TY - JOUR T1 - Why are there so many plant species in the Neotropics? JF - Taxon Y1 - 2011 A1 - Antonelli, Alexandre A1 - Sanmartín, I. SP - 403 EP - 414 VL - 60 ER - TY - JOUR T1 - Mass Extinction, Gradual Cooling, or Rapid Radiation? Reconstructing the Spatiotemporal Evolution of the Ancient Angiosperm Genus Hedyosmum (Chloranthaceae) Using Empirical and Simulated Approaches JF - Systematic Biology Y1 - 2011 A1 - Antonelli, Alexandre A1 - Sanmartín, Isabel SP - 596 EP - 615 AB - Chloranthaceae 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. VL - 60 UR - http://sysbio.oxfordjournals.org/content/60/5/596.abstract ER - TY - JOUR T1 - Revisiting taxonomy, morphological evolution, and fossil calibration strategies in Chloranthaceae JF - Journal of Systematics and Evolution Y1 - 2011 A1 - Zhang, Qiang A1 - Antonelli, Alexandre A1 - Feild, Taylor S. A1 - Kong, Hong-Zhi SP - 315–329 AB - Chloranthaceae 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. VL - 49 UR - http://www.jse.ac.cn/Abstract.aspx?id=2827 ER - TY - JOUR T1 - Diversification in the Andes: Age and origins of South American Heliotropium lineages (Heliotropiaceae, Boraginales) JF - Molecular Phylogenetics and Evolution Y1 - 2011 DO - 10.1016/j.ympev.2011.06.001 A1 - Luebert, F. A1 - Hilger, H. H. A1 - Weigend, M. SP - 90–102 VL - 61 UR - http://dx.doi.org/10.1016/j.ympev.2011.06.001 IS - 1 ER - TY - JOUR T1 - Phylogenetic relationships and morphological diversity in Neotropical Heliotropium (Heliotropiaceae) JF - Taxon Y1 - 2011 A1 - Luebert, F. A1 - Brokamp, G. A1 - Wen, J. A1 - Weigend, M. A1 - Hilger, H. H. SP - 663 EP - 680 VL - 60 UR - http://www.ingentaconnect.com/content/iapt/tax/2011/00000060/00000003/art00004 IS - 3 ER - TY - JOUR T1 - Underestimated endemic species diversity in the dry inter-Andean valley of the Río Marañón, northern Peru: An example from Mimosa (Leguminosae, Mimosoideae) JF - Taxon Y1 - 2011 A1 - Särkinen, T. E. A1 - Marcelo-Peña, José Luis A1 - Yomona, A. Daza A1 - Simon, Marcelo F. A1 - Pennington, R. Toby A1 - Hughes, Colin E. SP - 139 EP - 150 VL - 60 UR - - http://www.ingentaconnect.com/content/iapt/tax/2011/00000060/00000001/art00012 N1 - - 139 ER - TY - JOUR T1 - Recent oceanic long-distance dispersal and divergence in the amphi-Atlantic rain forest genus Renealmia L.f. (Zingiberaceae) JF - Molecular Phylogenetics and Evolution Y1 - 2007 A1 - Särkinen, T. E. A1 - Newman, M. F. A1 - Maas, P. J. M. A1 - Maas, H. A1 - Poulsen, A. D. A1 - Harris, D. J. A1 - Richardson, J. E. A1 - Clark, A. A1 - Hollingsworth, M. A1 - Pennington, R. T. SP - 968 EP - 980 AB - Renealmia L.f. (Zingiberaceae) is one of the few tropical plant genera with numerous species in both Africa and South America but not in Asia. Based on phylogenetic analysis of nuclear ribosomal internal transcribed spacer (ITS) and chloroplast trnL-F DNA, Rellealmia is shown to be monophyletic with high branch support. Low sequence divergence found in the two genome regions (ITS: 0-2.4%; trnL-F: 0-1.9%) suggests recent diversification within the genus. Molecular divergence age estimates give further support to the recent origin of the genus and show that Renealmia has attained its amphi-Atlantic distribution by an oceanic long-distance dispersal event from Africa to South America during the Miocene or Pliocene (15.8-2.7 My ago). Some support