André M. Amorim

Phylogenomics and a posteriori data partitioning resolve the Cretaceous angiosperm radiation Malpighiales

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.

Angiospermas em remanescentes de floresta montana no sul da Bahia, Brasil

A floristic study of three areas of montane Atlantic forest in southern Bahia, Brazil, was carried out. From 2004 to 2008 regular botanical collections were made, principally along trails in the interior of the forest fragments at: the Reserva Serra da Pedra Lascada (SPL), the Reserva Serra das Lontras (SLO) and the Reserva Particular do Patrimonio Natural Serra Bonita (SBO). The species richness of each area was compared to that of the other two, and together to other areas of Atlantic coastal forest in Bahia and southeastern Brazil. For all three areas, a total of 1129 species in 467 genera and 124 families were found. Trees represented 46.9% of the species, followed by herbs (20.1%), epiphytes (19.5%), and vines and lianas (13.5%). The families Araceae, Asteraceae, Bromeliaceae, Fabaceae, Lauraceae, Melastomataceae, Myrtaceae, Orchidaceae, Piperaceae, Poaceae, Rubiaceae, and Solanaceae showed the highest species richness for the three areas together. The genus Psychotria (Rubiaceae) had the highest number of species for all three areas (21 spp.), followed by Miconia (20 spp.), Solanum (20 spp.), Piper (19 spp.), Ocotea (16 spp.), Leandra (16 spp.), Peperomia (15 spp.), and Myrcia (14 spp.). The results confirm the high species diversity of angiosperms in southern Bahia and demonstrate for the first time the presence of species characteristic of montane regions of southeastern Brazil in this region.

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.

Amazon plant diversity revealed by a taxonomically verified species list

Significance Large floristic datasets that purportedly represent the diversity and composition of the Amazon tree flora are being widely used to draw conclusions about the patterns and evolution of Amazon plant diversity, but these datasets are fundamentally flawed in both their methodology and the resulting content. We have assembled a comprehensive dataset of Amazonian seed plant species from published sources that includes falsifiable data based on voucher specimens identified by taxonomic specialists. This growing list should serve as a basis for addressing the long-standing debate on the number of plant species in the Amazon, as well as for downstream ecological and evolutionary analyses aimed at understanding the origin and function of the exceptional biodiversity of the vast Amazonian forests. 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.

A New Species of Physeterostemon (Melastomataceae) from Bahia, Brazil, with Notes on the Phylogeny of the Genus

Abstract Physeterostemon thomasii is described from the southern Bahian Atlantic forest of Brazil. It differs from the other two species of the genus by the paleaceous trichomes on young stems and petioles, and by the strongly bullate/foveolate leaves. A phylogenetic analysis with all three species, based on rbcL and nahF DNA sequence data, showed that Physeterostemon forms a monophyletic group, sister to Eriocnema fulva, and this clade is placed in a polytomy at the base of the tribe Miconieae sensu stricto. However, there is no resolution within Physeterostemon, thus the phylogenetic relationships of the three species cannot be established.

Physeterostemon (Melastomataceae) : a new genus and two new species from the Bahian Atlantic Forest, Brazil

A new genus, Physeterostemon, with two new species, P. fiaschii and P. jardimii, is described from southern Bahian Atlantic forest of Brazil. The genus can be distinguished from all other Melastomataceae by its 6-merous and diplostemonous flowers, toothed and persistent calyx, inferior ovary and dry, capsular fruits. The androecium consists of stamens that are slightly unequal in size with connectives that are unappendaged or minutely ventrally bituberculate and not prolonged below the thecae but dorsally and apically thickened; the anthers are oblong and rounded apically in ventral view, slightly projecting backwards over the connective in lateral view, but with a single ventral pore.

Epiphytic angiosperms in a mountain forest in southern Bahia, Brazil

The Atlantic Forest in southern Bahia State, Brazil, has high levels of diversity and vascular plant endemism. There have been few floristic surveys of the mountain forests there, however, especially those focusing on herbs and canopy plants, with studies of Atlantic Forest epiphytes having been limited to the southern and southeastern region of that country. The present study therefore surveyed the epiphytic angiosperms in the Serra das Lontras National Park (SLNP), the distribution of their species among genera and families, and their biogeographical patterns. Fieldwork was performed between February 2011 and March 2012. Collections were made along roads and trails and phorophytes were occasionally climbed and fallen trees and branches examined in order to sample canopy species. The study site demonstrated high epiphyte richness (256 spp.), one of the highest recorded in the Atlantic Forest. The richest families are Orchidaceae, Bromeliaceae, and Araceae, reaffirming the patterns reported in previous major reviews on epiphytes. The species exhibit high degrees of endemism (45%) to the Atlantic Forest, especially among the Bromeliaceae and Orchidaceae. One new occurrence to Brazil, four to the Atlantic Forest and 30 to Bahia state are registered. The SLNP shares more species with areas of southern and southeastern Brazil than with other northeastern states.

Five new species of Heteropterys (Malpighiaceae) from Central and South America

Five-new taxa ofHeteropterys H. B. K. subsect.Aptychia Nied. are described, illustrated, and mapped:H. andina from Peru;H. minutiflora from Costa Rica; andH. bullata, H. capixaba, andH. oberdanii, from the Atlantic coastal forest of Brazil. The affinities and diagnostic characters of each species are discussed.ResumenCinco taxa deHeteropterys H. B. K. subsect.Aptychia Nied. são descritas como novas, ilustradas e mapeadas:H. andina do Peru;H. minutiflora da Costa Rica; eH. bullata, H. capixaba eH. oberdanii, da Floresta Atlântica no Brasil. São apontadas as afinidades e os caracteres diagnósticos de cada espécie.

Angiosperms and the Linnean shortfall: three new species from three lineages of Melastomataceae at one spot at the Atlantic Forest

Three new species of Angiosperms have been found in four short collection trips to the same protected reserve—“Estação Ecológica Estadual de Wenceslau Guimarães”—and neighboring areas in the Atlantic Forest in the south of the Brazilian state of Bahia. These new species belong to three genera from three distinct lineages in the family Melastomataceae: Huberia, Meriania and Physeterostemon. The description of these species represent a good example of a Linnean shortfall, i.e., the absence of basic knowledge about the biodiversity in the area, as well as in tropical forests as a whole. The description of these probably endemic species per se is a signal that this area deserves more attention regarding research and policies, but its consequences go farther: this area has a relevant role as a phylogenetic (both genetic and morphological) stock, and thus is also valuable as a phylogenetic conservation priority.

A First Record of Freziera (Pentaphylacaceae) from the Brazilian Atlantic Forest, with the Description of a New Species

Abstract Freziera atlantica is described and illustrated. The species resembles F. grisebachii in terms of the size and shape of its leaves but differs especially by the serrate and villous margin of the leaf blade and larger petals. The new species is known from two disjunct localities in the Atlantic Forest of Brazil, in extremely endangered environments. All known specimens of F. atlantica were collected within the last three years. This new generic record for the Brazilian Atlantic Forest highlights the need for further floristic studies of forest remnants in the states of Bahia and Espírito Santo.