mariariz

• Salazar, Maria Ariza; Engelstad, Mari; Lieungh, Eva; Laux, Marcele; Ready, Jonathan & Mauvisseau, Quentin [Show all 8 contributors for this article] (2024). Evaluating the feasibility of using plant-specific metabarcoding to assess forest types from soil eDNA. Applied Vegetation Science. ISSN 1402-2001. 27(4). doi: 10.1111/avsc.12806. Full text in Research Archive Show summary

  Questions An essential aspect of variation in natural systems is that species respond to complex environmental gradients. Recognizing plant composition gradients associated with abiotic factors (ecoclines) can be foundational for defining habitat types, which, in turn, helps map natural variation. Typically, ecoclinal structures are assessed through visual evaluation of above-ground vegetation and analysis of covarying abiotic factors. However, the correlation between ecological structures detected by soil eDNA plant assessments and those identified by visual assessment remains largely unexplored. Location Hvaler archipelago, southern Norway. Methods Plant diversity assessments were conducted using metabarcoding of the trnL (UUA) intron p6 loop and ITS2 from 31 soil samples collected across six forest types. These forest types span gradients related to drought risk and calcium richness. Results The barcode amplicons identified 70 plant taxa, primarily vascular plants (67), with most assigned to the species level (59), representing common forest taxa across the sites. Comparisons between soil eDNA compositions and theoretical forest-type compositions showed a low to medium correspondence (26% to 76%) between the two. Ordinations of soil eDNA compositions revealed two axes without clear ecological interpretation and correlated poorly with the calcium–richness gradient previously identified by visual assessments. Conclusions Overall, our results emphasize the necessity for comprehensive sequence reference libraries to conduct thorough plant biodiversity assessments. They also highlight the potential of soil eDNA to assess plant composition, which can aid in ecosystem mapping.

• Quintana, Itxaso; Cifuentes, Edgar F.; Dunnink, Jeffrey A.; Salazar, Maria Ariza; Martínez-Medina, Daniela & Fantacini, Felipe M. [Show all 8 contributors for this article] (2022). Severe conservation risks of roads on apex predators. Scientific Reports. 12(1). doi: 10.1038/s41598-022-05294-9. Full text in Research Archive Show summary

  The global expansion of road networks threatens apex predator conservation and ecosystem functioning. This occurs through wildlife-vehicle collisions, habitat loss and fragmentation, reduced genetic connectivity and increased poaching. We reviewed road impacts on 36 apex predator species and assessed their risk from current roads based on road exposure and species vulnerability. Our findings reveal all apex predators are exposed to road impacts. Eight of the ten species with the highest risk occur in Asia, although other high-risk species are present in the Americas, Africa and Europe. The sloth bear suffers the highest risk of all apex predators, followed by the tiger and dhole. Based on species risk from roads, we propose a widely applicable method to assess the potential impact of future roads on apex predators. We applied this method to proposed road developments in three areas: the Brazilian Amazon, Africa, and Nepal, to locate high-impact road segments. Roughly 500 protected areas will be intersected by these roads, threatening core apex predator habitats. We advocate the need for rigorous road development planning to apply effective mitigation measures as an urgent priority and to avoid construction in wilderness areas and predator strongholds.

• Salazar, Maria Ariza; Fouks, Bertrand; Mauvisseau, Quentin; Halvorsen, Rune; Alsos, Inger Greve & Boer, Hugo de (2022). Plant biodiversity assessment through soil eDNA reflects temporal and local diversity. Methods in Ecology and Evolution. 14(2), p. 415–430. doi: 10.1111/2041-210X.13865. Full text in Research Archive Show summary

