The angiosperm order Malpighiales includes ∼16,000 species and constitutes up to 40% of the understory tree diversity in tropical rain forests. Despite remarkable progress in angiosperm systematics during the last 20 y, relationships within Malpighiales remain poorly resolved, possibly owing to its rapid rise during the mid-Cretaceous. Using phylogenomic approaches, including analyses of 82 plastid genes from 58 species, we identified 12 additional clades in Malpighiales and substantially increased resolution along the backbone. This greatly improved phylogeny revealed a dynamic history of shifts in net diversification rates across Malpighiales, with bursts of diversification noted in the Barbados cherries (Malpighiaceae), cocas (Erythroxylaceae), and passion flowers (Passifloraceae). We found that commonly used a priori approaches for partitioning concatenated data in maximum likelihood analyses, by gene or by codon position, performed poorly relative to the use of partitions identified a posteriori using a Bayesian mixture model. We also found better branch support in trees inferred from a taxon-rich, data-sparse matrix, which deeply sampled only the phylogenetically critical placeholders, than in trees inferred from a taxon-sparse matrix with little missing data. Although this matrix has more missing data, our a posteriori partitioning strategy reduced the possibility of producing multiple distinct but equally optimal topologies and increased phylogenetic decisiveness, compared with the strategy of partitioning by gene. These approaches are likely to help improve phylogenetic resolution in other poorly resolved major clades of angiosperms and to be more broadly useful in studies across the Tree of Life. M alpighiales are one of the most surprising clades discovered in broad molecular phylogenetic studies of the flowering plants (1-3). The order contains ∼16,000 species and 42 families (2, 3) that exhibit remarkable morphological and ecological diversity. A few examples include cactus-like succulents (Euphorbiaceae), epiphytes (Clusiaceae), holoparasites (Rafflesiaceae), submerged aquatics (Podostemaceae), and windpollinated trees (temperate Salicaceae). The order is ecologically important: species in Malpighiales constitute up to 40% of the understory tree diversity in tropical rain forests worldwide (4). They also include many economically important species, such as Barbados nut (Jatropha curcas L., Euphorbiaceae), cassava (Manihot esculenta Crantz, Euphorbiaceae), castor bean (Ricinus communis L., Euphorbiaceae), coca (Erythroxylum coca Lam., Erythroxylaceae), flax (Linum usitatissimum L., Linaceae), the poplars (Populus spp., Salicaceae), and the rubber tree (Hevea brasiliensis Müll. Arg., Euphorbiaceae). Partially for this reason, genomic resources for Malpighiales are growing at a rapid pace and include whole-genome sequencing projects completed or near completion for Barbados nut (5), cassava, castor bean (6), flax, and poplar (7). Thus, a resolved phylogeny of Malpighiales is critical not only for evol...

Recent debates on the number of plant species in the vast lowland rain forests of the Amazon have been based largely on model estimates, neglecting published checklists based on verified voucher data. Here we collate taxonomically verified checklists to present a list of seed plant species from lowland Amazon rain forests. Our list comprises 14,003 species, of which 6,727 are trees. These figures are similar to estimates derived from nonparametric ecological models, but they contrast strongly with predictions of much higher tree diversity derived from parametric models. Based on the known proportion of tree species in neotropical lowland rain forest communities as measured in complete plot censuses, and on overall estimates of seed plant diversity in Brazil and in the neotropics in general, it is more likely that tree diversity in the Amazon is closer to the lower estimates derived from nonparametric models. Much remains unknown about Amazonian plant diversity, but this taxonomically verified dataset provides a valid starting point for macroecological and evolutionary studies aimed at understanding the origin, evolution, and ecology of the exceptional biodiversity of Amazonian forests.Amazonia | floristics | rain forests | seed plants | species diversity