is found for the hypothesis that speciation in neotropical Renealmia was influenced by the Andean orogeny. Speciation has been approximately simultaneous on both sides of the Atlantic, but increased taxon sampling is required to compare the speciation rates between the New World and Old World tropics. (c) 2007 Elsevier Inc. All rights reserved. VL - 44 SN - 1055-7903 UR - ://WOS:000249845400004 N1 - Times Cited: 7 ER - TY - JOUR T1 - Systematics and biogeography of Amicia Kunth (Leguminosae, Papilionoideae) JF - Systematic Botany Monographs Y1 - 2011 A1 - Särkinen, T. A1 - Hughes, C. E. VL - accepted pending revision ER - TY - JOUR T1 - Evolutionary islands in the Andes: persistence, isolation and endemism in Andean dry tropical forests JF - Submitted Y1 - 2011 A1 - Särkinen, T. A1 - Simon, M. F. A1 - Lavin, M. A1 - Pennington, R. T. A1 - Hughes, C. E. ER - TY - JOUR T1 - Origins of biodiversity response JF - Science Y1 - 2011 A1 - Hoorn, C. A1 - Wesselingh, F. P. A1 - ter Steege, H. A1 - Bermudez, M. A. A1 - Mora, A. A1 - Sevink, J. A1 - Sanmartín, I. A1 - Sanchez-Meseguer, A. A1 - Anderson, C. L. A1 - Figueiredo, J. P. A1 - Jaramillo, C. A1 - Riff, D. A1 - Negri, F. R. A1 - Hooghiemstra, H. A1 - Lundberg, J. A1 - Stadler, T. A1 - Särkinen, T. A1 - Antonelli, A. SP - 399 EP - 400 VL - 331 UR - ://WOS:000286635900027 N1 - Times Cited: 0 ER - TY - JOUR T1 - Contrasting plant diversification histories within the Andean biodiversity hotspot JF - Proceedings of the National Academy of Sciences of the United States of America Y1 - 2010 A1 - Pennington, R. T. A1 - Lavin, M. A1 - Särkinen, T. A1 - Lewis, G. P. A1 - Klitgaard, B. B. A1 - Hughes, C. E. SP - 13783 EP - 13787 AB - The Andes are the most species-rich global biodiversity hotspot. Most research and conservation attention in the Andes has focused on biomes such as rain forest, cloud forest, and paramo, where much plant species diversity is the hypothesized result of rapid speciation associated with the recent Andean orogeny. In contrast to these mesic biomes, we present evidence for a different, older diversification history in seasonally dry tropical forests (SDTF) occupying rain-shadowed inter-Andean valleys. High DNA sequence divergence in Cyathostegia mathewsii, a shrub endemic to inter-Andean SDTF, indicates isolation for at least 5 million years of populations separated by only ca. 600 km of high cordillera in Peru. In conjunction with fossil evidence indicating the presence of SDTF in the Andes in the late Miocene, our data suggest that the disjunct small valley pockets of inter-Andean SDTF have persisted over millions of years. These forests are rich in endemic species but massively impacted, and merit better representation in future plans for science and conservation in Andean countries. VL - 107 UR - ://WOS:000280605900043 N1 - Times Cited: 4 ER - TY - JOUR T1 - Amazonia through time: Andean uplift, climate change, landscape evolution, and biodiversity JF - Science Y1 - 2010 A1 - Hoorn, C. A1 - Wesselingh, F. P. A1 - ter Steege, H. A1 - Bermudez, M. A. A1 - Mora, A. A1 - Sevink, J. A1 - Sanmartín, I. A1 - Sanchez-Meseguer, A. A1 - Anderson, C. L. A1 - Figueiredo, J. P. A1 - Jaramillo, C. A1 - Riff, D. A1 - Negri, F. R. A1 - Hooghiemstra, H. A1 - Lundberg, J. A1 - Stadler, T. A1 - Särkinen, T. A1 - Antonelli, A. SP - 927 EP - 931 AB - The 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. VL - 330 UR - ://WOS:000284118000031 N1 - Times Cited: 1 ER - TY - CHAP T1 - Phylogeny and dating of Aframomum (Zingiberaceae) T2 - Diversity, Phylogeny, and Evolution in the Monocotyledons Y1 - 2010 A1 - Auvrey, G. A1 - Harris, D. J. A1 - Richardson, J. D. A1 - Newman, M. F. A1 - Särkinen, T. SP - 287 EP - 305 JF - Diversity, Phylogeny, and Evolution in the Monocotyledons PB - Aarhus University Press CY - Aarhus ER - TY - CHAP T1 - Phylogeny and dating of Aframomum (Zingiberaceae) T2 - Diversity, Phylogeny, and Evolution in the Monocotyledons Y1 - 2010 A1 - Auvrey, G. A1 - Harris, D. J. A1 - Richardson, J. D. A1 - Newman, M. F. A1 - Särkinen, T. SP - 287 EP - 305 JF - Diversity, Phylogeny, and Evolution in the Monocotyledons PB - Aarhus University Press CY - Aarhus ER - TY - JOUR T1 - Phylogenetic analysis of Fosterella L.B. Sm. (Pitcairnioideae, Bromeliaceae) based on four chloroplast DNA regions JF - Molecular Phylogenetics and Evolution Y1 - 2009 DO - 10.1016/j.ympev.2009.01.001 A1 - Rex, Martina A1 - Schulte, Katharina A1 - Zizka, Georg A1 - Peters, Jule A1 - Vásquez, Roberto A1 - Ibisch, Pierre L. A1 - Weising, Kurt SP - 472–485 VL - 51 ER - TY - JOUR T1 - Towards a taxonomic revision of the genus Fosterella (Bromeliaceae) JF - Selbyana Y1 - 2008 A1 - Peters, Jule A1 - Vásquez, Roberto A1 - Osinaga, Arturo A1 - Leme, Elton A1 - Weising, Kurt A1 - Ibisch, Pierre L. SP - 182–194 VL - 29 ER - TY - JOUR T1 - Inferring the diversification of the epiphytic fern genus Serpocaulon (Polypodiaceae) in South America using chloroplast sequences and amplified fragment length polymorphisms JF - Plant Systematics and Evolution Y1 - 2008 DO - 10.1007/s00606-008-0021-3 A1 - Kreier, H.-P A1 - Rex, M. A1 - Weising, Kurt A1 - Kessler, M. A1 - Smith, A. R. A1 - Schneider, H. SP - 1–16 VL - 274 ER - TY - JOUR T1 - AFLP analysis of genetic relationships in the genus Fosterella L.B. Smith (Pitcairnioideae, Bromeliaceae) JF - Genome Y1 - 2007 DO - 10.1139/G06-141 A1 - Rex, Martina A1 - Patzolt, Kerstin A1 - Schulte, Katharina A1 - Zizka, Georg A1 - Vásquez, Roberto A1 - Ibisch, Pierre L. A1 - Weising, Kurt SP - 90–105 VL - 50 ER - TY - CHAP T1 - Organizing specimen and tissue preservation in the field for subsequent molecular analyses T2 - Manual on field recording techniques and protocols for all taxa biodiversity: Inventories and monitoring Y1 - 2010 A1 - Gemeinholzer, Birgit A1 - Rey, Isabel A1 - Weising, Kurt A1 - Grundmann, Michael A1 - Muellner, Alexandra N. A1 - Zetzsche, Holger A1 - Droege, Gabriele A1 - Seberg, Ole A1 - Petersen, Gitte A1 - Rawson, David A1 - Weigt, Lee ED - Eymann, Jutta ED - Degreef, Jerome ED - Häuser, Christoph L. ED - Monje, Juan Carlos ED - Samyn, Yves ED - VandenSpiegel, Didier SP - 129–157 JF - Manual on field recording techniques and protocols for all taxa biodiversity: Inventories and monitoring T3 - ABC Taxa VL - 8 UR - http://www.abctaxa.be/volumes/volume-8-manual-atbi ER - TY - JOUR T1 - Epitypification of Heliotropium arborescens L. (Heliotropiaceae) JF - Taxon Y1 - 2010 A1 - Luebert, F. A1 - Weigend, M. A1 - Hilger, H. H. SP - 1263 EP - 1266 VL - 59 UR - http://www.ingentaconnect.com/content/iapt/tax/2010/00000059/00000004/art00023 ER - TY - JOUR T1 - Phylogenetic analysis and evolutionary diversification of Heliotropium