ORIGINAL ARTICLE Refugia and geographic barriers of populations of the desert poppy, Hunnemannia fumariifolia (Papaveraceae) Eduardo Ruiz-Sanchez & Flor Rodriguez-Gomez & Victoria Sosa Received: 18 July 2011 / Accepted: 22 March 2012 / Published online: 15 April 2012 # Gesellschaft für Biologische Systematik 2012 Abstract Phylogeographic data and divergence estimation times as well as current and past ecological niche modeling for the Mexican tulip poppy, Hunnemannia fumariifolia Sweet, were combined in order to understand its biogeo- graphic history. Divergence times were estimated to deter- mine if divergence occurred during the Pleistocene. Ecological niche modelling was used to determine if the last glacial maximum (LGM) was responsible for the southward movement of poppy populations into the Tehuacán-Cuicat- lán Valley. Analyses were performed to detect any geo- graphical barriers that might have caused genetic discontinuities among populations across the entire range of distribution. Current and Pleistocene ecological niche models were created for H. fumariifolia using eight envi- ronmental variables derived from temperature and precipi- tation. The evidence shows that divergence of the three main clades in H. fumariifolia occurred from the Early Pleisto- cene to Mid-Miocene. It was also found that gene flow between the populations of H. fumariifolia could have been limited by the LGM, by climate change during the Quater- nary, and by the complex topography of the Sierra Madre Oriental and the Trans-Mexican Volcanic Belt. Furthermore, all of these processes may have resulted in the patchy distribution of suitable microhabitats for H. fumariifolia in its geographical range. Ecological niche models constructed using the MIROC3 model indicated that populations did not move to the north but rather that they had suitable ecological habitats in the Chihuahuan Desert, which harbored Pinus- Juniperus forests during that period. Keywords Climate change . Ecological niche models . Last glacial maximum . Chihuahuan Desert . Sierra Madre Oriental . Trans-Mexican Volcanic Belt. Introduction An increasing number of biogeographic studies dealing with a diverse array of species from North America have identi- fied areas that served as refugia during the last glacial maximum (LGM) in the Late Pleistocene. Studies combine ecological niche modelling and molecular evidence to esti- mate the time of origin, divergence of populations, abiotic factors influencing adaptation to habitats and the historical events that have had an effect on the evolutionary processes of these taxa (e.g., Riddle et al. 2000; Carstens and Richards 2007; Castoe et al. 2007; McGuire et al. 2007; Knowles et al. 2007; Waltari et al. 2007; Morris et al. 2008, 2010; Cavender-Bares et al. 2011; Chan et al. 2011; Cosacov et al. 2010; Désamoré et al. 2011; Ornelas et al. 2010; Reber- nig et al. 2010a). The utilization of palaeoclimatic models and ecological niche models projected onto historical landscapes provides a spatial context for phylogeographic analyses (Carstens and Richards 2007; Waltari et al. 2007). These tools have been used widely to identify refugia during the Late Pleistocene E. Ruiz-Sanchez (*) University of California, Berkeley, Plant and Microbial Biology, 431 Koshland Hall, Berkeley, CA 94270, USA e-mail: [email protected]F. Rodriguez-Gomez : V. Sosa Instituto de Ecología, A. C., Biología Evolutiva, Apartado Postal 63, 91000, Xalapa, Veracruz, México Present Address: E. Ruiz-Sanchez Instituto de Ecología, A. C., Centro Regional de Bajío, Av. Lázaro Cárdenas 253, 61600, Pátzcuaro, Michoacán, México Org Divers Evol (2012) 12:133–143 DOI 10.1007/s13127-012-0089-z
Transcript
ORIGINAL ARTICLE
Refugia and geographic barriers of populations of the desertpoppy, Hunnemannia fumariifolia (Papaveraceae)
Eduardo Ruiz-Sanchez & Flor Rodriguez-Gomez &
Victoria Sosa
Received: 18 July 2011 /Accepted: 22 March 2012 /Published online: 15 April 2012# Gesellschaft für Biologische Systematik 2012
Abstract Phylogeographic data and divergence estimationtimes as well as current and past ecological niche modelingfor the Mexican tulip poppy, Hunnemannia fumariifoliaSweet, were combined in order to understand its biogeo-graphic history. Divergence times were estimated to deter-mine if divergence occurred during the Pleistocene.Ecological niche modelling was used to determine if the lastglacial maximum (LGM) was responsible for the southwardmovement of poppy populations into the Tehuacán-Cuicat-lán Valley. Analyses were performed to detect any geo-graphical barriers that might have caused geneticdiscontinuities among populations across the entire rangeof distribution. Current and Pleistocene ecological nichemodels were created for H. fumariifolia using eight envi-ronmental variables derived from temperature and precipi-tation. The evidence shows that divergence of the three mainclades in H. fumariifolia occurred from the Early Pleisto-cene to Mid-Miocene. It was also found that gene flowbetween the populations of H. fumariifolia could have beenlimited by the LGM, by climate change during the Quater-nary, and by the complex topography of the Sierra Madre
Oriental and the Trans-Mexican Volcanic Belt. Furthermore,all of these processes may have resulted in the patchydistribution of suitable microhabitats for H. fumariifolia inits geographical range. Ecological niche models constructedusing the MIROC3 model indicated that populations did notmove to the north but rather that they had suitable ecologicalhabitats in the Chihuahuan Desert, which harbored Pinus-Juniperus forests during that period.
An increasing number of biogeographic studies dealing witha diverse array of species from North America have identi-fied areas that served as refugia during the last glacialmaximum (LGM) in the Late Pleistocene. Studies combineecological niche modelling and molecular evidence to esti-mate the time of origin, divergence of populations, abioticfactors influencing adaptation to habitats and the historicalevents that have had an effect on the evolutionary processesof these taxa (e.g., Riddle et al. 2000; Carstens and Richards2007; Castoe et al. 2007; McGuire et al. 2007; Knowles etal. 2007; Waltari et al. 2007; Morris et al. 2008, 2010;Cavender-Bares et al. 2011; Chan et al. 2011; Cosacov etal. 2010; Désamoré et al. 2011; Ornelas et al. 2010; Reber-nig et al. 2010a).
The utilization of palaeoclimatic models and ecologicalniche models projected onto historical landscapes provides aspatial context for phylogeographic analyses (Carstens andRichards 2007; Waltari et al. 2007). These tools have beenused widely to identify refugia during the Late Pleistocene
E. Ruiz-Sanchez (*)University of California, Berkeley, Plant and Microbial Biology,431 Koshland Hall,Berkeley, CA 94270, USAe-mail: [email protected]
F. Rodriguez-Gomez :V. SosaInstituto de Ecología, A. C., Biología Evolutiva,Apartado Postal 63,91000, Xalapa, Veracruz, México
Present Address:E. Ruiz-SanchezInstituto de Ecología, A. C., Centro Regional de Bajío,Av. Lázaro Cárdenas 253,61600, Pátzcuaro, Michoacán, México
LGM (Hugall et al. 2002; Carstens and Richards 2007;Marske et al. 2011). Neogene vicariance, due largely toorogenesis, and Quaternary climate change have been postu-lated as drivers of evolutionary diversification in western NorthAmerica (Riddle and Hafner 2006) and Mexico (Bryson et al.2010b).
