| 1. |
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| 2. |
- Ralimanana, H., et al.
(author)
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Madagascar’s extraordinary biodiversity: Threats and opportunities
- 2022
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In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 378:6623
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Research review (peer-reviewed)abstract
- Madagascar’s unique biota is heavily affected by human activity and is under intense threat. Here, we review the current state of knowledge on the conservation status of Madagascar’s terrestrial and freshwater biodiversity by presenting data and analyses on documented and predicted species-level conservation statuses, the most prevalent and relevant threats, ex situ collections and programs, and the coverage and comprehensiveness of protected areas. The existing terrestrial protected area network in Madagascar covers 10.4% of its land area and includes at least part of the range of the majority of described native species of vertebrates with known distributions (97.1% of freshwater fishes, amphibians, reptiles, birds, and mammals combined) and plants (67.7%). The overall figures are higher for threatened species (97.7% of threatened vertebrates and 79.6% of threatened plants occurring within at least one protected area). International Union for Conservation of Nature (IUCN) Red List assessments and Bayesian neural network analyses for plants identify overexploitation of biological resources and unsustainable agriculture as the most prominent threats to biodiversity. We highlight five opportunities for action at multiple levels to ensure that conservation and ecological restoration objectives, programs, and activities take account of complex underlying and interacting factors and produce tangible benefits for the biodiversity and people of Madagascar.
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| 3. |
- Antonelli, Alexandre, 1978, et al.
(author)
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Madagascar's extraordinary biodiversity : Evolution, distribution, and use
- 2022
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In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 378:6623, s. 962-
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Journal article (peer-reviewed)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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| 4. |
- Gjesfjeld, E., et al.
(author)
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A quantitative workflow for modeling diversification in material culture
- 2020
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In: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 15:2
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Journal article (peer-reviewed)abstract
- Questions about the evolution of material culture are widespread in the humanities and social sciences. Statistical modeling of long-term changes in material culture is less common due to a lack of appropriate frameworks. Our goal is to close this gap and provide robust statistical methods for examining changes in the diversity of material culture. We provide an open-source and quantitative workflow for estimating rates of origination, extinction, and preservation, as well as identifying key shift points in the diversification histories of material culture. We demonstrate our approach using two distinct kinds of data: age ranges for the production of American car models, and radiocarbon dates associated with archaeological cultures of the European Neolithic. Our approach improves on existing frameworks by disentangling the relative contributions of origination and extinction to diversification. Our method also permits rigorous statistical testing of competing hypotheses to explain changes in diversity. Finally, we stress the value of a flexible approach that can be applied to data in various forms; this flexibility allows scholars to explore commonalities between forms of material culture and ask questions about the general properties of cultural change.
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| 5. |
- Gjesfjeld, E, et al.
(author)
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Competition and extinction explain the evolution of diversity in American automobiles
- 2016
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In: Palgrave Communications. - : Springer Science and Business Media LLC. - 2055-1045. ; 2
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Journal article (peer-reviewed)abstract
- One of the most remarkable aspects of our species is that while we show surprisingly little genetic diversity, we demonstrate astonishing amounts of cultural diversity. Perhaps most impressive is the diversity of our technologies, broadly defined as all the physical objects we produce and the skills we use to produce them. Despite considerable focus on the evolution of technology by social scientists and philosophers, there have been few attempts to systematically quantify technological diversity, and therefore the dynamics of technological change remain poorly understood. Here we show a novel Bayesian model for examining technological diversification adopted from palaeontological analysis of occurrence data. We use this framework to estimate the tempo of diversification in American car and truck models produced between 1896 and 2014, and to test the relative importance of competition and extrinsic factors in shaping changes in macro-evolutionary rates. Our results identify a four-fold decrease in the origination and extinction rates of car models, and a negative net diversification rate over the last 30 years. We also demonstrate that competition played a more significant role in car model diversification than either changes in oil prices or gross domestic product. Together our analyses provide a set of tools that can enhance current research on technological and cultural evolution by providing a flexible and quantitative framework for exploring the dynamics of diversification.
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| 6. |
- Harmon, L. J., et al.
