| 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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| 11. |
- Antonelli, Alexandre, 1978, et al.
(författare)
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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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Ingår i: Systematic biology. - : Oxford University Press (OUP). - 1076-836X .- 1063-5157. ; 66:2, s. 152-166
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Tidskriftsartikel (refereegranskat)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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| 12. |
- Aros-Mualin, D., et al.
(författare)
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Light, rather than circadian rhythm, regulates gas exchange in ferns and lycophytes
- 2023
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Ingår i: Plant Physiology. - : Oxford University Press (OUP). - 0032-0889 .- 1532-2548. ; 191:3, s. 1634-47
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Tidskriftsartikel (refereegranskat)abstract
- Circadian regulation plays a vital role in optimizing plant responses to the environment. However, while circadian regulation has been extensively studied in angiosperms, very little is known for lycophytes and ferns, leaving a gap in our understanding of the evolution of circadian rhythms across the plant kingdom. Here, we investigated circadian regulation in gas exchange through stomatal conductance and photosynthetic efficiency in a phylogenetically broad panel of 21 species of lycophytes and ferns over a 46 h period under constant light and a selected few under more natural conditions with day-night cycles. No rhythm was detected under constant light for either lycophytes or ferns, except for two semi-aquatic species of the family Marsileaceae (Marsilea azorica and Regnellidium diphyllum), which showed rhythms in stomatal conductance. Furthermore, these results indicated the presence of a light-driven stomatal control for ferns and lycophytes, with a possible passive fine-tuning through leaf water status adjustments. These findings support previous evidence for the fundamentally different regulation of gas exchange in lycophytes and ferns compared to angiosperms, and they suggest the presence of alternative stomatal regulations in Marsileaceae, an aquatic family already well known for numerous other distinctive physiological traits. Overall, our study provides evidence for heterogeneous circadian regulation across plant lineages, highlighting the importance of broad taxonomic scope in comparative plant physiology studies.
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| 13. |
- Bacon, Christine D., et al.
(författare)
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Biological evidence supports an early and complex emergence of the Isthmus of Panama
- 2015
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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. ; 112:19, s. 6110-6115
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Tidskriftsartikel (refereegranskat)abstract
- The linking of North and South America by the Isthmus of Panama had major impacts on global climate, oceanic and atmospheric currents, and biodiversity, yet the timing of this critical event remains contentious. The Isthmus is traditionally understood to have fully closed by ca. 3.5 million years ago (Ma), and this date has been used as a benchmark for oceanographic, climatic, and evolutionary research, but recent evidence suggests a more complex geological formation. Here, we analyze both molecular and fossil data to evaluate the tempo of biotic exchange across the Americas in light of geological evidence. We demonstrate significant waves of dispersal of terrestrial organisms at approximately ca. 20 and 6 Ma and corresponding events separating marine organisms in the Atlantic and Pacific oceans at ca. 23 and 7 Ma. The direction of dispersal and their rates were symmetrical until the last ca. 6 Ma, when northern migration of South American lineages increased significantly. Variability among taxa in their timing of dispersal or vicariance across the Isthmus is not explained by the ecological factors tested in these analyses, including biome type, dispersal ability, and elevation preference. Migration was therefore not generally regulated by intrinsic traits but more likely reflects the presence of emergent terrain several millions of years earlier than commonly assumed. These results indicate that the dramatic biotic turnover associated with the Great American Biotic Interchange was a long and complex process that began as early as the Oligocene–Miocene transition.
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| 14. |
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| 15. |
- Bacon, Christine D., et al.
(författare)
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The origin of modern patterns of continental diversity in Mauritiinae palms: the Neotropical museum and the Afrotropical graveyard
- 2022
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Ingår i: Biology Letters. - : The Royal Society. - 1744-9561 .- 1744-957X. ; 18:11
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Tidskriftsartikel (refereegranskat)abstract
- While the latitudinal diversity gradient has received much attention, biodiversity and species richness also vary between continents across similar latitudes. Fossil information can be used to understand the evolutionary mechanisms that generated such variation between continents of similar latitudes. We integrated fossil data into a phylogenetic analysis of the Mauritiinae palms, whose extant diversity is restricted to the Neotropics, but extended across Africa and India during most of the Cenozoic. Mauritiinae diverged from its sister lineage Raphiinae ca 106 Ma. Using ancestral state estimation and a lineage through time analysis, we found that diversity arose globally during the late Cretaceous and Palaeocene across South America, Africa and India. The Palaeocene-Eocene transition (ca 56 Ma) marked the end of global Mauritiinae expansion, and the beginning of their decline in both Africa and India. Mauritiinae disappeared from the Indian subcontinent and Africa at the end of the Eocene and the Miocene, respectively. By contrast, Neotropical diversity steadily increased over the last 80 Myr. Taken together, our results suggest that the Neotropics functioned as a continental-scale refuge for Mauritiinae palms, where lineages survived and diversified while global climatic changes that drastically reduced rainforests led to their demise on other continents.
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| 16. |
- Belluardo, F., et al.
