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Background: The angiosperm family Bromeliaceae comprises over 3.500 species characterized by exceptionally high morphological and ecological diversity, but a very low genetic variation. In many genera, plants are vegetatively very similar which makes determination of non flowering bromeliads difficult. This is particularly problematic with living collections where plants are often cultivated over decades without flowering. DNA barcoding is therefore a very promising approach to provide reliable and convenient assistance in species determination. However, the observed low genetic variation of canonical barcoding markers in bromeliads causes problems., Result: In this study the low-copy nuclear gene Agt1 is identified as a novel DNA barcoding marker suitable for molecular identification of closely related bromeliad species. Combining a comparatively slowly evolving exon sequence with an adjacent, genetically highly variable intron, correctly matching MegaBLAST based species identification rate was found to be approximately double the highest rate yet reported for bromeliads using other barcode markers., Conclusion: In the present work, we characterize Agt1 as a novel plant DNA barcoding marker to be used for barcoding of bromeliads, a plant group with low genetic variation. Moreover, we provide a comprehensive marker sequence dataset for further use in the bromeliad research community.

The saxicolous genus Orthophytum (∼60 species, Bromeliaceae) is endemic to eastern Brazil and diversified in xeric habitats of the Atlantic Rainforest, Caatinga and campos rupestres. Within the genus, two main groups are discerned based on the presence or absence of a pedunculate inflorescence, which are further subdivided into several morphological subgroups. However, these systematic hypotheses have not yet been tested in a molecular phylogenetic framework. Here we present the first phylogenetic analysis of Orthophytum using nuclear and plastid markers (phytochrome C, and trnH-psbA and trnL-trnF spacers). Forty species representing the two main groups and all subgroups of Orthophytum, and the related genera Cryptanthus (8 spp.) and Lapanthus (2 spp.) were analyzed. The phylogenetic reconstruction revealed a well-supported clade termed Eu-Orthophytum, containing species with pedunculate inflorescences only. The Orthophytum species with sessile inflorescence formed two clades: (1) the amoenum group and (2) the vagans group plus O. foliosum, the only pedunculate Orthophytum species found outside Eu-Orthophytum. The vagans clade is in sister group position to Eu-Orthophytum. Within the latter, the subgroup mello-barretoi was sister to the most diversified clade, termed Core Orthophytum. Morphological character state reconstructions of floral characters used in previous taxonomic treatments as key diagnostic characters (penduncle presence, corolla form, and petal appendage form) showed different levels of homoplasy., (Copyright © 2014 Elsevier Inc. All rights reserved.)

We present an integrative model predicting associations among epiphytism, the tank habit, entangling seeds, C₃ vs. CAM photosynthesis, avian pollinators, life in fertile, moist montane habitats, and net rates of species diversification in the monocot family Bromeliaceae. We test these predictions by relating evolutionary shifts in form, physiology, and ecology to time and ancestral distributions, quantifying patterns of correlated and contingent evolution among pairs of traits and analyzing the apparent impact of individual traits on rates of net species diversification and geographic expansion beyond the ancestral Guayana Shield. All predicted patterns of correlated evolution were significant, and the temporal and spatial associations of phenotypic shifts with orogenies generally accorded with predictions. Net rates of species diversification were most closely coupled to life in fertile, moist, geographically extensive cordilleras, with additional significant ties to epiphytism, avian pollination, and the tank habit. The highest rates of net diversification were seen in the bromelioid tank-epiphytic clade (D(crown) = 1.05 My⁻¹), associated primarily with the Serra do Mar and nearby ranges of coastal Brazil, and in the core tillandsioids (D(crown) = 0.67 My⁻¹), associated primarily with the Andes and Central America. Six large-scale adaptive radiations and accompanying pulses of speciation account for 86% of total species richness in the family. This study is among the first to test a priori hypotheses about the relationships among phylogeny, phenotypic evolution, geographic spread, and net species diversification, and to argue for causality to flow from functional diversity to spatial expansion to species diversity.

