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Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods(1,2). 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 genome(3,4). Many studies have drawn on this foundational work, such as classification and first insights into angiosperm diversification since their Mesozoic origins(5-7). 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 genes(8). This 15-fold increase in genus-level sampling relative to comparable nuclear studies(9) 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.

In the late 18 th century, the Danish government planned to establish plantations in Danish Guinea (now southeastern Ghana), and detailed botanical studies were initiated for this. Material of more than 600 species was collected, mostly preserved at C, with duplicates at B, BM, FI-W, G, G-D C, K, LE, M, P-JU and S. Duplicates were distributed and studied across Europe long before the publication of a treatment of the entire collection. Examples of research on duplicates at B, C, G and G-DC illustrate how the material was sometimes described under different names during this period, as when Augustin-Pyramus de Candolle in Geneva took up Thonning’s intended generic name TriclicerasThonn. ex DC. for a new genus, while Schumacher in Copenhagen named the same genus Wormskioldia Schumach. & Thonn. This example also illustrates the contacts between Danish botanists and Candolle in Geneva, both directly and via Marc Nicolas Puerari. A manuscript dealing with the entire Guinean collection was ready by 1819, but only published when the Royal Danish Academy of Sciences and Letters took responsibility for it. Archival studies document that, on 30 June 1826, the Academy decided to publish Beskrivelse but not when and how a preprint became available. In a range of libraries in Europe and USA there are copies of this preprint entitled Beskrivelse af Guineiske Planter and the year of publication given as “1827 ”, while in the regular series of the Academy’s publications the first 228 pages of Beskrivelseappeared in 1828 and the remaining 236 in 1829. The International Code of Nomenclature for Algae, Fungi and Plants stipulates that the priority of all new names published in a work must be counted from the year indicated as the year of publication on the work itself, unless this can be documented to be wrong, so 1827 must stand as the year of publication. Soon after that, Beskrivelse became an important source of information on West African plants.

In the late 18 th century, the Danish government planned to establish plantations in Danish Guinea (now southeastern Ghana), and detailed botanical studies were initiated for this. Material of more than 600 species was collected, mostly preserved at C, with duplicates at B, BM, FI-W, G, G-D C, K, LE, M, P-JU and S. Duplicates were distributed and studied across Europe long before the publication of a treatment of the entire collection. Examples of research on duplicates at B, C, G and G-DC illustrate how the material was sometimes described under different names during this period, as when Augustin-Pyramus de Candolle in Geneva took up Thonning’s intended generic name TriclicerasThonn. ex DC. for a new genus, while Schumacher in Copenhagen named the same genus Wormskioldia Schumach. & Thonn. This example also illustrates the contacts between Danish botanists and Candolle in Geneva, both directly and via Marc Nicolas Puerari. A manuscript dealing with the entire Guinean collection was ready by 1819, but only published when the Royal Danish Academy of Sciences and Letters took responsibility for it. Archival studies document that, on 30 June 1826, the Academy decided to publish Beskrivelse but not when and how a preprint became available. In a range of libraries in Europe and USA there are copies of this preprint entitled Beskrivelse af Guineiske Planter and the year of publication given as “1827 ”, while in the regular series of the Academy’s publications the first 228 pages of Beskrivelseappeared in 1828 and the remaining 236 in 1829. The International Code of Nomenclature for Algae, Fungi and Plants stipulates that the priority of all new names published in a work must be counted from the year indicated as the year of publication on the work itself, unless this can be documented to be wrong, so 1827 must stand as the year of publication. Soon after that, Beskrivelse became an important source of information on West African plants.

