Paul E. Berry

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.

ANCIENT VICARIANCE OR RECENT LONG-DISTANCE DISPERSAL? INFERENCES ABOUT PHYLOGENY AND SOUTH AMERICAN-AFRICAN DISJUNCTIONS IN RAPATEACEAE AND BROMELIACEAE BASED ON ndhF SEQUENCE DATA

Rapateaceae and Bromeliaceae each have a center of diversity in South America and a single species native to a sandstone area in west Africa that abutted the Guayana Shield in northern South America before the Atlantic rifted. They thus provide ideal material for examining the potential role of vicariance versus long‐distance dispersal in creating amphiatlantic disjunctions. Analyses based on ndhF sequence variation indicate that Rapateaceae and Bromeliaceae are each monophyletic and underwent crown radiation around 41 and 23 Ma, respectively. Both exhibit clocklike sequence evolution, with bromeliads evolving roughly one‐third more slowly than rapateads. Among rapateads, the divergence of west African Maschalocephalus dinklagei from its closest South American relatives implies that Maschalocephalus resulted via long‐distance dispersal 7 Ma, not ancient continental drift; only its sandstone habitat is vicariant. Rapateads arose first at low elevations in the Guayana Shield; the earliest divergent genera are widespread along riverine corridors there and, to a lesser extent, in Amazonia and the Brazilian Shield. Speciation at small spatial scales accelerated 15 Ma with the invasion of high‐elevation, insular habitats atop tepuis. Among bromeliads, Pitcairnia feliciana diverges little from its congeners and appears to be the product of long‐distance dispersal ca. 12 Ma. Brocchinia/Ayensua and then Lindmania are sister to all other bromeliads, indicating that the Guayana Shield was also the cradle of the bromeliads. Three lineages form an unresolved trichotomy representing all other bromeliads: (1) Till andsioideae, (2) Hechtia, and (3) a large clade including remaining genera of Pitcairnioideae and all Bromelioideae. The last includes a clade of pitcairnioid genera endemic to the Guayana and Brazilian Shields; a xeric group (Abromeitiella/Deuterocohnia/Dyckia/Encholirium/Fosterella) from southern South America and the southern Andes, sister to Pitcairnia; and Andean Puya, sister to Bromelioideae, with many of the latter native to the Brazilian Shield. Both Rapateaceae and Bromeliaceae appear to have arisen at low elevations in the Guayana Shield, experienced accelerated speciation after invading dissected mountainous terrain, and undergone long‐distance dispersal to west Africa recently. Bromeliad acquisition of key adaptations to drought (e.g., CAM photosynthesis, tank habit, tillandsioid leaf trichomes) 17 Ma appears to have coincided with and help cause the centripetal invasion of drier, more seasonal regions beyond the Guayana Shield, resulting in a wider familial range and dominance of the epiphytic adaptive zone. Geology, past and present climate, and proximity to South America help account for both families occurring in nearly the same area of Africa. We present a new classification for Rapateaceae, including a new tribe Stegolepideae, a new subfamily Monotremoideae, and revisions to tribe Saxofridericieae and subfamily Rapateoideae.

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 Websters 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.

The Use of Chloroplast DNA to Assess Biogeography and Evolution of Morphology, Breeding Systems, and Flavonoids in Fuchsia Sect, Skinnera (Onagraceae)

