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Phylogenetic estimation of the core Bromelioids with an emphasis on the genus Aechmea (Bromeliaceae

Phylogenetic estimation of the core Bromelioids with an emphasis on the genus Aechmea (Bromeliaceae
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  Phylogenetic estimation of the core Bromelioids with an emphasis on the genus  Aechmea  (Bromeliaceae) Chodon Sass a, * , Chelsea D. Specht a,b a Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA b University and Jepson Herbaria, Berkeley, CA 94720, USA a r t i c l e i n f o  Article history: Received 22 July 2009Revised 5 January 2010Accepted 5 January 2010Available online 11 January 2010 Keywords: Aechmea BromeliaceaeBromelioideaeETSg3pdhMolecular phylogenyNeotropical biogeographyrpb2 a b s t r a c t We developed a phylogeny of the core Bromelioideae including  Aechmea  and related genera, with thespecific goals of investigating the monophyly of   Aechmea  and its allied genera, redefining monophyleticlineages for taxonomic revision, and investigating the biogeographic history of the group. Chloroplast,nuclearribosomal,andlowcopynuclearDNAsequencesfrom150specieswithintheBromelioideaewereused to develop the phylogeny. Phylogenies constructed with the combined four gene dataset providedsufficient resolution for investigating evolutionary relationships among species. Many genera are nestedwithin  Aechmea , or are rendered para- or polyphyletic by inclusion of   Aechmea  species. Several generaand subgenera of   Aechmea  with species in disjunct geographic locations are found to be polyphyletic,divided into separate clades that reflect geographic distribution rather than morphological similarity.This suggests that certain morphological characteristics thought to be indicative of common ancestryhave instead evolved multiple times in parallel (i.e. ecological conservatism), possibly indicative of localadaptations to an epiphytic habit across the range of the Bromelioideae. These apparently homoplasticmorphological characters used to assign species to genera or subgenera may be useful taxonomicallywhen geography is also taken into account.   2010 Elsevier Inc. All rights reserved. 1. Introduction The Bromeliaceae is a morphologically and edaphically diverse,mostly neotropical family containing over 3100 species in 58 gen-era as currently defined (Luther, 2008). The family forms an early-diverging lineage within the Poales (APG II, 2003; Givnish et al.,2007). Bromeliaceae is historically divided into three subfamilies:Pitcairnioideae, Bromelioideae and Tillandsioideae. A recentmolecular phylogenetic study based on ndhF sequences suggeststhat Bromeliaceae may better be divided into eight monophyleticlineages (Givnish et al., 2007); however, this study and others(Ranker et al., 1990;Horres et al., 2000, 2007) consistentlysupport the monophyly of subfamily Bromelioideae.Bromelioideae contains species that are economically impor-tant, such as  Ananas comosus  (pineapple), the 4th most importanttropical fruit for commercial production after watermelon, bananaand mango (Chwee and Ahmad, 2008), as well as many other spe- cies valued locally as sources of fiber. Ecologically, Bromelioideaeare important sources of fleshy fruit, floral nectar, water (in leaf impounding tanks) and shelter for associated tropical mammals,amphibians, birds and insects (Benzing, 1998a; Galindo-Lealet al., 2003; Balke et al., 2008). Species of the Bromelioideae are typicallyrecognizedby havingserratedleaves coveredwith multi-cellular trichome scales, roots that function as holdfasts, baccate,indehiscent fruits (Givnishet al., 2007) with gelatinous seeds (Sajo et al., 2004), petals which are almost always appendaged, and ma-ture seeds which are unappendaged (Smith, 1988). The subfamilyis found throughout the neotropics and exists in all types of trop-ical biomes, from