Domingos Cardoso

A new subfamily classification of the leguminosae based on a taxonomically comprehensive phylogeny

The classification of the legume family proposed here addresses the long-known non-monophyly of the traditionally recognised subfamily Caesalpinioideae, by recognising six robustly supported monophyletic subfamilies. This new classification uses as its framework the most comprehensive phylogenetic analyses of legumes to date, based on plastid matK gene sequences, and including near-complete sampling of genera (698 of the currently recognised 765 genera) and ca. 20% (3696) of known species. The matK gene region has been the most widely sequenced across the legumes, and in most legume lineages, this gene region is sufficiently variable to yield well-supported clades. This analysis resolves the same major clades as in other phylogenies of whole plastid and nuclear gene sets (with much sparser taxon sampling). Our analysis improves upon previous studies that have used large phylogenies of the Leguminosae for addressing evolutionary questions, because it maximises generic sampling and provides a phylogenetic tree that is based on a fully curated set of sequences that are vouchered and taxonomically validated. The phylogenetic trees obtained and the underlying data are available to browse and download, facilitating subsequent analyses that require evolutionary trees. Here we propose a new community-endorsed classification of the family that reflects the phylogenetic structure that is consistently resolved and recognises six subfamilies in Leguminosae: a recircumscribed Caesalpinioideae DC., Cercidoideae Legume Phylogeny Working Group (stat. nov.), Detarioideae Burmeist., Dialioideae Legume Phylogeny Working Group (stat. nov.), Duparquetioideae Legume Phylogeny Working Group (stat. nov.), and Papilionoideae DC. The traditionally recognised subfamily Mimosoideae is a distinct clade nested within the recircumscribed Caesalpinioideae and is referred to informally as the mimosoid clade pending a forthcoming formal tribal and/or cladebased classification of the new Caesalpinioideae. We provide a key for subfamily identification, descriptions with diagnostic charactertistics for the subfamilies, figures illustrating their floral and fruit diversity, and lists of genera by subfamily. This new classification of Leguminosae represents a consensus view of the international legume systematics community; it invokes both compromise and practicality of use.

Revisiting the phylogeny of papilionoid legumes: New insights from comprehensively sampled early-branching lineages

UNLABELLED PREMISE OF STUDY Phylogenetic relationships of the papilionoid legumes (Papilionoideae) reveal that the early branches are more highly diverse in floral morphology than are other clades of Papilionoideae. This study attempts for the first time to comprehensively sample the early-branching clades of this economically and ecologically important legume subfamily and thus to resolve relationships among them. • METHODS Parsimony and Bayesian phylogenetic analyses of the plastid matK and trnL intron sequences included 29 genera not yet sampled in matK phylogenies of the Papilionoideae, 11 of which were sampled for DNA sequence data for the first time. • KEY RESULTS The comprehensively sampled matK phylogeny better resolved the deep-branching relationships and increased support for many clades within Papilionoideae. The potentially earliest-branching papilionoid clade does not include any genus traditionally assigned to tribe Swartzieae. Dipterygeae is monophyletic with the inclusion of Monopteryx. The genera Aldina and Amphimas represent two of the nine main but as yet unresolved lineages comprising the large 50-kb inversion clade within papilionoids. The quinolizidine-alkaloid-accumulating genistoid clade is expanded to include a strongly supported subclade containing Ormosia and the previously unplaced Clathrotropis s.s., Panurea, and Spirotropis. Camoensia is the first-branching genus of the core genistoids. • CONCLUSIONS The well-resolved phylogeny of the earliest-branching papilionoids generated in this study will greatly facilitate the efforts to redefine and stabilize the classification of this legume subfamily. Many key floral traits did not often predict phylogenetic relationships, so comparative studies on floral evolution and plant-animal interactions, for example, should also benefit from this study.

Identity and relationships of the Arboreal Caatinga among other floristic units of seasonally dry tropical forests (SDTFs) of north-eastern and Central Brazil

The tree species composition of seasonally dry tropical forests (SDTF) in north-eastern and central Brazil is analyzed to address the following hypotheses: (1) variations in species composition are related to both environment (climate and substrate) and spatial proximity; (2) SDTF floristic units may be recognized based on peculiar composition and environment; and (3) the Arboreal Caatinga, a deciduous forest occurring along the hinterland borders of the Caatinga Domain, is one of these units and its flora is more strongly related to the caatinga vegetation than to outlying forests. The study region is framed by the Brazilian coastline, 50th meridian west and 21st parallel south, including the Caatinga Domain and extensions into the Atlantic Forest and Cerrado Domains. Multivariate and geostatistic analyses were performed on a database containing 16,226 occurrence records of 1332 tree species in 187 georeferenced SDTF areas and respective environmental variables. Tree species composition varied significantly with both environmental variables and spatial proximity. Eight SDTF floristic units were recognized in the region, including the Arboreal Caatinga. In terms of species composition, its tree flora showed a stronger link with that of the Cerrado Dry Forest Enclaves. On the other hand, in terms of species frequency across sample areas, the links were stronger with two other units: Rock Outcrops Caatinga and Agreste and Brejo Dry Forests. There is a role for niche-based control of tree species composition across the SDTFs of the region determined primarily by the availability of ground water across time and secondarily by the amount of soil mineral nutrients. Spatial proximity also contributes significantly to the floristic cohesion of SDTF units suggesting a highly dispersal-limited tree flora. These units should be given the status of eco-regions to help driving the conservation policy regarding the protection of their biodiversity.