  1. Several studies have shown the potential of eDNA-based proxies for plant identification, but little is known about their spatial and temporal resolution. This limits its use for plant biodiversity assessments and monitoring of vegetation responses to environmental changes. Here we calibrate the temporal and spatial plant signals detected with soil eDNA surveys by comparing with a standard visual above-ground vegetation survey.<p> <p>2. Our approach compares vegetation in an old-growth boreal forest in southern Norway, surveyed in 100 permanent 1-m2 plots seven times over a 30-year period, with a single soil eDNA metabarcoding-based survey from soil samples collected at the same 100 plots in the year of the last vegetation survey. <p>3. On average, 60% and 10% of the vascular plants and bryophytes recorded across all vegetation surveys were detected by soil eDNA. Taxa detected by soil eDNA were more representative for the local taxa pool than for the specific plot, and corresponded to those surveyed over the 30-year period although most closely matched the current taxa composition. Soil eDNA detected abundant taxa better than rare ones although both rare taxa and taxa unrecorded by the visual survey were detected. <p>4. Our study highlights the potential of soil eDNA assessments for monitoring of vegetation responses over broad spatial and temporal scales. The method's ability to detect abundant taxa makes it suitable for assessment of vegetation composition in a specific area and for broad-scale plant diversity assessments.

• Polling, Marcel; Schure, Anna Theresia Maria Ter; Geel, Bas van; Bokhoven, Tom van; Boessenkool, Sanne & MacKay, Glen [Show all 13 contributors for this article] (2021). Multiproxy analysis of permafrost preserved faeces provides an unprecedented insight into the diets and habitats of extinct and extant megafauna. Quaternary Science Reviews. ISSN 0277-3791. 267, p. 1–16. doi: 10.1016/j.quascirev.2021.107084. Full text in Research Archive Show summary

  The study of faecal samples to reconstruct the diets and habitats of extinct megafauna has traditionally relied on pollen and macrofossil analysis. DNA metabarcoding has emerged as a valuable tool to complement and refine these proxies. While published studies have compared the results of these three proxies for sediments, this comparison is currently lacking for permafrost preserved mammal faeces. Moreover, most metabarcoding studies have focused on a single plant-specific DNA marker region. In this study, we target both the commonly used chloroplast trnL P6 loop as well as nuclear ribosomal ITS (nrITS). The latter can increase taxonomic resolution of plant identifications but requires DNA to be relatively well preserved because of the target length (∼300–500 bp). We compare DNA results to pollen and macrofossil analyses from permafrost and ice-preserved faeces of Pleistocene and Holocene megafauna. Samples include woolly mammoth, horse, steppe bison as well as Holocene and extant caribou. Most plant identifications were found using DNA, likely because the studied faeces contained many vegetative remains that could not be identified using macrofossils or pollen. Several taxa were, however, identified to lower taxonomic levels uniquely with macrofossil and pollen analysis. The nrITS marker provides species level taxonomic resolution for commonly encountered plant families that are hard to distinguish using the other proxies (e.g. Asteraceae, Cyperaceae and Poaceae). Integrating the results from all proxies, we are able to accurately reconstruct known diets and habitats of the extant caribou. Applying this approach to the extinct mammals, we find that the Holocene horse and steppe bison were not strict grazers but mixed feeders living in a marshy wetland environment. The mammoths showed highly varying diets from different non-analogous habitats. This confirms the presence of a mosaic of habitats in the Pleistocene ‘mammoth steppe’ that mammoths could fully exploit due to their flexibility in food choice.

• Zizka, Alexander; Silvestro, Daniele; Andermann, Tobias; Azevedo, Josue; Ritter, Camila Duarte & Edler, Daniel [Show all 14 contributors for this article] (2019). CoordinateCleaner: Standardized cleaning of occurrence records from biological collection databases. Methods in Ecology and Evolution. 10(5), p. 744–751. doi: 10.1111/2041-210X.13152. Full text in Research Archive

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• Salazar, Maria Ariza; Pastor, Sandra Garces & Boer, Hugo de (2022). Chapter 24. Environmental and biodiversity assessments. In Boer, Hugo de; Rydmark, Marcella Christine Orwick; Verstraete, Brecht & Gravendeel, Barbara (Ed.), Molecular identification of plants: from sequence to species. Pensoft Publishers. ISSN 9786192480912. doi: 10.3897/ab.e98875. Full text in Research Archive
• Salazar, Maria Ariza; Pastor, Sandra Garces & Boer, Hugo de (2022). Chapter 4. DNA from soil. In Boer, Hugo de; Rydmark, Marcella Christine Orwick; Verstraete, Brecht & Gravendeel, Barbara (Ed.), Molecular identification of plants: from sequence to species. Pensoft Publishers. ISSN 9786192480912. doi: 10.3897/ab.e98875. Full text in Research Archive

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