Geog aphy, clima e and shi s in
hos plan s dis ibu ion explain
he genomic a ia ion in he
cac us mo h
Daniel Po eda-Ma ı
´nez
1,2
*,Vı
´c o Nogue ales
3
,
S ephen D. High
4
, Guille mo Loga zo
1
, B en C. Eme son
3
,
Lau a Va one
1
†
and Es eban Hasson
2
†
1
Fundacio
´n pa a el Es udio de Especies In asi as (FuEDEI), Hu lingham, A gen ina,
2
Ins i u o de
Ecologı
´a Gene
´ ica y E olucio
´n de Buenos Ai es (IEGEBA-CONICET), Facul ad de Ciencias Exac as y
Na u ales, Uni e sidad de Buenos Ai es, Buenos Ai es, A gen ina,
3
Island Ecology and E olu ion
Resea ch G oup, Ins i u o de P oduc os Na u ales y Ag obiologı
´a (IPNA-CSIC), San C is o
´bal de La
Laguna, Cana y Islands, Spain,
4
The U.S. Depa men o Ag icul u e –Ag icul u al Resea ch Se ice
(USDA-ARS), Insec Beha io and Biocon ol Resea ch Uni (IBBRU), Tallahassee, FL, Uni ed S a es
Landscape he e ogenei y and he hos plan use a e ac o s sugges ed o play
de e minan oles in shaping he e olu iona y his o y o he bi o ous insec s.
Howe e , he ole o he econfigu a ion o hos plan s dis ibu ions linked o
Qua e na y clima e oscilla ions as d i e s o con empo a y popula ion gene ic
s uc u e is s ill poo ly unde s ood. He e, we o mally examine he ela i e
con ibu ion o such ac o s on in aspecific di e sifica ion using he Sou h
Ame ican cac us mo h, Cac oblas is cac o um, an he bi o e insec specialized
in he use o cac i as hos plan s. We assessed genomic a ia ion using genome-
wide SNPs and mi ochond ial da a in popula ions sampled ac oss a b oad
geog aphical g adien whe e mo hs eed on di e en cac us species. We
in eg a ed demog aphic simula ions and ecological niche modeling in o a
landscape genomics amewo k, o es al e na i e hypo heses o pas and
cu en popula ion connec i i y o bo h C. cac o um and i s hos plan s.
Regions exhibi ing highe genomic di e si y we e e alua ed o cong uence
wi h a eas whe e sui able clima ic condi ions emained s able h ough ime.
Ou esul s e ealed ha pas spa ial configu a ion o sui able habi a condi ions
and shi s o hos plan s dis ibu ions a e he ac o s ha be e explain he
in aspecific di e sifica ion. Genomic da a also suppo ed he hypo hesis ha
a eas o long- e m habi a s abili y se ed as e ugia o C. cac o um, enabling
he main enance o high le els o gene ic di e si y o e ime. O e all, ou s udy
highligh s he impo ance o in eg a ing in e -specific in e ac ions and hei
spa io- empo al dynamics o be e unde s and he ela i e impo ance o
abio ic and bio ic ac o s d i ing he di e sifica ion p ocesses in he bi o ous
insec s wi h b oad geog aphical and es ic ed hos anges.
KEYWORDS
cac us pes , cac oblas is cac o um, ddRAD, landscape genomics, paleoclima e, opun ia
F on ie s in Ecology and E olu ion on ie sin.o g01
OPEN ACCESS
EDITED BY
Zi ong Li,
Commonweal h Scien ific and Indus ial
Resea ch O ganisa ion (CSIRO), Aus alia
REVIEWED BY
Cui Wang,
Uni e si y o Helsinki, Finland
Jo dan Golubo ,
Uni e sidad Au o
´noma
Me opoli ana, Mexico
*CORRESPONDENCE
Daniel Po eda-Ma ı
´nez
[email p o ec ed]
†
These au ho s sha e las au ho ship
RECEIVED 18 July 2023
ACCEPTED 29 Augus 2023
PUBLISHED 19 Sep embe 2023
CITATION
Po eda-Ma ı
´nez D, Nogue ales V,
High SD, Loga zo G, Eme son BC,
Va one L and Hasson E (2023) Geog aphy,
clima e and shi s in hos plan s dis ibu ion
explain he genomic a ia ion in he
cac us mo h.
F on . Ecol. E ol. 11:1260857.
doi: 10.3389/ e o.2023.1260857
COPYRIGHT
©2023Po eda-Ma ı
´nez, Nogue ales, High ,
Loga zo, Eme son, Va one and Hasson. This
is an open-access a icle dis ibu ed unde
he e ms o he C ea i e Commons
A ibu ion License (CC BY). The use,
dis ibu ion o ep oduc ion in o he
o ums is pe mi ed, p o ided he o iginal
au ho (s) and he copy igh owne (s) a e
c edi ed and ha he o iginal publica ion in
his jou nal is ci ed, in acco dance wi h
accep ed academic p ac ice. No use,
dis ibu ion o ep oduc ion is pe mi ed
which does no comply wi h hese e ms.
TYPE O iginal Resea ch
PUBLISHED 19 Sep embe 2023
DOI 10.3389/ e o.2023.1260857
1 In oduc ion
The spa ial dis ibu ion o genomic a ia ion in na u al
popula ions is influenced by a a ie y o p ocesses, including he
dispe sal abili y o indi iduals, gene flow, bio ic in e ac ions, and
landscape ea u es. Un eiling he ela i e oles o hese p ocesses is
necessa y o unde s and how o ganisms in e ac wi h he
en i onmen and how he la e shapes hei genomic makeup. In
his ma e , he bi o ous insec s dis ibu ed along en i onmen al
g adien s eeding on a se o hos plan s o e he oppo uni y
o disen angling he ecological and geog aphical p ocesses d i ing
popula ion di e en ia ion and gene flow dynamics in he e ogeneous
landscapes (Bo e e al., 2012;Laukkanen e al., 2014).
Among he ecological ac o s, he use o al e na i e hos plan s is
hough o shape pa e ns o gene flow among popula ions in
he bi o ous insec s (Funk e al., 2006;Fo bes e al., 2017).
Mo eo e , changes in hos plan use oge he wi h adap a ion o
di e en en i onmen al condi ions can lead o ecological
specializa ion and di e sifica ion (isola ion by en i onmen , IBE;
Wang and B adbu d, 2014). Geog aphy (isola ion by dis ance, IBD;
Sla kin, 1993) and he spa ial dis ibu ion o sui able habi a s
(isola ion by esis ance, IBR; McRae, 2006;McRae and Beie , 2007)
may also be de e minan s o popula ion gene ic di e en ia ion ac oss
he landscape (Pe e man e al., 2014;Vidal e al., 2019).
