1
Supplementary analyses and results
1
Phylogenies
Psychotria_marginata
Psychotria_ graciliflora
Psycho tria_gra ndis
nens is
Psyc hotria _limo
tenu ifolia
Psy chot ria_
ifol ia
s
_ps ych otri
Psy cho triaotria_chagrensi
a
Psych ho tria _d efl ex
a
Ps yc _cyanococc
a
tria
cemos
Psycho tria_ra
in at a
nsis
Psychotri a_ ac um
iane rt ii
ho
Ps yc ourea_gu_s ei betalis
Palic M or in daccidenm m ia
ig e d ra
ea_o
cu rv e x a n ra
Faram
re a _re a _ h a rv if lo
li a
p
ss a
ti fo a
C o u C o u tarr h is _ri a _ la p h y ll m
a u e c ro e u a
C h imo s o q _ m a _ rocskiane ri
P
ia u m
ti
g o n m _bla p it u m
n ta c n e is a _ o s ta
P e a c ro Alseo y e nfo r marmaanaa
c _ _
s
M
T o r o n ndia mericb o sis s
d
m n
e n Ra a_a o r y me d u li sii
io d
nip _ c na _ e ye m
erg
Ge io u a _pa r t ia _ha a t ut u mm
nb
a a b e m c in o u a
se
A m ojo li u ir id er e n
r
Ro
A
lan _ c le p sp ros ca a
Bo
So m _ a _ a t e
n u m _ ia y n
la n u um bu ua i g a
S o o la lan abe ia_g _ g
S So T u ra
b e
be t h
Ta h a n
ic
Tr
s
u m si
o r en ii
e t am od
o
u m an rw i
_d p a er
ir a sis_a _ g i t t i r a
p
sis
t t e op o n i s _ if lo a
en v e
ar e r
u a m n n s lt er
G es s a n o p m u bif il is _tov ip li n
D o o _ se b ia t r s a
M n o la _ n o d m _ r o
U ir ola _ mie u m b
V ir o la h o m _ u g a
V ir sc m r a lo n
V eil n a n d o b ua y
B in ta a _ ern z z
C e c te _c _ fu ru la
N c o tea d r a b e e a ta ra
O co ta n _ p u li n if lo is
O e c te a ra _ c is s ens
N c o n d ra _ ian ra
num
O e c ta n d _gu c if lo d le y a
N e c ta na _ p a u s ta n ra
N iparu n a u m _ a p o
S ip a ru a ry s _ m
S s tr o c a rp u tr a ta p e jil o te
A e n o c _ ro s a _ te
O a le a e d o re
A tt a m a eifera s
C h eis_ol ar ro ni
Ela tr is _b aj or
B acct ris _m on ia ta
Ba ct ris _c ol xo rrh iza
Ba at ea _e
So cr aequale
Piper_ arb ore um
Pip er_ cor dul atu m
Pip er_ lonense
Piper_co icula tum
Pipe r_ret oanum
Piper_ carrill
Piper_perlasense
Ginkgo_biloba
Abarema_macradenia
Schizolobium_pa rahyba
Enterolo bium_sc
Inga_ acumi nata homburg kii
Inga _pez izife
ra
Inga _pu
Inga_coclncta ta
eensis
Ing a_
Ing a_ rui zia na
In ga ma rgi na
In ga _n ob ilis ta
In ga _o er st ed
_t
ia
In ga hi ba
na
In _s ap ud ia na
In ga _g ol in do id
In g a _ la dm an es
In g a _ sp u ri n a ii
C g a _ u e ct
T o jo b m b e a b ili s
Vaa c h iga _ ru fell if e ra
sc
S ch a li
A enn ellia _ v e e n s
D n d ir a_d _m rs ic
E ip te a _ ari elan o lo r
O r y th r y in e ens ocera
L r m r in x _ o rm is
s
O o n o s a _ le is
O r rmoc h o ia _ a c o s if e r a
c
P m
m ta
P la o sia a r p a r ic
P la t y s ia _c u s z o n e n
P te ty m is _ oc _ h ic s is
M t e r rocpod c ium a c cine e p taa
S y
ph
S w r o o c ar ium m r o c a
y ll
B wa art s p a r p pus _e _ p in a ly
us
r o r z e r u _ le n x
s i tzia ia_ m s _ be ga a t
m _ s u m r o liz n u m
u m s im _ h r en s
_ a imp ple f r u ii sis
t
x
l i c lex _ e s
a s _v v a c e
t r u ar r _ g n s
m _o r a
ch n d
na iflo
ce r a
a
H ie
Ce
se
en
an
ui i
_ g ne a na
um lle o li ica a
im bu it r if tar if o li i
o s s_ _ c os u s o e
Br icu u s s_c o b t pen a t a
F ic u _ o o n a sis
F ic u s _p r ig id en
F ic us _ t sip on a
F ic u s _in p im
F ic us yo a x z ii e n s is
F ic s_ m d u n a
F icu s _ to n g u ia an
c
ta ma
F u _ _
F icic u su ir a _cauarma ochy
F a q his ia_ nth
M rop en _xa inis s a
T ouls bea _aff m o
P ere cea ra c e ig n is li a
P oro is _ in s s if o
S ro p h p ia _ o b tu e s
T c ro ia _
g ip
C ee c ro p ia _ lo nb ic o lo r
C e c ro p m a _ ra
C u ro u accife i
P o ra_b ch ip pi ha
Ure tis _s ic ra nt fo lia
C el a_ m iv er si ac hy a
Tr em
ha _d
ro st
Ac al yp ha _m ac lia
ifo
Ac al yp
ne a_ lat
Al ch ora_ tril ob a
Ad eli
pita ns
Hu ra_ cre
oad leaf
Sap ium _br
dulo sum
Sap ium_ glan
ianus
Croto n_bil lberg
Hirtella _ameri cana
Hirtella_tria ndra
Licania_hypoleuca
M
H
a
yb
a R yt
L n in en
r o M ind t h u ore us
n y a r a c s _ a_ _
m ga ke p s sc
a _ r it r r u ylv hi
sp
a lc a r ia_ n i a pp
O
e
de ur h o ia _ la f o l tic ii
Te La
u i a
c
a
Ca tr a th is te L o sia_ tea r n e n o b rin u s
se y la m a z a sp _lu o id il is a
aria c iu _ n ia at c e
_ m a g _ hu en s
Ca com _ jo g r e gp it t ielata s
Z u se me h a a tu r
e la ari rs n s m i
on e n
L a n ia _a_arb
ia ii
L e ti a g u orena
C
Ca asea aetia _ th aid o n iaa
se
ria _p m
C aria_ _sy roc n ia
X y loaseari guianlvestrera
H a ss
s m a a_ac ens is
e lt ia _ o lig ulea is
ta
_
a
V is mM a ri lafl o ri b un d ra
ia _b _ la xi n d a
flo ra
Sy m phV is m ia ill be rg ia
on ia _g_b ac ci na
Ga rc in
lo liffe ra
ia _mbu
er
Ga rci nia
a
Ch rys
_in terad ru no
me dia
Ca lop hyloc hla my s_ ec
lip es
lum
Spachea_m_lo ng ifo lium
embranace
Malp ighia _rom
a
eroa na
Eryth roxyl um_p
anam ense
Erythro xylum_ macrop
hyllum
Cassipoure a_elliptica
Licania_platypus
Ap
he
la
Ae
n
T u gip Ja dra
r p hil car _s
P in a_ a in
T e T e r ic r ia _ pa nda cla
Co
r m a o n _ i
n o M o m in in am n iac c idam coprian
Co s t e g u r ir a li a li a _ _ la e n ens aia a
M ic nos ia _ i_ m _ a mo b t if ot a li is
o n teg c in y r t a z lo n li a s
ia ia n il o g
L e M _ h o _bra m olo id n ia a
a
ic n a m e
M icn d r a o n iad u r ctea e a s
_
e
M ic Mic o n ia d ic h_ a ff n s ista
o n on _ a rg o to in is
ia _ ia_ e m
im
C li d M ic Mic p enerv n te aa
e m o n on ti o osa
ia _ ia _ ia_ la ri
C li ds e p tu d o rs ilelatas
p
o
e
L a foC lid e mm ia _ oli n e rv b a
ia
P si di
V e n si ia _ c to n a
um _f oc hy si a _ p u nd e n ta ta
rie dr a_ fe ic if o
M yr ic hs th rr ug in lia
Euge ci a_ ga tual ia nuea
nia_oe ne ns m
Eugenia rstedi is
Eugenia
_nesiotana
_galalon
ica
Eu ge nia
ensis
_co
Ch am gua lor ad oe nsi
va_ sch ipp s
Cap pari s_fr
ond osaii
Sterculia_apet
ala
Pachira_quinata
Pseudob ombax_s eptenatu
m
Ochroma_pyram idale
Ceiba_pentandra
Cavanillesia_plat anifolia
Theobrom a_cacao
a
Herra nia_p urpure
lata
ndicu
Ham pea_ appe
lmif olia
Gua zum a_u
emanniiu
Luehea_se
tib ou rbo
Ap eib a_mb ran ac ea
ra
me
ma
a_
_a
Ap eib Quassia sp er a
_a
m
ni ck ia ui fo liuse
en
Tr at tin
am enns e
iu m _t
Pr ot m _p anta ri cesu
m
P ro tium _c osco n fu o fe ri
_
lk
P ro tiu
ti u m s _ ra d o m b in
ro
P n d ia s _ m o le n sm
S p op o n d iag ra v ec e ls uu m
S iu m _ _ e x e ri n u m
n
m
o
iu n ip lo s s e
A s tra c a rd m _ ju s e tu m e na n ii
A n x y lu lu m _p a n ae k mu la taa
o
y
_
_
n th o x m m e r c ll id ia
Z a a n th x y lu x y lu tu b _ p aidon li a
Z th o th o ia _ il ia gu if o zy
d z a
n
il h
Z a Z a n r ic h T r ic rea_ r a n _fu rat t ii
T
a _g ea do oa s
Gu r e a uar _o _ c r cen nii a
a G ela ia es an li a
Gu
dr li s ruf m if o re s
Ce T a ia_ see_ la t ine m u ra
_
n
c r lo
pa nia n iaia_ p e nif
Cuupa u p a an i l o s ter
C C up p s a_
C s _ ne
u oa
l
y l
ph S
lo
Al
Psychotria_horizontalis
Guettarda_ foliacea
Hameli a_axilla ris
Hame lia_p atens
Asp idos perm
a_sp ruce
Lac me lla_
pan am ens anu m
Ra uvo lfia
Ste mm _lit tor alis is
Ta be ad en ia_
Th ev rn ae mo gra nd iflo
C or diet ia _a honta na _a rb ra
or ea
ua i
C or a_ al
C or di a_ bi lio do ra
D e di a_ co lo r
A rdn d ro la si oc
A is ia p a n a al yx
A rd is ia _ b a rt x_ a rb
S rd is ia _ g u le tt ii o re u s
D ioty lo g y _ s ta nia n e n s
d le is
G s p ne
C usta y ro _ tu rb y a n
C h ry via s _ a a c a
P h ry s o p _su rt a n e n s
P ou s o h y perb th if is
P o u teri p h y ll u m a o li a
C o u te r a_ ll u _ a
C oo c c te r iaia _ sfossicm _ c arg e n
T c o _ ti
in te
G r ip c o lo r e p it ola it o u m
N u la lo b a ti c a ta
H e ap r is b a _ c u la
H e e a ira _ _ m o r o ta
A e is _ _ c u a n
A n is te a m sta m n z a ta
An nn axateriaria_ p li nd in g ia in e
no on go _c ac f o li aleya n a ll e n
s is
na
na a_ re on um
_s ac a_p cin ina
pr um an na ta
ag in a
ue ata me
ns
i
is
2
(a) Kress phylogeny
a ll
op
hy
lu
m s lo s _
a a p
lic li cy t en e s il
hy
h ir h an a n n ua _ o s
ir ia ia s t p
b
