| 1. |
- Antonelli, Alexandre, 1978, et al.
(author)
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Settling a family feud: a high-level phylogenomic framework for the Gentianales based on 353 nuclear genes and partial plastomes
- 2021
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In: American Journal of Botany. - : Wiley. - 0002-9122 .- 1537-2197. ; 108:7, s. 1143-1165
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Journal article (peer-reviewed)abstract
- Premise: Comprising five families that vastly differ in species richness—ranging from Gelsemiaceae with 13 species to the Rubiaceae with 13,775 species—members of the Gentianales are often among the most species-rich and abundant plants in tropical forests. Despite considerable phylogenetic work within particular families and genera, several alternative topologies for family-level relationships within Gentianales have been presented in previous studies. Methods: Here we present a phylogenomic analysis based on nuclear genes targeted by the Angiosperms353 probe set for approximately 150 species, representing all families and approximately 85% of the formally recognized tribes. We were able to retrieve partial plastomes from off-target reads for most taxa and infer phylogenetic trees for comparison with the nuclear-derived trees. Results: We recovered high support for over 80% of all nodes. The plastid and nuclear data are largely in agreement, except for some weakly to moderately supported relationships. We discuss the implications of our results for the order’s classification, highlighting points of increased support for previously uncertain relationships. Rubiaceae is sister to a clade comprising (Gentianaceae + Gelsemiaceae) + (Apocynaceae + Loganiaceae). Conclusions: The higher-level phylogenetic relationships within Gentianales are confidently resolved. In contrast to recent studies, our results support the division of Rubiaceae into two subfamilies: Cinchonoideae and Rubioideae. We do not formally recognize Coptosapelteae and Luculieae within any particular subfamily but treat them as incertae sedis. Our framework paves the way for further work on the phylogenetics, biogeography, morphological evolution, and macroecology of this important group of flowering plants.
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| 2. |
- Antonelli, Alexandre, 1978
(author)
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Spatiotemporal Evolution of Neotropical Organisms: New Insights into an Old Riddle.
- 2008
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Doctoral thesis (other academic/artistic)abstract
- Nowhere else on Earth are there so many species of plants and animals as in the Neotropical region. Yet, many questions remain concerning the causes underlying such outstanding diversification. In this thesis, I use a combination of molecular-based methods (phylogenetic inference, molecular dating, biogeographic reconstruction, analyses of diversification and extinction) together with geological, palaeontological, hydrological and climatological evidence to reconstruct the evolution of some Neotropical organisms in space and time. Diversification patterns obtained from case studies in the plant families Rubiaceae, Chloranthaceae and Campanulaceae are compared to published studies of other plants and animals, especially tetrapods (birds, non-avian reptiles, amphibians and mammals). The uplift of the Northern Andes in the Neogene (~23 Ma to today) is concluded to have played a major role in promoting Neotropical diversification, by fostering allopatric speciation of lowland organisms and inducing adaptive radiations in newly formed montane habitats. In addition, its formation caused the end of a lowland corridor episodically invaded by marine incursions that separated the Northern and Central Andes, enabling the southward dispersal of boreotropical groups already present in northwestern South America. The fact that most Neotropical plant groups are either Andean-centred or Amazonian-centred is explained by the long-lasting effect of the Palaeo-Orinoco and Lake Pebas as dispersal barriers between these two diversity centres. Finally, a new diversification model is proposed to explain the origin and evolution of organisms in two areas characterized today by unusually high levels of species richness and endemism: the Huancabamba region and western Amazonia. Under this model, speciation is proposed to have occurred over several million years in connection with the recolonization of previously submerged areas, by means of adaptive radiation of founder colonies and secondary contact of previously isolated populations.
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| 3. |
- Antonelli, Alexandre, 1978, et al.
(author)
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SUPERSMART: ecology and evolution in the era of big data
- 2014
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In: PeerJ PrePrints. - : PeerJ. - 2167-9843.
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Journal article (other academic/artistic)abstract
- Rapidly growing biological data volumes – including molecular sequences, species traits, geographic occurrences, specimen collections, and fossil records – hold an unprecedented, yet largely unexplored potential to reveal how ecological and evolutionary processes generate and maintain biodiversity. Most biodiversity studies integrating ecological data and evolutionary history use an idiosyncratic step-by-step approach for the reconstruction of time-calibrated phylogenies in light of ecological and evolutionary scenarios. Here we introduce a conceptual framework, termed SUPERSMART (Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa), and provide a proof of concept for dealing with the moving targets of biodiversity research. This framework reconstructs dated phylogenies based on the assembly of molecular datasets and collects pertinent data on ecology, distribution, and fossils of the focal clade. The data handled for each step are continuously updated as databases accumulate new records. We exemplify the practice of our method by presenting comprehensive phylogenetic and dating analyses for the orders Primates and the Gentianales. We believe that this emerging framework will provide an invaluable tool for a wide range of hypothesis-driven research questions in ecology and evolution.
