How do habitat amount and habitat fragmentation drive time-delayed responses of biodiversity to land-use change?

Land-use change is a root cause of the extinction crisis, but links between habitat change and biodiversity loss are not fully understood. While there is evidence that habitat loss is an important extinction driver, the relevance of habitat fragmentation remains debated. Moreover, while time delays of biodiversity responses to habitat transformation are well-documented, time-delayed effects have been ignored in the habitat loss versus fragmentation debate. Here, using a hierarchical Bayesian multi-species occupancy framework, we systematically tested for time-delayed responses of bird and mammal communities to habitat loss and to habitat fragmentation. We focused on the Argentine Chaco, where deforestation has been widespread recently. We used an extensive field dataset on birds and mammals, along with a time series of annual woodland maps from 1985 to 2016 covering recent and historical habitat transformations. Contemporary habitat amount explained bird and mammal occupancy better than past habitat amount. However, occupancy was affected more by the past rather than recent fragmentation, indicating a time-delayed response to fragmentation. Considering past landscape patterns is therefore crucial for understanding current biodiversity patterns. Not accounting for land-use history ignores the possibility of extinction debt and can thus obscure impacts of fragmentation, potentially explaining contrasting findings of habitat loss versus fragmentation studies.     

Evolution of habitat selection: stochastic acquisition of cognitive clues?

Different habitat preferences in animals have been interpreted mostly as a result of different adaptive design of the species and/or as a result of interspecific competition. We propose an alternative view of evolution of habitat preferences. Our model is based on progressive stochastic acquisition of cognitive clues discriminating habitat features which correlate with expected fitness. We assume that acquisition of each cognitive clue allowing discrimination of ‘better’ and ‘worse’ habitats (according to the average fitness in each habitat) will constrain further evolution, because each further clue will discriminate habitats only within previously acquired preferences. Simple simulation model shows that if it is the case, even the species with equal habitat-related fitness differences will rapidly diversify in their habitat preferences. Therefore, similarly as in the evolution of other species-specific traits, the evolution of animal–habitat relationship may be strongly affected by stochastic events and historical contingency. This revised version was published online in July 2006 with corrections to the Cover Date.     

Locality or habitat? Exploring predictors of biodiversity in Amazonia

Amazonia is an environmentally heterogeneous and biologically megadiverse region, and its biodiversity varies considerably over space. However, existing knowledge on Amazonian biodiversity and its environmental determinants stems almost exclusively from studies of macroscopic above‐ground organisms, notably vertebrates and trees. In contrast, diversity patterns of most other organisms remain elusive, although some of them, for instance microorganisms, constitute the overwhelming majority of taxa in any given location, both in terms of diversity and abundance. Here, we use DNA metabarcoding to estimate prokaryote and eukaryote diversity in environmental soil and litter samples from 39 survey plots in a longitudinal transect across Brazilian Amazonia using 16S and 18S gene sequences, respectively. We characterize richness and community composition based on operational taxonomic units (OTUs) and test their correlation with longitude and habitat. We find that prokaryote and eukaryote OTU richness and community composition differ significantly among localities and habitats, and that prokaryotes are more strongly structured by locality and habitat type than eukaryotes. Our results 1) provide a first large‐scale mapping of Amazonian soil biodiversity, suggesting that OTU richness patterns might follow substantially different patterns from those observed for macro‐organisms; and 2) indicate that locality and habitat factors interact in determining OTU richness patterns and community composition. This study shows the potential of DNA metabarcoding in unveiling Amazonia's outstanding diversity, despite the lack of complete reference sequence databases for the organisms sequenced.     

How do roads affect the habitat use of an assemblage of scavenging raptors?

Scavengers may benefit from the availability of dead animals along roads that result from collisions with vehicles. However, roads are also considered risky places for many species. Animal habitat selection patterns usually balance energy intake with mortality risk. In this work we analyzed the foraging space use of an assemblage of diurnal scavenging raptors in relation to distance from roads in northwest Patagonia. We selected patches at different distances from roads, and placed a sheep carcass in each patch during the night (n = 18 carcasses in total). In general, carcasses near roads were detected by diurnal scavenging raptors much faster than those far from roads. Smaller raptors such as southern caracaras (Caracara plancus), chimango caracaras (Milvago chimango), and black vultures (Coragyps atratus), were commonly associated with roads both in terms of overall detections and scavenging activities. Southern and chimango caracaras proved to be very good at detecting carcasses, were faster to land in order to feed from them, and were found in greater numbers near roads than far from them. Even though Andean condors (Vultur gryphus) and black-chested buzzard-eagles (Geranoaetus melanoleucus) flew all over the area, they chose to feed far from roads. Our work emphasizes that some scavengers have taken advantage of the novel food resources provided by roads whereas others are reluctant to feed near them. Within a scenario of an increasing number of roads, some species can extend their distributions favoring competition and biotic homogenization processes within original communities. We highlight the importance of taking into account large flying scavengers in land-use planning. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Effects of habitat configuration on host–parasitoid food web structure

