Phylogenomics and the rise of the angiosperms

Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods1,2. A robust understanding of angiosperm evolution is required to explain their rise to ecological dominance. So far, the angiosperm tree of life has been determined primarily by means of analyses of the plastid genome3,4. Many studies have drawn on this foundational work, such as classification and first insights into angiosperm diversification since their Mesozoic origins5-7. However, the limited and biased sampling of both taxa and genomes undermines confidence in the tree and its implications. Here, we build the tree of life for almost 8,000 (about 60%) angiosperm genera using a standardized set of 353 nuclear genes8. This 15-fold increase in genus-level sampling relative to comparable nuclear studies9 provides a critical test of earlier results and brings notable change to key groups, especially in rosids, while substantiating many previously predicted relationships. Scaling this tree to time using 200 fossils, we discovered that early angiosperm evolution was characterized by high gene tree conflict and explosive diversification, giving rise to more than 80% of extant angiosperm orders. Steady diversification ensued through the remaining Mesozoic Era until rates resurged in the Cenozoic Era, concurrent with decreasing global temperatures and tightly linked with gene tree conflict. Taken together, our extensive sampling combined with advanced phylogenomic methods shows the deep history and full complexity in the evolution of a megadiverse clade.

Dracontium nivosum (Lem.) G.H.Zhu (Araceae): range extension from Amazonia to a brejo forest refugium in Northeast Brazil confirmed

The 558 km range extension of the Amazonian aroid Dracontium nivosum (Lem.) G.H.Zhu into semi-arid Northeast Brazil is confirmed. This species occurs in Ceará in threatened fragments of brejo forest at ca. 580–870 m elevation. An illustrated taxonomic description is provided. The species’  Extent of Occurrence (EOO) is estimated as 356,392 km2 (meets Least Concern); the Area of Occupancy (AOO), 60 km2 using a 2×2 km cell (Endangered). Within Ceará the EOO is 41.4 km2 (Critically Endangered) and the AOO is 16 km2 (Endangered). 

Relationships within the Araceae: comparison of morphological patterns with molecular phylogenies

PREMISE OF THE STUDY

The first family-wide molecular phylogeny of the Araceae, a family of about 3800 published species in 120 genera, became available in 1995, followed by a cladistic analysis of morpho-anatomical data in 1997. The most recent and comprehensive family-wide molecular phylogeny was published in 2008 and included species from 102 genera. We reanalyzed the molecular data with a more complete genus sampling and compared the resulting phylogeny with morphological and anatomical data, with a view to contributing to a new formal classification of the Araceae.

METHODS

We analyzed 113 aroid genera and 4494 aligned nucleotides that resulted from adding 11 genera to the 2008 molecular matrix. We also analyzed 81 morphological characters in the context of the molecular phylogeny, using an extended version of the 1997 morpho-anatomical data set.

KEY RESULTS

The resulting maximum-likelihood phylogeny is well resolved and supported, and most of the 44 larger clades also have morphological or anatomical synapomorphies as well as ecological or geographic cohesion. Of the 44 clades, 16 are here newly circumscribed and informally named. However, some relationships remain poorly supported within the Aroideae subfamily. The most problematic placement is Calla within Aroideae, which conflicts with the distribution of morphological, anatomical, and palynological character states.

CONCLUSIONS

The comparison of the molecular analysis with morphological and anatomical data presented here represents an important basis for a new formal classification for the Araceae and for the understanding of the evolution of this ancient family, a monocot group known in the fossil record from the early Cretaceous.

Revisão taxonômica das espécies de Anthurium (Araceae) seção Urospadix subseção Flavescentiviridia

RESUMO Apresenta-se o estudo taxonômico de 35 espécies de Anthurium seção Urospadix subseção Flavescentiviridia, com base em análises dos caracteres morfológicos vegetativos e reprodutivos, a partir de material coletado em campo e de exsicatas de diversos herbários nacionais e internacionais. A subseção caracteriza-se pela lâmina foliar de consistência membranácea a cartácea, esverdeada discolor, com nervuras secundárias geralmente impressas adaxialmente e proeminentes abaxialmente em diversos graus, são geralmente ombrófilas e esciófilas. Registros inéditos de morfologia vegetativa e reprodutiva estão sendo apresentados, especialmente em relação às bagas (A. acutum, A. urvilleanum, A. hoehnei, A. ianthinopodum, A. loefgrenii, A. longicuspidatum, A. luschnathianum, A. marense e A. mourae). Apresenta-se uma chave para identificação das espécies, descrições detalhadas, comentários sobre a distribuição geográfica, ecologia, fenologia, conservação e ilustrações para cada uma delas.

Taxonomy as an eScience

The Internet has the potential to provide wider access to biological taxonomy, the knowledge base of which is currently fragmented across a large number of ink-on-paper publications dating from the middle of the eighteenth century. A system (the CATE project) is proposed in which consensus or consolidated taxonomies are presented in the form of Web-based revisions. The workflow is designed to allow the community to offer, online, additions and taxonomic changes ('proposals') to the consolidated taxonomies (e.g. new species and synonymies). A means of quality control in the form of online peer review as part of the editorial process is also included in the workflow. The CATE system rests on taxonomic expertise and judgement, rather than using aggregation technology to accumulate taxonomic information from across the Web. The CATE application and its system and architecture are described in the context of the wider aims and purpose of the project.

