Birds as surrogates for mammals and reptiles: Are patterns of cross-taxonomic associations stable over time in a human-modified landscape?

Cross-taxonomic surrogates can be feasible alternatives to direct measurements of biodiversity in conservation if validated with robust data and used with explicit goals. However, few studies of cross-taxonomic surrogates have examined how temporal changes in composition or richness in one taxon can drive variation in concordant patterns of diversity in another taxon, particularly in a dynamic and heavily modified landscape. We examined this problem by assessing changes in cross-taxonomic associations over time between the surrogate (birds) and target vertebrate taxa (mammals, reptiles) that demand high sampling effort, in a heterogeneous mosaic landscape comprising pine monoculture, eucalypt woodland remnants and agricultural land. Focussing on four study years (1999, 2001, 2011, 2013) from a dataset spanning 15 years, we: (1) investigated temporal changes in cross-taxonomic congruency among three animal taxa, (2) explored how temporal variation in composition and species richness of each taxon might account for variation in cross-taxonomic congruency, and (3) identified habitat structural variables that are strongly correlated with species composition of each taxon. We found the strength of cross-taxonomic congruency varied between taxa in response to both landscape context and over time. Among the three taxa, overall correlations were weak but were consistently positive and strongest between birds and mammals, while correlations involving reptiles were usually weak and negative. We also found that stronger species richness and composition correlations between birds and mammals were not only more prevalent in woodland remnants in the agricultural matrix, but they also increased in strength over time. Temporal shifts in species composition differed in rate and extent among the taxa even though these changes were significant over time, while important habitat structural correlates were seldom shared across taxa. Our study highlights the role of the landscape matrix and time in shaping animal communities and the resulting cross-taxonomic associations in the woodland remnants, especially after a major perturbation event (i.e. plantation establishment). In such dynamic landscapes, differing and taxon-specific shifts in diversity over time can influence the strength, direction and consistency of cross-taxonomic correlations, therefore posing a ‘temporal’ problem for the use of surrogates like birds in monitoring and assessments of biodiversity, and conservation management practices.     

Evaluating the benefits of CAP reforms: Can afforestations restore bird diversity in Mediterranean Spain?

Current Common Agricultural Policy (CAP) subsidies in the Mediterranean region tend to prioritize afforestation on former arable land with oaks rather than pines because pine plantations would maintain lower biological diversities than native forests. Nevertheless, no thorough evaluations of the conservation values of pine plantations as compared to oak remnants have been carried out to date. We analyze the diversity and conservation value of bird assemblages breeding in 200 remnants of Holm oak Quercus ilex woodlands and 82 mature (>50-year-old) pine plantations in central Spain, a Mediterranean region mostly devoted to arable farming. Species–area relationships were compared between forest types. The conservation value of bird assemblages was assessed using the “Species of European Conservation Concern” (SPEC) classification of Burfield and van Bommel [(2004). Birds in Europe: Populations estimates, trends and conservation status. Cambridge: BirdLife International]. Overall numbers of bird species maintained by oak and pine archipelagoes were rather similar, but species–area relationships differed between forest types. Intercepts were higher in oak fragments, whereas slopes were steeper in pine plantations. Small oak fragments held more species (mainly Mediterranean Sylvia warblers) than plantations, whereas large plantations held more species than large oak remnants. Differences in species–area relationships seemed to be due to differences in vegetation structure, especially understorey shrub cover and tree height and cover. We recorded nine SPECs, all exclusive (6) or near-exclusive (3) to oak woodlands, although such woodlands do not appear to be critical for their conservation. Hence, we conclude that pine afforestations have played a role for maintaining and restoring forest bird communities in the farming landscapes of central Spain. Promoting large and shrubby plantations would enhance their conservation value for breeding birds, together with promoting growth, regeneration and expansion of Holm oak remnants by means of set-aside measures previous or alternative to oak reafforestation. The increasing importance of non-commercial as compared to commercial values of Mediterranean forests would justify subsidizing the proposed policy.     

Dendrochronological assessment of British veteran sweet chestnut (Castanea sativa) trees: Successful cross-matching,and cross-dating with British and French oak (Quercus) chronologies

Across Britain and continental Europe there are many ancient Castanea sativa trees of great significance for natural and cultural heritage, yet scant assessment has been made of them for dendrochronological information. This paper describes the dendrochronological analysis of 28 Castanea sativa trees (veteran historic trees, forest trees and coppice stems) sampled from 15 sites in southern Britain: 56 growth-ring sequences were collected for analysis, by boring living trees and by cutting transverse sections from dead fallen trees and previously cut stumps. Twenty-three single-tree sequences from 14 sites were cross-matched (t ≥3.5) and then cross-dated with 17 oak Quercus reference chronologies from England and northern France: a Castanea sativa master chronology spanning AD 1660–2014 has been created. The results demonstrate the viability of dendrochronological analysis of Castanea sativa wood; and confirm that Castanea sativa can be cross-dated with oak Quercus reference chronologies, inter-regionally and inter-nationally. The findings provide the potential means for dating Castanea sativa timbers sampled from palaeoenvironmental and historical contexts. The extraction of sawn sections from long-dead (up to 60 years in this study) trees and stumps is proven to be a reliable method for dating veteran trees in cultural landscapes and ancient woodlands; and for revealing the growth history of historic/iconic trees. The germination dates calculated for the Castanea sativa trees in this study span the period AD 1640–1943. The inaccuracy of estimating veteran Castanea sativa tree ages from girth measurements is highlighted.     

