00429nas a2200121   4500008004100000245005900041210005800100300001200158490000700170100002500177700001900202856008600221       2011                        eng d00aWhy are there so many plant species in the Neotropics?0 aWhy are there so many plant species in the Neotropics  a403-4140 v601 aAntonelli, Alexandre1 aSanmartín, I.  uhttps://nnb.myspecies.info/content/why-are-there-so-many-plant-species-neotropics02376nas a2200145   4500008004100000245020200041210006900243260002000312300001200332490000700344520176800351100002502119700002302144856006302167       2011                        eng d00aMass Extinction, Gradual Cooling, or Rapid Radiation? Reconstructing the Spatiotemporal Evolution of the Ancient Angiosperm Genus Hedyosmum (Chloranthaceae) Using Empirical and Simulated Approaches0 aMass Extinction Gradual Cooling or Rapid Radiation Reconstructin  cOctober 1, 2011  a596-6150 v603 aChloranthaceae is a small family of flowering plants (65 species) with an extensive fossil record extending back to the Early Cretaceous. Within Chloranthaceae, Hedyosmum is remarkable because of its disjunct distribution–1 species in the Paleotropics and 44 confined to the Neotropics–and a long "temporal gap" between its stem age (Early Cretaceous) and the beginning of the extant radiation (late Cenozoic). Is this gap real, reflecting low diversification and a recent radiation, or the signature of extinction? Here we use paleontological data, relaxed-clock molecular dating, diversification analyses, and parametric ancestral area reconstruction to investigate the timing, tempo, and mode of diversification in Hedyosmum. Our results, based on analyses of plastid and nuclear sequences for 40 species, suggest that the ancestor of Chloranthaceae and the Hedyosmum stem lineages were widespread in the Holarctic in the Late Cretaceous. High extinction rates, possibly associated with Cenozoic climatic fluctuations, may have been responsible for the low extant diversity of the family. Crown group Hedyosmum originated c. 36–43 Ma and colonized South America from the north during the Early-Middle Miocene (c. 20 Ma). This coincided with an increase in diversification rates, probably triggered by the uplift of the Northern Andes from the Mid-Miocene onward. This study illustrates the advantages of combining paleontological, phylogenetic, and biogeographic data to reconstruct the spatiotemporal evolution of an ancient lineage, for which the extant diversity is only a remnant of past radiations. It also shows the difficulties of inferring patterns of lineage diversification when incomplete taxon sampling is combined with high extinction rates.1 aAntonelli, Alexandre1 aSanmartín, Isabel  uhttp://sysbio.oxfordjournals.org/content/60/5/596.abstract02479nas a2200157   4500008004100000245010200041210006900143300001400212490000700226520195800233100001702191700002502208700002202233700001902255856004702274       2011                        eng d00aRevisiting taxonomy, morphological evolution, and fossil calibration strategies in Chloranthaceae0 aRevisiting taxonomy morphological evolution and fossil calibrati  a315–3290 v493 aChloranthaceae is one of the earliest diverging angiosperm families and is comprised of approximately 75 species in four genera (Chloranthus, Sarcandra, Ascarina, and Hedyosmum). This family has received considerable attention because of its seemingly primitive morphology, disjunct tropical distribution in Asia and America, and extensive fossil record from the Early Cretaceous. In the present study, we reconstructed the phylogeny of Chloranthaceae based on a combined dataset of three plastid DNA regions and 56 species. We then estimated divergence times in the family using two relaxed molecular clock methods (BEAST and penalized likelihood). We focused on testing the influence of fossil taxa in calibrating the molecular phylogeny, and on assessing the current taxonomy of the family in light of the phylogenetic results. Our results indicate that most intrageneric divisions within Ascarina and Hedyosmum are not monophyletic. The results from the dating analysis suggest that the Hedyosmum-like fossil Asteropollis represents a stem lineage of Hedyosmum, as has been suggested previously from morphological analyses. In contrast, our results indicate that the Chloranthus-like fossil Chloranthistemon, previously suggested on morphological grounds to be a stem relative of Chloranthus, may, instead, belong to the branch leading to the clade Chloranthus+Sarcandra. The median crown ages of Chloranthus, Sarcandra, Ascarina, and Hedyosmum estimated in the BEAST analysis were 26.3, 9.5, 31.0 and 45.8 million years ago (Ma), respectively, whereas the divergence between Chloranthus and Sarcandra, the splitting of Ascarina with the former two genera, and Hedyosmum separating from the three genera