sect. Cochranea (Heliotropiaceae) in the Atacama Desert JF - Systematic Botany Y1 - 2008 DO - 10.1600/036364408784571635 A1 - Luebert, F. A1 - Wen, J. SP - 390 EP - 402 VL - 33 UR - http://www.bioone.org/doi/abs/10.1600/036364408784571635 IS - 2 ER - TY - JOUR T1 - Systematic placement and biogeographical relationships of the monotypic genera Gypothamnium and Oxyphyllum (Asteraceae: Mutisioideae) from the Atacama Desert JF - Botanical Journal of the Linnean Society Y1 - 2009 DO - 10.1111/j.1095-8339.2008.00926.x A1 - Luebert, F. A1 - Wen, J. A1 - Dillon, M. O. SP - 32 EP - 51 VL - 159 UR - http://onlinelibrary.wiley.com/doi/10.1111/j.1095-8339.2008.00926.x/abstract ER - TY - JOUR T1 - Origins of Biodiversity–Response JF - Science Y1 - 2011 A1 - Hoorn, C. A1 - Wesselingh, F. P. A1 - Steege, H. Ter A1 - Bermudez, M. A. A1 - Mora, A. A1 - Sevink, J. A1 - Sanmartín, I. A1 - Sanchez-Meseguer, A. A1 - Anderson, C. L. A1 - Figueiredo, J. P. A1 - Jaramillo, C. A1 - Riff, D. A1 - Negri, F. R. A1 - Hooghiemstra, H. A1 - Lundberg, J. A1 - Stadler, T. A1 - Särkinen, T. A1 - Antonelli, Alexandre SP - 399 EP - 400 VL - 331 UR - http://www.sciencemag.org/content/331/6016/399.short ER - TY - JOUR T1 - Vicariance or long-distance dispersal: historical biogeography of the pantropical subfamily Chrysophylloideae (Sapotaceae) JF - Journal of Biogeography Y1 - 2011 A1 - Bartish, Igor V. A1 - Antonelli, Alexandre A1 - Richardson, James E. A1 - Swenson, Ulf SP - 177 EP - 190 KW - Africa KW - Australasia KW - land bridges KW - Late Cretaceous KW - long-distance dispersal KW - molecular dating KW - Neotropics KW - Sapotaceae KW - Tertiary KW - vicariance AB - Abstract 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. PB - Blackwell Publishing Ltd VL - 38 SN - 1365-2699 UR - http://dx.doi.org/10.1111/j.1365-2699.2010.02389.x ER - TY - JOUR T1 - On the origin of Amazonian landscapes and biodiversity: a synthesis JF - In Hoorn, C., Wesselingh, F.P.: Amazonia, Landscape and Species Evolution, 1st edition. Blackwell publishing Y1 - 2010 A1 - Wesselingh, F. P. A1 - Hoorn, C. A1 - Kroonenberg, S.B. A1 - Antonelli, Alexandre A1 - Lundberg, J.G. A1 - Vonhof, H.B. A1 - Hooghiemstra, H. SP - 421 EP - 431 AB - In 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. ER - TY - JOUR T1 - Amazonia Through Time: Andean Uplift, Climate Change, Landscape Evolution, and Biodiversity JF - Science Y1 - 2010 A1 - Hoorn, C. A1 - Wesselingh, F. P. A1 - ter Steege, H. A1 - Bermudez, M. A. A1 - Mora, A. A1 - Sevink, J. A1 - Sanmartín, I. A1 - Sanchez-Meseguer, A. A1 - Anderson, C. L. A1 - Figueiredo, J. P. A1 - Jaramillo, C. A1 - Riff, D. A1 - Negri, F. R. A1 - Hooghiemstra, H. A1 - Lundberg, J. A1 - Stadler, T. A1 - Särkinen, T. A1 - Antonelli, Alexandre SP - 927 EP - 931 AB - The 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. VL - 330 UR - http://www.sciencemag.org/cgi/content/abstract/330/6006/927 ER - TY - JOUR T1 - 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) JF - BMC Evolutionary Biology Y1 - 2010 A1 - Gustafsson, A.L.S. A1 - Verola, C.F. A1 - Antonelli, Alexandre SP - 177 AB - 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 (~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. VL - 10 SN - 1471-2148 UR - http://www.biomedcentral.com/1471-2148/10/177 ER - TY - JOUR T1 - Climate cooling promoted the