(författare)
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Slow and steady wins the race: Diversification rate is independent from body size and lifestyle in Malagasy skinks (Squamata: Scincidae: Scincinae)
- 2023
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Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903. ; 178
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Tidskriftsartikel (refereegranskat)abstract
- Most of the unique and diverse vertebrate fauna that inhabits Madagascar derives from in situ diversification from colonisers that reached this continental island through overseas dispersal. The endemic Malagasy Scincinae lizards are amongst the most species-rich squamate groups on the island. They colonised all bioclimatic zones and display many ecomorphological adaptations to a fossorial (burrowing) lifestyle. Here we propose a new phylogenetic hypothesis for their diversification based on the largest taxon sampling so far compiled for this group. We estimated divergence times and investigated several aspects of their diversification (diversification rate, body size and fossorial lifestyle evolution, and biogeography). We found that diversification rate was constant throughout most of the evolutionary history of the group, but decreased over the last 6-4 million years and independently from body size and fossorial lifestyle evolution. Fossoriality has evolved from fully quadrupedal ancestors at least five times independently, which demonstrates that even complex morphological syndromes - in this case involving traits such as limb regression, body elongation, modification of cephalic scalation, depigmentation, and eyes and ear-opening regression - can evolve repeatedly and independently given enough time and eco-evolutionary advantages. Initial diversification of the group likely occurred in forests, and the divergence of sand-swimmer genera around 20 Ma appears linked to a period of aridification. Our results show that the large phenotypic variability of Malagasy Scincinae has not influenced diversification rate and that their rich species diversity results from a constant accumulation of lineages through time. By compiling large geographic and trait-related datasets together with the computation of a new time tree for the group, our study contributes important insights on the diversification of Malagasy vertebrates.
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| 17. |
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| 18. |
- Calió, Maria Fernanda, et al.
(författare)
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Spatio-temporal evolution of the catuaba clade in the Neotropics: Morphological shifts correlate with habitat transitions
- 2022
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Ingår i: Journal of Biogeography. - : Wiley. - 0305-0270 .- 1365-2699. ; 49:6, s. 1086-1098
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Tidskriftsartikel (refereegranskat)abstract
- Aim The biotic assembly of one of the most species-rich savannas, the Brazilian Cerrado, has involved recruitment of lineages from several surrounding regions. However, we lack a clear understanding about the timing and pathways of biotic exchanges among these regions and about the role those interchanges had in the assembly of Neotropical biodiversity. We investigated the timing and routes of species movements between wet or seasonally dry habitats across Neotropical regions and assessed the potential for ecological adaptation by evaluating the habitat transitions correlated with morphological shifts. Location Neotropics. Taxon The plant genus Anemopaegma (Bignonieae, Bignoniaceae). Methods We inferred a Bayesian molecular phylogeny of Anemopaegma using one nuclear and two chloroplast markers. We sampled more than 90% of the known species diversity of Anemopaegma, covering its full geographical range. We estimated divergence times using a Bayesian relaxed-clock approach and inferred ancestral ranges as well as shifts in habitat and morphological characters. Results Phylogenetic analyses recovered seven main clades within Anemopaegma. The genus likely originated in Amazonia in the late Oligocene. Early-diverging lineages diversified in situ in Amazonia, particularly during the Miocene, with independent dispersal events to the Andes, Atlantic Forest and Cerrado. Shifts from seasonally dry forest to savanna habitats were correlated with shifts from liana to shrub and the loss of tendrils. Main Conclusions The timing of diversification of major lineages within Anemopaegma is consistent with major geological and climatic events that occurred during the late Palaeogene and Neogene, such as the Andean uplift and the Middle Miocene Climatic Optimum. Movements across different regions within the Neotropics were relatively common but shifts between habitats were not. The correlation in the evolution of the shrubby habit, the loss of tendrils and the shifts from forest to savanna are consistent with a scenario of ecological adaptation.
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| 19. |
- Carlisle, E., et al.
(författare)
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A timescale for placental mammal diversification based on Bayesian modeling of the fossil record
- 2023
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Ingår i: Current Biology. - 0960-9822. ; 33:15
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Tidskriftsartikel (refereegranskat)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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| 20. |
- Carrillo, Juan D., et al.
(författare)
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Disproportionate extinction of South American mammals drove the asymmetry of the Great American Biotic Interchange
- 2020
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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. ; 117:42, s. 26281-26287
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Tidskriftsartikel (refereegranskat)abstract
- The interchange between the previously disconnected faunas of North and South America was a massive experiment in biological invasion. A major gap in our understanding of this invasion is why there was a drastic increase in the proportion of mammals of North American origin found in South America. Four nonmutually exclusive mechanisms may explain this asymmetry: 1) Higher dispersal rate of North American mammals toward the south, 2) higher origination of North American immigrants in South America, 3) higher extinction of mammals with South American origin, and 4) similar dispersal rate but a larger pool of native taxa in North versus South America. We test among these mechanisms by analyzing similar to 20,000 fossil occurrences with Bayesian methods to infer dispersal and diversification rates and taxonomic selectivity of immigrants. We find no differences in the dispersal and origination rates of immigrants. In contrast, native South American mammals show higher extinction. We also find that two clades with North American origin (Carnivora and Artiodactyla) had significantly more immigrants in South America than other clades. Altogether, the asymmetry of the interchange was not due to higher origination of immigrants in South America as previously suggested, but resulted from higher extinction of native taxa in southern South America. These results from one of the greatest biological invasions highlight how biogeographic processes and biotic interactions can shape continental diversity.
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| 21. |
- Carvalho, M. R., et al.
(författare)
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Extinction at the end-Cretaceous and the origin of modern Neotropical rainforests
- 2021
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 372:6537
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Tidskriftsartikel (refereegranskat)abstract
- The end-Cretaceous event was catastrophic for terrestrial communities worldwide, yet its long-lasting effect on tropical forests remains largely unknown. We quantified plant extinction and ecological change in tropical forests resulting from the end-Cretaceous event using fossil pollen (>50,000 occurrences) and leaves (>6000 specimens) from localities in Colombia. Late Cretaceous (Maastrichtian) rainforests were characterized by an open canopy and diverse plant-insect interactions. Plant diversity declined by 45% at the Cretaceous-Paleogene boundary and did not recover for similar to 6 million years. Paleocene forests resembled modern Neotropical rainforests, with a closed canopy and multistratal structure dominated by angiosperms. The end-Cretaceous event triggered a long interval of low plant diversity in the Neotropics and the evolutionary assembly of today's most diverse terrestrial ecosystem.
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| 22. |
- Claudel, C., et al.
