Lessons Learned While Integrating Habitat,Dispersal, Disturbance,and Life-History Traits into Species Habitat Models Under Climate Change

We present an approach to modeling potential climate-driven changes in habitat for tree and bird species in the eastern United States. First, we took an empirical-statistical modeling approach, using randomForest, with species abundance data from national inventories combined with soil, climate, and landscape variables, to build abundance-based habitat models for 134 tree and 147 bird species. We produced lists of species for which suitable habitat tends to increase, decrease, or stay the same for any region. Independent assessments of trends of large trees versus seedlings across the eastern U.S. show that 37 of 40 species in common under both studies are currently trending as modeled. We developed a framework, ModFacs, in which we used the literature to assign default modification factor scores for species characteristics that cannot be readily assessed in such models, including 12 disturbance factors (for example, drought, fire, insect pests), nine biological factors (for example, dispersal, shade tolerance), and assessment scores of novel climates, long-distance extrapolations, and output variability by climate model and emission scenario. We also used a spatially explicit cellular model, SHIFT, to calculate colonization potentials for some species, based on their abundance, historic dispersal distances, and the fragmented nature of the landscape. By combining results from the three efforts, we can create projections of potential climate change impacts over the next 100 years or so. Here we emphasize some of the lessons we have learned over 16 years in hopes that they may help guide future experiments, modeling efforts, and management.     

Prey Distribution,Physical Habitat Features,and Guild Traits Interact to Produce Contrasting Shorebird Assemblages among Foraging Patches

Worldwide declines in shorebird populations, driven largely by habitat loss and degradation, motivate environmental managers to preserve and restore the critical coastal habitats on which these birds depend. Effective habitat management requires an understanding of the factors that determine habitat use and value to shorebirds, extending from individuals to the entire community. While investigating the factors that influenced shorebird foraging distributions among neighboring intertidal sand flats, we built upon species-level understandings of individual-based, small-scale foraging decisions to develop more comprehensive guild- and community-level insights. We found that densities and community composition of foraging shorebirds varied substantially among elevations within some tidal flats and among five flats despite their proximity (all located within a 400-m stretch of natural, unmodified inlet shoreline). Non-dimensional multivariate analyses revealed that the changing composition of the shorebird community among flats and tidal elevations correlated significantly (ρ_s = 0.56) with the spatial structure of the benthic invertebrate prey community. Sediment grain-sizes affected shorebird community spatial patterns indirectly by influencing benthic macroinvertebrate community compositions. Furthermore, combining sediment and macroinvertebrate information produced a 27% increase in correlation (ρ_s = 0.71) with shorebird assemblage patterns over the correlation of the bird community with the macroinvertebrate community alone. Beyond its indirect effects acting through prey distributions, granulometry of the flats influenced shorebird foraging directly by modifying prey availability. Our study highlights the importance of habitat heterogeneity, showing that no single patch type was ideal for the entire shorebird community. Generally, shorebird density and diversity were greatest at lower elevations on flats when they became exposed; these areas are at risk from human intervention by inlet sand mining, construction of groins and jetties that divert sediments from flats, and installation of seawalls on inlet shorelines that induce erosion of flats.     