open sand dunes to humid montane cloudforests.Since the recognition of the subfamily in 1828 (Reichenbach,1828),andinthemostrecentmonographoftheBromeliaceaepub-lishedinFloraNeotropicabySmithandDownsin1979,ithasbeenapparent that many generic circumscriptions within Bromelioi-deae do not represent true genealogical relationships (Smith andDowns, 1979; Smith, 1988; Smith and Kress, 1990; Smith andSpencer, 1992). Within the subfamily, species are assigned to gen-era mostly on the basis of floral characteristics, with a major divi-sion made between those species that have symmetric versusasymmetric sepals (Smith, 1988). Recent re-examinations of someBromelioideae species have made progress in defining monophy-letic lineages, such as the identification of a Nidularioide lineage(Leme, 2000a), the confirmation of the monophyly of the genus Lymania  based on a morphological and chloroplast gene regionanalyses (Faria et al., 2004b; de Oliveira et al., 2007; de Sousa and Wendt, 2008), and the re-establishment of the genus  Andrea 1055-7903/$ - see front matter   2010 Elsevier Inc. All rights reserved.doi:10.1016/j.ympev.2010.01.005 *  Correspondingauthor.Address:UniversityofCalifornia,Berkeley,111KoshlandHall, Berkeley, CA 94720, USA. Fax: +1 510 642 4995. E-mail address: (C. Sass).Molecular Phylogenetics and Evolution 55 (2010) 559–571 Contents lists available at ScienceDirect Molecular Phylogenetics and Evolution journal homepage:  (Brown and Leme, 2005). However, phylogenies resulting from theanalysis of chloroplast gene regions, AFLPs, and morphologicalcharacters for a more extensive sampling within Bromelioideae(Faria et al., 2004b; Schulte et al., 2005; Horres et al., 2007) have low resolution and/or lack support for the monophyly of many rec-ognized genera. These studies show both paraphyly and polyphylyof genera, and often the few monophyletic genera are nested with-in larger generic groups, rendering the latter para- or polyphyletic.Taxonomic issues are especially untenable in the largest genus,  Aechmea  (Greek: ‘‘speared leaf”), which currently comprises over240 species (Luther, 2008) and is characterized generally by thepresence of asymmetric sepals. Many of the characters used to as-sign species to subgenera or identify species within  Aechmea  arethe same characters used to specify species belonging to other gen-era, confounding taxonomic delineations (Smith, 1988; Faria et al.,2004b). These characters include branching of inflorescence, sepaland petal connation and armament, pollen characteristics, pres-ence or absence of pedicels and inflorescence and floral bract mor-phology. Efforts to overcome historical taxonomic issues byelevating the eight recognized subgenera of   Aechmea  to genera(Smith and Kress, 1989, 1990) or by creating new genera (Read and Baensch, 1994) werecontroversial,as subgenericdelimitationswithin  Aechmea  were also found to be artificial (Smith and Downs,1979; Izquierdo and Pinero, 1998; Faria et al., 2004b). Leme (1997) has suggested that the characters listed above cannot be appliedsingularly to delineate genera or subgenera, but rather that a com-bination or suite of characters must be used to evaluate every spe-cies. Unfortunately, such extensive re-evaluations of theBromelioideae are few (Leme, 1997, 1998, 2000b; Wendt, 1997;de Sousa and Wendt, 2008; de Sousa et al., 2008) and limited intaxonomic sampling – often including only species of the subgen-era or genera that are native to Brazil.Due tothehistoricdifficultiesin usingmorphologicalcharactersto delineate genera within this subfamily, a well-sampled molecu-lar phylogeny that can delineate evolutionary relationships amongspecies offers promise to resolve taxonomic difficulties and assignspecies to monophyletic genera. Previous molecular phylogeneticstudies of Bromelioideae have relied solely on chloroplast gene re-gions (Schulte et al., 2005; de Oliveira