(author)
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Detecting the macroevolutionary signal of species interactions
- 2019
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In: Journal of Evolutionary Biology. - : Wiley. - 1010-061X .- 1420-9101. ; 32:8, s. 769-782
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Journal article (peer-reviewed)abstract
- Species interactions lie at the heart of many theories of macroevolution, from adaptive radiation to the Red Queen. Although some theories describe the imprint that interactions will have over long timescales, we are still missing a comprehensive understanding of the effects of interactions on macroevolution. Current research shows strong evidence for the impact of interactions on macroevolutionary patterns of trait evolution and diversification, yet many macroevolutionary studies have only a tenuous relationship to ecological studies of interactions over shorter timescales. We review current research in this area, highlighting approaches that explicitly model species interactions and connect them to broad-scale macroevolutionary patterns. We also suggest that progress has been made by taking an integrative interdisciplinary look at individual clades. We focus on African cichlids as a case study of how this approach can be fruitful. Overall, although the evidence for species interactions shaping macroevolution is strong, further work using integrative and model-based approaches is needed to spur progress towards understanding the complex dynamics that structure communities over time and space. © 2019 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2019 European Society For Evolutionary Biology
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| 7. |
- Pino, K., et al.
(author)
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Regional landscape change triggered by Andean uplift: The extinction of Sparassodonta (Mammalia, Metatheria) in South America
- 2022
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In: Global and Planetary Change. - : Elsevier BV. - 0921-8181. ; 210
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Journal article (peer-reviewed)abstract
- Sparassodonta, a Metatherian monophyletic group, was the main mammalian carnivore predator clade in South America from the Paleogene to the Early Pliocene (c. 66–3.5 Ma). However, there is still no consensus on the causes of their demise. Here, we use the fossil record and Bayesian diversification models to infer the origination and extinction rates for Sparassodonta. Then, we evaluate if their demise can be attributed to global temperature changes, Andean uplift, biotic interactions with their competitor and prey clades, and body mass evolution. That is biotic aspects in the context of the Red Queen model, abiotic aspects in the context of the Court Jester model, and an intrinsic lineage attribute. Our results show that this lineage is characterized by a positive near-zero net diversification rate indicating that the clade maintained a relatively low but stable diversity until the Middle Miocene when an increase in extinction rate drove them to decline and eventual extinction. Moreover, our results support the idea that a drastic regional landscape change triggered by the Andean uplift process affected their diversification dynamics, eventually driving them to extinction. These environmental changes could explicitly affect Sparassodonta lineages due to their ever-present vulnerability to extinction by near-zero net diversification rate and their highly specialized ecology that could have constrained adaptation to new South American landscapes. © 2022 Elsevier B.V.
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| 8. |
- Richard-Bollans, A., et al.
(author)
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Machine learning enhances prediction of plants as potential sources of antimalarials
- 2023
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In: Frontiers in Plant Science. - 1664-462X. ; 14
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Journal article (peer-reviewed)abstract
- Plants are a rich source of bioactive compounds and a number of plant-derived antiplasmodial compounds have been developed into pharmaceutical drugs for the prevention and treatment of malaria, a major public health challenge. However, identifying plants with antiplasmodial potential can be time-consuming and costly. One approach for selecting plants to investigate is based on ethnobotanical knowledge which, though having provided some major successes, is restricted to a relatively small group of plant species. Machine learning, incorporating ethnobotanical and plant trait data, provides a promising approach to improve the identification of antiplasmodial plants and accelerate the search for new plant-derived antiplasmodial compounds. In this paper we present a novel dataset on antiplasmodial activity for three flowering plant families - Apocynaceae, Loganiaceae and Rubiaceae (together comprising c. 21,100 species) - and demonstrate the ability of machine learning algorithms to predict the antiplasmodial potential of plant species. We evaluate the predictive capability of a variety of algorithms - Support Vector Machines, Logistic Regression, Gradient Boosted Trees and Bayesian Neural Networks - and compare these to two ethnobotanical selection approaches - based on usage as an antimalarial and general usage as a medicine. We evaluate the approaches using the given data and when the given samples are reweighted to correct for sampling biases. In both evaluation settings each of the machine learning models have a higher precision than the ethnobotanical approaches. In the bias-corrected scenario, the Support Vector classifier performs best - attaining a mean precision of 0.67 compared to the best performing ethnobotanical approach with a mean precision of 0.46. We also use the bias correction method and the Support Vector classifier to estimate the potential of plants to provide novel antiplasmodial compounds. We estimate that 7677 species in Apocynaceae, Loganiaceae and Rubiaceae warrant further investigation and that at least 1300 active antiplasmodial species are highly unlikely to be investigated by conventional approaches. While traditional and Indigenous knowledge remains vital to our understanding of people-plant relationships and an invaluable source of information, these results indicate a vast and relatively untapped source in the search for new plant-derived antiplasmodial compounds.
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| 9. |
- Rolland, J., et al.
