| 1. |
- Andermann, Tobias, et al.
(författare)
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Estimating Alpha, Beta, and Gamma Diversity Through Deep Learning
- 2022
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Ingår i: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 13
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Tidskriftsartikel (refereegranskat)abstract
- The reliable mapping of species richness is a crucial step for the identification of areas of high conservation priority, alongside other value and threat considerations. This is commonly done by overlapping range maps of individual species, which requires dense availability of occurrence data or relies on assumptions about the presence of species in unsampled areas deemed suitable by environmental niche models. Here, we present a deep learning approach that directly estimates species richness, skipping the step of estimating individual species ranges. We train a neural network model based on species lists from inventory plots, which provide ground truth data for supervised machine learning. The model learns to predict species richness based on spatially associated variables, including climatic and geographic predictors, as well as counts of available species records from online databases. We assess the empirical utility of our approach by producing independently verifiable maps of alpha, beta, and gamma plant diversity at high spatial resolutions for Australia, a continent with highly heterogeneous diversity patterns. Our deep learning framework provides a powerful and flexible new approach for estimating biodiversity patterns, constituting a step forward toward automated biodiversity assessments.
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| 2. |
- Andermann, Tobias, et al.
(författare)
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iucn_sim: a new program to simulate future extinctions based on IUCN threat status
- 2021
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Ingår i: Ecography. - : Wiley. - 0906-7590 .- 1600-0587. ; 44:2, s. 162-176
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Tidskriftsartikel (refereegranskat)abstract
- The ongoing environmental crisis poses an urgent need to forecast the who, where and when of future species extinctions, as such information is crucial for targeting conservation efforts. Commonly, such forecasts are made based on conservation status assessments produced by the International Union for Conservation of Nature (IUCN). However, when researchers apply these IUCN conservation status data for predicting future extinctions, important information is often omitted, which can impact the accuracy of these predictions. Here we present a new approach and a software for simulating future extinctions based on IUCN conservation status information, which incorporates generation length information of individual species when modeling extinction risks. Additionally, we explicitly model future changes in conservation status for each species, based on status transition rates that we estimate from the IUCN assessment history of the last decades. Finally, we apply a Markov chain Monte Carlo algorithm to estimate extinction rates for each species, based on the simulated future extinctions. These estimates inherently incorporate the chances of conservation status changes and the generation length for each given species and are specific to the simulated time frame. We demonstrate the utility of our approach by estimating future extinction rates for all bird species. Our average extinction rate estimate for the next 100 yr across all birds is 6.98 x 10(-4) extinctions per species-year, and we predict an expected biodiversity loss of between 669 and 738 bird species within that time frame. Further, the rate estimates between species sharing the same IUCN status show larger variation than the rates estimated with alternative approaches, which reflects expected differences in extinction risk among taxa of the same conservation status. Our method demonstrates the utility of applying species-specific information to the estimation of extinction rates, rather than assuming equal extinction risks for species assigned to the same conservation status.
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| 3. |
- Andermann, Tobias, et al.
(författare)
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The origin and evolution of open habitats in North America inferred by Bayesian deep learning models
- 2022
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 13:1
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Tidskriftsartikel (refereegranskat)abstract
- Some of the most extensive terrestrial biomes today consist of open vegetation, including temperate grasslands and tropical savannas. These biomes originated relatively recently in Earth’s history, likely replacing forested habitats in the second half of the Cenozoic. However, the timing of their origination and expansion remains disputed. Here, we present a Bayesian deep learning model that utilizes information from fossil evidence, geologic models, and paleoclimatic proxies to reconstruct paleovegetation, placing the emergence of open habitats in North America at around 23 million years ago. By the time of the onset of the Quaternary glacial cycles, open habitats were covering more than 30% of North America and were expanding at peak rates, to eventually become the most prominent natural vegetation type today. Our entirely data-driven approachdemonstrates how deep learning can harness unexplored signals from complex data sets to provide insights into the evolution of Earth’s biomes in time and space.
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| 4. |
- Andermann, Tobias, et al.