et al., 2007; Givnish et al., 2007) or AFLPs (Horres et al., 2007). In both a large morphological study encompassing several distinct Bromelioid genera endemic toeastern Brazil and in a recent study of the Bromelioideae using thelow copy nuclear gene PRK, the Bromelioideae were divided intotwo major groups: (1) the core Bromelioideae and (2) earlierdiverging lineages (Leme, 1997, 1998, 2000b; Schulte et al.,2009). These two lineages correspond to the two major groupsidentified based on sepal morphology (Smith, 1988).The current study focuses within the core Bromelioideae on thegenus  Aechmea , including those genera that have shown affinity orclose relationship to  Aechmea  in previous morphological, chloro-plast or AFLP based studies (Izquierdo and Pinero, 1998; Duvalet al., 2003; Faria et al., 2004b; Brown and Leme, 2005; Schulte et al., 2005, 2009; de Oliveira et al., 2007; Horres et al., 2007). Be- cause chloroplast gene regions have demonstrated a lack of suffi-cient phylogenetic signal to resolve relationships among fast-evolving plant lineages in general (Doyle, 1992; Sang, 2002; Steele et al., 2008) and among Bromelioideae specifically (Horres et al.,2000, 2007; Schulte et al., 2005), several additional markers that are phylogenetically informative in various groups of angiosperms(ETS (Baldwin and Markos, 1998), rpb2 (Denton et al., 1998), and g3pdh (Olsen and Schaal, 1999)) were used along with the chloro-plast intron of the trnL gene and the intergenic spacer betweentrnL and trnF (trnLF).Beyond the promise of elucidating relationships within a sub-family that has challenged taxonomists for decades, a well-sam-pled molecular phylogeny can be used to further understand theinteresting morphological and biogeographical features of thischarismatic group (Felsenstein, 1985; Schluter et al., 1997; Pagel, 1999; Blomberg and Garland, 2002). Understanding evolutionary histories holds the promise to reveal general patterns that affectbiodiversity such as differential rates of evolution, (Edwardset al., 2007; Smith and Donoghue, 2008; Smith et al., 2009) and ecological conservatism (Losos, 2008; Crisp et al., 2009). At the phylogenetic scaleofspecies,climatictolerancesmayplayanespe-cially important role in the diversification patterns of epiphytes,organisms highly dependent on atmospheric conditions for nutri-ents and water (Benzing, 1998b; Pierce et al., 2002; Pounds and Masters,2009), butthesepatternsofdiversificationcan onlybeob-served and tested after evolutionary relationships are betterunderstood.Here we use a combined four gene molecular phylogeneticanalysis to investigate the evolution of   Aechmea  and related gen-era, and discuss the taxonomic consequences and biogeographicpatterns resulting from this analysis. The current study encom-passes the broadest species-level and genomic level sampling of this taxonomically challenging group. 2. Materials and methods  2.1. Taxon sampling  Species from all eight subfamilies of   Aechmea  and at least onemember of 18 remaining genera of Bromelioideae were sampled,for a total of 150 species (Supp. Table 1). Sampling was concen-trated on species native to Central America and northern SouthAmerica, and focused on genera within the Bromelioideae thathad been shown to have morphological affinity to  Aechmea  species(Supp. Table 2) or a close relationship to  Aechmea  based on previ-ous phylogenetic studies. Based on previous work, several Brome-lioideae genera are consistently separated from  Aechmea  ( Bromelia ,  Acanthostachys ,  Fascicularia ,  Griegia ,  Cryptanthus ,  Deinacanthon , and Ochagavia ) and as such were not the focus of ingroup sampling inthis study. At least one member of   Bromelia ,  Acanthostachys , and Fascicularia  were included for the purposes of outgroup rooting.  