A major problem in establishing effective protocols for conserving Madagascar's biodiversity is the lack of reliable information for the identification of priority sites in need of protection. Analyses of field data and information from herbarium collections for members of the plant family Pandanaceae (85 spp. of Pandanus; 6 spp. of Martellidendron) showed how risk of extinction assessments can inform conservation planning. Application of IUCN Red List categories and criteria showed that 91% of the species are threatened. Mapping occurrence revealed centres of richness and rarity as well as gaps in Madagascar's existing protected area network. Protection of 10 additional sites would be required to encompass the 19 species currently lacking representation in the reserve network, within which east coast littoral forests are particularly under represented and important. The effect of scale on assessments of risk of extinction was explored by applying different grid cell sizes to estimate area of occupancy. Using a grid cell size within the range suggested by IUCN overestimates threatened status if based solely upon specimen data. For poorly inventoried countries such as Madagascar measures of range size based on such data should be complemented with field observations to determine population size, sensitivity to disturbance, and specific threats to habitat and therefore potential population decline. The analysis of such data can make an important contribution to the conservation planning process by identifying threatened species and revealing the highest priority sites for their conservation

Smith & al. (2010) have suggested that the apportionment of institutional votes for the Nomenclature Section of the International Botanical Congress based upon taxonomic activity represents a "colonial legacy" that disadvantages developing nations, and that institutional votes should instead be distributed based at least in part upon a country's human population and the size of its flora. While we agree that increasing participation by developing-country taxonomists is an important goal, we believe that Smith & al. fail to support their claim that the current practice of plant nomenclature is harmful to developing nations. No evidence has been offered of regional biases regarding proposals to change the wording of the Code, which represent the vast majority of the votes taken at any Nomenclature Section, nor has the current process of apportionment of institutional votes been shown to be biased. The reform measures proposed by Smith & al. would, as we show, introduce explicit discrimination based on nationality into the International code of botanical nomenclature, undermining the international cooperation among taxonomists that is necessary for the smooth functioning of a universally accepted system of nomenclature. Rather than making hasty and perhaps harmful changes to the current means of voting, we suggest that the international taxonomic community should consider carefully what measures will best facilitate participation without creating new sources of injustice.

Background and aims Recent studies have adopted a broad definition of Sapindaceae that includes taxa traditionally placed in Aceraceae and Hippocastanaceae, achieving monophyly but yielding a family difficult to characterize and for which no obvious morphological synapomorphy exists. This expanded circumscription was necessitated by the finding that the monotypic, temperate Asian genus Xanthoceras, historically placed in Sapindaceae tribe Harpullieae, is basal within the group. Here we seek to clarify the relationships of Xanthoceras based on phylogenetic analyses using a dataset encompassing nearly 3/4 of sapindaceous genera, comparing the results with information from morphology and biogeography, in particular with respect to the other taxa placed in Harpullieae. We then re-examine the appropriateness of maintaining the current broad, morphologically heterogeneous definition of Sapindaceae and explore the advantages of an alternative family circumscription. Methods Using 243 samples representing 104 of the 142 currently recognized genera of Sapindaceae s. lat. (including all in Harpullieae), sequence data were analyzed for nuclear (ITS) and plastid (matK, rpoB, trnD-trnT, trnK-matK, trnL-trnF and trnS-trnG) markers, adopting the methodology of a recent family-wide study, performing single-gene and total evidence analyses based on maximum likelihood (ML) and maximum parsimony (MP) criteria, and applying heuristic searches developed for large datasets, viz, a new strategy implemented in RAxML (for ML) and the parsimony ratchet (for MP). Bootstrap analyses were performed for each method to test for congruence between markers. Key results Our findings support earlier suggestions that Harpullieae are polyphyletic: Xanthoceras is confirmed as sister to all other sampled taxa of Sapindaceae s. lat.; the remaining members belong to three other clades within Sapindaceae s. lat., two of which correspond respectively to the groups traditionally treated as Aceraceae and Hippo, authorCount :6