Insec s wi h na ow die b ead hs and en i onmen al
equi emen s a e expec ed o exhibi ma ked gene ic s uc u e as
a consequence o gene flow dis up ion be ween popula ions
exploi ing al e na i e hos s (Vidal and Mu phy, 2018) and/o
inhabi ing a agmen ed landscape o sui able habi a s (O ego
e al., 2021). Howe e , in widely dis ibu ed insec s eeding on a
na ow a ay o hos plan s ac oss he landscape, con empo a y
pa e ns o genomic a ia ion can also be influenced by a ange o
ac o s, including dispe sal abili y, pa e ns o hos plan use and/o
componen s o landscape he e ogenei y. Mo eo e , less s udied
spa io-ecological ac o s, such as dis ibu ional shi s o hos
plan s d i en by clima e oscilla ions h oughou he Qua e na y
pe iod, may ha e also p omo ed cycles o geog aphical isola ion and
seconda y con ac , shaping con empo a y pa e ns o gene ic
a ia ion in he bi o ous insec s (Nogue ales e al., 2018). Ye , he
ela i e con ibu ion o hese ecological ac o s and spa io- empo al
landscape dynamics in d i ing popula ions di e en ia ion in axa
wi h b oad clima ic niches and na ow eeding equi emen s a e
s ill open ques ions in e olu iona y biology. To unde s and he ole
o such spa ial-ecological p ocesses in species di e sifica ion and
shaping gene flow in he e ogeneous landscapes, an in eg a i e
app oach is necessa y, aking in o accoun his o ical and
con empo a y en i onmen al da a, combined wi h a sui able
insec model wi h na ow ophic equi emen s and dis ibu ed
along en i onmen al g adien s.
He e, we in es iga e pa e ns o genomic a ia ion in he cac us
mo h, Cac oblas is cac o um (Be g) (Lepidop e a: Py alidae), a
sou he n Sou h Ame ican he bi o e insec , ha inhabi s
he e ogeneous landscapes, aces a a ie y o clima e condi ions,
and eeds on se e al species o he genus Opun ia (Cac aceae,
Opun ioideae). This mo h can be ound ac oss wide la i udinal
and longi udinal g adien s, om he a id and semi-a id lands o
no hwes e n and no heas e n Chaco, o he g asslands o he
Pampa, and no h o he Pa agonian s eppe (McFadyen, 1985;
Mo one, 2014;Va one e al., 2014). Along such b oad
dis ibu ion, C. cac o um eeds on na i e species, such as O.
anacan ha Speg., O. bonae ensis Speg., O. ela a Link & O o ex
Salm-Dyck, O. megapo amica A echa ., O. penicillige a Speg., O.
quimilo K. Schum., and O. iopla ense Fon ., and also he cul i a ed
O. ficus-indica (L.) Mille , an exo ic species in he egion (Va one
e al., 2012;Va one e al., 2014).
Soon a e i s in oduc ion he p ickly pea O. ficus-indica was
quickly adop ed as a c op in sou he n Sou h Ame ica (E in, 2012).
The a ailabili y o his new hos plan ep esen s a ela i ely ecen
expansion o hos use o C. cac o um. Cu en ly his mo h is a
se ious h ea o he egional indus y o p ickly pea ui
p oduc ion (Ochoa e al., 2007). The in oduc ion o he new hos
led o he sugges ion ha he sp ead o O. ficus-indica p omo ed he
dispe sion and geog aphical ange expansion o C. cac o um
(Va one e al., 2014).
P e ious s udies e ealed ha popula ions o C. cac o um a e
gene ically di e en ia ed in a leas ou haplog oups co ela ed
wi h geog aphy and a iable le els o gene ic di e si y among na i e
and non-na i e mo h popula ions (Ma sico e al., 2011), and ha
pa e ns o colo a ion o ma u e la ae and hos plan use a y
ac oss egions (B ooks e al., 2012). Howe e , only limi ed
conclusions can be d awn om hese s udies since (i) only a
single mi ochond ial gene ic ma ke was used; (ii) sampling did
no co e he en i e species ange; and (iii) he ela i e abundance o
hos species was no conside ed (McFadyen, 1985;Ma sico e al.,
2011;B ooks e al., 2012). Mo e ecen ly, an ex ensi e su ey
e alua ing hos plan p e e ences ac oss he b oad ange o C.
cac o um concluded ha pa e ns o hos use eflec a ia ion in
hos a ailabili y a he han emale p e e ence (Va one e al., 2014).
In his s udy, we use high- h oughpu nuclea sequence da a and
Sange sequence da a o mi ochond ial DNA o in es iga e he
p ocesses ha shaped pa e ns o di e sifica ion in he cac us mo h,
C. cac o um. Ou sampling s a egy ex ended o e a b oad geog aphic
ange aking ca e o including he di e si y o na i e and non-na i e
hos s. We combine in e ences om phylogenomics and demog aphic
modeling o unco e he empo and mode o di e sifica ion, pa e ns
o gene flow and popula ion gene ic s uc u e. By in eg a ing
ecological niche modeling in o a landscape genomic amewo k, we
es a comp ehensi e sui e o compe ing scena ios o popula ion
isola ion. Specifically we e alua e he hypo heses ha con empo a y
spa ial pa e ns o popula ion gene ic di e en ia ion in C. cac o um
a e p edominan ly a consequence o he spa ial econfigu a ion o
sui able a eas and shi s in he dis ibu ion o hos plan s caused by
Qua e na y clima ic oscilla ions whils he cu en pa e n o hos
plan use and opoclima ic ac o s a e less influen ial in i s
di e sifica ion. Since we es ima ed his o ical and con empo a y
habi a sui abili y, and long- e m sui able en i onmen s end o
suppo la ge e ec i e popula ion sizes (Ca na al e al., 2009;
Soley-Gua dia e al., 2019), we also add ess whe he egions whe e
sui able habi a condi ions emained s able since he las glacial
maximum (LGM, ca. 21 ka) o he p esen exhibi g ea e gene ic
di e si y han popula ions h i ing in less s able a eas. Finally, we
e alua ed whe he he expansion o O. ficus-indica acili a ed
Po eda-Ma ı
´nez e al. 10.3389/ e o.2023.1260857
F on ie s in Ecology and E olu ion on ie sin.o g02
con empo a y gene flow among geog aphically dis an popula ions.
In his ma e , ou expec a ion is o find oo p in s o gene ic
admix u e among dis an egions, especially among a eas highly
impac ed by p ickly pea ag oindus y.
