Phylogeny, Adaptive Radiation, and Historical Biogeography of Bromeliaceae Inferred from ndhF Sequence Data

Cladistic analysis of ndhF sequences identifies eight major bromeliad clades arranged in ladderlike fashion. The traditional subfamilies Tillandsioideae and Bromelioideae are monophyletic, but Pitcairnioideae are paraphyletic, requiring the description of four new subfamilies, recircumscription of Pitcairnioideae and Navioideae, the sinking of Ayensua, and description of the new genus Sequencia. Brocchinioideae are basalmost, followed by Lindmanioideae, both restricted to the Guayana Shield. Next is an unresolved trichotomy involving Hechtioideae from Central America, Tillandsioideae, and the remaining bromeliads in subfamilies Navioideae, Pitcairnioideae, Puyoideae, and Bromelioideae. Bromeliads arose as C3 terrestrial plants on moist infertile sites in the Guayana Shield roughly 70 Mya, spread centripetally in the New World, and reached tropical West Africa (Pitcairnia feliciana) via long-distance dispersal about 10 Mya. Modern lineages began to diverge from each other 19 Mya and invaded drier areas in Central and South America beginning 15 Mya, coincident with a major adaptive radiation involving the repeated evolution of epiphytism, CAM photosynthesis, impounding leaves, several features of leaf/trichome anatomy, and accelerated diversification at the generic level. This ‘‘bromeliad revolution’’ occurred after the uplift of the northern Andes and shift of the Amazon to its present course. Epiphytism may have accelerated speciation by increasing ability to colonize along the length of the Andes, while favoring the occupation of a cloud-forest landscape frequently dissected by drier valleys. Avian pollination (mainly by hummingbirds) evolved at least twice ca. 13 Mya; entomophily was ancestral. Hechtia, Abromeitiella–Deuterocohnia–Dyckia–Encholirium, and Puya exhibit a remarkable pattern of concerted convergence in six anatomical and physiological leaf traits adapted to drought

Giant lobelias exemplify convergent evolution

Giant lobeliads on tropical mountains in East Africa and Hawaii have highly unusual, giant-rosette growth forms that appear to be convergent on each other and on those of several independently evolved groups of Asteraceae and other families. A recent phylogenetic analysis by Antonelli, based on sequencing the widest selection of lobeliads to date, raises doubts about this paradigmatic example of convergent evolution. Here I address the kinds of evidence needed to test for convergent evolution and argue that the analysis by Antonelli fails on four points. Antonelli's analysis makes several important contributions to our understanding of lobeliad evolution and geographic spread, but his claim regarding convergence appears to be invalid. Giant lobeliads in Hawaii and Africa represent paradigmatic examples of convergent evolution

Phylogeny, Adaptive Radiation, and Historical Biogeography in Bromeliaceae: Insights from an Eight-Locus Plastid Phylogeny

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

Phylogeny, Genome Size, and Chromosome Evolution of Asparagales

Asparagales are a diverse monophyletic order that has numerous species (ca. 50% of monocots) including important crop plants such as Allium, Asparagus, and Vanilla, and a host of ornamentals such as irises, hyacinths, and orchids. Historically, Asparagales have been of interest partly because of their fascinating chromosomal evolution. We examine the evolutionary dynamics of Asparagales genomes in an updated phylogenetic framework that combines analyses of seven gene regions (atp1, atpB, matK, ndhF, rbcL, trnL intron, and trnL-F intergenic spacer) for 79 taxa of Asparagales and outgroups. Asparagales genomes are evolutionarily labile for many characters, including chromosome number and genome size. The history and causes of variation in chromosome number and genome size remain unclear, primarily because of the lack of data in small clades in the phylogenetic tree and the lack of comparative genetic maps, apart from Allium and Asparagus. Genomic tools such as bacterial artificial chromosome (BAC) libraries should be developed, as both molecular cytogenetic markers and a source of nuclear genes that can be widely used by evolutionary biologists and plant breeders alike to decipher mechanisms of chromosomal evolution

Phylogenetic Relationships of Monocots Based on the Highly Informative Plastid Gene ndhF

