Reassessing the temporal evolution of orchids with new fossils and a Bayesian relaxed clock, with implications for the diversification of the rare South American genus Hoffmannseggella (Orchidaceae: Epidendroideae)

BACKGROUND: The temporal origin and diversification of orchids (family Orchidaceae) has been subject to intense debate in the last decade. The description of the first reliable fossil in 2007 enabled a direct calibration of the orchid phylogeny, but little attention has been paid to the potential influence of dating methodology in obtaining reliable age estimates. Moreover, two new orchid fossils described in 2009 have not yet been incorporated in a molecular dating analysis. Here we compare the ages of major orchid clades estimated under two widely used methods, a Bayesian relaxed clock implemented in BEAST and Penalized Likelihood implemented in r8s. We then perform a new family-level analysis by integrating all 3 available fossils and using BEAST. To evaluate how the newly estimated ages may influence the evolutionary interpretation of a species-level phylogeny, we assess divergence times for the South American genus Hoffmannseggella (subfam. Epidendroideae), for which we present an almost complete phylogeny (40 out of 41 species sampled). RESULTS: Our results provide additional support that all extant orchids shared a most recent common ancestor in the Late Cretaceous (approximately 77 million years ago, Ma). However, we estimate the crown age of the five orchid subfamilies to be generally (approximately1-8 Ma) younger than previously calculated under the Penalized Likelihood algorithm and using a single internal fossil calibration. The crown age of Hoffmannseggella is estimated here at approximately 11 Ma, some 3 Ma more recently than estimated under Penalized Likelihood. CONCLUSIONS: Contrary to recent suggestions that orchid diversification began in a period of global warming, our results place the onset of diversification of the largest orchid subfamilies (Orchidoideae and Epidendroideae) in a period of global cooling subsequent to the Early Eocene Climatic Optimum. The diversification of Hoffmannseggella appears even more correlated to late Tertiary climatic fluctuations than previously suggested. With the incorporation of new fossils in the orchid phylogeny and the use of a method that is arguably more adequate given the present data, our results represent the most up-to-date estimate of divergence times in orchids

Returns to R&D

R&D is generally modeled as a stock of knowledge resulting from the accumulation of past R&D expenditure that enters as a factor of production in an extended production function. It can also be seen as an input in a production function of knowledge whose output can be measured by patents, new products or new processes. R&D then affects productivity in an indirect way increasing the choice or the quality of products. R&D can also be conceived as attempts to improve technologies and productivity with an uncertainty rate of success. Returns to R&D may vary depending on the sectors, the level of development, and the opportunity factor. Econometric estimates may depend on whether they are based on cross-sectional or time-series variation in the data. R&D can generate spillover effects by creating or destroying economic rents elsewhere in the economy or by transmitting knowledge to other firms. R&D spillovers play an essential role in endogenous growth models

R&D tax incentives

Tax incentives are widely used to incentivize firms to engage in research and development or to increase their R&D efforts. They can be volume-based or incremental. More and more countries have also adopted the patent box, which is an ex-post tax reward for successful innovators. Two broad methods are used in evaluating the effectiveness of tax incentives: the price elasticity of a user cost of R&D and counterfactual methods. In evaluating tax incentives a major question is whether there is crowding in or crowding out. More thorough evaluations do a cost-benefit analysis incorporating R&D spillover, the cost of financing tax expenditure, as well as administrative and compliance costs in the computation of the bang for the buck. Some studies look beyond the effect on R&D at the effect on innovation and productivity. R&D tax incentives are in principle neutral, but they are sometimes used to stimulate a particular type of R&D. They can also give rise to tax competition to attract R&D performers

Placement of Kuhlmanniodendron Fiaschi & Groppo in Lindackerieae (Achariaceae, Malpighiales) confirmed by analyses of rbcL sequences, with notes on pollen morphology and wood anatomy