Fuchsia sect. Skinnera, the only Old World group in the genus, comprises three species in New Zealand and one in Tahiti. These species include a tree, a large shrub, a climbing-scandent shrub, and a creeping, barely woody plant. The section is extremely distinct from the New World species of Fuchsia, and several sharply contrasting models depicting the evolutionary history of these species and the character state changes associated with habit, breeding systems, and chemistry have been proposed. A chloroplast DNA restriction site analysis of sect Skinnera and two outgroup sections was performed, generating a single tree depicting maternal relationships. This tree is congruent with one previously proposed model and demonstrates that the rare F. procumbens of New Zealand is the sister group to all other species in the section, while F. cyrtandroides of Tahiti is the sister taxon of the two remaining New Zealand species. Based on the chloroplast DNA analysis, a critical reevaluation was made of character state changes in the section relating to morphology, breeding systems, and flavonoid compounds. Phylogenetic analysis of plants using chloroplast DNA (cpDNA) is increasingly providing detailed and often unexpected evidence of evolutionary relationships at many taxonomic levels (Jansen and Palmer 1987a, 1988; Palmer 1986; Palmer and Zamir 1982; Palmer et al. 1983, 1985, 1988; Rieseberg et al. 1988; Smith and Sytsma 1990; Soltis et al. 1988; Sytsma 1990; Sytsma and Gottlieb 1986a, 1986b; Sytsma and Schaal 1985; Sytsma and Smith 1988; Sytsma et al. 1990). A major strength of cpDNA restriction fragment analysis is that it provides numerous, independent molecular characters that can often rigorously define monophyletic lineages. The utility of cpDNA, as well as other molecular markers, in phylogenetic studies can involve two separate steps. The first consists of defining monophyletic lineages, refining estimates of historical genealogies, and changing taxonomic groupings as needed; that is, addressing questions about phylogenetic relationships. The second step involves the application of the resulting cladogram or phylogeny to questions such as the evolution of morphology, breeding systems, and biogeography; that is, addressing questions about character evolution (where, when, and how the character states arose). Through this secondary application, molecular phylogenetics is having a considerable impact on many aspects of systematics, evolution, genetics, and ecology. This two-step process is especially crucial and informative when dealing with groups of species that show tremendous divergence and radiation in morphology, chemicals, and ecology (Sytsma 1990). Analysis of non-molecular characters in such groups can often be phylogenetically uninformative or even misleading because of the operation of strong selection and resulting homoplasy, difficulty in ordering or even polarizing character states, the high number of autapomorphies, and the lack of well defined synapomorphies. An exemplary model of a lineage that has undergone extraordinary radiation but is difficult to interpret in an evolutionary sense is Fuchsia sect. Skinnera. This section has been the focus of several competing hypotheses concerning the evolution and relationships of component taxa and the nature of changes in habit, morphology, floral biology, flavonoids, and distribution. The genus Fuchsia, distinctive in the Onagraceae by its fleshy fruits, corolloid calyx, and unspecialized features in floral and vegetative

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.

A worldwide molecular phylogeny and classification of the leafy spurges, Euphorbia subgenus Esula (Euphorbiaceae)

The leafy spurges, Euphorbia subg. Esula, make up one of four main lineages in Euphorbia. The subgenus comprises about 480 species, most of which are annual or perennial herbs, but with a small number of dendroid shrubs and nearly leafless, pencil-stemmed succulents as well. The subgenus constitutes the primary northern temperate radiation in Euphorbia. While the subgenus is most diverse from central Asia to the Mediterranean region, members of the group also occur in Africa, in the Indo-Pacific region, and in the New World. We have assembled the largest worldwide sampling of the group to date (273 spp.), representing most of the taxonomic and geographic breadth of the subgenus. We performed phylogenetic analyses of sequence data from the nuclear ribosomal ITS and plastid ndhF regions. Our individual and combined analyses produced well-resolved phylogenies that confirm many of the previously recognized clades and also establish a number of novel groupings and place- ments of previously enigmatic species. Euphorbia subg. Esula has a clear Eurasian center of diversity, and we provide evidence for four independent arrivals to the New World and three separate colonizations of tropical and southern Africa. One of the latter groups further extends to Madagascar and New Zealand, and to more isolated islands such as Reunion and Samoa. Our results confirm that the dendroid shrub and stem-succulent growth forms are derived conditions in E. subg. Esula. Stem- succulents arose twice in the subgenus and dendroid shrubs three times. Based on the molecular phylogeny, we propose a new classification for E. subg. Esula that recognizes 21 sections (four of them newly described and two elevated from subsectional rank), and we place over 95% of the accepted species in the subgenus into this new classification.

