Force of habit: shrubs, trees and contingent evolution of wood anatomical diversity using Croton (Euphorbiaceae) as a model system.

Background and Aims: Wood is a major innovation of land plants, and is usually a central component of the body plan for two major plant habits: shrubs and trees. Wood anatomical syndromes vary between shrubs and trees, but no prior work has explicitly evaluated the contingent evolution of wood anatomical diversity in the context of these plant habits. Methods: Phylogenetic comparative methods were used to test for contingent evolution of habit, habitat and wood anatomy in the mega-diverse genus Croton (Euphorbiaceae), across the largest and most complete molecular phylogeny of the genus to date. Key Results: Plant habit and habitat are highly correlated, but most wood anatomical features correlate more strongly with habit. The ancestral Croton was reconstructed as a tree, the wood of which is inferred to have absent or indistinct growth rings, confluent-like axial parenchyma, procumbent ray cells and disjunctive ray parenchyma cell walls. The taxa sampled showed multiple independent origins of the shrub habit in Croton , and this habit shift is contingent on several wood anatomical features (e.g. similar vessel-ray pits, thick fibre walls, perforated ray cells). The only wood anatomical trait correlated with habitat and not habit was the presence of helical thickenings in the vessel elements of mesic Croton . Conclusions: Plant functional traits, individually or in suites, are responses to multiple and often confounding contexts in evolution. By establishing an explicit contingent evolutionary framework, the interplay between habit, habitat and wood anatomical diversity was dissected in the genus Croton . Both habit and habitat influence the evolution of wood anatomical characters, and conversely, the wood anatomy of lineages can affect shifts in plant habit and habitat. This study hypothesizes novel putatively functional trait associations in woody plant structure that could be further tested in a variety of other taxa.

Adaptive radiation, correlated and contingent evolution, and net species diversification in Bromeliaceae.

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.

Phylogenetics and the evolution of major structural characters in the giant genus Euphorbia L. (Euphorbiaceae).

Euphorbia is among the largest genera of angiosperms, with about 2000 species that are renowned for their remarkably diverse growth forms. To clarify phylogenetic relationships in the genus, we used maximum likelihood, bayesian, and parsimony analyses of DNA sequence data from 10 markers representing all three plant genomes, averaging more than 16kbp for each accession. Taxon sampling included 176 representatives from Euphorbioideae (including 161 of Euphorbia). Analyses of these data robustly resolve a backbone topology of four major, subgeneric clades--Esula, Rhizanthium, Euphorbia, and Chamaesyce--that are successively sister lineages. Ancestral state reconstructions of six reproductive and growth form characters indicate that the earliest Euphorbia species were likely woody, non-succulent plants with helically arranged leaves and 5-glanded cyathia in terminal inflorescences. The highly modified growth forms and reproductive features in Euphorbia have independent origins within the subgeneric clades. Examples of extreme parallelism in trait evolution include at least 14 origins of xeromorphic growth forms and at least 13 origins of seed caruncles. The evolution of growth form and inflorescence position are significantly correlated, and a pathway of evolutionary transitions is supported that has implications for the evolution of Euphorbia xerophytes of large stature. Such xerophytes total more than 400 species and are dominants of vegetation types throughout much of arid Africa and Madagascar.

Molecular phylogenetics and character evolution of the "sacaca" clade: novel relationships of Croton section Cleodora (Euphorbiaceae).

Phylogenetic relationships of Croton section Cleodora (Klotzsch) Baill. were evaluated using the nuclear ribosomal ITS and the chloroplast trnL-F and trnH-psbA regions. Our results show a strongly supported clade containing most previously recognized section Cleodora species, plus some other species morphologically similar to them. Two morphological synapomorphies that support section Cleodora as a clade include pistillate flowers in which the sepals overlap to some degree, and styles that are connate at the base to varying degrees. The evolution of vegetative and floral characters that have previously been relied on for taxonomic decisions within this group are evaluated in light of the phylogenetic hypotheses. Within section Cleodora there are two well-supported clades, which are proposed here as subsections (subsection Sphaerogyni and subsection Spruceani). The resulting phylogenetic hypothesis identifies the closest relatives of the medicinally important and essential oil-rich Croton cajucara Benth. as candidates for future screening in phytochemical and pharmacological studies.

Phylogenetics of the Chamaesyce clade (Euphorbia, Euphorbiaceae): reticulate evolution and long-distance dispersal in a prominent C4 lineage.