A multilocus phylogenetic analysis reveals the monophyly of a recircumscribed papilionoid legume tribe Diocleae with well-supported generic relationships ☆

Deciphering the phylogenetic relationships within the species-rich Millettioid clade has persisted as one of the major challenges in the systematics and evolutionary history of papilionoid legumes (Leguminosae, Papilionoideae). Historically, the predominantly neotropical lianas of subtribe Diocleinae in the Millettioid legumes have been taxonomically tangled together with the largely heterogeneous tribe Phaseoleae. This work presents a comprehensive molecular phylogenetic analysis based on nuclear and chloroplast markers and includes all genera ever referred to Diocleae except for the monospecific Philippine Luzonia, resolving several key generic relationships within the Millettioid legumes. The first of two separate analyses includes 310 matK accessions and strongly supports the reestablishment of tribe Diocleae as a branch of the Millettioid clade. This work sheds greater light on the higher-level phylogeny of Diocleae and allows the recognition of three major lineages: the Canavalia, Dioclea, and Galactia clades. The second set of phylogenetic analyses utilized nuclear (ITS/5.8S and ETS) and plastid (matK and trnT-Y) DNA sequences to reveal (i) the monophyly of Canavalia and Cleobulia; (ii) the monophyly of Bionia with the exclusion of Bionia bella; (iii) the paraphyly of Dioclea with respect to Cleobulia, Cymbosema, and Macropsychanthus; (iv) the paraphyly of Cratylia with respect to the broadly polyphyletic Camptosema; and (v) the polyphyly of Galactia with species scattered widely across the tree.

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 Synopsis, New Combinations, and Synonyms in Acanthocladus (Polygalaceae)

Abstract A synopsis of the American genus Acanthocladus Klotzsch ex Hassk. (Polygalaceae), based primarily on herbarium studies, is presented, along with an identification key to the currently accepted eight species. Two new synonyms and the following new combinations are presented: A. dukei (Barringer) J. F. B. Pastore & D. B. O. S. Cardoso, A. pulcherrimus (Kuhlm.) J. F. B. Pastore & D. B. O. S. Cardoso, and A. santosii (Wurdack) J. F. B. Pastore & D. B. O. S. Cardoso. The names A. brasiliensis Klotzsch ex Hassk. and A. pulcherrimus are lectotypified.

Filling in the gaps of the papilionoid legume phylogeny: the enigmatic Amazonian genus Petaladenium is a new branch of the early-diverging Amburaneae clade.

Recent deep-level phylogenies of the basal papilionoid legumes (Leguminosae, Papilionoideae) have resolved many clades, yet left the phylogenetic placement of several genera unassessed. The phylogenetically enigmatic Amazonian monospecific genus Petaladenium had been believed to be close to the genera of the Genistoid Ormosieae clade. In this paper we provide the first DNA phylogenetic study of Petaladenium and show it is not part of the large Genistoid clade, but is a new branch of the Amburaneae clade, one of the first-diverging lineages of the Papilionoideae phylogeny. This result is supported by the chemical observation that the quinolizidine alkaloids, a chemical synapomorphy of the Genistoids, are absent in Petaladenium. Parsimony and Bayesian phylogenetic analysis of nuclear ITS/5.8S and plastid matK and trnL intron agree with a new interpretation of morphology that Petaladenium is sister to Dussia, a genus comprising ∼18 species of trees largely confined to rainforests in Central America and northern South America. Petaladenium, Dussia, and Myrospermum have papilionate flowers in a clade otherwise with radial floral symmetry, loss of petals or incompletely differentiated petals. Our phylogenetic analyses also revealed well-supported resolution within the three main lineages of the ADA clade (Angylocalyceae, Dipterygeae, and Amburaneae). We also discuss further molecular phylogenetic evidence for the undersampled Amazonian genera Aldina and Monopteryx, and the tropical African Amphimas, Cordyla, Leucomphalos, and Mildbraediodendron.