两种热带木质藤本幼苗形态、生长和光合能力对光强和养分的响应

比较了两种不同攀援习性,卷须缠绕种薄叶羊蹄甲（Bauhinia tenuiflora）和茎缠绕种刺果藤（Byttneria aspera）,木质藤本植物的形态、生长及光合特性对不同光强（4％、35％和全光照）和土壤养分（高和低）的响应。两种藤本植物大部分表型特征主要受光照的影响,而受土壤养分的影响较小。弱光促进地上部分生长,弱光下两种植物均具有较大的比叶面积（specific leaf area,SLA）、茎生物量比（stem mass ratio,SMR）和平均叶面积比（mean leaf area ratio,LARm）。高光强下,两种植物的总生物量和投入到地下部分的比重增加,具有更大的根生物量比（root mass ratio,RMR）、更多的分枝数、更高的光合能力（maximum photosynthetic rate,Pmax）和净同化速率（net assimilation rate,NAR）,综合表现为相对生长速率（relative growth rate,RGR）增加。两种藤本植物的Pmax与叶片含氮量的相关性均未达显著水平,但刺果藤的Pmax与SU志间呈显著的正相关,而薄叶羊蹄甲的Pmax与SLA之间相关性不显著。在相同光照强度和土壤养分条件下,卷须缠绕种薄叶羊蹄甲的RGR显著高于茎缠绕种刺果藤。薄叶羊蹄甲的RGR与NAR呈显著正相关,其RGR与SLA、平均叶面积比（EARm）及Pmax之间相关性不显著。刺果藤的RGR与NAR呈显著的正相关,而与SLA存在显著的负相关。上述结果表明,与土壤养分相比,光照强度可能是决定木质藤本分布更为重要的生态因子。卷须缠绕种薄叶羊蹄甲由于具有特化的攀援器官,在形态上和生理上具有更大的可塑性,这使得卷须缠绕种木质藤本在与其它植物的竞争中更具优势。     

Phylogeny of the Malus (Apple Tree) Species,Inferred from the Morphological Traits and Molecular DNA Analysis

Some debated issues of the genus Malus (apple) taxonomy were examined using a variety of species from the collection of the Maikop Experimental Station, Vavilon Research Institute of Plant Industry (Krasnodar krai). Phylogenetic relationships among these species were studied using traditional analysis of morphological traits, RAPD, and complete sequencing of the 5"- internal transcribed spacer (ITS1), 5.8S rRNA, 3"- internal transcribed spacer (ITS2) (constituting a cluster of the rRNA genes), and the terminal fragment of the matK gene encoding chloroplast maturase. The results showed that the Sorbomalussection was polyphyletic; the American apple M. fusca was closely related to the species contributing to the East Asian center of the genus origin, and the American speciesM. angustifolia, M. coronaria, and M. ioensis were closely related to the M. trilobata relict species, whose assignment to the genus Malus is debated by some authors. Molecular analysis of the species relationships showed that the Middle Asian apple M. sieversii is the species from which apple domestication started.     

Optimal Foraging: Field Tests of Diet Choice and Habitat Switching

The application of optimal foraging theory to questions of predatorbehavior, and evidence bearing on the utility of this construct,are reviewed. Experimental tests of simple models predictingprey choice are examined with particular reference to the size-selectionof prey by fish. Laboratory estimates of model parameters arethen used to predict prey choice in the field and data fromseveral field tests are presented which corroborate these predictions.When parameters are habitat specific this permits predictionsof net return from foraging in different habitats and consequentlypredictions of habitat use and switching. Field data gatheredto test these predictions demonstrate that fish feed in thericher habitats and switch habitats when the profitability ofone drops below that of another. Examples are provided showinghow these models can then be used to relate behavioral and morphologicaldifferences between species and questions at higher levels suchas the nature of species interactions and community structure.It is suggested that this may be one of the more useful applicationsof optimal foraging theory. Finally, some of the criticismsof the theory and important questions requiring further studyare discussed.     

Sensory Information and Encounter Rates of Interacting Species

Most motile organisms use sensory cues when searching for resources, mates, or prey. The searcher measures sensory data and adjusts its search behavior based on those data. Yet, classical models of species encounter rates assume that searchers move independently of their targets. This assumption leads to the familiar mass action-like encounter rate kinetics typically used in modeling species interactions. Here we show that this common approach can mischaracterize encounter rate kinetics if searchers use sensory information to search actively for targets. We use the example of predator-prey interactions to illustrate that predators capable of long-distance directional sensing can encounter prey at a rate proportional to prey density to the power (where is the dimension of the environment) when prey density is low. Similar anomalous encounter rate functions emerge even when predators pursue prey using only noisy, directionless signals. Thus, in both the high-information extreme of long-distance directional sensing, and the low-information extreme of noisy non-directional sensing, encounter rate kinetics differ qualitatively from those derived by classic theory of species interactions. Using a standard model of predator-prey population dynamics, we show that the new encounter rate kinetics derived here can change the outcome of species interactions. Our results demonstrate how the use of sensory information can alter the rates and outcomes of physical interactions in biological systems.     