(författare)
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Patterns and drivers of heat production in the plant genus Amorphophallus
- 2023
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Ingår i: Plant Journal. - 0960-7412. ; 115:4, s. 874-894
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Tidskriftsartikel (refereegranskat)abstract
- Thermogenesis - the ability to generate metabolic heat - is much more common in animals than in plants, but it has been documented in several plant families, most prominently the Araceae. Metabolic heat is produced in floral organs during the flowering time (anthesis), with the hypothesised primary functions being to increase scent volatilisation for pollinator attraction, and/or to provide a heat reward for invertebrate pollinators. Despite in-depth studies on the thermogenesis of single species, no attempts have yet been made to examine plant thermogenesis across an entire clade. Here, we apply time-series clustering algorithms to 119 measurements of the full thermogenic patterns in inflorescences of 80 Amorphophallus species. We infer a new time-calibrated phylogeny of this genus and use phylogenetic comparative methods to investigate the evolutionary determinants of thermogenesis. We find striking phenotypic variation across the phylogeny, with heat production in multiple clades reaching up to 15 degrees C, and in one case 21.7 C-degrees above ambient temperature. Our results show that the thermogenic capacity is phylogenetically conserved and is also associated with inflorescence thickness. Our study paves the way for further investigations of the eco-evolutionary benefits of thermogenesis in plants.
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| 23. |
- Condamine, F. L., et al.
(författare)
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The rise of angiosperms pushed conifers to decline during global cooling
- 2020
-
Ingår i: 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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Tidskriftsartikel (refereegranskat)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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| 24. |
- Cruz, G. A. S., et al.
(författare)
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Molecular phylogeny, character evolution and historical biogeography of Cryptanthus Otto & A. Dietr. (Bromeliaceae)
- 2017
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Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 107, s. 152-165
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Tidskriftsartikel (refereegranskat)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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| 25. |
- del Cid, Carlos Calderon, et al.
(författare)
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Challenges in estimating species' age from phylogenetic trees
- 2024
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Ingår i: GLOBAL ECOLOGY AND BIOGEOGRAPHY. - 1466-822X .- 1466-8238.
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Tidskriftsartikel (refereegranskat)abstract
- AimSpecies age, the elapsed time since origination, can give insight into how species longevity might influence eco-evolutionary dynamics, which has been hypothesized to influence extinction risk. Traditionally, species' ages have been estimated from fossil records. However, numerous studies have recently used the branch lengths of time-calibrated phylogenies as estimates of the ages of extant species. This approach poses problems because phylogenetic trees only contain direct information about species identity at the tips and not along the branches. Here, we show that incomplete taxon sampling, extinction and different assumptions about speciation modes can significantly alter the relationship between true species age and phylogenetic branch lengths, leading to high error rates. We found that these biases can lead to erroneous interpretations of eco-evolutionary patterns derived from comparing phylogenetic age and other traits, such as extinction risk.InnovationFor bifurcating speciation, the default assumption in most analyses of species age, we propose a probabilistic approach based on the properties of a birth-death process to improve the estimation of species ages. Our approach can reduce the error by one order of magnitude under cases of high extinction and a high percentage of unsampled extant species.Main conclusionOur results call for caution in interpreting the relationship between phylogenetic ages and eco-evolutionary traits, as this can lead to biased and erroneous conclusions. We show that, under the assumption of bifurcating speciation, we can obtain unbiased approximations of species age by combining information from branch lengths with the expectations of a birth-death process.
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| 26. |
- del Cid, Carlos Calderon, et al.
(författare)
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The Clade Replacement Theory: a framework to study age-dependent extinction
- 2024
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Ingår i: JOURNAL OF EVOLUTIONARY BIOLOGY. - 1010-061X .- 1420-9101. ; 37:3, s. 290-301
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Tidskriftsartikel (refereegranskat)abstract
- There is no scientific consensus about whether and how species' evolutionary age, or the elapsed time since their origination, might affect their probability of going extinct. Different age-dependent extinction (ADE) patterns have been proposed in theoretical and empirical studies, while the existence of a consistent and universal pattern across the tree of life remains debated. If evolutionary age predicts species extinction probability, then the study of ADE should comprise the elapsed time and the ecological process acting on species from their origin to their extinction or to the present for extant species. Additionally, given that closely related species share traits associated with fitness, evolutionary proximity could generate similar ADE patterns. Considering the historical context and extinction selectivity based on evolutionary relatedness, we build on previous theoretical work to formalize the Clade Replacement Theory (CRT) as a framework that considers the ecological and evolutionary aspects of species age and extinction probability to produce testable predictions on ADE patterns. CRT's domain is the diversification dynamics of two or more clades competing for environmental space throughout time, and its propositions or derived hypotheses are as follows: (i) incumbency effects by an early arriving clade that limit the colonization and the diversification of a younger clade leading to a negative ADE scenario (younger species more prone to extinction than older ones) and (ii) an ecological shift triggered by an environmental change that imposes a new selective regime over the environmental space and leads to a positive ADE scenario (extinction probability increasing with age). From these propositions, we developed the prediction that the ADE scenario would be defined by whether an ecological shift happens or not. We discuss how the CRT could be tested with empirical data and provide examples where it could be applied. We hope this article will provide a common ground to unify results from different fields and foster new empirical tests of the mechanisms derived here while providing insights into CRT theoretical structuration.
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| 27. |
- Di Giacomo, Michele, et al.