ce a n rinte ll ate ll _h _ p_ se r ne r
sp th uor _ a _yp lac h if lom
v ised ou s _ea a m tr olet y ip ru s
es ra p _s e ia up up iia
v
m
is
sy
ia _ia_ te r u ylvr ic n d c s
m p vm ia
a n
a a
h o is m_ bm ascpa_thluif oaliticn ar a
il
c
n
g m ia ia _ lb ero p hulaenussa
c a c h ryg a rca rc ina ri_lag lobba crg
y ll ta
ia _ u lic ifia
e ry e ry thlo p hs o c hin ia
na
th ro ro xyy ll u la m_ in_ mla
raa
feera
a dx if lo
xy lu lu m _ y ste rm
m _ lo n _ e eru nra
ca ssm _ m
p a n g if c lipd iao
ip
a
o
la ci st loou recr o pa m eli uems
n se
em za a_ h yl lu
zu a_ agni a_elpilip tic
te tra th xy loel an ia
gr eg tti erm
sm a__g ui
at umai
yla ciu
do
ol ig an
m_ joh
ni a
lin da ck
eri a_an
sedr
lae tia
niia
_thlau
lae tia_
amrin
casear
niaa
pro
cer
ia_sylve
casearia
a
stris
case aria_
_guianensis
comm
erso niana
casearia_ar
borea
casearia
_aculea
ta
banara_gu
ianensis
spachea_membranace
a
malpighia_romeroana
rauvolfia_littoralis
stemmadenia_grandi
tabernaem ontana_arbflora
orea
thevetia _ahoua
i
cestru m_me
sola num
hyllum
_arbgalop
sola num
oreu m
sola
_as peru
num _cir
m
sol
anu
so
m_ haycina tum
lan
um
co
esi i
rdi a_
co
all_s tey erm
rd ia_
co
ark ii
rd ia
biciod
de nd
oloora
as io
r
sc
ro_l
he ffl
pa
ca
ko
lyx
na
an
ve rb oper a_ x_ ar
ar
m or bo re
inhy
ot
rddiissies
a_llo
aard
gi n_ w etot onus
iaa_ ba
cshtyryloisgia __ fe nrt lega
nt eam oriei
s oy n eg u iadnle ritt ii
pcoh ry
en
tesrio pphh y_lltu rb
ppoo uute
y ll uu m a csies
ri aa _ fo
gduio su te
_
cte
_ ca rgnes is
rns tapvyriroa __sre tis sm
o
ic
c
a
s
c
o c c tr ia s _ ti p c u o la in itn te
gtr ip
c o o _ a it la
o um
hn eua la o lolo be ms u p rt a a ta ta
ahee ise apirr is b aa _ ia _ e rbn th
aannnnaisx tete_r aam__s c u_ mc o r ote p a if o li
noonagriaia _ p litanm ina n zn a e z a a
naa_or _ca c fo dle g iain eta p o
_s acea onu mli a ya n a ll e te
pr um_p cin in a na n s is
a
ag in n na ta
ue at am
i a en
sis
rauvolfia_littoralis
stemmadenia_grandi
tabernaem ontana_arbflora
orea
thevetia _ahoua
i
cestru m_me
galop hyllum
solan um_
arbo
sola num
reum
sola
_as peru
num _cir
m
sol
anu
so
m_ haycina tum
lan
um
co
rdi a_
i
teyesi
co
all_s
erm
rd ia_
iod
co rd
ark ii
de
oloora
_lbic
ndia
as io
r
sc
ro
he
pa
ca
ko an ffl er na lyx
ve
rb op hya_ mx_ ar bo
aar
re us
rddi sies in a_llo n_or ot ot on
ba rtgi ga w et m i
satyrd isis iaa_
_ fe
le tt nt ea or ei
n d le
cchh rylo gia
ii
y _ g u ia
n e ri
ppoo urytessoo pnhe _ tu
te ri ap h yy ll u rb an si s
dpioo uute
ens
s p ririaa __ follsu mm _ acrg
teg u s ta
c
is
re
_
y
rn
s
_
c
o
c o c s v iaro s s ti ti c ic o a ine n te
c cc o tr o _ _ a p it u la la it o u m
gtr ip
hn eua la o lolo be ms u p rt a a ta ta
ahee ise apirr is b aa _ ia _ e rbn th
aannnnaisx tete_r aam__s c u_ mc o rote p a if o li
noonagriaia _ p litanm ina n zn a e z a a
naa_or _ca c fo dle g iain eta p o
_s acea onu mli a ya n a ll e te
pr um_p cin in a na n s is
ag inan na ta
ue at am
i a en
sis
(b) Phylomatic phylogeny
sis
enu m
amt o r i
an e ie r h a
_pu mit t n ta
e
u lar v
sis_ d _ pc r alo r n s is
n dli n e
oepr ias ism alt ife r am e p eip
a
p
m
u
if
t
_
a
s t o ia m b in ia __ trif lo r
dgeunaolon pla __ sseu rie du mis s z y ta a
ux yir oo lala _ h mo ma _ cfu ze a u re
vv irir oil s ca m d r ra __ li nu rp
vb e n ta nn dd ra _ p uag a
rn
la
cnine cc tata nn d ra
is
ce lo n ru
nnee cc ta
a__ o bu b ee i n e n sra
noecootete aa __pw hgitu iau c if lo
_
oocc oote
te annaa _ puaa leu m
e
oscip aaru
e q re um
ru
r_ a rb one ns
atlis
spip
ip ee r_ aco lord ulria
co pe se ns e
ppiippe r_
r_
pe r_ im
rla ul at um
um
m
pi
pe r_ pe
ea nund ley an
pi
re tic
pe
hi ed
pi
sta
pe r_
m_ac
r_ scryu
ea
pi
pe
tyr nis
pi
tro ca
a_ bu
as
aleis_
ba rro
att
lon iata
is
ctr _co
ba
lora don
bac tris
_co
or
bac tris
maj
rea_ tepe jilote
bac tris_
cham aedo
era
elaeis _oleif
apora
oenoca rpus_m
socratea_e xorrhiza ii
mosannona_garwood
abarema_macradenia
acacia_melanoceras
andira_ine rmis
cojoba_ rufesce
ns
dipter yx_ol
eifera
ente rolob
ium_ scho mbu
eryt hrin
a_c
ing
osta
rgkii
a_a cum
ing
a_c ocl
ina tarice nsis
ing
een
a_ go
ing a_
sis
ing
lauldm
rin aan ii
in
ma rg
gaa_
in
_m
ina ta
ga _n
uc un
in
ga
ob
a
in
_o er
ili
ga
s
in
_p
ga _p ezst ed
in ga
iz ife ia na
in
g a __r uiun ct
in
ra
at
g
zi
in g a _ sa p an a
in
sp e in d a
g aa _ th
lo
c h_ u mib actua boiliid e s
ynro
omrm
b e d ia s
rm o ssopcea rp
oorm
ll if n
pplala oo s iaia _ rm uu s _e raa
pp r iotyty ms ia __ caom am _hfre p ta
m ac c z o n u te p h
sp tete r r iap o is c iu
in
sswecnh izr oocc a_ cdoiu m
mc ro e a ic a s c ey ll u s
t
r
a
ns
b a n o a p p _ _p ca
ficb r or ocsh igr t za_dlo br p uuss _a if ee le gin nly
x
iu _ o ff r a a a tu
uss imim a liia _arie
_a uu m_ vs im nm _ rpo h ic in n s m
ur m _ e r p sis a r r ii a li
s
ea_ g a li s ic le x a h
yb
u iac a o lo
a
n es t r r
n su m
e
ei a ae a
e no li in an
u ll r if b r ric a a
_ bc ito lusta id a o li
u s s __ cco s ipx ims if a e i
f icf ic uuusss___inm ab tur tuesn oz ii s isa is a
ic
n
o
s
f
fifciccuuuss __ ppeo pn doun ec tonrie nc h y m
fifi cc u ss __ too p_ ti nu ia th oa ta
fifi ccuu ss _ yraa _ gx a nrm
fifi c ua c luu ire a _ia _ aff inaisn as a
b e na _ a u c m o is
mm a qrels
a
s lia
ppeo uro c eis __cra cines iggnip efo
stroo pphh isp ia __ lo nb tu sio lo r
tr o c ro p ia _ o b ic
o
_
e
c
cr
ife ra
o puiam acc
ce
ii ha sa
cr
ppnt
ce
u ro
a_ ba
puroer
sc hi
ic ra du lolia
lti s_
a_ ma_ gl anrs ifo chya
ce
tre mbr in _d ive sta
cro
lu
ha
s
co
a_ma
al ypph
a
ice nsi
ac
ob
alya_ trila_
ac
cos tarlia
eli
ad
_la tifo
ho rne
alc
neallbe
rgia nus
yi
alc hor
_bi_sta ndle
s
cro ton
_alch orne oide
dryp etes
hiero nyma
ans
hura_ crepit
obilis
margar itaria_n
sapium_br oadleaf
sapium_glandulosum
op
hy
lu
m s lo s _
a a p
lic li cy t en e s il
hy
h a a n a_ o
b ir h ir nian iau s t s p
ce a n rinte ll ate ll _h _ p_ se r ne r
sp th uor _ a _yp lac h if lom
ed o s ea a m tr o t y ip ru s
v is
u
_
_
e
m iasiara p r sye ria nleup up iia
s y v is m
_ _ teau n lv ic a d cas
m p v ia
h o is m_ bm ascpa_thluif oaliticn ar a
il
c
n
g m ia ia _ lb ero p hulaenussa
c a c h ryg a rca rc ina ri_lag lobba crg
y ll ta
ia _ u lic ifia
e ry e ry thlo p hs o c hin ia
na
th ro ro xyy ll u la m_ in_ mla
raa
feera
a dx if lo
xy lu lu m _ y ste rm
m _ lo n _ e eru nra
ca ssm _ m
p
if c lipd iao
a cra n agm
la ci st iploou re
o p h oelinuems
em a_za nia_ el
yl
se
lu m
zu
ag gra_ pilip
te tra th xy loel an ia
a
ttitic
eg at
er
sm a__g ui
yla ciu
i
um
do ni
ol ig an
m_ joh
lin da ck
a
eri a_an
sedr
lae tia
niia
_thlau
lae tia_
amrin
casear
niaa
pro
cer
ia_sylve
casearia
a
case aria_
_guianestris
comm
nsis
erso niana
casearia_ar
borea
casearia
_aculea
ta
banara_gu
ianensis
spachea_membranacea
malpighia_romeroana
sis
ae ta
enu m
t u gip jabeb
amt o r i
te t er p hil ca u
an e ie r h a
la r m r min ia a_ra ia_
_pu mit t n ta
e
v fo in in _ p n g
u lar v
sis_ d _ pc r alo r n s is
m o c he n a li a lio c anda_ua
n dli n e
o u y s ia a a c idamc ya
oepr ias ism alt ife r am e p eip
a
s ia _ _ a _ o e eop c
r
r
p
m
_
u
if
t
_
a
m ir i_
s t o ia m b in ia _ trif lo
_ p m b n n aa
mm
o nm icico o nm yfe ru n ica zlo nt a lisisian
icic
dgeunaolon pla __ sseu rie du mis s z y ta a
o
z
c
ia
n
ux yir oo lala _ h mo ma _ fu e a u re
n ia r ti r u if o n g s
m ia _ _ imia _ _ p ll og ino li iaa
vv irir oil s ca m d r ra __ li nu rp
m ic m h o p n e r a id e a
vb e n ta nn dd ra _ p uag a
c o n le ic oo n iaic onnd euti orv os ineasa
rn
la
cnine cc tata nn d ra
o s te a n m icn ia __ d oia _re nla ris a
coeb lobne rui n s is
e
_
c
nn e c ta
a _ u e n e ra
cl idco n o g iad_ra _o n iaa rgrs ileolastaiss
noecootete aa __pw hgitu iau c if lo
e m st e c ind ic _ ae n b a
_
te
a
c
ia
a
g
h
ff inte a
ps id
ia _ n a mo to
oo c oo te n aa _ pu a le m
is
cl_ se p tu
b o mm
iu m
n e q re u e
oscip aaru
ru
em pra
_f riecl idid
um
linctee aetaaa
r_ a rb one ns
atlis
dr icem iaia _o
spip
ip ee r_ aco lord ulria
