Pedro Beja

Ecological impacts of early 21st century agricultural change in Europe – A review

The impacts of agricultural land use are far-reaching and extend to areas outside production. This paper provides an overview of the ecological status of agricultural systems across the European Union in the light of recent policy changes. It builds on the previous review of 2001 devoted to the impacts of agricultural intensification in Western Europe. The focus countries are the UK, The Netherlands, Boreal and Baltic countries, Portugal, Hungary and Romania, representing a geographical spread across Europe, but additional reference is made to other countries. Despite many adjustments to agricultural policy, intensification of production in some regions and concurrent abandonment in others remain the major threat to the ecology of agro-ecosystems impairing the state of soil, water and air and reducing biological diversity in agricultural landscapes. The impacts also extend to surrounding terrestrial and aquatic systems through water and aerial contamination and development of agricultural infrastructures (e.g. dams and irrigation channels). Improvements are also documented regionally, such as successful support of farmland species, and improved condition of watercourses and landscapes. This was attributed to agricultural policy targeted at the environment, improved environmental legislation, and new market opportunities. Research into ecosystem services associated with agriculture may provide further pressure to develop policy that is targeted at their continuous provisioning, fostering motivation of land managers to continue to protect and enhance them.

Conservation of Mediterranean temporary ponds under agricultural intensification: an evaluation using amphibians

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.

Birds of prey as limiting factors of gamebird populations in Europe: a review

Whether predators can limit their prey has been a topic of scientific debate for decades. Traditionally it was believed that predators take only wounded, sick, old or otherwise low‐quality individuals, and thus have little impact on prey populations. However, there is increasing evidence that, at least under certain circumstances, vertebrate predators may indeed limit prey numbers. This potential role of predators as limiting factors of prey populations has created conflicts between predators and human hunters, because the hunters may see predators as competitors for the same resources. A particularly acute conflict has emerged over the past few decades between gamebird hunters and birds of prey in Europe. As a part of a European‐wide research project, we reviewed literature on the relationships between birds of prey and gamebirds. We start by analysing available data on the diets of 52 European raptor and owl species. There are some 32 species, mostly specialist predators feeding on small mammals, small passerine birds or insects, which never or very rarely include game animals (e.g. hares, rabbits, gamebirds) in their diet. A second group (20 species) consists of medium‐sized and large raptors which prey on game, but for which the proportion in the diet varies temporally and spatially. Only three raptor species can have rather large proportions of gamebirds in their diet, and another seven species may utilise gamebirds locally to a great extent. We point out that the percentage of a given prey species in the diet of an avian predator does not necessarily reflect the impact of that predator on densities of prey populations. Next, we summarise available data on the numerical responses of avian predators to changing gamebird numbers. In half of these studies, no numerical response was found, while in the remainder a response was detected such that either raptor density or breeding success increased with density of gamebirds. Data on the functional responses of raptors were scarce. Most studies of the interaction between raptors and gamebird populations give some estimate of the predation rate (per cent of prey population taken by predator), but less often do they evaluate the subsequent reduction in the pre‐harvest population or the potential limiting effect on breeding numbers. The few existing studies indicate that, under certain conditions, raptor predation may limit gamebird populations and reduce gamebird harvests. However, the number and extent of such studies are too modest to draw firm conclusions. Furthermore, their geographical bias to northern Europe, where predator–prey communities are typically simpler than in the south, precludes extrapolation to more diverse southern European ecosystems. There is an urgent need to develop further studies, particularly in southern Europe, to determine the functional and numerical responses of raptors to gamebird populations in species and environments other than those already evaluated in existing studies. Furthermore, additional field experiments are needed in which raptor and possibly also mammalian predator numbers are manipulated on a sufficiently large spatial and temporal scale. Other aspects that have been little studied are the role of predation by the non‐breeding part of the raptor population, or floaters, on the breeding success and survival of gamebirds, as well as the effect of intra‐guild predation. Finally there is a need for further research on practical methods to reduce raptor predation on gamebirds and thus reduce conflict between raptor conservation and gamebird management.

An analysis of otter Lutra lutra predation on introduced American crayfish Procambarus clarkii in Iberian streams

1. Patterns of otter, Lutra lutra, predation on introduced American crayfish, Pro-cambarus clarkii, were examined in an Iberian intermittent stream over a 2-year period, in order to assess the relative importance to otters of this new food resource. Diet was described from spraints collected monthly, and the importance of different prey types was determined in terms of their relative numeric and energetic contributions to the diet. Monthly fluctuations in diet and abundance of principal prey species were compared. 2. Energetically, the crayfish ranked second after eels, accounting for 18% of the estimated annual intake of energy. Crayfish and eels were particularly important in the diet from April to October. For the rest of the year, crayfish accounted for < 10% of the monthly energetic intake, and cyprinids and toads were the most important prey. The seasonality of crayfish consumption, as well as that of cyprinids, toads and frogs, was highly correlated with fluctuations in their availability. However, the consumption of eels during their period of maximum availability was unexpectedly small, probably because this was also when crayfish were most abundant. 3. In spite of this, crayfish and eels co-occurred more frequently in spraints from the same months than could be expected from chance, whereas crayfish and fish other than eels tended to occur separately. It is suggested that when feeding on crayfish, otters also have a high likelihood of catching eels (a preferred prey for otters). 4. Although the introduction of the crayfish apparently increased the availability of prey to otters from spring to early autumn, there were no perceptible increases in food resources for the remainder of the year. Otter populations inhabiting Iberian streams may still be limited by indigenous prey species, such as cyprinids, which make up the bulk of the diet in late autumn and winter. The maintenance of indigenous prey should thus be considered a major issue in otter conservation strategies, even in areas holding abundant populations of introduced American crayfish.