(författare)
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Microbial Community Structure and Dynamics of Dark Fire-Cured Tobacco Fermentation
- 2007
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Ingår i: Applied and Environmental Microbiology. - : ASM. - 0099-2240 .- 1098-5336. ; 73:3, s. 825-837
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Tidskriftsartikel (refereegranskat)abstract
- The Italian Toscano cigar production includes a fermentation step that starts when dark fire-cured tobacco leaves are moistened and mixed with ca. 20% prefermented tobacco to form a 500-kg bulk. The dynamics of the process, lasting ca. 18 days, has never been investigated in detail, and limited information is available on microbiota involved. Here we show that Toscano fermentation is invariably associated with the following: (i) an increase in temperature, pH, and total microbial population; (ii) a decrease in reducing sugars, citric and malic acids, and nitrate content; and (iii) an increase in oxalic acid, nitrite, and tobacco-specific nitrosamine content. The microbial community structure and dynamics were investigated by culture-based and culture-independent approaches, including denaturing gradient gel electrophoresis and single-strand conformational polymorphism. Results demonstrate that fermentation is assisted by a complex microbial community, changing in structure and composition during the process. During the early phase, the moderately acidic and mesophilic environment supports the rapid growth of a yeast population predominated by Debaryomyces hansenii. At this stage, Staphylococcaceae (Jeotgalicoccus and Staphylococcus) and Lactobacillales (Aerococcus, Lactobacillus, and Weissella) are the most commonly detected bacteria. When temperature and pH increase, endospore-forming low-G+C content gram-positive bacilli (Bacillus spp.) become evident. This leads to a further pH increase and promotes growth of moderately halotolerant and alkaliphilic Actinomycetales (Corynebacterium and Yania) during the late phase. To postulate a functional role for individual microbial species assisting the fermentation process, a preliminary physiological and biochemical characterization of representative isolates was performed.
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| 28. |
- Dib, L., et al.
(författare)
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Evolutionary footprint of coevolving positions in genes
- 2014
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Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 30:9, s. 1241-1249
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Tidskriftsartikel (refereegranskat)abstract
- Motivation: The analysis of molecular coevolution provides information on the potential functional and structural implication of positions along DNA sequences, and several methods are available to identify coevolving positions using probabilistic or combinatorial approaches. The specific nucleotide or amino acid profile associated with the coevolution process is, however, not estimated, but only known profiles, such as the Watson-Crick constraint, are usually considered a priori in current measures of coevolution. Results: Here, we propose a new probabilistic model, Coev, to identify coevolving positions and their associated profile in DNA sequences while incorporating the underlying phylogenetic relationships. The process of coevolution is modeled by a 16 X 16 instantaneous rate matrix that includes rates of transition as well as a profile of coevolution. We used simulated, empirical and illustrative data to evaluate our model and to compare it with a model of `independent' evolution using Akaike Information Criterion. We showed that the Coev model is able to discriminate between coevolving and non-coevolving positions and provides better specificity and specificity than other available approaches. We further demonstrate that the identification of the profile of coevolution can shed new light on the process of dependent substitution during lineage evolution.
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| 29. |
- Edler, Daniel, et al.
(författare)
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raxmlGUI 2.0: A graphical interface and toolkit for phylogenetic analyses using RAxML
- 2021
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Ingår i: Methods in Ecology and Evolution. - : John Wiley & Sons. - 2041-210X. ; 12:2, s. 373-377
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Tidskriftsartikel (refereegranskat)abstract
- raxmlGUI is a graphical user interface to RAxML, one of the most popular and widely used softwares for phylogenetic inference using maximum likelihood. Here we present raxmlGUI 2.0, a complete rewrite of the GUI which seamlessly integrates RAxML binaries for all major operating systems with an intuitive graphical front-end to setup and run phylogenetic analyses. Our program offers automated pipelines for analyses that require multiple successive calls of RAxML, built-in functions to concatenate alignment files while automatically specifying the appropriate partition settings, and one-click model testing to select the best substitution models using ModelTest-NG. In addition to RAxML 8.x, raxmlGUI 2.0 also supports the new RAxML-NG, which provides new functionality and higher performance on large datasets. raxmlGUI 2.0 facilitates phylogenetic analyses by coupling an intuitive interface with the unmatched performance of RAxML. © 2020 The Authors. Methods in Ecology and Evolution published by John Wiley & Sons Ltd on behalf of British Ecological Society
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| 30. |
- Farina, B. M., et al.
(författare)
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Dollo meets Bergmann: morphological evolution in secondary aquatic mammals
- 2023
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Ingår i: Proceedings of the Royal Society B-Biological Sciences. - 0962-8452. ; 290:2002
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Tidskriftsartikel (refereegranskat)abstract
- Secondary transitions to aquatic environments are common among vertebrates, and aquatic lineages display several adaptations to this realm, some of which might make these transitions irreversible. At the same time, discussions about secondary transitions often focus only on the marine realm, comparing fully terrestrial with fully aquatic species. This, however, captures only a fraction of land-to-water transitions, and freshwater and semi-aquatic groups are often neglected in macroevolutionary studies. Here, we use phylogenetic comparative methods to unravel the evolution of different levels of aquatic adaptations across all extant mammals, testing if aquatic adaptations are irreversible and if they are related to relative body mass changes. We found irreversible adaptations consistent with Dollo's Law in lineages that rely strongly on aquatic environments, while weaker adaptations in semi-aquatic lineages, which still allow efficient terrestrial movement, are reversible. In lineages transitioning to aquatic realms, including semi-aquatic ones, we found a consistent trend towards an increased relative body mass and a significant association with a more carnivorous diet. We interpret these patterns as the result of thermoregulation constraints associated with the high thermal conductivity of water leading to body mass increase consistently with Bergmann's rule and to a prevalence of more nutritious diets.
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| 31. |
- Faurby, Sören, 1981, et al.