Premise: Bromeliaceae form a large, ecologically diverse family of angiosperms native to the New World. We use a bromeliad phylogeny based on eight plastid regions to analyze relationships within the family, test a new, eight-subfamily classification, infer the chronology of bromeliad evolution and invasion of different regions, and provide the basis for future analyses of trait evolution and rates of diversification., Methods: We employed maximum-parsimony, maximum-likelihood, and Bayesian approaches to analyze 9341 aligned bases for four outgroups and 90 bromeliad species representing 46 of 58 described genera. We calibrate the resulting phylogeny against time using penalized likelihood applied to a monocot-wide tree based on plastid ndhF sequences and use it to analyze patterns of geographic spread using parsimony, Bayesian inference, and the program S-DIVA., Results: Bromeliad subfamilies are related to each other as follows: (Brocchinioideae, (Lindmanioideae, (Tillandsioideae, (Hechtioideae, (Navioideae, (Pitcairnioideae, (Puyoideae, Bromelioideae))))))). Bromeliads arose in the Guayana Shield ca. 100 million years ago (Ma), spread centrifugally in the New World beginning ca. 16-13 Ma, and dispersed to West Africa ca. 9.3 Ma. Modern lineages began to diverge from each other roughly 19 Ma., Conclusions: Nearly two-thirds of extant bromeliads belong to two large radiations: the core tillandsioids, originating in the Andes ca. 14.2 Ma, and the Brazilian Shield bromelioids, originating in the Serro do Mar and adjacent regions ca. 9.1 Ma.

Phylogenetic relationships within subfamily Bromelioideae (Bromeliaceae, Poales) were inferred using DNA sequence data from the low-copy nuclear gene phosphoribulokinase (PRK) and five plastid loci (matK gene, 3'trnK intron, trnL intron, trnL-trnF spacer, atpB-rbcL spacer). The PRK dataset exhibited a considerably higher proportion of potentially informative characters than the plastid dataset (16.9% vs. 3.1%), leading to a higher resolution and improved nodal support of the resulting phylogenies. Bromelia is resolved as sister to the remainder of the subfamily, albeit this relationship receives only weak nodal support. The basal position of Bromelia, as well as Deinacanthon, Greigia, Ochagavia, Fascicularia and Fernseea within the subfamily is corroborated and the remainder of the subfamily forms a highly supported clade (the eu-bromelioids). By the inclusion of nuclear data the sister group position of Fernseea to the eu-bromelioids is now highly supported. Within the eu-bromelioids the resolution of the clade representing the more advanced core bromelioids has increased and further demonstrates the highly problematic generic concept of Aechmea as well as Quesnelia. Moreover, the data were used to examine the evolution of sepal symmetry and the tank habit. Tracing of character transitions onto the molecular phylogeny implies that both characters have undergone only few transitions within the subfamily and thus are not as homoplasious as previously assumed. The character state reconstruction reveals the great importance of the evolution of the tank habit for the diversification of the core bromelioids.

Understanding the spatial and temporal frameworks of species diversification is fundamental in evolutionary biology. Assessing the geographic origin and dispersal history of highly diverse lineages of rapid diversification can be hindered by the lack of appropriately sampled, resolved, and strongly supported phylogenetic contexts. The use of currently available cost-efficient sequencing strategies allows for the generation of a substantial amount of sequence data for dense taxonomic samplings, which together with well-curated geographic information and biogeographic models allow us to formally test the mode and tempo of dispersal events occurring in quick succession. Here, we assess the spatial and temporal frameworks for the origin and dispersal history of the expanded clade K, a highly diverse Tillandsia subgenus Tillandsia (Bromeliaceae, Poales) lineage hypothesized to have undergone a rapid radiation across the Neotropics. We assembled full plastomes from Hyb-Seq data for a dense taxon sampling of the expanded clade K plus a careful selection of outgroup species and used them to estimate a time- calibrated phylogenetic framework. This dated phylogenetic hypothesis was then used to perform biogeographic model tests and ancestral area reconstructions based on a comprehensive compilation of geographic information. The expanded clade K colonized North and Central America, specifically the Mexican transition zone and the Mesoamerican dominion, by long-distance dispersal from South America at least 4.86 Mya, when most of the Mexican highlands were already formed. Several dispersal events occurred subsequently northward to the southern Nearctic region, eastward to the Caribbean, and southward to the Pacific dominion during the last 2.8 Mya, a period characterized by pronounced climate fluctuations, derived from glacial--interglacial climate oscillations, and substantial volcanic activity, mainly in the Trans-Mexican Volcanic Belt. Our taxon sampling design allowed us to calibrate for the first time several nodes, not only within the expanded clade K focal group but also in other Tillandsioideae lineages. We expect that this dated phylogenetic framework will facilitate future macroevolutionary studies and provide reference age estimates to perform secondary calibrations for other Tillandsioideae lineages. [ABSTRACT FROM AUTHOR]