Molecular Phylogenetics and Biogeography of the Caribbean-Centered Croton Subgenus Moacroton (Euphorbiaceae s.s.)

Initial molecular phylogenetic studies established the monophylly of the large genus Croton (Euphorbiaceae s.s.) and suggested that the group originated in the New World. A denser and more targeted sampling of Croton species points to a South American origin for the genus. The nuclear and chloroplast genomes indicate a different rooting for the phylogeny of Croton. Although we favor the rooting indicated by the chloroplast data our conclusions are also consistent with the topology inferred from the nuclear data. The satellite genera Cubacroton and Moacroton are embedded within Croton. These two genera are synonimized into Croton and a new subgenus, Croton subgenus Moacroton, is circumscribed to include them and their allied Croton species. Croton subgenus Moacroton is morphologically characterized by a primarily lepidote indumentum, bifid or simple styles, and pistillate flowers with sepals that are connate at the base. This newly circumscribed subgenus is found from North America to South America, and in contrast to the majority of Croton species most of its members are found in mesic habitats. The group is most diverse in the greater Caribbean basin. A molecular clock was calibrated to the phylogeny using the available Euphorbiaceae fossils. The timing and pattern of diversification of Croton is consistent with both the GAARlandia and Laurasian migration hypotheses. A single species, Croton poecilanthus from Puerto Rico, is placed incongruently by its nuclear and chloroplast genomes. The possibility of this species being of hybrid origin is discussed.ResumenEstudios moleculares preliminares establecieron que el género grande Croton (Euphorbiaceae s.s.) es monofilético y sugirieron que el grupo origino en el Nuevo Mundo. Un muestreo mas denso y especifico de especies de Croton apunta a un origen Suraméricano para el género. Los genomas nucleares y del cloroplasto indican una diferente raíz para la filogenia de Croton. Aunque favoramos la raíz indicada por los datos del cloroplasto nuestras conclusiones también son consistentes con la topología deducida por los datos nucleares. Los géneros satélite Cubacroton y Moacroton están encajados dentro de Croton. Estos dos géneros son synonimizados dentro de Croton y un nuevo subgénero, Croton subgénero Moacroton, es circunscrito para incluirlos y las especies aliadas de Croton. Croton subgénero Moacroton esta caracterizada morfológicamente por un indumento mayormente lepidoto, estilos bifidos o simples, y flores pistiladas con sépalos unidos en la base. Este nuevamente circunscrito subgénero esta distribuido desde Norteamérica hasta Suramérica, y en contraste con la mayoría de las especies de Croton la mayoría de sus especies se encuentran en habitats húmedos. El grupo es mas diverso en la zona del Caribe. Un reloj molecular fue calibrado a la filogenia utilizando los fósiles de Euphorbiaceae disponibles. La sincronización y patrón de la diversificación de Croton son consistentes con las hipótesis de GAARlandia y la migración Laurasiana. Una especie, Croton poecilanthus de Puerto Rico, es puesto incongruentemente por sus genomas nucleares y del cloroplasto. La posibilidad de que esta especie tiene un origen hibrido es discutido.

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

UNLABELLED 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.

Phylogenetics, morphological evolution, and classification of Euphorbia subgenus Euphorbia

Euphorbia subg. Euphorbia is the largest and most diverse of four recently recognized subgenera within Euphorbia and is distributed across the tropics and subtropics. Relationships within this group have been difficult to discern due mainly to homoplasious morphological characters and inadequate taxon sampling in previous phylogenetic studies. Here we present a phylogenetic analysis of E. subg. Euphorbia, using one nuclear and two plastid regions, for the most complete sampling of molecular sequence data to date. We assign 661 species to the subgenus and show that it is comprised of four highly supported clades, including a single New World clade and multiple independent lineages on Madagascar. Using this phylogenetic framework we discuss patterns of homoplasy in morphological evolution and general patterns of biogeography. Finally, we present a new sectional classification of E. subg. Euphorbia comprising 21 sections, nine of them newly described here.

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.