The genetic analysis and germplasm identification of the gametophytes of Undaria pinnatifida (Phaeophyceae) with RAPD method

Eleven pairs of Undaria pinnatifida (Harv.) Suringar gametophytes were identified with random amplified polymorphic DNA (RAPD) technique. After screening 100 primers, 20 ten-base primers were determined for the RAPD analysis. A total of 312 polymorphic loci were obtained, of which 97.7% were polymorphic. The primer S198 was found to distinguish all the selected Undaria pinnatifida gametophytes. The genetic distances between each two of the twenty-two U. pinnatifida gametophytes ranged from 0.080 to 0.428, while the distances to the Laminaria was 0.497 on average. After reexamination, two sequences characterized amplification region (SCAR) markers were successfully converted, which could be applied to U. pinnatifida germplasm identification. All these results demonstrated the feasibility of applying RAPD markers to germplasm characterization and identification of U. pinnatifida gametophytes, and to provide a molecular basis for Undaria breeding.

Sectoral impacts on the diversity of carabid beetles (Coleoptera: Carabidae) and their associated ecosystem service of biocontrol

This thesis aimed to provide an understanding of how human-induced changes in the economic sectors of agriculture and transport affect carabid diversity, potential carabidmediated biocontrol and predator-pest interactions. The research involved both observational and manipulative laboratory and field-based studies. Observational research consisted of two large-scale investigations of (1) the impact of Miscanthus and oilseed rape production (n=45) and (2) the impact of horticultural and ecological based landscaping of roadside verges (n=64). This research is the first record of carabid diversity, potential biocontrol and community assemblage with respect to bioenergy crop production and roadside landscaping in an Irish context and it is also an important addition to the limited knowledge of carabid populations in these ecosystems internationally. Manipulative work involved the examination of the role predator identity, diversity and biomass play in the suppression of pollen beetle larvae (an economically damaging insect pest of oilseed rape in Europe), using a novel experimental design called ‘simplex’. To complement this research, an additional field study on the impact of low and high oilseed rape pesticide management on carabid species richness and abundance, and crop yield, was also conducted. This research is a great contribution to the existing understanding of what constitutes the important components of predator biodiversity and expands the knowledge of the usefulness of carabid predators in the context of pollen beetle larvae control. In particular, the work shows that the abundance or biomass of beetles has an effect that is far larger than the effect of diversity on the capacity of beetles to consume prey. In turn, the field study showed that pesticide applications had little impact on yield, or carabid richness, but that carabid abundance/biomass declined drastically. The work provides compelling evidence that management practices erode the useful components of biodiversity that are essential for the delivery of biocontrol services.

Habitat Isolation Reduces the Temporal Stability of Island Ecosystems in the Face of Flood Disturbance

Natural ecosystems are increasingly exposed to multiple anthropogenic stressors, including land-use change, deforestation, agricultural intensification, and urbanisation, all of which have led to widespread habitat fragmentation, which is also likely to be amplified further by predicted climate change. The potential interactive effects of these different stressors cannot be determined by studying each in isolation, although such synergies have been largely ignored in ecological field studies to date. Here, we use a model system of naturally fragmented islands in a braided river network, which is exposed to periodic inundation, to investigate the interactive effects of habitat isolation and flood disturbance. Food web structure was similar across the islands during periods of hydrological stability, but several key properties were altered in the aftermath of flood disturbance, based on distance of the islands from the regional source pool of species: taxon richness and mean food chain length declined with habitat isolation after flooding, while the proportion of basal species increased. Greater species turnover through time reflected the slower process of re-colonisation on the more distant islands following disturbance. Increased variability of several food web properties over a 1-year period highlighted the reduced temporal stability of isolated habitat fragments. Many of these effects reflected the differential successes of predator and prey species at re-colonising the islands: even though larger, more mobile consumers may reach the more distant islands first, they cannot establish populations until the lower trophic levels have successfully reassembled. These results highlight the susceptibility of fragmented ecosystems to environmental perturbations. © 2013 Elsevier Ltd.

