Taxonomic and functional diversity of farmland bird communities across Europe:Effects of biogeography and agricultural intensification

In eight European study sites (in Spain, Ireland, Netherlands, Germany, Poland, Estonia and Sweden), abundance of breeding farmland bird territories was obtained from 500 × 500 m survey plots (30 per area, N = 240) using the mapping method. Two analyses were performed: (I) a Canonical Correspondence Analysis of species abundance in relation to geographical location and variables measuring agricultural intensification at field and farm level to identify significant intensification variables and to estimate the fractions of total variance in bird abundance explained by geography and agricultural intensification; (II) several taxonomic and functional community indices were built and analysed using GLM in relation to the intensification variables found significant in the CCA. The geographical location of study sites alone explains nearly one fifth (19. 5%) of total variation in species abundance. The fraction of variance explained by agricultural intensification alone is much smaller (4. 3%), although significant. The intersection explains nearly two fifths (37. 8%) of variance in species abundance. Community indices are negatively affected by correlates of intensification like farm size and yield, whereas correlates of habitat availability and quality have positive effects on taxonomic and functional diversity of assemblages. Most of the purely geographical variation in farmland bird assemblage composition is associated to Mediterranean steppe species, reflecting the bio-geographical singularity of that assemblage and reinforcing the need to preserve this community. Taxonomic and functional diversity of farmland bird communities are negatively affected by agricultural intensification and positively affected by increasing farmland habitat availability and quality. © 2011 Springer Science+Business Media B.V.

PLUMED 2: New feathers for an old bird

Enhancing sampling and analyzing simulations are central issues in molecular simulation. Recently, we introduced PLUMED, an open-source plug-in that provides some of the most popular molecular dynamics (MD) codes with implementations of a variety of different enhanced sampling algorithms and collective variables (CVs). The rapid changes in this field, in particular new directions in enhanced sampling and dimensionality reduction together with new hardware, require a code that is more flexible and more efficient. We therefore present PLUMED 2 here a,complete rewrite of the code in an object-oriented programming language (C++). This new version introduces greater flexibility and greater modularity, which both extends its core capabilities and makes it far easier to add new methods and CVs. It also has a simpler interface with the MD engines and provides a single software library containing both tools and core facilities. Ultimately, the new code better serves the ever-growing community of users and contributors in coping with the new challenges arising in the field.

Program summary

Program title: PLUMED 2

Catalogue identifier: AEEE_v2_0

Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEEE_v2_0.html

Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland

Licensing provisions: Yes

No. of lines in distributed program, including test data, etc.: 700646

No. of bytes in distributed program, including test data, etc.: 6618136

Distribution format: tar.gz

Programming language: ANSI-C++.

Computer: Any computer capable of running an executable produced by a C++ compiler.

Operating system: Linux operating system, Unix OSs.

Has the code been vectorized or parallelized?: Yes, parallelized using MPI.

RAM: Depends on the number of atoms, the method chosen and the collective variables used.

Classification: 3, 7.7, 23. Catalogue identifier of previous version: AEEE_v1_0.

Journal reference of previous version: Comput. Phys. Comm. 180 (2009) 1961.

External routines: GNU libmatheval, Lapack, Bias, MPI. (C) 2013 Elsevier B.V. All rights reserved.

The modularity of seed dispersal: differences in structure and robustness between bat- and bird-fruit networks