expansion and radiation of a threatened group of South American orchids (Epidendroideae: Laeliinae) JF - Biological Journal of the Linnean Society Y1 - 2010 A1 - Antonelli, Alexandre A1 - Verola, C.F. A1 - Parisod, C. A1 - Gustafsson, A.L.S. SP - 597 EP - 607 AB - 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 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. VL - 100 SN - 1095-8312 UR - http://dx.doi.org/10.1111/j.1095-8312.2010.01438.x N1 - 10.1111/j.1095-8312.2010.01438.x ER - TY - JOUR T1 - Molecular studies and phylogeography of Amazonian tetrapods and their relation to geological and climatic models JF - In Hoorn, C., Wesselingh, F.: Amazonia, Landscape and Species Evolution, 1st edition. Blackwell publishing Y1 - 2010 A1 - Antonelli, Alexandre A1 - Quijada-Mascareñas, A. A1 - Crawford, A. J. A1 - Bates, J. M. A1 - Velazco, P.M. A1 - Wüster, W. SP - 386 EP - 404 AB - Explaining 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. ER - TY - JOUR T1 - Brazil Should Facilitate Research Permits JF - Conservation Biology Y1 - 2009 A1 - Antonelli, Alexandre A1 - Victor Rodriguez SP - 1068 EP - 1069 VL - 23 SN - 1523-1739 UR - http://dx.doi.org/10.1111/j.1523-1739.2009.01300.x N1 - 10.1111/j.1523-1739.2009.01300.x ER - TY - JOUR T1 - Tracing the impact of the Andean uplift on Neotropical plant evolution JF - Proceedings of the National Academy of Sciences Y1 - 2009 A1 - Antonelli, Alexandre A1 - Nylander, Johan A. A. A1 - Persson, Claes A1 - Sanmartín, Isabel SP - 9749 EP - 9754 AB - Recent 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. VL - 106 UR - http://www.pnas.org/content/106/24/9749.abstract ER - TY - JOUR T1 - Have giant lobelias evolved several times independently? Life form shifts and historical biogeography of the cosmopolitan and highly diverse subfamily Lobelioideae (Campanulaceae) JF - Bmc Biology Y1 - 2009 A1 - Antonelli, Alexandre SP - 82 AB - BACKGROUND: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. VL - 7 SN - 1741-7007 UR - http://www.biomedcentral.com/1741-7007/7/82 ER - TY - JOUR T1 - Higher level phylogeny and evolutionary trends in Campanulaceae subfam. Lobelioideae: Molecular signal overshadows morphology JF - Molecular Phylogenetics and Evolution Y1 - 2008 A1 - Antonelli, Alexandre SP - 1 EP - 18 KW - Bayesian inference KW - Campanulaceae KW - Fruit evolution KW - Lobelioideae (Lobeliaceae) KW - ndhF KW - rbcL KW - SH test KW - Systematics KW - trnL-F AB - Relationships 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. VL - 46 UR - http://www.scopus.com/scopus/inward/record.url?eid=2-s2.0-37249069472&partnerID=40&rel=R7.0.0 N1 - 10557903 (ISSN)Export Date: 28 January 2008Source: ScopusCODEN: MPEVEdoi: 10.1016/j.ympev.2007.06.015Language of Original Document: EnglishCorrespondence Address: Antonelli, A.; Department of Plant and Environmental Sciences; Go?teborg University; P.O. Box 461 SE-405 30 Go?teborg, Sweden; email: alexandre.antonelli@dpes.gu.seReferences: Albach, D.C., Soltis, P.S., Soltis, D.E., Olmstead, R.G., Phylogenetic analysis of asterids based on sequences of four genes (2001) Ann. Mo. Bot. Gard., 88, pp. 163-212; Andersson, L., Antonelli, A., Phylogeny of the tribe Cinchoneae (Rubiaceae), its position in Cinchonoideae, and description of a new genus, Ciliosemina (2005) Taxon, 54 (1), pp. 17-28; Andersson, L., Chase, M.W., Phylogeny