(författare)
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Brain expansion in early hominins predicts carnivore extinctions in East Africa
- 2020
-
Ingår i: Ecology Letters. - : Wiley. - 1461-023X .- 1461-0248. ; 23:3, s. 537-544
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Tidskriftsartikel (refereegranskat)abstract
- While the anthropogenic impact on ecosystems today is evident, it remains unclear if the detrimental effect of hominins on co-occurring biodiversity is a recent phenomenon or has also been the pattern for earlier hominin species. We test this using the East African carnivore fossil record. We analyse the diversity of carnivores over the last four million years and investigate whether any decline is related to an increase in hominin cognitive capacity, vegetation changes or climatic changes. We find that extinction rates in large carnivores correlate with increased hominin brain size and with vegetation changes, but not with precipitation or temperature changes. While temporal analyses cannot distinguish between the effects of vegetation changes and hominins, we show through spatial analyses of contemporary carnivores in Africa that only hominin causation is plausible. Our results suggest that substantial anthropogenic influence on biodiversity started millions of years earlier than currently assumed.
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| 32. |
- Flannery-Sutherland, J. T., et al.
(författare)
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Global diversity dynamics in the fossil record are regionally heterogeneous
- 2022
-
Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 13:1
-
Tidskriftsartikel (refereegranskat)abstract
- Global diversity trends in the fossil record vary regionally through time and space, affecting our ability to interpret macroevolutionary history. Here, the authors propose a method to eliminate spatial sampling bias, estimate origination and extinction rates, and generate diversity estimates, applying this method to the Late Permian to Early Jurassic marine fossil record. Global diversity patterns in the fossil record comprise a mosaic of regional trends, underpinned by spatially non-random drivers and distorted by variation in sampling intensity through time and across space. Sampling-corrected diversity estimates from spatially-standardised fossil datasets retain their regional biogeographic nuances and avoid these biases, yet diversity-through-time arises from the interplay of origination and extinction, the processes that shape macroevolutionary history. Here we present a subsampling algorithm to eliminate spatial sampling bias, coupled with advanced probabilistic methods for estimating origination and extinction rates and a Bayesian method for estimating sampling-corrected diversity. We then re-examine the Late Permian to Early Jurassic marine fossil record, an interval spanning several global biotic upheavals that shaped the origins of the modern marine biosphere. We find that origination and extinction rates are regionally heterogenous even during events that manifested globally, highlighting the need for spatially explicit views of macroevolutionary processes through geological time.
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| 33. |
- Gaboriau, T., et al.
(författare)
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A multi-platform package for the analysis of intra- and interspecific trait evolution
- 2020
-
Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 11:11, s. 1439-1447
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Tidskriftsartikel (refereegranskat)abstract
- Evolutionary forces affect the distribution of phenotypes both within and among species. Yet, at the macro-evolutionary scale, the evolution of intraspecific variance is rarely considered. Here, we present an r and a BEAST 2 implementation that extends the JIVE (Joint inter- and Intraspecific Variance Evolution) model aimed at the analysis of continuous trait evolution at both inter- and intraspecific level. Using a hierarchical Bayesian approach, we implemented a range of models for continuous trait evolution that operate independently on species means and variances along a phylogeny. The package uses Markov chain Monte Carlo for the inference of parameters and the evaluation of model fit. JIVE is available in the bite (Bayesian Integrative models of Trait Evolution) r package, as well as in BEAST 2. The two implementations offer the same continuous trait evolutionary models, but differ in their use and types of analyses. The r implementation allows for faster analyses by taking the phylogeny as data, while providing graphical and statistical functions as part of tools for model comparison, result parsing and summary, and plotting. In the BEAST 2 implementation, the species tree is a parameter, and both its topology and divergence times are jointly estimated with trait model parameters. The bite package and the BEAST 2 implementation introduce new frameworks within comparative phylogenetics that explicitly model intraspecific variance. These tools allow users to tackle long-standing questions in evolutionary biology, such as the identification of key evolutionary processes determining niche conservatism, niche partitioning, and life-history strategies. © 2020 British Ecological Society
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| 34. |
- Gjesfjeld, E., et al.
(författare)
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A quantitative workflow for modeling diversification in material culture
- 2020
-
Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 15:2
-
Tidskriftsartikel (refereegranskat)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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| 35. |
- Gjesfjeld, E, et al.
(författare)
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Competition and extinction explain the evolution of diversity in American automobiles
- 2016
-
Ingår i: Palgrave Communications. - : Springer Science and Business Media LLC. - 2055-1045. ; 2
-
Tidskriftsartikel (refereegranskat)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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| 36. |
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| 37. |
- Harmon, L. J., et al.
(författare)
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Detecting the macroevolutionary signal of species interactions
- 2019
-
Ingår i: Journal of Evolutionary Biology. - : Wiley. - 1010-061X .- 1420-9101. ; 32:8, s. 769-782
-
Tidskriftsartikel (refereegranskat)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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| 38. |
- Hauffe, T., et al.
(författare)
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A quantitative framework to infer the effect of traits, diversity and environment on dispersal and extinction rates from fossils
- 2022
-
Ingår i: Methods in Ecology and Evolution. - : Wiley. - 2041-210X. ; 13:6, s. 1201-1213
-
Tidskriftsartikel (refereegranskat)abstract
- Speciation, dispersal and extinction govern the spatial and temporal dynamics of biodiversity. The fossil record offers the opportunity to directly estimate range expansion and contraction via dispersal and extinction, respectively. However, due to the incomplete occurrence record, determining the dynamics of these processes and the biotic and abiotic factors influencing them remains challenging. The dispersal-extinction-sampling (DES) model infers dispersal and extinction rates from present and past geographical ranges of taxa while accounting for the incompleteness of the fossil record via jointly estimated sampling rates. Here, we expand the DES framework to a new suite of models that (a) incorporate heterogeneity in fossil sampling across taxa, (b) reconstruct diversity trajectories through time and across regions, and (c) link rates of range evolution with biotic and abiotic covariates. These models integrate the effects of competitive interaction, traits and environmental change on dispersal and extinction while controlling for phylogenetic effects through higher level taxonomy. We validate our framework through simulations and find that likelihood-based model testing has the power to discriminate among models with or without biotic and abiotic effects on dispersal and extinction. Among the tested models, we found that trait-dependent models yielded the most accurate parameter estimates. We then assess the factors influencing geographical range evolution for Eurasian and North American terrestrial carnivores. We identify substantial variation in the fossil sampling rates of carnivore genera and find that global cooling increased their extinction risk while their dispersal rate varied among families and increased with larger body size. The expanded suite of DES models for fossil biogeography is a powerful tool to test hypotheses about the factors influencing geographical range evolution using fossil data.