were estimated to 63.8, 95.7 and 111.1 Ma. The present study sheds further light on the temporal evolution of Chloranthaceae and exemplifies how molecular dating analyses may be used to explore alternative phylogenetic placements of fossil taxa.1 aZhang, Qiang1 aAntonelli, Alexandre1 aFeild, Taylor, S.1 aKong, Hong-Zhi  uhttp://www.jse.ac.cn/Abstract.aspx?id=282700879nas a2200325   4500008004100000245003900041210003900080260002100119300001200140490000800152100001400160700002300174700001600197700002100213700001300234700001500247700001900262700002500281700002100306700002300327700001800350700001300368700001800381700002100399700001700420700001600437700001800453700002500471856005700496       2011                        eng d00aOrigins of Biodiversity–Response0 aOrigins of Biodiversity–Response  cJanuary 28, 2011  a399-4000 v3311 aHoorn, C.1 aWesselingh, F., P.1 aSteege, Ter1 aBermudez, M., A.1 aMora, A.1 aSevink, J.1 aSanmartín, I.1 aSanchez-Meseguer, A.1 aAnderson, C., L.1 aFigueiredo, J., P.1 aJaramillo, C.1 aRiff, D.1 aNegri, F., R.1 aHooghiemstra, H.1 aLundberg, J.1 aStadler, T.1 aSärkinen, T.1 aAntonelli, Alexandre  uhttp://www.sciencemag.org/content/331/6016/399.short03145nas a2200301   4500008004100000020001400041245012700055210006900182260002900251300001200280490000700292520222800299653001102527653001602538653001702554653002002571653002802591653002102619653001502640653001502655653001302670653001502683100002202698700002502720700002602745700001702771856005502788       2011                        eng d  a1365-269900aVicariance or long-distance dispersal: historical biogeography of the pantropical subfamily Chrysophylloideae (Sapotaceae)0 aVicariance or longdistance dispersal historical biogeography of   bBlackwell Publishing Ltd  a177-1900 v383 aAbstract Aim  Continental disjunctions in pantropical taxa have been explained by vicariance or long-distance dispersal. The relative importance of these explanations in shaping current distributions may vary, depending on historical backgrounds or biological characteristics of particular taxa. We aimed to determine the geographical origin of the pantropical subfamily Chrysophylloideae (Sapotaceae) and the roles vicariance and dispersal have played in shaping its modern distribution. Location  Tropical areas of Africa, Australasia and South America. Methods  We utilized a recently published, comprehensive data set including 66 species and nine molecular markers. Bayesian phylogenetic trees were generated and dated using five fossils and the penalized likelihood approach. Distributional ranges of nodes were estimated using maximum likelihood and parsimony analyses. In both biogeographical and molecular dating analyses, phylogenetic and branch length uncertainty was taken into account by averaging the results over 2000 trees extracted from the Bayesian stationary sample. Results  Our results indicate that the earliest diversification of Chrysophylloideae was in the Campanian of Africa c. 73–83 Ma. A narrow time interval for colonization from Africa to the Neotropics (one to three dispersals) and Australasia (a single migration) indicates a relatively rapid radiation of this subfamily in the latest Cretaceous to the earliest Palaeocene (c. 62–72 Ma). A single dispersal event from the Neotropics back to Africa during the Neogene was inferred. Long-distance dispersal between Australia and New Caledonia occurred at least four times, and between Africa and Madagascar on multiple occasions. Main conclusions  Long-distance dispersal has been the dominant mechanism for range expansion in the subfamily Chrysophylloideae. Vicariance could explain South American–Australian disjunction via Antarctica, but not the exchanges between Africa and South America and between New Caledonia and Australia, or the presence of the subfamily in Madagascar. We find low support for the hypothesis that the North Atlantic land bridge facilitated range expansions at the Palaeocene/Eocene boundary.10aAfrica10aAustralasia10aland bridges10aLate Cretaceous10along-distance dispersal10amolecular dating10aNeotropics10aSapotaceae10aTertiary10avicariance1 aBartish, Igor, V.1 aAntonelli, Alexandre1 aRichardson, James, E.1 aSwenson, Ulf  uhttp://dx.doi.org/10.1111/j.1365-2699.2010.02389.x02591nas a2200181   4500008004100000245007200041210006400113300001200177520198500189100002302174700001402197700002202211700002502233700001902258700001702277700002102294856009402315       2010                        eng d00aOn the origin of Amazonian landscapes and biodiversity: a synthesis0 aorigin of Amazonian landscapes and biodiversity a synthesis  a421-4313 aIn northern South America the Cenozoic was a period of intense tectonic and climatic interaction that resulted in a dynamic Amazonian landscape dominated by lowlands with local and shield-derived rivers. These drainage