Anthropogenic transformation of the biomes, 1700 to 2000

Aim To map and characterize anthropogenic transformation of the terrestrial biosphere before and during the Industrial Revolution, from 1700 to 2000. Location Global. Methods Anthropogenic biomes (anthromes) were mapped for 1700, 1800, 1900 and 2000 using a rule‐based anthrome classification model applied to gridded global data for human population density and land use. Anthropogenic transformation of terrestrial biomes was then characterized by map comparisons at century intervals. Results In 1700, nearly half of the terrestrial biosphere was wild, without human settlements or substantial land use. Most of the remainder was in a seminatural state (45%) having only minor use for agriculture and settlements. By 2000, the opposite was true, with the majority of the biosphere in agricultural and settled anthromes, less than 20% seminatural and only a quarter left wild. Anthropogenic transformation of the biosphere during the Industrial Revolution resulted about equally from land‐use expansion into wildlands and intensification of land use within seminatural anthromes. Transformation pathways differed strongly between biomes and regions, with some remaining mostly wild but with the majority almost completely transformed into rangelands, croplands and villages. In the process of transforming almost 39% of earth's total ice‐free surface into agricultural land and settlements, an additional 37% of global land without such use has become embedded within agricultural and settled anthromes. Main conclusions Between 1700 and 2000, the terrestrial biosphere made the critical transition from mostly wild to mostly anthropogenic, passing the 50% mark early in the 20th century. At present, and ever more in the future, the form and process of terrestrial ecosystems in most biomes will be predominantly anthropogenic, the product of land use and other direct human interactions with ecosystems. Ecological research and conservation efforts in all but a few biomes would benefit from a primary focus on the novel remnant, recovering and managed ecosystems embedded within used lands.     

Adaptive Patch Searching Strategies in Fragmented Landscapes

The search strategies dispersers employ to search for new habitat patches affect individuals’ search success and subsequently landscape connectivity and metapopulation viability. Some evidence indicates that individuals within the same species may display a variety of behavioural patch searching strategies rather than one species-specific strategy. This may result from landscape heterogeneity. We modelled the evolution of individual patch searching strategies in different landscapes. Specifically, we analysed whether evolution can favour different, co-existing, behavioural search strategies within one population and to what extent this coexistence of multiple strategies was dependent on landscape configuration. Using an individual-based simulation model, we studied the evolution of patch searching strategies in three different landscape configurations: uniform, random and clumped. We found that landscape configuration strongly influenced the evolved search strategy. In uniform landscapes, one fixed search strategy evolved for the entire spatially structured population, while in random and clumped landscapes, a set of different search strategies emerged. The coexistence of several search strategies also strongly depended on the dispersal mortality. We show that our result can affect landscape connectivity and metapopulation dynamics. Co-ordinating editor: N. Yamamura     

Complexity of free energy landscapes of peptides revealed by nonlinear principal component analysis

Employing the recently developed hierarchical nonlinear principal component analysis (NLPCA) method of Saegusa et al. (Neurocomputing 2004;61:57-70 and IEICE Trans Inf Syst 2005;E88-D:2242-2248), the complexities of the free energy landscapes of several peptides, including triglycine, hexaalanine, and the C-terminal beta-hairpin of protein G, were studied. First, the performance of this NLPCA method was compared with the standard linear principal component analysis (PCA). In particular, we compared two methods according to (1) the ability of the dimensionality reduction and (2) the efficient representation of peptide conformations in low-dimensional spaces spanned by the first few principal components. The study revealed that NLPCA reduces the dimensionality of the considered systems much better, than did PCA. For example, in order to get the similar error, which is due to representation of the original data of beta-hairpin in low dimensional space, one needs 4 and 21 principal components of NLPCA and PCA, respectively. Second, by representing the free energy landscapes of the considered systems as a function of the first two principal components obtained from PCA, we obtained the relatively well-structured free energy landscapes. In contrast, the free energy landscapes of NLPCA are much more complicated, exhibiting many states which are hidden in the PCA maps, especially in the unfolded regions. Furthermore, the study also showed that many states in the PCA maps are mixed up by several peptide conformations, while those of the NLPCA maps are more pure. This finding suggests that the NLPCA should be used to capture the essential features of the systems.     