The Brazilian Atlantic Forest is considered one of the world's most important sites for biodiversity conservation, and within this biome there are regions with diVering levels of species richness, species composition, and endemism. The present study was undertaken in southern Bahia, Brazil, and employed a standardized sampling method to compare the density of arboreal species in this region with other areas throughout the world known for their high tree species density. A total of 144 tree species with DBH > 4.8 cm were sampled within a 0.1 ha plot of old-growth forest (OGF), and these data were then compared with 22 other world sites that had been sampled using the same methodology and likewise demonstrated high densities of arboreal species. Only one site of ombrophilous forest in Colombia demonstrated a higher tree species density (148 spp. in 0.1 ha) than was encountered in southern Bahia. Other areas of Brazil, including other Atlantic Forest sites, showed signiWcantly inferior tree species densities. These results indicate that this region of southern Bahia has one of the greatest numbers of tree species in Brazil and in the world. These results, associated with the high levels of endemism there, indicate the high biological importance of this region. It is therefore fundamental

Foi realizado um levantamento florístico de três remanescentes de floresta montana localizados na Mata Atlântica do sul da Bahia. Durante os anos de 2004 a 2008 foram feitas coletas periódicas de material botânico, principalmente ao longo de trilhas no interior dos fragmentos das áreas: Reserva Serra da Pedra Lascada - SPL, Reserva Serra das Lontras - SLO e Reserva Particular do Patrimônio Natural Serra Bonita - SBO. A riqueza florística em cada área foi comparada entre si e com outras áreas de Mata Atlântica na Bahia e no Sudeste do Brasil. Foi registrado um total de 1.129 espécies em 467 gêneros e 124 famílias. O hábito arbóreo representou 46,9% das espécies, seguido de herbáceas (20,1%), epífitas (19,5%) e trepadeiras (13,5%). As famílias Araceae, Asteraceae, Bromeliaceae, Fabaceae, Lauraceae, Melastomataceae, Myrtaceae, Orchidaceae, Piperaceae, Poaceae, Rubiaceae e Solanaceae apresentaram a maior riqueza florística nas três áreas em conjunto. O gênero Psychotria (Rubiaceae) apresentou o maior número de espécies em todas as áreas (21 spp.), destacando-se também Miconia (20 spp.), Solanum (20 spp.), Piper (19 spp.), Ocotea (16 spp.), Leandra (16 spp.), Peperomia (15 spp.) e Myrcia (14 spp.). Os resultados confirmam a elevada riqueza de angiospermas no sul da Bahia e evidenciam, pela primeira vez, a ocorrência de espécies características de regiões montanhosas da Mata Atlântica do Sudeste do Brasil nessa região.

Whole-genome duplications (WGDs) are widespread and prevalent in vascular plants and frequently coincide with major episodes of global and climatic upheaval, including the mass extinction at the Cretaceous-Tertiary boundary (c. 65 Ma) and during more recent periods of global aridification in the Miocene (c. 10-5 Ma). Here, we explore WGDs in the diverse flowering plant clade Malpighiales. Using transcriptomes and complete genomes from 42 species, we applied a multipronged phylogenomic pipeline to identify, locate, and determine the age of WGDs in Malpighiales using three means of inference: distributions of synonymous substitutions per synonymous site (K ) among paralogs, phylogenomic (gene tree) reconciliation, and a likelihood-based gene-count method. We conservatively identify 22 ancient WGDs, widely distributed across Malpighiales subclades. Importantly, these events are clustered around the Eocene-Paleocene transition (c. 54 Ma), during which time the planet was warmer and wetter than any period in the Cenozoic. These results establish that the Eocene Climatic Optimum likely represents a previously unrecognized period of prolific WGDs in plants, and lends further support to the hypothesis that polyploidization promotes adaptation and enhances plant survival during episodes of global change, especially for tropical organisms like Malpighiales, which have tight thermal tolerances.