2 Me hods
2.1 Popula ion sampling and
DNA ex ac ion
Be ween 2018 and 2019, we collec ed 140 indi iduals o C.
cac o um om 28 sampling si es spanning a b oad ange o i s
na i e dis ibu ion in sou he n Sou h Ame ica (Figu e 1;Table S1).
Indi iduals we e collec ed di ec ly om hos plan s, including se en
na i e axa, O. anacan ha, O. bonae ensis, O. ela a, O.
megapo amica, O. penicillige a, O. iopla ense, and O. quimilo,
and he exo ic O. ficus-indica. To a oid he inclusion o siblings,
only a single indi idual pe sampled plan and eggs ick was used o
gene ic analysis. Be o e DNA ex ac ion, indi idual la ae we e
dissec ed o emo e any ood esidue, and ~30 mg o clean issue
was used o DNA ex ac ion wi h Qiagen DNeasy Blood & Tissue
Ki ollowing manu ac u e ’s ins uc ions (Qiagen, Inc.).
2.2 Genomic lib a ies p epa a ion, fil e ing
and assembling
Indi iduals we e p ocessed in o wo genomic lib a ies ollowing
he double diges es ic ion-si e Associa ed DNA (ddRAD)
p ocedu e desc ibed in Pe e son e al. (2012). Genomic DNA was
agmen ed using NspI and MboI es ic ion enzymes, and hen
pu ified and liga ed o ba coded adap e s. Lib a ies we e sequenced
in pai ed-end 125 bp mode on a HiSeq2500 Illumina ins umen .
Demul iplexed aw eads we e checked, compiled and
summa ized on Mul iQC 1.10.1 (Ewels e al., 2016). Reads we e
assembled wi h IPYRAD .0.9.59 (Ea on and O e cas , 2020). A
e e ence based assembly me hod was implemen ed o mapping
he fil e ed eads agains he C. cac o um e e ence genome. DNA
ex ac ed om an adul male (clean DNA, ee o ood
con aminan s can be ob ained om males, as hey do no eed)
was used o lib a y p epa a ion and sequenced in an Illumina
No aSeq 6000 pla o m. The de no o assembly was accomplished
wi h CLC Genomics Wo kbench 7.1 (see Po eda-Ma ınez e al.,
2022 o de ails). Thus, he e e ence genome se ed also as a fil e
o exogenous eads de i ed om la al ood.
In subsequen IPYRAD assembly s eps, we allowed 20% o
SNPs pe RAD locus, and sha ed he e ozygous si es occu ing
ac oss a maximum o 25% o samples. A minimum o 90% was
se o he minimum numbe o samples sco ed pe locus. We used
c ools 1.15 (Danecek e al., 2011) o emo eSNPswi h
minimum allele equency lowe han 3%, missing da a pe si e
ac oss indi iduals exceeding 25%, and o keep SNPs wi h ead
dep hs be ween 6× and 100×. Indi iduals wi h mo e han 20%
missing da a we e excluded om u he analyses. To p une SNPs
in linkage disequilib ium, PLINK 1.9 (Pu cell e al., 2007) was used
wi h a window size o 50 bp, window shi o 5 and VIF h eshold o
2. SNPs unde selec ion we e iden ified using Bayescan .2.1 (Foll
and Gaggio i, 2008) and excluded om he da ase . A agmen o
he mi ochond ial gene encoding he Cy och ome oxidase subuni I
AB
C
FIGURE 1
Geog aphic loca ion and hos species o he Cac oblas is cac o um popula ions sampled in his s udy (A). Regions ep esen biogeog aphic
p o inces acco ding o Mo one e al. (2014). Panels (B, C) ep esen he maps o habi a sui abili y o C. cac o um du ing he p esen (B) and du ing
he Las Glacial Maximum (LGM, ca. 21ky) (C) as in e ed by he mos -suppo ed ENM model in MAXENT.
Po eda-Ma ı
´nez e al. 10.3389/ e o.2023.1260857
F on ie s in Ecology and E olu ion on ie sin.o g03
(COI) (m DNA) was amplified using p ime s C1-J-2183 and Pa II.
Amplifica ions, PCR-p oduc pu ifica ion and sequencing we e
pe o med as de ailed in Po eda-Ma ınez e al. (2022).
2.3 Assessing genomic
popula ion s uc u e
Popula ion gene ic s uc u e was in e ed using genome-wide
SNP da a (nDNA he ea e ) and he spa se non-nega i e ma ix
ac o iza ion app oach (sNMF) (F icho e al., 2014), as
implemen ed in R using he LEA package (F icho and F ancois,
2015). The numbe o gene ic clus e s ha bes desc ibed ou da a
was assessed wi h 100 epe i ions o each possible K alue ( om
K = 1 o K = 10) and using he c oss-en opy c i e ion. In addi ion
o sNMF, gene ic s uc u e was app oxima ed by using he majo
axes o genomic a ia ion ob ained om a P incipal Componen
Analysis (PCA), as implemen ed in he hie s a (Goude , 2005)R
package. We used m DNA da a o cons uc a haplo ype ne wo k
using he Median Joining algo i hm (Bandel e al., 1999)as
implemen ed in PopA .1.7.1 (Leigh and B yan , 2015).
2.4 Phylogene ic analyses
Phylogene ic ela ionships we e econs uc ed among he main
gene ic g oups as in e ed in sNMF using nDNA da a and he
coalescen -based me hod implemen ed in SNAPP (B yan e al.,
2012). Due o compu a ional bu den, SNAPP analyses we e un
including only fi e indi iduals pe gene ic clus e , selec ing hose
wi h an ances y coe ficien highe han 0.85, acco ding o sNMF,
and indi iduals ha had he lowes p opo ion o missing da a. One
SNP pe locus was andomly selec ed esul ing in a new ma ix o
2,086 SNPs sha ed ac oss ips. This allows o ensu e independen
biallelic ma ke s as well as ai ly spaced SNPs as equi ed in SNAPP
(B yan e al., 2012). The de aul model pa ame e s we e used in
SNAPP o U and V equal o one, and he analysis was un o
5,000,000 MCMC gene a ions, sampling e e y 1000 gene a ions in
Beas .2.5.2 (Bouckae e al., 2014). The comple e se o ees was
isualized in Densi ee .2.2.5 (Bouckae , 2010), emo ing he fi s
10% o he ees as bu n-in. A maximum c edibili y ee was
gene a ed using T eeAnno a o .1.7.5 (D ummond e al., 2012).