rv ia
ct on
eum
ci hs th_d
en
co pe se ns e
ppiippe r_
geyr
al ia
ta taa
ni a_ ga
im rla at um m
pe r_
nu
oe rstu ne
pi
ul ea nu ley an um
eu eu gea_
m
pe r_
nia
r_ pe
pi
te dins
nia _g
re tic
eu gege
nd
is
_n
pe
ed
r_
hi
an
pi
sta
es
nia _c ala lon iot icaa
pe r_ scryu m_ac ea
pi
ch am
pe
tyr nis
rad oeen sis
pi
guolo
tro ca
av a_
a_ bu
cap
as
rro
ns
ale
tric
par
sch
ba
is
hos per muis_ fro ndo
att
ipp
is
ctr is__co lon iata
ba
m_ gal eotsaii
lora don
theo brom
bac tris
_co
or
bac tris
maj
sterc ulia_a_c
acatii
o
rea_ tepe jilote
bac tris_
quara ribea_
apet
ala
cham aedo
astero
era
pseudo bombax
elaeis _oleif
apora
_septen lepis
oenoca rpus_m
pachira_seatum
ssilis
socratea_e xorrhiza ii
pachira_quinata
mosannona_garwood
ochroma_pyramidale
abarema_macradenia
acacia_melanoceras
luehea_seemannii
andira_ine rmis
urpurea
herrania_p
cojoba_ rufesce ns
unda
dipter yx_ol
hasselt ia_florib
culata
eifera
ente rolob
ea_ap pendi
ifolia
hamp
_ulm
ium_
eryt
hrin a_c ostascho mbu rgkii
ndraa
guaz uma
ing a_a
entaifoli
cum ina tarice nsis
ceib a_p
ing
a_c ocl
pla tan
boua
ing
ourace
lles ia_
een sis
a_ go
ing
iba _tib
cav aniape
ldm
um
a_ lau
mb ran
ing
tul os
rin aan ii
a_ me
in
en seii
ma rg
gaa_
m_ se
am
ap eib
in
_m
an_e
ina ta
ga _n
kmatan
uc un
ox ylu
in
ga
lum _p
ob
in mum
ar aa
za nth
in
lu m
_o er
m_a
ili s a
ga _p
ho xyho xy_a
cuba
aria
in
ga
za ntza
nt lu m ou
in
_p ezst
a_laam
tif ol
iz ed
in
na
xysi m ar assia_
ladtaa
ife ia
_r uiun ct
gga
ho
in
ra
a
cu
nt
_
qu
at
g
zi
ni
er
in g a _ sa p an a
a lli
za
o nliiaa
am_t uba _upid
in
sp e in d a
g aa _ th
lo
pi cr
liaic h ili
g n duiflloa ta
ct a o id
n
ta
_
_
m
hi
ib
c
a
u
y roh m ba u db ili e s
o rm
tr ic tru a re_ g ra
_ b o rae ra
e ll if ia ns
rm o ssopcea rp
g re a a re a_ o da sepn suisme
oorm
a
p
la
o
a
_
e
u
ia
u
rm
p lala o s ia _ a u s _ hra
g u ge d re k ian a mif o lie nnss em i
ia __ c om am _ e p
c n icp a n ua mc e s u r
ppter iotytypmsis
p
fr
ta
in
_
z
m ac c o n u te p h
tt is te n rin fu o feb in
s te r r ia o c iu
ns
in
tr aa s tru m __ poas ta
oa d lko m
sswecnh izr oocc a_ cdoiu m
le u ms
mc_ro ce a ic a s c ey ll u s
c
m
t
ti
c
g
r
_
r
a
n
m o ls e p a
a ro u _
b an o a p p _ p a
s
s _s _a v ec e cvonsnniis
te tr pp rotitiu mti u m
ficb r or ocsh igr t za_dlo br p uuss _a if ee le gin nly
x
iu _ o ff r a a a tu
o d ia ia g r e x r iner a e li aa
uss imim a liia _arie
p ro p rp o no n dm _m _ia _ p_nemesct if oere
_a uu m_ vs im nm _ rpo h ic in n s m
s s pn iud iuli s sia se uf la in
ur m _ e r p sis a r r ii a li
_ r _ c
s
tr o a r tatanliiaia_n iaia_
ea_ g a li s ic le x a h
yb
a sn a c
u iac a o lo
n
a
n
a
p ap a
a
a
n es t r r
cucupc u up
c
n su m
e
ei a ae a
e no li in an
u ll r if b r ric a a
_ bc ito lusta id a o li
u s s __ cco s ipx ims if a i
e
f icf ic uuusss___inm ab tur tuesn oz ii s isa is a
f icc u s _ o e p u e n rie n sh y m
p
d
fi
o
to
n
u
s
n
_
f ic
fificccuu ss __ptoo p_oti nucia nth oacta
fifi ccuu ss _ yraa _ gx a nrm
fifi c ua c luu ire a _ia _ aff inaisn as a
b e na _ a u c m o is
mm a qrels
a
s lia
ppeo uro c eis __cra cines iggnip efo
stroo pphh isp ia __ lo nb tu sio lo r
o
trcoe c roo ppia
ia _a _ b icra
cr
ife
o
m
u
ce
ii
ccpp
cr
ce
u ro
nt ha sa
a_ ba
p oer
sc hi
ic ra du lo
s_
an
oli a
ur
m
lti
a_in
a_ gl er sifstachya
ce
mbr
trelu
cro
a_ div
co
a_ma
aly ph
a tar ice nsi s
phtril
ac
ob
alya_
ac
cos
a__la
eli
tifo lia
ad
ho rne
alc
neallbe
rgia nus
yi
alc hor
_bi_sta ndle
s
cro ton
_alch orne oide
dryp etes
hiero nyma
ans
hura_ crepit
obilis
margar itaria_n
sapium_bro adleaf
sapium_glandulosum
a ll
s
lacmellea_panamensi
anum
ma_spruce
ri
aspidospertocoyen
a_pittiem
on_fo rmosu
rmat aa
rosen bergio dendrrand ia_a
tenu ifoli
osa
tria_
chotria
lia
psy cho
_ra cem
iifo
tie ri
ych otrpit
psy _ps
tria
ina ta
otr ia_
psy cho ps ych
entasis
_m arg
lisa
onon
tria
limriz
hotri
a_ho
s
ps ycho
gi an
dira
eg
tri a_an ns
ps ycho
gr an
lif lo xa
ffm tri a_
ps yc
ra cief le si s
a_ hoyc ho
ia _gia _dgr en a ta
tr
in
ho tri psho
lia
m
ho tr ha
ps yc
ti fo ll a
a cu
ps ycps yctr iaia_c
_ la p h y s iss
hoo tr e_ri a
c ro n e n u m
ns
ycch
pssy
q u m a u ia saete
p la rie a
p p o s on ia _a _ gm _aro
o re u _ x il a c n as
ta gc o u e mm elilia __afoeliri cnatadliraia
e a m e an m ra
p e np a lic ro c nh am
a id
is
h ae tt a rd
a _o c ch e xevmif lon sr ti ia
ma
g ue neipa _re au_rvpiga r m eibbeo snliasa
g m ta c _ n a s em kiau e a
u _ is a _ y c d t n a
fa rac oa re ar r ha _ pn iac o rbla _ e airniase
u _ _ ia ig ro
s a
u s im o jop p a is r t _ g cla_
c o c hb o r aa io ulseli b er asinuia
a a he _ b
am
n td r a b e
h alan ta
t r iche
ap
lacmellea_panamensi s
ri
aspidosper ma_spruce anum
a_pittie
tocoyen
m
on_fo rmosu
rmat aa
rosen bergio dendrrand ia_a
tenu ifoli
osa
tria_
chotria
lia
psy cho
_ra cem
iifo
tie ri
ych otrpit
psy _ps
tria
ina ta
otr ia_
psy cho ps ych
entasis
_m arg
lis
onon
tria
limriz
hotri
a_ho
an as
ps ycho
eg gi
an dira
tri a_an ns
ps ycho
a_ gr lif lo xa
ci
ffm
le
s
tri
ps yc
ra
a_ hoyctrho
ta
_d ef insi
a lia
ia _g
ho tri psho
tr iaha grmen
ho
ps yc
ti fo ll a
a cu
ps ycps yctr iaia_c
_ la p h y s iss
hoo tr e_ri a
c ro n e n u m
ns
ycch
pssy
q u m a u ia saete
p la rie a
p p o s on ia _a _ gm _aro
o re u _ x il a c n as
ta gc o u e mm elilia __afoeliri cnatadliraia
e a m e an m ra
p e np a lic ro c nh am
a id
is
h ae tt a rd
a _o c ch e xevmif lon sr ti ia
ma
g u n ipa _ a _rv iga r m eib eo snas
re
g em eta
c u _ p a e b iau li a
u _ is a n _ s y mck d t enaa
fa rac o re a r h _ p ia o r la _ e a niase
r
s a a a u n_ c _b ia ig irro
u s im o jop p a is r t _ g cla_
c o c hb o r aa io ulseli b er asinuia
a a he _ b
am
n td r a b e
h alan ta
t r iche
ap
ae ta
t u gip jabeb
te t er p hil ca u
la r m r min ia a_ra ia_
v fo in in _ p n g
m o c he n a li a lio c anda_ua
o u y s ia a a c idamc ya
r
ir s ia _ _ a _ o e eop c
mm ic i_ m_ fep u m ab lon t nsaiaan
mm
icic
o no n iaic o no n iay r tir rnuic ifz o nagli sis
n
m ia _ _ imia _ _ p ll og ino li iaa
m ic m h o p n e r a id e a
c o n le ic oo n iaic onnd euti orv os ineasa
o s te a n m icn ia __ d oia _re nla ris a
cl idco n o g iad_ra _o n iaa rgrs ileolastaiss
e m st e c ind ic _ ae n b a
ia _ g ia n a h o ff inte a
ps id
_ b ram oto m is
cl se p tu
iu m
me a
em
_f riecl idid
ct
p
lin
e
dr icem iaia _o cte rva taa
eum
onia
ci hs th_d
en ta
geyr
al ia
ni a_ ga
taa
nu m
oe rstu ne
eu eu gea_
te dins
nia nia _n
eu gege
anis
es iot
nia _c_g ala
lon en
icaa
ch am
rad
guolo
oe nssis
av a_
tric hoscap
sch
ippis
perpar is_
m_fro
saii
galndo
theomu
eot
brom
tii
sterc ulia_a_c
aca o
quara ribea_
apet
ala
astero
pseudo bombax
_septen lepis
pachira_seatum
ssilis
pachira_quinata
ochroma_pyramidale
luehea_seemannii
herrania_p urpurea
unda
hasselt ia_florib
pendi culata
ifolia
hamp ea_ap
_ulm
ndra
guaz uma
enta
lia
a_plata
nifo
ceiba_p
boua
ourace
lesiiba _tib
cav anilape
ume
mb ran
tul osns
a_ me
ii
m_ sena me
ap eib
kmatan
ox ylum_ pa
in mum
ar aa
za nthox yluxy
lu m _e
m_a
aria
ho m _a cuba
za nth
za nt
lu ar ou sia_laam
tif ol
ladtaa
asni a_er cu
ho xysi mqu
nt
a lli
za
o nliiaa
am_t uba _upid
pi cr
liaic h ili
g n duiflloa ta
ta
_
hi
a
tr ic tru a re_ g ra
_ b o rae ra
g re a a re a_ o da sepn suisme
_
li s
g u a geud re la
k ia a m o n s e
c n icp a nn u ifm ee n u mr i
tt inis _ te n a rincfu so feb in
n sms
tr aa s tru m __ poas ta
oa d lko m
c
m
o le
ti
c
g
_
r
ls ue p a
m
u
a ro
_
s _s _a v ec e cvonsnniis
te tr pp rotitiu mti u m
o d ia ia g r e x r iner a e li aa
p ro p rp o no n dm _m _ia _ p_nemesct if oere
s s pn iud iuli s sia se uf la in
_ r _ c
tr o a r tatanliiaia_n iaia_
a sn a c
n
a
n
a
a
p p a
a
cucupc u up
c
(c) Control Phylogeny
Fig. A1: The three phylogenies used in the study. Note the lack of resolution in the
Phylomatic (b) and control (c) phylogenies, as compared to the Kress phylogeny (a). Newick
files of the phylogenies are in a separate files in in the Supplementary Materials.