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We studied the epiphytic species Tillandsia capillaris and T. virescens that grow as neotenic forms with autogamous and cleistogamous flowers. They have expanded in Andean mountain environments, where they grow sympatrically across most of their ranges in arid regions of Peru, central-western Bolivia and north-central Argentina and Chile. We studied the relationships between the two species and populations within each of them, the morphological boundaries and the climatic characterization of distinct genetic entities. We analysed 125 and 102 individuals from 25 and 27 populations of T. virescens and T. capillaris , respectively, by means of haplotype networks, phylogenetic and genetic structure analyses, using the plastid gene ycf1 (c. 4500 bp) to define genetic groups. Morphological studies by discriminant analyses and correlation with climatic variables extracted from WorldClim were used to test differentiations among the genetic groups within each species. We confirm that T. capillaris is a distinct entity and that T. virescens consists of three groups that diverged by vicariance from widespread ancestors. The high genetic diversity found in both species is consistent with the complex geography of the Andes and the Pleistocene glaciation cycles that have driven ecological speciation in both species reflected in the timing of divergence of the clusters. [ABSTRACT FROM AUTHOR]

Subtribe Vrieseinae comprise four genera, Alcantarea , Stigmatodon , Vriesea s.s. and Waltillia , encompassing c. 20% of species in Tillandsioideae (Bromeliaceae), almost all of which are exclusive to Brazil. Here, we explore the biogeographic history of Vrieseinae, sampling 21 of the 22 genera of Tillandsioideae (130 terminals) and three DNA sequence markers (two plastid: rps16-trnK and matK ; one nuclear: PHYC). We inferred a dated phylogeny and the ancestral areas of this lineage through RASP (reconstruct ancestral state in phylogeny) analyses. Vrieseinae were recovered as monophyletic, but tribe Vrieseeae (subtribe Vrieseinae + subtribe Cipuropsidinae) were not. A vicariant event between the Andes and Brazilian Shield probably occurred c. 10 Mya, when two clades, Cipuropsidineae + Tillandsieae and Vrieseineae, diverged. The Atlantic Forest plus the Chacoan region is recognized as the ancestral area for Vrieseinae. The results confirmed the recent origin of genera of Vrieseinae, with estimated crown ages in the Pliocene (5.3–2.6 Mya). We propose that the Paranaean Sea influenced the divergence of the main clades; Pleistocene events were probably responsible for the diversification of the most recent clades. This study sheds light on the biogeographic history of a key group of Neotropical plants, providing a new hypothesis for the evolution of bromeliads. [ABSTRACT FROM AUTHOR]

Since the first description of the genus in 1754, the taxonomy of Ananas underwent many fundamental changes and it is still the subject of a vivid debate. We present a phylogeny comprising all seven known Ananas taxa, Pseudananas sagenarius as well as closely related members of Bromelioideae (Aechmea subg. Chevaliera) based on three nuclear markers (agt1, ETS, phyC), five plastid markers (atpB-rbcL, trnL-trnF, matK, two segments of ycf1) and AFLP data. This study reveals a close relationship between Ananas, P. sagenarius, Aechmea tayoensis and Disteganthus basilateralis, and proposes novel relationship of the Ananas clade and Aechmea fernandae. Taxonomic implications of our analysis in particular the recognition of species versus varieties in Ananas are discussed. Furthermore, we could show that the evolution of two traits (scape bracts and the apical coma of the inflorescence) might be interlinked. [ABSTRACT FROM AUTHOR]