(författare)
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The past and future human impact on mammalian diversity
- 2020
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Ingår i: Science Advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 6:36
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Tidskriftsartikel (refereegranskat)abstract
- To understand the current biodiversity crisis, it is crucial to determine how humans have affected biodiversity in the past. However, the extent of human involvement in species extinctions from the Late Pleistocene onward remains contentious. Here, we apply Bayesian models to the fossil record to estimate how mammalian extinction rates have changed over the past 126,000 years, inferring specific times of rate increases. We specifically test the hypothesis of human-caused extinctions by using posterior predictive methods. We find that human population size is able to predict past extinctions with 96% accuracy. Predictors based on past climate, in contrast, perform no better than expected by chance, suggesting that climate had a negligible impact on global mammal extinctions. Based on current trends, we predict for the near future a rate escalation of unprecedented magnitude. Our results provide a comprehensive assessment of the human impact on past and predicted future extinctions of mammals.
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| 5. |
- Antonelli, Alexandre, 1978, et al.
(författare)
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Amazonia is the primary source of Neotropical biodiversity
- 2018
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424. ; 115:23, s. 6034-6039
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Tidskriftsartikel (refereegranskat)abstract
- The American tropics (the Neotropics) are the most species-rich realm on Earth, and for centuries, scientists have attempted to understand the origins and evolution of their biodiversity. It is now clear that different regions and taxonomic groups have responded differently to geological and climatic changes. However, we still lack a basic understanding of how Neotropical biodiversity was assembled over evolutionary timescales. Here we infer the timing and origin of the living biota in all major Neotropical regions by performing a cross-taxonomic biogeographic analysis based on 4,450 species from six major clades across the tree of life (angiosperms, birds, ferns, frogs, mammals, and squamates), and integrate > 1.3 million species occurrences with large-scale phylogenies. We report an unprecedented level of biotic interchange among all Neotropical regions, totaling 4,525 dispersal events. About half of these events involved transitions between major environmental types, with a predominant directionality from forested to open biomes. For all taxonomic groups surveyed here, Amazonia is the primary source of Neotropical diversity, providing > 2,800 lineages to other regions. Most of these dispersal events were to Mesoamerica (similar to 1,500 lineages), followed by dispersals into open regions of northern South America and the Cerrado and Chaco biomes. Biotic interchange has taken place for > 60 million years and generally increased toward the present. The total amount of time lineages spend in a region appears to be the strongest predictor of migration events. These results demonstrate the complex origin of tropical ecosystems and the key role of biotic interchange for the assembly of regional biotas.
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| 6. |
- Antonelli, Alexandre, 1978, et al.
(författare)
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An engine for global plant diversity: Highest evolutionary turnover and emigration in the American tropics
- 2015
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Ingår i: Frontiers in Genetics. - : Frontiers Media SA. - 1664-8021. ; 6:130
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Tidskriftsartikel (refereegranskat)abstract
- Understanding the processes that have generated the latitudinal biodiversity gradient and the continental differences in tropical biodiversity remains a major goal of evolutionary biology. Here we estimate the timing and direction of range shifts of extant flowering plants (angiosperms) between tropical and non-tropical zones, and into and out of the major tropical regions of the world. We then calculate rates of speciation and extinction taking into account incomplete taxonomic sampling. We use a recently published fossil calibrated phylogeny and apply novel bioinformatic tools to code species into user-defined polygons. We reconstruct biogeographic history using stochastic character mapping to compute relative numbers of range shifts in proportion to the number of available lineages through time. Our results, based on the analysis of c. 22,600 species and c. 20 million geo-referenced occurrence records, show no significant differences between the speciation and extinction of tropical and non-tropical angiosperms. This suggests that at least in plants, the latitudinal biodiversity gradient primarily derives from other factors than differential rates of diversification. In contrast, the outstanding species richness found today in the American tropics (the Neotropics), as compared to tropical Africa and tropical Asia, is associated with significantly higher speciation and extinction rates. This suggests an exceedingly rapid evolutionary turnover, i.e., Neotropical species being formed and replaced by one another at unparalleled rates. In addition, tropical America stands out from other continents by having "pumped out" more species than it received through most of the last 66 million years. These results imply that the Neotropics have acted as an engine for global plant diversity. © 2015 Antonelli, Zizka, Silvestro, Scharn, Cascales-Miñana and Bacon.
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| 7. |
- Antonelli, Alexandre, 1978, et al.