PREMISE OF THE STUDY: The Chamaesyce clade of Euphorbia is the largest lineage of C(4) plants among the eudicots, with 350 species including both narrow endemics and cosmopolitan weeds. We sampled this group worldwide to address questions about subclade relationships, the origin of C(4) photosynthesis, the evolution of weeds, and the role of hybridization and long-distance dispersal in the diversification of the group. • METHODS: Two nuclear (ITS and exon 9 of EMB2765) and three chloroplast markers (matK, rpl16, and trnL-F) were sequenced for 138 ingroup and six outgroup species. Exon 9 of EMB2765 was cloned in accessions with >1% superimposed peaks. • KEY RESULTS: The Chamaesyce clade is monophyletic and consists of three major subclades [1(2,3)]: (1) the Acuta clade, containing three North American species with C(3) photosynthesis and C(3)-C(4) intermediates; (2) the Peplis clade, mostly North American and entirely C(4); and (3) the Hypericifolia clade, all C(4), with both New World and Old World groups. Incongruence between chloroplast and ITS phylogenies and divergent cloned copies of EMB2765 exon 9 suggest extensive hybridization, especially in the Hawaiian Islands radiation. • CONCLUSIONS: The Chamaesyce clade originated in warm, arid areas of North America, where it evolved C(4) photosynthesis. From there, it diversified globally with extensive reticulate evolution and frequent long-distance dispersals. Although many species are weedy, there are numerous local adaptations to specific substrates and regional or island radiations, which have contributed to the great diversity of this group.

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.

Amazon tree dominance across forest strata.

The forests of Amazonia are among the most biodiverse plant communities on Earth. Given the immediate threats posed by climate and land-use change, an improved understanding of how this extraordinary biodiversity is spatially organized is urgently required to develop effective conservation strategies. Most Amazonian tree species are extremely rare but a few are common across the region. Indeed, just 227 'hyperdominant' species account for >50% of all individuals >10 cm diameter at 1.3 m in height. Yet, the degree to which the phenomenon of hyperdominance is sensitive to tree size, the extent to which the composition of dominant species changes with size class and how evolutionary history constrains tree hyperdominance, all remain unknown. Here, we use a large floristic dataset to show that, while hyperdominance is a universal phenomenon across forest strata, different species dominate the forest understory, midstory and canopy. We further find that, although species belonging to a range of phylogenetically dispersed lineages have become hyperdominant in small size classes, hyperdominants in large size classes are restricted to a few lineages. Our results demonstrate that it is essential to consider all forest strata to understand regional patterns of dominance and composition in Amazonia. More generally, through the lens of 654 hyperdominant species, we outline a tractable pathway for understanding the functioning of half of Amazonian forests across vertical strata and geographical locations.

Molecular phylogeny, divergence time estimates, and historical biogeography of Circaea (Onagraceae) in the Northern Hemisphere.

Circaea (Onagraceae) consists of eight species and six subspecies distributed in Eurasia and North America. The sister group of Circaea was recently shown to be Fuchsia, which comprises 107 species primarily distributed in montane Central and South America, including four species occurring in the South Pacific islands. Three plastid markers (petB-petD, rpl16, and trnL-F) and nrITS sequences from 13 of the 14 taxa of Circaea were sequenced and used to reconstruct the phylogenetic and biogeographic history of the genus. Parsimony and Bayesian analyses support that (1) Circaea is monophyletic; (2) the bilocular group is a weakly supported clade nested within the unilocular grade; (3) neither the C. alpina complex nor the C. canadensis complex is monophyletic; and (4) the western North American C. alpina subsp. pacifica diverged first in the genus. Divergence time estimates based on the Bayesian "relaxed" clock methods suggest that the earliest Circaea divergence occurred minimally at 16.17 mya (95% HPD: 7.69-24.53 mya). Biogeographic analyses using divergence-vicariance analysis (DIVA) and a likelihood method support the New World origin of Circaea. Three independent dispersal events between Eurasia and North America via the Bering land bridge were inferred within Circaea. Higher taxon diversity of Circaea in eastern Asia was probably caused by geologic and ecological changes during the late Tertiary in the Northern Hemisphere.

Repeated range expansion and niche shift in a volcanic hotspot archipelago: Radiation of C4 Hawaiian Euphorbia subgenus Chamaesyce (Euphorbiaceae).

Woody perennial plants on islands have repeatedly evolved from herbaceous mainland ancestors. Although the majority of species in Euphorbia subgenus Chamaesyce section Anisophyllum (Euphorbiaceae) are small and herbaceous, a clade of 16 woody species diversified on the Hawaiian Islands. They are found in a broad range of habitats, including the only known C4 plants adapted to wet forest understories. We investigate the history of island colonization and habitat shift in this group. We sampled 153 individuals in 15 of the 16 native species of Hawaiian Euphorbia on six major Hawaiian Islands, plus 11 New World close relatives, to elucidate the biogeographic movement of this lineage within the Hawaiian island chain. We used a concatenated chloroplast DNA data set of more than eight kilobases in aligned length and applied maximum likelihood and Bayesian inference for phylogenetic reconstruction. Age and phylogeographic patterns were co-estimated using BEAST. In addition, we used nuclear ribosomal ITS and the low-copy genes LEAFY and G3pdhC to investigate the reticulate relationships within this radiation. Hawaiian Euphorbia first arrived on Kaua`i or Ni`ihau ca. 5 million years ago and subsequently diverged into 16 named species with extensive reticulation. During this process Hawaiian Euphorbia dispersed from older to younger islands through open vegetation that is disturbance-prone. Species that occur under closed vegetation evolved in situ from open vegetation of the same island and are only found on the two oldest islands of Kaua`i and O`ahu. The biogeographic history of Hawaiian Euphorbia supports a progression rule with within-island shifts from open to closed vegetation.

