The bioassessment of aquatic ecosystems is currently based on various biotic indices that use the occurrence and/or abundance of selected taxonomic groups to define ecological status. These ...conventional indices have some limitations, often related to difficulties in morphological identification of bioindicator taxa. Recent development of DNA barcoding and metabarcoding could potentially alleviate some of these limitations, by using DNA sequences instead of morphology to identify organisms and to characterize a given ecosystem. In this paper, we review the structure of conventional biotic indices, and we present the results of pilot metabarcoding studies using environmental DNA to infer biotic indices. We discuss the main advantages and pitfalls of metabarcoding approaches to assess parameters such as richness, abundance, taxonomic composition and species ecological values, to be used for calculation of biotic indices. We present some future developments to fully exploit the potential of metabarcoding data and improve the accuracy and precision of their analysis. We also propose some recommendations for the future integration of DNA metabarcoding to routine biomonitoring programs.
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•Current biomonitoring approaches are widely used but have some limitations.•DNA metabarcoding provides a new complementary tool for biomonitoring.•Metabarcoding allows extending the range of taxa used as bioindicators.•Metabarcoding data could be used to establish molecular metrics and indices.•Future work should standardise procedures and improve data analysis.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
DNA metabarcoding is increasingly used in dietary studies to estimate diversity, composition and frequency of occurrence of prey items. However, few studies have assessed how technical and biological ...replication affect the accuracy of diet estimates. This study addresses these issues using the European free‐tailed bat Tadarida teniotis, involving high‐throughput sequencing of a small fragment of the COI gene in 15 separate faecal pellets and a 15‐pellet pool per each of 20 bats. We investigated how diet descriptors were affected by variability among (a) individuals, (b) pellets of each individual and (c) PCRs of each pellet. In addition, we investigated the impact of (d) analysing separate pellets vs. pellet pools. We found that diet diversity estimates increased steadily with the number of pellets analysed per individual, with seven pellets required to detect ~80% of prey species. Most variation in diet composition was associated with differences among individual bats, followed by pellets per individual and PCRs per pellet. The accuracy of frequency of occurrence estimates increased with the number of pellets analysed per bat, with the highest error rates recorded for prey consumed infrequently by many individuals. Pools provided poor estimates of diet diversity and frequency of occurrence, which were comparable to analysing a single pellet per individual, and consistently missed the less common prey items. Overall, our results stress that maximizing biological replication is critical in dietary metabarcoding studies and emphasize that analysing several samples per individual rather than pooled samples produce more accurate results.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
The application of DNA metabarcoding to dietary analysis of trophic generalists requires using multiple markers in order to overcome problems of primer specificity and bias. However, limited ...attention has been given to the integration of information from multiple markers, particularly when they partly overlap in the taxa amplified, and vary in taxonomic resolution and biases. Here, we test the use of a mix of universal and specific markers, provide criteria to integrate multi‐marker metabarcoding data and a python script to implement such criteria and produce a single list of taxa ingested per sample. We then compare the results of dietary analysis based on morphological methods, single markers, and the proposed combination of multiple markers. The study was based on the analysis of 115 faeces from a small passerine, the Black Wheatears (Oenanthe leucura). Morphological analysis detected far fewer plant taxa (12) than either a universal 18S marker (57) or the plant trnL marker (124). This may partly reflect the detection of secondary ingestion by molecular methods. Morphological identification also detected far fewer taxa (23) than when using 18S (91) or the arthropod markers IN16STK (244) and ZBJ (231), though each method missed or underestimated some prey items. Integration of multi‐marker data provided far more detailed dietary information than any single marker and estimated higher frequencies of occurrence of all taxa. Overall, our results show the value of integrating data from multiple, taxonomically overlapping markers in an example dietary data set.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
Este texto procura formular, de maneira provisória, entendimentos acerca das potencialidades narrativas presentes nas formas plásticas desenvolvidas pelo escritor angolano José Luandino Vieira. A ...título de estudo de caso, propõe-se analisar o desenho "Portrait of a sauvage as a youg sic girl", recolhido do livro Papéis da Prisão (2015), como um gesto narrativo estético que condensa tópicos críticos sobre o empreendimento colonial português e que pavimenta, em pequenos traçados, a relação entre palavra e experiência. Os desenhos aqui são compreendidos não como ilustrações ou rascunhos, mas discurso sobre um método daquilo que definiremos como um pensamento visual.