systems constantly changed shape and size. During the entire Cenozoic, the Brazilian and Guiana Shields were stable mountainous areas. Andean-derived river systems increased in importance especially in the Neogene. A remarkable feature in western Amazonian history is the waxing and waning of large lake systems and embayments. By the Late Miocene (about 11 Ma), the Andes were connected with the Atlantic through an incipient Amazon River, and from c. 7 Ma Andean-derived river systems became fully established in central and eastern Amazonia and the modern landscape configuration had developed. Rainforests already existed in northern South America during the Paleogene, but the modern rainforests – with resemblance to the Present forest – only developed during the Miocene. The western Amazonian Miocene record contains very diverse aquatic faunas (molluscs, ostracods, turtles, crocodiles, fishes) as well as terrestrial mammals. Remarkable gigantic forms thrived in Amazonian ecosystems at the time. Since the Late Miocene, edaphically heterogeneous lands emerged in western Amazonia in areas previously occupied by lake systems. At the same time nutrient-rich deposits spread over central and eastern Amazonia, an event that, based on molecular phylogenetic studies on extant taxa, coincided with diversification of terrestrial taxa. Molecular-based time estimates confirm the steady diversification and mostly pre-Quaternary origin of extant Amazonian taxa. A significant portion of the current species richness is attributed to a combination of relatively constant wet and warm climates and a heterogeneous edaphic substrate. The Quaternary was a time of distribution shifts, but can no longer be considered a time of diversification in Amazonia. 1 aWesselingh, F., P.1 aHoorn, C.1 aKroonenberg, S.B.1 aAntonelli, Alexandre1 aLundberg, J.G.1 aVonhof, H.B.1 aHooghiemstra, H.  uhttps://nnb.myspecies.info/content/origin-amazonian-landscapes-and-biodiversity-synthesis01792nas a2200337   4500008004100000245009600041210006900137260002100206300001200227490000800239520080700247100001401054700002301068700001601091700002101107700001301128700001501141700001901156700002501175700002101200700002301221700001801244700001301262700001801275700002101293700001701314700001601331700001801347700002501365856006401390       2010                        eng d00aAmazonia Through Time: Andean Uplift, Climate Change, Landscape Evolution, and Biodiversity0 aAmazonia Through Time Andean Uplift Climate Change Landscape Evo  cNovember 12, 201  a927-9310 v3303 aThe Amazonian rainforest is arguably the most species-rich terrestrial ecosystem in the world, yet the timing of the origin and evolutionary causes of this diversity are a matter of debate. We review the geologic and phylogenetic evidence from Amazonia and compare it with uplift records from the Andes. This uplift and its effect on regional climate fundamentally changed the Amazonian landscape by reconfiguring drainage patterns and creating a vast influx of sediments into the basin. On this "Andean" substrate, a region-wide edaphic mosaic developed that became extremely rich in species, particularly in Western Amazonia. We show that Andean uplift was crucial for the evolution of Amazonian landscapes and ecosystems, and that current biodiversity patterns are rooted deep in the pre-Quaternary.1 aHoorn, C.1 aWesselingh, F., P.1 aSteege, ter1 aBermudez, M., A.1 aMora, A.1 aSevink, J.1 aSanmartín, I.1 aSanchez-Meseguer, A.1 aAnderson, C., L.1 aFigueiredo, J., P.1 aJaramillo, C.1 aRiff, D.1 aNegri, F., R.1 aHooghiemstra, H.1 aLundberg, J.1 aStadler, T.1 aSärkinen, T.1 aAntonelli, Alexandre  uhttp://www.sciencemag.org/cgi/content/abstract/330/6006/92702855nas a2200157   4500008004100000020001400041245021900055210006900274300000800343490000700351520222400358100002302582700001702605700002502622856005002647       2010                        eng d  a1471-214800aReassessing 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)0 aReassessing the temporal evolution of orchids with new fossils a  a1770 v103 aBACKGROUND: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 (~77 million years ago, Ma). However, we estimate the crown age of the five orchid subfamilies to be generally younger (~1-8 Ma) than previously calculated under the Penalized Likelihood algorithm and using a single internal fossil calibration. The crown age of Hoffmannseggella is estimated at ~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.1 aGustafsson, A.L.S.1 aVerola, C.F.1 aAntonelli, Alexandre  uhttp://www.biomedcentral.com/1471-2148/10/17702420nas a2200169   4500008004100000020001400041245013300055210006900188300001200257490000800269520183700277100002502114700001702139700001602156700002302172856005502195       2010                        eng d  a1095-831200aClimate cooling promoted the expansion and radiation of a threatened group of South American orchids (Epidendroideae: Laeliinae)0 aClimate cooling promoted the expansion and radiation of a threat  a597-6070 v1003 aThe 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 11201314†Mya). The region corresponding today to southern Minas Gerais acted as a main 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.