and classification of Marantaceae (2001) Bot. J. Linn. Soc., 135, pp. 275-287; Andersson, L., Rova, J.H.E., The rps16 intron and the phylogeny of the Rubioideae (Rubiaceae) (1999) Pl. Syst. Evol., 214, pp. 161-186; Batterman, M.R.W., Lammers, T.G., Branched foliar trichomes of Lobelioideae (Campanulaceae) and the infrageneric classification of Centropogon (2004) Syst. Bot., 29, pp. 448-458; Bolmgren, K., Eriksson, O., Fleshy fruits-origins, niche shifts, and diversification (2005) Oikos, 109, pp. 255-272; Bremer, B., Bremer, K., Heidari, N., Erixon, P., Olmstead, R.G., Anderberg, A.A., Ka?llersjo?, M., Barkhordarian, E., Phylogenetics of asterids based on 3 coding and 3 non-coding chloroplast DNA markers and the utility of non-coding DNA at higher taxonomic levels (2002) Mol. Phylogenet. Evol., 24, pp. 274-301; Bremer, K., Friis, E.M., Bremer, B., Molecular phylogenetic dating of asterid flowering plants shows early Cretaceous diversification (2004) Syst. Biol., 53, pp. 496-505; Buss, C.C., Lammers, T.G., Wise, R.R., Seed coat morphology and its systematic implications in Cyanea and other genera of Lobelioideae (Campanulaceae) (2001) Amer. J. Bot., 88, pp. 1301-1308; Candolle, A.P.d., (1830) Prodromus Systematis Naturalis Regni Vegetabilis, , Treutell and Wiirtz, Paris; Chase, M.W., Albert, V.A., A perspective on the contribution of plastid rbcL sequences to Angiosperm phylogenetics (1998) Molecular Systematics of Plants II-DNA Sequencing, pp. 488-507. , Soltis D.E., Soltis P.S., and Doyle J.J. (Eds), Kluwer Academic Publishers, Massachusetts; Cosner, M.E., Jansen, R.K., Lammers, T.G., Phylogenetic relationships in the Campanulales based on rbcL sequences (1994) Pl. Syst. Evol., 190, pp. 79-95; Darlu, P., Lecointre, G., When does the incongruence length difference test fail? (2002) Mol. Biol. Evol., 19 (4), pp. 432-437; Dolphin, K., Belshaw, R., Orme, C.D.L., Quicke, D.L.J., Noise and incongruence: interpreting results of the incongruence length difference test (2000) Mol. Phylogenet. Evol., 17 (3), pp. 401-406; Farris, J.S., Ka?llersjo?, M., Kluge, A.G., Bult, C., Testing significance of incongruence (1995) Cladistics, 10, pp. 315-319; Goldman, N., Anderson, J.P., Rodrigo, A.G., Likelihood-based tests of topologies in phylogenetics (2000) Syst. Biol., 49 (4), pp. 652-670; Givnish, T.J., Sytsma, K.J., Smith, J.F., Hahn, W.J., Molecular evolution, adaptive radiation, and geographic speciation in Cyanea (Campanulaceae, Lobelioideae) (1995) Hawaiian Biogeography: Evolution on a Hot Spot Archipelago, pp. 288-337. , Wagner W.L., and Funk V.A. (Eds), Smithsonian Institution Press, Washington; Gustafsson, M.H.G., Backlund, A., Bremer, B., Phylogeny of the Asterales sensu lato based on rbcL sequences with particular reference to the Goodeniaceae (1996) Pl. Syst. Evol., 199 (3-4), pp. 217-242; Hipp, A.L., Hall, J.C., Sytsma, K.J., Congruence versus phylogenetic accuracy: revisiting the incongruence length difference test (2004) Syst. Biol., 53 (1), pp. 81-89; Huelsenbeck, J.P., Ronquist, F., MRBAYES: bayesian inference of phylogeny (2001) Bioinformatics, 17, pp. 754-755; Janson, C.H., Measuring evolutionary constraints: a markov model for phylogenetic transitions among seed dispersal syndromes (1992) Evolution, 46 (1), pp. 136-158; Judd, W.S., Campbell, C.S., Kellogg, E.A., Stevens, P.F., Donoughue, M.J., (2002) Plant Systematics: A Phylogenetic Approach. second ed., , Sinauer Associates, Sunderland; Katoh, K., Kuma, K.