Crop type influences edge effects on the reproduction of songbirds in sagebrush habitat near agriculture

Extensive fragmentation of the sagebrush shrubsteppe of western North America could be contributing to observed population declines of songbirds in sagebrush habitat. We examined whether habitat fragmentation impacts the reproduction of songbirds in sagebrush edge habitat near agriculture, and if potential impacts vary depending on the adjacent crop type. Specifically, we evaluated whether nest abundance and nest survival varied between orchard edge habitat, vineyard edge habitat, and interior habitat. We then examined whether the local nest predator community and vegetation could explain the differences detected. We detected fewer nests in edge than interior habitat. Nest abundance per songbird was also lower in edge than interior habitat, although only adjacent to vineyards. Nest predation was more frequent in orchard edge habitat than vineyard edge or interior habitat. Predators identified with nest cameras were primarily snakes, however, reduced nest survival in orchard edge habitat was not explained by differences in the abundance of snakes or any other predator species identified. Information theoretic analysis of daily survival rates showed that greater study plot shrub cover and lower grass height at nests were partially responsible for the lower rate of predation-specific daily nest survival rate (PDSR) observed in orchard edge habitat, but additional factors are likely important. Results of this study suggest that different crop types have different edge effects on songbirds nesting in sagebrush shrubsteppe, and that these reproductive edge effects may contribute to observed declines of these species. Habitat managers should avoid the creation of new orchard-sagebrush habitat edges to avoid further impacts on already declining songbird populations.

Forest structure in a mosaic of rainforest sites: The effect of fragmentation and recovery after clear cut

A variety of human-induced disturbances such as forest fragmentation and recovery after deforestation for pasture or agricultural activities have resulted in a complex landscape mosaic in the Una region of northeastern Brazil. Using a set of vegetation descriptors, we investigated the main structural changes observed in forest categories that comprise the major components of the regional landscape and searched for potential key descriptors that could be used to discriminate among different forest categories. We assessed the forest structure of five habitat categories defined as (I) interiors and (2) edges of large fragments of old-growth forest (>1000 ha), (3) interiors and (4) edges of small forest fragments (<100 ha), and (5) early secondary forests. Forest descriptors used here were: frequency of herbaceous lianas and woody climbers, number of standing dead trees, number of fallen trunks, litter depth, number of pioneer plants (early secondary and shade-intolerant species), vertical foliage stratification profile and distribution Of trees in different diameter classes. Edges and interiors of forest fragments were significantly different only in the number of standing dead trees. Secondary forests and edges of fragments showed differences in litter depth, fallen trunks and number of pioneer trees, and secondary forests were significantly different from fragment interiors in the number of standing dead trees and the number of pioneer trees. Horizontal and vertical structure evaluated via ordination analysis showed that fragment interiors, compared to secondary forests, were characterized by a greater number of medium (25-35 cm) and large (35-50 cm) trees and smaller numbers of thin trees (5-10 cm). There was great heterogeneity at the edges of small and large fragments, as these sites were distributed along almost the entire gradient. Most interiors of large and small fragments presented higher values of foliage densities at higher strata ( 15-20 m and at 20-25 m height), and lower densities at 1-5 m. All secondary forests and some fragment edge sites showed an opposite tendency. A discriminant function highlighted differences among forest categories, with transects of large fragment interiors and secondary forests representing two extremes along a disturbance gradient determined by foliage structure (densities at 15-20 m and 20-25 m), with the edges of both large and small fragments and the interiors of small fragments scattered across the gradient. The major underlying processes determining patterns of forest disturbance in the study region are discussed, highlighting the importance of forest fragments, independently of its size, as forests recovery after clear cut show a greatly distinct structure, with profound implications on fauna movements. (C) 2009 Elsevier BY. All rights reserved.

Fragmentation drives tropical forest fragments to early successional states: A modelling study for Brazilian Atlantic forests

Land use leads to massive habitat destruction and fragmentation in tropical forests. Despite its global dimensions the effects of fragmentation on ecosystem dynamics are not well understood due to the complexity of the problem. We present a simulation analysis performed by the individual-based model FORMIND. The model was applied to the Brazilian Atlantic Forest, one of the world`s biodiversity hot spots, at the Plateau of Sao Paulo. This study investigates the long-term effects of fragmentation processes on structure and dynamics of different sized remnant tropical forest fragments (1-100 ha) at community and plant functional type (PFT) level. We disentangle the interplay of single effects of different key fragmentation processes (edge mortality, increased mortality of large trees, local seed loss and external seed rain) using simulation experiments in a full factorial design. Our analysis reveals that particularly small forest fragments below 25 ha suffer substantial structural changes, biomass and biodiversity loss in the long term. At community level biomass is reduced up to 60%. Two thirds of the mid- and late-successional species groups, especially shade-tolerant (late successional climax) species groups are prone of extinction in small fragments. The shade-tolerant species groups were most strongly affected; its tree number was reduced more than 60% mainly by increased edge mortality. This process proved to be the most powerful of those investigated, explaining alone more than 80% of the changes observed for this group. External seed rain was able to compensate approximately 30% of the observed fragmentation effects for shade-tolerant species. Our results suggest that tropical forest fragments will suffer strong structural changes in the long term, leading to tree species impoverishment. They may reach a new equilibrium with a substantially reduced subset of the initial species pool, and are driven towards an earlier successional state. The natural regeneration potential of a landscape scattered with forest fragments appears to be limited, as external seed rain is not able to fully compensate for the observed fragmentation-induced changes. Our findings suggest basic recommendations for the management of fragmented tropical forest landscapes. (C) 2011 Elsevier B.V. All rights reserved.