2.2. Genomic sampling  Leaf tissue was clipped from live plants, dried in silica, andstored at   80   C. Whole genomic DNA was extracted with a mod-ified sodium dodecyl sulfate (SDS) and sodium chloride protocol,followedbywashingwithethanol(Edwards etal.,1991; KoniecznyandAusubel,1993). DNAqualityand quantitywas verifiedby mea-suring its absorbance at 260 and 280 nm with a NanoDrop  ND-1000 (NanoDrop Technologies, Wilmington, DE). Three nucleargenes and one chloroplast region were sampled: the nuclear ribo-somal external transcribed spacer (ETS), the 23rd intron of RNApolymerase beta subunit II (rpb2), the region between the 8thand 10th exons of glyceraldehydes-3-phosphate-dehydrogenase(g3pdh), and the chloroplast region including the trnL intron andthe intergenic spacer between trnL and trnF (trnLF). PCR amplifica-tion was performed from genomic DNA with iProof™ High-FidelityDNA polymerase or iTaq™ DNA polymerase (Bio-Rad, Hercules,CA). Amplification primers and annealing temperatures are listedin Table 1. For some gene regions (ETS and g3pdh), universal orpreviously published primers were used to amplify and sequencethe gene region from two to five taxa, from which bromeliad spe-cific primers and amplification conditions were developed andused for the remaining taxa (Table 1). For g3pdh, initial PCR condi-tions amplified two copies of g3pdh, which were clearly distin-guishable by their introns. A second set of primers was designedto amplify only one of these copies. Amplified products were in- 560  C. Sass, C.D. Specht/Molecular Phylogenetics and Evolution 55 (2010) 559–571  spected on 1% agarose/TAE gels. When necessary, amplicons werecloned using the CloneJET™ PCR cloning kit (Fermentas, Glen Bur-nie, MD). Colonies were chosen at random and inserts were ampli-fied with vector specific primers using EconoTaq™ (Lucigen,Middleton, WI). Prior to sequencing, all amplicons were cleanedby digestion with exonuclease and shrimp alkaline phosphataseor through gel extraction using the QiaQuick™ Gel Extraction Kit(Qiagen, Valencia, CA). Cycle sequencing was performed using BigDye v.3.1 sequencing chemistry and sequencing was performedon an ABI 3100 sequencer (Applied Biosystems, Foster City, CA).  2.3. Sequence alignment  Sequence editing and contig generation were performed inSequencher (Gene Codes Corp., Ann Arbor, MI). Additional se-quences for trnLF were downloaded from GenBank (see Supp. Ta-ble 1). Gene regions were individually aligned with CLUSTAL X(Thompson et al., 1994) and manually adjusted in MacClade (Sina-uer Associates, Inc., Sunderland, MA). Gaps were treated as missingdata and regions of questionable homology were omitted fromphylogenetic estimations. The multi-gene concatenated alignmentwith a total of 2457 characters (including gaps) used for tree esti-mations is stored in TreeBASE.  2.4. Phylogenetic reconstruction Separate and combined analyses for each of the four gene re-gions were performed using parsimony in PAUP   4.0b (Swofford,2003), maximum-likelihood in Garli v0.96 (Zwickl, 2006) and Bayesian inference in MrBayes v3.2 (Huelsenbeck and Ronquist,2001). In the combined parsimony analysis, consensus trees weregenerated from heuristic searches with 100 random addition rep-licates with tree bisection and reconnection (TBR) branch swap-ping, MULTREES on, and steepest descent in effect, with no morethan 7500 trees saved per replicate. Support was assessed with113 bootstrap replicates each with 10 random addition, TBR branch swapping, MULTREES on, and no more than 10,000 treessaved per pseudoreplicate. For maximum-likelihood and Bayesiananalyses, individual and combined datasets were tested for theappropriate model of nucleotide evolution with ModelTest v3.7(Posada and Crandall, 1998) using the Akaike Information Criterion (AIC) (Akaike, 1974; de Queiroz and Gatesy, 2007). Garli was run remotelythroughtheCIPRESPortal2.0 at theSan DiegoSupercom-puting Center (Miller et al., 2009) using the general time reversiblemodel of nucleotide