To understand the biogeographic history of the Mexicantulip poppy Hunnemannia fumariifolia, we combined diver-gence time estimation and palaeoclimatic models to inves-tigate if Neogene orogenesis and Quaternary climaticchange has influenced the distribution patterns of popula-tions of the Mexican tulip poppy. Our previous phylogeo-graphic study found that allopatric fragmentation had aneffect on genetic divergence in populations of the tulippoppy in the Sierra Madre Oriental, and that this divergencemay be a reflection of the complex geology of the area overwhich this species is distributed (Sosa et al. 2009). More-over, our results suggested that the areas located in the northof the Sierra Madre Oriental acted as post-glacial refugia forsome populations of H. fumariifolia (Sosa et al. 2009).However, divergence time was not estimated for popula-tions, nor were further analyses conducted to confirm theserefugia or to discover the geographic barriers that preventedgene flow.
The tulip poppy is an herbaceous perennial, growing inxerophytic habitats at middle elevations in Mexico. In thenorth, populations are distributed in the Chihuahuan Desertand the Sierra Madre Oriental and, crossing the Trans-Mexican Volcanic Belt, there are populations in the south,in the Tehuacán-Cuicatlán Valley (Sosa et al. 2009). Hun-nemannia forms part of a North American clade in thePapaveraceae, together with Eschscholzia and Dendrome-con (Hoot et al. 1997).
An analysis of the biogeographic history of the populationsof the Mexican tulip poppy may help to understand pastchanges in plant distribution in the deserts of Mexico. It hasbeen suggested that the habitats of the western highlands of theSierra Madre Oriental and the Chihuahuan Desert fluctuateddramatically during the Pleistocene, and that this has resultedin the cyclical downward displacement and retraction of thepine-oak-juniper forests (Van Devender 1990; Metcalfe et al.2000; Metcalfe 2006). As a result of forest shifts, populationsexpanded their range during glacial periods and remainedisolated in refugia at high elevations during interglacial peri-ods. Moreover, these events caused subsequent postglacialfragmentation that prevented gene flow (Bryson et al. 2010a).
During the Early Pliocene the Chihuahuan Desert, alongwith the other North American deserts, attained its maxi-mum area but it decreased during the moist Late Plioceneand during the Pleistocene pluvial intervals (Riddle andHafner 2006). As a result of the uplift of the Sierra MadreOccidental and the Mexican Plateau, the Chihuahuan Desertwas separated from the Sonoran and Mojave Deserts,
causing vicariance events that separated, for example, her-petofauna, rodents and some plant populations from bothdeserts (Riddle et al. 2000; Jaeger et al. 2005; Riddle andHafner 2006; Castoe et al. 2007; Leaché and Mulcahy 2007;Bryson et al. 2010a; Rebernig et al. 2010a). The Chihua-huan Desert also acted as a barrier between the Sierra MadreOccidental and Oriental for some gymnosperms, such asPinus (Moreno-Letelier and Piñero 2009).
The distribution of the Mexican tulip poppy is complexdue to the presence of three mountain ranges: the Trans-Mexican Volcanic Belt in the south, the Sierra Madre Occi-dental to the northwest and the Sierra Madre Oriental innorth-eastern Mexico. In the middle of these mountains, theChihuahuan Desert is located on the Mexican Plateau. TheSierra Madre Oriental has the most complicated geologicalhistory of the three formations, originating in the Laramideformation during the Late Cretaceous to the Palaeogene(80–55 Ma). This formation resulted from an orogenic eventthat gave rise to the Rocky Mountain fold, the thrust belt inCanada, the Sierra Madre Oriental fold and the thrust belt inMexico (English et al. 2003). Erosion in the foothills of thismountain range occurred during the Palaeogene-Eocene andsubsequently either during the Oligocene or the Neogene(Roure et al. 2009). In contrast, the Sierra Madre Occidentalresulted from volcano-tectonic events that occurred after theend of the Laramide orogeny and before the episode peaksof the Sierra Madre Occidental volcanic events in the Oli-gocene. The volcano-tectonic peaks occurred in three mainepisodes from the mid-late Oligocene to the early Miocene,at about 32–30 Ma, 30–28 Ma and 26–25 Ma (Tristán-González et al. 2009). The western area of the Trans-Mexican Volcanic Belt originated during the Miocene andthe eastern area during the Holocene (Ferrari et al. 2000;García-Polomo et al. 2002). Palaeorecords from the Mio-cene and Pliocene at the end of the Tertiary (2–20 Ma)indicate that plant communities reached elevated complexityat that time, reflecting a warmer, more humid, and relativelystable climate compared to that of the Quaternary (Tausch etal. 1993). Furthermore, it has been postulated that the oro-genesis that occurred from the Palaeogene to the Neogeneand the Quaternary climate change were the drivers of plantdiversification in North America (Bryson et al., 2010a).
Our study focuses on several aspects of the evolutionaryhistory of Hunnemannia fumariifolia populations: (1) esti-mating the time of divergence of its populations to deter-mine if divergence occurred during the Pleistocene; (2)establishing whether the LGM was responsible for thesouthward movement of populations into the Tehuacán-Cuicatlán Valley; (3) detecting the geographical barriers thatcaused genetic discontinuities among populations acrossthis species’ entire range of distribution; and (4) identifyingthe geographic areas that served as refugia for itspopulations.
134 E. Ruiz-Sanchez et al.
Methods
Sampling and DNA sequences
The DNA sequences of three plastid spacers: trnH-psbA(EF464658–EF464664), rpl32-trnL (UAG) (EU169024–EU169030) and ndhF-rpl32 (EU169018–EU169023) pub-lished previously by Sosa et al. (2009) corresponding to 17populations with a total of 85 individuals were included in theanalyses. In addition, for molecular dating, DNA sequencesfrom two plastid genes: atpB (U86384, U86386-U86401,AF293860, AF092116, AF092115, AF093396, AF093384,FJ026454, FJ026397, AF093375, DQ359689, AF093382,AF093393 and D8955) and rbcL (86621-86632; L01943,L01951, L08764, L12645, AF197599, AF093720,AF093719, AF093731, AF093726, HQ260807, L37920,AF093723, DQ359689, L75849, AF093730 andGQ997596) from 15 representative taxa of Papaveraceae wereused as the ingroup based on Hoot et al. (1997). For theoutgroup, we chose representative taxa of Berberidaceae,Circaeasteraceae, Eupetalaceae, Lardizabalaceae, Menisper-maceae and Ranunculaceae of Order Ranunculales, in addi-tion to Platanus occidentalis and Nelumbo nucifera ofProteales andCeratophyllum submersum, based on a previousphylogenetic study by Bell et al. (2010).