Effects of fragmented habitat and fire on the distribution and ecology of the swamp antechinus (Antechinus minimus maritimus) in the Eastern Otways, Victoria

This study investigated the distribution, habitat and population dynamics of the swamp antechinus (Antechinus minimus maritimus) in the eastern Otway Ranges. The species has a restricted, disjunct distribution and has been recorded at 25 sites between 1969 and 1999. All sites were located within 7 km of the coast, occurred at altitudes up to 80 m above sea level and within 10 m of a gully. Analysis of landscape site variables identified sun index as being significant in determination of the probability of occurrence of A. minimus. The presence of A. minimus is negatively associated with sun index, occuring at sites that have a southerly aspect and gentle slope. A. minimus was located in a range of structural vegetation including Open Forest, Low Woodland, Shrubland and Hummock Grassland and a number of floristic groups, some characterised by high frequencies of sclerophyll shrubs, others by high frequencies of Pteridium esculentum, hummock grasses and herbaceous species. A. minimus occurs in fragmented, small populations with maximum population densities of 1.1–18 ha^–1. Populations at inland sites became extinct after the 1983 wildfire which burnt 41 000 ha. These sites have not been recolonised since, while on the coast the species did not re-establish until 1993–97. One population that is restricted to a narrow coastal strip of habitat is characterised by high levels of transient animals. The species is subject to extinction in the region due to habitat fragmentation, coastal developments and fire. Management actions to secure the present populations and ensure long-term survival of the species in the area are required and include implementation of appropriate fire regimes, prevention of habitat fragmentation, revegetation of habitat, and establishment of corridor habitat.

The response of ground and bark foraging insectivorous birds across an urban–forest gradient

This paper assesses the response of four common species of forest dependant insectivorous birds to an urban–forest gradient. The presence or absence was recorded for each species in landscapes that varied in landscape and site level attributes. Landscapes were classified into three categories based on their level of urbanisation. Broad comparisons across the landscapes were used to determine species specific response to increasing levels of urbanisation. Site level attributes were modelled to predict the patch occupancy for each species in each of the landscape types. Two broad trends were identified: the superb fairy wren (Malurus cyaneus) and white-browed scrubwren (Sericornis frontalis) displayed a tolerance to urbanisation and the eastern yellowrobin (Eosaltrica australis) and white throated treecreeper (Cormobates leucophaeus) demonstrated a threshold response to urbanisation. The density of roads (−ve) and the extent of tree cover (+ve) in a landscape were highly correlated with the occurrence of urban sensitive species while at the site level the density of roads and density of rivers were the strongest contributors to their presence. The marked differences in the isolation and connectivity of patches where the threshold for urban sensitive species ceases are the likely contributors to their decline and sensitivity to suburban habitats. Conservation and management of urban sensitive species is largely dependant on the way urban development is managed. Of critical importance is careful planning in urban-fringe environments.

Habitat patch size modulates terrestrial mammal activity patterns in Amazonian forest fragments

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Atlantic forest fragmentation and genetic diversity of an isolated population of the Blue-manakin, Chiroxiphia caudata (Pipridae), assessed by microsatellite analyses

Habitat fragmentation is predicted to restrict gene flow, which can result in the loss of genetic variation and inbreeding depression. The Brazilian Atlantic forest has experienced extensive loss of habitats since European settlement five centuries ago, and many bird populations and species are vanishing. Genetic variability analysis in fragmented populations could be important in determining their long-term viability and for guiding management plans. Here we analyzed genetic diversity of a small understory bird, the Blue-manakins Chiroxiphia caudata (Pipridae), from an Atlantic forest fragment (112 ha) isolated 73 years ago, and from a 10,000 ha continuous forest tract (control), using orthologous microsatellite loci. Three of the nine loci tested were polymorphic. No statistically significant heterozygote loss was detected for the fragment population. Although genetic diversity, which was estimated by expected heterozygosity and allelic richness, has been lower in the fragment population in relation to the control, it was not statistically significant, suggesting that this 112 ha fragment can be sufficient to maintain a blue-manakin population large enough to avoid stochastic effects, such as inbreeding and/or genetic drift. Alternatively, it is possible that 73 years of isolation did not accumulate sufficient generations for these effects to be detected. However, some alleles have been likely lost, specially the rare ones, what is expected from genetic drift for such a small and isolated population. A high genetic differentiation was detected between populations by comparing both allelic and genotypic distributions. Only future studies in continuous areas are likely to answer if such a structure was caused by the isolation resulted from the forest fragmentation or by natural population structure.