(författare)
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Conceptual and empirical advances in Neotropical biodiversity research
- 2018
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Ingår i: PeerJ. - : PeerJ. - 2167-8359. ; 2018:10
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Tidskriftsartikel (refereegranskat)abstract
- The unparalleled biodiversity found in the American tropics (the Neotropics) has attracted the attention of naturalists for centuries. Despite major advances in recent years in our understanding of the origin and diversification of many Neotropical taxa and biotic regions, many questions remain to be answered. Additional biological and geological data are still needed, as well as methodological advances that are capable of bridging these research fields. In this review, aimed primarily at advanced students and early-career scientists, we introduce the concept of "trans-disciplinary biogeography," which refers to the integration of data from multiple areas of research in biology (e.g., community ecology, phylogeography, systematics, historical biogeography) and Earth and the physical sciences (e.g., geology, climatology, palaeontology), as a means to reconstruct the giant puzzle of Neotropical biodiversity and evolution in space and time. We caution against extrapolating results derived from the study of one or a few taxa to convey general scenarios of Neotropical evolution and landscape formation. We urge more coordination and integration of data and ideas among disciplines, transcending their traditional boundaries, as a basis for advancing tomorrow's ground-breaking research. Our review highlights the great opportunities for studying the Neotropical biota to understand the evolution of life.
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| 8. |
- Antonelli, Alexandre, 1978, et al.
(författare)
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Integrating machine learning, remote sensing and citizen science to create an early warning system for biodiversity
- 2022
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Ingår i: Plants People Planet. - : Wiley. - 2572-2611. ; 5:3, s. 307-16
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Tidskriftsartikel (refereegranskat)abstract
- Application of machine learning approaches is aiding biodiversity conservation and research at a time of rapid global change. Two emerging topics and their data requirements are presented. First, to identify areas of priority protection for preventing biodiversity loss, reinforcement learning is used by training models that take into account human disturbance and climate change under recurrent monitoring schemes. Second, neural networks are used to approximate classification of species into Red List categories of the International Union for Conservation of Nature, offering the possibility of real-time re-classification after events such as widespread fires and deforestation. We discuss how the identification of areas and species most at risk could be integrated into an ‘early warning system’ based on climatic monitoring, remotely sensed land-use changes and near-real time biological and threat data from citizen science initiatives. Such system would help guide actions to prevent biodiversity loss at the speed required for effective conservation.
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| 9. |
- Antonelli, Alexandre, 1978, et al.
(författare)
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Madagascar's extraordinary biodiversity : Evolution, distribution, and use
- 2022
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 378:6623, s. 962-
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Tidskriftsartikel (refereegranskat)abstract
- Madagascar's biota is hyperdiverse and includes exceptional levels of endemicity. We review the current state of knowledge on Madagascar's past and current terrestrial and freshwater biodiversity by compiling and presenting comprehensive data on species diversity, endemism, and rates of species description and human uses, in addition to presenting an updated and simplified map of vegetation types. We report a substantial increase of records and species new to science in recent years; however, the diversity and evolution of many groups remain practically unknown (e.g., fungi and most invertebrates). Digitization efforts are increasing the resolution of species richness patterns and we highlight the crucial role of field- and collections-based research for advancing biodiversity knowledge and identifying gaps in our understanding, particularly as species richness corresponds closely to collection effort. Phylogenetic diversity patterns mirror that of species richness and endemism in most of the analyzed groups. We highlight humid forests as centers of diversity and endemism because of their role as refugia and centers of recent and rapid radiations. However, the distinct endemism of other areas, such as the grassland-woodland mosaic of the Central Highlands and the spiny forest of the southwest, is also biologically important despite lower species richness. The documented uses of Malagasy biodiversity are manifold, with much potential for the uncovering of new useful traits for food, medicine, and climate mitigation. The data presented here showcase Madagascar as a unique " living laboratory" for our understanding of evolution and the complex interactions between people and nature. The gathering and analysis of biodiversity data must continue and accelerate if we are to fully understand and safeguard this unique subset of Earth's biodiversity.
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| 10. |
- Antonelli, Alexandre, 1978, et al.
(författare)
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SUPERSMART: ecology and evolution in the era of big data
- 2014
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Ingår i: PeerJ PrePrints. - : PeerJ. - 2167-9843.
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)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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