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| 39. |
- Huang, S., et al.
(författare)
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Mammal body size evolution in North America and Europe over 20 Myr: similar trends generated by different processes
- 2017
-
Ingår i: Proceedings of the Royal Society B - Biological Sciences. - : The Royal Society. - 0962-8452 .- 1471-2954. ; 284:1849
-
Tidskriftsartikel (refereegranskat)abstract
- Because body size interacts with many fundamental biological properties of a species, body size evolution can be an essential component of the generation and maintenance of biodiversity. Here we investigate how body size evolution can be linked to the clade-specific diversification dynamics in different geographical regions. We analyse an extensive body size dataset of Neogene large herbivores (covering approx. 50% of the 970 species in the orders Artiodactyla and Perissodactyla) in Europe and North America in a Bayesian framework. We reconstruct the temporal patterns of body size in each order on each continent independently, and find significant increases of minimum size in three of the continental assemblages (except European perissodactyls), suggesting an active selection for larger bodies. Assessment of trait-correlated birth-death models indicates that the common trend of body size increase is generated by different processes in different clades and regions. Larger-bodied artiodactyl species on both continents tend to have higher origination rates, and both clades in North America show strong links between large bodies and low extinction rate. Collectively, our results suggest a strong role of species selection and perhaps of higher-taxon sorting in driving body size evolution, and highlight the value of investigating evolutionary processes in a biogeographic context.
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| 40. |
- Häggi, C., et al.
(författare)
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GDGT distribution in tropical soils and its potential as a terrestrial paleothermometer revealed by Bayesian deep-learning models
- 2023
-
Ingår i: Geochimica Et Cosmochimica Acta. - 0016-7037. ; 362, s. 41-64
-
Tidskriftsartikel (refereegranskat)abstract
- Branched and isoprenoidal glycerol dialkyl glycerol tetraethers (br- and isoGDGTs) are membrane lipids produced by bacteria and archaea, respectively. These lipids form the basis of several frequently used paleoclimatic proxies. For example, the degree of methylation of brGDGTs (MBT'5Me) preserved in mineral soils (as well as peats and lakes) is one of the most important terrestrial paleothermometers, but features substantial variability that is so far insufficiently constrained. The distribution of isoGDGTs in mineral soils has received less attention and applications have focused on the use of the relative abundance of the isoGDGT crenarchaeol versus brGDGTs (BIT index) as an indicator of aridity. To expand our knowledge of the factors that can impact the br- and isoGDGT distribution in mineral soils, including the MBT'5Me index, and to improve isoGDGT-based precipitation reconstructions, we surveyed the GDGT distribution in a large collection of mineral surface soils (n = 229) and soil profiles (n = 22) across tropical South America. We find that the MBT'5Me index is significantly higher in grassland compared to forest soils, even among sites with the same mean annual air temperature. This is likely a result of a lack of shading in grasslands, leading to warmer soils. We also find a relationship between MBT'5Me and soil pH in tropical soils. Together with existing data from arid areas in mid-latitudes, we confirm the relationship between the BIT-index and aridity, but also find that the isoGDGT distribution alone is aridity dependent. The combined use of the BIT-index and isoGDGTs can strengthen reconstructions of past precipitation in terrestrial archives. In terms of site-specific variations, we find that the variability in BIT and MBT'5Me is larger at sites that show on average lower BIT and MBT'5Me values. In combination with modelling results, we suggest that this pattern arises from the mathematical formulation of these proxies that amplifies variability for intermediate values and mutes it for values close to saturation (value of 1). Soil profiles show relatively little variation with depth for the brGDGT indices. On the other hand, the isoGDGT distribution changes significantly with depth as does the relative abundance of br- versus isoGDGTs. This pattern is especially pronounced for the isoGDGTIsomerIndex where deeper soil horizons show a near absence of isoGDGT isomers. This might be driven by archaeal community changes in different soil horizons, potentially driven by the difference between aerobic and anaerobic archaeal communities. Finally, we use our extensive new dataset and Bayesian neural networks (BNNs) to establish new brGDGT-based temperature models. We provide a tropical soil calibration that removes the pH dependence of tropical soils (n = 404; RMSE = 2.0 degrees C) and global peat and soil models calibrated against the temperature of the months above freezing (n = 1740; RMSE = 2.4) and mean annual air temperature (n = 1740; RMSE = 3.6). All models correct for the bias found in arid samples. We also successfully test the new calibrations on Chinese loess records and tropical river sediments. Overall, the new calibrations provide improved temperature reconstructions for terrestrial archives.
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| 41. |
- Jaramillo, Carlos, et al.
(författare)
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Comment (1) on "Formation of the Isthmus of Panama" by O'Dea et al.
- 2017
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Ingår i: Science advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 3:6
-
Tidskriftsartikel (refereegranskat)abstract
- A review and reanalysis of geological, molecular, and paleontological data led O'Dea et al. (1) to propose (i) that reports by Montes et al. (2) and Bacon et al. (3) regarding a middle Miocene closure of the Central American Seaway (CAS) are unsupported, and (ii) a new age of the formation of the Isthmus at 2.8 million years ago (Ma). Here, we reject both of these conclusions.
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| 42. |
- Jäpelt, Rie Bak, et al.