-i., Toh, H., Miyata, T., MAFFT version 5: improvement in accuracy of multiple sequence alignment (2005) Nucleic Acids Res., 33 (2), pp. 511-518; Kim, K.-J., Jansen, R.K., ndhF sequence evolution and the major clades in the sunflower family (1995) Evolution, 92, pp. 10379-10383; Knox, E.B., Downie, S.R., Palmer, J.D., Chloroplast genome rearrangements and the evolution of giant lobelias from herbaceous ancestors (1993) Mol. Biol. Evol., 10 (2), pp. 414-430; Koopman, M.M., Ayers, T.J., Nectar spur evolution in the Mexican lobelias (Campanulaceae: Lobelioideae) (2005) Am. J. Bot., 92, pp. 558-562; Ka?llersjo?, M., Sta?hl, B., Phylogeny of the Theophrastaceae (Ericales s.l.) (2003) Int. J. Plant. Sci., 164, pp. 579-591; Lammers, T.G., Sequential paedomorphosis among the endemic Hawaiian Lobelioideae (Campanulaceae) (1990) Taxon, 39, pp. 206-211; Lammers, T.G., Campanulaceae (1990) Manual of the Flowering Plants of Hawaii, , Wagner W.L., Herbst D.R., and Sohmer D.R. (Eds), University of Hawaii Press, Honolulu; Lammers, T.G., Hensold, N., Chromosome numbers of Campanulaceae. II. The Lobelia tupa complex of Chile (1992) Am. J. Bot., 79, pp. 585-588; Lammers, T.G., Chromosome numbers of Campanulaceae. III. Review and integration of data for subfamily Lobelioideae (1993) Am. J. Bot., 80, pp. 660-675; Lammers, T.G., Review of the Neotropical endemics Burmeistera, Centropogon, and Siphocampylus (Campanulaceae: Lobelioideae), with description of 18 new species and a new section (1998) Brittonia, 50, pp. 233-262; Lammers, T.G., Nemacladoideae, a new subfamily of Campanulaceae (1998) Novon, 8, pp. 36-37; Lammers, T.G., Revision of Lobelia sect. Tupa (Campanulaceae: Lobelioideae) (2000) Sida, 19, pp. 87-110; Lammers, T.G., Revision of Lobelia sect. Homochilus (Campanulaceae:Lobelioideae) (2004) Sida, 21 (2), pp. 591-623; Lammers, T.G., Campanulaceae (2007) World checklist and bibliography of Campanulaceae, , Kubitzki K. (Ed), Kew Publishing; Luteyn, J.L., A new Burmeistera (Campanulaceae: Lobelioideae) from western Colombia (1986) Syst. Bot., 11, pp. 474-476; Mabberley, D.J., The pachycaul lobelias of Africa and St. Helena (1974) Kew Bull., 29, pp. 535-584; McVaugh, R., Studies in South American Lobelioideae (Campanulaceae) with special reference to Colombian species (1949) Brittonia, 6, pp. 450-493; Murata, J., Systematic implication of seed coat morphology in Lobelia (Campanulaceae-Lobelioideae) (1992) J. Fac. Sci. Univ. Tokyo (Sect. 3), 15 (2), pp. 155-172; Murata, J., A revision of infrageneric classification of Lobelia (Campanulaceae-Lobelioideae) with special reference to seed coat morphology (1995) J. Fac. Sci. Univ. Tokyo (Sect. 3), 15, pp. 349-371; Nylander, J.A.A., (2004) MrModeltest v2. Program distributed by the author, , Evolutionary Biology Centre, Uppsala University; Olmstead, R.G., Sweere, J.A., Combining data in phylogenetic systematics: an empirical approach using three molecular data sets in the solanaceae (1994) Syst. Biol., 43 (4), pp. 467-481; Olmstead, R.G., Kim, K., Jansen, R.K., Wagstaff, S.J., The phylogeny of the Asteridae sensu lato based on chloroplast ndhF gene sequences (2000) Mol. Phylogenet. Evol., 16 (1), pp. 96-112; Pepper, A.S.R., Gustafsson, M.H.G., Albert, V.A., Molecular systematics of neotropical Lobelioideae (Campanulaceae), with emphasis on Burmeistera, Centropogon, and Siphocampylus, and the utility of fruit and floral characters in lobelioid classification (1997) Am. J. Bot., 84 (SUPPL. 