The dispersal of organisms among patches affects community structure in spatially heterogeneous habitats. The enhancement of dispersal frequency among patches can be expected to increase potential interaction between organisms in food webs. However, it has been difficult to fairly evaluate the effects of dispersal on the food web structure because the quantification of actual dispersal is difficult. In this study, in order to manipulate the dispersal frequency, two oak plantations (each with 100 oak trees) were established as high-patch connectivity (1-m interval) and low-patch connectivity (3-m interval) plots. Quantitative food webs of herbivores and their parasitoids were constructed for the high- and low-connectivity plots, and quantitative measures of food web metrics as indices of structure were calculated for both webs to examine dispersal effects on food web complexity. In the entire web, 86 herbivore species (Lepidoptera and Coleoptera) were attacked by 50 parasitoid species (Hymenoptera and Diptera). As a result, although we found no significant difference in herbivore abundance between high- and low-connectivity plots, a higher parasitism rate and greater complexity in web structure were observed in many food web metrics for the high-connectivity plot. Furthermore, the parasitoid overlap diagram showed a higher potential for indirect interactions among herbivore species in the high-connectivity plot. These results imply that the increase in dispersal frequency among habitat patches facilitates food web complexity, and the role of dispersal as a determinant of food web structure should be considered in food web ecology.     

The interpretation of habitat preference metrics under use�Cavailability designs

Models of habitat preference are widely used to quantify animal–habitat relationships, to describe and predict differential space use by animals, and to identify habitat that is important to an animal (i.e. that is assumed to influence fitness). Quantifying habitat preference involves the statistical comparison of samples of habitat use and availability. Preference is therefore contingent upon both of these samples. The inferences that can be made from use versus availability designs are influenced by subjectivity in defining what is available to the animal, the problem of quantifying the accessibility of available resources and the framework in which preference is modelled. Here, we describe these issues, document the conditional nature of preference and establish the limits of inferences that can be drawn from these analyses. We argue that preference is not interpretable as reflecting the intrinsic behavioural motivations of the animal, that estimates of preference are not directly comparable among different samples of availability and that preference is not necessarily correlated with the value of habitat to the animal. We also suggest that preference is context-dependent and that functional responses in preference resulting from changing availability are expected. We conclude by describing advances in analytical methods that begin to resolve these issues.     

Predictive quality of macroinvertebrate — habitat associations in lower navigation pools of the Mississippi River

Macroinvertebrate community structure was compared between habitat types within a navigation pool and between navigation pools of the Upper Mississippi River. Bottom samples were taken using a grab or Wilding sampler from 40 and 14 stations on Pool 19 and 26, respectively. In both Pools, distinct communities developed based on substrate type or the presence of aquatic macrophytes rather than specific habitats as defined by river morphometry. Areas with sand substrates usually had communities of low density and diversity. Communities of the highest density, including Hexagenia or Musculium or both, occurred in habitats with silt-sand substrates. However, these areas were low in diversity. High diversity was found in both vegetated areas and habitats with coarse substrates, the latter dominated by net-spinning caddisfly larvae. Due to pool age and longitudinal distribution of species, community similarity between Pools 19 and 26 was not significant, p < 0.05, but functional feeding similarities occurred between communities from the same type of substrate.     

The heterospecific habitat copying hypothesis: can competitors indicate habitat quality?

According to the "habitat copying" hypothesis, animals use thereproductive performance of conspecifics to assess habitat suitabilityand choose their future breeding site. This is because conspecificsshare ecological needs and thus indicate habitat suitability.Here, we propose the "heterospecific habitat copying" hypothesis,which states that animals should use public information (i.e.,information derived from the performance of others) from con-and heterospecifics sharing ecological needs. In a correlationalapproach we test some assumptions and predictions of this hypothesiswith a data set from two sympatric bird populations, rollers(Coracias garrulus) and kestrels (Falco tinnunculus), usingthe same nest-boxes and exploiting similar food resources. Sincekestrels are residents and breed earlier, we assumed that theyare dominant over rollers for nest-box acquisition. The environmentappears to be patchy for both species and temporally predictablefor kestrels only. Two results suggest that the use of heterospecificpublic information in breeding habitat selection may be at work:(1) an increase in the reoccupancy probability by kestrels ofprevious roller nests with increasing nest success, and (2)an increase in roller breeding population with increasing localkestrel success. Most of the other observed patterns could beexplained by alternative mechanisms such as natal philopatry,breeding fidelity, conspecific attraction, intraspecific habitatcopying, and the effect of interspecific competition.     

