ORCID Profile
0000-0003-3414-5155
Current Organisations
Università degli Studi di Milano
,
Université Grenoble Alpes
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Publisher: Wiley
Date: 28-08-2023
DOI: 10.1002/EDN3.467
Abstract: Environmental DNA studies have proliferated over the last decade, with promising data describing the ersity of organisms inhabiting aquatic and terrestrial ecosystems. The recovery of DNA present in the sediment of aquatic systems (sedDNA) has provided short‐ and long‐term data on a wide range of biological groups (e.g., photosynthetic organisms, zooplankton species) and has advanced our understanding of how environmental changes have affected aquatic communities. However, substantial challenges remain for recovering the genetic material of macro‐organisms (e.g., fish) from sediments, preventing complete reconstructions of past aquatic ecosystems, and limiting our understanding of historic, higher trophic level interactions. In this review, we outline the biotic and abiotic factors affecting the production, persistence, and transport of fish DNA from the water column to the sediments, and address questions regarding the preservation of fish DNA in sediment. We identify sources of uncertainties around the recovery of fish sedDNA arising during the sedDNA workflow. This includes methodological issues related to experimental design, DNA extraction procedures, and the selected molecular method (quantitative PCR, digital PCR, metabarcoding, metagenomics). By evaluating previous efforts (published and unpublished works) to recover fish sedDNA signals, we provide suggestions for future research and propose troubleshooting workflows for the effective detection and quantification of fish sedDNA. With further research, the use of sedDNA has the potential to be a powerful tool for inferring fish presence over time and reconstructing their population and community dynamics.
Publisher: Wiley
Date: 04-2019
DOI: 10.1111/MEC.15060
Publisher: Wiley
Date: 06-08-2015
DOI: 10.1111/COBI.12559
Abstract: After their failure to achieve a significant reduction in the global rate of bio ersity loss by 2010, world governments adopted 20 new ambitious Aichi bio ersity targets to be met by 2020. Efforts to achieve one particular target can contribute to achieving others, but different targets may sometimes require conflicting solutions. Consequently, lack of strategic thinking might result, once again, in a failure to achieve global commitments to bio ersity conservation. We illustrate this dilemma by focusing on Aichi Target 11. This target requires an expansion of terrestrial protected area coverage, which could also contribute to reducing the loss of natural habitats (Target 5), reducing human-induced species decline and extinction (Target 12), and maintaining global carbon stocks (Target 15). We considered the potential impact of expanding protected areas to mitigate global deforestation and the consequences for the distribution of suitable habitat for >10,000 species of forest vertebrates ( hibians, birds, and mammals). We first identified places where deforestation might have the highest impact on remaining forests and then identified places where deforestation might have the highest impact on forest vertebrates (considering aggregate suitable habitat for species). Expanding protected areas toward locations with the highest deforestation rates (Target 5) or the highest potential loss of aggregate species' suitable habitat (Target 12) resulted in partially different protected area network configurations (overlapping with each other by about 73%). Moreover, the latter approach contributed to safeguarding about 30% more global carbon stocks than the former. Further investigation of synergies and trade-offs between targets would shed light on these and other complex interactions, such as the interaction between reducing overexploitation of natural resources (Targets 6, 7), controlling invasive alien species (Target 9), and preventing extinctions of native species (Target 12). Synergies between targets must be identified and secured soon and trade-offs must be minimized before the options for co-benefits are reduced by human pressures.
Publisher: Wiley
Date: 23-03-2015
DOI: 10.1111/MEC.13136
Abstract: Paleoenvironmental studies are essential to understand bio ersity changes over long timescales and to assess the relative importance of anthropogenic and environmental factors. Sedimentary ancient DNA (sedaDNA) is an emerging tool in the field of paleoecology and has proven to be a complementary approach to the use of pollen and macroremains for investigating past community changes. SedaDNA-based reconstructions of ancient environments often rely on indicator taxa or expert knowledge, but quantitative ecological analyses might provide more objective information. Here, we analysed sedaDNA to investigate plant community trajectories in the catchment of a high-elevation lake in the Alps over the last 6400 years. We combined data on past and present plant species assemblages along with sedimentological and geochemical records to assess the relative impact of human activities through pastoralism, and abiotic factors (temperature and soil evolution). Over the last 6400 years, we identified significant variation in plant communities, mostly related to soil evolution and pastoral activities. An abrupt vegetational change corresponding to the establishment of an agropastoral landscape was detected during the Late Holocene, approximately 4500 years ago, with the replacement of mountain forests and tall-herb communities by heathlands and grazed lands. Our results highlight the importance of anthropogenic activities in mountain areas for the long-term evolution of local plant assemblages. SedaDNA data, associated with other paleoenvironmental proxies and present plant assemblages, appear to be a relevant tool for reconstruction of plant cover history. Their integration, in conjunction with classical tools, offers interesting perspectives for a better understanding of long-term ecosystem dynamics under the influence of human-induced and environmental drivers.