Habitat Use by Weddell Seals and Emperor Penguins Foraging in the Ross Sea, Antarctica

The only apex predators that live year-round at high latitudesof the Ross Sea are the Weddell seal and emperor penguin. Theseasonal distribution, foraging depths, and diet of these twospecies appear to overlap. What makes it possible for emperorpenguins and Weddell seals to co-exist at high latitude throughoutthe winter when other marine tetrapods apparently cannot? Bothspecies have similar adaptations for exploitation of the deep-waterhabitat, forage on the same species, and routinely make longand deep dives. Yet, despite these similarities, there is probablylittle trophic overlap between the adults of both species dueto geographical and seasonal differences in habitat use. Forexample, during the winter months while female emperor penguinsare ranging widely in the pack ice, adult seals are foragingand fattening for the upcoming summer fast, literally beneaththe feet of the male penguins. However, there is more extensiveoverlap between juvenile seals and adult penguins, and shiftsin prey abundance and/or distribution would likely affect thesetwo groups similarly. In contrast, juvenile penguins appearto avoid inter- and intra- specific competition by leaving theRoss Sea once they molt.     

Digging Behaviour while Foraging by the European Badger,Meles meles,in a Mediterranean Habitat

Digging behaviour while foraging by the European badger (Meles meles) was studied in the Maremma Natural Park, central Italy, during late winter and spring of 1984 and 1985. Badgers digging for Lamellicornia larvae were successful in approximately 77% of the observed digging attempts. Digging success was similar among individuals and months and was positively correlated with the depth of the hole. A change of position while digging was associated with successful digging. Badgers always started their digging activity using only a foreleg at a constant rate and at a later stage used both forelegs alternately at a higher rate. The adoption of such technique is regarded as adaptive since it maximizes the chance of capturing the prey while reducing the energy expenditure due to digging. The reduced availability of those resources to be collected on the ground surface during late winter and spring is suggested as the possible cause of the energetically expensive digging behaviour.     

Visual and Olfactory Responses of Seven Butterfly Species During Foraging

Foraging responses of seven butterfly species were determined for flower models that differed in color, size, and depth of artificial corolla. We measured frequency of visits to flowers of various colors (red, orange, yellow, purple, and white) with or without the application of honey water to flower models. We found that the relative strength of butterfly response to visual versus olfactory cues differed among butterfly species. We suggest that the seven butterfly species tested exhibit four different patterns in how visual and olfactory cues were combined as determinants of foraging importance: (1) vision was given priority over olfaction (in Cethosia cyane and Danaus chrysippus); (2) olfaction was given priority over vision (Cethosia biblis, Idea leuconoe, and Tirumala limniace); (3) olfaction and vision were equally important (Catopsilia pomona); and (4) only olfaction was used (e.g., Danaus genutia, which was not sensitive to the five colors tested but very sensitive to the smell of honey in our experiments). In tests with flower models of different sizes, the visitation frequency of C. cyane, I. leuconoe, and D. chrysippus increased with increasing corolla diameter, provided flowers were sprayed with honey water. C. cyane and D. chrysippus showed this trend because of their strong dependence on visual cues. In contrast, I. leuconoe with its large body size preferred larger flowers, it could be that butterflies need more nectar to support its large body size. Catopsilia pomona tended to visit large and middle-sized flowers because it used both vision and odor to detect food, large or middle-sized flowers could have more vision and odor stimulation than small flowers for foraging butterfly. The other three butterfly species did not show that trend because of lack of dependence on visual cues. There was no correlation between visitation frequency and corolla depth within particular butterfly species. In conclusion, the foraging strategies of butterflies are not only mainly determined by the weights given to visual and olfactory cues, but also affected by body size.     