Does habitat specialization shape the evolutionary potential of wild bird populations?

Because specialist species evolved in more temporally and spatially homogeneous environments than generalist species, they are supposed to experience less fluctuating selection. For this reason, we expect specialists to show lower overall genetic variation as compared to generalists. We also expect populations from specialist species to be smaller and more fragmented, with lower neutral genetic diversity. We tested these hypotheses by investigating patterns of genetic diversity along a habitat specialization gradient in wild birds, based on estimates of heritability, coefficients of variation of additive genetic variance, and heterozygosity available in the literature. We found no significant effect of habitat specialization on any of the quantitative genetic estimators but generalists had higher heterozygosity. This effect was mainly a consequence of the larger population size of generalists. Our results suggest that evolutionary potential does not differ at the population level between generalist and specialist species, but the trend observed in heterozygosity levels and population sizes may explain their difference in susceptibility to extinction.     

Can models of density-dependent habitat selection be applied for trap-building predators?

Density-dependent habitat selection theory was mainly tested on active foragers and therefore its applicability to trap-building predators is poorly understood. The high sensitivity of trap-building predators to changes in their physical environment, combined with their limited movement capability, can lead to habitat specialization, reducing their utilization of alternative habitats. We studied density-dependent habitat selection in two pit-building antlions, differing in their habitat utilization spectrum. The habitat generalist, Myrmeleon hyalinus, inhabits and performs equally well in both sand- and loess-derived soils, although preferring the former, more productive coarse-grained soils. In contrast, the habitat specialist, Cueta lineosa, only inhabits fine-grained soils such as loess, while showing reduced foraging performance in coarse-grained sandy soils. We allowed larvae to select between these two soils, while manipulating con-specific density and initial stocking position. Irrespective of the initial stocking position, the number of M. hyalinus pits in the sand was positively correlated with the number of con-specific pits in the loess, implying that this species is a density-dependent habitat selector. Furthermore, these patterns of density-dependence were consistent with the expectations of ideal pre-emptive distribution (i.e., strong non-linearity in the distribution of antlions between soils with increased total density), suggesting that interference competition largely dictates habitat selection in this species. In contrast, the habitat specialist showed constant habitat selectivity, as neither con-specific density nor initial stocking positions influenced its habitat preference. Although mainly tested on active foragers, habitat selection theory can be applicable for trap-building predators, demonstrating how mechanisms operating at the individual level influence spatial distribution patterns.     

Does habitat heterogeneity affect the diversity of epigaeic arthropods in vineyards?

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The biology of habitat dominance; can microbes behave as weeds?

Competition between microbial species is a product of, yet can lead to a reduction in, the microbial diversity of specific habitats. Microbial habitats can resemble ecological battlefields where microbial cells struggle to dominate and/or annihilate each other and we explore the hypothesis that (like plant weeds) some microbes are genetically hard‐wired to behave in a vigorous and ecologically aggressive manner. These ‘microbial weeds’ are able to dominate the communities that develop in fertile but uncolonized – or at least partially vacant – habitats via traits enabling them to out‐grow competitors; robust tolerances to habitat‐relevant stress parameters and highly efficient energy‐generation systems; avoidance of or resistance to viral infection, predation and grazers; potent antimicrobial systems; and exceptional abilities to sequester and store resources. In addition, those associated with nutritionally complex habitats are extraordinarily versatile in their utilization of diverse substrates. Weed species typically deploy multiple types of antimicrobial including toxins; volatile organic compounds that act as either hydrophobic or highly chaotropic stressors; biosurfactants; organic acids; and moderately chaotropic solutes that are produced in bulk quantities (e.g. acetone, ethanol). Whereas ability to dominate communities is habitat‐specific we suggest that some microbial species are archetypal weeds including generalists such as: Pichia anomala, Acinetobacter spp. and Pseudomonas putida; specialists such as Dunaliella salina, Saccharomyces cerevisiae, Lactobacillus spp. and other lactic acid bacteria; freshwater autotrophs Gonyostomum semen and Microcystis aeruginosa; obligate anaerobes such as Clostridium acetobutylicum; facultative pathogens such as Rhodotorula mucilaginosa, Pantoea ananatis and Pseudomonas aeruginosa; and other extremotolerant and extremophilic microbes such as Aspergillus spp., Salinibacter ruber and Haloquadratum walsbyi. Some microbes, such as Escherichia coli, Mycobacterium smegmatis and Pseudoxylaria spp., exhibit characteristics of both weed and non‐weed species. We propose that the concept of nonweeds represents a ‘dustbin’ group that includes species such as Synodropsis spp., Polypaecilum pisce, Metschnikowia orientalis, Salmonella spp., and Caulobacter crescentus. We show that microbial weeds are conceptually distinct from plant weeds, microbial copiotrophs, r‐strategists, and other ecophysiological groups of microorganism. Microbial weed species are unlikely to emerge from stationary‐phase or other types of closed communities; it is open habitats that select for weed phenotypes. Specific characteristics that are common to diverse types of open habitat are identified, and implications of weed biology and open‐habitat ecology are discussed in the context of further studies needed in the fields of environmental and applied microbiology.     