evolution with a gamma distributed rateparameter and 1000 bootstrap replicates to test for clade support,with default settings for the combined analysis. For individualanalyses, Garli was run with the models as listed in Table 1, withdefault parameters except that starting tree was set to random,replicate runs were set to 10, and the automatic run terminationlimits were increased: significance of change set to 0.05 and num-ber of runs without significant change set to 1 million. In the com-bined Bayesian estimation, 4 independent runs of 30 milliongenerations, sampled every 100th generation, each with threeheated chains and one cold chain were run with data partitionedby gene region according to models of nucleotide evolution indi-cated in Table 1. All parameters except topology and branch lengthwere allowed to vary across partitions. Likelihood values weremonitored to assess burnin, and only post-burnin trees were usedto generate a consensus tree to estimate the posterior probability(as a measure of clade support) and average branch lengths inMrBayes. The individual Bayesian analyses were run as in the com-bined analysis except with two independent runs for 5 milliongenerations.Congruence among the independent gene regions for the sam-pled species was examined using the Incongruence Length Differ-ence (ILD) test (Farris et al., 1994) as implemented in PAUP  with 1000 bootstrap replicates, each with 10 random addition rep-  Table 1 Details of primers, amplification conditions, character information, and evolutionary models for gene regions used in this analysis. GeneregionFwd.primerRev.primerIntern.Fwd.Annealingtemp. (  C)Length of amplifiedproduct (  bp)Reference ParsimonyInformativeCharactersModel of nucleotideevolutionrpb2 a,b CAR CCA GCA 52.5 (1streaction)350 Denton et al., 1998; Roncal et al., 2005;Lagomarsino, unpublished50 GTR+GGAR CGC TCAGAT ATC TGGATG TGA GAACCA TAT AAG 48.5 (2ndreaction)TGG CCA TTGAC C CTETS c GTT CAA N/A 63.5touchdown to58600 Baldwin and Markos, 1998; Kay et al., 2005 234 GTR+G TCG CCAGCC GGTTCC AGCCAG ATGTCT TCCAGC TTT Gg3pdh c CAT GCT N/A 65touchdown to591000–1100 Strand et al., 1997 108 HKY+GCTA GAAGCA GATAGG ACCACT TGCGGA TGTGAG G CAC CtrnL-F CGA ATT N/A 55 1000 Taberlet et al., 1991 58 GTR+I+GAAT TGACGG ACTTAG GGTACG GACCTA ACGCG AG a Nested PCR reaction required. b PCR primer developed for use in  Heliconia. c PCR primers developed for this project. C. Sass, C.D. Specht/Molecular Phylogenetics and Evolution 55 (2010) 559–571  561  licates after non-parsimony informative characters had been re-moved. The ILD test was performed between all four gene regions,and between ETS and the three remaining gene regions. Signifi-cance of topological incongruence was tested between 16 plausibletopologies (4 gene combined ML and Bayesian ML tree, 3 genecombined ML and Bayesian ML tree, individual ML and BayesianML trees, individual Bayesian consensus trees) with the Shimoda-ira–Hasegawa (SH) test (Shimodaira and Hasegawa, 1999) asimplemented in PAUP with the model of evolution indicated in Ta-ble 1, with 1000 RELL bootstrap repetitions.  2.5. Morphological and biogeographic character evaluation Publishedliteratureandonlinedatabasesweresearchedtocodemorphological character states of sampled species in order to per-form a preliminary re-evaluation of morphological affinities, iden-tify synapomorphies, and search for biogeographic trends.Literature sources included Flora Neotropica (Smith and Downs,1979), The Journal of the Bromeliad Society (Read, 1982; Leme,1986;Read and Baensch,1994;Luther andNorton, 2008), Selbyana(Gilmartin, 1981; Read and Luther, 1991; Espejo-Serna et al.,2004b), Bromelienstuden series (Bohme, 1988; Gross, 1988), The Bromeliads of the Atlantic Forest series (Leme, 1997, 1998,2000b), Bromelien (Rauh et al., 1973), Families and Genera of Vas- cular Plants (Kubitzki et al., 1998), and other published