Advances in Legume Systematics 14. Classification of Caesalpinioideae. Part 2: Higher-level classification.

Caesalpinioideae is the second largest subfamily of legumes (Leguminosae) with ca. 4680 species and 163 genera. It is an ecologically and economically important group formed of mostly woody perennials that range from large canopy emergent trees to functionally herbaceous geoxyles, lianas and shrubs, and which has a global distribution, occurring on every continent except Antarctica. Following the recent re-circumscription of 15 Caesalpinioideae genera as presented in Advances in Legume Systematics 14, Part 1, and using as a basis a phylogenomic analysis of 997 nuclear gene sequences for 420 species and all but five of the genera currently recognised in the subfamily, we present a new higher-level classification for the subfamily. The new classification of Caesalpinioideae comprises eleven tribes, all of which are either new, reinstated or re-circumscribed at this rank: Caesalpinieae Rchb. (27 genera / ca. 223 species), Campsiandreae LPWG (2 / 5-22), Cassieae Bronn (7 / 695), Ceratonieae Rchb. (4 / 6), Dimorphandreae Benth. (4 / 35), Erythrophleeae LPWG (2 /13), Gleditsieae Nakai (3 / 20), Mimoseae Bronn (100 / ca. 3510), Pterogyneae LPWG (1 / 1), Schizolobieae Nakai (8 / 42-43), Sclerolobieae Benth. & Hook. f. (5 / ca. 113). Although many of these lineages have been recognised and named in the past, either as tribes or informal generic groups, their circumscriptions have varied widely and changed over the past decades, such that all the tribes described here differ in generic membership from those previously recognised. Importantly, the approximately 3500 species and 100 genera of the former subfamily Mimosoideae are now placed in the reinstated, but newly circumscribed, tribe Mimoseae. Because of the large size and ecological importance of the tribe, we also provide a clade-based classification system for Mimoseae that includes 17 named lower-level clades. Fourteen of the 100 Mimoseae genera remain unplaced in these lower-level clades: eight are resolved in two grades and six are phylogenetically isolated monogeneric lineages. In addition to the new classification, we provide a key to genera, morphological descriptions and notes for all 163 genera, all tribes, and all named clades. The diversity of growth forms, foliage, flowers and fruits are illustrated for all genera, and for each genus we also provide a distribution map, based on quality-controlled herbarium specimen localities. A glossary for specialised terms used in legume morphology is provided. This new phylogenetically based classification of Caesalpinioideae provides a solid system for communication and a framework for downstream analyses of biogeography, trait evolution and diversification, as well as for taxonomic revision of still understudied genera.

Precipitation is the main axis of tropical plant phylogenetic turnover across space and time.

Early natural historians-Comte de Buffon, von Humboldt, and De Candolle-established environment and geography as two principal axes determining the distribution of groups of organisms, laying the foundations for biogeography over the subsequent 200 years, yet the relative importance of these two axes remains unresolved. Leveraging phylogenomic and global species distribution data for Mimosoid legumes, a pantropical plant clade of c. 3500 species, we show that the water availability gradient from deserts to rain forests dictates turnover of lineages within continents across the tropics. We demonstrate that 95% of speciation occurs within a precipitation niche, showing profound phylogenetic niche conservatism, and that lineage turnover boundaries coincide with isohyets of precipitation. We reveal similar patterns on different continents, implying that evolution and dispersal follow universal processes.

Systematics of Ditaxinae and Related Lineages within the Subfamily Acalyphoideae (Euphorbiaceae) Based on Molecular Phylogenetics.

The subtribe Ditaxinae in the plant family Euphorbiaceae is composed of five genera (Argythamnia, Caperonia, Chiropetalum, Ditaxis and Philyra) and approximately 120 species of perennial herbs (rarely annual) to treelets. The subtribe is distributed throughout the Americas, with the exception of Caperonia, which also occurs in tropical Africa and Madagascar. Under the current classification, Ditaxinae includes genera with a questionable morphology-based taxonomy, especially Argythamnia, Chiropetalum and Ditaxis. Moreover, phylogenetic relationships among genera are largely unexplored, with previous works sampling <10% of taxa, showing Ditaxinae as paraphyletic. In this study, we inferred the phylogenetic relationships within Ditaxinae and related taxa using a dataset of nuclear (ETS, ITS) and plastid (petD, trnLF, trnTL) DNA sequences and a wide taxon sampling (60%). We confirmed the paraphyly of Ditaxinae and Ditaxis, both with high support. Following our phylogenetic results, we combined Ditaxis in Argythamnia and upgraded Ditaxinae to the tribe level (Ditaxeae). We also established and described the tribe Caperonieae based on Caperonia, and transferred Philyra to the tribe Adelieae, along with Adelia, Garciadelia, Lasiocroton and Leucocroton. Finally, we discuss the main morphological synapomorphies for the genera and tribes and provide a taxonomic treatment, including all species recognized under each genus.