Knowledge of the geographic distribution of plants is essential to underpin the understanding of global biodiversity patterns. Vascular epiphytes are important components of diversity and functionality of Neotropical forests but, unlike their terrestrial counterparts, they are under-represented in large-scale diversity and biogeographic analyses. This is the case for the Atlantic Forest - one of the most diverse and threatened biomes worldwide. We provide the first comprehensive species list of Atlantic Forest vascular epiphytes; their endemism patterns and threatened species occurrence have also been analyzed. A list with 2,256 species of (hemi-)epiphytes - distributed in 240 genera and 33 families - is presented based on the updated Brazilian Flora Checklist. This represents more than 15% of the total vascular plant richness in the Atlantic Forest. Moreover, 256 species are included on the Brazilian Red List. More than 93% of the overall richness is concentrated in ten families, with 73% represented by Orchidaceae and Bromeliaceae species alone. A total of 78% of epiphytic species are endemic to the Atlantic Forest, in contrast to overall vascular plant endemism in this biome estimated at 57%. Among the non-endemics, 13% of epiphytic species also occur either in the Amazon or in the Cerrado - the other two largest biomes of Brazil – and only 8% are found in two or more Brazilian biomes. This pattern of endemism, in addition to available dated phylogenies of some genera, indicate the dominance of recent radiations of epiphytic groups in the Atlantic Forest, showing that the majority of divergences dating from the Pliocene onwards are similar to those that were recently reported for other Neotropical plants.

No abstract

-(Floristic composition and structure of the arboreal component of a transitional area of Atlantic forest in southern Bahia, Brazil). The purpose of this study was to attempt to detect a floristic transition in forest along an altitudinal gradient on a mountain side in southern Bahia, Brazil. The study site is located at the east-west transition from tropical moist to semideciduous forests. A belt transect of one hectare (10 × 1000 m) was established running up the slope (from ca. 350 m to 750 m elevation). All included trees and lianas ≥ 5 cm in diameter at breast height were numbered, collected, and measured. Density, dominance, frequency, and importance values (IV) were calculated for each species. We encountered 1400 individuals and 264 species of woody plants in 56 families. Cariniana legalis (Mart.) Kuntze had the highest IV, based on the dominance of a small number of trees. Discocarpus pedicellatus Fiaschi & Cordeiro and Ampelocera glabra Kuhlm. were the most frequent trees, with 90 and 86 individuals respectively. Ninety-six species were represented by a single individual. The Fabaceae and Myrtaceae were the most diverse families with 37 and 31 species respectively. Cluster analysis and correspondence analysis (DCA) revealed that the composition of the forest along the uppermost 30 percent of the transect was distinct from the rest. The lower and upper forests can be considered respectively as semideciduous and moist forests. Although there are some well-marked floristic differences between these forests, both clearly belong to the southern Bahian sector of the Atlantic coastal forests.Key words -altitudinal gradient, Atlantic coastal forest, Bahia, tropical semi-deciduous forest RESUMO -(Composição florística e estrutura do componente arbóreo de uma área transicional de Floresta Atlântica no sul da Bahia, Brasil). O objetivo deste estudo foi averiguar a existência de uma possível transição florística ao longo de um gradiente altitudinal numa floresta serrana do sul da Bahia, Brasil. A área amostrada situa-se em uma zona de transição (leste-oeste) entre florestas ombrófilas e estacionais. Um transecto linear abrangendo um hectare (10 × 1.000 m) foi situado na encosta da serra (de ca. 350 a 750 m.s.m.). Todas as árvores e lianas com DAP ≥ 5 foram numeradas, coletadas e medidas. Foram calculados valores de densidade, dominância, frequência e valor de importância (VI) para cada espécie amostrada. Foram amostrados 1.400 indivíduos agrupados em 264 espécies e 56 famílias de angiospermas. Cariniana legalis (Mart.) Kuntze teve o maior VI, devido à elevada dominância de poucos indivíduos. Discocarpus pedicellatus Fiaschi & Cordeiro e Ampelocera glabra Kuhlm. foram as espécies mais frequentes, com 90 e 86 indivíduos respectivamente. Noventa e seis espécies foram representadas por apenas um indivíduo. As famílias mais diversas foram Fabaceae e Myrtaceae com 37 e 31 espécies respectivamente. Análises de agrupamento e correspondência (DCA) revelaram que a composição florística da floresta situada na porção...