Macroinvertebrate assemblages in an artificial habitat—a settling basin of a hydroelectric power plant: comparison with a natural riffle habitat

The macroinvertebrate assemblages in an artificial habitat, the settling basin of a hydroelectric power plant, were investigated and compared with those in a natural habitat, riffles in a nearby river. This study showed that macroinvertebrate density was much higher in the settling basin than in the riffles. Macroinvertebrate assemblage composition differed between the settling basin and the riffles. The difference was probably due to the widespread bryophyte beds in the settling basin. Cincticostella, Brachycentrus, Ephmerella, and chironomid midges, which are usually abundant in bryophyte beds, were present at much higher densities in the settling basin. Cheumatopsyche and Taeniopterygidae were also present at higher densities in the settling basin than in the natural riffles. In contrast, Epeorus was present at lower density in the settling basin than in the natural riffles. This study suggests that the settling basin increases β-diversity in riverine ecosystems.     

Does lack of available suitable habitat explain the patchy distributions of rare calcicole fern species?

In Canada, as in many countries, a relatively large number of fern species occur in specialized habitats and have low numbers of known populations containing few individuals. It has been suggested that the distribution of ferns is mostly determined by factors of climate and habitat due to relatively low limitations in ferns for dispersal and establishment. Here, we attempt to explain whether the local patchy distribution of three calcicole fern species rare in Canada ( Asplenium ruta-muraria , Pellaea atropurpurea and Woodsia obtusa ) is due to a lack of available habitat. Analyses based on micro-scale differences between sites occupied by the ferns and nearby, unoccupied sites did not reveal any significant differences, thereby indicating that the rarity of these species is not entirely driven by the rarity of their microhabitat at a local scale. Our results suggest that the widely accepted premise that ferns are not limited by dispersal or establishment should be reconsidered, as such limitations are the only likely explanation for empty available and suitable habitat.     

Utility of mesohabitat features for determining habitat associations of subadult sharks in Georgia’s estuaries

We examined the affects of selected water quality variables on the presence of subadult sharks in six of nine Georgia estuaries. During 231 longline sets, we captured 415 individuals representing nine species. Atlantic sharpnose shark (Rhizoprionodon terranovae), bonnethead (Sphyrna tiburo), blacktip shark (Carcharhinus limbatus) and sandbar shark (C. plumbeus) comprised 96.1% of the catch. Canonical correlation analysis (CCA) was used to assess environmental influences on the assemblage of the four common species. Results of the CCA indicated Bonnethead Shark and Sandbar Shark were correlated with each other and with a subset of environmental variables. When the species occurred singly, depth was the defining environmental variable; whereas, when the two co-occurred, dissolved oxygen and salinity were the defining variables. Discriminant analyses (DA) were used to assess environmental influences on individual species. Results of the discriminant analyses supported the general CCA findings that the presence of bonnethead and sandbar shark were the only two species that correlated with environmental variables. In addition to depth and dissolved oxygen, turbidity influenced the presence of sandbar shark. The presence of bonnethead shark was influenced primarily by salinity and turbidity. Significant relationships existed for both the CCA and DA analyses; however, environmental variables accounted for <16% of the total variation in each. Compared to the environmental variables we measured, macrohabitat features (e.g., substrate type), prey availability, and susceptibility to predation may have stronger influences on the presence and distribution of subadult shark species among sites.     