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| 4. |
- Antonelli, Alexandre, 1978, et al.
(author)
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The pitfalls of taking science to the public
- 2018
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In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 359
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Journal article (other academic/artistic)
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| 5. |
- Antonelli, Alexandre, 1978
(author)
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The rise and fall of Neotropical biodiversity
- 2022
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In: Botanical Journal of the Linnean Society. - : Oxford University Press (OUP). - 0024-4074 .- 1095-8339. ; 199:1, s. 8-24
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Journal article (peer-reviewed)abstract
- The exceptional levels of biodiversity found today in the American tropics are the outcome of tens of millions of years of evolution, shaped by the tumultuous geological history of the region, its heterogeneous habitats, climate change, ecological interactions and, in recent millennia, human influence. Although our understanding of diversity patterns and their underlying processes grows steadily in breadth and depth, Neotropical biodiversity is rapidly breaking down. Here, I contrast the long-term evolution of Neotropical biodiversity with its recent and rapid deterioration due to anthropogenic factors. I consider the impacts of the early arrival of humans to the region and the modern intensification of land-use change (primarily driven by agriculture) and other drivers of biodiversity loss, such as direct exploitation, invasive species and climate change. Together, these threats have led to 33% of all Neotropical species for which sufficient data are available being currently threatened with extinction. I outline emerging opportunities for conservation and restoration under the post-2020 Global Biodiversity Framework and call for urgent action from the biodiversity community, for the benefit of people and nature.
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| 6. |
- Antonelli, Alexandre, 1978, et al.
(author)
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The science and ethics of extinction
- 2018
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In: Nature Ecology and Evolution. - : Springer Science and Business Media LLC. - 2397-334X. ; 2
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Journal article (other academic/artistic)
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| 7. |
- Antonelli, Alexandre, 1978, et al.
(author)
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Toward a Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa.
- 2017
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In: Systematic biology. - : Oxford University Press (OUP). - 1076-836X .- 1063-5157. ; 66:2, s. 152-166
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Journal article (peer-reviewed)abstract
- Rapidly growing biological data-including molecular sequences and fossils-hold an unprecedented potential to reveal how evolutionary processes generate and maintain biodiversity. However, researchers often have to develop their own idiosyncratic workflows to integrate and analyze these data for reconstructing time-calibrated phylogenies. In addition, divergence times estimated under different methods and assumptions, and based on data of various quality and reliability, should not be combined without proper correction. Here we introduce a modular framework termed SUPERSMART (Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa), and provide a proof of concept for dealing with the moving targets of evolutionary and biogeographical research. This framework assembles comprehensive data sets of molecular and fossil data for any taxa and infers dated phylogenies using robust species tree methods, also allowing for the inclusion of genomic data produced through next-generation sequencing techniques. We exemplify the application of our method by presenting phylogenetic and dating analyses for the mammal order Primates and for the plant family Arecaceae (palms). We believe that this framework will provide a valuable tool for a wide range of hypothesis-driven research questions in systematics, biogeography, and evolution. SUPERSMART will also accelerate the inference of a "Dated Tree of Life" where all node ages are directly comparable. [Bayesian phylogenetics; data mining; divide-and-conquer methods; GenBank; multilocus multispecies coalescent; next-generation sequencing; palms; primates; tree calibration.].
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| 8. |
- Antonelli, Alexandre, 1978, et al.
(author)
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Tracing the impact of the Andean uplift on Neotropical plant evolution
- 2009
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In: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424. ; 106:24, s. 9749-9754
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Journal article (peer-reviewed)abstract
- 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.
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| 9. |
- Antonelli, A, et al.
(author)
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Tracing the impact of the Andean uplift on Neotropical plant evolution : evidence from the coffee family
- 2009
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In: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 106:24, s. 9749-9754
-
Journal article (peer-reviewed)abstract
- 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
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| 10. |
- Antonelli, Alexandre, 1978, et al.
(author)
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We must protect biodiversity
- 2017
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In: Washington Post. - 0190-8286. ; :Dec 15
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Journal article (pop. science, debate, etc.)
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