2
Density Plots
8
3
Assemblage Size (m)
6
5
10
50
4
All BCI
100 m
50 m
0
2
Density
Source Pool Size
0.6
0.8
1.0
1.2
D
8
(a) Phylomatic Phylogeny
Assemblage Size (m)
6
5
10
50
4
All BCI
100 m
50 m
0
2
Density
Source Pool Size
0.6
0.8
1.0
1.2
D
(b) Control Phylogeny
Fig. A2: Density plots of D with different assemblage and source pool sizes in the Phylomatic
and Control phylogenies.
3
Source Pool Size
All BCI
100 m
50 m
0.8
0.4
0.6
5
10
50
0.0
0.2
Density
Assemblage Size (m)
−3
−2
−1
0
1
2
3
2
3
SESMPD
Assemblage Size (m)
5
10
50
Source Pool Size
0.4
All BCI
100 m
50 m
0.0
0.2
Density
0.6
0.8
(a) Phylomatic Phylogeny
−3
−2
−1
0
1
SESMPD
(b) Control Phylogeny
Fig. A3: Density plots of SESM P D with different assemblage and source pool sizes in the
Phylomatic and control phylogenies.
4
5
10
50
Source Pool Size
0.2
All BCI
100 m
50 m
0.0
0.1
Density
0.3
0.4
Assemblage Size (m)
−3
−2
−1
0
1
2
3
2
3
SESMNTD
Assemblage Size (m)
5
10
50
Source Pool Size
0.2
0.3
All BCI
100 m
50 m
0.0
0.1
Density
0.4
0.5
(a) Phylomatic Phylogeny
−3
−2
−1
0
1
SESMNTD
(b) Control Phylogeny
Fig. A4: Density plots of SESM N T D with different assemblage and source pool sizes in the
Phylomatic and control phylogenies.
5
80
40
5
10
50
0
20
Density
60
Assemblage
Size (m)
0.74
0.76
0.78
0.80
0.82
0.84
PSV
50
50
(a) Kress Phylogeny
Assemblage
Assemblage
Size (m)
30
5
10
50
0
0
10
20
Density
20
30
5
10
50
10
Density
40
40
Size (m)
0.60
0.65
0.70
0.75
0.80
0.60
PSV
0.65
0.70
0.75
0.80
PSV
(b) Phylomatic Phylogeny
(c) Control Phylogeny
Fig. A5: Density plots of PSV with different assemblage sizes in all three phylogenies. PSV
was calculated using the function psv in the R package picante (Kembel et al., 2010), using
the same community definitions as described in the main text. See the next figure for an
explanation of how source pool size was assessed using PSV.
6
All BCI
100 m
50 m
80
40
60
5
10
50
Source Pool Size
0
20
Density
Assemblage Size (m)
−0.10
−0.05
0.00
0.05
0.10
PSVcorrected
80
80
(a) Kress Phylogeny
Assemblage Size (m)
60
Density
40
All BCI
100 m
50 m
Assemblage Size (m)
5
10
50
Source Pool Size
All BCI
100 m
50 m
0
0
20
40
Source Pool Size
20
Density
60
5
10
50
−0.10
−0.05
0.00
0.05
0.10
−0.10
PSVcorrected
−0.05
0.00
0.05
0.10
PSVcorrected
(b) Phylomatic Phylogeny
(c) Control Phylogeny
Fig. A6: Density plots of corrected PSV with different assemblage sizes in all three phylogenies. Since PSV values are calculated across a phylogeny of present species, we subtracted
the mean PSV of 1000 randomly-assembled assemblages with the same species richness from
each assemblage’s source pool to give ‘corrected PSV ’.
7
4
Mixed effects models
Assemblage
5
5
5
10
10
10
50
50
Source Pool
50
100
All BCI
50
100
All BCI
100
All BCI
Phylomatic
0.97 ± 0.0052
0.95 ± 0.0052
0.90 ± 0.0052
0.95 ± 0.0074
0.92 ± 0.0074
0.88 ± 0.0074
0.94 ± 0.0181
0.86 ± 0.0181
Control
0.97 ± 0.0070
0.95 ± 0.0070
0.90 ± 0.0070
0.93 ± 0.0074
0.91 ± 0.0074
0.89 ± 0.0074
0.93 ± 0.0154
0.88 ± 0.0154
(a) D Values
Assemblage Source Pool
5
50
5
100
5
All BCI
10
50
10
100
10
All BCI
50
100
50
All BCI
Phylomatic
-0.13 ± 0.0215
-0.13 ± 0.0215
-0.03 ± 0.0215
-0.30 ± 0.0394
-0.30 ± 0.0394
–0.11 ± 0.0394
-0.10 ± 0.1099
0.40 ± 0.1089
Control
0.03 ± 0.0290
0.06 ± 0.0290
0.16 ± 0.0290
-0.01 ± 0.0409
0.05 ± 0.0409
0.23 ± 0.0409
0.39 ± 0.1026
0.73 ± 0.1017
(b) SESM P D Values
Assemblage Source Pool
5
50
5
100
5
All BCI
10
50
10
100
10
All BCI
50
100
50
All BCI
Phylomatic
-0.19 ± 0.0218
-0.17 ± 0.0218
0.04 ± 0.0218
0.04 ± 0.0388
0.12 ± 0.0388
0.44 ± 0.0388
0.51 ± 0.1072
0.84 ± 0.1071
Control
-0.11580 ± 0.0270
-0.06508 ± 0.0270
0.13488 ± 0.0270
0.08723 ± 0.0417
0.19955 ± 0.0417
0.52777 ± 0.0417
0.64197 ± 0.1090
1.04558 ± 0.1090
(c) SESM N T D Values
Table A1: Mixed effects model estimates of of mean values (± SE) of D, SESM P D , and
SESM N T D values across BCI in the Phylomatic and control phylogenies. D Phylomatic (AIC
— -22886 vs. -21496; p-value of likelihood ratio test < 0.0001) and control (AIC — -24604
vs. -22896; p-value of likelihood ratio test < 0.0001) models showed statistically significant
effects of source pool and assemblage size when compared with a null model containing
neither variable. SESM P D Phylomatic (AIC — 44678 vs. 44848; p-value of likelihood ratio
test < 0.0001) and control (AIC — 41518 vs. 41778; p-value of likelihood ratio test <
0.0001) models showed statistically significant effects of source pool and assemblage size
when compared with a null model containing neither variable.
8
Assemblage
10
5
50
AICmodel
AICnull
LRT p-value
Source
0.79 ±
0.79 ±
0.79 ±
Pool
Phylomatic
Control
0.0008 0.70 ± 0.0011 0.70 ± 0.0014
0.0006 0.70 ± 0.0008 0.70 ± 0.0011
0.0030 0.71 ± 0.0046 0.70 ± 0.0047
-30961
-25450
-30958
-25451
0.028
0.275
-25382
-25382
0.101
(a) PSV Values
Assemblage
10
10
10
5
5
5
50
50
AICmodel
AICnull
LRT p-value
Source Pool
50
All BCI
100
50
All BCI
100
All BCI
100
Kress
-0.01 ± 0.0011
0.00 ± 0.0011
0.00± 0.0011
-0.01 ± 0.0007
0.00 ± 0.0007
0.00± 0.0007
0.00 ± 0.0031
0.00 ± 0.0031
-89790
-88842
<0.0001
Phylomatic
-0.01 ± 0.0014
0.00± 0.0014
-0.01 ± 0.0014
-0.01 ± 0.0008
0.00 ± 0.0008
0.00± 0.0008
0.01 ± 0.0039
0.00 ± 0.0039
-80758
-80581
<0.0001
Control
0.00± 0.0016
0.01 ± 0.0016
0.00 ± 0.0016
0.00 ± 0.0011
0.01 ± 0.0011
0.00 ± 0.0011
0.01 ± 0.0040
0.01 ± 0.0040
-79999
-79651
<0.0001
(b) Corrected PSV Values
Table A2: Mixed effects model estimates of of mean values (± SE) of PSV and corrected
PSV values across BCI in the three phylogenies. Mixed effect model AIC and LRT p-values
are given in the final three rows for each dataset; each was calculated as described in the text
for D and SESM P D . The exception to this is PSV (but not corrected PSV ); no random
effect term was fitted for each 5m radius circle, since these uncorrected values do not allow
for variation in source pool size, and so fitting such a model would fit a random effect term
for each 5m radius assemblage and so cause fitting errors. Note that the estimates for PSV
do not change appreciably with spatial scale; therefore there is no danger that a change in
the way in which spatial variation was accounted for led to an artifactual increase in effect
size.
