Daniele Silvestro

Last Name

Silvestro

First Name

Daniele

ORCID

0000-0003-0100-0961

Organisational unit

09490 - Stadler, Tanja / Stadler, Tanja

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Publications 1 - 10 of 138

DeepDiveR—A software for deep learning estimation of palaeodiversity from fossil occurrences
Cooper, Rebecca B.; Allen, Bethany; Silvestro, Daniele (2025)
Methods in Ecology and Evolution
1. The incompleteness of the fossil record, in particular variation in preservation and sampling through space and time, presents a barrier to estimating changes in biodiversity which standard statistical methods struggle to account for. 2. Here we present DeepDiveR, an R package companion for the DeepDive Python program, facilitating estimation of biodiversity from fossil occurrence data. The method uses a simulation-trained deep neural network to generate predictions of biodiversity change through time, while accounting for temporal, spatial, and taxonomic heterogeneities in preservation and sampling. 3. DeepDive and DeepDiveR can be readily used to explore the extinct biodiversity of different clades. We demonstrate the pipeline to build and customise analyses in R, including consideration of changes in biogeography, before running them in Python. We also further develop the DeepDive model to integrate information about modern diversity in the case of extant clades and introduce a function that automatically adjusts the parameterisation of the simulations to generate training data that reflect the distribution of empirical datasets. 4. To demonstrate the software, we analyse the fossil record of the order Carnivora through the Cenozoic, finding a peak in diversity in the Late Miocene and a 31% species loss since the Pleistocene. Our implementation includes the generation of summary statistics and plots that allow for an evaluation of the model performance and diversity estimations, and a configuration file that captures all parameters required to guarantee the full reproducibility of the results.
Eco-Evolutionary Dynamics of Plant-Soil Feedbacks Explain the Spread Potential of a Plant Invader Under Climate Warming and Biocontrol Herbivory
Sun, Yan; Silvestro, Daniele; Mathes, Gregor H.; et al. (2025)
Global change biology
Plant–soil feedbacks (PSFs) can contribute to the success of invasive plants. Despite strong evidence that plant genetic traits influence soil microbial communities and vice versa, empirical evidence exploring these feedbacks over evolutionary timescales, especially under climate change, remains limited. We conducted a 5-year field study of the annual invasive plant, Ambrosia artemisiifolia L., to examine how selection under climate warming and biocontrol insect herbivory shapes plant population genetics, soil properties, and microbial communities. After four generations under warming and herbivory, we collected seeds of the F4 plant populations together with their conditioned soil for a common garden PSF experiment to explore how resulting PSFs patterns are influencing the performance and spread potential of Ambrosia under changing environmental conditions. This is especially relevant because our recent predictions point to a northward spread of Ambrosia in Europe and Asia under climate change, outpacing the spread of its insect biocontrol agent. We discovered that warming and herbivory significantly but differentially altered plant genetic composition and its soil microbial communities, with less pronounced effects on soil physicochemical properties. Our results indicate that both herbivory and warming generated negative PSFs. These negative PSFs favored plant growth of the seeds from the persistent soil seed bank growing in the conditioned soil under insect herbivory, and by this maintaining the Ambrosia population genetic diversity. They also enhanced the spread potential of warming-selected plant offspring, especially from warmer (southern) to colder (northern) climates. This can be explained by the observed decrease in soil pathogens occurrence under insect herbivory and by the especially strong genetic changes in plant populations under climate warming. Our findings provide insights into how climate warming and biocontrol management affect eco-evolutionary interactions between invasive plant populations and their soil environments, which are critical for predicting invasion dynamics in the context of global change.
Early arrival and climatically-linked geographic expansion of New World monkeys from tiny African ancestors
Silvestro, Daniele; Tejedor, Marcelo F.; Serrano-Serrano, Martha L.; et al. (2019)
Systematic Biology
New World Monkeys (NWM) (platyrrhines) are one of the most diverse groups of primates, occupying today a wide range of ecosystems in the American tropics and exhibiting large variations in ecology, morphology, and behavior. Although the relationships among the almost 200 living species are relatively well understood, we lack robust estimates of the timing of origin, ancestral morphology, and geographic range evolution of the clade. Herein, we integrate paleontological and molecular evidence to assess the evolutionary dynamics of extinct and extant platyrrhines. We develop novel analytical frameworks to infer the evolution of body mass, changes in latitudinal ranges through time, and species diversification rates using a phylogenetic tree of living and fossil taxa. Our results show that platyrrhines originated 5–10 million years earlier than previously assumed, dating back to the Middle Eocene. The estimated ancestral platyrrhine was small—weighing 0.4 kg—and matched the size of their presumed African ancestors. As the three platyrrhine families diverged, we recover a rapid change in body mass range. During the Miocene Climatic Optimum, fossil diversity peaked and platyrrhines reached their widest latitudinal range, expanding as far South as Patagonia, favored by warm and humid climate and the lower elevation of the Andes. Finally, global cooling and aridification after the middle Miocene triggered a geographic contraction of NWM and increased their extinction rates. These results unveil the full evolutionary trajectory of an iconic and ecologically important radiation of monkeys and showcase the necessity of integrating fossil and molecular data for reliably estimating evolutionary rates and trends.