Phylogenetic analyses
Bayesian inference (BI) was conducted with MRBAYES v.3.1.2 (Ronquist & Huelsenbeck 2003). The software jMo-delTest 0.1.1 (Posada 2008) was run to determine the modelof evolution that best fit using the AICc values for Papaver-aceae and the outgroup taxa for the combined matrices(atpB, rbcL) was GTR + I + G and for each one of the threechloroplast markers (trnH-psbA 0 F81; rpl32-trnL (UAG) 0TIM1; ndhF-rpl32 0 TVM) for analyses at the populationlevel. Two different analyses were performed—the first forthe family level based on the combined data matrix and thesecond based on the concatenated data matrix of H. fumar-iifolia. Two independent runs were conducted to assess therepeatability of stationarity between runs for each analysis.For each run, one cold and three heated chains were set for10,000,000 runs, sampling one tree every 1,000 generations.Stationarity was determined based on the likelihood scoresfor time to convergence and sample points collected prior tostationarity were eliminated (10 %). Posterior probabilitiesfor supported clades were determined by a 50 % majority-rule consensus of the trees retained after burn-in.
Molecular dating
Divergence time was estimated with a Bayesian approach asimplemented in BEAST v. 1.5.4 (Drummond and Rambaut
2007), and evolutionary models were determined with jMo-delTest 0.1.1 (Posada 2008). Two estimates of divergencetime were worked out. First, divergence was assessed at thefamily level. The evolutionary model GTR + I + G wasselected based on the AICc result from jModelTest 0.1.1(Posada 2008) for the combined chloroplast matrices (atpBand rbcL) and analyses were run under an uncorrelatedlognormal relaxed clock model. The Yule speciation processwas used as a prior to model the tree. We used five calibra-tion points for this level, we treated all calibration points asminimum age constraints. Three secondary points derivedfrom the Bell et al. (2010) analysis were utilized, with anormal distribution. For the root node we used a mean ageof 136 Ma, SD 2.8 (130–142 Ma), for the Eucotyledoneae amean of 129 Ma, SD 3.2 (123–134 Ma), and for Ranuncu-lales a mean of 100 Ma, SD 7.5 (85–115 Ma). We con-strained Proteales with the fossil of Platanocarpusbrookensis (98 Ma) (Bell et al. 2010) modelled with a meanof 1 and an offset of 98 (hard bound constraint), whichequalled the minimum age of the fossil (Ho and Philips2009). We then constrained the divergence of Menisperma-ceae from Ranunculaceae/Berberidaceae with the fossil ofPrototinomiscium vangerowii (91 Ma) (Anderson et al.2005) with a mean of 1 and an offset of 91. The secondestimate of divergence time was conducted at the populationlevel in Hunnemannia fumariifolia. We used the HKY + Gmodel of sequence evolution and the three chloroplastspacers [trnH-psbA, rpl32-trnL(UAG) and ndhF-rpl32], un-der an uncorrelated lognormal relaxed clock model andcoalescent model assuming exponential population growth.To calibrate the root, we used the results of the first diver-gence time analysis. We used the mean (16.03 Ma; 95 % HDP
0 4.6–30) divergence time of the separation between Hunne-mannia-Eschscholzia. We used a lognormal distributionwith a mean of 2.78, SD 0.3, zero offset; range of 4.6-30.For both estimates four independent 107 generation runswere performed with random starting trees, sampling every1,000 generations. TRACER v. 1.5 (http://tree.bio.ed.ac.uk/software/tracer/) was used to assess convergence and effec-tive sample sizes (ESS) for all parameters and also forcombining tree files from the four runs performed withBEAST. Results were summarized in a single tree visualizedwith FIGTREE v. 1.5.4 (http://tree.bio.ed.ac.uk/software/figtree/).
Geographic barriers
BARRIER 2.2 (Manni et al. 2004) based on Monmonier’salgorithm (Monmonier 1973) was used to determine geo-graphic barriers within the Hunnemannia fumariifolia local-ities. These barriers represent zones of abrupt changes in thepattern of genetic variation among sample populations in thepresence of isolating factors (geography) is likely to weaken
Refugia and geographic barriers in Hunnemannia fumariifolia 135
the gene flow by increasing the chances of finding signifi-cant barriers (Manni et al. 2004). First the combined cpDNAmatrix was transformed into a distance matrix using the F84model of nucleotide substitution implemented in DNADISTand then SEQBOOTwas used to generate 100 bootstrappeddistance matrices from DNA sequences to evaluate supportfor the observed barriers, both programs are included in thePHYLYP 3.69 package (Felsenstein 1989).
Ecological niche modelling
Current and Pleistocene ENMs were created for Hunneman-nia fumariifolia using eight environmental variables derivedfrom temperature and precipitation data obtained fromWorld-Clim 1.4 (Hijmans et al. 2005) (Mean diurnal range, Temper-ature seasonality, Temperature annual range, Meantemperature of warmest quarter, Mean temperature of coldestquarter, Precipitation seasonality, Precipitation of wettestquarter and Precipitation of coldest quarter) with a resolutionof 1 km2. These variables are not highly correlated (pairwise
r<0.7 based on all sample locations) (Peterson 2007; Naka-zato et al. 2010). Two general atmospheric circulation models(GCM) were used to generate past climate scenarios for LGM:the Community Climate System Model (CCSM) and theModel for Interdisciplinary Research on Climate (MIROC3).The original GCM data were downloaded from thePMIP2 website (http:// www.pmip2.cnrs-gif.fr/) (Braconnotet al. 2007). One Last Inter-Glacial (LIG; 120,000–140,000 years BP) was used to generate past climate scenariosfor LIG; the data was downloaded from WorldClim (http://www.worldclim.org/past). The models were run in Maxent3.3.2 (Phillips et al. 2006; http://www.cs.princeton. edu/~schapire/maxent/). Maxent employs a maximum likelihoodmethod that estimates the species’ distribution that has max-imum entropy, subject to the constraint that the environmentalvariables for the predicted distribution must match the empir-ical average (Elith et al. 2006; Phillips et al. 2006).