9
5
Quantile Regressions
Assemblage Source Pool
5
50
5
100
5
All BCI
10
50
10
100
10
All BCI
50
100
50
All BCI
Range
τ =0.10
0.74
0.74
0.71
0.78
0.78
0.75
0.76
0.75
0.07
τ =0.25
0.87
0.86
0.82
0.87
0.85
0.81
0.86
0.80
0.07
τ =0.50
0.99
0.97
0.92
0.95
0.93
0.89
0.95
0.86
0.13
τ =0.75
1.10
1.06
1.00
1.04
1.01
0.95
1.03
0.89
0.21
τ =0.90
1.18
1.13
1.05
1.11
1.06
1.00
1.08
0.92
0.26
τ =0.75
1.12
1.08
1.02
1.04
1.01
0.98
1.03
0.92
0.20
τ =0.90
1.22
1.17
1.09
1.12
1.08
1.03
1.12
0.97
0.25
(a) Phylomatic Phylogeny
Assemblage Source Pool
5
50
5
100
5
All BCI
10
50
10
100
10
All BCI
50
100
50
All BCI
Range
τ =0.10
0.71
0.72
0.70
0.73
0.75
0.75
0.74
0.79
0.09
τ =0.25
0.85
0.85
0.82
0.84
0.84
0.83
0.87
0.84
0.05
τ =0.50
1.00
0.98
0.94
0.95
0.93
0.91
0.96
0.89
0.11
(b) Control Phylogeny
Table A3: Quantile regression of D values across BCI in the Phylomatic and control phylogenies.
10
Assemblage Source Pool
10
50
10
All BCI
10
100
5
50
5
All BCI
5
100
50
All BCI
50
100
τ =0.10
0.0080
0.0091
0.0093
0.0090
0.0088
0.0090
0.0383
0.0279
τ =0.25
0.0054
0.0065
0.0066
0.0062
0.0058
0.0062
0.0124
0.0112
τ =0.50
0.0042
0.0054
0.0060
0.0050
0.0046
0.0050
0.0085
0.0134
τ =0.75
0.0042
0.0048
0.0055
0.0049
0.0046
0.0047
0.0119
0.0144
τ =0.90
0.0053
0.0064
0.0068
0.0062
0.0057
0.0058
0.0059
0.0087
τ =0.50
0.0059
0.0057
0.0056
0.0051
0.0069
0.0061
0.0149
0.0122
τ =0.75
0.0053
0.0051
0.0050
0.0046
0.0063
0.0056
0.0069
0.0046
τ =0.90
0.0064
0.0063
0.0062
0.0057
0.0074
0.0074
0.0329
0.0074
τ =0.75
0.0052
0.0072
0.0059
0.0060
0.0060
0.0056
0.0089
0.0054
τ =0.90
0.0078
0.0090
0.0089
0.0085
0.0083
0.0081
0.0678
0.0261
(a) Kress Phylogeny
Assemblage Source Pool
5
50
5
100
5
All BCI
10
50
10
100
10
All BCI
50
100
50
All BCI
τ =0.10
0.0105
0.0102
0.0099
0.0088
0.0103
0.0098
0.0533
0.0248
τ =0.25
0.0067
0.0064
0.0063
0.0055
0.0074
0.0071
0.0109
0.0194
(b) Phylomatic Phylogeny
Assemblage Source Pool
10
50
10
100
10
All BCI
5
50
5
100
5
All BCI
50
100
50
All BCI
τ =0.10
0.0069
0.0094
0.0086
0.0097
0.0090
0.0086
0.0149
0.0305
τ =0.25
0.0062
0.0079
0.0080
0.0080
0.0073
0.0072
0.0077
0.0158
τ =0.50
0.0060
0.0073
0.0071
0.0072
0.0068
0.0065
0.0217
0.0170
(c) Control Phylogeny
Table A4: Standard errors of quantile regression of D values across BCI in all three phylogenies.
11
Assemblage Source Pool
5
50
5
100
5
All BCI
10
50
10
100
10
All BCI
50
100
50
All BCI
Range
τ =0.10
-1.34
-1.34
-1.24
-1.56
-1.54
-1.36
-1.45
-1.09
0.47
τ =0.25
-0.80
-0.79
-0.71
-0.96
-0.98
-0.87
-0.62
-0.18
0.80
τ =0.50
-0.20
-0.21
-0.12
-0.36
-0.34
-0.14
-0.07
0.32
0.68
τ =0.75
0.40
0.39
0.51
0.31
0.28
0.49
0.40
1.03
0.75
τ =0.90
0.98
0.96
1.10
0.84
0.85
1.08
1.12
1.66
0.82
τ =0.75
0.52
0.55
0.63
0.50
0.52
0.70
0.65
1.04
0.54
τ =0.90
1.08
1.10
1.20
1.02
1.04
1.24
1.23
1.73
0.71
(a) Phylomatic Phylogeny
Assemblage Source Pool
5
50
5
100
5
All BCI
10
50
10
100
10
All BCI
50
100
50
All BCI
Range
τ =0.10
-1.12
-1.07
-0.96
-1.29
-1.19
-1.00
-1.19
-0.44
0.85
τ =0.25
-0.62
-0.58
-0.48
-0.76
-0.66
-0.51
-0.51
0.08
0.84
τ =0.50
-0.06
-0.01
0.08
-0.13
-0.04
0.12
0.27
0.56
0.69
(b) Control Phylogeny
Table A5: Quantile regression of SESM P D values across BCI in the Phylomatic and Control
phylogenies.
12
Assemblage Source Pool
10
50
10
100
10
All BCI
5
50
5
100
5
All BCI
50
100
50
All BCI
τ =0.10
0.0454
0.0588
0.0565
0.0492
0.0500
0.0491
0.0539
0.3776
τ =0.25
0.0373
0.0522
0.0478
0.0405
0.0401
0.0399
0.4235
0.0726
τ =0.50
0.0320
0.0465
0.0429
0.0350
0.0347
0.0351
0.1351
0.0837
τ =0.75
0.0339
0.0459
0.0463
0.0372
0.0359
0.0367
0.0462
0.1402
τ =0.90
0.0272
0.0455
0.0409
0.0315
0.0317
0.0317
0.1549
0.1055
τ =0.50
0.0300
0.0451
0.0421
0.0343
0.0339
0.0339
0.1103
0.1907
τ =0.75
0.0333
0.0450
0.0465
0.0386
0.0373
0.0385
0.0396
0.0512
τ =0.90
0.0537
0.0670
0.0772
0.0583
0.0580
0.0567
0.2841
0.4082
τ =0.75
0.0277
0.0466
0.0457
0.0331
0.0314
0.0326
0.0905
0.0405
τ =0.90
0.0402
0.0640
0.0600
0.0466
0.0460
0.0470
0.0908
0.2588
(a) Kress Phylogeny
Assemblage Source Pool
10
50
10
All BCI
10
100
5
All BCI
5
50
5
100
50
100
50
All BCI
τ =0.10
0.0382
0.0614
0.0652
0.0430
0.0425
0.0428
0.1061
0.2991
τ =0.25
0.0370
0.0571
0.0534
0.0407
0.0408
0.0409
0.2361
0.0693
(b) Phylomatic Phylogeny
Assemblage Source Pool
10
50
10
100
10
All BCI
5
50
5
100
5
All BCI
50
100
50
All BCI
τ =0.10
0.0440
0.0658
0.0593
0.0472
0.0484
0.0480
0.0697
0.1424
τ =0.25
0.0366
0.0542
0.0513
0.0398
0.0392
0.0394
0.1562
0.0753
τ =0.50
0.0352
0.0437
0.0451
0.0383
0.0382
0.0386
0.1165
0.0732
(c) Control Phylogeny
Table A6: Standard errors of quantile regression of SESM P D values across BCI in all three
phylogenies.
13
Assemblage Source Pool
5
50
5
100
5
All BCI
10
50
10
100
10
All BCI
50
100
50
All BCI
Range
τ =0.10
-1.37
-1.31
-1.09
-1.19
-1.10
-0.78
-0.92
-0.62
0.75
τ =0.25
-0.83
-0.80
-0.57
-0.66
-0.57
-0.22
-0.55
0.14
0.52
τ =0.50
-0.23
-0.21
0.00
-0.02
0.05
0.37
0.63
0.81
1.04
τ =0.75
0.39
0.40
0.58
0.64
0.69
1.01
1.30
1.38
0.99
τ =0.90
0.92
0.92
1.11
1.26
1.28
1.59
1.79
1.81
0.89
τ =0.75
0.47
0.50
0.69
0.67
0.75
1.07
1.21
1.37
0.90
τ =0.90
0.99
1.04
1.20
1.35
1.41
1.73
1.43
1.86
0.87
(a) Phylomatic Phylogeny
Assemblage Source Pool
5
50
5
100
5
All BCI
10
50
10
100
10
All BCI
50
100
50
All BCI
Range
τ =0.10
-1.33
-1.26
-1.05
-1.18
-1.05
-0.71
-0.79
-0.26
1.07
τ =0.25
-0.78
-0.73
-0.51
-0.66
-0.52
-0.17
-0.21
0.38
1.16
τ =0.50
-0.15
-0.09
0.10
-0.01
0.10
0.44
0.55
0.83
0.98
(b) Control Phylogeny
Table A7: Quantile regression of SESM N T D values across BCI in the Phylomatic and Control
phylogenies.
14
Assemblage Source Pool
5
50
5
100
5
All BCI
10
50
10
100
10
All BCI
50
100
50
All BCI
τ =0.10
0.0211
0.0230
0.0204
0.0391
0.0380
0.0512
0.0953
0.0642
τ =0.25
0.0179
0.0178
0.0187
0.0363
0.0431
0.0487
0.1292
0.0753
τ =0.50
0.0167
0.0163
0.0160
0.0291
0.0276
0.0272
0.1047
0.0701
τ =0.75
0.0165
0.0157
0.0159
0.0374
0.0345
0.0364
0.1041
0.1853
τ =0.90
0.0156
0.0166
0.0190
0.0405
0.0294
0.0460
0.0452
0.6051
τ =0.50
0.0154
0.0152
0.0154
0.0341
0.0347
0.0297
0.0614
0.0377
τ =0.75
0.0168
0.0167
0.0163
0.0410
0.0347
0.0365
0.0969
0.1310
τ =0.90
0.0209
0.0204
0.0206
0.0636
0.0573
0.0497
0.2038
0.0310
τ =0.75
0.0172
0.0177
0.0173
0.0454
0.0387
0.0465
0.0736
0.0738
τ =0.90
0.0223
0.0187
0.0186
0.0506
0.0447
0.0489
0.0762
0.0547
(a) Kress Phylogeny
Assemblage Source Pool
5
50
5
100
5
All BCI
10
50
10
100
10
All BCI
50
100
50
All BCI
τ =0.10
0.0223
0.0212
0.0198
0.0367
0.0382
0.0357
0.0074
0.0769
τ =0.25
0.0155
0.0164
0.0144
0.0300
0.0285
0.0280
0.1468
0.3560
(b) Phylomatic Phylogeny
Assemblage Source Pool
5
50
5
100
5
All BCI
10
50
10
100
10
All BCI
50
100
50
All BCI
τ =0.10
0.0204
0.0163
0.0186
0.0339
0.0356
0.0345
0.4747
0.3204
τ =0.25
0.0166
0.0179
0.0173
0.0309
0.0346
0.0302
0.0258
0.0506
τ =0.50
0.0163
0.0163
0.0150
0.0271
0.0307
0.0254
0.2407
0.1084
(c) Control Phylogeny
Table A8: Standard errors of quantile regression of SESM N T D values across BCI in all three
phylogenies.
