0.58 0 4 +117.7 33.8 0.0%DIVALIKE 0.17 1E+12 0.64 2.81 0 1 0 0.87 0 5 +109.3 20.1 0.0%
BAYAREALIKE 6.40 3.70 0 4.13 2.37 1 0 0 0 4 +129.7 57.8 0.0%BAYAREALIKE 5.34 3.70 0.95 4.14 2.38 1 0 0 0 5 +122.3 46.2 0.0%BAYAREALIKE 3.32 3.91 0 2.67 0 1 0 0 0 3 +130.8 57.2 0.0%BAYAREALIKE 3.34 3.91 0.78 2.67 0 1 0 0 0 4 +123.0 44.4 0.0%BAYAREALIKE 4.36 3.46 0 5.66 2.45 1 0 0.98 0 5 +129.9 61.4 0.0%BAYAREALIKE 0.09 0.16 0.35 9.24 3.01 1 0 0.42 0 6 +97.51 0.0 96.5%BAYAREALIKE 3.36 2.66 0 2.61 0 1 0 0.00 0 4 +132.5 63.5 0.0%BAYAREALIKE 0.07 1E+12 0.14 2.59 0 1 0 0.14 0 5 +103.4 8.4 1.5%
Black:>free>parameter>that>is>estimated.>Gray:>fixed>parameter.
Results: Model choice
Base%model rate%of%ran
ge%%%%expan
sion
rate%of%ran
ge%loss
weight%o
f%fou
nder5event%
speciatio
n
rate%of%flight%5>
%flightlessne
ss
rate%of%flightlessne
ss%5>
%flight
dispersal%m
ultip
lier%w
hen%
trait=1%(flight)
dispersal%m
ultip
lier%w
hen%
trait=2%(flightless)
rate%of%switch%to%flightlessne
ss%
durin
g%foun
der%e
vent
rate%of%switch%to%flight%during%
foun
der%e
vent
numbe
r%of%free%pa
rameters
log5likelihoo
d
delta
%AICc
mod
el%weight
d e j t12 t21 m1 m2 jt12 jt21 np LnL dAICc mw
DEC 3.84 1.94 0 3.31 0.94 1 0 0 0 4 +119.6 37.6 0.0%DEC 0.18 0.00 0.28 5.18 1.65 1 0 0 0 5 +103.9 9.4 0.9%DEC 3.81 2.01 0 2.58 0 1 0 0 0 3 +120.3 36.2 0.0%DEC 0.15 0.00 0.16 2.84 0 1 0 0 0 4 +107.5 13.5 0.1%DEC 2.50 1.69 0 3.60 1.28 1 0 1.00 0 5 +119.4 40.3 0.0%DEC 0.18 0.00 0.82 4.37 1.12 1 0 0.75 0 6 +104.2 13.3 0.1%DEC 3.31 1.98 0 2.57 0 1 0 1.00 0 4 +120.2 38.9 0.0%DEC 0.15 1E+12 0.16 2.84 0 1 0 0.00 0 5 +107.5 16.6 0.0%
DIVALIKE 1.99 0.82 0 5.16 1.48 1 0 0 0 4 +115.2 28.9 0.0%DIVALIKE 0.24 0.00 0.22 5.73 1.71 1 0 0 0 5 +104.1 9.8 0.7%DIVALIKE 2.68 1.50 0 2.60 0 1 0 0 0 3 +117.7 31.0 0.0%DIVALIKE 0.16 0.00 0.10 2.61 0 1 0 0 0 4 +109.3 17.1 0.0%DIVALIKE 2.35 0.90 0 4.38 1.11 1 0 0.91 0 5 +115.3 32.2 0.0%DIVALIKE 0.24 0.00 0.49 5.49 1.49 1 0 0.62 0 6 +104.1 13.2 0.1%DIVALIKE 2.56 1.45 0 2.70 0 1 0 0.58 0 4 +117.7 33.8 0.0%DIVALIKE 0.17 1E+12 0.64 2.81 0 1 0 0.87 0 5 +109.3 20.1 0.0%
BAYAREALIKE 6.40 3.70 0 4.13 2.37 1 0 0 0 4 +129.7 57.8 0.0%BAYAREALIKE 5.34 3.70 0.95 4.14 2.38 1 0 0 0 5 +122.3 46.2 0.0%BAYAREALIKE 3.32 3.91 0 2.67 0 1 0 0 0 3 +130.8 57.2 0.0%BAYAREALIKE 3.34 3.91 0.78 2.67 0 1 0 0 0 4 +123.0 44.4 0.0%BAYAREALIKE 4.36 3.46 0 5.66 2.45 1 0 0.98 0 5 +129.9 61.4 0.0%BAYAREALIKE 0.09 0.16 0.35 9.24 3.01 1 0 0.42 0 6 +97.51 0.0 96.5%BAYAREALIKE 3.36 2.66 0 2.61 0 1 0 0.00 0 4 +132.5 63.5 0.0%BAYAREALIKE 0.07 1E+12 0.14 2.59 0 1 0 0.14 0 5 +103.4 8.4 1.5%
Black:>free>parameter>that>is>estimated.>Gray:>fixed>parameter.