A total of 65 unique records with georeferences werecompiled. Georeferenced data obtained from the previousphylogeographic study by Sosa et al. (2009) and data from
Menispermun candense
Tinospora esiangkara
Ranunculus macranthus
Coptis trifolia
Hydrastis candensis
Glaucidium palmatum
Nandina domestica
Sargentodoxa cuneata
Kingdonia uniflora
Circaeaster agrestis
Euptelea polyandra
Hunnemannia fumariifolia
Eschscholzia californica
Dendromecon rigidum
Macleaya cordata
Sanguinaria candensis
Glaucium flavum
Dicranostigma franchetiana
Stylophorum diphyllum
Romneya coulteri
Corydalis nobilis
Hypecoum imberba
Papaver orientalis
Platystemon californicus
Argemone mexicana
Pteridophyllum racemosum
Platanus occidentalis
Nelumbo nucifera
Ceratophyllum submersum
Cretaceous Paleogene NeogenePaleocene Eocene Oligocene Miocene Pli Ple
02550100125 75 Ma
E/H
EA
EC
AR
EV
AP
AP
SE
LA
LU
CL
UN
AR
EA
EN
OD
EL
YT
OC
UE
PROTEALES
02550100125 75 Ma
Cretaceous Paleogene NeogenePaleocene Eocene Oligocene Miocene Pli Ple
0.78
1.0
1.01.0
1.01.0
1.0
0.98
1.0
0.84
1.0
1.0
1.0
0.78
1.0
0.96
1.0
0.67
1.0
1.0
1.0
1.0
1.0
Fig. 1 Chronogram of the Papaveraceae family based on a Bayesianapproach. Gray bars 95 % confidence intervals for node age estimates.Brackets identify Eucotyledoneae clade, Ranunculales clade, Protealesclade, Papaveracae family clade and the H/E Hunnemannia/
Escholscholzia clade. Black stars secondary calibration points, blackcrosses fossil calibration points. Numbers below the branches Bayesianposterior probabilities (PP). Pli Pliocene, Ple Pleistocene, Ma Millionyears
the "National Biodiversity Information Network" (REMIB;http://www.conabio.gob.mx/remib_ingles/doctos/remib_ing.html; accessed May 2010). The Maxent logistic modeloutput for a given species is a continuous surface of valuesranging from 0 to 1, where high values indicate a highersuitability for a given species. Maxent was run with defaultsettings, ensuring that we had only one locality per grid cell.To evaluate model performance, we set aside a randomsubset of 25 % of the total unique records and mea-sured the area under the curve (AUC) of the receiveroperating characteristic, a threshold-independent measureof performance.
Results
Phylogenetic analyses
Results of the family level phylogenetic analysis are shownin Fig. 1. This chronogram is similar to the 50 % majorityconsensus tree that resulted from the Bayesian analysis(posterior probabilities, PP are indicated). In this tree, Papa-veraceae is depicted as monophyletic (1.0 PP); it also showsthat Hunnemannia is closely related to Eschscholzia (1.0PP). Papaveraceae is the sister group to the rest of thefamilies in the order Ranunculales (1.0 PP), and the repre-sentative taxa of Proteales was found to have an affinitywith Ranunculales (1.0 PP); representative taxa in Eucoty-ledoneae were the sister group to Ceratophyllum submersumwithout support.
The results of intra-specific phylogenetic relationshipsshow the relationship between haplotypes of Hunnemanniafumariifolia and are depicted in the 50 % majority consen-sus tree shown in Fig. 2. Haplotypes are grouped into threemain clades that received good support in an unresolvedgeneral topology. These clades correspond to the three areasof its distribution: Chihuahuan Desert, Tehuacán-CuicatlánValley and Sierra Madre Oriental. Within the Sierra MadreOriental two sub-clades were retrieved (SMO 1; 0.94 PP andSMO 2; 0.87 PP) and a clade grouped the haplotypes fromthe Chihuahuan Desert and Tehuacán-Cuicatlán ValleyCH/T-C; 1.0 PP). The only exception is a single haplotypefrom the Ciudad del Maíz (Chihuahuan Desert) nested with-in the SMO 1 clade, which shares haplotypes with the SMO1 and CH/T-V clades (Figs. 2, 3). The SMO 1 clade groupedpopulations from the southern and northernmost localities ofthe Sierra Madre Oriental, while the SMO 2 clade haspopulations only from the northern part of the SMO.
Divergence times
Divergence time estimates at the family level, calculatedwith the Yule speciation process, are shown in Fig. 1.
Papaveraceae is estimated to have diverged in the Mid-to-Late Cretaceous (mean096 Ma; 95 % HDP072–116). The cladeformed by Hunnemannia-Eschscholzia is estimated to havediverged from the Early Oligocene to the Pliocene(16.03 Ma; 95 % HDP04.6–30 MA) (Fig. 1). Divergence esti-mates for Hunnemannia fumariifolia using a coalescentmodel and assuming exponential population growth areshown in Fig. 4. The divergence of Hunnemannia fumarii-folia occurred during the Early to Late Miocene (12.8 Ma;
95 % HDP06-20 Ma) (Fig. 4). Within the tulip poppy, theoldest clade is SMO 1 with a divergence time of 6.5 Ma(95 % HDP01.8-12.3), during the Mid-Pleistocene to Mid-Miocene. It was followed by the CH/T-V clade (5.5 Ma;95 % HDP01.2-11.1) and a similar divergence was foundfor the SMO and SMO 2 clades, which diverged during theEarly Pleistocene to Late Miocene (4 Ma; 95 % HDP00.5-8.4) (Fig. 4).
Eschscholzia spArteaga-14Cd. Maiz-13Bonanza-2Real de Catorce-4
Coixtlahuaca-6Tequixtepec-17Real de Catorce-4Cd. Maiz-13Cerro Tahti-5Cienega-9Cd. Maiz-13Escondida-3
Zaragoza-12Escondida-3Mezquititlan-16
Tolantongo-15Cienega-9La Luz-8San Isidro-7
San Isidro-7
Mezquititlan-16Altares-10Galeana-1
Galeana-1Zaragoza-12Rio San Jose-11
0.99
0.99
0.94
1.0
0.99
0.94
0.97
0.97
0.97
1.0
0.95
0.87
2O
MS
1O
MS
C-T/
HC
B
C
O
N
N
C
B
E
D
H
F
I
J
J
L
L
G
G
G
Q
M
A
A
A
K
P
Fig. 2 Bayesian 50 % majority-rule consensus tree based on concat-enated chloroplast [trnH-psbA, rpl32-trnL(UAG) and ndhF-rpl32]spacer sequence data, showing the relationships among haplotypesfrom the populations of Hunnemannia fumariifolia. The three mainclades are identified in brackets: CH/T-C, Chihuahuan Desert/Tehua-cán Cuicatlán Valley; SMO 1, Sierra Madre Oriental 1 and SMO 2,Sierra Madre Oriental 2. Circled letters at the end of the rows are thehaplotypes indicated in Table 1 of Sosa et al. (2009). Numbers belowthe branches Bayesian posterior probabilities (PP)
Refugia and geographic barriers in Hunnemannia fumariifolia 137
The geographic boundaries revealed by the program Barrier2.2 are displayed in Fig. 5. There are several boundarieswith the greatest bootstrap support (thick bars). Amongthem, a barrier separated the populations of Tehuacán-Cui-catlán from the rest of the populations in the SMO and CH(Fig. 5) while another barrier separated the southern SMOpopulations from those of the CH (Fig. 5). In addition, acomplex pattern of boundaries separated the rest of thepopulations of the SMO from the populations in CH(Fig. 5). Fragmentation was particularly evident in theSMO, with several barriers separating populations fromthose in the southern, central and northernmost parts of theSMO (Fig. 5).