6), p. 222. , [abstract]; Pol, D., Empirical problems of the Hierarchical likelihood ratio test for model selection (2004) Syst. Biol., 53 (6), pp. 949-962; Posada, D., Buckley, T., Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests (2004) Syst. Biol., 53 (5), pp. 793-808; Rova, J.H.E., Delprete, P.G., Andersson, L., Albert, V.A., A trnL-F cpDNA sequence study of the Condamineeae-Rondeletieae-Sipaneeae complex with implications on the phylogeny of the Rubiaceae (2002) Am. J. Bot., 89, pp. 145-159; Ruas, P.M., Vanzela, A.L.L., Vieira, A.O.S., Bernini, C., Ruas, C.R., Karyotype studies in Brazilian species of Lobelia L., subgenus Tupa (Campanulaceae) (2001) Rev. Bras. Bot., 24, pp. 249-254; Schultheis, L.M., Systematics of Downingia (Campanulaceae) based on molecular sequence data: implications for floral and chromosome evolution (2001) Syst. Bot., 26 (3), pp. 603-621; Shimodaira, H., Hasegawa, M., Multiple comparisons of log-likelihoods with applications to phylogenetic inference (1999) Mol. Biol. Evol., 16 (8), pp. 1114-1116; Soltis, D.E., Soltis, P.S., Choosing an approach and an appropriate gene for phylogenetic analysis (1998) Molecular Systematics of Plants II-DNA Sequencing, pp. 1-42. , Soltis D.E., Soltis P.S., and Doyle J.J. (Eds), Kluwer Academic Publishers, Massachusetts; Stace, H.M., James, S.H., Another perspective on cytoevolution in Lobelioideae (Campanulaceae) (1996) Am. J. Bot., 83, pp. 1356-1364; Stein, B.A., Synopsis of the genus Burmeistera (Campanulaceae: Lobelioideae) in Peru (1987) Ann. Mo. Bot. Gard., 74, pp. 494-496; Swofford, D.L., (1999) PAUP*. Phylogenetic Analysis Using Parsimony (* and other methods), , Sinauer Associates, Sunderland, Massachusetts; Taberlet, P., Gielly, L., Pautou, G., Bouvet, J., Universal primers for amplification of three non-coding regions of chloroplast DNA (1991) Pl. Mol. Biol., 17, pp. 1105-1109; Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., Higgins, D.G., The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools (1997) Nucleic Acids Res., 24, pp. 4876-4882; Wiens, J.J., Missing data, incomplete taxa, and phylogenetic accuracy (2003) Syst. Biol., 52 (4), pp. 528-538; Wimmer, F.E., Campanulaceae-Lobelioideae, II Teil (1953) Das Pflanzenreich, IV.276b, , Stubbe H., and Noach K. (Eds), Akademie Verlag, Berlin; Wimmer, F.E., Campanulaceae-Cyphioideae (1968) Das Pflanzenreich, IV.276c, , Stubbe H. (Ed), Akademie Verlag, Berlin; Zander, R.H., Minimal values for reliability of bootstrap and jackknife proportions, decay index, and bayesian posterior probability (2004) Phyloinformatics, 2, pp. 1-13 ER - TY - JOUR T1 - Physiological diversity and biogeography of vascular epiphytes at Río Changuinola, Panama JF - Flora - Morphology, Distribution, Functional Ecology of Plants Y1 - 2011 DO - DOI: 10.1016/j.flora.2010.01.011 A1 - Stefan Wester A1 - Glenda Mendieta-Leiva A1 - Lars Nauheimer A1 - Wolfgang Wanek A1 - Holger Kreft A1 - Gerhard Zotz SP - 66 EP - 79 KW - Floristic composition VL - 206 UR - http://www.sciencedirect.com/science/article/B7GX0-5178VJS-1/2/8dc2de2078fe376c49fb71252ed0d933 ER -