articles(Smith, 1972, 1988; Smith and Spencer, 1992; Wendt, 1997; Faria et al., 2004a,b; de Oliveira et al., 2007; de Sousa and Wendt, 2008). Species were coded as present or absent from countries (or statesin the case of Mexico and Brazil) based on recorded herbariumspecimens listed in Flora Neotropica (Smith and Downs, 1979),Flora Mesoamerica (Davidse et al., 1994), Bromeliaceae in the her-barium database of Marie-Selby Botanical Garden (downloaded in2007), Bromeliaceae in the online herbarium database of the NewYork Botanical Garden (downloaded in 2009), Bromeliaceae foundintheGBIFonlinedatabasedownloadedin2009(AccessedthroughGBIF data portal, 2009), and geographic descriptions found in theliterature cited above as well as from other sources (Espejo-Sernaet al., 2004a; Acevedo-Rodriguez and Strong, 2005; Aguirre-Sant-oro and Betancur, 2008). 3. Results  3.1. Taxon sampling  With  Fascicularia  and  Bromelia as outgroups, the eu-Bromelioids(sensu Schulte et al. (2009): see Fig. 1) were found to be monophy- letic. The relationship between  Acanthostachys  and  Ananas  couldnot be resolved in the Bayesian analysis, but  Acanthostachys  wassister to all other eu-Bromelioids and formed a basal grade with Fascicularia  and  Bromelia  (Fig. 1) in the strict consensus parsimonyand maximum-likelihood estimations.The core Bromelioids(sensuLeme (1997) and Schulte et al. (2009)) are monophyletic with the surprising exception of the relatively newly described  Aechmeatayoensis  (Gilmartin, 1981) from Ecuador, which nests within  Ananas .Within thecore Bromelioids, three majordivisionsare wellsupported, Clades A, B, and C (Fig. 1). Members of   Aechmea  arefound in each of these clades, corroborating the lack of monophylyshown in previous studies of the genus (Fig. 1).  3.2. Genomic sampling ETS:  The external transcribed spacer aligned dataset consistedof 609 characters (includinggaps) with 234 parsimony informativecharacters, 110 variable characters that are parsimony-uninforma-tive, and 518 unique site patterns for 135 OTUs.  g3pdh:  Several re-gions of the sequenced length of g3pdh contained ambiguouslyalignedgapsandlongsinglenucleotideruns,particularlyintronse-quences close to the 8th and 10th exons. Data used for analyseswas limited to unambiguous regions surrounding the 9th exon.The final alignment for g3pdh consisted of 511 characters (includ-ing gaps) for a total of 119 taxa and contained 108 parsimonyinformative characters, 116 variable characters that are parsi-mony-uninformative, and 346 unique site patterns.  rpb2:  Analigneddatasetof 334characters(includinggaps) for106 taxacon-tained 50 parsimony informative characters, 49 variable charactersthat are parsimony-uninformative, and 182 unique site patterns. trnLF:  The aligned dataset for trnLF consisted of 1003 characters(including gaps) for 113 taxa, and contained 58 parsimony infor-mative characters, 88 variable characters that are parsimony-unin-formative, and 442 unique site patterns.The combined aligned dataset had a total of 2457 characters,450 of which were parsimony informative and 363 of which werevariable but parsimony-uninformative, and 1473 unique site pat-terns, with a total of 22% missing data. The alignment file withall ambiguous regions excluded is stored on TreeBASE.  3.3. Phylogenetic reconstruction In the combined parsimony analysis, a total of 330,000 trees of 1842 steps were saved. Fifty-six percent of random addition repli-cates did not find a tree with an optimal score. The ML estimationgenerated a tree with a log-likelihood of    15528.35. In the com-bined Bayesian analysis, burnin was set to 10,000 trees after exam-ining the log-likelihood scores and seeing that stationarity hadbeen reached. The total mean tree length was 29.497 with a vari-ance of 2.96. The average standard deviation of split frequenciesafter 30 million generations was 0.016 and the average potentialscale