(författare)
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LC–MS/MS with atmospheric pressure chemical ionisation to study the effect of UV treatment on the formation of vitamin D3 and sterols in plants
- 2011
-
Ingår i: Food Chemistry. - : Elsevier. - 0308-8146 .- 1873-7072. ; 129:1, s. 217-225
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Tidskriftsartikel (refereegranskat)abstract
- Some plant species are known to cause calcium intoxification in grazing animals. This has been attributed to the presence of vitamin D3-like activity. However, research into the presence of vitamin D3 in plants has been limited. One reason for this may be limitations in the analytical methods available for unambiguous detection and quantification of vitamin D3. This paper presents a new method for determining vitamin D3 and its sterol precursors. The method is based on saponification and extraction followed by solid phase clean-up of the compounds from plant leaves and detection by APCI-MS. Recoveries ranged from 101% to 114% and precision from 3% to 12%. Detection limits were 2–8 ng/g fresh weight for the substances tested. In a pilot study we found that Solanum glaucohyllum Desf. and Solanum lycopersicum L. produced vitamin D3 after UV-treatment. The preliminary results presented suggest that vitamin D3 formation in plants is dependent on light exposure.
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| 43. |
- Jäpelt, Rie Bak, et al.
(författare)
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Quantification of vitamin D3 and its hydroxylated metabolites in waxy leaf nightshade (Solanum glaucophyllum Desf.), tomato (Solanum lycopersicum L.) and bell pepper (Capsicum annuum L.)
- 2013
-
Ingår i: Food Chemistry. - : Elsevier. - 0308-8146 .- 1873-7072. ; 138:2-3, s. 1206-1211
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Tidskriftsartikel (refereegranskat)abstract
- Changes in vitamin D3 and its metabolites were investigated following UVB- and heat-treatment in the leaves of Solanum glaucophyllum Desf., Solanum lycopersicum L. and Capsicum annuum L. The analytical method used was a sensitive and selective liquid chromatography electrospray ionisation tandem mass spectrometry (LC–ESI-MS/MS) method including Diels–Alder derivatisation. Vitamin D3 and 25-hydroxy vitamin D3 were found in the leaves of all plants after UVB-treatment. S. glaucophyllum had the highest content, 200 ng vitamin D3/g dry weight and 31 ng 25-hydroxy vitamin D3/g dry weight, and was the only plant that also contained 1,25 dihydroxy vitamin D3 in both free (32 ng/g dry weight) and glycosylated form (17 ng/g dry weight).
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| 44. |
- Kehoe, Laura, et al.
(författare)
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Make EU trade with Brazil sustainable
- 2019
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 364:6438, s. 341-
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 45. |
- Kostikova, A., et al.
(författare)
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Bridging Inter- and Intraspecific Trait Evolution with a Hierarchical Bayesian Approach
- 2016
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Ingår i: Systematic Biology. - : Oxford University Press (OUP). - 1063-5157 .- 1076-836X. ; 65:3, s. 417-431
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Tidskriftsartikel (refereegranskat)abstract
- The evolution of organisms is crucially dependent on the evolution of intraspecific variation. Its interactions with selective agents in the biotic and abiotic environments underlie many processes, such as intraspecific competition, resource partitioning and, eventually, species formation. Nevertheless, comparative models of trait evolution neither allow explicit testing of hypotheses related to the evolution of intraspecific variation nor do they simultaneously estimate rates of trait evolution by accounting for both trait mean and variance. Here, we present a model of phenotypic trait evolution using a hierarchical Bayesian approach that simultaneously incorporates interspecific and intraspecific variation. We assume that species-specific trait means evolve under a simple Brownian motion process, whereas species-specific trait variances are modeled with Brownian or Ornstein-Uhlenbeck processes. After evaluating the power of the method through simulations, we examine whether life-history traits impact evolution of intraspecific variation in the Eriogonoideae (buckwheat family, Polygonaceae). Our model is readily extendible to more complex scenarios of the evolution of inter-and intraspecific variation and presents a step toward more comprehensive comparative models for macroevolutionary studies.
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| 46. |
- Laursen, Tomas, et al.
(författare)
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Characterization of a dynamic metabolon producing the defense compound dhurrin in sorghum
- 2016
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Ingår i: Science. - : American Association for the Advancement of Science. - 0036-8075 .- 1095-9203. ; 354:6314, s. 890-893
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Tidskriftsartikel (refereegranskat)abstract
- Metabolic highways may be orchestrated by the assembly of sequential enzymes into protein complexes, or metabolons, to facilitate efficient channeling of intermediates and to prevent undesired metabolic cross-talk while maintaining metabolic flexibility. Here we report the isolation of the dynamic metabolon that catalyzes the formation of the cyanogenic glucoside dhurrin, a defense compound produced in sorghum plants. The metabolon was reconstituted in liposomes, which demonstrated the importance of membrane surface charge and the presence of the glucosyltransferase for metabolic channeling. We used in planta fluorescence lifetime imaging microscopy and fluorescence correlation spectroscopy to study functional and structural characteristics of the metabolon. Understanding the regulation of biosynthetic metabolons offers opportunities to optimize synthetic biology approaches for efficient production of high-value products in heterologous hosts.
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| 47. |
- Lehtonen, S., et al.
(författare)
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Environmentally driven extinction and opportunistic origination explain fern diversification patterns
- 2017
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- Combining palaeontological and neontological data offers a unique opportunity to investigate the relative roles of biotic and abiotic controls of species diversification, and the importance of origination versus extinction in driving evolutionary dynamics. Ferns comprise a major terrestrial plant radiation with an extensive evolutionary history providing a wealth of modern and fossil data for modelling environmental drivers of diversification. Here we develop a novel Bayesian model to simultaneously estimate correlations between diversification dynamics and multiple environmental trajectories. We estimate the impact of different factors on fern diversification over the past 400 million years by analysing a comprehensive dataset of fossil occurrences and complement these findings by analysing a large molecular phylogeny. We show that origination and extinction rates are governed by fundamentally different processes: originations depend on within-group diversity but are largely unaffected by environmental changes, whereas extinctions are strongly affected by external factors such as climate and geology. Our results indicate that the prime driver of fern diversity dynamics is environmentally driven extinction, with origination being an opportunistic response to diminishing ecospace occupancy.