Didactic games in the teaching of Botany: Enraizando and Batalha Algal / Jogos Didáticos no Ensino de Botânica: Enraizando e Batalha Algal

Botany is neglected in Biology teaching for elementary and high school. Based on this context, the Botanical Games Teaching Project, of the Laboratório de Sistemática e Evolução de Plantas da Universidade Federal de Pelotas, was created to approach the teaching of Botany in a fun way, seeking to make matters related to the plant kingdom more interesting and closer to the community. In this sense, didactic games were developed in order to present the subjects in a simple and attractive way for students. The game Enraizando was inspired by a dynamic chessboard, making the teaching of plant physiology more interesting for students. The game Batalha Algal was inspired by the game naval battle, streamlining the contents related to algae. This study presents didactic proposals in the teaching of Botany, in order to help teachers in a more effective and playful didactic transposition.

A Botânica é negligenciada no ensino de Biologia para o ensino fundamental e médio. Dessa forma, o Projeto de Ensino Jogos Botânicos, do Laboratório de Sistemática e Evolução de Plantas da Universidade Federal de Pelotas, foi criado para abordar o ensino de Botânica de forma lúdica, buscando tornar os assuntos relacionados ao reino das plantas mais interessantes e próximos da comunidade. Nesse sentido, foram elaborados jogos didáticos com intuito de apresentar os assuntos de forma simples e atraente aos estudantes. O jogo Enraizando foi inspirado em um tabuleiro dinâmico de xadrez, tornando o ensino de fisiologia vegetal mais interessante aos alunos. Da mesma forma, o jogo Batalha Algal foi inspirado no jogo batalha naval, dinamizando os conteúdos referentes às algas. Este trabalho apresenta propostas didáticas no ensino de Botânica, a fim de auxiliar os professores, do ensino fundamental e médio, em uma transposição didática mais efetiva e de maneira lúdica.

A new generic circumscription of Hydrochorea (Leguminosae, Caesalpinioideae, mimosoid clade) with an amphi-Atlantic distribution.

Hydrochorea and Balizia were established to accommodate four and three species, respectively, that were previously included in different ingoid genera, based primarily on differences in fruit morphology. Both genera have Amazonia as their centre of diversity, extending to Central America and the Brazilian Atlantic Rainforest. Previous phylogenetic evidence showed Balizia to be paraphyletic with respect to Hydrochorea, and species of Hydrochorea and Balizia were placed in a large unresolved polytomy with species of Jupunba. Here we present a new phylogenomic analysis based on 560 exons, from which 686 orthologous alignments were derived for gene tree inference. This analysis confirms a paraphyletic Balizia in relation to Hydrochorea, together with two African species formerly placed in Albizia nested within the clade. Jupunbamacradenia was resolved as sister to the clade combining those taxa. However, quartet support is low for several of the branches at the base of the clade combining the genera Jupunba, Balizia and Hydrochorea, suggesting that rapid initial divergence in this group led to extensive incomplete lineage sorting and consequently poor phylogenetic resolution. Because of these phylogenomic complexities, we decided to use morphology as the main guide to consider Hydrochorea as a distinct genus from Jupunba, and Balizia as a new synonym for Hydrochorea. The taxonomic treatment includes the study of collections from various herbaria and fieldwork expeditions. We present a re-circumscribed Hydrochorea accommodating a total of 10 species, including six new combinations, five new synonyms, one new taxonomic status, two corrections of nomenclature category for lectotypes, and a second step lectotype and three new lectotypes. A new species from the Brazilian Amazon is described and illustrated. An identification key for all species of Hydrochorea is presented, together with comments and illustrations.

Phylogenomic analysis of 997 nuclear genes reveals the need for extensive generic re-delimitation in Caesalpinioideae (Leguminosae).