From local monitoring to a broad-scale viability assessment: a case study for the Bonelli's Eagle in western Europe

Population viability analysis (PVA) has become a basic tool of current conservation practice. However, if not accounted for properly, the uncertainties inherent to PVA predictions can decrease the reliability of this type of analysis. In the present study, we performed a PVA of the whole western European population (France, Portugal, and Spain) of the endangered Bonellis Eagle (Aquila fasciata), in which we thoroughly explored the consequences of uncertainty in population processes and parameters on PVA predictions. First, we estimated key vital rates (survival, fertility, recruitment, and dispersal rates) using monitoring, ringing, and bibliographic data from the period 1990-2009 from 12 populations found throughout the studied geographic range. Second, we evaluated the uncertainty about model structure (i.e., the assumed processes that govern individual fates and population dynamics) by comparing the observed growth rates of the studied populations with model predictions for the same period. Third, using the model structures suggested in the previous step, we assessed the viability of both the local populations and the overall population. Finally, we analyzed the effects of model and parameter uncertainty on PVA predictions. Our results strongly support the idea that all local populations in western Europe belong to a single, spatially structured population operating as a source- sink system, whereby the populations in the south of the Iberian Peninsula act as sources and, thanks to dispersal, sustain all other local populations, which would otherwise decline. Predictions regarding population dynamics varied considerably, and models assuming more constrained dispersal predicted more pessimistic population trends than models assuming greater dispersal. Model predictions accounting for parameter uncertainty revealed a marked increase in the risk of population declines over the next 50 years. Sensitivity analyses indicated that adult and pre-adult survival are the chief vital rates regulating these populations, and thus, the conservation efforts aimed at improving these survival rates should be strengthened in order to guarantee the long-term viability of the European populations of this endangered species. Overall, the study provides a framework for the implementation of multi-site PVAs and highlights the importance of dispersal processes in shaping the population dynamics of long-lived birds distributed across heterogeneous landscapes.

Seasonal patterns of spatial variation in understory bird assemblages across a mosaic of flooded and unflooded Amazonian forests.

We examined seasonal patterns of spatial variation in understory bird assemblages across a mosaic of upland and floodplain forests in central Amazonia, where variation in flooding patterns and floodwater nutrient load shapes a marked spatial heterogeneity in forest structure and composition. Despite great differences in productivity due to flooding by either nutrient-rich “white waters” (várzea) or nutrient-poor “black waters” (igapó), bird assemblages in the two floodplain forest types were relatively similar, showing lower abundances than adjacent upland forests (terra firme) and sharing a set of species that were absent or scarce elsewhere. Species that breed in pensile nests overhanging water were abundant in floodplain forests, whereas species that feed on the ground were generally scarce. Flooding affected assemblage dynamics in floodplain forests, with some influx of ground-dwelling species such as ant-following birds from adjacent upland during the low-water season, and the occupation by riverine and aquatic species such as kingfishers during floods. Spatial configuration influenced the seasonal pattern of assemblage structuring, with movements from terra firme occurring primarily to adjacent igapó forests. No such influx was detected in várzea forests that were farther from terra firme and isolated by wide river channels. Results support the view that habitat heterogeneity created by flooding strongly contributes to maintain diverse vertebrate assemblages in Amazonia forest landscapes, even in the case of largely sedentary species such as understory forest birds. Including both upland and floodplain forests in Amazonia reserves may thus be essential to preserve bird diversity at the landscape scale.

Structuring of Amazonian bat assemblages: the roles of flooding patterns and floodwater nutrient load