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| 48. |
- Liu, Xiaokang, et al.
(författare)
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Heterogeneous selectivity and morphological evolution of marine clades during the Permian-Triassic mass extinction
- 2024
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Ingår i: NATURE ECOLOGY & EVOLUTION. - 2397-334X. ; 8:1248–1258
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Tidskriftsartikel (refereegranskat)abstract
- Morphological disparity and taxonomic diversity are distinct measures of biodiversity, typically expected to evolve synergistically. However, evidence from mass extinctions indicates that they can be decoupled, and while mass extinctions lead to a drastic loss of diversity, their impact on disparity remains unclear. Here we evaluate the dynamics of morphological disparity and extinction selectivity across the Permian-Triassic mass extinction. We developed an automated approach, termed DeepMorph, for the extraction of morphological features from fossil images using a deep learning model and applied it to a high-resolution temporal dataset encompassing 599 genera across six marine clades. Ammonoids, brachiopods and ostracods experienced a selective loss of complex and ornamented forms, while bivalves, gastropods and conodonts did not experience morphologically selective extinctions. The presence and intensity of morphological selectivity probably reflect the variations in environmental tolerance thresholds among different clades. In clades affected by selective extinctions, the intensity of diversity loss promoted the loss of morphological disparity. Conversely, under non-selective extinctions, the magnitude of diversity loss had a negligible impact on disparity. Our results highlight that the Permian-Triassic mass extinction had heterogeneous morphological selective impacts across clades, offering new insights into how mass extinctions can reshape biodiversity and ecosystem structure. Using a deep learning method that extracts morphological features from images of marine fossils, the authors explore morphological disparity dynamics over a time series of 4 million years, spanning the Permian-Triassic mass extinction event.
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| 49. |
- Loiseau, O., et al.
(författare)
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Slowly but surely: gradual diversification and phenotypic evolution in the hyper-diverse tree fern family Cyatheaceae
- 2020
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Ingår i: Annals of Botany. - : Oxford University Press (OUP). - 0305-7364 .- 1095-8290. ; 125:1, s. 93-103
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Tidskriftsartikel (refereegranskat)abstract
- Background and Aims The tremendously unbalanced distribution of species richness across clades in the tree of life is often interpreted as the result of variation in the rates of diversification, which may themselves respond to trait evolution. Even though this is likely a widespread pattern, not all diverse groups of organisms exhibit heterogeneity in their dynamics of diversification. Testing and characterizing the processes driving the evolution of clades with steady rates of diversification over long periods of time are of importance in order to have a full understanding of the build-up of biodiversity through time. Methods We studied the macroevolutionary history of the species-rich tree fern family Cyatheaceae and inferred a time-calibrated phylogeny of the family including extinct and extant species using the recently developed fossilized birth-death method. We tested whether the high diversity of Cyatheaceae is the result of episodes of rapid diversification associated with phenotypic and ecological differentiation or driven by stable but low rates of diversification. We compared the rates of diversification across clades, modelled the evolution of body size and climatic preferences and tested for trait-dependent diversification. Key Results This ancient group diversified at a low and constant rate during its long evolutionary history. Morphological and climatic niche evolution were found to be overall highly conserved, although we detected several shifts in the rates of evolution of climatic preferences, linked to changes in elevation. The diversification of the family occurred gradually, within limited phenotypic and ecological boundaries, and yet resulted in a remarkable species richness. Conclusions Our study indicates that Cyatheaceae is a diverse clade which slowly accumulated morphological, ecological and taxonomic diversity over a long evolutionary period and provides a compelling example of the tropics as a museum of biodiversity.
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| 50. |
- Marek, Magdalena, et al.
(författare)
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Serum albumin promotes ATP-binding cassette transporter-dependent sterol uptake in yeast
- 2014
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Ingår i: FEMS yeast research (Print). - : Oxford Academic. - 1567-1356 .- 1567-1364. ; 14:8, s. 1223-1233
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Tidskriftsartikel (refereegranskat)abstract
- Sterol uptake in fungi is a multistep process that involves interaction between external sterols and the cell wall, incorporation of sterol molecules into the plasma membrane, and subsequent integration into intracellular membranes for turnover. ATP-binding cassette (ABC) transporters have been implicated in sterol uptake, but key features of their activity remain to be elucidated. Here, we apply fluorescent cholesterol (NBD-cholesterol) to monitor sterol uptake under anaerobic and aerobic conditions in two fungal species, Candida glabrata (Cg) and Saccharomyces cerevisiae (Sc). We found that in both fungal species, ABC transporter-dependent uptake of cholesterol under anaerobic conditions and in mutants lacking HEM1 gene is promoted in the presence of the serum protein albumin that is able to bind the sterol molecule. Furthermore, the C. glabrataABC transporter CgAus1p expressed in S. cerevisiae requires the presence of serum or albumin for efficient cholesterol uptake. These results suggest that albumin can serve as sterol donor in ABC transporter-dependent sterol uptake, a process potentially important for growth of C. glabrata inside infected humans.Serum albumin can serve as sterol donor in ATP-binding cassette-transporter-dependent sterol uptake, a process potentially important for growth of Candida glabrata inside infected humans.Serum albumin can serve as sterol donor in ATP-binding cassette-transporter-dependent sterol uptake, a process potentially important for growth of Candida glabrata inside infected humans.
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