2.5 Demog aphic his o y
A coalescen -based simula ion app oach was implemen ed in
Fas simcoal2 (Exco fie e al., 2013) based on he si e equency
spec um (SFS) o nDNA da a o u he in es iga e he
demog aphic his o y o he h ee main lineages iden ified in
clus e ing analysis and species ee in e ence (Cen e , Eas and
Sou h, see esul s sec ion). Ini ially, o u he e alua e he
consis ency o phylogene ic ela ionships among C. cac o um
popula ions in e ed in SNAPP, models ep esen ing he h ee
possible opologies (A, B and C) we e conside ed in each one o
he subsequen models o gene flow (Figu e S1). Fo each opology,
di e gence imes, con empo a y and ancien e ec i e popula ion
sizes we e es ima ed, as well as al e na i e scena ios o gene flow.
Models 1–3 conside ed no gene flow among lineages; models 4–6
con empla ed scena ios o symme ic gene flow among lineages,
while models 7–9 conside ed scena ios o asymme ic gene flow
among lineages. Fo hese analyses, 20 indi iduals we e selec ed
wi h he highes ances y coe ficien (>0.85) acco ding o sNMF
(e.g., O ego e al., 2021). The olded join SFS was calcula ed
conside ing a single SNP pe locus using he Py hon sc ip w i en
by Isaac O e cas and a ailable a Gi Hub (h ps://gi hub.com/
isaaco e cas /easySFS). To emo e missing da a and minimize
e o s wi h allele equency es ima es, each gene ic clus e was
downsampled o 16 indi iduals yielding a o al o 2,565 a iable
si es. Assuming ha in a iable si es we e no conside ed in he SFS
calcula ion, we used he “ emo eZe oSFS”op ion in Fas simcoal2
and fixed he e ec i e popula ion size o one o he demes (Sou h
lineage, NE
SOUTH
= 824,626) o enable he es ima ion o o he
pa ame e s wi h Fas simcoal2. NE
SOUTH
was calcula ed acco ding
o he equa ion NE = p/4m(Lynch and Cone y, 2003). Nucleo ide
di e si y (p= 0.004) was es ima ed using a ian and in a ian si es
wi h DNAsp 6 (Rozas e al., 2017). The mu a ion a e (m) was
conside ed o be 2.9 × 10
−9
subs i u ions pe si e pe gene a ion, as
p e iously es ima ed o he bu e flyHeliconius melpomene
(Keigh ley e al., 2015) (Lepidop e a: Nymphalidae). Each model
was un wi h 50 eplica es, conside ing 100,000–250,000
simula ions o he calcula ion o he composi e likelihood, 10–40
expec a ion–condi ional maximiza ion (ECM) cycles, and a
s opping c i e ion o 0.001. Once maximum likelihood was
es ima ed pe un, he bes demog aphic model was selec ed
acco ding o Akaike’s in o ma ion c i e ion (AIC). AIC alues
we e escaled in e ms o AIC di e ences (Di) acco ding o he
o mula: Di = AICi −AICmin. A model wi h a DAIC alue o 0 and
he highes AIC weigh (wi) se ed as he bes model. A pa ame ic
boo s apping app oach was used o cons uc 95% confidence
in e als o he es ima ed pa ame e s unning 100 boo s ap
eplica es using ini ialized alues om he bes model (Exco fie
e al., 2013).
2.6 En i onmen al niche modeling
An en i onmen al niche modeling app oach was implemen ed
o p edic con empo a y and his o ical geog aphic dis ibu ions o
sui able a eas o he cac us mo h in i s na i e ange. En i onmen al
niche models (ENMs) we e used o de e mine he impac o
his o ical and con empo a y componen s o landscape
he e ogenei y on C. cac o um di e sifica ion as is de ailed below
in he landscape genomic analysis sec ion. ENMs we e buil using
MaxEn .3.4.1 (Phillips e al., 2006) and he bioclima ic da a
a ailable in CHELSA .1.2 da abase (h ps://chelsa-clima e.o g/
bioclim/). Model pa ame e s in MaxEn we e selec ed and
op imized using he kuenm (Cobos e al., 2019) R package. Fo
bo h empo al bioclima ic condi ions, p esen -day and Las Glacial
Maximum (LGM, ca. 21 kya), we e alua ed 15 en i onmen al
a iables e ie ed a 30 a c-sec (~1 km) o esolu ion. Fou
bioclima ic a iables (Bio 8, 9, 18 and 19) we e disca ded o
Po eda-Ma ı
´nez e al. 10.3389/ e o.2023.1260857
F on ie s in Ecology and E olu ion on ie sin.o g04
ha ing a ificial b eaks (Oli ei a e al., 2020). Highly co ela ed
a iables (R > 0.9) acco ding o a iance infla ion ac o c i e ion
we e excluded o downs eam analyses esul ing in a final da ase
o six bioclima ic a iables (Bio 2, 3, 5, 13, 14 and 15). Sui abili y
maps du ing he LGM we e ob ained by p ojec ing he p esen -day
ENM on o LGM bioclima ic condi ions de i ed om he
Communi y Clima e Sys em Model (CCSM4; B aconno e al.,
2007) esul ing in wo sui abili y maps based on bioclima ic
a iables da a (Se 1, Clima ic
CURR
and Clima ic
LGM
om he ea e ).
Addi ionally, we cons uc ed ENMs o fi e o he se en na i e
hos species o C. cac o um conside ing he a o emen ioned
app oach o a iable selec ion and model building. ENM o O.
penicillige a and O. bonae ensis could no be implemen ed due o
limi ed occu ence da a. The esul ing ENMs ob ained o cu en
and LGM condi ions om each hos species we e used as a iables
o build an addi ional ENM o C. cac o um (Se 2, Hos
CURR
and
Hos
LGM
om he ea e ). A hi d ENM was cons uc ed o C.
cac o um conside ing he inpu o bo h he bioclima ic a iables
(Se 1) and he hos plan ENMs (Se 2) (Se 3; Clima ic-Hos
CURR
and Clima ic-Hos
LGM
om he ea e ).
Occu ence da a o he hos species and C. cac o um we e
ob ained om field su eys made om 2007 o 2019 and
complemen ed, a e de ailed cu a ion, wi h dis ibu ion
in o ma ion a ailable a GBIF (www.gbi .o g). Redundan
occu ences (e.g. poin s occu ing wi hin 1,500 km
2
)we e
excluded using spThin (Aiello-Lammens e al., 2015) R package.
A e hinning occu ence da a, 81 eco ds o C. cac o um loca ions
and hei associa ed occu ance o 205 hos species emained [O.
quimilo (50), O. megapo amica (47), O. iopla ense (39), O. ela a
(38), and O. anacan ha (31)] and we e used o conduc ENMs.