Practical tool for landscape planning? An empirical investigation of network based models of habitat fragmentation

This study presents a graph-theoretical modelling approach using daily movements and habitat demands of different target bird species in an urban context to assess: 1) habitable land cover types, 2) threshold distances between patches of habitat, 3) the required minimum accessible habitat areas and 4) the effects of barriers and stepping stones. The modelling approach is tested using empirical data from field surveys in the urban area of Stockholm, Sweden.
The results show that groups of small habitat patches can house the same species as larger contiguous patches as long as they are perceived as functionally connected by the inhabitant organisms. Furthermore, we found that binary habitat/non-habitat representations of the landscape could roughly explain the variation in species occurrence, as long as habitat was properly defined. However, the explanatory power of the landscape models increased when features of matrix heterogeneity such as stepping stones and barriers were accounted for.
Synthesis and application: in a world where forest ecosystems are becoming increasingly fragmented there is an urgent need to find comprehensive and scientifically relevant methods for managing and planning ecosystems. This study shows that: 1) groups of well placed small habitat patches can, together, be sufficient to attract birds in intensively developed areas, 2) the presented modelling approach can help identify such groups of patches, 3) matrix heterogeneity should preferably be accounted for, and 4) proper assessments of habitable land cover types are important. Finally, we argue that the modelling approach applied here may substantially improve landscape management and planning at scales ranging from whole landscapes down to neighbourhoods.     

What is an edge species? The implications of sensitivity to habitat edges

For decades, researchers have categorized species as “edge‐loving” or “edge‐avoiding”, but recent studies that show inconsistencies in responses have called these labels into question and led to a sense that edge effects are idiosyncratic and difficult to understand. We suggest that species would be better categorized according to their sensitivity to edges, not the direction of observed responses because no species should be expected to show the same response to all edge types. Measures of edge sensitivity will apply widely across taxa and landscapes and allow metrics that are broadly comparable, making generalities easier to discern. Finally, while the direction of observed edge responses remains a critical (but largely understood) dynamic, most reported edge responses are neutral, so discovering when species are least likely to respond to edges will increase our understanding of edge ecology and associated fragmentation effects. We offer a case study that measures edge sensitivity of 15 butterfly species at 12 edge types. We found that sensitivity is weakly related to vulnerability to predation, but more importantly we show how our results generate new predictions about edge sensitivity that can be explored in future studies.     

Elevational replacement of two Himalayan titmice: interspecific competition or habitat preference?

Elevational species replacement is a widely documented pattern in montane species. Although interspecific competition has been shown to be important in setting species elevational limits in tropical habitats, its effect in species of temperate regions is poorly studied. We tested the role of interspecific competition for space in the breeding season and for food in the non‐breeding season in mediating the distribution of two resident titmice species in the Himalayas. We show that high elevation green‐backed tits Parus monticolus are behaviourally dominant over low elevation cinereous tits Parus cinereus in both song playback and feeder trials. Despite being subordinate, at their elevational upper limit, cinereous tits occur in sympatry in human modified habitats. Our study suggests that the loss of natural habitats in the sympatric zone, not interspecific competition, might be limiting the distribution of the high‐elevation green‐backed tits and facilitating an upward range shift through human association in cinereous tits.     

Loss of habitat specialists despite conservation management in fen remnants 1995–2006

Many ecosystems of high conservation value have been shaped by human impacts over centuries. Today, traditional management of semi-natural habitats is a common conservation measure in Europe. However, despite traditional management, habitat remnants may still loose specialist species due to surrounding land-use change or atmospheric nitrogen deposition. To detect trends in species density (2-m² plot scale) and habitat quality in calcareous fens in the pre-Alps of Switzerland, we surveyed 36 traditionally managed fens in 1995/97 and again in 2005/06 (five plots per fen). The fens occurred at three altitudinal levels (800–1000, 1000–1200, 1200–1400 m asl) and were either extensively grazed or mown once a year. Despite these traditional management regimes, species density of fen specialists and of all bryophytes decreased during this decade (vascular plant specialists: ?9.4%, bryophyte specialists: ?14.9%, all bryophytes: ?5.7%). Management had no effect on the number of Red-List species and habitat specialists of vascular plants per plot. However, bryophyte species density was more strongly reduced in grazed fens. Species density of vascular plant generalists increased between the two surveys (+8.2%) but not of bryophytes. Among vascular plants, Red-List species decreased from 1.01 to 0.78 species per plot. Furthermore, between the two surveys aboveground plant biomass, mean plant-community indicator values for nutrients and species density of nutrient indicators increased, whereas mean plant indicator values for soil moisture, light and peat, and species density for peat indicators, decreased. We attribute these changes and the loss of specialist species over the past decade mainly to land-use change in the surrounding area and to nutrient inputs. Thus, despite traditional management, calcareous fens in the pre-Alps suffer from ongoing habitat deterioration and endangered plant species remain threatened. For their long-term protection, we suggest to reduce nutrient inputs and, where necessary, to restore hydrology and adjust grazing management.