In networks of plant-animal mutualisms, different animal groups interact preferentially with different plants, thus forming distinct modules responsible for different parts of the service. However, what we currently know about seed dispersal networks is based only on birds. Therefore, we wished to fill this gap by studying bat-fruit networks and testing how they differ from bird-fruit networks. As dietary overlap of Neotropical bats and birds is low, they should form distinct mutualistic modules within local networks. Furthermore, since frugivory evolved only once among Neotropical bats, but several times independently among Neotropical birds, greater dietary overlap is expected among bats, and thus connectance and nestedness should be higher in bat-fruit networks. If bat-fruit networks have higher nestedness and connectance, they should be more robust to extinctions. We analyzed 1 mixed network of both bats and birds and 20 networks that consisted exclusively of either bats (11) or birds (9). As expected, the structure of the mixed network was both modular (M = 0.45) and nested (NODF = 0.31); one module contained only birds and two only bats. In 20 datasets with only one disperser group, bat-fruit networks (NODF = 0.53 +/- A 0.09, C = 0.30 +/- A 0.11) were more nested and had a higher connectance than bird-fruit networks (NODF = 0.42 +/- A 0.07, C = 0.22 +/- A 0.09). Unexpectedly, robustness to extinction of animal species was higher in bird-fruit networks (R = 0.60 +/- A 0.13) than in bat-fruit networks (R = 0.54 +/- A 0.09), and differences were explained mainly by species richness. These findings suggest that a modular structure also occurs in seed dispersal networks, similar to pollination networks. The higher nestedness and connectance observed in bat-fruit networks compared with bird-fruit networks may be explained by the monophyletic evolution of frugivory in Neotropical bats, among which the diets of specialists seem to have evolved from the pool of fruits consumed by generalists.

Consequences of Simulated Loss of Open Cerrado Areas to Bird Functional Diversity

Over the past 35 years, more than two thirds of the Cerrado`s original expanse has been taken by agriculture. Even if some attempts have been made to conserve closed cerrado physiognomies, open cerrado physiognomies, richer in species and more fragile, have been systematically ignored. These open physiognomies are used by almost half of the Cerrado bird species, many of which being endemics. Using data from 11 surveys carried out in Cerrado landscapes, we asked what would happen to bird functional diversity if open cerrado species became extinct. Open cerrado birds would be able to keep on average 59% of the functional diversity. If they became extinct, on average 27% of the functional diversity would be lost. In this case, the remaining functional diversity would be lower than what would be expected by chance in five sites. Although many functions were shared by both open cerrado and forest species, there was some degree of complementarity between them, highlighted by the decrease in functional diversity when the former became extinct. Destruction of open cerrado physiognomies would lead to a habitat simplification, decrease in bird functional diversity, and, ultimately, to a considerable impact on community functioning. Thus, open cerrado physiognomies must receive much more conservation attention than they are currently receiving, because they maintain a high bird functional diversity that would otherwise be considerably diminished Were open cerrado species to become extinct.

Towards a set of priorities for bird conservation and research in Australia : the perceptions of ornithologists

Australian delegates at the Australasian Ornithological Conference (2007) were surveyed by questionnaire to determine their perceived research and conservation priorities for Australian birds (n = 134). Respondents were honours or postgraduate students (37.4%), academics (26.2%), wildlife managers (6.5%), land managers (6.5%), environmental consultants (5.6%), independent wildlife researchers (5.6%) or had ‘other’ occupations not relevant to birds or their management (12.1%). Respondents rated their priorities on a predetermined set of issues, and were invited to add additional priorities. ‘Conservation of threatened species’ was considered the highest priority, followed by ‘Conservation of birds and biodiversity in general’, ‘Monitoring’, ‘Management’ and ‘Working with communities’. ‘Animal welfare/rights’ was regarded as comparatively less important. Eight of 11 conservation strategies were regarded as of high importance, these included habitat protection and rehabilitation, threat abatement, research, advocacy and education. This study documents the view of the ornithological community with respect to priority issues facing birds and could potentially feed into government and other policies aimed at conserving and understanding Australia’s birds.