Model pe o mance o each scena io was e alua ed independen ly
based on s a is ical significance (Pa ial ROC), omission a es (OR),
and he Akaike in o ma ion c i e ion co ec ed o small sample
sizes (AICc) using he kuenm (Cobos e al., 2019) R package.
2.7 Landscape genomic analyses
A landscape genomic app oach was implemen ed o s udy
po en ial ac o s ha could explain pa e ns o gene ic
di e en ia ion wi hin C. cac o um.Asameasu eo gene ic
di e en ia ion, pai wise F
ST
es ima es we e de i ed om genome-
wide SNP da a using he Wei and Cocke ham (1984) me hod wi h
he S AMPP (Pemble on e al., 2013) R package and 9,999 boo s ap
eplica es. We e alua ed se e al plausible scena ios o popula ion
connec i i y based on his o ical and con empo a y spa ial and
ecological da a.
Isola ion by esis ance scena ios (IBR) we e es ed by
calcula ing esis ance su aces based on he sui abili y maps
ob ained om ENMs o p esen -day and LGM condi ions
conside ing di e en subse s o ac o s: (i) only clima ic a iables
(Clima ic
CURR
and Clima ic
LGM
); (ii) clima e-based habi a
sui abili y maps conside ing he hos species dis ibu ion
(Hos
CURR
and Hos
LGM
); and (iii) combining clima ic a iables
and clima e-based habi a sui abili y maps o hos species
dis ibu ion (Clima ic-Hos
CURR
and Clima ic-Hos
LGM
).
Resis ance dis ances o all pai s o popula ions we e calcula ed
using an eigh -neighbo cell connec ion scheme in Ci cui scape .5
(Hall e al., 2021) h ough Julia .1.5.2 (h ps://julialang.o g/). We
also calcula ed esis ance dis ances based on a “fla landscape”
whe e all cells ha e an equal esis ance alue (=1) ep esen ing a
null model o isola ion by esis ance (IBR
NULL
).
An isola ion by dis ance scena io was also e alua ed using
weigh ed opog aphic dis ances (IBD
WTD
), which inco po a e an
addi ional o e land dis ance co e ed by an o ganism due o changes
in ele a ion imposed by he opog aphy. The IBD
WTD
dis ance
ma ix was calcula ed on a digi al ele a ion model (DEM) a ~1 km
o esolu ion e ie ed om Wo ldClim .2.1 (Fick and Hijmans,
2017) da ase using he TopoWeigh edDis unc ion implemen ed
in he opoDis ance (Fick and Hijmans, 2017;Wang, 2020)R
package. We assumed a linea unc ion o weigh aspec changes
(hFunc ion pa ame e ) and an exponen ial unc ion o weigh he
slope ( Func ion pa ame e ) (e.g. Nogue ales e al., 2021).
Clima ic dissimila i ies we e es ima ed be ween popula ions o
e alua e an isola ion by en i onmen scena io (IBE
CLI
).
En i onmen al da a was ex ac ed om he 15 CHELSA
bioclima ic a iables o each o he 28 sampling si es, as well as
om 500 andom poin s co e ing ou s udy a ea o a oid po en ial
biases esul ing om only conside ing condi ions a ocal si es. Due
o collinea i y among he bioclima ic a iables, we an a PCA using
he ade4 R package and summa ized he en i onmen al a ia ion in
he h ee fi s axes accoun ing o ca. 82% (PC1 = 43.79%;
PC2 = 23.96%; PC3 = 14.31%) o o al a ia ion. The
en i onmen al dissimila i y ma ix was ob ained by calcula ing
he Euclidean dis ances o PC sco es be ween pai s o sampling
si es (O ego e al., 2021).
To es he ela i e ole o hos use in popula ion gene ic
s uc u e in C. cac o um, a hos plan dis ance ma ix (IBH) was
buil conside ing he hos species whe e mo hs we e collec ed. We
cons uc ed a bina y ma ix coded wi h each hos species pe
sampling si e, and an a PCA using he ade4 R package o build a
dis ance ma ix wi h o al PCs a ia ion. IBH was ob ained by
calcula ing he Euclidean dis ances o PC sco es be ween pai s o
sampling si es.
Rela ionships be ween explana o y dis ance ma ices based on
landscape he e ogenei y (IBRs, IBD
WTD
,IBE
CLI
), and he
con empo a y pa e ns o hos use (IBH) wi h he gene ic
di e en ia ion be ween C. cac o um popula ions (F
ST
)we e
e alua ed using uni a ia e and mul iple ma ix eg essions wi h
andomiza ion using he unc ion MMRR (Wang, 2013)as
implemen ed in R. An ini ial ull model was cons uc ed
conside ing all significan explana o y e ms iden ified p e iously
in uni a ia e analysis, and a final bes -fi model was selec ed using a
backwa d-s epwise p ocedu e by p og essi ely emo ing non
significan a iables un il all e ained e ms wi hin he model
we e significan (Wang, 2013;O ego e al., 2014). The esul was
he minimal mos adequa e model o explaining he a iabili y in
he esponse a iable, whe e only he significan explana o y e ms
we e e ained.
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2.8 Popula ion gene ic di e si y and
clima e/habi a s abili y
Gi en ha sui able en i onmen s end o suppo la ge e ec i e
popula ion sizes (Ca na al e al., 2009), we es ed whe he he egions
exhibi ing high gene ic di e si y we e hose whe e sui able clima ic
condi ions emained s able h ough ime, om he LGM o he p esen .
To es his hypo hesis, en i onmen al s abili y maps we e cons uc ed
by a e aging cu en and LGM sui abili y maps ollowing Soley-
Gua dia e al. (2019). Fo each sampling si e, alues o clima e/
habi a s abili y we e ex ac ed o each o he h ee scena ios
conside ing (i) only clima ic a iables (S abili y
ENV
), (ii) clima e-
based habi a sui abili y maps o hos species (S abili y
HOST
), and
(iii) combining clima ic a iables and clima e-based habi a sui abili y
maps o hos species (S abili y
ENV-HOST
). Ras e calcula ions we e
conduc ed using he as e R package.