(author)
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Conceptual and empirical bridges between micro- and macroevolution
- 2023
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In: Nature Ecology and Evolution. - 2397-334X. ; 7, s. 1181-1193
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Journal article (peer-reviewed)abstract
- This Perspective discusses four questions of evolutionary biology that bridge macro and microevolution perspectives and proposes future research avenues to link evolutionary mechanisms and processes. Explaining broad molecular, phenotypic and species biodiversity patterns necessitates a unifying framework spanning multiple evolutionary scales. Here we argue that although substantial effort has been made to reconcile microevolution and macroevolution, much work remains to identify the links between biological processes at play. We highlight four major questions of evolutionary biology whose solutions require conceptual bridges between micro and macroevolution. We review potential avenues for future research to establish how mechanisms at one scale (drift, mutation, migration, selection) translate to processes at the other scale (speciation, extinction, biogeographic dispersal) and vice versa. We propose ways in which current comparative methods to infer molecular evolution, phenotypic evolution and species diversification could be improved to specifically address these questions. We conclude that researchers are in a better position than ever before to build a synthesis to understand how microevolutionary dynamics unfold over millions of years.
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| 10. |
- Rozzi, R., et al.
(author)
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Dwarfism and gigantism drive human-mediated extinctions on islands
- 2023
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In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 379:6636, s. 1054-1058
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Journal article (peer-reviewed)abstract
- Islands have long been recognized as distinctive evolutionary arenas leading to morphologically divergent species, such as dwarfs and giants. We assessed how body size evolution in island mammals may have exacerbated their vulnerability, as well as how human arrival has contributed to their past and ongoing extinctions, by integrating data on 1231 extant and 350 extinct species from islands and paleo islands worldwide spanning the past 23 million years. We found that the likelihood of extinction and of endangerment are highest in the most extreme island dwarfs and giants. Extinction risk of insular mammals was compounded by the arrival of modern humans, which accelerated extinction rates more than 10-fold, resulting in an almost complete demise of these iconic marvels of island evolution.
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| 11. |
- Woutersen, A., et al.
(author)
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A novel approach to study the morphology and chemistry of pollen in a phylogenetic context, applied to the halophytic taxon Nitraria L.(Nitrariaceae)
- 2018
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In: PeerJ. - : PeerJ. - 2167-8359. ; 6
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Journal article (peer-reviewed)abstract
- Nitraria is a halophytic taxon (i.e., adapted to saline environments) that belongs to the plant family Nitrariaceae and is distributed from the Mediterranean, across Asia into the south-eastern tip of Australia. This taxon is thought to have originated in Asia during the Paleogene (66-23 Ma), alongside the proto-Paratethys epicontinental sea. The evolutionary history of Nitraria might hold important clues on the links between climatic and biotic evolution but limited taxonomic documentation of this taxon has thus far hindered this line of research. Here we investigate if the pollen morphology and the chemical composition of the pollen wall are informative of the evolutionary history of Nitraria and could explain if origination along the proto-Paratethys and dispersal to the Tibetan Plateau was simultaneous or a secondary process. To answer these questions, we applied a novel approach consisting of a combination of Fourier Transform Infrared spectroscopy (FTIR), to determine the chemical composition of the pollen wall, and pollen morphological analyses using Light Microscopy (LM) and Scanning Electron Microscopy (SEM). We analysed our data using ordinations (principal components analysis and non-metric multidimensional scaling), and directly mapped it on the Nitrariaceae phylogeny to produce a phylomorphospace and a phylochemospace. Our LM, SEM and FTIR analyses show clear morphological and chemical differences between the sister groups Peganum and Nitraria. Differences in the morphological and chemical characteristics of highland species (Nitraria schoberi, N. sphaerocarpa, N. sibirica and N. tangutorum) and lowland species (Nitraria billardierei and N. retusa) are very subtle, with phylogenetic history appearing to be a more important control on Nitraria pollen than local environmental conditions. Our approach shows a compelling consistency between the chemical and morphological characteristics of the eight studied Nitrariaceae species, and these traits are in agreement with the phylogenetic tree. Taken together, this demonstrates how novel methods for studying fossil pollen can facilitate the evolutionary investigation of living and extinct taxa, and the environments they represent.
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| 12. |
- Carlisle, E., et al.
