@article {94,
	title = {Contrasting plant diversification histories within the Andean biodiversity hotspot},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	volume = {107},
	number = {31},
	year = {2010},
	note = {Times Cited: 4},
	pages = {13783-13787},
	abstract = {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.},
	url = {<Go to ISI>://WOS:000280605900043},
	author = {Pennington, R. T. and Lavin, M. and S{\"a}rkinen, T. and Lewis, G. P. and Klitgaard, B. B. and Hughes, C. E.}
}
@article {92,
	title = {Amazonia through time: Andean uplift, climate change, landscape evolution, and biodiversity},
	journal = {Science},
	volume = {330},
	number = {6006},
	year = {2010},
	note = {Times Cited: 1},
	pages = {927-931},
	abstract = {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.},
	url = {<Go to ISI>://WOS:000284118000031},
	author = {Hoorn, C. and Wesselingh, F. P. and ter Steege, H. and Bermudez, M. A. and Mora, A. and Sevink, J. and Sanmart{\'\i}n, I. and Sanchez-Meseguer, A. and Anderson, C. L. and Figueiredo, J. P. and Jaramillo, C. and Riff, D. and Negri, F. R. and Hooghiemstra, H. and Lundberg, J. and Stadler, T. and S{\"a}rkinen, T. and Antonelli, A.}
}
@inbook {91,
	title = {Phylogeny and dating of <i>Aframomum </i>(Zingiberaceae)},
	booktitle = {Diversity, Phylogeny, and Evolution in the Monocotyledons},
	year = {2010},
	pages = {287-305},
	publisher = {Aarhus University Press},
	organization = {Aarhus University Press},
	address = {Aarhus},
	author = {Auvrey, G. and Harris, D. J. and Richardson, J. D. and Newman, M. F. and S{\"a}rkinen, T.}
}
@inbook {90,
	title = {Phylogeny and dating of <i>Aframomum </i>(Zingiberaceae)},
	booktitle = {Diversity, Phylogeny, and Evolution in the Monocotyledons},
	year = {2010},
	pages = {287-305},
	publisher = {Aarhus University Press},
	organization = {Aarhus University Press},
	address = {Aarhus},
	author = {Auvrey, G. and Harris, D. J. and Richardson, J. D. and Newman, M. F. and S{\"a}rkinen, T.}
}
@inbook {Gemeinholzer.2010,
	title = {Organizing specimen and tissue preservation in the field for subsequent molecular analyses},
	booktitle = {Manual on field recording techniques and protocols for all taxa biodiversity: Inventories and monitoring},
	series = {ABC Taxa},
	volume = {8},
	year = {2010},
	pages = {129{\textendash}157},
	url = {http://www.abctaxa.be/volumes/volume-8-manual-atbi},
	author = {Gemeinholzer, Birgit and Rey, Isabel and Weising, Kurt and Grundmann, Michael and Muellner, Alexandra N. and Zetzsche, Holger and Droege, Gabriele and Seberg, Ole and Petersen, Gitte and Rawson, David and Weigt, Lee},
	editor = {Eymann, Jutta and Degreef, Jerome and H{\"a}user, Christoph L. and Monje, Juan Carlos and Samyn, Yves and VandenSpiegel, Didier}
}
@article {61,
	title = {Epitypification of Heliotropium arborescens L. (Heliotropiaceae)},
	journal = {Taxon},
	volume = {59},
	number = {4},
	year = {2010},
	pages = {1263-1266},
	url = {http://www.ingentaconnect.com/content/iapt/tax/2010/00000059/00000004/art00023},
	author = {Luebert, F. and Weigend, M. and Hilger, H. H.}
}
@article {36,
	title = {On the origin of Amazonian landscapes and biodiversity: a synthesis},
	journal = {In Hoorn, C., Wesselingh, F.P.: Amazonia, Landscape and Species Evolution, 1st edition. Blackwell publishing},
	year = {2010},
	pages = {421-431},
	abstract = {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 {\textendash} with resemblance to the Present forest {\textendash} 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. },
	author = {Wesselingh, F. P. and Hoorn, C. and Kroonenberg, S.B. and Antonelli, Alexandre and Lundberg, J.G. and Vonhof, H.B. and Hooghiemstra, H.}
}
@article {37,
	title = {Amazonia Through Time: Andean Uplift, Climate Change, Landscape Evolution, and Biodiversity},
	journal = {Science},
	volume = {330},
	number = {6006},
	year = {2010},
	month = {November 12, 201},
	pages = {927-931},
	abstract = {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.},
	url = {http://www.sciencemag.org/cgi/content/abstract/330/6006/927},
	author = {Hoorn, C. and Wesselingh, F. P. and ter Steege, H. and Bermudez, M. A. and Mora, A. and Sevink, J. and Sanmart{\'\i}n, I. and Sanchez-Meseguer, A. and Anderson, C. L. and Figueiredo, J. P. and Jaramillo, C. and Riff, D. and Negri, F. R. and Hooghiemstra, H. and Lundberg, J. and Stadler, T. and S{\"a}rkinen, T. and Antonelli, Alexandre}
}
@article {38,
	title = {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)},
	journal = {BMC Evolutionary Biology},
	volume = {10},
	number = {1},
	year = {2010},
	pages = {177},
	abstract = {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.},
	isbn = {1471-2148},
	url = {http://www.biomedcentral.com/1471-2148/10/177},
	author = {Gustafsson, A.L.S. and Verola, C.F. and Antonelli, Alexandre}
}
@article {39,
	title = {Climate cooling promoted the expansion and radiation of a threatened group of South American orchids (Epidendroideae: Laeliinae)},
	journal = {Biological Journal of the Linnean Society},
	volume = {100},
	number = {3},
	year = {2010},
	note = {10.1111/j.1095-8312.2010.01438.x},
	pages = {597-607},
	abstract = {The Brazilian Cerrado is the most species-rich tropical savanna in the world. Within this biome, the Campos Rupestres ({\textquoteright}rocky savannas{\textquoteright}) 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{\textdagger}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{\textdagger}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.{\textdagger}{\textdagger}{\textcopyright} 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 100, 5972013607.},
	isbn = {1095-8312},
	url = {http://dx.doi.org/10.1111/j.1095-8312.2010.01438.x},
	author = {Antonelli, Alexandre and Verola, C.F. and Parisod, C. and Gustafsson, A.L.S.}
}
@article {40,
	title = {Molecular studies and phylogeography of Amazonian tetrapods and their relation to geological and climatic models},
	journal = {In Hoorn, C., Wesselingh, F.: Amazonia, Landscape and Species Evolution, 1st edition. Blackwell publishing},
	year = {2010},
	pages = {386-404},
	abstract = {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.},
	author = {Antonelli, Alexandre and Quijada-Mascare{\~n}as, A. and Crawford, A. J. and Bates, J. M. and Velazco, P.M. and W{\"u}ster, W.}
}