Nuclea and mi ochond ial di e si y we e cha ac e ized o
each o he 28 sampling si es. Gene ic di e si y es ima es we e
no malized o h ee indi iduals pe sampling loca ion o a oid
po en ial bias esul ing om une en popula ion sample size ( ange:
3–11 indi iduals). Fo nDNA, expec ed he e ozygosi ies (H
E
) and
nucleo ide di e si y (p) we e calcula ed using he di eRsi y (Keenan
e al., 2013) R package, and DNAsp 6 (Rozas e al., 2017),
espec i ely. We also es ima ed pand haplo ype di e si y (H
d
) o
m DNA da a using DNAsp. Co ela ions be ween s abili y alues
and es ima es o nuclea (H
E
,p) and m DNA (H
D
,p) popula ion
gene ic di e si y we e es ed using linea eg essions. Longi ude and
la i ude we e also included as explana o y ac o s o accoun o
po en ial geog aphical clines o gene ic di e si y (Guo, 2012).
3 Resul s
3.1 Genomic da a
We success ully geno yped 138 indi iduals o C. cac o um using
ddRAD sequencing which a e ep esen a i e o popula ions eeding on
bo h exo ic O. ficus-indica (71 indi iduals), and na i e hos plan s O.
megapo amica (34), O. iopla ense (11), O. ela a (10), O. bonae ensis
(4), O. penicillige a (3), O. quimilo (3), and O. anacan ha (2) along
h ee biogeog aphic egions. A e fil e ing s eps, he a e age numbe o
pai ed-end eads e ained pe indi idual was 1,859,116, o which an
a e age o 1,253,277 eads mapped o he C. cac o um e e ence
genome. A e disca ding loci in linkage disequilib ium and unde
selec ion, we eco e ed a o al o 3,506 biallelic SNPs wi h an a e age
co e age o 30× (Table S2). A o al o 143 indi iduals om he same 28
loca ions we e success ully sequenced o a agmen o 790 bp o he
COI gene. The analysis o m DNA da a e ealed 66 haplo ypes, 171
a iable si es, 97 o which we e pa simony-in o ma i e sample-wide.
3.2 Assessing popula ion
genomic s uc u e
Clus e ing analysis wi h sNMF indica ed K = 6 as he mos
likely numbe o gene ic clus e s. While all gene ic g oups we e
spa ially s uc u ed (No h, Cen al, Wes e n, Sou heas , Sou hwes
and Eas ), no gene ic s uc u e based on hos plan s was obse ed.
Popula ion gene ic s uc u e analyses also e ealed a ce ain deg ee
o admix u e among geog aphic g oups; some No he n and
Cen al indi iduals exhibi ed a ela i ely high deg ee o admix u e
wi h bo h he Wes e n and Eas e n clus e s (Figu es 2A–C).
In e es ingly, No he n, Cen al and Wes e n popula ions
appea ed o o m a unique clus e (Cen al lineage om
he ea e ) when assuming K = 3, whe eas bo h Sou he n (Sou h
lineage om he ea e ) and Eas e n (Eas lineage om he ea e )
popula ions emained as sepa a ed panmic ic g oups. Wi h K = 4,
he Sou he n popula ion appea ed subdi ided in o wo geog aphic
uni s; Sou heas e n and Sou hwes e n. Finally, wi h K = 5, No he n
popula ions appea ed sepa a ed om he Cen al ones (Figu e S2).
In he PCA he Eas e n lineage appea s sepa a ed om he Cen al
and Sou h lineages along PC1, whe eas he Sou h lineage can be
dis inguished om he Cen al lineage along PC2 (Figu e 2D).
The median-joining ne wo k ob ained wi h m DNA sequence
da a e ealed s ong spa ial gene ic s uc u e consis en wi h he
clus e s iden ified wi h nDNA da a (Figu e 2E). The Cen al
haplog oup iden ified wi h a s a -like pa e n had one o he mos
equen haplo ypes and was sepa a ed by se en mu a ional s eps
om he Eas e n haplog oup, whe eas a leas ou mu a ional s eps
sepa a ed he Cen al and No he n haplog oups. Wes e n,
sou heas e n and Sou hwes e n haplog oups appea ed close o he
Cen al haplog oup sepa a ed by ew mu a ional s eps (Figu e 2E).
3.3 Species ee econs uc ion
Phylogene ic ela ionships in e ed wi h SNAPP we e
consis en wi h he hie a chical spa ial gene ic s uc u e obse ed
wi h sNMF (Figu es 2B,C;Figu e S2). The mos ances al spli
co esponded o he sepa a ion o Sou h and Eas lineages om he
Cen al lineage. Sou hwes e n and Sou heas e n clus e s, as well as
Wes , Cen al and No h clus e s di e ged subsequen ly om hei
espec i e lineages, as obse ed in clus e ing analyses.
3.4 Demog aphic in e ence using
coalescen -based simula ions
The scena io conside ing ull asymme ic in e lineage gene flow
(model 8) was he mos suppo ed among he nine demog aphic
models es ed wi h Fas simcoal2 (Table S3). Unde his model,
di e gence among he h ee main lineages o C. cac o um was
es ima ed o ha e occu ed du ing he La e Pleis ocene (Figu e 3;
Table 1). Specifically, his model in ol es an ini ial spli (T
DIV1
)o
he Cen al lineage ~75 kya (conside ing wo gene a ions pe yea in
na i e hos species, as epo ed by Va one e al., 2014), and a mo e
ecen spli (T
DIV2
) sepa a ing he Sou h and Eas lineages
occu ing ~19 kya. Demog aphic simula ions es ima ed an
e ec i e popula ion size close o 250,000 o he Cen al lineage
(NE
CENTER
), which was six imes highe han he alue ob ained o
he Eas lineage (NE
EAST
= 41,551). Es ima es o gene flow a es
a ied among lineages wi h he highes a e o con empo a y gene
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FIGURE 3
Visual ep esen a ion o he mos suppo ed demog aphic model (Model 8) es ima ed using Fas simcoal2. Pa ame e es ima es included iming o
popula ion di e gence (T
DIV1
and T
DIV2
), his o ical and con empo a y e ec i e popula ion sizes (NE
ANC1
and NE
ANC2
), and asymme ic a es o gene
flow (M
SC
,M
CS
;M
ES
,M
SE
;M
CE
, and M
EC
).
A
B
D
E
C
FIGURE 2
Popula ion gene ic s uc u e and phylogene ic ela ionships o he C. cac o um popula ions. (A) Pie cha s ep esen he a e age ances y coe ficien
o indi iduals belonging o each o 28 sampling si es dis ibu ed along h ee biogeog aphic egions. (B) Species ee econs uc ed by SNAPP;
numbe s in nodes deno e pos e io p obabili y. (C) Resul s o indi idual assignmen in gene ic clus e s using sNMF. Ve ical ba s ep esen he
ances y coe ficien o each indi idual o he co esponding gene ic clus e . (D) PCA using he wo majo axes o genomic a ia ion. (E) Median-
joining ne wo k ob ained wi h m DNA da a. Image shows an adul male o C.cac o um..