Flowering ecology of a Box-Ironbark Eucalyptus community

Box-Ironbark forests occur on the inland hills of the Great Dividing Range in Australia, from western Victoria to southern Queensland. These dry, open forests are characteristically dominated by Eucalyptus species such as Red Ironbark E. tricarpa, Mugga Ironbark E. sideroxylon and Grey Box E. microcarpa. Within these forests, several Eucalyptus species are a major source of nectar for the blossom-feeding birds and marsupials that form a distinctive component of the fauna. In Victoria, approximately 83% of the original pre - European forests of the Box-Ironbark region have been cleared, and the remaining fragmented forests have been heavily exploited for gold and timber. This exploitation has lead to a change in the structure of these forests, from one dominated by large 80-100 cm diameter, widely -spaced trees to mostly small (≥40 cm DBH), more densely - spaced trees. This thesis examines the flowering ecology of seven Eucalyptus species within a Box-Ironbark community. These species are characteristic of Victorian Box-Ironbark forests; River Red Gum E. camaldulensis, Yellow Gum E. leucoxylon, Red Stringybark E. macrorhyncha, Yellow Box E. melliodora, Grey Box E. microcarpa, Red Box E. polyanthemos and Red Ironbark E. tricarpa. Specifically, the topics examined in this thesis are: (1) the floral character traits of species, and the extent to which these traits can be associated with syndromes of bird or insect pollination; (2) the timing, frequency, duration, intensity, and synchrony of flowering of populations and individual trees; (3) the factors that may explain variation in flowering patterns of individual trees through examination of the relationships between flowering and tree-specific factors of individually marked trees; (4) the influence of tree size on the flowering patterns of individually marked trees, and (5) the spatial and temporal distribution of the floral resources of a dominant species, E. tricarpa. The results are discussed in relation to the evolutionary processes that may have lead to the flowering patterns, and the likely effects of these flowering patterns on blossom-feeding fauna of the Box-Ironbark region. Flowering observations were made for approximately 100 individually marked trees for each species (a total of 754 trees). The flower cover of each tree was assessed at a mean interval of 22 (+ 0.6) days for three years; 1997, 1998 and 1999. The seven species of eucalypt each had characteristic flowering seasons, the timing of which was similar each year. In particular, the timing of peak flowering intensity was consistent between years. Other spatial and temporal aspects of flowering patterns for each species, including the percentage of trees that flowered, frequency of flowering, intensity of flowering and duration of flowering, displayed significant variation between years, between forest stands (sites) and between individual trees within sites. All seven species displayed similar trends in flowering phenology over the study, such that 1997 was a relatively 'poor' flowering year, 1998 a 'good' year and 1999 an 'average' year in this study area. The floral character traits and flowering seasons of the seven Eucalyptus species suggest that each species has traits that can be broadly associated with particular pollinator types. Differences between species in floral traits were most apparent between 'summer' and 'winter' flowering species. Winter - flowering species displayed pollination syndromes associated with bird pollination and summer -flowering species displayed syndromes more associated with insect pollination. Winter - flowering E. tricarpa and E. leucoxylon flowers, for example, were significantly larger, and contained significantly greater volumes of nectar, than those of the summer flowering species, such as E. camaldulensis and E. melliodom. An examination of environmental and tree-specific factors was undertaken to investigate relationships between flowering patterns of individually marked trees of E. microcarpa and E. tricarpa and a range of measures that may influence the observed patterns. A positive association with tree-size was the most consistent explanatory variable for variation between trees in the frequency and intensity of flowering. Competition from near-neighbours, tree health and the number of shrubs within the canopy area were also explanatory variables. The relationship between tree size and flowering phenology was further examined by using the marked trees of all seven species, selected to represent five size-classes. Larger trees (≥40 cm DBH) flowered more frequently, more intensely, and for a greater duration than smaller trees. Larger trees provide more abundant floral resources than smaller trees because they have more flowers per unit area of canopy, they have larger canopies in which more flowers can be supported, and they provide a greater abundance of floral resources over the duration of the flowering season. Heterogeneity in the distribution of floral resources was further highlighted by the study of flowering patterns of E. tricarpa at several spatial and temporal scales. A total of approximately 5,500 trees of different size classes were sampled for flower cover along transects in major forest blocks at each of five sample dates. The abundance of flowers varied between forest blocks, between transects and among tree size - classes. Nectar volumes in flowers of E. tricarpa were sampled. The volume of nectar varied significantly among flowers, between trees, and between forest stands. Mean nectar volume per flower was similar on each sample date. The study of large numbers of individual trees for each of seven species was useful in obtaining quantitative data on flowering patterns of species' populations and individual trees. The timing of flowering for a species is likely to be a result of evolutionary selective forces tempered by environmental conditions. The seven species' populations showed a similar pattern in the frequency and intensity of flowering between years (e.g. 1998 was a 'good' year for most species) suggesting that there is some underlying environmental influence acting on these aspects of flowering. For individual trees, the timing of flowering may be influenced by tree-specific factors that affect the ability of each tree to access soil moisture and nutrients. In turn, local weather patterns, edaphic and biotic associations are likely to influence the available soil moisture. The relationships between the timing of flowering and environmental conditions are likely to be complex. There was no evidence that competition for pollinators has a strong selective influence on the timing of flowering. However, as there is year-round flowering in this community, particular types of pollinators may be differentiated along a temporal gradient (e.g. insects in summer, birds in winter). This type of differentiation may have resulted in the co-evolution of floral traits and pollinator types, with flowers displaying adaptations that match the morphologies and energy requirements of the most abundant pollinators in any particular season. Spatial variation in flowering patterns was evident at several levels. This is likely to occur because of variation in climate, weather patterns, soil types, degrees of disturbance and biotic associations, which vary across the Box-Ironbark region. There was no consistency among sites between years in flowering patterns suggesting that factors affecting flowering at this level are complex. Blossom-feeding animals are confronted with a highly spatially and temporally patchy resource. This patchiness has been increased with human exploitation of these forests leading to a much greater abundance of small trees and fewer large trees. Blossom-feeding birds are likely to respond to this variation in different ways, depending upon diet-breadth, mobility and morphological and behavioural characteristics. Future conservation of the blossom-feeding fauna of Box-Ironbark forests would benefit from the retention of a greater number of large trees, the protection and enhancement of existing remnants, and revegetation with key species, such as E. leucoxylon, E. microcarpa and E. tricarpa. The selective clearing of summer flowering species, which occur on the more fertile areas, may have negatively affected the year-round abundance and distribution of floral resources. The unpredictability of the spatial distribution of flowering patches within the region means that all remnants are likely to be important foraging areas in some years.