Publisher: Wiley
Date: 16-12-2016
DOI: 10.1111/COBI.12813
Publisher: MDPI AG
Date: 09-10-2021
DOI: 10.3390/DATA6100107
Abstract: Most of the world’s mountain glaciers have been retreating for more than a century in response to climate change. Glacier retreat is evident on all continents, and the rate of retreat has accelerated during recent decades. Accurate, spatially explicit information on the position of glacier margins over time is useful for analyzing patterns of glacier retreat and measuring reductions in glacier surface area. This information is also essential for evaluating how mountain ecosystems are evolving due to climate warming and the attendant glacier retreat. Here, we present a non-comprehensive spatially explicit dataset showing multiple positions of glacier fronts since the Little Ice Age (LIA) maxima, including many data from the pre-satellite era. The dataset is based on multiple historical archival records including topographical maps repeated photographs, paintings, and aerial or satellite images with a supplement of geochronology and own field data. We provide ESRI shapefiles showing 728 past positions of 94 glacier fronts from all continents, except Antarctica, covering the period between the Little Ice Age maxima and the present. On average, the time series span the past 190 years. From 2 to 46 past positions per glacier are depicted (on average: 7.8).
Publisher: Elsevier BV
Date: 05-2019
DOI: 10.1016/J.SCITOTENV.2019.02.191
Abstract: An excessive supply of sediment is observed in numerous rivers across the world where it leads to deleterious impacts. Information on the sources delivering this material to waterbodies is required to design effective management measures, and sediment tracing or fingerprinting techniques are increasingly used to quantify the amount of sediment derived from different sources. However, the current methods used to identify the land use contributions to sediment have a limited discrimination power. Here, we investigated the potential of environmental DNA (eDNA) to provide more detailed information on the plant species found in sediment source areas as a next generation fingerprint. To this end, flood sediment deposits (n = 12) were collected in 2017 in two catchments impacted by the Fukushima radioactive fallout along differing river sections draining forests, cropland or a mix of both land uses. Conventional fingerprints (i.e. fallout radionuclides and organic matter properties) were also measured in these s les. The conventional fingerprint model results showed that most sediment s les contained a dominant proportion of subsoil material. Nevertheless, the eDNA information effectively discriminated the three above-mentioned groups of sediment, with the dominance of tree, shrub and fern species in sediment s led in rivers draining forests versus a majority of grass, algae and cultivated plant species in sediment collected in rivers draining cropland. Based on these encouraging results, future research should examine the potential of eDNA in mixed land use catchments where the contribution of topsoil to sediment dominates and where the cultivation of land has not been abandoned in order to better characterize the memory effect of eDNA in soils and sediment.
Publisher: Springer Science and Business Media LLC
Date: 25-03-2020
DOI: 10.1038/S41586-020-2138-7
Abstract: Environmental change is rapidly accelerating, and many species will need to adapt to survive
Publisher: Wiley
Date: 03-04-2017
DOI: 10.1111/NPH.14470
Abstract: Contents Summary 924 I. Introduction 925 II. Environmental and temporal limits for survival of aDNA 925 III. Lake sediments 927 IV. Perspective for plant aDNA research 929 V. Perspective for plant aDNA research 930 VI. Pollen DNA 930 VII. Sedimentary aDNA 931 VIII. Recent key findings and future methods using HTS techniques 933 IX. Challenges when studying aDNA from lake sediments 935 X. Bioinformatic processing 936 XI. Conclusions and directions for future research 938 Acknowledgements 938 References 938 Recent advances in sequencing technologies now permit the analyses of plant DNA from fossil s les (ancient plant DNA , plant aDNA ), and thus enable the molecular reconstruction of palaeofloras. Hitherto, ancient frozen soils have proved excellent in preserving DNA molecules, and have thus been the most commonly used source of plant aDNA . However, DNA from soil mainly represents taxa growing a few metres from the s ling point. Lakes have larger catchment areas and recent studies have suggested that plant aDNA from lake sediments is a more powerful tool for palaeofloristic reconstruction. Furthermore, lakes can be found globally in nearly all environments, and are therefore not limited to perennially frozen areas. Here, we review the latest approaches and methods for the study of plant aDNA from lake sediments and discuss the progress made up to the present. We argue that aDNA analyses add new and additional perspectives for the study of ancient plant populations and, in time, will provide higher taxonomic resolution and more precise estimation of abundance. Despite this, key questions and challenges remain for such plant aDNA studies. Finally, we provide guidelines on technical issues, including lake selection, and we suggest directions for future research on plant aDNA studies in lake sediments.