Disjunctive distributions across paleotropical regions in the Indian Ocean Basin (IOB) often invoke dispersal/vicariance debates. Exacum (Gentianaceae, tribe Exaceae) species are spread around the IOB, in Africa, Madagascar, Socotra, the Arabian peninsula, Sri Lanka, India, the Himalayas, mainland Southeast Asia including southern China and Malaysia, and northern Australia. The distribution of this genus was suggested to be a typical example of vicariance resulting from the breakup of the Gondwanan supercontinent. The molecular phylogeny of Exacum is in principle congruent with morphological conclusions and shows a pattern that resembles a vicariance scenario with rapid divergence among lineages, but our molecular dating analysis demonstrates that the radiation is too recent to be associated with the Gondwanan continental breakup. We used our dating analysis to test the results of DIVA and found that the program predicted impossible vicariance events. Ancestral area reconstruction suggests that Exacum originated in Madagascar, and divergence dating suggests its origin was not before the Eocene. The Madagascan progenitor, the most recent common ancestor of Exacum, colonized Sri Lanka and southern India via long-distance dispersals. This colonizer underwent an extensive range expansion and spread to Socotra-Arabia, northern India, and mainland Southeast Asia in the northern IOB when it was warm and humid in these regions. This widespread common ancestor retreated subsequently from most parts of these regions and survived in isolation in Socotra-Arabia, southern India–Sri Lanka, and perhaps mainland Southeast Asia, possibly as a consequence of drastic climatic changes, particularly the spreading drought during the Neogene. Secondary diversification from these surviving centers and Madagascar resulted in the extant main lineages of the genus. The vicariance-like pattern shown by the phylogeny appears to have resulted from long-distance disper

The economically important soapberry family (Sapindaceae) comprises about 1900 species mainly found in the tropical regions of the world, with only a few genera being restricted to temperate areas. The infrafamilial classification of the Sapindaceae and its relationships to the closely related Aceraceae and Hippocastanaceae – which have now been included in an expanded definition of Sapindaceae (i.e., subfamily Hippocastanoideae) – have been debated for decades. Here we present a phylogenetic analysis of Sapindaceae based on eight DNA sequence regions from the plastid and nuclear genomes and including 85 of the 141 genera defined within the family. Our study comprises 997 new sequences of Sapindaceae from 152 specimens. Despite presenting 18.6% of missing data our complete data set produced a topology fully congruent with the one obtained from a subset without missing data, but including fewer markers. The use of additional information therefore led to a consistent result in the relative position of clades and allowed the definition of a new phylogenetic hypothesis. Our results confirm a high level of paraphyly and polyphyly at the subfamilial and tribal levels and even contest the monophyletic status of several genera. Our study confirms that the Chinese monotypic genus Xanthoceras is sister to the rest of the family, in which subfamily Hippocastanoideae is sister to a clade comprising subfamilies Dodonaeoideae and Sapindoideae. On the basis of the strong support demonstrated in Sapindoideae, Dodonaeoideae and Hippocastanoideae as well as in 14 subclades, we propose and discuss informal groupings as basis for a new classification of Sapindaceae.

Malagasy Dracaena (Ruscaceae) are divided into four species and 14 varieties, all of them showing a high level of morphological diversity and a putatively artefactual circumscription. In order to reveal relationships between those entangled entities, a span of Malagasy Dracaena were sampled and analyzed using cpDNA sequences and AFLP. The cpDNA analyses resolved three biogeographic clades that are mostly inconsistent with morphology, since similar phenotypes are found across the three clades. Bayesian inference clustering analyses based on the AFLP were not in accordance with the cpDNA analysis. This result might be explained by (1) a recent origin of the Malagasy species of Dracaena with an incomplete sorting of chloroplast lineages; (2) a high amount of hybridizations; (3) a complex migration pattern. Interestingly, when the AFLP are analyzed using the parsimony criterion, a trend towards a directional evolution of inflorescence types and ecological features was observed. This might be considered either as phenotypic plasticity and/or as the result of fast evolution in flower characters according to habitat preferences. Overall, our results point to the difficulty of defining evolutionarily significant units in Malagasy Dracaena, emphasizing the complex speciation processes taking place in tropical regions.