Ecological Niche Modelling
The area under the curve (AUC) was 0.983, and the mod-elled distribution corresponds to the known distribution ofH. fumariifolia. Ecological niche modelling (ENM) for thecurrent climate variables predicted an accurate distributionof H. fumariifolia, with the exception of areas in the north-eastern SMO and one in the eastern part of the Trans-
Mexican Volcanic Belt (Fig. 6) where plants have neverbeen collected. However, when the models were projectedonto past climate (21 K) layers, two different scenarios wereretrieved (Fig. 6). For the climate layers based on MIROC3,a large area of suitable habitats in the central and northernparts of the SMO and the central area of the ChihuahuanDesert was predicted, with no connection to the Tehuacán-Cuicatlán Valley. Predictions based on CCSM suggest aslight connection between the Chihuahuan Desert-SierraMadre Oriental and the Tehuacán-Cuicatlán Valley, and alsopredicted an area of suitable habitat in the northernmost partof the Chihuahuan Desert. The model projected onto 120-140 K revealed a highly fragmented scenario, includingareas of suitable habitats in the Trans-Mexican VolcanicBelt and in the Tehuacán-Cuicatlán Valley; however, noareas were predicted in the SMO or in the ChihuahuanDesert.
Discussion
Our phylogenetic reconstruction for Papaveraceae and relat-ed families based on two chloroplast genes retrieved a wellresolved tree, with a topology similar to analyses based on a
Fig. 3 Geographical distribution of the population of H. fumariifolia. Population numbers correspond to those in Sosa et al. (2009). Enclosed areascorrespond to clades in Fig. 1
138 E. Ruiz-Sanchez et al.
larger number of molecular markers (Wang et al. 2009; Bellet al. 2010).
The Mexican tulip poppy populations were grouped intothree main clades that clearly share geographical areas(Fig. 3). The southernmost populations were grouped in theSierra Madre Oriental (Clade 1), while the northern popula-tions of the Sierra were in Clade 2, and the Chihuahuan Desertand Tehuacán-Cuicatlán Valley populations formed part of amore inclusive clade (CH/T-C). The linkage between thepopulations of the Chihuahuan Desert and the northern pop-ulations of the Sierra Madre Oriental corresponded to a hap-lotype from Ciudad del Maíz (13). These results coincide withprevious findings for taxa from North American deserts (BajaCalifornia, Colorado Plateau, and the Chihuahuan, Mojaveand Sonoran deserts). Those studies found patterns in thedistribution of the phylogroups: Eastern (Chihuahuan Desertand Western of the Sierra Madre Oriental) vs Eastern (BajaCalifornia, Colorado Plateau, Mojave and Sonoran deserts)groups (Riddle et al. 2000; Jaeger et al. 2005; Leaché andMulcahy 2007; Castoe et al. 2007; Moore and Jansen 2007;Rebernig et al. 2010a, b).
Our estimate of divergence times for the Papaveraceaebased on five calibration points (three secondary points andtwo fossils) indicate a mean age of 96 Ma (95 % HDP072–116).The estimations of Anderson et al. (2005) that included thisgroup in their analyses of Eudicots using penalized likeli-hood and nonparametric rate smoothing found a mean agefor the stem and crown groups of 114–106 Ma and 121–119,respectively. Furthermore, Bell et al. (2010) found a meanage of 88 Ma (95 % HDP070–106 Ma) using a Bayesianmethod (BEAST). Our results are more similar to those ofBell et al. (2010). However, as stressed by Graur and Martin(2004), the associated error must be considered when usingsecondary calibration and fossil points, as well as the errorbars around each node. Our estimate of the divergence timebetween Hunnemannia and Eschscholzia indicates that itoccurred during the Early Oligocene to the Pliocene(16.03 Ma; 95 % HDP04.6–30 Ma), coinciding with the lastvolcanic-tectonic peak in the Sierra Madre Occidental, 26–25 Ma (Tristán-González et al. 2009). The rise of the SierraMadre Occidental could be responsible for the separation ofpopulations of Hunnemannia in the Chihuahuan Desert and
Arteaga-14
Cd. Maiz-13
Bonanza-2
Real de Catorce-4
Coixtlahuaca-6
Tequixtepec-17
Real de Catorce-4
Cd. Maiz-13
Cerro Tahti-5
Cienega-9
Cd. Maiz-13
Escondida-3
Zaragoza-12
Escondida-3
Mezquititlan-16
Tolantongo-15
Cienega-9
La Luz-8
San Isidro-7
San Isidro-7
Mezquititlan -16
Altares-10
Galeana-1
Galeana-1
Zaragoza-12
Rio San Jose-11
2O
MS
1O
MS
C-T/
HC
0 Ma2.57.5 512.5 1017.5 1520
0 Ma2.57.5 512.5 1017.5 1520
Miocene Pliocene Pleistocene Hol
Miocene Pliocene Pleistocene Hol
B
C
N
O
N
C
B
E
D
H
M
G
G
G
Q
L
L
I
J
J
F
A
K
A
A
P
Fig. 4 Chronogram based on Bayesian approach of the H. fumariifoliaphylogeography. Gray bars 95 % confidence intervals for node ageestimates. Brackets identify clades as given in Fig 2. Circled letters at
the end of the rows are the haplotypes indicated in Table 1 of Sosa et al.(2009). Hol Holocene, Ma Million years
Refugia and geographic barriers in Hunnemannia fumariifolia 139
Sierra Madre Oriental from Eschscholzia in the SonoranDesert and the California Province where most of the speciesof this genus are found (Hoot et al. 1997). Themean divergencetime for each of the three main clades in H. fumariifoliaindicates divergence occurred from the Early Pleistocene toMid-Miocene. This coincides with the Quaternary glacial-interglacial climate cycles and with the contraction and expan-sion of the pine-oak forest in the Sierra Madre Oriental, theSierra Madre Occidental and the Chihuahuan Desert (Metcalfeet al. 2000, 2002; Lozano-Garcia et al. 2002; Bryson et al.2010a, b). However, there are other geological/climatic eventsthat could explain the H. fumariifolia divergence and the sep-aration of Hunnemannia-Eschscholzia, between them is theerosion of the foothills of the SMOr during the Oligocene tothe Neogene (Roure et al. 2009), the aridification during thePliocene and the major temperature decline in the mid-Miocene(Braun 1950; Graham 1999). This same period also coincideswith the divergence of other desert and highland taxa in NorthAmerica (Riddle et al. 2000; Leaché andMulcahy 2007; Castoeet al. 2007; Bryson et al. 2010a, b; Rebernig et al. 2010a, b).