reduction factor was 1.001. The harmonic mean of marginallikelihoods was   15626.89 and the arithmetic mean was  15489.98. Three of four independent runs reached marginal like-lihoodof   15489.69(arithmeticmean), with onlyonerun havingalower log-likelihood of    15523.95. Examination of the topologiesof the consensus of each of the four independent runs revealedno differences in topology, except that the single lower log-likeli-hood analysis placed Central American Clade I (within Clade A,highlighted in Fig. 4) as sister to the remaining members of CladeA (Fig. 1) without support (BPP = 0.52). The only topological differences between the three methods of phylogenetic estimation were in resolution. The Bayesian post-burnin majority-rule consensus tree had greater resolution thanthe strict consensus of most parsimonious trees (Fig. 1) with oneexception: in the parsimony analysis,  Acanthostachys  was sisterto all other eu-Bromelioids and formed a basal grade with  Fascicu-laria  and  Bromelia , whereas in the Bayesian estimation, the rela-tionship between  Acanthostachys  and  Ananas  is unresolved. Themaximum-likelihood tree also had  Acanthostachys  in this basalgrade position. A second difference in resolutionbetween the max-imum-likelihood tree and the Bayesian majority-rule consensustree was that the Central American Clade I (Fig. 4C) was found sis-tertoClade Ain themaximum-likelihoodtopology(as inthesinglelower likelihood run of the combined Bayesian analysis), but thisrelationship was not found in the strict consensus of parsimonytrees. Minor differences in the placement of taxa in the maxi-mum-likelihood estimation are also indicated in Fig. 1.In the Bayesian analyses of individual gene regions with burninset to 10% of the trees, the ETS consensus phylogeny had a meantree length of 18.113058 with variance 1.536881 and arithmeticmean of the log-likelihood of    6385.03; g3pdh had a mean treelength of 29.179115 with variance 2.865855 and arithmetic meanof the log-likelihood of    3729.35; rpb2 had a mean tree length of 29.708372with variance 2.983664 and arithmetic mean of the log- 562  C. Sass, C.D. Specht/Molecular Phylogenetics and Evolution 55 (2010) 559–571  Fig. 1.  Majority rule consensus tree showing average branch lengths of a post-burnin Bayesian analysis run for 30 million generations of 151 taxa in the Bromelioideae. Thedataset was partitioned by gene region with models of nucleotide evolution as listed in Table 1. Branches that collapse in the strict consensus of most parsimonious trees arethin. Branches that are not supported by the maximum-likelihood topology are dashed. Bayesian posterior probabilities (BPP) are shown above each branch, and maximum-likelihood (MLB) and parsimony (PB) bootstrap probabilities are shown below each branch, in that order. Taxon names and subtending branches are colored by genus orsubgenus. The names of the clades ‘‘eu-Bromelioids” and ‘‘core Bromelioids” are as from Schulte et al. (2009). Clades within the core Bromelioids are labeled A, B or C. The treeis divided into two pages, with Clade A shown in A and with outgroups and Clades B and C shown in B. The biogeographic grid was coded based on presence in broadgeographic categories based on available data from herbarium specimens and published monographs (see Section 2). Brazil is divided into the following subregions: south-east Brazil includes the states on the Atlantic coast from Rio Grande do Sul to Espírito Santo, and Minas Gerais; mid-east Brazil includes the states along the Atlantic coastfrom Bahia to Pará, and inland from Goiás to Tocantins; northern Brazil includes the states of Amapá and Roraima; mid-west Brazil includes the states of Amazonas and Acre.Abbreviation: IT, Isthmus Tehuantepec. C. Sass, C.D. Specht/Molecular Phylogenetics and Evolution 55 (2010) 559–571  563
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