Challenges in estimating species' age from phylogenetic trees
Calderón del Cid, Carlos; Hauffe, Torsten; Carrillo, Juan D.; et al. (2024)
Global Ecology and Biogeography
Aim Species 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. Innovation For 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 conclusion Our 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.
Evolutionary footprint of coevolving positions in genes
Dib, Linda; Silvestro, Daniele; Salamin, Nicolas (2014)
Bioinformatics
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 × 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.
Fossil-informed models reveal a boreotropical origin and divergent evolutionary trajectories in the walnut family (Juglandaceae)
Zhang, Qiuyue; Ree, Richard H.; Salamin, Nicolas; et al. (2022)
Systematic Biology
Temperate woody plants in the Northern Hemisphere have long been known to exhibit high species richness in East Asia and North America and significantly lower diversity in Europe, but the causes of this pattern remain debated. Here, we quantify the roles of dispersal, niche evolution, and extinction in shaping the geographic diversity of the temperate woody plant family Juglandaceae (walnuts and their relatives). Integrating evidence from molecular, morphological, fossil, and (paleo)environmental data, we find strong support for a Boreotropical origin of the family with contrasting evolutionary trajectories between the temperate subfamily Juglandoideae and the tropical subfamily Engelhardioideae. Juglandoideae rapidly evolved frost tolerance when the global climate shifted to ice-house conditions from the Oligocene, with diversification at high latitudes especially in Europe and Asia during the Miocene. Subsequent range contraction at high latitudes and high levels of extinction in Europe driven by global cooling led to the current regional disparity in species diversity. Engelhardioideae showed temperature conservatism while adapting to increased humidity, tracking tropical climates to low latitudes since the middle Eocene with comparatively little diversification, perhaps due to high competition in the tropical zone. The biogeographic history of Juglandaceae shows that the North Atlantic land bridge and Europe played more critical roles than previously thought in linking the floras of East Asia and North America, and showcases the complex interplay among climate change, niche evolution, dispersal, and extinction that shaped the modern disjunct pattern of species richness in temperate woody plants. [Boreotropical origin; climatic niche evolution; disjunct distribution; dispersal; diversity anomaly; extinction; Juglandaceae.]
Bridging inter- and intraspecific trait evolution with a hierarchical Bayesian approach
Kostikova, Anna; Silvestro, Daniele; Pearman, Peter B.; et al. (2016)
Systematic Biology
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.
Patterns and drivers of heat production in the plant genus Amorphophallus
Claudel, Cyrille; Loiseau, Oriane; Silvestro, Daniele; et al. (2023)
The Plant Journal
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°C, and in one case 21.7°C 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.
Heterogeneous selectivity and morphological evolution of marine clades during the Permian–Triassic mass extinction
Liu, Xiaokang; Chu, Daoliang; Wang, Fengyu; et al. (2024)
Nature Ecology & Evolution
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.
Selective extinction against redundant species buffers functional diversity
Pimiento, Catalina; Bacon, Christine D.; Silvestro, Daniele; et al. (2020)
Proceedings of the Royal Society B: Biological Sciences
The extinction of species can destabilize ecological processes. A way to assess the ecological consequences of species loss is by examining changes in functional diversity. The preservation of functional diversity depends on the range of ecological roles performed by species, or functional richness, and the number of species per role, or functional redundancy. However, current knowledge is based on short timescales and an understanding of how functional diversity responds to long-term biodiversity dynamics has been limited by the availability of deep-time, trait-based data. Here, we compile an exceptional trait dataset of fossil molluscs from a 23-million-year interval in the Caribbean Sea (34 011 records, 4422 species) and develop a novel Bayesian model of multi-trait-dependent diversification to reconstruct mollusc (i) diversity dynamics, (ii) changes in functional diversity, and (iii) extinction selectivity over the last 23 Myr. Our results identify high diversification between 23–5 Mya, leading to increases in both functional richness and redundancy. Conversely, over the last three million years, a period of high extinction rates resulted in the loss of 49% of species but only 3% of functional richness. Extinction rates were significantly higher in small, functionally redundant species suggesting that competition mediated the response of species to environmental change. Taken together, our results identify long-term diversification and selective extinction against redundant species that allowed functional diversity to grow over time, ultimately buffering the ecological functions of biological communities against extinction.

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Daniele Silvestro

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