We studied the genetic diversity and structure of the Tillandsia capillaris complex, a morphologically diverse group of highly specialized epiphytes, across the distribution range in arid mountain regions of central Peru, Chile, Bolivia and central Argentina. To elucidate the phylogenetic relationships in the complex and to explore the taxon boundaries among populations, we used three plastid markers ( rpoB-trnC-petN, trnK-matK-trnK, ycf1, c. 8100 bp in total) and one single-copy nuclear gene ( PHYC, c. 1200 bp) for 69 populations and 96 individuals of the T. capillaris complex plus 16 outgroup taxa. Bayesian inference of plastid DNA data indicates the existence of two evolutionary core lineages, which can be recognized as two distinct species: T. capillaris and T. virescens (as proposed previously on the basis of morphological characters). Tillandsia capillaris is a monophyletic and homogeneous group, widely distributed and less genetically variable, whereas T. virescens (including T. kuehhasii) is genetically more divergent with most of the forms growing at high elevation in arid areas, except for the small clade including T. virescens s.s. (= T. cordobensis), which grows in lower, more humid habitats. The nuclear analysis resulted in a polytomy with some individuals showing incongruent positions between plastid and nuclear topologies. The high haplotype diversity, consisting of 63 plastid DNA haplotypes in 69 populations, was resolved as two core lineages occurring from north to south, allowing us to establish a preliminary view of the genetic variation overlapping between the two taxa. The results suggest that the genetic differentiation into two main clades is consistent with morphological variation in this Andean complex. [ABSTRACT FROM AUTHOR]

We performed a phylogenetic analysis using maximum parsimony and Bayesian inference of three plastid DNA markers and the external transcribed spacer ( ETS) of nuclear ribosomal DNA to assess the species composition of the Tillandsia utriculata complex and their phylogenetic relationships, and to reconstruct patterns of character evolution and biogeography. The results showed that species of the T. utriculata complex are nested in a clade composed mainly of Mexican and Central American species of T. subgenus Tillandsia (Mexican Clade), and are organized in two lineages: the T. utriculata clade and the T. limbata clade. The ancestor of the core Mexican Clade was probably a T. utriculata-like epiphyte (Group II-type remote flowers and flexuous rachises). The T. utriculata clade is defined morphologically by the presence of acute petals. In this clade, there are two lineages: one of high-elevation, saxicolous, grey-leaved plants from the Mexican Plateau; and one which is more widespread and found from the Gulf of Mexico to Venezuela. The T. limbata clade probably arose in western Mesoamerica and is defined by rounded petals. These species are found mainly in tropical dry forests, but one species colonized wet environments of eastern Mesoamerica. Finally, analyses based on the ETS region allowed us to distinguish between T. utriculata and T. pringlei. [ABSTRACT FROM AUTHOR]

The article introduces Tillandsia lechneri, a new epilithic Tillandsia from Central Bolivia, named after Peter Lechner of the Agricultural University in Vienna, Austria who observed the plant during a botanical field trip in September 2007. It notes differences from its close relatives T. lotteae and T. xiphioides in terms of floral bract color, sepal and petal lengths, and scent. A diagram showing the maximum likelihood phylogram containing T. lechneri and its relatives is presented.

The article discusses a study on the Tillandsia L., the largest genus of Bromeliaceae with more than 620 pieces in six subgenera ranging from Southeastern U.S. to subtropical Argentine and Chile inhabiting tropical rainforests and deserts from the lowlands to the highlands. It aims to elucidate the aspects belonging to Tillandsia subs. Tillandsia and the phylogenetic relationships of taxa within the subgenus. Variation and information within 8 plastid DNA markers were assessed.