Predicting Species Distributions Using Record Centre Data: Multi-Scale Modelling of Habitat Suitability for Bat Roosts

Conservation increasingly operates at the landscape scale. For this to be effective, we need landscape scale information on species distributions and the environmental factors that underpin them. Species records are becoming increasingly available via data centres and online portals, but they are often patchy and biased. We demonstrate how such data can yield useful habitat suitability models, using bat roost records as an example. We analysed the effects of environmental variables at eight spatial scales (500 m – 6 km) on roost selection by eight bat species (Pipistrellus pipistrellus, P. pygmaeus, Nyctalus noctula, Myotis mystacinus, M. brandtii, M. nattereri, M. daubentonii, and Plecotus auritus) using the presence-only modelling software MaxEnt. Modelling was carried out on a selection of 418 data centre roost records from the Lake District National Park, UK. Target group pseudoabsences were selected to reduce the impact of sampling bias. Multi-scale models, combining variables measured at their best performing spatial scales, were used to predict roosting habitat suitability, yielding models with useful predictive abilities. Small areas of deciduous woodland consistently increased roosting habitat suitability, but other habitat associations varied between species and scales. Pipistrellus were positively related to built environments at small scales, and depended on large-scale woodland availability. The other, more specialist, species were highly sensitive to human-altered landscapes, avoiding even small rural towns. The strength of many relationships at large scales suggests that bats are sensitive to habitat modifications far from the roost itself. The fine resolution, large extent maps will aid targeted decision-making by conservationists and planners. We have made available an ArcGIS toolbox that automates the production of multi-scale variables, to facilitate the application of our methods to other taxa and locations. Habitat suitability modelling has the potential to become a standard tool for supporting landscape-scale decision-making as relevant data and open source, user-friendly, and peer-reviewed software become widely available.     

New Method for Estimating Bacterial Cell Abundances in Natural Samples by Use of Sublimation

We have developed a new method based on the sublimation of adenine from Escherichia coli to estimate bacterial cell counts in natural samples. To demonstrate this technique, several types of natural samples, including beach sand, seawater, deep-sea sediment, and two soil samples from the Atacama Desert, were heated to a temperature of 500°C for several seconds under reduced pressure. The sublimate was collected on a cold finger, and the amount of adenine released from the samples was then determined by high-performance liquid chromatography with UV absorbance detection. Based on the total amount of adenine recovered from DNA and RNA in these samples, we estimated bacterial cell counts ranging from ~10⁵ to 10⁹ E. coli cell equivalents per gram. For most of these samples, the sublimation-based cell counts were in agreement with total bacterial counts obtained by traditional DAPI (4,6-diamidino-2-phenylindole) staining.     

Population Structure of Morphological Traits in Clarkia Dudleyana I. Comparison of F(st) between Allozymes and Morphological Traits

The X-linked white gene when transposed to autosomes retains only partial dosage compensation. One copy of the gene in males expresses more than one copy but less than two copies in females. When inserted in ectopic X chromosome sites, the mini-white gene of the CaspeR vector can be fully dosage compensated and can even achieve hyperdosage compensation, meaning that one copy in males gives more expression than two copies in females. As sequences are removed gradually from the 5' end of the gene, we observe a progressive transition from hyperdosage compensation to full dosage compensation to partial dosage compensation. When the deletion reaches -17, the gene can no longer dosage compensate fully even on the X chromosome. A deletion reaching +173, 4 bp preceeding the AUG initiation codon, further reduces dosage compensation both on the X chromosome and on autosomes. This truncated gene can still partially dosage compensate on autosomes, indicating the presence of dosage compensation determinants in the protein coding region. We conclude that full dosage compensation requires an X chromosome environment and that the white gene contains multiple dosage-compensation determinants, some near the promoter and some in the coding region.     