Our previous results with populations of H. fumariifoliafound molecular evidence of northern refugia in the SMO
(Sosa et al. 2009). The ENM reconstructions of the Pleisto-cene LGM based on two different climate scenarios (CCSMand MIROC3) performed for this study with populations ofthe Mexican tulip poppy, agree with the refugia identified bymolecular data. However, the results of the MIROC3 modelsuggested that populations had suitable ecological habitatsin the Chihuahuan Desert, where there were Pinus-Juniperusforests during that period, whereas the latter were not locatedin the north (Metcalfe et al. 2000, 2002; Lozano-Garcia et al.2002; Bryson et al. 2010a, b). Recent phylogeographic studieswith desert plants (e.g., Euphorbia lomelii andMelampodiumleucanthum) based onmolecular data and ENM (Garrick et al.2009; Rebernig et al. 2010a), demonstrated the movement ofpopulations from northern to southern refugia, contrary to ourresults, which showed thatH. fumariifolia populations movedto western and northern refugia. Other phylogeographic stud-ies of trees and vertebrates in North America, however, show acommon pattern of movement from north to south (Carstensand Richards 2007; Waltari et al. 2007; Morris et al. 2010;Cavender-Bares et al. 2011). Recent studies based on fossiland molecular data of Pseudotsuga menziesii indicate verticalmigration in the southern Rocky Mountains and California(Gugger and Sugita 2010; Gugger et al. 2010). It is possiblethat the pattern of migration of the tulip poppy populationswere similar in the northern SMO and in the west in the CH;however, fossils are needed to test this hypothesis.
Sosa et al. (2009) found that the historical processes thatinfluence the geographical pattern of genetic variation in H.fumariifolia could be result of the complex geologic historyof the SMO, while the refugia could be a consequence ofclimate change in the Pleistocene. Here, we used the samedata and combined divergence estimates and palaeoclimaticmodels to test these hypotheses, and found that Neogeneorogenesis in the SMO could be the historical processresponsible for the geographical pattern. Furthermore, Qua-ternary climate change might have had an influence onpopulations of H. fumariifolia, which remained in in-siturefugia in the north of the SMO. Using molecular dating andecological niche modelling with the Crotalus triseriatusgroup, Bryson et al. (2010b) found similar results, indicatingthat the Neogene orogenesis and Quaternary climaticchange drove the evolutionary diversification of this groupof snakes.
Results of the Barrier Analysis indicated that the Trans-Mexican Volcanic Belt was the geographic barrier that sep-arated the populations of the Tehuacán-Cuicatlán Valleyfrom those in the SMO and the Chihuahuan Desert. Twoadditional geographic barriers were detected in the SMO:the Río Pánuco River Basin and the Cerritos-Arista andSaladan Filter Barriers. These same three geographical bar-riers were also identified for populations of the snake Cro-talus triseriatus (Bryson et al. 2010a). The results ofMonmonier’s algorithm for populations of the Mexican tulip
8
10
12
13
14
15
17
7
1
4
5
6
2
311
Tehuacán-Cuicatlán Valley
9
16tleBcinaclovsnarT
Chihuahuan
Desert
latneirOerdaMarreiS
40-60
Bootstrap values
81-9070-80
91-100
Fig. 5 Geographic breaks identified in the distribution of H. fumar-iifolia using Monmonier’s algorithm. The sampling populations of H.fumariifolia are outlined by filled circles, with breaks as recovered bythe software program Barrier 2.2 (Manni et al., 2004) indicated withblack bars. The confidence level of the barrier is indicated by theweight of the line, with heavy lines indicating the best-supportedbreaks as determined by analyses run on boot-strapped distance matri-ces. Population numbers correspond to those in Sosa et al. (2009)
140 E. Ruiz-Sanchez et al.
poppy detected even more geographic barriers preventinggene flow. A barrier separated Bonanza-2 populations fromthe Real de Catorce-4 population in the Chihuahuan Desert.Another separated populations in the central area from thenorthern area of the SMO, and a barrier coinciding with thesouthernmost part of the Sierra Gorda separated the southernpopulations of the SMO from those of the ChihuahuanDesert. For example, the uplift of the Cascades and theSierra Nevada caused the vicariance between the RockyMountain and the west coast populations of Pseudotsugamenziesii (Gugger et al. 2010). Thus, we suggest that thecomplex orogeny of the Sierra Madre Oriental that arose atdifferent periods (English et al. 2003; Roure et al. 2009)gave rise to a diverse array of geographical barriers prevent-ing gene flow in populations of H. fumariifolia (Fig. 5).
Conclusions
In this study we found evidence that the divergence of thethree main clades of populations in H. fumariifolia occurredfrom Early Pleistocene to Mid-Miocene. Gene flow betweenthe populations of H. fumariifolia was also found to belimited by the LGM, climate change during the Quaternary,the complex topography caused by the Neogene orogenesisof the SMO and the Trans-Mexican Volcanic Belt, and that
all of these processes may have resulted in the patchydistribution of suitable microhabitats for H. fumariifolia.ENM with the MIROC3 model indicated that populationsdid not move to the north but rather that they had suitableecological habitats in the Chihuahuan Desert, where Pinus-Juniperus forests existed during that period.
Acknowledgments We are particularly grateful to Sasa Stefanovicand two anonymous reviewers, whose comments improved this man-uscript significantly. We thank Bianca Delfosse for revising the Englishand Tania Hernandez for help with the molecular dating analyses.
References
Anderson, C. L., Bremer, K., & Friis, E. M. (2005). Dating phyloge-netically basal eudicots using rbcL sequences and multiple fossilreference points. American Journal of Botany, 92, 1737–1748.
Bell, C. D., Soltis, D. E., & Soltis, P. S. (2010). The age and diversi-fication of the angiosperm re-revisited. American Journal of Bot-any, 97, 1296–1303.
Braconnot, P., Otto-Bliesner, B., Harrison, S., Joussaume, S.,Peterchmitt, J.-Y., Abe-Ouchi, A., Crucifix, M., Driesschaert,E., Fichefet, T., Hewitt, C. D., et al. (2007). Results ofPMIP2 coupled simulations of the Mid-Holocene and LastGlacial Maximum—Part 1: experiments and large-scale fea-tures. Climate of the Past, 3, 261–277.
Braun, E. L. (1950). Deciduous forests of Eastern North America.Philadelphia: Blakiston.
Fig. 6 a–d. Ecological niche models for H. fumariifolia populations. aPrediction of suitable habitat in the current environment. b Predictionprojected onto past climatic layers (LGM; CCSM). c Prediction under
past climate conditions (LGM; MIROC3). d Prediction projected ontopast climatic layers during an interglacial period (120–140 ka). Filledcircles sampling sites
Refugia and geographic barriers in Hunnemannia fumariifolia 141
Bryson, R. W., Nieto-Montes, A., Jaeger, J. R., & Riddle, B. R. (2010).Elucidation of cryptic diversity in a widespread Nearctic treefrogreveals episodes of mitochondrial gene capture as frogs diversi-fied across a dynamic landscape. Evolution, 64, 2315–2330.
Bryson, R. W., Jr., Murphy, R. W., Lathrop, A., & Lazcano-Villareal,D. (2010). Evolutionary drivers of phylogeographical diversity inthe highlands of Mexico: a case study of the Crotalus triseriatusspecies group of montane rattlesnakes. Journal of Biogeography,38, 697–710.