The phylogenetic placement of Kuhlmanniodendron Fiaschi & Groppo (Achariaceae) within Malpighiales was investigated with rbcL sequence data. This genus was recently created to accommodate Carpotroche apterocarpa Kuhlm., a poorly known species from the rainforests of Espirito Santo, Brazil. One rbcL sequence was obtained from Kuhlmanniodendron and analyzed with 73 additional sequences from Malpighiales, and 8 from two closer orders, Oxalidales and Celastrales, all of which were available at Genbank. Phylogenetic analyses were carried out with maximum parsimony and Bayesian inference; bootstrap analyses were used in maximum parsimony to evaluate branch support. The results confirmed the placement of Kuhlmanniodendron together with Camptostylus, Lindackeria, Xylotheca, and Caloncoba in a strongly supported clade (posterior probability = 0.99) that corresponds with the tribe Lindackerieae of Achariaceae (Malpighiales). Kuhlmanniodendron also does not appear to be closely related to Oncoba (Salicaceae), an African genus with similar floral and fruit morphology that has been traditionally placed among cyanogenic Flacourtiaceae (now Achariaceae). A picrosodic paper test was performed in herbarium dry leaves, and the presence of cyanogenic glycosides, a class of compounds usually found in Achariaceae, was detected. Pollen morphology and wood anatomy of Kuhlmanniodendron were also investigated, but both pollen (3-colporate and microreticulate) and wood, with solitary to multiple vessels, scalariform perforation plates and other features, do not seem to be useful to distinguish this genus from other members of the Achariaceae and are rather common among the eudicotyledons as a whole. However, perforated ray cells with scalariform plates, an uncommon wood character, present in Kuhlmanniodendron are similar to those found in Kiggelaria africana (Pangieae, Achariaceae), but the occurrence of such cells is not mapped among the angiosperms, and it is not clear how homoplastic this character could be.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)FAPESP[2000/07401-0]FAPESP[2006/03170-0]Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Universidade de São Paulo (USP)Universidade de São Paulo USP-ProIPCNPq (GDE)[200682/2006-7]Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Virginia Commonwealth University (VCU)Virginia Commonwealth University (VCU)Carl Tryggers StiftelseCarl Tryggers StiftelseHelge Axson Johnsons StiftelseHelge Axson Johnsons Stiftels

Placement of kuhlmanniodendron fiaschi & groppo in lindackerieae (achariaceae, malpighiales) confirmed by analyses of rbcL sequences, with notes on pollen morphology and wood anatomy

The phylogenetic placement of Kuhlmanniodendron Fiaschi & Groppo (Achariaceae) within Malpighiales was investigated with rbcL sequence data. This genus was recently created to accommodate Carpotroche apterocarpa Kuhlm., a poorly known species from the rainforests of Espírito Santo, Brazil. One rbcL sequence was obtained from Kuhlmanniodendron and analyzed with 73 additional sequences from Malpighiales, and 8 from two closer orders, Oxalidales and Celastrales, all of which were available at Genbank. Phylogenetic analyses were carried out with maximum parsimony and Bayesian inference; bootstrap analyses were used in maximum parsimony to evaluate branch support. The results confirmed the placement of Kuhlmanniodendron together with Camptostylus, Lindackeria, Xylotheca, and Caloncoba in a strongly supported clade (posterior probability = 0.99) that corresponds with the tribe Lindackerieae of Achariaceae (Malpighiales). Kuhlmanniodendron also does not appear to be closely related to Oncoba (Salicaceae), an African genus with similar floral and fruit morphology that has been traditionally placed among cyanogenic Flacourtiaceae (now Achariaceae). A picrosodic paper test was performed in herbarium dry leaves, and the presence of cyanogenic glycosides, a class of compounds usually found in Achariaceae, was detected. Pollen morphology and wood anatomy of Kuhlmanniodendron were also investigated, but both pollen (3-colporate and microreticulate) and wood, with solitary to multiple vessels, scalariform perforation plates and other features, do not seem to be useful to distinguish this genus from other members of the Achariaceae and are rather common among the eudicotyledons as a whole. However, perforated ray cells with scalariform plates, an uncommon wood character, present in Kuhlmanniodendron are similar to those found in Kiggelaria africana (Pangieae, Achariaceae), but the occurrence of such cells is not mapped among the angiosperms, and it is not clear how homoplastic this character could be2862737CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO - CNPQFUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULO - FAPESP200682/2006-72000/07401-0; 2006/03170-

Climate cooling promoted the expansion and radiation of a threatened group of South American orchids (Epidendroideae: Laeliinae)

The Brazilian Cerrado is the most species-rich tropical savanna in the world. Within this biome, the Campos Rupestres ('rocky savannas') constitute a poorly studied and highly threatened ecosystem. To better understand how plants characteristic of this vegetation have evolved and come to occupy the now widely-separated patches of rocky formations in eastern Brazil, we reconstruct the biogeographical history of the rare orchid genus Hoffmannseggella. We apply parsimony and Bayesian methods to infer the phylogenetic relationships among 40 out of the 41 described species. Absolute divergence times are calculated under penalized likelihood and compared with estimates from a Bayesian relaxed clock. Ancestral ranges are inferred for all nodes of the phylogeny using Fitch optimization and statistical dispersal vicariance analysis. In all analyses, phylogenetic uncertainty is taken into account by the independent analysis of a large tree sample. The results obtained indicate that Hoffmannseggella underwent rapid radiation around the Middle/Late Miocene (approximately 1114 Mya). The region corresponding today to southern Minas Gerais acted as amain source area for several independent range expansions north- and eastwards via episodic corridors. These results provide independent evidence that climate cooling following the Middle Miocene Climatic Optimum (approximately 15 Mya) led to important vegetational shifts in eastern Brazil, causing an increase in the dominance of open versus closed habitats. Polyploidy following secondary contact of previously isolated populations may have been responsible for the formation of many species, as demonstrated by the high ploidy levels reported in the genus