Biology subjects

De Angelis, D.

Publications and source records attributed to De Angelis, D..

4 recordsLinked to original sources

bioRxiv2024

Standardizing marine habitat modelling practices to enhance inter-comparability across biological observations

In recent years, the volume of accessible marine pelagic observations has increased exponentially and now incorporates a wealth of new data types, including information derived from metagenomics and quantitative imaging. This calls for standardized modelling protocol across taxonomically harmonized observations, to better predict biogeographic patterns in space and time, and thus investigate marine ecosystem structure and functioning on a macroecological scale. In this context, we introduce CEPHALOPOD (Comprehensive Ensemble Pipeline for Habitat modelling Across Large-scale Ocean Pelagic Observation Datasets), a standardized and flexible framework to perform multi-species marine habitat modelling across data types and data sources. We built this new framework on observational data from federating initiatives such as AtlantECO, OBIS, GBIF, associated with already existing statistical and machine learning methods that enable to extract and model information from heterogeneous, scarce, and biased field observations. Here, we first document our statistical ensemble modelling approach and then assess its strength and limitations with a virtual ecologist approach. We show how our framework performs in reproducing a range of distributions from biased field samples. Then, we illustrate its performance and comparability across data types by investigating the global diversity patterns of coccolithophores from both abundance and metagenomic data. Our modelling framework serves as a foundation for the consistent generation of Essential Biodiversity and Ocean Variables (EBVs and EOVs) and carries the potential to significantly advance our comprehension of biodiversity and marine ecosystems functioning. Finally, it provides an unprecedented opportunity to foster collaborations in the field of marine science, sustainable ecological practices, and, ultimately, contribute to the preservation of global marine biodiversity.

ecology↗

bioRxiv2023

Including biotic interactions in species distribution models improves the understanding of species niche: a case of study with the brown bear in Europe

Biotic interactions are expected to influence species responses to climate change, but they are usually not included when predicting future range shifts. We assessed the importance of biotic interactions to understand future consequences of climate and land use change for biodiversity using as a model system the brown bear (Ursus arctos) in Europe. By including biotic interactions using the spatial variation of energy contribution and habitat models of each food species, we showed that the use of biotic factors considerably improves our understanding of the distribution of brown bears. Predicted future range shifts, which included changes in the distribution of food species, varied greatly when considering various scenarios of change in biotic factors, warning about future indirect climate change effects. Our study confirmed that advancing our understanding of ecological networks of species interactions will improve future scenarios of biodiversity change, which is key for conserving biodiversity and ecosystem services.

ecology↗

bioRxiv2022

Stable population structure in Europe since the Iron Age, despite high mobility

Ancient DNA research in the past decade has revealed that European population structure changed dramatically in the prehistoric period (14,000-3,000 years before present, YBP), reflecting the widespread introduction of Neolithic farmer and Bronze Age Steppe ancestries. However, little is known about how population structure changed from the historical period onward (3,000 YBP - present). To address this, we collected whole genomes from 204 individuals from Europe and the Mediterranean, many of which are the first historical period genomes from their region (e.g. Armenia and France). We found that most regions show remarkable inter-individual heterogeneity. At least 7% of historical individuals carry ancestry uncommon in the region where they were sampled, some indicating cross-Mediterranean contacts. Despite this high level of mobility, overall population structure across western Eurasia is relatively stable through the historical period up to the present, mirroring geography. We show that, under standard population genetics models with local panmixia, the observed level of dispersal would lead to a collapse of population structure. Persistent population structure thus suggests a lower effective migration rate than indicated by the observed dispersal. We hypothesize that this phenomenon can be explained by extensive transient dispersal arising from drastically improved transportation networks and the Roman Empires mobilization of people for trade, labor, and military. This work highlights the utility of ancient DNA in elucidating finer scale human population dynamics in recent history.

genetics↗

bioRxiv2022

A Genetic History of Continuity and Mobility in the Iron Age Central Mediterranean

The Iron Age was a dynamic period in central Mediterranean history, with the expansion of Greek and Phoenician colonies and the growth of Carthage into the dominant maritime power of the Mediterranean. These events were facilitated by the ease of long-distance travel following major advances in seafaring. We know from the archaeological record that trade goods and materials were moving across great distances in unprecedented quantities, but it is unclear how these patterns correlate with human mobility. To investigate population mobility and interactions directly, we sequenced the genomes of 30 ancient individuals from coastal cities around the central Mediterranean, in Tunisia, Sardinia, and central Italy. We observe a meaningful contribution of autochthonous populations, as well as highly heterogeneous ancestry including many individuals with non-local ancestries from other parts of the Mediterranean region. These results highlight both the role of local populations and the extreme interconnectedness of populations in the Iron Age Mediterranean. By studying these trans-Mediterranean neighbors together, we explore the complex interplay between local continuity and mobility that shaped the Iron Age societies of the central Mediterranean.

genomics↗