The endangered species Brycon orbignyanus: genetic analysis and definition of priority areas for conservation

Currently, biodiversity is threatened by several factors often associated with human population growth and the extension of areas occupied by human activity. In particular, freshwater fish fauna is affected by overfishing, deforestation, water pollution, introduction of exotic species and habitat fragmentation promoted by hydroelectric dams, among other environmental impact factors. Several action plans to preserve ichthyofauna biodiversity have been adopted; however, these plans frequently cover only a small number of species, and decisions are often made without strong scientific support. This study aimed to evaluate the genetic aspects of wild groups of Brycon orbignyanus, an endangered fish species, using microsatellites and D-loop regions to identify the genetic structure of the samples and to establish priority areas for conservation based on the genetic patterns of this species. The results indicated that the samples showed levels of genetic variability compatible with others studies with Neotropical fishes. However, the results obtained in the analysis of molecular variance (AMOVA) for microsatellites (F (ST) = 0.258) and D-loop (F (ST) = 0.234) and the interpopulation fixation index revealed that B. orbignyanus was structured in different subpopulations in the La Plata River basin; the areas with better environmental conditions also showed subgroups with higher rates of genetic variability. Future conservation actions addressing these sites should consider two different management units: the complex formed by the Ivinhema River, Upper Parana, Camargo Port and Ilha Grande groups; and the complex formed by the Verde River and Sucuriu River groups.

Natural enemies depend on remnant habitat size in agricultural landscapes

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Landscape connectivity, habitat structure and activity of bat guilds in farmland-dominated matrices

Agricultural intensification has caused a decline in structural elements in European farmland, where natural habitats are increasingly fragmented. The loss of habitat structures has a detrimental effect on biodiversity and affects bat species that depend on vegetation structures for foraging and commuting. We investigated the impact of connectivity and configuration of structural landscape elements on flight activity, species richness and diversity of insectivorous bats and distinguished three bat guilds according to species-specific bioacoustic characteristics. We tested whether bats with shorter-range echolocation were more sensitive to habitat fragmentation than bats with longer-range echolocation. We expected to find different connectivity thresholds for the three guilds and hypothesized that bats prefer linear over patchy landscape elements. Bat activity was quantified using repeated acoustic monitoring in 225 locations at 15 study plots distributed across the Swiss Central Plateau, where connectivity and the shape of landscape elements were determined by spatial analysis (GIS). Spectrograms of bat calls were assigned to species with the software batit by means of image recognition and statistical classification algorithms. Bat activity was significantly higher around landscape elements compared to open control areas. Short- and long-range echolocating bats were more active in well-connected landscapes, but optimal connectivity levels differed between the guilds. Species richness increased significantly with connectivity, while species diversity did not (Shannon's diversity index). Total bat activity was unaffected by the shape of landscape elements. Synthesis and applications. This study highlights the importance of connectivity in farmland landscapes for bats, with shorter-range echolocating bats being particularly sensitive to habitat fragmentation. More structurally diverse landscape elements are likely to reduce population declines of bats and could improve conditions for other declining species, including birds. Activity was highest around optimal values of connectivity, which must be evaluated for the different guilds and spatially targeted for a region's habitat configuration. In a multi-species approach, we recommend the reintroduction of structural elements to increase habitat heterogeneity should become part of agri-environment schemes.

Habitat selection and breeding success in a forest-nesting Alcid, the marbled murrelet, in two landscapes with different degrees of forest fragmentation

We studied habitat selection and breeding success in marked populations of a protected seabird (family Alcidae), the marbled murrelet (Brachyramphus marmoratus), in a relatively intact and a heavily logged old-growth forest landscape in south-western Canada. Murrelets used old-growth fragments either proportionately to their size frequency distribution (intact) or they tended to nest in disproportionately smaller fragments (logged). Multiple regression modelling showed that murrelet distribution could be explained by proximity of nests to landscape features producing biotic and abiotic edge effects. Streams, steeper slopes and lower elevations were selected in both landscapes, probably due to good nesting habitat conditions and easier access to nest sites. In the logged landscape, the murrelets nested closer to recent clearcuts than would be expected. Proximity to the ocean was favoured in the intact area. The models of habitat selection had satisfactory discriminatory ability in both landscapes. Breeding success (probability of nest survival to the middle of the chick rearing period), inferred from nest attendance patterns by radio-tagged parents, was modelled in the logged landscape. Survivorship was greater in areas with recent clearcuts and lower in areas with much regrowth, i.e. it was positively correlated with recent habitat fragmentation. We conclude that marbled murrelets can successfully breed in old-growth forests fragmented by logging.