The influence of unburnt patches and distance from refuges on post-fire bird communities

Predicting the response of faunal communities to fire presents a challenge for land managers worldwide because the post-fire responses of species may vary between locations and fire events. Post-fire recovery can occur via nucleated recovery from in situ surviving populations or by colonization from ex situ populations. Fine-scale spatial patterns in the patchiness of fires and the proximity of burnt sites to source populations may contribute to both the variability in post-fire responses and the processes by which populations recover. We examined the avifauna at recently burnt sites within extensive semi-arid shrublands of south-eastern Australia, including 72 sites < 5 years since fire and 26 sites 10 years since fire. Study sites represented a gradient of increasing distance from ‘unburnt’ vegetation (i.e. > 27 years since fire) and varied in the presence or absence of small (25–900 m2) unburnt patches of vegetation. For sites < 5 years since fire, species richness was higher at sites closer to unburnt vegetation and at sites containing unburnt patches. These patterns were no longer evident at sites of 10 years since fire. The probability of occurrence of three of seven bird species modelled decreased with increasing distance to unburnt vegetation, but this pattern was evident only at sites burnt uniformly. One species was found almost exclusively at patchily burnt sites. These results are consistent with the hypothesis that proximity to unburnt vegetation enhances post-fire occupancy, and that colonization from ex situ populations is an important process for post-fire recovery of avifauna. Additionally, small unburnt patches enhance the rapid recovery of assemblages post-fire. These patterns are important for understanding the dynamics of post-fire population recovery. We recommend that management of fire for ecological purposes should explicitly consider the role that the spatial attributes of fires play in determining the post-fire community.