15
Assemblage
5
10
50
Range
τ =0.25 τ =0.50
0.76
0.78
0.77
0.78
0.78
0.79
0.02
0.01
τ =0.75
0.79
0.80 0.82
0.79
0.80 0.80
0.79
0.80 0.80
0
0
0.02
(a) Kress Phylogeny
Assemblage
5
10
50
Range
τ =0.25 τ =0.50
0.66
0.68
0.67
0.68
0.69
0.70
0.03
0.02
τ =0.75
0.70
0.72 0.74
0.70
0.71 0.73
0.70
0.71 0.72
0
0.01 0.02
(b) Phylomatic Phylogeny
Assemblage Source Pool τ =0.25
5
0.66
0.68
10
0.67
0.68
50
0.69
0.70
Range
0.03
0.02
τ =0.50 τ =0.75
0.70
0.72
0.75
0.70
0.71
0.73
0.70
0.71
0.71
0
0.01
0.04
(c) Control Phylogeny
Table A9: Quantile regression of PSV values across BCI in all three phylogenies.
16
Assemblage τ =0.25 τ =0.50
5
0.0006 0.0004
10
0.0006 0.0004
50
0.0019 0.0005
τ =0.75
0.0004 0.0004 0.0006
0.0005 0.0005 0.0006
0.0006 0.0008 0.0000
(a) Kress Phylogeny
Assemblage τ =0.25 τ =0.50
5
0.0008 0.0006
10
0.0011 0.0008
50
0.0005 0.0018
τ =0.75
0.0006 0.0008 0.0009
0.0007 0.0008 0.0011
0.0016 0.0008 0.0020
(b) Phylomatic Phylogeny
Assemblage τ =0.25 τ =0.50
5
0.0009 0.0006
10
0.0010 0.0008
50
0.0008 0.0007
τ =0.75
0.0006 0.0007 0.0010
0.0007 0.0008 0.0011
0.0007 0.0011 0.0008
(c) Control Phylogeny
Table A10: Standard errors of quantile regression of PSV values across BCI in all three
phylogenies.
17
Assemblage Source Pool
5
50
5
100
5
All BCI
10
50
10
100
10
All BCI
50
100
50
All BCI
Range
τ =0.10
-0.06
-0.03
-0.03
-0.06
-0.02
-0.02
-0.01
-0.01
0.05
τ =0.25
-0.03
-0.02
-0.01
-0.02
-0.01
-0.01
0.00
0.00
0.03
τ =0.50
-0.01
0.00
0.00
-0.01
0.00
0.00
0.00
0.00
0.01
τ =0.75
0.01
0.01
0.01
0.00
0.00
0.01
0.00
0.01
0.01
τ =0.90
0.02
0.03
0.03
0.01
0.01
0.01
0.00
0.01
0.02
τ =0.50
-0.01
0.00
-0.01
-0.01
0.00
-0.01
0.00
0.00
0.01
τ =0.75
0.01
0.01
0.01
0.01
0.02
0.01
0.01
0.00
0.02
τ =0.90
0.02
0.02
0.02
0.04
0.04
0.04
0.01
0.01
0.03
τ =0.75
0.02
0.02
0.03
0.01
0.01
0.02
0.00
0.01
0.03
τ =0.90
0.04
0.05
0.05
0.02
0.02
0.03
0.01
0.02
0.04
(a) Kress Phylogeny
Assemblage Source Pool
10
50
10
All BCI
10
200
5
50
5
All BCI
5
100
50
All BCI
50
100
Range
τ =0.10
-0.04
-0.03
-0.03
-0.05
-0.04
-0.05
-0.01
-0.01
0.04
τ =0.25
-0.02
-0.02
-0.02
-0.03
-0.03
-0.03
0.00
0.00
0.03
(b) Phylomatic Phylogeny
Assemblage Source Pool
5
50
5
100
5
All BCI
10
50
10
100
10
All BCI
50
100
50
All BCI
Range
τ =0.10
-0.05
-0.04
-0.04
-0.03
-0.03
-0.02
-0.01
0.00
0.05
τ =0.25
-0.03
-0.02
-0.02
-0.02
-0.02
-0.01
0.00
0.00
0.03
τ =0.50
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.01
0.01
(c) Control Phylogeny
Table A11: Quantile regression of corrected PSV values across BCI in the Phylomatic and
Control phylogenies.
18
Assemblage Source Pool
5
50
5
100
5
All BCI
10
50
10
100
10
All BCI
50
100
50
All BCI
τ =0.10
0.0012
0.0006
0.0006
0.0021
0.0007
0.0006
0.0006
0.0030
τ =0.25
0.0007
0.0004
0.0004
0.0007
0.0004
0.0005
0.0004
0.0003
τ =0.50
0.0004
0.0004
0.0004
0.0005
0.0004
0.0005
0.0003
0.0003
τ =0.75
0.0004
0.0004
0.0004
0.0004
0.0004
0.0005
0.0007
0.0005
τ =0.90
0.0005
0.0006
0.0006
0.0006
0.0005
0.0006
0.0006
0.0003
τ =0.50
0.0006
0.0006
0.0006
0.0007
0.0006
0.0007
0.0011
0.0010
τ =0.75
0.0007
0.0007
0.0008
0.0007
0.0007
0.0009
0.0011
0.0004
τ =0.90
0.0008
0.0008
0.0009
0.0009
0.0012
0.0013
0.0014
0.0017
τ =0.75
0.0007
0.0006
0.0007
0.0008
0.0009
0.0007
0.0005
0.0009
τ =0.90
0.0011
0.0011
0.0010
0.0009
0.0010
0.0009
0.0010
0.0006
(a) Kress Phylogeny
Assemblage Source Pool
5
50
5
100
5
All BCI
10
50
10
100
10
All BCI
50
100
50
All BCI
τ =0.10
0.0010
0.0008
0.0009
0.0009
0.0015
0.0010
0.0000
0.0004
τ =0.25
0.0007
0.0006
0.0006
0.0010
0.0007
0.0007
0.0012
0.0010
(b) Phylomatic Phylogeny
Assemblage Source Pool
5
50
5
100
5
All BCI
10
50
10
100
10
All BCI
50
100
50
All BCI
τ =0.10
0.0009
0.0009
0.0009
0.0012
0.0009
0.0010
0.0008
0.0009
τ =0.25
0.0006
0.0006
0.0005
0.0008
0.0008
0.0008
0.0003
0.0004
τ =0.50
0.0006
0.0006
0.0006
0.0007
0.0006
0.0007
0.0008
0.0003
(c) Control Phylogeny
Table A12: Standard errors of quantile regression of corrected PSV values across BCI in all
three phylogenies.
19
Phylogenetic Depth Plots
2
3
6
●
1
D
●
●
●
●●
●
●●
●
●
●
●
● ●
●
●
●
●
●
●
●
●
●
●
●● ●● ●
●●
●
●
●
●
●
●
●
−1
0
●
Root Node
−−>
Tips of Phylogeny
2
3
(a) Phylomatic Phylogeny
●
1
D
●
●
●
●●
●
●●
●
●
●
●
● ●
●
●
●
●
●
●
●
●
●
●
●● ●● ●
●●
●
●
●
●
●
●
●
−1
0
●
Root Node
−−>
Tips of Phylogeny
(b) Control Phylogeny
Fig. A7: Phylogenetic depth plots of D for the observed and simulated assemblages in the
Phylomatic and Control phylogenies. These plots seem much more discrete than those of
the Kress phylogeny, reflecting the poor resolution of both these phylogenies.
20
●
●
0.01
0.00
●
−0.01
Observed Slopes
0.02
●
●
●
●
●
●
●
● ● ● ●● ● ●●
●●
● ●
● ●●●
●
●
● ●● ● ●
●●
●
●●
●
●●● ●●●●
● ●●
● ● ●●
●
●
●
●
●
●● ●
●
● ● ●
●
●
●
●
●
● ● ●●
●
● ● ●● ●● ● ● ●
●● ● ●
●
●
●
●
●
●
●
●
●
●●●●●● ●
●●●●
●●
● ● ● ● ●
●●●
●
●●●
● ● ●●●
●
●
●
●
●●●
●●
●●
●
●
● ●●
● ●
●●
●
● ● ●●
●● ● ●
●
●
●
●
●
●
●
Phylogeny
●
●
−0.02
●
Phylomatic
Control
●
−0.010
−0.005
0.000
0.005
0.010
0.015
0.020
Simulated Slopes
Fig. A8: Plot of observed and simulated slopes for regressions of D on clade age in the
Phylomatic and control phylogenies. The red dashed line passes through the origin with a
slope of 1 (the null expectation). Note the difference in scale of these figures in comparison
with figure 5 in the main text; these slope estimates are extremely small.
21
7
Density plots
8
7.1
Edge Results
Assemblage Size (m)
6
5
10
50
Source Pool Size
0
2
4
Density
All BCI
100 m
50 m
0.6
0.8
1.0
1.2
D
8
8
(a) Kress Phylogeny
Assemblage Size (m)
Assemblage Size (m)
6
5
10
50
6
5
10
50
Source Pool Size
4
All BCI
100 m
50 m
0
0
2
4
Density
All BCI
100 m
50 m
2
Density
Source Pool Size
0.6
0.8
1.0
1.2
0.6
D
0.8
1.0
1.2
D
(b) Phylomatic Phylogeny
(c) Control Phylogeny
Fig. A9: Density plots of D with different assemblage and source pool sizes in all three
phylogenies, with assemblages whose source pools that cross the boundary of BCI removed
from the analysis.
22
0.8
Assemblage Size (m)
Source Pool Size
All BCI
100 m
50 m
0.0
0.2
0.4
Density
0.6
5
10
50
−3
−2
−1
0
1
2
3
SESMPD
0.8
Assemblage Size (m)
Source Pool Size
Density
5
10
50
Source Pool Size
All BCI
100 m
50 m
0.0
0.0
0.2
0.4
All BCI
100 m
50 m
Assemblage Size (m)
0.4
0.6
5
10
50
0.2
Density
0.6
0.8
(a) Kress Phylogeny
−3
−2
−1
0
1
2
3
−3
SESMPD
−2
−1
0
1
2
3
SESMPD
(b) Phylomatic Phylogeny
(c) Control Phylogeny
Fig. A10: Density plots of SESM P D with different assemblage and source pool sizes in
all three phylogenies, with assemblages whose source pools that cross the boundary of BCI
removed from the analysis.
23
0.5
Assemblage Size (m)
0.4
5
10
50
Source Pool Size
0.0
0.1
0.2
Density
0.3
All BCI
100 m
50 m
−3
−2
−1
0
1
2
3
SESMNTD
0.5
Assemblage Size (m)
All BCI
100 m
50 m
0.2
Density
5
10
50
Source Pool Size
0.0
0.0
0.1
0.2
0.3
All BCI
100 m
50 m
Assemblage Size (m)
0.3
0.4
5
10
50
Source Pool Size
0.1
Density
0.4
0.5
(a) Kress Phylogeny
−3
−2
−1
0
1
2
3
−3
SESMNTD
−2
−1
0
1
2
3
SESMNTD
(b) Phylomatic Phylogeny
(c) Control Phylogeny
Fig. A11: Density plots of SESM N T D with different assemblage and source pool sizes in
all three phylogenies, with assemblages whose source pools that cross the boundary of BCI
removed from the analysis.