Analysis of Genetic Variation in Natural Populations of Medicago truncatula of Southern Tunisian Ecological Areas, Using Morphological Traits and SSR Markers

We used 19 quantitative traits and 14 microsatellite markers (SSRs) to analyze the genetic variation in four natural populations of the model legume Medicago truncatula sampled in southern Tunisia. The greatest genetic variation of quantitative traits and molecular markers occurred within populations (>71%). In contrast to quantitative population differentiation (Q _ST ?=?0.09), a high level of molecular differentiation (F _ST ?=?0.23) was found among populations. The majority of quantitative traits exhibited Q _ST values significantly less than F _ST values, suggesting that selection may be acting to suppress differentiation for these traits. There was no significant correlation between genetic variation of quantitative traits and molecular markers within populations. On the other hand, significant correlations were found between measured quantitative characters and the site-of-origin environmental factors. The eco-geographical factors with the greatest influence on the variation of measured traits among populations were altitude, followed by soil texture, assimilated phosphorus (P₂O₅) and organic matter. Nevertheless, there were no consistent patterns of associations between gene diversity (He) and eco-geographical factors.     

Predicting the Potential Future Distribution of Four Tree Species in Ohio Using Current Habitat Availability and Climatic Forcing

Weinvestigated the effect of habitat loss on the ability of trees to shift in distribution across a landscape dominated by agriculture. The potential distribution shifts of four tree species (Diospyros virginiana, Oxydendron arboreum, Pinus virginiana, Quercus falcata var. falcata) whose northern distribution limits fall in the southern third of Ohio were used to assess possible distribution shift scenarios as a result of global warming. Our predictions derive from the results of simulations using (a) forest inventory based estimates of current distribution and abundance of target species; (b) a satellite-based estimate of forest habitat availability; and (c) a tree migration model (SHIFT). The current distribution and abundance of trees was estimated using USDA Forest Service's Forest Inventory Analysis data and distribution maps from the late 1960s; pre-European settlement forest–nonforest maps were used to represent the fully forested condition for calibration and comparison. Habitat-availability estimates in Ohio were estimated using classified Landsat Thematic Mapper (TM) data from 1994. Tree abundance, forest availability and migration were modeled using a 1-km² pixel size. Forest availability was estimated as the proportion of forested TM pixels within each cell. The probability of a migrating species colonizing an unoccupied cell is modeled as a function of forest availability and distance to occupied cells. The results of the migration models suggest that the species studied are capable of colonizing virtually any forested location within Ohio over the next 100 years if climatic controls over the current distribution that may currently inhibit northward movement are relaxed. The contiguous distribution of these species, however, is not likely to shift more than 10 km during the next century regardless of the magnitude of the climate change. Examining the sensitivity of our simulations by varying critical model attributes, we found that whereas the variables controlling the amount of long-distance dispersal have strong effects on migration rates in the fully forested 1800 situation, they have significantly lesser effects on projections of future migration into highly fragmented forests. The low forest availability that characterizes much of the current Ohio landscape, along with the low likelihood of long distance dispersal, result in potential distribution shifts that are concentrated within the principally forested corridors in southeastern Ohio. We propose that in contrast to the past, future tree migrations are likely to be spatially and temporally correlated as a result of large climatic forcing and channelization through limited regions of available habitat. With respect to the management of biodiversity, this result suggests that it may be very difficult to discern plant migrations of native forest species owing to exceedingly slow rates of movement. Received 19 September 2000; Accepted 2 March 2001.     