Subfamily Caesalpinioideae with ca. 4,600 species in 152 genera is the second-largest subfamily of legumes (Leguminosae) and forms an ecologically and economically important group of trees, shrubs and lianas with a pantropical distribution. Despite major advances in the last few decades towards aligning genera with clades across Caesalpinioideae, generic delimitation remains in a state of considerable flux, especially across the mimosoid clade. We test the monophyly of genera across Caesalpinioideae via phylogenomic analysis of 997 nuclear genes sequenced via targeted enrichment (Hybseq) for 420 species and 147 of the 152 genera currently recognised in the subfamily. We show that 22 genera are non-monophyletic or nested in other genera and that non-monophyly is concentrated in the mimosoid clade where ca. 25% of the 90 genera are found to be non-monophyletic. We suggest two main reasons for this pervasive generic non-monophyly: (i) extensive morphological homoplasy that we document here for a handful of important traits and, particularly, the repeated evolution of distinctive fruit types that were historically emphasised in delimiting genera and (ii) this is an artefact of the lack of pantropical taxonomic syntheses and sampling in previous phylogenies and the consequent failure to identify clades that span the Old World and New World or conversely amphi-Atlantic genera that are non-monophyletic, both of which are critical for delimiting genera across this large pantropical clade. Finally, we discuss taxon delimitation in the phylogenomic era and especially how assessing patterns of gene tree conflict can provide additional insights into generic delimitation. This new phylogenomic framework provides the foundations for a series of papers reclassifying genera that are presented here in Advances in Legume Systematics (ALS) 14 Part 1, for establishing a new higher-level phylogenetic tribal and clade-based classification of Caesalpinioideae that is the focus of ALS14 Part 2 and for downstream analyses of evolutionary diversification and biogeography of this important group of legumes which are presented elsewhere.

Hybrid capture of 964 nuclear genes resolves evolutionary relationships in the mimosoid legumes and reveals the polytomous origins of a large pantropical radiation.

PREMISE: Targeted enrichment methods facilitate sequencing of hundreds of nuclear loci to enhance phylogenetic resolution and elucidate why some parts of the "tree of life" are difficult (if not impossible) to resolve. The mimosoid legumes are a prominent pantropical clade of ~3300 species of woody angiosperms for which previous phylogenies have shown extensive lack of resolution, especially among the species-rich and taxonomically challenging ingoids. METHODS: We generated transcriptomes to select low-copy nuclear genes, enrich these via hybrid capture for representative species of most mimosoid genera, and analyze the resulting data using de novo assembly and various phylogenomic tools for species tree inference. We also evaluate gene tree support and conflict for key internodes and use phylogenetic network analysis to investigate phylogenetic signal across the ingoids. RESULTS: Our selection of 964 nuclear genes greatly improves phylogenetic resolution across the mimosoid phylogeny and shows that the ingoid clade can be resolved into several well-supported clades. However, nearly all loci show lack of phylogenetic signal for some of the deeper internodes within the ingoids. CONCLUSIONS: Lack of resolution in the ingoid clade is most likely the result of hyperfast diversification, potentially causing a hard polytomy of six or seven lineages. The gene set for targeted sequencing presented here offers great potential to further enhance the phylogeny of mimosoids and the wider Caesalpinioideae with denser taxon sampling, to provide a framework for taxonomic reclassification, and to study the ingoid radiation.

Amazon plant diversity revealed by a taxonomically verified species list.

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.

Forgotten forests--issues and prospects in biome mapping using Seasonally Dry Tropical Forests as a case study.

BACKGROUND: South America is one of the most species diverse continents in the world. Within South America diversity is not distributed evenly at both local and continental scales and this has led to the recognition of various areas with unique species assemblages. Several schemes currently exist which divide the continental-level diversity into large species assemblages referred to as biomes. Here we review five currently available biome maps for South America, including the WWF Ecoregions, the Americas basemap, the Land Cover Map of South America, Morrone's Biogeographic regions of Latin America, and the Ecological Systems Map. The comparison is performed through a case study on the Seasonally Dry Tropical Forest (SDTF) biome using herbarium data of habitat specialist species. RESULTS: Current biome maps of South America perform poorly in depicting SDTF distribution. The poor performance of the maps can be attributed to two main factors: (1) poor spatial resolution, and (2) poor biome delimitation. Poor spatial resolution strongly limits the use of some of the maps in GIS applications, especially for areas with heterogeneous landscape such as the Andes. Whilst the Land Cover Map did not suffer from poor spatial resolution, it showed poor delimitation of biomes. The results highlight that delimiting structurally heterogeneous vegetation is difficult based on remote sensed data alone. A new refined working map of South American SDTF biome is proposed, derived using the Biome Distribution Modelling (BDM) approach where georeferenced herbarium data is used in conjunction with bioclimatic data. CONCLUSIONS: Georeferenced specimen data play potentially an important role in biome mapping. Our study shows that herbarium data could be used as a way of ground-truthing biome maps in silico. The results also illustrate that herbarium data can be used to model vegetation maps through predictive modelling. The BDM approach is a promising new method in biome mapping, and could be particularly useful for mapping poorly known, fragmented, or degraded vegetation. We wish to highlight that biome delimitation is not an exact science, and that transparency is needed on how biomes are used as study units in macroevolutionary and ecological research.