24
80
60
5
10
50
Source Pool Size
All BCI
100 m
50 m
0
20
40
Density
Assemblage Size (m)
−0.10
−0.05
0.00
0.05
0.10
PSVcorrected
60
50
(a) Kress Phylogeny
Assemblage Size (m)
Assemblage Size (m)
40
50
5
10
50
30
Density
0
0
10
10
20
20
Density
30
40
5
10
50
0.60
0.65
0.70
0.75
0.80
0.60
PSV
0.65
0.70
0.75
0.80
PSV
(b) Phylomatic Phylogeny
(c) Control Phylogeny
Fig. A12: Density plots of PSV with different assemblage and source pool sizes in all three
phylogenies, with assemblages whose source pools that cross the boundary of BCI removed
from the analysis.
25
7.2
Mixed Effects Models
Assemblage
5
5
5
10
10
10
50
50
AICmodel
AICnull
Source Pool
50
100
All BCI
50
100
All BCI
100
All BCI
Kress
0.96 ±
0.94 ±
0.92 ±
0.96 ±
0.94 ±
0.92 ±
0.95 ±
0.89 ±
-15196
-14855
0.0059
0.0060
0.0057
0.0087
0.0093
0.0084
0.0247
0.0143
Phylomatic
0.96 ± 0.0055
0.95 ± 0.0058
0.90 ± 0.0052
0.94 ± 0.0079
0.92 ± 0.0088
0.89 ± 0.0073
0.94 ± 0.0302
0.86 ± 0.0162
-13604
-13131
Control
0.97 ± 0.0073
0.95 ± 0.0075
0.91 ± 0.0071
0.92 ± 0.0080
0.91 ± 0.0086
0.89 ± 0.0077
1.02 ± 0.0254
0.90 ± 0.0169
-13816
-13109
Phylomatic
-0.19 ± 0.0240
-0.18 ± 0.0266
0.04 ± 0.0220
0.05 ± 0.0425
0.13 ± 0.0489
0.44 ± 0.0387
0.38 ± 0.1863
0.80 ± 0.0968
23656
23792
Control
-0.10 ± 0.0283
-0.07 ± 0.0306
0.14 ± 0.0265
0.12 ± 0.0450
0.20 ± 0.0511
0.52 ± 0.0413
0.70 ± 0.1886
1.03 ± 0.0987
21641
21819
(a) D Values
Assemblage
5
5
5
10
10
10
50
50
AICmodel
AICnull
Source Pool
50
100
All BCI
50
100
All BCI
100
All BCI
Kress
0.02 ± 0.0227
0.00 ± 0.0255
0.17 ± 0.0204
-0.03 ± 0.0420
-0.05 ± 0.0487
0.23 ± 0.0379
0.26 ± 0.1909
-0.13 ± 0.0987
20043
20175
(b) SESM P D Values
Assemblage
5
5
5
10
10
10
50
50
AICmodel
AICnull
Source Pool
50
100
All BCI
50
100
All BCI
100
All BCI
Kress
0.02257 ± 0.02265
-0.00222 ± 0.02545
0.16646 ± 0.02038
-0.03044 ± 0.04201
-0.05332 ± 0.04867
0.22546 ± 0.03794
0.26091 ± 0.19088
-0.13081 ± 0.09868
20043
20175
Phylomatic
0.05 ± 0.0425
0.13 ± 0.0489
0.44 ± 0.0387
-0.19 ± 0.0240
-0.18 ± 0.0266
0.04 ± 0.0220
0.38 ± 0.186
0.80 ± 0.0968
23656
23792
Control
-0.10 ± 0.0283
-0.07 ± 0.0306
0.14 ± 0.0265
0.12 ± 0.0450
0.20 ± 0.0511
0.52 ± 0.0413
0.70 ± 0.1886
1.03 ± 0.0987
21641
21819
(c) SESM N T D Values
Table A13: Mixed effects models of D, SESM P D , and SESM N T D values across BCI, with assemblages whose source pools that cross the boundary of BCI removed from the analysis. Estimates of
mean values (± SE) for each assemblage/source pool combination, with a different table for each
dispersion measure, subdivided within each table according to the phylogeny used. AIC values
for each model are given the last two rows of each table; all likelihood ratio tests had p-values <
0.0001.
26
Assemblage
10
5
50
AICmodel
AICnull
LRT p-value
Kress
Phylomatic
Control
0.79 ± 0.0008
0.70 ± 0.0011 0.70 ± 0.0014
0.79 ± 0.0006375 0.70 ± 0.0008 0.70 ± 0.0011
0.79 ± 0.0030
0.71 ± 0.0046 0.70 ± 0.0047
-30961
-25450
-25382
-30958
-25451
-25382
0.028
0.275
0.101
(a) PSV Values
Assemblage
10
10
10
5
5
5
50
50
AICmodel
AICnull
LRT p-value
Source Pool
50
All BCI
100
50
All BCI
100
All BCI
100
Kress
-0.01 ± 0.0012
0.00 ± 0.0011
0.00± 0.0013
-0.01 ± 0.0008
0.00 ± 0.0008
0.00± 0.0009
0.00 ± 0.0026
0.00± 0.0050
-50893
-50653
<0.0001
Phylomatic
-0.01 ± 0.0016
0.00 ± 0.0014
-0.01 ± 0.0018
0.00 ± 0.0009
0.00 ± 0.0008
0.00 ± 0.0010
0.01 ± 0.0036
0.00 ± 0.0069
-43857
-43753
<0.0001
Control
0.00 ± 0.0018
0.01 ± 0.0016
0.00 ± 0.0020
0.00 ± 0.0012
0.01 ± 0.0012
0.00 ± 0.0013
0.01 ± 0.0037
0.00 ± 0.0070
-43599
-43443
<0.0001
(b) Corrected PSV Values
Table A14: Mixed effects models of PSV values across BCI, with assemblages whose source
pools that cross the boundary of BCI removed from the analysis. Estimates of mean values (±
SE) for each assemblage/source pool combination, with a different table for each dispersion
measure, subdivided within each table according to the phylogeny used. AIC values for each
model and likelihood ratio test p-values are given the last two rows of each table.
27
7.3
Quantile Regressions
Assemblage
5
5
5
10
10
10
50
50
Range
Source Pool
50
100
All BCI
50
100
All BCI
100
All BCI
τ =0.25
0.86
0.85
0.85
0.88
0.87
0.86
0.89
0.86
0.04
τ =0.50
0.97
0.95
0.93
0.97
0.95
0.92
0.96
0.89
0.08
τ =0.75
1.07
1.04
1.00
1.04
1.01
0.98
1.05
0.92
0.15
τ =0.50
0.99
0.97
0.92
0.94
0.93
0.89
0.92
0.86
0.13
τ =0.75
1.09
1.06
1.00
1.03
1.01
0.95
0.97
0.89
0.20
(a) Kress Phylogeny
Assemblage
5
5
5
10
10
10
50
50
Range
Source Pool
50
100
All BCI
50
100
All BCI
100
All BCI
τ =0.25
0.86
0.86
0.82
0.85
0.85
0.81
0.86
0.80
0.06
(b) Phylomatic Phylogeny
Assemblage
5
5
5
10
10
10
50
50
Range
Source Pool
50
100
All BCI
50
100
All BCI
100
All BCI
τ =0.25
0.85
0.84
0.82
0.84
0.85
0.83
0.94
0.84
0.12
τ =0.50
1.00
0.97
0.94
0.94
0.94
0.91
0.98
0.89
0.11
τ =0.75
1.12
1.09
1.02
1.04
1.01
0.98
1.04
0.92
0.20
(c) Control Phylogeny
Table A15: Quantile regression of D values across BCI in all three phylogenies, with assemblages whose source pools that cross the boundary of BCI removed from the analysis.
28
Assemblage
5
5
5
10
10
10
50
50
Source Pool
50
100
All BCI
50
100
All BCI
100
All BCI
τ =0.25
0.0060
0.0059
0.0023
0.0082
0.0080
0.0035
0.0055
0.0144
τ =0.50
0.0045
0.0055
0.0020
0.0089
0.0075
0.0036
0.0209
0.0082
τ =0.75
0.0047
0.0039
0.0020
0.0059
0.0077
0.0025
0.0272
0.0135
τ =0.50
0.0047
0.0052
0.0022
0.0074
0.0108
0.0033
0.0365
0.0178
τ =0.75
0.0056
0.0045
0.0020
0.0068
0.0105
0.0032
0.3063
0.0103
(a) Kress Phylogeny
Assemblage
5
5
5
10
10
10
50
50
Source Pool
50
100
All BCI
50
100
All BCI
100
All BCI
τ =0.25
0.0057
0.0057
0.0031
0.0071
0.0085
0.0049
0.0704
0.0340
(b) Phylomatic Phylogeny
Assemblage
10
10
10
5
5
5
50
50
Source Pool
50
100
All BCI
50
100
All BCI
100
All BCI
τ =0.25
0.0088
0.0074
0.0052
0.0060
0.0077
0.0038
0.0417
0.0127
τ =0.50
0.0075
0.0062
0.0040
0.0050
0.0053
0.0027
0.0331
0.0250
τ =0.75
0.0073
0.0077
0.0028
0.0037
0.0053
0.0020
0.1345
0.0013
(c) Control Phylogeny
Table A16: Standard errors of quantile regression of D values across BCI in all three phylogenies, with assemblages whose source pools that cross the boundary of BCI removed from
the analysis.
29
Assemblage
5
5
5
10
10
10
50
50
Range
Source Pool
50
100
All BCI
50
100
All BCI
100
All BCI
τ =0.25
-0.60
-0.65
-0.50
-0.75
-0.89
-0.59
-1.41
-0.27
1.14
τ =0.50
-0.02
-0.09
0.00
-0.15
-0.27
-0.07
-0.77
0.20
0.97
τ =0.75
0.53
0.43
0.51
0.36
0.30
0.43
0.56
0.91
0.61
τ =0.50
-0.14
-0.11
-0.12
-0.30
-0.26
-0.14
-0.44
0.31
0.73
τ =0.75
0.54
0.53
0.51
0.37
0.35
0.49
0.25
1.03
0.78
(a) Kress Phylogeny
Assemblage
5
5
5
10
10
10
50
50
Range
Source Pool
50
100
All BCI
50
100
All BCI
100
All BCI
τ =0.25
-0.77
-0.75
-0.71
-0.92
-0.80
-0.87
-1.15
-0.18
0.97
(b) Phylomatic Phylogeny
Assemblage
5
5
5
10
10
10
50
50
Range
Source Pool
50
100
All BCI
50
100
All BCI
100
All BCI
τ =0.25
-0.60
-0.60
-0.48
-0.68
-0.74
-0.51
-1.03
0.08
1.11
τ =0.50
0.02
-0.02
0.08
-0.03
-0.03
0.12
-0.23
0.54
0.77
τ =0.75
0.62
0.57
0.63
0.57
0.60
0.70
0.51
1.04
0.53
(c) Control Phylogeny
Table A17: Quantile regression of SESM P D values across BCI in the Phylomatic and Control
phylogenies, with assemblages whose source pools that cross the boundary of BCI removed
from the analysis.