Results: Model choice
Base%model rate%of%ran
ge%%%%expan
sion
rate%of%ran
ge%loss
weight%o
f%fou
nder5event%
speciatio
n
rate%of%flight%5>
%flightlessne
ss
rate%of%flightlessne
ss%5>
%flight
dispersal%m
ultip
lier%w
hen%
trait=1%(flight)
dispersal%m
ultip
lier%w
hen%
trait=2%(flightless)
rate%of%switch%to%flightlessne
ss%
durin
g%foun
der%e
vent
rate%of%switch%to%flight%during%
foun
der%e
vent
numbe
r%of%free%pa
rameters
log5likelihoo
d
delta
%AICc
mod
el%weight
d e j t12 t21 m1 m2 jt12 jt21 np LnL dAICc mw
DEC 3.84 1.94 0 3.31 0.94 1 0 0 0 4 +119.6 37.6 0.0%DEC 0.18 0.00 0.28 5.18 1.65 1 0 0 0 5 +103.9 9.4 0.9%DEC 3.81 2.01 0 2.58 0 1 0 0 0 3 +120.3 36.2 0.0%DEC 0.15 0.00 0.16 2.84 0 1 0 0 0 4 +107.5 13.5 0.1%DEC 2.50 1.69 0 3.60 1.28 1 0 1.00 0 5 +119.4 40.3 0.0%DEC 0.18 0.00 0.82 4.37 1.12 1 0 0.75 0 6 +104.2 13.3 0.1%DEC 3.31 1.98 0 2.57 0 1 0 1.00 0 4 +120.2 38.9 0.0%DEC 0.15 1E+12 0.16 2.84 0 1 0 0.00 0 5 +107.5 16.6 0.0%
DIVALIKE 1.99 0.82 0 5.16 1.48 1 0 0 0 4 +115.2 28.9 0.0%DIVALIKE 0.24 0.00 0.22 5.73 1.71 1 0 0 0 5 +104.1 9.8 0.7%DIVALIKE 2.68 1.50 0 2.60 0 1 0 0 0 3 +117.7 31.0 0.0%DIVALIKE 0.16 0.00 0.10 2.61 0 1 0 0 0 4 +109.3 17.1 0.0%DIVALIKE 2.35 0.90 0 4.38 1.11 1 0 0.91 0 5 +115.3 32.2 0.0%DIVALIKE 0.24 0.00 0.49 5.49 1.49 1 0 0.62 0 6 +104.1 13.2 0.1%DIVALIKE 2.56 1.45 0 2.70 0 1 0 0.58 0 4 +117.7 33.8 0.0%DIVALIKE 0.17 1E+12 0.64 2.81 0 1 0 0.87 0 5 +109.3 20.1 0.0%
BAYAREALIKE 6.40 3.70 0 4.13 2.37 1 0 0 0 4 +129.7 57.8 0.0%BAYAREALIKE 5.34 3.70 0.95 4.14 2.38 1 0 0 0 5 +122.3 46.2 0.0%BAYAREALIKE 3.32 3.91 0 2.67 0 1 0 0 0 3 +130.8 57.2 0.0%BAYAREALIKE 3.34 3.91 0.78 2.67 0 1 0 0 0 4 +123.0 44.4 0.0%BAYAREALIKE 4.36 3.46 0 5.66 2.45 1 0 0.98 0 5 +129.9 61.4 0.0%BAYAREALIKE 0.09 0.16 0.35 9.24 3.01 1 0 0.42 0 6 +97.51 0.0 96.5%BAYAREALIKE 3.36 2.66 0 2.61 0 1 0 0.00 0 4 +132.5 63.5 0.0%BAYAREALIKE 0.07 1E+12 0.14 2.59 0 1 0 0.14 0 5 +103.4 8.4 1.5%
Black:>free>parameter>that>is>estimated.>Gray:>fixed>parameter.
Base model matters too!