Composição florística e análise fitogeográfica de uma floresta semidecídua na Bahia, Brasil

Resumo (Composicâo floristica e analise fitogeografica de urna floresta semidecidua na Bahia, Brasil) As florestas semideciduas na Bahia mostram-se bastante fragmentadas e tem sido pouco estudadas em relacâo a floristica e a fitogeografia. Estas florestas estâo situadas principalmente no semi-arido e isoladas da Mata Atlantica costeira por extensas areas de caatinga. Este trabalho apresenta o levantamento floristico de um fragmento de floresta semidecidua na Serra da Fazenda Retiro (SFR), localizada no municipio de Feira de Santana, Bahia, com o objetivo principal de avahar a sua posicâo fitogeografica em relacâo as caatingas e a Mata Atlantica. Foram amostradas 173 especies incluidas em 143 generos e 59 familias. Myrtaceae foi a familia que apresentou o maior numero de especies (15 spp.), seguida por Euphorbiaceae (13), Leguminosae (12), Malvaceae (7), Orchidaceae (7) e Rubiaceae (7). Alem disso, foram coletadas tres novas especies dos generos Neomarica (Iridaceae), Pseudobombax (Malvaceae) e Solarium (Solanaceae). As analises de agrupamento pelo metodo UPGMA e de composicâo de especies da SFR mostram que a area, apesar de estar situada dentro do Bioma Caatinga, apresenta urna maior relacâo floristica com as florestas semideciduas do Dominio da Floresta Atlantica. Palavras-chave: fitogeograna, flora, florestas secas, Mata Atlantica, semi-arido. Abstract (Floristic composition andphytogeographical analysis of a semideciduous forest in Bahia State, Brazil) The semideciduous forests of Bahia occur as highly fragmented areas and have only received a little attention from floristic and phytogeographical studies. These areas are mainly situated within the semi-arid region and isolated from the Coastal Atlantic Forest by the surrounding dry vegetation of the caatinga domain. This paper presents a floristic survey of a semideciduous forest fragment at Serra da Fazenda Retiro (SFR), Feira de Santana, Bahia State, in order to assess its phytogeographical relationships in comparison to caatinga vegetation and Atlantic Forest. The survey identified 173 species belonging to 143 genera and 59 families. Myrtaceae presented the highest species number (15 spp.), followed by Euphorbiaceae (13), Leguminosae (12), Malvaceae (7), Orchidaceae (7), and Rubiaceae (7). Additionally, three new species of the genera Neomarica (Iridaceae), Pseudobombax (Malvaceae), and Solarium (Solanaceae) were sampled. In spite of the studied area being located within the circumscription of the Caatinga Biome, analysis of similarity (UPGMA) and of the SFR species composition showed that it is more floristically related to semideciduous forest of the Atlantic Forest domain rather than to caatinga vegetation.

Three new species of Luetzelburgia (Leguminosae, Papilionoideae) from the caatinga of Bahia, Brazil and an identification key to all species of the genus

SummaryThree new species of the Brazilian genus Luetzelburgia Harms (Leguminosae, Papilionoideae, Sophoreae sensu lato (Vataireoid clade)) are described and illustrated under the names Luetzelburgia harleyi D. Cardoso, L. P. Queiroz & H. C. Lima, L. neurocarpa D. Cardoso, L. P. Queiroz & H. C. Lima and L. purpurea D. Cardoso, L. P. Queiroz & H. C. Lima. All three occur in the caatinga vegetation of the State of Bahia, Eastern Brazil. A discussion of the morphological characters distinguishing the new species from their close relatives, as well as an identification key to all known species of Luetzelburgia, are presented.ResumoTrês espécies novas do gênero Luetzelburgia Harms (Leguminosae, Papilionoideae, Sophoreae sensu lato (clado Vataireóide)) são descritas e ilustradas sob os nomes de Luetzelburgia harleyi D. Cardoso, L. P. Queiroz & H. C. Lima, L. neurocarpa D. Cardoso, L. P. Queiroz & H. C. Lima e L. purpurea D. Cardoso, L. P. Queiroz & H. C. Lima. Todas elas ocorrem na vegetação de caatinga do Estado da Bahia, Brasil. Uma discussão dos caracteres morfológicos que distinguem as novas espécies das mais relacionadas, bem como uma chave de identificação para todas as espécies de Luetzelburgia, são apresentadas.

Correlations Between Indigenous Brazilian Folk Classifications of Fungi and Their Systematics

Abstract Folk classification is largely based on a long history of observing and harvesting living organisms. Although epistemologically undervalued by Western modern science, the study of ethnomycological classifications by indigenous populations has recently received increased attention. The classification criteria for fungi of several Brazilian indigenous groups, including the Caiabi, Txicão, Txucarramãe, Tupi-Guarani, and Yanomami, are similar to those used in classical, morphology-based taxonomy. The Yanomami, due to their long history of mycophilic behavior, show impressive knowledge of fungal classification similar in some cases to the recently proposed phylogenetic classification. This suggests that indigenous traditional knowledge may be helpful in the development of fungal systematics, reinforcing the epistemological validity of these distinct forms of knowledge of the natural world.