Associations of Forest Cover, Fragment Area, and Connectivity with Neotropical Understory Bird Species Richness and Abundance

Theoretical and empirical studies demonstrate that the total amount of forest and the size and connectivity of fragments have nonlinear effects on species survival. We tested how habitat amount and configuration affect understory bird species richness and abundance. We used mist nets (almost 34,000 net hours) to sample birds in 53 Atlantic Forest fragments in southeastern Brazil. Fragments were distributed among 3 10,800-ha landscapes. The remaining forest in these landscapes was below (10% forest cover), similar to (30%), and above (50%) the theoretical fragmentation threshold (approximately 30%) below which the effects of fragmentation should be intensified. Species-richness estimates were significantly higher (F = 3715, p = 0.00) where 50% of the forest remained, which suggests a species occurrence threshold of 30-50% forest, which is higher than usually occurs (<30%). Relations between forest cover and species richness differed depending on species sensitivity to forest conversion and fragmentation. For less sensitive species, species richness decreased as forest cover increased, whereas for highly sensitive species the opposite occurred. For sensitive species, species richness and the amount of forest cover were positively related, particularly when forest cover was 30-50%. Fragment size and connectivity were related to species richness and abundance in all landscapes, not just below the 30% threshold. Where 10% of the forest remained, fragment size was more related to species richness and abundance than connectivity. However, the relation between connectivity and species richness and abundance was stronger where 30% of the landscape was forested. Where 50% of the landscape was forested, fragment size and connectivity were both related to species richness and abundance. Our results demonstrated a rapid loss of species at relatively high levels of forest cover (30-50%). Highly sensitive species were 3-4 times more common above the 30-50% threshold than below it; however, our results do not support a unique fragmentation threshold.

Land use imperils plant and animal community stability through changes in asynchrony rather than diversity

Human land use may detrimentally affect biodiversity, yet long-term stability of species communities is vital for maintaining ecosystem functioning. Community stability can be achieved by higher species diversity (portfolio effect), higher asynchrony across species (insurance hypothesis) and higher abundance of populations. However, the relative importance of these stabilizing pathways and whether they interact with land use in real-world ecosystems is unknown. We monitored inter-annual fluctuations of 2,671 plant, arthropod, bird and bat species in 300 sites from three regions. Arthropods show 2.0-fold and birds 3.7-fold higher community fluctuations in grasslands than in forests, suggesting a negative impact of forest conversion. Land-use intensity in forests has a negative net impact on stability of bats and in grasslands on birds. Our findings demonstrate that asynchrony across species—much more than species diversity alone—is the main driver of variation in stability across sites and requires more attention in sustainable management.

Seawater carbonate chemistry in Hog reef and calcification rate in the Bermuda reef community, 2010

Despite the potential impact of ocean acidification on ecosystems such as coral reefs, surprisingly, there is very limited field data on the relationships between calcification and seawater carbonate chemistry. In this study, contemporaneous in situ datasets of seawater carbonate chemistry and calcification rates from the high-latitude coral reef of Bermuda over annual timescales provide a framework for investigating the present and future potential impact of rising carbon dioxide (CO2) levels and ocean acidification on coral reef ecosystems in their natural environment. A strong correlation was found between the in situ rates of calcification for the major framework building coral species Diploria labyrinthiformis and the seasonal variability of [CO32-] and aragonite saturation state omega aragonite, rather than other environmental factors such as light and temperature. These field observations provide sufficient data to hypothesize that there is a seasonal "Carbonate Chemistry Coral Reef Ecosystem Feedback" (CREF hypothesis) between the primary components of the reef ecosystem (i.e., scleractinian hard corals and macroalgae) and seawater carbonate chemistry. In early summer, strong net autotrophy from benthic components of the reef system enhance [CO32-] and omega aragonite conditions, and rates of coral calcification due to the photosynthetic uptake of CO2. In late summer, rates of coral calcification are suppressed by release of CO2 from reef metabolism during a period of strong net heterotrophy. It is likely that this seasonal CREF mechanism is present in other tropical reefs although attenuated compared to high-latitude reefs such as Bermuda. Due to lower annual mean surface seawater [CO32-] and omega aragonite in Bermuda compared to tropical regions, we anticipate that Bermuda corals will experience seasonal periods of zero net calcification within the next decade at [CO32-] and omega aragonite thresholds of ~184 micro moles kg-1 and 2.65. However, net autotrophy of the reef during winter and spring (as part of the CREF hypothesis) may delay the onset of zero NEC or decalcification going forward by enhancing [CO32-] and omega aragonite. The Bermuda coral reef is one of the first responders to the negative impacts of ocean acidification, and we estimate that calcification rates for D. labyrinthiformis have declined by >50% compared to pre-industrial times.