††© 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 100, 5972013607.1 aAntonelli, Alexandre1 aVerola, C.F.1 aParisod, C.1 aGustafsson, A.L.S.  uhttp://dx.doi.org/10.1111/j.1095-8312.2010.01438.x02540nas a2200169   4500008004100000245011700041210006900158300001200227520187300239100002502112700002802137700002102165700001802186700001802204700001602222856013202238       2010                        eng d00aMolecular studies and phylogeography of Amazonian tetrapods and their relation to geological and climatic models0 aMolecular studies and phylogeography of Amazonian tetrapods and   a386-4043 aExplaining the origins and evolution of Amazonian biodiversity continues to be an outstanding question in evolutionary biology. A plethora of mechanisms for promoting diversification has been proposed, generally invoking ecological and vicariance processes associated with major geological, hydrological and climatic events in the history of the Amazon drainage basin. Here, we review recent advances on this topic in the light of a rich new source of information: molecular phylogenetics and especially phylogeography. We present a comparison of phylogeographical studies covering over 50 clades of amphibians, birds, non-avian reptiles and mammals, focusing on studies where estimates of divergence times were explicitly calculated. We then discuss the congruence of the speciation patterns found in these studies with previous hypotheses of diversification. Based on the estimates of crown group ages, we conclude that a high proportion of present-day diversity is a result of Neogene diversification. The origin of most species clearly predates the Pleistocene by a considerable margin, refuting the long-held hypothesis that repeated expansion and contraction of lowland forests during Pleistocene climatic changes would be responsible for most of the Amazonian biodiversity. However, some evidence from phylogenetic and distributional patterns suggests that climate cycles did trigger speciation. Speciose lineages of tetrapods tend to be older than groups containing one to a few species, with a few notable exceptions. Considering each tetrapod group alone, amphibians and non-avian reptiles are generally older than birds, while mammals contain both recent and ancient clades of approximately the same number of species. Finally, we make recommendations about future research approaches and animal systems that deserve further attention from phylogeographers.1 aAntonelli, Alexandre1 aQuijada-Mascareñas, A.1 aCrawford, A., J.1 aBates, J., M.1 aVelazco, P.M.1 aWüster, W.  uhttps://nnb.myspecies.info/content/molecular-studies-and-phylogeography-amazonian-tetrapods-and-their-relation-geological-and-c00404nas a2200133   4500008004100000020001400041245004600055210004600101300001400147490000700161100002500168700002200193856005500215       2009                        eng d  a1523-173900aBrazil Should Facilitate Research Permits0 aBrazil Should Facilitate Research Permits  a1068-10690 v231 aAntonelli, Alexandre1 aRodriguez, Victor  uhttp://dx.doi.org/10.1111/j.1523-1739.2009.01300.x02093nas a2200169   4500008004100000245007500041210006900116260001800185300001400203490000800217520155100225100002501776700002701801700001901828700002301847856005301870       2009                        eng d00aTracing the impact of the Andean uplift on Neotropical plant evolution0 aTracing the impact of the Andean uplift on Neotropical plant evo  cJune 16, 2009  a9749-97540 v1063 aRecent phylogenetic studies have revealed the major role played by the uplift of the Andes in the extraordinary diversification of the Neotropical flora. These studies, however, have typically considered the Andean uplift as a single, time-limited event fostering the evolution of highland elements. This contrasts with geological reconstructions indicating that the uplift occurred in discrete periods from west to east and that it affected different regions at different times. We introduce an approach for integrating Andean tectonics with biogeographic reconstructions of Neotropical plants, using the coffee family (Rubiaceae) as a model group. The distribution of this family spans highland and montane habitats as well as tropical lowlands of Central and South America, thus offering a unique opportunity to study the influence of the Andean uplift on the entire Neotropical flora. Our results suggest that the Rubiaceae originated in the Paleotropics and used the boreotropical