A Nomenclator of Croton (Euphorbiaceae) in Madagascar, the Comoros Archipelago, and the Mascarene Islands.

All published names of Croton from Madagascar, the Comoros, and the Mascarenes are treated here. We indicate which names are currently accepted (123 native species and 1 introduced), which ones we consider to be heterotypic synonyms (188), which ones are doubtful (25), and which ones should be excluded (5). We newly designate lectotypes for 108 names, and epitypes for C. anisatus Baill., C. nobilis Baill., and C. submetallicus Baill. A total of 133 names are newly treated as synonyms. One new combination is made, Croton basaltorum (Leandri) P.E.Berry for C. antanosiensis var. basaltorum Leandri, and one new name is proposed, Croton toliarensis B.W.vanEe & Kainul. for C. tranomarensis var. rosmarinifolius Radcl.-Sm.

An integrated assessment of the vascular plant species of the Americas.

The cataloging of the vascular plants of the Americas has a centuries-long history, but it is only in recent decades that an overview of the entire flora has become possible. We present an integrated assessment of all known native species of vascular plants in the Americas. Twelve regional and national checklists, prepared over the past 25 years and including two large ongoing flora projects, were merged into a single list. Our publicly searchable checklist includes 124,993 species, 6227 genera, and 355 families, which correspond to 33% of the 383,671 vascular plant species known worldwide. In the past 25 years, the rate at which new species descriptions are added has averaged 744 annually for the Americas, and we can expect the total to reach about 150,000.

Evolutionary bursts in Euphorbia (Euphorbiaceae) are linked with photosynthetic pathway.

The mid-Cenozoic decline of atmospheric CO2 levels that promoted global climate change was critical to shaping contemporary arid ecosystems. Within angiosperms, two CO2 -concentrating mechanisms (CCMs)-crassulacean acid metabolism (CAM) and C4 -evolved from the C3 photosynthetic pathway, enabling more efficient whole-plant function in such environments. Many angiosperm clades with CCMs are thought to have diversified rapidly due to Miocene aridification, but links between this climate change, CCM evolution, and increased net diversification rates (r) remain to be further understood. Euphorbia (∼2000 species) includes a diversity of CAM-using stem succulents, plus a single species-rich C4 subclade. We used ancestral state reconstructions with a dated molecular phylogeny to reveal that CCMs independently evolved 17-22 times in Euphorbia, principally from the Miocene onwards. Analyses assessing among-lineage variation in r identified eight Euphorbia subclades with significantly increased r, six of which have a close temporal relationship with a lineage-corresponding CCM origin. Our trait-dependent diversification analysis indicated that r of Euphorbia CCM lineages is approximately threefold greater than C3 lineages. Overall, these results suggest that CCM evolution in Euphorbia was likely an adaptive strategy that enabled the occupation of increased arid niche space accompanying Miocene expansion of arid ecosystems. These opportunities evidently facilitated recent, replicated bursts of diversification in Euphorbia.

Are spurred cyathia a key innovation? Molecular systematics and trait evolution in the slipper spurges (Pedilanthus clade: Euphorbia, Euphorbiaceae).

The study of traits that play a key role in promoting diversification is central to evolutionary biology. Floral nectar spurs are among the few plant traits that correlate with an enhanced rate of diversification, supporting the claim that they are key innovations. Slight changes in spur morphology could confer some degree of premating isolation, explaining why clades with spurs tend to include more species than their spurless close relatives. We explored whether the cyathial nectar spur of the Pedilanthus clade (Euphorbia) may also function as a key innovation. We estimated the phylogeny of the Pedilanthus clade using one plastid (matK) and three nuclear regions (ITS and two G3pdh loci) and used our results and a Yule model of diversification to test the hypothesis that the cyathial spur correlates with an increased diversification rate. We found a lack of statistical support for the key innovation hypothesis unless specific assumptions regarding the phylogeny apply. However, the young age (hence small size) of the group may limit our ability to detect a significant increase in diversification rate. Additionally, our results confirm previous species designations, indicate higher homoplasy in cyathial than in vegetative features, and suggest a possible Central American origin of the group.