(author)
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A timescale for placental mammal diversification based on Bayesian modeling of the fossil record
- 2023
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In: Current Biology. - 0960-9822. ; 33:15
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Journal article (peer-reviewed)abstract
- The timing of the placental mammal radiation has been the focus of debate over the efficacy of competing methods for establishing evolutionary timescales. Molecular clock analyses estimate that placental mammals originated before the Cretaceous-Paleogene (K-Pg) mass extinction, anywhere from the Late Cretaceous to the Jurassic. However, the absence of definitive fossils of placentals before the K-Pg boundary is compatible with a post-Cretaceous origin. Nevertheless, lineage divergence must occur before it can be manifest phenotypically in descendent lineages. This, combined with the non-uniformity of the rock and fossil records, requires the fossil record to be interpreted rather than read literally. To achieve this, we introduce an extended Bayesian Brownian bridge model that estimates the age of origination and, where applicable, extinction through a probabilistic interpretation of the fossil record. The model estimates the origination of placentals in the Late Cretaceous, with ordinal crown groups originating at or after the K-Pg boundary. The results reduce the plausible interval for placental mammal origination to the younger range of molecular clock estimates. Our findings support both the Long Fuse and Soft Explosive models of placental mammal diversification, indicating that the placentals originated shortly prior to the K-Pg mass extinction. The origination of many modern mammal lineages overlapped with and followed the K-Pg mass extinction.
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| 13. |
- Condamine, F. L., et al.
(author)
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The rise of angiosperms pushed conifers to decline during global cooling
- 2020
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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. ; 117:46, s. 28867-28875
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Journal article (peer-reviewed)abstract
- Competition among species and entire clades can impact species diversification and extinction, which can shape macroevolutionary patterns. The fossil record shows successive biotic turnovers such that a dominant group is replaced by another. One striking example involves the decline of gymnosperms and the rapid diversification and ecological dominance of angiosperms in the Cretaceous. It is generally believed that angiosperms outcompeted gymnosperms, but the macroevolutionary processes and alternative drivers explaining this pattern remain elusive. Using extant time trees and vetted fossil occurrences for conifers, we tested the hypotheses that clade competition or climate change led to the decline of conifers at the expense of angiosperms. Here, we find that both fossil and molecular data show high congruence in revealing 1) low diversification rates, punctuated by speciation pulses, during warming events throughout the Phanerozoic and 2) that conifer extinction increased significantly in the MidCretaceous (100 to 110 Ma) and remained high ever since. Their extinction rates are best explained by the rise of angiosperms, rejecting alternative models based on either climate change or time alone. Our results support the hypothesis of an active clade replacement, implying that direct competition with angiosperms increased the extinction of conifers by pushing their remaining species diversity and dominance out of the warm tropics. This study illustrates how entire branches on the Tree of Life may actively compete for ecological dominance under changing climates.
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| 14. |
- Cruz, G. A. S., et al.
(author)
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Molecular phylogeny, character evolution and historical biogeography of Cryptanthus Otto & A. Dietr. (Bromeliaceae)
- 2017
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In: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 107, s. 152-165
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Journal article (peer-reviewed)abstract
- Cryptanthus comprises 72 species endemic to eastern Brazil with a center of diversity in the Atlantic Forest. The majority of the species are threatened due to habitat loss. We reconstructed phylogenetic relationships in Cryptanthus based on amplified fragment length polymorphisms (AFLP) including 48 species and 109 accessions. The Bayesian phylogenetic analysis revealed four major lineages in Cryptanthus and provided further evidence for the paraphyly of subgen. Hoplocryptanthus, while subgenus Cryptanthus was resolved as monophyletic. Monophyly of previously recognized morphological species groups at sectional level could not be confirmed. Based on the phylogenetic reconstruction we inferred the evolution of the sex system in Cryptanthus via maximum likelihood (ML) ancestral character reconstruction. Homoecy, the possession of hermaphrodite flowers only, was reconstructed as the ancestral state in the genus and characterizes three of the four main lineages within Cryptanthus. Andromonoecy, the possession of male and hermaphrodite flowers on the same plant, evolved only once and represents a synapomorphy of the fourth main lineage, C. subgen. Cryptanthus. The ancestral biome analysis reconstructed Cerrado (semiarid scrublands and forests) and campos rupestres (rock fields) as the most likely ancestral biomes for the genus. A shift to the Atlantic Forest biome was reconstructed to have occurred twice, in the ancestor of the first diverging lineage within the genus and in the ancestor of the C. subgen. Cryptanthus clade. A shift to the Caatinga (tropical dryland savanna) and one reversal to Cerrado (campos rupestres - rock fields) was reconstructed to have occurred once, in C. bahianus and C. arelii, respectively. The ancestral biome reconstruction indicates a high degree of niche conservatism within Cryptanthus with rare biome shifts throughout the evolution of the genus. Further, our results imply that the current infrageneric taxonomy of Cryptanthus is problematic and requires revision. © 2016 Elsevier Inc.
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| 15. |
- Kehoe, Laura, et al.