Agricultural policies in the European Union (EU) are increasingly promoting organic management and integrated pest management (IPM) as environmentally friendly alternatives to high-input conventional ...management. While there is consensus that organic management is largely beneficial for biodiversity, including the natural enemies of crop pests, IPM has been much less scrutinized. We conducted a meta-analysis based on 294 observations extracted from 18 studies to compare the effects of conventional, IPM and organic management on biocontrol potential and herbivore pressure in olive, an important cash crop in the EU. Information about the management practices used was also compiled to assess differences in intensity between the three management strategies. Results suggest that IPM is predominantly based on intensive practices, employing chemical control rather than preventive measures as a first resort. Biocontrol potential and herbivore pressure were similar in conventional management and IPM. Moreover, biocontrol potential was higher in organic crops than in crops under IPM, especially when considering canopy-dwelling natural enemies. Although organic management enhanced biocontrol potential, it also benefitted some olive pests, and in both cases effects were more pronounced at warmer temperatures. Our results suggest that, in its current form, IPM might not significantly affect biocontrol potential or herbivore pressure when compared with conventional olive crop management. A shift to a more comprehensive implementation of IPM practices is thus needed, involving the use of proactive measures to promote natural enemies and regulate olive pests before resorting to chemical control. Moreover, greater use of non-chemical inputs might be required for effective regulation of olive pests in organic olive crops.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Abstract
Mediterranean pastures are experiencing strong changes in management, involving shifts from sheep to cattle-based livestock systems. The impacts of such shifts on biodiversity are still ...poorly understood. Here, we sought to contrast the grazing regime, vegetation structure, bird species richness and abundance, between sheep and cattle grazed parcels, to understand the mechanisms through which management decisions impact farmland birds. During spring 2019, we characterized livestock management, bird populations and sward structure in 23 cattle and 27 sheep grazed parcels. We used a Structural Equation Model to infer the direct and indirect effects of sheep and cattle grazing on birds. Although no effects were found on overall species richness, there were species-specific responses to sheep and cattle grazed systems. Grazing pressure (variable integrating stocking rate and the number of days in the parcel) had negative impacts on the prevalence/abundance of Zitting Cisticola, Corn Bunting and Little Bustard, either directly or indirectly, through the effects of grazing pressure on vegetation height. Animal density and vegetation cover had direct positive effects in
Galerida
spp. and Common Quail, respectively. Zitting Cisticola and Little Bustard also showed a direct response to livestock type. Our study emphasizes the importance of grazing pressure as a driver of negative impacts for bird populations in Mediterranean grasslands. Since the ongoing transition from sheep to cattle-based systems involves increases in stocking rate, and therefore potentially higher grazing pressure, we propose a policy change to cap the maximum allowed grazing pressure. At the landscape scale, a mix of sheep and cattle grazed fields would be beneficial for maintaining bird diversity.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
Despite its importance for reducing wildlife-vehicle collisions, there is still incomplete understanding of factors responsible for high road mortality. In particular, few empirical studies examined ...the idea that spatial variation in roadkills is influenced by a complex interplay between road-related factors, and species-specific habitat quality and landscape connectivity.
In this study we addressed this issue, using a 7-year dataset of tawny owl (Strix aluco) roadkills recorded along 37 km of road in southern Portugal. We used a multi-species roadkill index as a surrogate of intrinsic road risk, and we used a Maxent distribution model to estimate habitat suitability. Landscape connectivity was estimated from least-cost paths between tawny owl territories, using habitat suitability as a resistance surface. We defined 10 alternative scenarios to compute connectivity, based on variation in potential movement patterns according to territory quality and dispersal distance thresholds. Hierarchical partitioning of a regression model indicated that independent variation in tawny owl roadkills was explained primarily by the roadkill index (70.5%) and, to a much lesser extent, by landscape connectivity (26.2%), while habitat suitability had minor effects (3.3%). Analysis of connectivity scenarios suggested that owl roadkills were primarily related to short range movements (<5 km) between high quality territories. Tawny owl roadkills were spatially autocorrelated, but the introduction of spatial filters in the regression model did not change the type and relative contribution of environmental variables.