Carstens, B. C., & Richards, C. L. (2007). Integrating coalescent andecological niche modeling in comparative phylogeography. Evo-lution, 61, 1439–1454.
Castoe, T. A., Spencer, C. L., & Parkinson, C. L. (2007). Phylogeo-graphic structure and historical demography of the western dia-mondback rattlesnake (Crotalus atrox): a perspective on NorthAmerican desert biogeography. Molecular Phylogenetics andEvolution, 42, 193–212.
Cavender-Bares, J., Gonzalez-Rodriguez, A., Pahlich, A., Koehler, K.,& Deacon, N. (2011). Phylogeography and climatic niche evolu-tion in live oaks (Quercus series Virentes) from the tropics to thetemperate zone. Journal of Biogeography, 38, 962–981.
Chan, L. M., Brown, J. L., & Yoder, A. D. (2011). Integrating statis-tical genetic and geospatial methods brings new power to phylo-geography.Molecular Phylogenetics and Evolution, 59, 523–537.
Cosacov, A., Sérsic, A. N., Johnson, L., Sosa, V., & Cocucci, A. A.(2010). Multiple periglacial refugia in the Patagonian steppe andpost-glacial colonization of the Andes: the phylogeography ofCalceolaria polyrhiza. Journal of Biogeography, 37, 1463–1477.
Désamoré, A., Laenen, B., Devos, N., Popp, M., González-Mancebo,J. M., Carine, M., & Vanderpoorten, A. (2011). Out of Africa:north-westwards Pleistocene expansions of the heather Ericaarborea. Journal of Biogeography, 38, 164–176.
Drummond, A. J., & Rambaut, A. (2007). BEAST: Bayesian evolu-tionary analysis by sampling trees. BMC Evolutionary Biology, 7,214.
Elith, J., Graham, C. H., Anderson, R. P., Dudik, M., Ferrier, S.,Guisan, A., Hijmans, R. J., Huettmann, F., Leathwick, J. R.,Lehmann, A., Li, J., Lohmann, L. G., Loiselle, B. A., Manion,G., Moritz, C., Nakamura, M., Nakazawa, Y., Overton, J. M.,Peterson, A. T., Phillips, S. J., Richardson, K., Scachetti-Pereira,R., Schapire, R. E., Soberon, J., Williams, S., Wisz, M. S.,Zimmermann, N. E., et al. (2006). Novel methods improve pre-diction of species’ distributions from occurrence data. Ecography,29, 129–151.
English, J. M., Johnston, S. T., & Wang, K. (2003). Thermal modelingof the Laramide orogeny: Testing the flat-slab subduction hypoth-esis. Earth and Planetary Science Letters, 214, 619–632.
Ferrari, L., Conticelli, S., Vaggelli, C., Petrone, C., & Manetti, P.(2000). Late Miocene mafic volcanism and intra-arc tectonicsduring the early development of the Trans-Mexican Volcanic Belt.Tectonophysics, 318, 161–185.
García-Palomo, A., Macías, J. L., Tolson, G., Valdez, G., & Mora, J. C.(2002). Volcanic stratigraphy and geological evolution of theApan region, east-central sector of the Trans-Mexican VolcanicBelt. Geofísica Internacional, 41, 133–150.
Garrick, R. C., Nason, J. D., Meadows, C. A., & Dyer, R. J. (2009).Not just vicariance: phylogeography of a Sonoran Desert euphorbindicates a major role of range expansion along the Baja penin-sula. Molecular Ecology, 18, 1916–1931.
Graham, A. (1999). Studies in Neotropical paleobotany. XIII. AnOligo-Miocene palynoflora from Simojovel (Chiapas, Mexico).American Journal of Botany, 86, 17–31.
Graur, D., & Martin, W. (2004). Reading the entrails of chickens:molecular timescales of evolution and the illusion of precision.Trends in Genetics, 20, 80–86.
Gugger, P. F., & Sugita, S. (2010). Glacial populations and postglacialmigration of Douglas-fir based on fossil pollen and macrofossilevidence. Quaternary Science Reviews, 29, 2052–2070.
Gugger, P. F., Sugita, S., & Cavender-Bares, J. (2010). Phylogeogra-phy of Douglas-fir based on mitochondrial and chloroplast DNAsequences: testing hypotheses from the fossil record. MolecularEcology, 19, 1877–1897.
Hijmans, R. J., Cameron, S. E., Parra, J. L., Jones, P. G., & Jarvis, A.(2005). Very high resolution interpolated climate surfaces forglobal land areas. International Journal of Climatology, 25,1965–1978.
Ho, S. Y. W., & Philips, M. J. (2009). Accounting for calibrationuncertainty in phylogenetic estimation of evolutionary divergencetimes. Systematic Biology, 58, 367–380.
Hoot, S. B., Kadereit, J. W., Blattner, F. B., Jork, K. B., Schwarzbach,A. E., & Crane, P. R. (1997). Data congruence and phylogeny ofthe Papaveraceae s.l., based on four data sets: atpB and rbcLsequences, trnK restriction sites, and morphological characters.Systematic Botany, 22, 575–590.
Hugall, A., Moritz, C., Moussalli, A., & Stanisic, J. (2002). Reconcil-ing paleodistribution models and comparative phylogeography inthe wet tropics rainforest land snail Gnarosophia bellendenker-ensis. Proceedings of the National Academy of Sciences USA, 99,6112–6117.
Jaeger, J. R., Riddle, B. R., & Bradford, D. F. (2005). Cryptic Neogenevicariance and Quaternary dispersal of the red-spotted toad (Bufopunctatus): insights on the evolution of North American warmdesert biotas. Molecular Ecology, 14, 3033–3048.
Knowles, L. L., Carstens, B. C., & Keat, M. L. (2007). Coupling geneticand ecological-niche models to examine how past population dis-tributions contribute to divergence. Current Biology, 17, 1–7.
Leaché, A. D., & Mulcahy, D. G. (2007). Phylogeny, divergence timesand species limits of spiny lizards (Sceloporus magister speciesgroup) in western North American deserts and Baja California.Molecular Ecology, 16, 5216–5233.
Lozano-García, S., Ortega-Guerrero, B., & Sosa-Nájera, S. (2002).Mid- to Late-Wisconsin pollen record of San Felipe Basin, BajaCalifornia. Quaternary Research, 58, 84–92.
Manni, F., Guérard, E., & Heyer, E. (2004). Geographic patterns of(genetic, morphologic, linguistic) variation: how barriers can bedetected by using Monmonier’s algorithm. Human Biology, 76,173–190.
Marske, K. A., Leschen, R. A. B., & Buckley, T. R. (2011). Reconcil-ing phylogeography and ecological niche models for New Zea-land beetles: looking beyond glacial refugia. MolecularPhylogenetics and Evolution, 59, 89–102.