(author)
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Make EU trade with Brazil sustainable
- 2019
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In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 364:6438, s. 341-
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Journal article (other academic/artistic)
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| 16. |
- Nyman, T., et al.
(author)
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The early wasp plucks the flower: disparate extant diversity of sawfly superfamilies (Hymenoptera: "Symphyta') may reflect asynchronous switching to angiosperm hosts
- 2019
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In: Biological Journal of the Linnean Society. - : Oxford University Press (OUP). - 0024-4066 .- 1095-8312. ; 128:1, s. 1-19
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Journal article (peer-reviewed)abstract
- The insect order Hymenoptera originated during the Permian nearly 300 Mya. Ancestrally herbivorous hymenopteran lineages today make up the paraphyletic suborder Symphyta', which encompasses c. 8200 species with very diverse host-plant associations. We use phylogeny-based statistical analyses to explore the drivers of diversity dynamics within the Symphyta', with a particular focus on the hypothesis that diversification of herbivorous insects has been driven by the explosive radiation of angiosperms during and after the Cretaceous. Our ancestral-state estimates reveal that the first symphytans fed on gymnosperms, and that shifts onto angiosperms and pteridophytes - and back - have occurred at different time intervals in different groups. Trait-dependent analyses indicate that average net diversification rates do not differ between symphytan lineages feeding on angiosperms, gymnosperms or pteridophytes, but trait-independent models show that the highest diversification rates are found in a few angiosperm-feeding lineages that may have been favoured by the radiations of their host taxa during the Cenozoic. Intriguingly, lineages-through-time plots show signs of an early Cretaceous mass extinction, with a recovery starting first in angiosperm-associated clades. Hence, the oft-invoked assumption of herbivore diversification driven by the rise of flowering plants may overlook a Cretaceous global turnover in insect herbivore communities during the rapid displacement of gymnosperm- and pteridophyte-dominated floras by angiosperms.
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| 17. |
- Wilke, T., et al.
(author)
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Deep drilling reveals massive shifts in evolutionary dynamics after formation of ancient ecosystem
- 2020
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In: Science Advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 6:40
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Journal article (peer-reviewed)abstract
- The scarcity of high-resolution empirical data directly tracking diversity over time limits our understanding of speciation and extinction dynamics and the drivers of rate changes. Here, we analyze a continuous species-level fossil record of endemic diatoms from ancient Lake Ohrid, along with environmental and climate indicator time series since lake formation 1.36 million years (Ma) ago. We show that speciation and extinction rates nearly simultaneously decreased in the environmentally dynamic phase after ecosystem formation and stabilized after deep-water conditions established in Lake Ohrid. As the lake deepens, we also see a switch in the macroevolutionary trade-off, resulting in a transition from a volatile assemblage of short-lived endemic species to a stable community of long- lived species. Our results emphasize the importance of the interplay between environmental/climate change, ecosystem stability, and environmental limits to diversity for diversification processes. The study also provides a new understanding of evolutionary dynamics in long-lived ecosystems.
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| 18. |
- Woutersen, A., et al.
(author)
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The evolutionary history of the Central Asian steppe-desert taxon Nitraria (Nitrariaceae) as revealed by integration of fossil pollen morphology and molecular data
- 2023
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In: Botanical Journal of the Linnean Society. - : Oxford University Press (OUP). - 0024-4074 .- 1095-8339. ; 202:2, s. 195-214
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Journal article (peer-reviewed)abstract
- The transition from a greenhouse to an icehouse world at the Eocene-Oligocene Transition (EOT) coincided with a large decrease of pollen from the steppe-adapted genus Nitraria. This genus, now common along the Mediterranean coast, Asia and Australia, has a proposed coastal origin and a geographically widespread fossil record. Here we investigated the evolution, taxonomic diversity and morphological disparity of Nitraria throughout the Cenozoic by integrating extant taxa and fossil palynological morphotypes into a unified phylogenetic framework based on both DNA sequences and pollen morphological data. We present the oldest fossil pollen grain of Nitraria, at least 53 Myr old. This fossil was found in Central Asian deposits, providing new evidence for its origin in this area. We found that the EOT is an evolutionary bottleneck for Nitraria, coinciding with retreat of the proto-Paratethys Sea, a major global cooling event and a turnover in Central Asian steppe vegetation. We infer the crown age of modern Nitraria spp. to be significantly younger (Miocene) than previously estimated (Palaeocene). The diversity trajectory of Nitraria inferred from extant-only taxa differs markedly from one that also considers extinct taxa. Our study demonstrates it is therefore critical to apply an integrative approach to fully understand the plant evolutionary history of Nitrariaceae.
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