Overall, results suggest that road-related factors may have a dominant influence on roadkill patterns, particularly in areas like ours where habitat quality and landscape connectivity are globally high for the study species. Nevertheless, the study supported the view that functional connectivity should be incorporated whenever possible in roadkill models, as it may greatly increase their power to predict the location of roadkill hotspots.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Arthropod declines have been linked to agricultural intensification. However, information about the impacts of intensification is still limited for many crops, as is our understanding of the ...responses of different arthropod taxa and trophic groups, thus hindering the development of effective mitigation measures. We investigated the impacts of olive farming intensification on canopy-dwelling arthropods in the Mediterranean region. Intensification involves the increased use of agrochemicals, mechanisation and irrigation, but also structural changes from traditional orchards with low densities of large and old trees, to intensive and superintensive orchards with high to very high densities of smaller and younger trees, respectively. Canopy arthropods were vacuum-sampled at 53 sites representing the three orchard intensification levels, in spring, summer and autumn 2017. We evaluated how the arthropod community varied across intensification levels, and in response to orchard structure, management and landscape context. We found no changes in the diversity of arthropod taxa across intensification levels after correcting for sample coverage, but arthropod abundance declined markedly along the intensification gradient. Decreased abundance was associated with changes in orchard structure, lower herbaceous cover, and higher herbicide and insecticide use. The abundance of a specialized olive pest was lower in landscapes with higher woodland cover. The negative effects of intensification were stronger in spring and summer than in autumn, and parasitoids and predators were particularly affected. Overall, results suggest that retaining herbaceous cover, reducing agrochemical inputs and preserving natural woody elements in the landscape, may contribute to mitigate impacts of olive farming intensification on canopy arthropods, particularly on beneficial species.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
Aerial photographs have been systematically collected from as early as the 1930s, providing a unique resource to describe changes in vegetation and land cover over extended periods of time. However, ...their use is often limited by technical constraints, such as the lack of ground control information and precise camera parameters, which hamper an accurate orthorectification of the raw imagery. Here, we describe the historical aerial photographs orthorectification (HAPO) workflow, based on a conventional photogrammetric procedure (the direct linear transformation (DLT) Method), integrated as a geographic information systems (GIS) procedure, in order to perform the image orientation and orthorectification, thereby converting historical aerial imagery into high-definition historical orthoimages. HAPO implementation is illustrated with an application to a rugged landscape in Portugal, where we aimed to produce land-cover maps using an aerial photograph coverage from 1947, as part of a study on long-term socioecological dynamics. We show that HAPO produces highly accurate orthoimages and discuss the wider usefulness of our framework in long-term socioecological research.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
This study examined responses of amphibians breeding in Mediterranean temporary ponds to a gradient of agricultural intensification, aiming to identify land uses and management prescriptions ...favouring the conservation of these habitats in farmed landscapes. Larval amphibian assemblages and habitat attributes were sampled at 57 ponds, 10 of which had been converted into permanent irrigation reservoirs. Species richness increased with area and hydroperiod in temporary ponds, with the addition of rare species to ponds with long hydroperiods resulting in a tendency for the less widespread species (e.g. Triturus marmoratus and T. boscai) to occur in the most species-rich ponds, while species-poor ponds consisted predominantly of widespread species only (nested pattern). However, one species (Pelodytes punctatus) was largely restricted to the most ephemeral ponds, whereas permanent irrigation reservoirs were species-poor and lacked most species occurring in temporary waters. The strongest negative correlates of amphibian abundances were the intensification of agricultural land uses, the transformation of ponds into permanent reservoirs and the introduction of exotic predators (fish and crayfish) from the irrigation channels. The results suggest that conservation of temporary pond amphibian assemblages in Mediterranean farmland requires networks of ponds with diverse hydroperiods, where the natural hydrologic regimes, less intensive land uses and isolation from irrigation waters should be preserved.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
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