McGuire, J., Linkem, C., Koo, M., Hutchison, D., Lappin, K., Orange,D., Lemos-Espinal, J., Riddle, B., & Jaeger, J. (2007). Mitochon-drial introgression and incomplete lineage sorting through spaceand time: phylogenetics of crotaphytid lizards. Evolution, 61,2879–2897.
Metcalfe, S. E. (2006). Late Quaternary environments of the northerndeserts and central Transvolcanic Belt of Mexico. Annals of theMissouri Botanical Garden, 93, 258–273.
Metcalfe, S. E., O’Hara, S. L., Caballero, M., & Davies, S. J. (2000).Records of Late Pleistocene–Holocene climatic change inMexico—a review. Quaternary Science Reviews, 19, 699–721.
Metcalfe, S. E., Say, A., Black, S., McCulloch, R., & O’Hara, S.(2002). Wet conditions during the last glaciation in the Chi-huahuan Desert, Alta Babicora Basin, Mexico. QuaternaryResearch, 57, 91–101.
142 E. Ruiz-Sanchez et al.
Monmonier, M. S. (1973). Maximum-difference barriers: an alternativenumerical regionalizationmethod.Geographical Analysis, 5, 245–261.
Moore, M. J., & Jansen, R. K. (2007). Origins and biogeography ofgypsophily in the Chihuahuan Desert plant group Tiquilia Subg.Eddya (Boraginaceae). Systematic Botany, 32, 392–414.
Moreno-Letelier, A., & Piñero, D. (2009). Phylogeographic structureof Pinus strobiformis Engelm. across the Chihuahuan Desertfilter-barrier. Journal of Biogeography, 36, 121–131.
Morris, A. B., Ickert, S. M., Brunson, B. D., Soltis, D. E., & Soltis, P.S. (2008). Phylogeographical structure and temporal complexityin American sweetgum (Liquidambar styraciflua; Altingiaceae).Molecular Ecology, 17, 3889–3900.
Morris, A. M., Graham, C. H., Soltis, D. E., & Soltis, P. S. (2010).Reassessment of phylogeographical structure in an eastern NorthAmerican tree using Monmonier’s algorithm and ecological nichemodelling. Journal of Biogeography, 37, 167–1667.
Nakazato, T., Warren, D. L., & Moyle, L. C. (2010). Ecological andgeographic modes of species divergence in wild tomatoes. Amer-ican Journal of Botany, 97, 680–693.
Ornelas, J. F., Ruiz-Sanchez, E., & Sosa, V. (2010). Phylogeography ofPodocarpus matudae (Podocarpaceae): pre-Quaternary relicts innorthern Mesoamerican cloud forests. Journal of Biogeography,37, 2384–2396.
Peterson, A. T. (2007). Why not WhyWhere: the need for morecomplex models of simpler environmental spaces. EcologicalModelling, 203, 527–530.
Phillips, S. J., Anderson, R. P., & Schapire, R. E. (2006). Maximumentropy modeling of species geographic distributions. EcologicalModelling, 190, 231–259.
Posada, D. (2008). jModelTest: Phylogenetic model averaging. Molec-ular Biology and Evolution, 25, 1253–1256.
Rebernig, C. A., Schneeweiss, G. M., Bardy, K. E., Schönswetter, P.,Villaseñor, J. L., Obermayer, R., Stuessy, T. F., & Weiss-Schneeweiss, H. (2010a). Multiple Pleistocene refugia and Holo-cene range expansion of an abundant south-western Americandesert plant species (Melampodium leucanthum, Asteraceae).Mo-lecular Ecology, 19, 3421–3443.
Rebernig, C. A., Weiss-Schneeweiss, H., Schneeweiss, G., Schönswetter,P., Obermayer, R., Villaseñor, J. L., & Stuessy, T. F. (2010b).Quaternary range dynamics and polyploid evolution in an aridbrushland plant species (Melampodium cinereum, Asteraceae).Mo-lecular Phylogenetics and Evolution, 54, 594–606.
Riddle, B. R., & Hafner, D. J. (2006). A step-wise approach tointegrating phylogeographic and phylogenetic biogeographic
perspectives on the history of a core North American warmdeserts biota. Journal of Arid Environments, 66, 435–461.
Riddle, B. R., Hafner, D. J., & Alexander, L. F. (2000). Comparativephylogeography of Baileys’ pocket mouse (Chaetodipus bailey)and the Peromyscus eremicus species group: historical vicarianceof the Baja California Peninsular Desert.Molecular Phylogeneticsand Evolution, 17, 161–172.
Ronquist, F., & Huelsenbeck, J. P. (2003). MrBayes 3: Bayesianphylogenetic inference under mixed models. Bioinformatics, 19,1572–1574.
Roure, F., Alzaga-Ruiz, H., Callot, J. P., Ferket, H., Granjeon, D.,Gonzalez-Mercado, G. E., Guilhaumou, N., Lopez, M., Mougin,P., Ortuño-Arzate, S., & Séranne, M. (2009). Long lasting inter-actions between tectonic loading, unroofing, post-rift thermalsubsidence and sedimentary transfer along the eastern margin ofthe Gulf of Mexico: Some insights from integrated quantitativestudies. Tectonophysics, 475, 169–189.
Sosa, V., Ruiz-Sanchez, E., & Rodriguez-Gomez, F. C. (2009). Hiddenphylogeographic complexity in the Sierra Madre Oriental: thecase of the Mexican tulip poppy Hunnemannia fumariifolia(Papaveraceae). Journal of Biogeography, 36, 18–27.
Tausch, R. J., Wigand, P. E., & Burkhardt, J. W. (1993). Viewpoint:Plant community thresholds, multiples steady states successionalpathways: legacy of the Quaternary? Journal of Range Manage-ment, 46, 439–447.
Tristán-González, M., Aguirre-Díaz, G. J., Labarthe-Hernández, G.,Torres-Hernández, J. R., & Hervé Bellon, H. (2009). Post-Laramide and pre-Basin and Range deformation and implicationsfor Paleogene (55–25 Ma) volcanism in central Mexico: A geo-logical basis for a volcano-tectonic stress model. Tectonophysics,471, 136–152.
Van Devender, T. R. (1990). Late Quaternary vegetation and climate ofthe Chihuahuan Desert, United States and Mexico. In BetancourtJL, T. R. Van Devender, & P. S. Martin (Eds.), Packrat Middens:The last 40,000 years of biotic change (pp. 104–133). Tucson:University of Arizona.
Waltari, E., Hijmans, R. J., Peterson, A. T., Nyari, A. S., Perkins, S. L.,& Guralnick, R. P. (2007). Locating Pleistocene refugia: compar-ing phylogeographic and ecological niche model predictions.PLoS ONE, 2, e563.
Wang, W., Lu, A. M., Ren, Y., Endress, M. E., & Chen, Z. D. (2009).Phylogeny and classification of Ranunculales: evidence from fourmolecular loci and morphological data. Perspectives in PlantEcology, Evolution and Systematics, 11, 81–110.
Refugia and geographic barriers in Hunnemannia fumariifolia 143