Phylogeny and biogeography of Croton alabamensis (Euphorbiaceae), a rare shrub from Texas and Alabama, using DNA sequence and AFLP data.

Croton alabamensis (Euphorbiaceae s.s.) is a rare plant species known from several populations in Texas and Alabama that have been assigned to var. texensis and var. alabamensis, respectively. We performed maximum parsimony, maximum likelihood, and Bayesian analyses of DNA sequences from the nuclear ribosomal internal transcribed spacer (ITS) and 5.8S regions and chloroplast trnL-trnF regions from collections of the two varieties of C. alabamensis and from outgroup taxa. C. alabamensis emerges alone on a long branch that is sister to Croton section Corylocroton and the Cuban endemic genus Moacroton. Molecular clock analysis estimates the split of C. alabamensis from its closest relatives in sect. Corylocroton at 41 million years ago, whereas the split of the two varieties of C. alabamensis occurred sometime in the Quaternary. Amplified fragment length polymorphism (AFLP) analyses were performed using two selective primer pairs on a larger sampling of accessions (22 from Texas, 17 from Alabama) to further discriminate phylogenetic structure and quantify genetic diversity. Using both neighbour joining and minimum evolution, the populations from the Cahaba and Black Warrior watersheds in Alabama form two well-separated groups, and in Texas, geographically distinct populations are recovered from Fort Hood, Balcones Canyonlands, and Pace Bend Park. Most of the molecular variance is accounted for by variance within populations. Approximately equal variance is found among populations within states and between states (varieties). Genetic distance between the Texas populations is significantly less than genetic distance between the Alabama populations. Both sequence and AFLP data support the same relationships between the varieties of C. alabamensis and their outgroup, while the AFLP data provide better resolution among the different geographical regions where C. alabamensis occurs. The conservation implications of these findings are discussed.

Molecular phylogenetics of the giant genus Croton and tribe Crotoneae (Euphorbiaceae sensu stricto) using ITS and TRNL-TRNF DNA sequence data.

Parsimony, likelihood, and Bayesian analyses of nuclear ITS and plastid trnL-F DNA sequence data are presented for the giant genus Croton (Euphorbiaceae s.s.) and related taxa. Sampling comprises 88 taxa, including 78 of the estimated 1223 species and 29 of the 40 sections previously recognized of Croton. It also includes the satellite genus Moacroton and genera formerly placed in tribe Crotoneae. Croton and all sampled segregate genera form a monophyletic group sister to Brasiliocroton, with the exception of Croton sect. Astraea, which is reinstated to the genus Astraea. A small clade including Moacroton, Croton alabamensis, and C. olivaceus is sister to all other Croton species sampled. The remaining Croton species fall into three major clades. One of these is entirely New World, corresponding to sections Cyclostigma, Cascarilla, and Velamea sensu Webster. The second is entirely Old World and is sister to a third, also entirely New World clade, which is composed of at least 13 of Webster's sections of Croton. This study establishes a phylogenetic framework for future studies in the hyper-diverse genus Croton, indicates a New World origin for the genus, and will soon be used to evaluate wood anatomical, cytological, and morphological data in the Crotoneae tribe.

Phylogenetic relationships and biogeography of Fuchsia (Onagraceae) based on noncoding nuclear and chloroplast DNA data.

To examine relationships and test previous sectional delimitations within Fuchsia, this study used parsimony and maximum likelihood analyses with nuclear ITS and chloroplast trnL-F and rpl16 sequence data for 37 taxa representing all sections of Fuchsia and four outgroup taxa. Results support previous sectional delimitations, except for F. verrucosa, which is related to a Central American clade rather than to section Fuchsia and is described here as a new section Verrucosa. The basal relationships within Fuchsia are poorly resolved, suggesting an initial rapid diversification of the genus. Among the species sampled, there is strong support for a single South Pacific lineage, a southern South American/southern Brazilian lineage, a tropical Andean lineage, and one or two Central American and Mexican lineages. There is no clear support for an austral origin of the genus, as previously proposed, which is more consistent with Fuchsia's sister group relationship with the boreal Circaea. An ultrametric molecular clock analysis (all minimal dates) places the split between Fuchsia and Circaea at 41 million years ago (mya), with the diversification of the modern-day lineages of Fuchsia beginning at 31 mya. The South Pacific Fuchsia lineage branches off around 30 mya, consistent with fossil records from Australia and New Zealand. The large Andean section Fuchsia began to diversify around 22 mya, preceded by the divergence of the Caribbean F. triphylla at 25 mya. The Brazilian members of section Quelusia separated from the southern Andean F. magellanica around 13 mya, and the ancestor of the Tahitian F. cyrtandroides split off from the New Zealand species of section Skinnera approximately 8 mya.