1. River system dynamics results in ecological heterogeneities that play a central role in maintaining biodiversity in riverine regions. In central Amazonia, large expanses of forest are seasonally flooded by nutrient-rich water (várzea forests) or by nutrient-poor water (igapó forests). Inundation patterns and the nutrient load of floodwaters are perhaps the most important abiotic factors determining spatial ecological variations in lowland Amazonia, and so they are expected to strongly influence the structuring of animal communities. 2. We examined how inundation patterns and water-nutrient load influence the structure of neotropical assemblages of bats, one of the most diverse vertebrate groups in tropical forests. Bat assemblages were sampled with mist nets in central Brazilian Amazonia, across a mosaic of várzea, igapó, and non-flooding nutrient-poor terra firme forests in the low- and high-water seasons. 3. An ordination analysis clearly separated the assemblages of the three forest types, demonstrating the structural relevance of both flooding and floodwater-nutrient load. Flooded forests had lower species richness because of the absence or rarity of species that make roosts out of leaves of understorey plants, and of those that feed on fruits of shrubs. Gleaning insectivores, also partly dependent on the understorey, were less abundant in flooded forests, but aerial insectivores more abundant, presumably because they benefited from a less cluttered foraging environment. These differences suggest that flooding affects bat assemblages mostly because it reduces the availability of niches associated with understorey vegetation, which tends to be sparser in flooded forests. 4. Nutrient-rich várzea forests had a bat biomass twice that of nutrient-poor igapó and unflooded forests. This difference was not only mostly due to a greater overall abundance of bats, but also attributable to a disproportionate higher abundance of large-bodied bat species. 5. We concluded that both flooding and floodwater-nutrient load are very important in the structuring of lowland Amazonian bat assemblages, with inundation mostly constraining the species composition of the assemblages, and water-nutrient load mostly influencing the abundance of species. The distinctiveness of bat assemblages associated with flooding emphasizes the need to preserve inundated forests, which are under particular pressure in Amazonia.

Structure and Seasonal Fluctuations of Rocky Littoral Fish Assemblages in South-Western Portugal: Implications for Otter Prey Availability

The fish assemblages of rocky intertidal and subtidal ( (Lutra lutra L., Mammalia) in south-western Portugal, and to compare these with other areas in Europe. A total of 475 fish of 14 species was captured over 150 d of trapping (788 trap-days), and 1575 fish of 15 species were captured over 24 d of angling (76.3h). Hand-netting was carried out occasionally, to supplement the observations from the other methods, and only 96 fish of seven species were captured. The three methods yielded different patterns of the fish assemblage: giant gobies (Gobius cobitis Pallas, 33.7%) and rock gobies (G. paganellus L., 22.9%) were the most frequently trapped fish; corkwing wrasse (Symphodus melons (L.), 81.2%) were the usual species caught by angling; shannies (Lipophrys pholis (L.), 42.7%) and Montagus blennies (Coryphoblennius galerita (L.), 28.1%) were the most frequently netted species. Conger eels ( Conger conger (L.)), giant gobies and shannies showed an uneven distribution along the coast, occurring most frequently in schist shelves, rather than in areas of large sandstone boulders. There was a large seasonal variation, with the catches of most species peaking in winter and early spring, including the majority of those most important in the diet of otters: conger eels, shore rocklings (Gaidropsarus mediterraneus L.), rock gobies and corkwing wrasse. This was also the period when the individuals of several species were heaviest.

Optimizing sampling design to deal with mist-net avoidance in Amazonian birds and bats.

Mist netting is a widely used technique to sample bird and bat assemblages. However, captures often decline with time because animals learn and avoid the locations of nets. This avoidance or net shyness can substantially decrease sampling efficiency. We quantified the day-to-day decline in captures of Amazonian birds and bats with mist nets set at the same location for four consecutive days. We also evaluated how net avoidance influences the efficiency of surveys under different logistic scenarios using re-sampling techniques. Net avoidance caused substantial declines in bird and bat captures, although more accentuated in the latter. Most of the decline occurred between the first and second days of netting: 28% in birds and 47% in bats. Captures of commoner species were more affected. The numbers of species detected also declined. Moving nets daily to minimize the avoidance effect increased captures by 30% in birds and 70% in bats. However, moving the location of nets may cause a reduction in netting time and captures. When moving the nets caused the loss of one netting day it was no longer advantageous to move the nets frequently. In bird surveys that could even decrease the number of individuals captured and species detected. Net avoidance can greatly affect sampling efficiency but adjustments in survey design can minimize this. Whenever nets can be moved without losing netting time and the objective is to capture many individuals, they should be moved daily. If the main objective is to survey species present then nets should still be moved for bats, but not for birds. However, if relocating nets causes a significant loss of netting time, moving them to reduce effects of shyness will not improve sampling efficiency in either group. Overall, our findings can improve the design of mist netting sampling strategies in other tropical areas.

Application of indicator kriging to the complementary use of bioindicators at three trophic levels.

The use of biological indicators is widespread in environmental monitoring, although it has long been recognised that each bioindicator is generally associated with a range of potential limitations and shortcomings. To circumvent this problem, this study adopted the complementary use of bioindicators representing different trophic levels and providing different type of information, in an innovative approach to integrate knowledge and to estimate the overall health state of ecosystems. The approach is illustrated using mercury contamination in primary producers (mosses), primary consumers (domestic pigeons and red-legged partridges) and top predators (Bonellis eagles) in southern Portugal. Indicator kriging geostatistics was used to identify the areas where mercury concentration was higher than the median for each species, and to produce an index that combines mercury contamination across trophic levels. Spatial patterns of mercury contamination were consistent across species. The combined index provided a new level of information useful in incorporating measures of overall environmental contamination into pollution studies.