The ‘Design’ of Mediterranean Landscapes: A Millennial Story of Humans and Ecological Systems during the Historic Period

What makes the structure and dynamics of coupled natural and human systems difficult to interpret in the Mediterranean is the extreme diversity in space and time of both environments and human societies. The succession of civilizations that waxed and waned in the Mediterranean Basin over several millennia has had great impacts on biota and ecosystems everywhere in the basin. A complex ‘coevolution’ has been claimed to shape the interactions between ecosystem components and human societies. Two opposing schools of thought traditionally have considered the consequences of human pressures on Mediterranean ecosystems. The ‘Ruined Landscape’ or ‘Lost Eden theory’ argues that human action resulted in a cumulative degradation and desertification of Mediterranean landscapes. The second school argues that humans actually contributed to keeping Mediterranean landscapes diverse since the last glacial episode. With this debate in mind, I show the following: (1) One cannot understand the components and dynamics of current biodiversity in the Mediterranean without taking into account the history of human-induced changes; (2) The various systems of land use and resource management that provided a framework for the blossoming of Mediterranean civilizations also had profound consequences on the distribution and dynamics of species, communities, and landscapes; (3) The processes of domestication of plant and animal species, which first occurred in the eastern Mediterranean area some 10,000 years ago, contributed to the increase of certain components of biodiversity at several spatial scales. Positive and negative feedback cycles between cultural practices and natural systems at the local and regional levels have kept ecosystems robust and resilient; (4) Assuming that human action can, to a certain extent, be considered a large-scale surrogate for natural sources of ecosystem disturbance, such patterns give support to the diversity-disturbance hypothesis—specifically, intermediate levels of disturbance have promoted biological diversity; (5) Intraspecific adaptive variation increased as a result of human-induced habitat changes over millennia, resulting in bursts of differentiation during the later Holocene of local ecotypes and gene pools of domesticated and wild plant and animal species, with region-specific characters fitting them to local climate and environmental conditions. High intraspecific adaptive variation also arose from earlier natural processes of the Pleistocene, mainly from a combination of periodic refugia formation and climate dynamics. During the Holocene, the main sources of disturbance came increasingly from humans, specifically from the coupled cultural and natural modifications of community and landscape structure. It is concluded that a high degree of resilience of Mediterranean ecosystems resulted in a dynamic coexistence of human and natural living systems, which in some cases provided stability, while fostering diversity and productivity (Blondel and Aronson, 1999). The word “design” used in the title and elsewhere in this paper metaphorically indicates that the long-lasting influence of human impacts resulted in an unintentional shaping of individual components of landscapes.     

Importance of Interhabitat Gaps and Stepping-Stones for Lesser Woodcreepers (Xiphorhynchus fuscus) in the Atlantic Forest, Brazil

Translocation experiments showed that a woodcreeper bird species is able to move between isolated forest fragments, but this ability is limited by increasing interpatch distances. Larger distances (> 100 m) were overcome by using small stepping‐stones (isolated trees), which enhance connectivity and are useful for the species conservation in fragmented landscapes.     

Human disturbance promotes herbivory by leaf‐cutting ants in the Caatinga dry forest

Anthropogenic disturbances are known to modify plant–animal interactions such as those involving the leaf‐cutting ants, the most voracious and proliferating herbivore across human‐modified landscapes in the Neotropics. Here, we evaluate the effect of chronic anthropogenic disturbance (e.g., firewood collection, livestock grazing) and vegetation seasonality on foraging area, foliage availability in the foraging area, leaf consumption and herbivory rate of the leaf‐cutting ant Atta opaciceps in the semiarid Caatinga, a mosaic of dry forest and scrub vegetation in northeast Brazil. Contrary to our initial expectation, the foraging area was not affected by either disturbance intensity or the interaction between season and disturbance intensity. However, leaf consumption and herbivory rate were higher in more disturbed areas. We also found a strong effect of seasonality, with higher leaf consumption and herbivory rate in the dry season. Our results suggest that the foraging ecology of leaf‐cutting ants is modulated by human disturbance and seasonality as these two drivers affect the spectrum and the amount of resources available for these ants in the Caatinga. Despite the low productivity of Caatinga vegetation, the annual rates of biomass consumption by A. opaciceps are similar to those reported from other leaf‐cutting ants in rain forests and savannas. This is made possible by maintaining high foraging activity even in the peak of the dry season and taking benefit from any resource available, including low‐quality items. Such compensation highlights the adaptive capacity of LCA to persist or even proliferate in human‐modified landscapes from dry to rain forests.     

Effect of double-stranded DNA on maturation of dendritic cells in vitro

A preparation of human genomic fragmented double-stranded DNA (dsDNA) was used as maturation stimulus in cultures of human dendritic cells (DCs) generated in compliance with the interferon protocol. Culturing of the DCs in medium with 5 μg/ml of the DNA preparation was associated with a decrease in the relative proportion of CD14 + cells and an increase in that of CD83 + cells. These changes are markers of DC maturation. The efficiency with which the DNA preparation was able to elicit DC maturation was commensurate with that of lypopolysaccharide from bacterial cell, the standard inducer of DC maturation. Generated ex vivo, matured in the presence of the human DNA preparation, pulsed with tumor antigens mouse DCs were used as a vaccine in biological tests for its antitumor activity. The experimental results demonstrate that reinfusion of mature pulsed with tumor antigens DCs cause a statistically significant suppression of tumor graft growth.