Molecular phylogenetic studies of seven plastid DNA regions were used to resolve circumscriptions at generic and infrageneric levels in subfamily Tillandsioideae of Bromeliaceae. One hundred and ten tillandsioid samples were analyzed, encompassing 10 genera, 104 species, and two cultivars. Two species of Bromelioideae, eight species of the polymorphic Pitcairnioideae, and two species of Rapateaceae were selected as outgroups. Parsimony analysis was based on sequence variation of five noncoding (partial 5' and 3' trnK intron, rps16 intron, trnL intron, trnL-trnF intergenic spacer, atpB-rbcL intergenic spacer) and two coding plastid regions (rbcL and matK). Phylogenetic analyses of individual regions produced congruent, but mostly weakly supported or unresolved clades. Results of the combined data set, however, clearly show that subfamily Tillandsioideae is monophyletic. The earliest divergence separates a lineage comprised of Glomeropitcairnia and Catopsis from the "core" tillandsioids. In their present circumscriptions, genera Vriesea and Tillandsia, and their subgenera or sections, as well as Guzmania and Mezobromelia, are poly- and/or paraphyletic. Genera Alcantarea, Werauhia, Racinaea, and Viridantha appear monophyletic, but separation of these from Vriesea and Tillandsia makes the remainder paraphyletic. Nevertheless, Tillandsioideae separates into four main clades, which are proposed as tribes, viz., Catopsideae, Glomeropitcairnieae, Vrieseeae, and Tillandsieae. [ABSTRACT FROM AUTHOR]

An amendment to this paper has been published and can be accessed via the original article. [ABSTRACT FROM AUTHOR]

The subgenus Tillandsia (Bromeliaceae) belongs to one of the fastest radiating clades in the plant kingdom and is characterized by the repeated evolution of Crassulacean acid metabolism (CAM). Despite its complex genetic basis, this water-conserving trait has evolved independently across many plant families and is regarded as a key innovation trait and driver of ecological diversification in Bromeliaceae. By producing high-quality genome assemblies of a Tillandsia species pair displaying divergent photosynthetic phenotypes, and combining genome-wide investigations of synteny, transposable element (TE) dynamics, sequence evolution, gene family evolution, and temporal differential expression, we were able to pinpoint the genomic drivers of CAM evolution in Tillandsia. Several large-scale rearrangements associated with karyotype changes between the 2 genomes and a highly dynamic TE landscape shaped the genomes of Tillandsia. However, our analyses show that rewiring of photosynthetic metabolism is mainly obtained through regulatory evolution rather than coding sequence evolution, as CAM-related genes are differentially expressed across a 24-h cycle between the 2 species but are not candidates of positive selection. Gene orthology analyses reveal that CAM-related gene families manifesting differential expression underwent accelerated gene family expansion in the constitutive CAM species, further supporting the view of gene family evolution as a driver of CAM evolution. The genomes of 2 species belonging to the Tillandsia radiation reveal gene family expansion as a potential driver of CAM evolution. [ABSTRACT FROM AUTHOR]

The genus Stigmatodon occurs in vertical and bare granite slopes, typical of the inselbergs of the Brazilian Atlantic Forest. Here, we present the first broad phylogenetic analysis focused on Stigmatodon, sampling a total of 83 terminals, including 16 of the 20 species of the genus and the morphologically similar species of Vriesea. We conducted a phylogenetic analysis using two plastid markers (matK and rps16-trnK) and the nuclear gene PHYC to infer phylogenetic relationships and reconstruct ancestral states for ecological and morphological characters. Our results suggest the monophyly of Stigmatodon as originally circumscribed is only possible with the inclusion of morphologically and ecologically similar Vriesea species. In addition, the morphological and anatomical traits led us to propose a new circumscription for the genus, combining eight species of Vriesea to Stigmatodon as S. andaraiensis, S. freicanecanus, S. lancifolius, S. limae, S. oliganthus, S. pseudoliganthus, S. vellozicolus, and S. zonatus. The stomata positioned above the ordinary epidermal cells, the adaxial water-storage parenchyma with axially elongated cells, the stamens positioned in two groups of three on each side of the corolla, and the tubo-laciniate stigma are exclusive to Stigmatodon in its new circumscription. These new morphological and phylogenetic results constitute a relevant contribution to the taxonomy and evolution of Bromeliaceae, one of the most diverse and ecologically important families of flowering plants of the Neotropics. [ABSTRACT FROM AUTHOR]