We used ndhF sequence variation to reconstruct relationships across 282 taxa representing 78 monocot families and all 12 orders. The resulting tree is highly resolved and places commelinids sister to Asparagales, with both sister to Liliales—Pandanales in the strict consensus; Pandanales are sister to Dioscoreales in the bootstrap majority-rule tree, just above Petrosaviales. Acorales are sister to all other monocots, with Alismatales sister to all but Acorales. Relationships among the four major clades of commelinids remain unresolved. Relationships within orders are consistent with those based on rbcL, alone or in combination with atpB and 18S nrDNA, and generally better supported: ndhF contributes more than twice as many informative characters as rbcL, and nearly as many as rbcL, atpB, and 18S nrDNA combined. Based on functional arguments, we hypothesized that net venation and fleshy fruits should both evolve—and thus undergo concerted convergence—in shaded habitats, and revert to parallel venation and dry, passively dispersed fruits in open, sunny habitats. Our data show that net venation arose at least 26 times and disappeared 9 times, whereas fleshy fruits arose 22 times and disappeared 11 times. Both traits arose together at least 15 times and disappeared together 5 times. They thus show a highly significant pattern of concerted convergence (P \u3c 10-9) and are each even more strongly associated with shaded habitats (P \u3c 10-10 to 10-23); net venation is also associated, as predicted, with broad-leaved aquatic plants. Exceptions to this pattern illustrate the importance of other selective constraints and phylogenetic inertia

Multigene Analyses of Monocot Relationships

We present an analysis of supra-familial relationships of monocots based on a combined matrix of nuclear I8S and partial 26S rDNA, plastid atpB, matK, ndhF, and rbcL, and mitochondrial atp1 DNA sequences. Results are highly congruent with previous analyses and provide higher bootstrap support for nearly all relationships than in previously published analyses. Important changes to the results of previous work are a well-supported position of Petrosaviaceae as sister to all monocots above Acorales and Alismatales and much higher support for the commelinid clade. For the first time, the spine of the monocot tree has some bootstrap support, although support for paraphyly of liliids is still only low to moderate (79-82%). Dioscoreales and Pandanales are sister taxa (moderately supported, 87- 92%), and Asparagales are weakly supported (79%) as sister to the commelinids. Analysis of just the four plastid genes reveals that addition of data from the other two genomes contributes to generally better support for most clades, particularly along the spine. A new collection reveals that previous material of Petermannia was misidentified, and now Petermanniaceae should no longer be considered a synonym of Colchicaceae. Arachnitis (Corsiaceae) falls into Liliales, but its exact position is not well supported. Sciaphila (Triuridaceae) falls with Pandanales. Trithuria (Hydatellaceae) falls in Poales near Eriocaulaceae, Mayacaceae, and Xyridaceae, but until a complete set of genes are produced for this taxon, its placement will remain problematic. Within the commelinid clade, Dasypogonaceae are sister to Poales and Arecales sister to the rest of the commelinids, but these relationships are only weakly supported

A process-based model of conifer forest structure and function with special emphasis on leaf lifespan

We describe the University of Sheffield Conifer Model (USCM), a process-based approach for simulating conifer forest carbon, nitrogen, and water fluxes by up-scaling widely applicable relationships between leaf lifespan and function. The USCM is designed to predict and analyze the biogeochemistry and biophysics of conifer forests that dominated the ice-free high-latitude regions under the high pCO2 “greenhouse” world 290–50 Myr ago. It will be of use in future research investigating controls on the contrasting distribution of ancient evergreen and deciduous forests between hemispheres, and their differential feedbacks on polar climate through the exchange of energy and materials with the atmosphere. Emphasis is placed on leaf lifespan because this trait can be determined from the anatomical characteristics of fossil conifer woods and influences a range of ecosystem processes. Extensive testing of simulated net primary production and partitioning, leaf area index, evapotranspiration, nitrogen uptake, and land surface energy partitioning showed close agreement with observations from sites across a wide climatic gradient. This indicates the generic utility of our model, and adequate representation of the key processes involved in forest function using only information on leaf lifespan, climate, and soils