Disjunctive distributions across paleotropical regions in the Indian Ocean Basin (IOB) often invoke dispersal/vicariance debates. Exacum (Gentianaceae, tribe Exaceae) species are spread around the IOB, in Africa, Madagascar, Socotra, the Arabian peninsula, Sri Lanka, India, the Himalayas, mainland Southeast Asia including southern China and Malaysia, and northern Australia. The distribution of this genus was suggested to be a typical example of vicariance resulting from the breakup of the Gondwanan supercontinent. The molecular phylogeny of Exacum is in principle congruent with morphological conclusions and shows a pattern that resembles a vicariance scenario with rapid divergence among lineages, but our molecular dating analysis demonstrates that the radiation is too recent to be associated with the Gondwanan continental breakup. We used our dating analysis to test the results of DIVA and found that the program predicted impossible vicariance events. Ancestral area reconstruction suggests that Exacum originated in Madagascar, and divergence dating suggests its origin was not before the Eocene. The Madagascan progenitor, the most recent common ancestor of Exacum, colonized Sri Lanka and southern India via long-distance dispersals. This colonizer underwent an extensive range expansion and spread to Socotra-Arabia, northern India, and mainland Southeast Asia in the northern IOB when it was warm and humid in these regions. This widespread common ancestor retreated subsequently from most parts of these regions and survived in isolation in Socotra-Arabia, southern India–Sri Lanka, and perhaps mainland Southeast Asia, possibly as a consequence of drastic climatic changes, particularly the spreading drought during the Neogene. Secondary diversification from these surviving centers and Madagascar resulted in the extant main lineages of the genus. The vicariance-like pattern shown by the phylogeny appears to have resulted from long-distance disper

The economically important soapberry family (Sapindaceae) comprises about 1900 species mainly found in the tropical regions of the world, with only a few genera being restricted to temperate areas. The infrafamilial classification of the Sapindaceae and its relationships to the closely related Aceraceae and Hippocastanaceae – which have now been included in an expanded definition of Sapindaceae (i.e., subfamily Hippocastanoideae) – have been debated for decades. Here we present a phylogenetic analysis of Sapindaceae based on eight DNA sequence regions from the plastid and nuclear genomes and including 85 of the 141 genera defined within the family. Our study comprises 997 new sequences of Sapindaceae from 152 specimens. Despite presenting 18.6% of missing data our complete data set produced a topology fully congruent with the one obtained from a subset without missing data, but including fewer markers. The use of additional information therefore led to a consistent result in the relative position of clades and allowed the definition of a new phylogenetic hypothesis. Our results confirm a high level of paraphyly and polyphyly at the subfamilial and tribal levels and even contest the monophyletic status of several genera. Our study confirms that the Chinese monotypic genus Xanthoceras is sister to the rest of the family, in which subfamily Hippocastanoideae is sister to a clade comprising subfamilies Dodonaeoideae and Sapindoideae. On the basis of the strong support demonstrated in Sapindoideae, Dodonaeoideae and Hippocastanoideae as well as in 14 subclades, we propose and discuss informal groupings as basis for a new classification of Sapindaceae.

A major problem in establishing effective protocols for conserving Madagascar's biodiversity is the lack of reliable information for the identification of priority sites in need of protection. Analyses of field data and information from herbarium collections for members of the plant family Pandanaceae (85 spp. of Pandanus; 6 spp. of Martellidendron) showed how risk of extinction assessments can inform conservation planning. Application of IUCN Red List categories and criteria showed that 91% of the species are threatened. Mapping occurrence revealed centres of richness and rarity as well as gaps in Madagascar's existing protected area network. Protection of 10 additional sites would be required to encompass the 19 species currently lacking representation in the reserve network, within which east coast littoral forests are particularly under represented and important. The effect of scale on assessments of risk of extinction was explored by applying different grid cell sizes to estimate area of occupancy. Using a grid cell size within the range suggested by IUCN overestimates threatened status if based solely upon specimen data. For poorly inventoried countries such as Madagascar measures of range size based on such data should be complemented with field observations to determine population size, sensitivity to disturbance, and specific threats to habitat and therefore potential population decline. The analysis of such data can make an important contribution to the conservation planning process by identifying threatened species and revealing the highest priority sites for their conservation