Habitat Characteristics and Lemur Species Richness in Madagascar1

In the extant lemur communities of Madagascar the number of lemur species increases with increasing number of tree species. In forests with few tree species lemurs use patches with higher number of tree species than average. However, in forest plots with high number of tree species, lemurs stay in places with lower number of tree species than average. At low tree species diversity a minimum number of different tree species seems to be required within the animals' home range to assure year-round food availability. At high tree species diversity tree species essential for survival might be diluted by resources which are of no use for lemurs, thus increasing energetic expenses for traveling between suitable patches. According to the present analyses, structural diversity is of subordinate importance to the number of tree species as a correlate of lemur species richness. Within limits of disturbance intensity and on a small geographic scale, disturbances increase forest productivity. Lemurs reach higher species numbers and population densities in slightly disturbed areas compared with undisturbed sites. This peaked curve of the number of lemur species over disturbance, however, may not only be a consequence of “resource dilution” in undisturbed sites and higher food abundance in slightly disturbed areas, but also a consequence of selective extinction of lemur species which were unable to cope with the disturbance regime exaggerated by human interference over the last few hundred or thousand years.     

Long-Term Changes in Species Composition and Relative Abundances of Sharks at a Provisioning Site

Diving with sharks, often in combination with food baiting/provisioning, has become an important product of today’s recreational dive industry. Whereas the effects baiting/provisioning has on the behaviour and abundance of individual shark species are starting to become known, there is an almost complete lack of equivalent data from multi-species shark diving sites. In this study, changes in species composition and relative abundances were determined at the Shark Reef Marine Reserve, a multi-species shark feeding site in Fiji. Using direct observation sampling methods, eight species of sharks (bull shark Carcharhinus leucas, grey reef shark Carcharhinus amblyrhynchos, whitetip reef shark Triaenodon obesus, blacktip reef shark Carcharhinus melanopterus, tawny nurse shark Nebrius ferrugineus, silvertip shark Carcharhinus albimarginatus, sicklefin lemon shark Negaprion acutidens, and tiger shark Galeocerdo cuvier) displayed inter-annual site fidelity between 2003 and 2012. Encounter rates and/or relative abundances of some species changed over time, overall resulting in more individuals (mostly C. leucas) of fewer species being encountered on average on shark feeding dives at the end of the study period. Differences in shark community composition between the years 2004–2006 and 2007–2012 were evident, mostly because N. ferrugineus, C. albimarginatus and N. acutidens were much more abundant in 2004–2006 and very rare in the period of 2007–2012. Two explanations are offered for the observed changes in relative abundances over time, namely inter-specific interactions and operator-specific feeding protocols. Both, possibly in combination, are suggested to be important determinants of species composition and encounter rates, and relative abundances at this shark provisioning site in Fiji. This study, which includes the most species from a spatially confined shark provisioning site to date, suggests that long-term provisioning may result in competitive exclusion among shark species.     

The Importance of Species Traits for Species Distribution on Oceanic Islands

Understanding species'' ability to colonize new habitats is a key knowledge allowing us to predict species'' survival in the changing landscapes. However, most studies exploring this topic observe distribution of species in landscapes which are under strong human influence being fragmented only recently and ignore the fact that the species distribution in these landscapes is far from equilibrium. Oceanic islands seem more appropriate systems for studying the relationship between species traits and its distribution as they are fragmented without human contribution and as they remained unchanged for a long evolutionary time. In our study we compared the values of dispersal as well as persistence traits among 18 species pairs from the Canary Islands differing in their distribution within the archipelago. The data were analyzed both with and without phylogenetic correction. The results demonstrate that no dispersal trait alone can explain the distribution of the species in the system. They, however, also suggest that species with better dispersal compared to their close relatives are better colonizers. Similarly, abundance of species in the archipelago seems to be an important predictor of species colonization ability only when comparing closely related species. This implies that analyses including phylogenetic correction may provide different insights than analyses without such a correction and both types of analyses should be combined to understand the importance of various plant traits for species colonization ability.