connection to reach South America. The biogeographic patterns found corroborate the existence of a long-lasting dispersal barrier between the Northern and Central Andes, the "Western Andean Portal". The uplift of the Eastern Cordillera ended this barrier, allowing dispersal of boreotropical lineages to the South, but gave rise to a huge wetland system ("Lake Pebas") in western Amazonia that prevented in situ speciation and floristic dispersal between the Andes and Amazonia for at least 6 million years. Here, we provide evidence of these events in plants.1 aAntonelli, Alexandre1 aNylander, Johan, A. A.1 aPersson, Claes1 aSanmartín, Isabel  uhttp://www.pnas.org/content/106/24/9749.abstract02448nas a2200133   4500008004100000020001400041245018400055210006900239300000700308490000600315520192000321100002502241856004802266       2009                        eng d  a1741-700700aHave giant lobelias evolved several times independently? Life form shifts and historical biogeography of the cosmopolitan and highly diverse subfamily Lobelioideae (Campanulaceae)0 aHave giant lobelias evolved several times independently Life for  a820 v73 aBACKGROUND:The tendency of animals and plants to independently develop similar features under similar evolutionary pressures - convergence - is a widespread phenomenon in nature. In plants, convergence has been suggested to explain the striking similarity in life form between the giant lobelioids (Campanulaceae, the bellflower family) of Africa and the Hawaiian Islands. Under this assumption these plants would have developed the giant habit from herbaceous ancestors independently, in much the same way as has been suggested for the giant senecios of Africa and the silversword alliance of Hawaii.RESULTS:Phylogenetic analyses based on plastid (rbcL, trnL-F) and nuclear (internal transcribed spacer [ITS]) DNA sequences for 101 species in subfamily Lobelioideae demonstrate that the large lobelioids from eastern Africa the Hawaiian Islands, and also South America, French Polynesia and southeast Asia, form a strongly supported monophyletic group. Ancestral state reconstructions of life form and distribution, taking into account phylogenetic uncertainty, indicate their descent from a woody ancestor that was probably confined to Africa. Molecular dating analyses using Penalized Likelihood and Bayesian relaxed clock approaches, and combining multiple calibration points, estimate their first diversification at ~25-33 million years ago (Ma), shortly followed by several long-distance dispersal events that resulted in the current pantropical distribution.CONCLUSION:These results confidently show that lobelioid species, commonly called 'giant', are very closely related and have not developed their giant form from herbaceous ancestors independently. This study, which includes the hitherto largest taxon sampling for subfamily Lobelioideae, highlights the need for a broad phylogenetic framework for testing assumptions about morphological development in general, and convergent evolution in particular.1 aAntonelli, Alexandre  uhttp://www.biomedcentral.com/1741-7007/7/8201753nas a2200229   4500008004100000245013000041210006900171300000900240490000700249520099400256653002301250653001801273653002001291653003101311653000901342653000901351653001201360653001601372653001101388100002501399856009901424       2008                        eng d00aHigher level phylogeny and evolutionary trends in Campanulaceae subfam. Lobelioideae: Molecular signal overshadows morphology0 aHigher level phylogeny and evolutionary trends in Campanulaceae   a1-180 v463 aRelationships within the subfamily Lobelioideae in Campanulaceae are inferred from DNA sequence variation in the rbcL and ndhF genes, and the trnL-F region including the trnL intron and the trnL-F intergenic spacer. Results derived from Bayesian and parsimony analyses provide evidence for the long-suspected paraphyly of the genus Lobelia, comprising over 400 species as presently circumscribed. The perennial dwarf herbs belonging to the Andean genus Lysipomia are sister to a group comprising the Neotropical shrubs Burmeistera, Centropogon, and Siphocampylus. Giant lobelioids from the Hawaiian Islands, Brazil, Africa, and Sri Lanka form a strongly supported group. Character optimizations on the phylogenetic tree reveal that shifts in fruit types and lignification have occurred much more commonly than generally assumed. The main clades in the subfamily are outlined, which largely contradict previous classifications based on morphology. © 2007 Elsevier Inc. All rights reserved.10aBayesian inference10aCampanulaceae10aFruit evolution10aLobelioideae (Lobeliaceae)10andhF10arbcL10aSH test10aSystematics10atrnL-F1 aAntonelli, Alexandre  uhttp://www.scopus.com/scopus/inward/record.url?eid=2-s2.0-37249069472&partnerID=40&rel=R7.0.0 