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F on ie s in Ecology and E olu ion on ie sin.o g07
flow es ima ed o occu om he Cen al o he Eas lineage
(M
CE
= 1.50 × 10
−5
mig a ion a e by gene a ion) and he lowes
om he Cen al lineage o he Sou h lineages (M
CS
= 2.71 × 10
−8
mig a ion a e by gene a ion) (Table 1).
3.5 Ecological niche modeling
h ough ime
Ecological niche models (ENMs) o he ocal species (C.
cac o um) and hos species exhibi ed an o e all good pe o mance
as sugges ed by he ela i ely high AUC sco es (Tables S4,S5).
Sui abili y maps o hos species we e conco dan wi h hei
espec i e cu en dis ibu ions (Figu e S3). Among hos species,
he a eas o highe sui abili y o Opun ia megapo amica we e
p edic ed in cen al and sou he n A gen ina; o O. ela a in cen al-
eas e n, and o O. iopla ense in eas e n A gen ina (in he a ea o
influence o he Pa ana-La Pla a i e basin). Opun ia anacan ha and
O. quimilo ha e mo e es ic ed sui abili y a eas in no hwes e n and
cen al A gen ina, espec i ely. P ojec ions du ing he LGM indica ed
changes in hos dis ibu ion (Figu e S3) ha sugges an inc eased
habi a sui abili y o almos all hos plan s, excep o O. anacan ha
whose sui abili y a eas ha e been es ic ed o he cen al-eas e n
egion du ing he LGM. Ins ead, habi a sui abili y o O.
megapo amica and O. ela a appea s ex ended in o he no he n
egion, whe eas he p ojec ions indica e an ex ended dis ibu ion in
cen al A gen ina o O. quimilo. Finally, sui able habi a s o O.
iopla ense ex ended o no he n and cen al A gen ina.
Models o C. cac o um (Se 1: Clima ic
CURR
,Se 2:Hos
CURR
,Se 3:
Clima ic-Hos
CURR
) indica ed simila p edic ed dis ibu ions (Figu e S4).
Howe e , he mos suppo ed model o C. cac o um acco ding o AIC
alues was one ha conside ed as inpu a iables he p edic ed
dis ibu ion o he hos plan s (Hos
CURR
). Addi ional in o ma ion on
he esul s o ENMs o bo h C. cac o um and hos species a e de ailed in
Tables S4,S5. The p esen -day dis ibu ion in e ed by he mos
suppo ed scena io (Hos
CURR
) was in line wi h he con empo a y
ange o he mo h. Unde his model, highe sui abili y a eas we e
p edic ed in bo h Chaco and no h o Pampa biogeog aphic egions
whe eas a eas o lowe sui abili y we e p edic ed in he sou he n po ions
o he Pampas and he Mon e biogeog aphic egions (Figu e 1B). O he
biogeog aphic p o inces (Yungas, Puna and P epuna) had ex emely low
sui abili y alues o C. cac o um. P ojec ions o ENM o LGM p edic ed
high en i onmen al sui abili y along he Chaco biogeog aphic p o ince
o he mos sou he n po ion o Pampas, wi h a eas o low sui abili y
loca ed in eas e n A gen ina, a confluencezoneo LaPla a i e
basin (Figu e 1C).
3.6 Landscape genomic analyses
Es ima es o gene ic di e en ia ion (F
ST
) among sampling si es
anged om 0.023 o 0.448 o nDNA da a (Table S6). Uni a ia e
ma ix eg essions indica ed ha nuclea gene ic di e en ia ion was
significan ly co ela ed wi h all dis ance ma ices excep wi h he
cu en pa e n o hos plan use (IBH) consis en wi h clus e ing
analysis, and bo h explana o y e ms o landscape he e ogenei y:
Clima ic
CURR
and Clima ic-Hos
CURR
(Table S7). Ye , only
Clima ic-Hos
LGM
was significan ly e ained in he bes -fi model
in he backwa d-s epwise p ocedu e (Table 2).
3.7 Popula ion gene ic di e si y and
clima e/habi a s abili y
We ound highe nuclea and mi ochond ial di e si y in
No he n, Cen al and Eas e n popula ions, han in Sou he n
TABLE 1 Pa ame e s in e ed om coalescen simula ions wi h Fas simcoal2 unde he bes -suppo ed demog aphic model (Model 8; Figu e 3).
Model 8 95% Confidence in e al
Pa ame e Poin es ima e Lowe bound Uppe bound
NE
ANC1
3,504,318 2,576,620 3,858,949
NE
ANC2
11,746 3,773 21,102
NE
CENTER
245,957 208,570 380,730
NE
EAST
41,551 35,596 54,151
T
DIV2
75,513 61,524 120,375
T
DIV1
19,207 17,202 23,310
M
ES
1.18 × 10
−6
8.86 × 10
−7
1.75 × 10
−6
M
SE
4.68 × 10
−8
5.41 × 10
−11
1.65 × 10
−6
M
CS
2.71 × 10
−8
3.55 × 10
−11
6.83 × 10
−8
M
SC
6.37 × 10
−6
4.37 × 10
−6
7.32 × 10
−6
M
CE
1.50 × 10
−5
1.23 × 10
−5
1.67 × 10
−5
M
EC
2.98 × 10
−5
3.78 × 10
−11
1.42 × 10
−6
Fo each pa ame e , poin es ima e and lowe and uppe 95% confidence in e als a e shown. T
DIV1
and T
DIV2
, popula ion di e gence; NE
ANC1
and NE
ANC2
, his o ical and con empo a y e ec i e
popula ion sizes; M
SC
,M
CS
,M
ES
,M
SE
,M
CE
, and M
EC
, asymme ic a es o gene flow among lineages.
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F on ie s in Ecology and E olu ion on ie sin.o g08
popula ions (Figu e 4;Table S8). Linea eg ession analyses
e ealed ha nuclea gene ic di e si y was significan ly co ela ed
wi h la i ude bu no wi h longi ude (Table 3). Likewise, es ima es o
nuclea gene ic di e si y o bo h H
E
and pwe e posi i ely
co ela ed wi h he h ee en i onmen al s abili y es ima es
(S abili y
ENV
, S abili y
HOST
and S abili y
ENV-HOST
) o he LGM
(~21 Kya) o he p esen . Con e sely, mi ochond ial gene ic
di e si y es ima ed wi h H
D
and pwe e no co ela ed wi h
geog aphic a iables no en i onmen al s abili y (Table 3;Figu e 4).