30
Assemblage
5
5
5
10
10
10
50
50
Source Pool
50
100
All BCI
50
100
All BCI
100
All BCI
τ =0.25
0.0261
0.0352
0.0149
0.0546
0.0650
0.0325
0.3056
0.0964
τ =0.50
0.0252
0.0305
0.0142
0.0489
0.0785
0.0291
0.0328
0.1107
τ =0.75
0.0263
0.0179
0.0140
0.0533
0.0577
0.0318
1.6307
0.1489
τ =0.50
0.0252
0.0327
0.0164
0.0542
0.0590
0.0354
0.0984
0.2350
τ =0.75
0.0347
0.0367
0.0199
0.0551
0.0782
0.0326
0.3733
0.1455
(a) Kress Phylogeny
Assemblage
5
5
5
10
10
10
50
50
Source Pool
50
100
All BCI
50
100
All BCI
100
All BCI
τ =0.25
0.0278
0.0341
0.0164
0.0491
0.0771
0.0432
0.4939
0.2130
(b) Phylomatic Phylogeny
Assemblage
5
5
5
10
10
10
50
50
Source Pool
50
100
All BCI
50
100
All BCI
100
All BCI
τ =0.25
0.0281
0.0277
0.0147
0.0760
0.0766
0.0339
0.2534
0.1436
τ =0.50
0.0289
0.0333
0.0153
0.0597
0.0450
0.0300
0.4484
0.0899
τ =0.75
0.0290
0.0320
0.0165
0.0479
0.1025
0.0340
0.0257
0.0787
(c) Control Phylogeny
Table A18: Standard errors of quantile regression of SESM P D values across BCI in all three
phylogenies, with assemblages whose source pools that cross the boundary of BCI removed
from the analysis.
31
Assemblage
5
5
5
10
10
10
50
50
Range
Source Pool
50
100
All BCI
50
100
All BCI
100
All BCI
τ =0.25
-1.16
-1.20
-0.99
-1.24
-1.32
-0.92
-0.67
-1.07
τ =0.50
-0.61
-0.61
-0.45
-0.69
-0.72
-0.39
-0.48
-0.70
τ =0.75
0.04
0.01
0.19
-0.09
-0.03
0.24
0.19
-0.19
0.66
0.64
0.76
0.55
0.52
0.82
0.92
0.41
1.14
1.10
1.26
1.06
1.07
1.39
1.28
1.19
τ =0.75
-0.22
-0.20
0.00
0.02
0.37
0.08
0.64
0.80
0.44
0.43
0.58
0.72
1.01
0.72
0.98
1.38
1.00
0.95
1.11
1.42
1.59
1.44
1.33
1.80
τ =0.75
-0.11
-0.05
0.10
0.73
0.44
0.15
0.36
0.83
0.53
0.56
0.69
1.51
1.07
0.79
1.04
1.37
1.09
1.09
1.20
(a) Kress Phylogeny
Assemblage
5
5
5
10
10
10
50
50
Range
Source Pool
50
100
All BCI
50
All BCI
100
100
All BCI
τ =0.25
-1.34
-1.27
-1.09
-1.16
-0.78
-1.04
-0.77
-0.63
τ =0.50
-0.80
-0.74
-0.57
-0.65
-0.22
-0.54
-0.59
0.14
(b) Phylomatic Phylogeny
Assemblage
5
5
5
10
10
10
50
50
Range
Source Pool
50
100
All BCI
50-1.18
All BCI
100
100
All BCI
τ =0.25
-1.28
-1.24
-1.05
-0.62
-0.71
-1.10
-0.50
-0.27
τ =0.50
-0.72
-0.69
-0.51
0.03
-0.17
-0.48
-0.20
0.38
1.73
1.70
1.39
1.86
(c) Control Phylogeny
Table A19: Quantile regression of SESM N T D values across BCI in the Phylomatic and
Control phylogenies, with assemblages whose source pools that cross the boundary of BCI
removed from the analysis.
32
Assemblage
5
5
5
10
10
10
50
50
Source Pool
50
100
All BCI
50
100
All BCI
100
All BCI
τ =0.25
0.0318
0.0352
0.0183
0.0588
0.0844
0.0441
0.3776
0.2412
τ =0.50
0.0270
0.0309
0.0156
0.0420
0.0554
0.0279
0.0500
0.1633
τ =0.75
0.0279
0.0340
0.0160
0.0583
0.0571
0.0352
1.4701
0.2777
τ =0.50
0.0271
0.0308
0.0153
0.0481
0.0581
0.0295
0.1506
0.2027
τ =0.75
0.0246
0.0308
0.0153
0.0804
0.1092
0.0359
0.5413
0.2189
(a) Kress Phylogeny
Assemblage
5
5
5
10
10
10
50
50
Source Pool
50
100
All BCI
50
100
All BCI
100
All BCI
τ =0.25
0.0269
0.0270
0.0151
0.0555
0.0699
0.0277
1.6673
0.4964
(b) Phylomatic Phylogeny
Assemblage
5
5
5
10
10
10
50
50
Source Pool
50
100
All BCI
50
100
All BCI
100
All BCI
τ =0.25
0.0243
0.0298
0.0170
0.0539
0.0867
0.0293
1.3553
0.1631
τ =0.50
0.0290
0.0381
0.0155
0.0454
0.0628
0.0261
0.0055
0.2032
τ =0.75
0.0331
0.0365
0.0171
0.0804
0.0780
0.0433
0.0929
0.1518
(c) Control Phylogeny
Table A20: Standard errors of quantile regression of SESM N T D values across BCI in all three
phylogenies, with assemblages whose source pools that cross the boundary of BCI removed
from the analysis.
33
Assemblage
5
10
50
Range
τ =0.25 τ =0.50 τ =0.75
0.78
0.79
0.80
0.78
0.79
0.80
0.79
0.79
0.80
0.01
0
0
(a) Kress Phylogeny
Assemblage τ =0.25
5
0.68
10
0.68
50
0.70
Range
0.02
τ =0.50
0.70
0.70
0.70
0
τ =0.75
0.72
0.71
0.71
0.01
(b) Phylomatic Phylogeny
Assemblage
5
10
50
Range
τ =0.25 τ =0.50 τ =0.75
0.68
0.70
0.72
0.68
0.70
0.71
0.70
0.70
0.71
0.02
0
0.01
(c) Control Phylogeny
Table A21: Quantile regression of PSV values across BCI in the Phylomatic and Control
phylogenies, with assemblages whose source pools that cross the boundary of BCI removed
from the analysis.
34
Assemblage
5
10
50
τ =0.25 τ =0.50 τ =0.75
0.0004 0.0004 0.0004
0.0004 0.0005 0.0005
0.0005 0.0006 0.0008
(a) Kress Phylogeny
Assemblage
5
10
50
τ =0.25 τ =0.50 τ =0.75
0.0006 0.0006 0.0008
0.0008 0.0007 0.0008
0.0018 0.0016 0.0008
(b) Phylomatic Phylogeny
Assemblage
5
10
50
τ =0.25 τ =0.50 τ =0.75
0.0006 0.0006 0.0007
0.0008 0.0007 0.0008
0.0007 0.0007 0.0011
(c) Control Phylogeny
Table A22: Standard errors of quantile regression of PSV values across BCI in all three
phylogenies, with assemblages whose source pools that cross the boundary of BCI removed
from the analysis.
35
Assemblage
5
5
5
10
10
10
50
50
Range
Source Pool
50
100
All BCI
50
100
All BCI
100
All BCI
τ =0.25
-0.02
-0.02
-0.01
-0.01
-0.01
-0.01
-0.01
0.00
0.01
τ =0.50
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0
τ =0.75
0.01
0.01
0.01
0.00
0.00
0.01
0.00
0.01
0.01
τ =0.50
-0.01
0.00
0.00
-0.01
-0.01
0.00
0.00
0.00
0.01
τ =0.75
0.02
0.02
0.02
0.01
0.01
0.01
0.00
0.01
0.01
(a) Kress Phylogeny
Assemblage
5
5
5
10
10
10
50
50
Range
Source Pool
50
100
All BCI
50
100
All BCI
100
All BCI
τ =0.25
-0.03
-0.03
-0.03
-0.02
-0.02
-0.02
-0.01
0.00
0.03
(b) Phylomatic Phylogeny
Assemblage
5
5
5
10
10
10
50
50
Range
Source Pool
50
100
All BCI
50
100
All BCI
100
All BCI
τ =0.25
-0.02
-0.02
-0.02
-0.02
-0.02
-0.01
-0.01
0.00
0.02
τ =0.50
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.01
0.01
τ =0.75
0.02
0.02
0.03
0.01
0.01
0.02
0.00
0.01
0.03
(c) Control Phylogeny
Table A23: Quantile regression of corrected PSV values across BCI in all three phylogenies,
with assemblages whose source pools that cross the boundary of BCI removed from the
analysis.
36
Assemblage
5
5
5
10
10
10
50
50
τ =0.25
50
100
All BCI
50
100
All BCI
100
All BCI
τ =0.50
0.0010
0.0008
0.0004
0.0012
0.0010
0.0005
0.0011
0.0006
τ =0.75
0.0007
0.0009
0.0004
0.0006
0.0012
0.0005
0.0006
0.0005
0.0007
0.0007
0.0004
0.0007
0.0008
0.0005
0.0066
0.0011
τ =0.75
0.0009
0.0013
0.0006
0.0011
0.0010
0.0007
0.0012
0.0016
0.0013
0.0014
0.0008
0.0012
0.0012
0.0008
0.0003
0.0009
(a) Kress Phylogeny
Assemblage
5
5
5
10
10
10
50
50
τ =0.25
50
100
All BCI
50
100
All BCI
100
All BCI
τ =0.50
0.0011
0.0014
0.0006
0.0011
0.0014
0.0008
0.0061
0.0014
(b) Phylomatic Phylogeny
Assemblage
5
5
5
10
10
10
50
50
Source Pool
50
100
All BCI
50
100
All BCI
100
All BCI
τ =0.25
0.0010
0.0011
0.0005
0.0017
0.0014
0.0008
0.0010
0.0007
τ =0.50
0.0012
0.0013
0.0006
0.0012
0.0009
0.0008
0.0023
0.0008
τ =0.75
0.0013
0.0014
0.0007
0.0010
0.0028
0.0007
0.0003
0.0014
(c) Control Phylogeny
Table A24: Standard errors of quantile regressions of corrected PSV values across BCI in
the all three phylogenies, with assemblages whose source pools that cross the boundary of
BCI removed from the analysis.
37
Small assemblage simulations
2
5
10
20
No. spp. in source pool
25
50
100
All
1.0
1.5
No. spp. in assemblage
0.0
0.5
Density
2.0
2.5
8
−1
0
1
2
3
D
Fig. A13: Simulated small assemblages’ D values. 30 randomly selected source pools containing 25, 50, 100, and all species in BCI, within with 30 different assemblages containing 2,
5, 10, and 20 species were created. D values were calculated for all 14400 assemblages, and
are plotted above. A two-way ANOVA of D against assemblage and source pool size was
significant (F15,14384 = 1.739), but only had an r2 of 0.18%. This likely reflects the poorer
resolution of D in assemblages containing only two species.
38
References
Kembel, S.W., Cowan, P.D., Helmus, M.R., Cornwell, W.K., Morlon, H., Ackerly, D.D.,
Blomberg, S.P. & Webb, C.O. (2010) Picante: R tools for integrating phylogenies and ecology. Bioinformatics 26, 1463–1464.
39