Gallirallus_pendiculentusGallirallus_philippensis_melloGallirallus_philippensis_19403Gallirallus_philippensis_42507Gallirallus_ripleyiGallirallus_wakensisTricholimnas_sylvestris_1896Gallirallus_rovianae_28014Gallirallus_rovianae_826433Nesoclopeus_woodfordi_immaculaGallirallus_owstoniHabropteryx_insignisHabropteryx_torquatus_celebensHabropteryx_torquatus_sulcirosHabropteryx_torquatus_torquatuHabropteryx_okinawaeCabalus_modestusEulabeornis_castaneoventrisGallirallus_australis_australiGallirallus_australis_greyiTricholimnas_lafresnayanusHabroptila_wallaciiGallirallus_calayanensisGallirallus_striatusGallirallus_pectoralisAramidopsis_plateni
1 0.8 0.6 0.4 0.2 0Millions of years ago
Not
Not
Not
Not
Not
Not
Not
Not
Not
Not
NotNot
Fly
NotNot
NotNot
NotNot
FlyFly
NotNot
NotFly
NotFlyFlyFlyNotNotNotNotNotNotNotNotFlyFlyFlyNotNotFlyNotNotNotNotNotFlyFlyNot
BioGeoBEARS BAYAREALIKE on traitonly M0_unconstrainedancstates: global optim, 1 areas max. a=1.1954; j=0; LnL=−14.83
Not
NotNot
Not
Not
Not
Not
Not
Not
Not
Not
Not
Fly
NotNot
NotNot
NotNot
FlyFly
NotNot
NotFly
Not
Not
Not
Not
Not
Not
Not
Not
Not
NotNotNot
Fly
NotNot
NotNot
NotNot
FlyFly
NotNot
NotFly
Flying:
Non-‐flying:
Distribu4on of flight in Pacific Rails
(standard trait model)
Flying:
Non-‐flying:
Distribu4on of flight in Pacific Rails
(standard trait model)
Gallirallus_pendiculentusGallirallus_philippensis_melloGallirallus_philippensis_19403Gallirallus_philippensis_42507Gallirallus_ripleyiGallirallus_wakensisTricholimnas_sylvestris_1896Gallirallus_rovianae_28014Gallirallus_rovianae_826433Nesoclopeus_woodfordi_immaculaGallirallus_owstoniHabropteryx_insignisHabropteryx_torquatus_celebensHabropteryx_torquatus_sulcirosHabropteryx_torquatus_torquatuHabropteryx_okinawaeCabalus_modestusEulabeornis_castaneoventrisGallirallus_australis_australiGallirallus_australis_greyiTricholimnas_lafresnayanusHabroptila_wallaciiGallirallus_calayanensisGallirallus_striatusGallirallus_pectoralisAramidopsis_plateni
1 0.8 0.6 0.4 0.2 0Millions of years ago
Not
Not
Fly
Fly
Fly
Fly
Fly
Fly
Fly
Fly
FlyFly
Fly
FlyFly
FlyNot
FlyFly
FlyFly
FlyNot
NotNot
NotFlyFlyFlyNotNotNotNotNotNotNotNotFlyFlyFlyNotNotFlyNotNotNotNotNotFlyFlyNot
BioGeoBEARS DEC+J+t12+t21+jt12+m1 on Pacific Rail flightancstates: global optim, 1 areas max. d=0.0935; e=0.1565; j=0.3493; t12=9.2439; t21=3.0112; jt12=0.4168; LnL=−97.51
Not
NotFly
Fly
Fly
Fly
Fly
Fly
Fly
Fly
Fly
Fly
Fly
FlyFly
FlyNot
FlyFly
FlyFly
FlyNot
NotNot
Not
Not
Fly
Fly
Fly
Fly
Fly
Fly
Fly
FlyFlyFly
Fly
FlyFly
FlyNot
FlyFly
FlyFly
FlyNot
NotNot
1. Trait-‐based dispersal models are feasible, at least for moderate-‐sized problems (key issue: size of matrices)
2. Trait evo. & its influence on dispersal can be revealed by parameter es@ma@on 3. Combinable with distance, etc. 4. Adding to BioGeoBEARS; email me to try it: [email protected]
Conclusions
Adolf Meyer (1898), The Birds of Celebes and the neighbouring islands. https://
en.wikipedia.org/wiki/Snoring_rail
Snoring rail, Aramidopsis plateni (flightless, Sulawesi)
Thanks! I welcome quesCons/comments/collaboraCons at: [email protected]
BioGeoBEARS Funding: NSF “Bivalves in Time and Space” UC Berkeley Wang Fellowship UC Berkeley Tien Fellowship Google Summer of Code NIMBioS ARC DECRA
TRY BIOGEOBEARS AT: h_p://phylo.wikidot.com/biogeobears
Thanks especially to:
Jeremy Kirchman
Craig Moritz ANU ARC DECRA
NIMBioS Brian O’Meara Jeremy Beaulieu KaGe Massana Michael Landis
Thanks! I welcome quesCons/comments/collaboraCons at: [email protected]
BioGeoBEARS Funding: NSF “Bivalves in Time and Space” UC Berkeley Wang Fellowship UC Berkeley Tien Fellowship Google Summer of Code NIMBioS ARC DECRA
TRY BIOGEOBEARS AT: h_p://phylo.wikidot.com/biogeobears
Thanks especially to:
Jeremy Kirchman
Craig Moritz ANU ARC DECRA
NIMBioS Brian O’Meara Jeremy Beaulieu KaGe Massana Michael Landis