Seawater carbonate chemistry and calcification rate in the Bermuda reef community, 2010

Despite the potential impact of ocean acidification on ecosystems such as coral reefs, surprisingly, there is very limited field data on the relationships between calcification and seawater carbonate chemistry. In this study, contemporaneous in situ datasets of seawater carbonate chemistry and calcification rates from the high-latitude coral reef of Bermuda over annual timescales provide a framework for investigating the present and future potential impact of rising carbon dioxide (CO2) levels and ocean acidification on coral reef ecosystems in their natural environment. A strong correlation was found between the in situ rates of calcification for the major framework building coral species Diploria labyrinthiformis and the seasonal variability of [CO32-] and aragonite saturation state omega aragonite, rather than other environmental factors such as light and temperature. These field observations provide sufficient data to hypothesize that there is a seasonal "Carbonate Chemistry Coral Reef Ecosystem Feedback" (CREF hypothesis) between the primary components of the reef ecosystem (i.e., scleractinian hard corals and macroalgae) and seawater carbonate chemistry. In early summer, strong net autotrophy from benthic components of the reef system enhance [CO32-] and omega aragonite conditions, and rates of coral calcification due to the photosynthetic uptake of CO2. In late summer, rates of coral calcification are suppressed by release of CO2 from reef metabolism during a period of strong net heterotrophy. It is likely that this seasonal CREF mechanism is present in other tropical reefs although attenuated compared to high-latitude reefs such as Bermuda. Due to lower annual mean surface seawater [CO32-] and omega aragonite in Bermuda compared to tropical regions, we anticipate that Bermuda corals will experience seasonal periods of zero net calcification within the next decade at [CO32-] and omega aragonite thresholds of ~184 micro moles kg-1 and 2.65. However, net autotrophy of the reef during winter and spring (as part of the CREF hypothesis) may delay the onset of zero NEC or decalcification going forward by enhancing [CO32-] and omega aragonite. The Bermuda coral reef is one of the first responders to the negative impacts of ocean acidification, and we estimate that calcification rates for D. labyrinthiformis have declined by >50% compared to pre-industrial times.

Bird species recorded in an untrained observer survey (UOS) and an expert observer survey (EOS) in 2011 in SE Peru

To evaluate the potential of community-based bird surveys in the tropics, we compared the species richness and abundances of bird functional groups that would be detected by a basic untrained observer (untrained observer survey, UOS) to a comprehensive bird species list compiled by a professional bird guide, in a coffee agroforestry landscape in the Peruvian East Andean foothills and compared functional signatures to global functional signatures of tropical bird assemblages. The submitted data comprises the transect counts of the UOS, the comprehensive bird list, ecological data of the recorded birds and information regarding the conservation status of the recorded birds from the IUCN Red List.

Higher temporal variability of forest breeding bird communities in fragmented landscapes

Understanding the relationship between animal community dynamics and landscape structure has become a priority for biodiversity conservation. In particular, predicting the effects of habitat destruction that confine species to networks of small patches is an important prerequisite to conservation plan development. Theoretical models that predict the occurrence of species in fragmented landscapes, and relationships between stability and diversity do exist. However, reliable empirical investigations of the dynamics of biodiversity have been prevented by differences in species detection probabilities among landscapes. Using long-term data sampled at a large spatial scale in conjunction with a capture-recapture approach, we developed estimates of parameters of community changes over a 22-year period for forest breeding birds in selected areas of the eastern United States. We show that forest fragmentation was associated not only with a reduced number of forest bird species, but also with increased temporal variability in the number of species. This higher temporal variability was associated with higher local extinction and turnover rates. These results have major conservation implications. Moreover, the approach used provides a practical tool for the study of the dynamics of biodiversity.

Finches and Bamboo: bird at left

Emperor Huizong; handscroll, ink and color on silk

Jar with bird-shaped finial

H: 7 43/64 in.; gilt silver