Publisher: Wiley
Date: 24-02-2015
DOI: 10.1111/CONL.12158
Publisher: Wiley
Date: 19-07-2023
DOI: 10.1111/CSP2.12988
Abstract: The problem of global hibian declines has prompted extensive research over the last three decades. Initially, the focus was on identifying and characterizing the extent of the problem, but more recently efforts have shifted to evidence‐based research designed to identify best solutions and to improve conservation outcomes. Despite extensive accumulation of knowledge on hibian declines, there remain knowledge gaps and disconnects between science and action that h er our ability to advance conservation efforts. Using input from participants at the ninth World Congress of Herpetology, a U.S. Geological Survey Powell Center symposium, hibian on‐line forums for discussion, the International Union for Conservation of Nature Assisted Reproductive Technologies and Gamete Biobanking group, and respondents to a survey, we developed a list of 25 priority research questions for hibian conservation at this stage of the Anthropocene. We identified hibian conservation research priorities while accounting for expected tradeoffs in geographic scope, costs, and the taxonomic breadth of research needs. We aimed to solicit views from in iduals rather than organizations while acknowledging inequities in participation. Emerging research priorities (i.e., those under‐represented in recently published hibian conservation literature) were identified, and included the effects of climate change, community‐level (rather than single species‐level) drivers of declines, methodological improvements for research and monitoring, genomics, and effects of land‐use change. Improved inclusion of under‐represented members of the hibian conservation community was also identified as a priority. These research needs represent critical knowledge gaps for hibian conservation although filling these gaps may not be necessary for many conservation actions.
Publisher: Wiley
Date: 10-11-2014
Abstract: Environmental DNA (eDNA) metabarcoding is increasingly used to study the present and past bio ersity. eDNA analyses often rely on lification of very small quantities or degraded DNA. To avoid missing detection of taxa that are actually present (false negatives), multiple extractions and lifications of the same s les are often performed. However, the level of replication needed for reliable estimates of the presence/absence patterns remains an unaddressed topic. Furthermore, degraded DNA and PCR/sequencing errors might produce false positives. We used simulations and empirical data to evaluate the level of replication required for accurate detection of targeted taxa in different contexts and to assess the performance of methods used to reduce the risk of false detections. Furthermore, we evaluated whether statistical approaches developed to estimate occupancy in the presence of observational errors can successfully estimate true prevalence, detection probability and false-positive rates. Replications reduced the rate of false negatives the optimal level of replication was strongly dependent on the detection probability of taxa. Occupancy models successfully estimated true prevalence, detection probability and false-positive rates, but their performance increased with the number of replicates. At least eight PCR replicates should be performed if detection probability is not high, such as in ancient DNA studies. Multiple DNA extractions from the same s le yielded consistent results in some cases, collecting multiple s les from the same locality allowed detecting more species. The optimal level of replication for accurate species detection strongly varies among studies and could be explicitly estimated to improve the reliability of results.
Publisher: Springer Science and Business Media LLC
Date: 29-06-2020
DOI: 10.1038/S41598-020-67452-1
Abstract: eDNA refers to DNA extracted from an environmental s le with the goal of identifying the occurrence of past or current biological communities in aquatic and terrestrial environments. However, there is currently a lack of knowledge regarding the soil memory effect and its potential impact on lake sediment eDNA records. To investigate this issue, two contrasted sites located in cultivated environments in France were studied. In the first site, soil s les were collected (n = 30) in plots for which the crop rotation history was documented since 1975. In the second site, s les were collected (n = 40) to compare the abundance of currently observed taxa versus detected taxa in cropland and other land uses. The results showed that the last cultivated crop was detected in 100% of the s les as the most abundant. In addition, weeds were the most abundant taxa identified in both sites. Overall, these results illustrate the potential of eDNA analyses for identifying the recent ( 10 years) land cover history of soils and outline the detection of different taxa in cultivated plots. The capacity of detection of plant species grown on soils delivering sediments to lacustrine systems is promising to improve our understanding of sediment transfer processes over short timescales.
No related grants have been discovered for Gentile Francesco Ficetola.