Phylogenetic relationships of aroids and duckweeds (Araceae) inferred from coding and noncoding plastid DNA

Familial, subfamilial, and tribal monophyly and relationships of aroids and duckweeds were assessed by parsimony and Bayesian phylogenetic analyses of five regions of coding (rbcL, matK) and noncoding plastid DNA (partial trnK intron, trnL intron, trnL-trnF spacer) for exemplars of nearly all aroid and duckweed genera. Our analyses confirm the position of Lemna and its allies (formerly Lemnaceae) within Araceae as the well-supported sister group of all aroids except Gymnostachydoideae and Orontioideae. The last two subfamilies form the sister clade of the rest of the family. Monophyly of subfamilies Orontioideae, Pothoideae, Monsteroideae, and Lasioideae is supported, but Aroideae are paraphyletic if Calla is maintained in its own subfamily (Calloideae). Our results suggest expansion of the recently proposed subfamily Zamioculcadoideae (Zamioculcas, Gonatopus) to include Stylochaeton and identify problems in the current delimitation of tribes Anadendreae, Heteropsideae, and Monstereae (Monsteroideae), Caladieae/Zomicarpeae, and Colocasieae (Aroideae). Canalization of traits of the spathe and spadix considered typical of Araceae evolved after the split of Gymnostachydoideae, Orontioideae, and Lemnoideae. An association with aquatic habitats is a plesiomorphic attribute in Araceae, occurring in the helophytic Orontioideae and free-floating Lemnoideae, but evolving independently in various derived aroid lineages including free-floating Pistia (Aroideae).

Population differentiation and species cohesion in two closely related plants adapted to neotropical high-altitude 'inselbergs', Alcantarea imperialis and Alcantarea geniculata (Bromeliaceae)

Isolated granitic rock outcrops or 'inselbergs' may provide a window into the molecular ecology and genetics of continental radiations under simplified conditions, in analogy to the use of oceanic islands in studies of species radiations. Patterns of variability and gene flow in inselberg species have never been thoroughly evaluated in comparison to related taxa with more continuous distribution ranges, or to other species in the same kingdom in general. We use nuclear microsatellites to study population differentiation and gene flow in two diploid, perennial plants adapted to high-altitude neotropical inselbergs, Alcantarea imperialis and Alcantarea geniculata (Bromeliaceae). Population differentiation is pronounced in both taxa, especially in A. imperialis. Gene flow in this species is considerably lower than expected from the literature on plants in general and Bromeliaceae in particular, and too low to prevent differentiation due to drift (N(e)m < 1), unless selection coefficients/effect sizes of favourable alleles are great enough to maintain species cohesion. Low gene flow in A. imperialis indicates that the ability of pollinating bats to promote gene exchange between inselbergs is smaller than previously assumed. Population subdivision in one inselberg population of A. imperialis appears to be associated with the presence of two colour morphs that differ in the coloration of rosettes and bracts. Our results indicate a high potential for inselbergs as venues for studies of the molecular ecology and genetics of continental radiations, such as the one that gave rise to the extraordinary diversity of adaptive strategies and phenotypes seen in Bromeliaceae.

Combined genotypic–phenotypic phylogeny of the tribe Spathicarpeae (Araceae) with reference to independent events of invasion to Andean regions

The Neotropical tribe Spathicarpeae is noteworthy within the family Araceae for having members occurring in very dry and/or very high (above 3000m) areas in South America. Considering the small size of previously included genera in the tribe (10 geophytic genera, none with more than 15 described species), generic circumscription has been considered troublesome. To address these issues, we sequenced two cpDNA markers (matK and trnL-F) and reconstructed the phylogeny of the tribe using two approaches: Maximum parsimony and Bayesian Inference. We also evaluated the effect of adding phenotypic characters in a "total evidence" analysis. Our results confirm the previous suggestion that the two non-geophytic genera Dieffenbachia and Bognera should be included in Spathicarpeae, but the precise placement of Bognera within the tribe is still unresolved. Our results also support the segregation of Asterostigma pavonii and Asterostigma integrifolium, recently described as new monospecific genera (Incarum and Croatiella, respectively). The reconstructed phylogenies suggest that the invasion of the Andean range by the Spathicarpeae occurred in at least two independent events. The inclusion of phenotypic characters in a combined analysis has improved both internal resolution and the number of strongly supported clades.

NOMENCLATURE AND TAXONOMY OF PHILODENDRON HASTATUM K. KOCH & SELLO

ABSTRACT The paper discusses the taxonomy and nomenclature of Philodendron hastatum and aims to clarify the status of some other names often used to name specimens with similar leaf blade shape. A description of the species is provided based on the study of herbarium material.

The Latina Breast Cancer Control Study, year one: factors predicting screening mammography utilization by urban Latina women in Massachusetts

This study identifies factors associated with screening mammography utilization for Latina women age 40 and older in two Massachusetts cities, who are predominantly of Caribbean origin. It is a cross-sectional survey based on an area probability sample, using bilingual Latina interviewers. Sixty-one percent of the sample was Latina, 99% of whom were interviewed in Spanish. Ethnicity, educational attainment, and acculturation were unrelated to recent screening. While distinct healing traditions were found among some Latinas, their use was unrelated to screening. Higher fatalism scores had a bivariate association with lower probability of screening. In a logistic regression, predictors were having health insurance or access to free care; having discussed mammography with a physician in the past 2 years; the difference between 67 and respondent's age (negative coefficient); and city of residence. Having a regular source of care was a predictor when substituted for insurance status. Insurance status and age principally determine whether subjects are screened, mediated by access to physician services and whether physicians recommend screening. Results suggest that universal medical insurance, and efforts to influence physician practices, are key to promoting screening mammography among this population.