4 Discussion
Nuclea SNPs and m DNA da a e ealed significan popula ion
s uc u e in C. cac o um. Landscape genomic analyses p o ided
suppo o he hypo hesis ha habi a connec i i y based on a
combina ion o clima ic condi ions and habi a sui abili y,
influenced by shi s in hos species dis ibu ions du ing LGM, was
he main ac o shaping popula ion gene ic s uc u e. Al hough
pa e ns o hos species use appea ed o be non influen ial on C.
cac o um di e sifica ion, shi s in he dis ibu ion o Opun ia hos s,
media ed by clima ic changes du ing he Qua e na y, had a di ec
influence on he dis ibu ion and genomic a ia ion o he ocal
species. Such shi s in hos dis ibu ions may ha e gene a ed
agmen ed anges ha led o educ ions o gene flow among
mo h popula ions, p omo ing gene ic di e en ia ion. Ou esul s
also suppo ed he habi a s abili y hypo hesis, whe eby popula ions
inhabi ing egions o g ea e habi a sui abili y du ing he las
21,000 yea s ha bo ed mo e gene ic di e si y han hose ha
pe sis ed in a eas o lowe habi a s abili y. The hypo hesis ha
he geog aphically widesp ead cul i a ion o O. ficus-indica
acili a ed con empo a y gene flow among o he wise
geog aphically dis an popula ions can be ejec ed, on he basis o
he esul s o popula ion genomic analyses e ealing limi ed gene ic
admix u e and a hie a chical pa e n o popula ion di e en ia ion
mainly conco dan wi h geog aphy.
4.1 E ec s o Qua e na y landscape
composi ion on popula ions di e en ia ion
Gene ic clus e ing analyses e ealed h ee majo lineages defined
by geog aphy: Cen al, Eas and Sou h (Figu es 2 and 3). Coalescen -
based demog aphic modeling sugges ed ha hese lineages began o
di e ge du ing he La e Qua e na y, app oxima ely 75 kya. The
ea lies spli in ol ed popula ions o he Chacoan biogeog aphic
domain (he ea e “Chaco”), including popula ions om No h,
Wes and Cen al A gen ina, om he Pampean biogeog aphic
egion (he ea e “Pampa”) ha includes he Sou h and Eas
lineages (Figu es 1,2). P io o his spli , he egional con ac ion
o sub opical and opical biomes made he Chaco and he Pampa
biomes mo e alike (O iz-Jau eguiza and Clade a, 2006).
Subsequen ly, du ing he Qua e na y, majo clima ic shi s ook
place in he a ea, leading o he isola ion o he Chacoan xe ic
woodlands om he ypical g asslands o he Pampean egion.
Such clima ic changes we e p omo ed by he opog aphic
econfigu a ion o Andean and sub-Andean Piedmon and he
upli o he eas e n o og aphic sys ems (known as he Sie as
Pampeanas) associa ed wi h he Pe ipampasic o ogenic a c (O iz-
Jau eguiza and Clade a, 2006;Spe anza e al., 2007;Cala ayud-
Masca ell e al., 2022). These e en s p oduced a ain-shadow e ec
ha esul ed in he ex eme xe ic condi ions ha p e ailed in his
a ea. Clima e changes du ing he Qua e na y, which included cold,
d y glacial cycles al e na ing wi h wa m, mois in e glacial pe iods,
a ec ed hese egions causing he expansion and con ac ion o open
woodlands and g asslands (O iz-Jau eguiza and Clade a, 2006).
This dynamic likely p omo ed changes in flo is ic composi ion o
such egions, a ec ing he dis ibu ions o hos species and
consequen habi a sui abili y o C. cac o um,p omo ing he
di e gence be ween he Cen al lineage (Chaco) and Eas , Sou h
lineages (Pampean) (Figu es 2,3).
The spli be ween Eas and Sou h lineages was es ima ed o ha e
occu ed app oxima ely 19 kya. Regional clima e models sugges
ha his iming is coinciden wi h an inc ease in p ecipi a ion along
he eas e n oo hills o he Andes (Cook and Vizy, 2006;O iz-
Jau eguiza and Clade a, 2006). These opog aphical ea u es
oge he wi h Qua e na y clima ic dynamics in he egion
main ained a agmen ed dis ibu ion o C. cac o um hos species
om he Pampa (Mou elle and Ezcu a, 1997). This likely limi ed
dispe sal o C. cac o um, es ic ing he Eas lineage o he mo e
humid en i onmen s wi h deep e ile soils ypical o he Pampa,
and he Sou h lineage o he d ie g asslands o he no he n bo de
o he Pa agonian s eppe, bo h egions wi h di e se pa e ns o hos
species composi ion (Va one e al., 2014).
TABLE 2 Resul s o mul iple ma ix eg ession wi h andomiza ion
(MMRR) es ing o he ela ionships be ween popula ion gene ic
di e en ia ion (F
ST
) and explana o y a iables ep esen ing weigh ed
opog aphic dis ance (isola ion by dis ance, IBD
WTD
), clima ic
dissimila i y (isola ion by en i onmen , IBE
CLI
), hos plan dis ance (*IBH),
and al e na i e isola ion by esis ance (IBR) scena ios.
Va iable R
2
p
Explana o y e m
LGM
ENV-HOST
0.416 16.365 0.001
Rejec ed e ms
Clima ic dissimila i y (IBE
CLI
)−0.476 0.831
Topog aphic dis ance (IBD
WTD
)−2.058 0.301
IBR –Hos
CURR
3.251 0.278
IBR –Clima ic
LGM
4.808 0.117
IBR –Hos
LGM
−5.834 0.087
Fla landscape –IBR
NULL
−3.654 0.278
IBR scena ios consis o cu en and pas habi a sui abili y based on (i) only clima ic a iables
(*Clima ic
CURR
, and Clima ic
LGM
), (ii) clima e-based habi a sui abili y maps o hos species
(Hos
CURR
and Hos
LGM
), and (iii) combining clima ic a iables clima e-based habi a
sui abili y maps o hos species (*Clima ic-Hos
CURR
and Clima ic-Hos
LGM
). IBR
NULL
ep esen s an IBR scena io whe e all pixel alues a e equal o 1 (fla landscape). R
2
,
eg ession coe ficien ; , -s a is ic; p, significance le el.
*Clima ic
CURR
, Clima ic-Hos
CURR
, and cu en pa e n o hos use (IBH) we e excluded om he
ini ial ull model due o hese e ms esul ed non-significan in hei espec i e uni a ia e analysis.
Po eda-Ma ı
´nez e al. 10.3389/ e o.2023.1260857
F on ie s in Ecology and E olu ion on ie sin.o g09