Assessing detectability for monitoring of rare species: a case study of the cobblestone tiger beetle (Cicindela marginipennis Dejean)

Interpreting data on distribution or population trends may be difficult unless detection probability is accounted for. We wished to determine the detectability of the rare and patchily distributed cobblestone tiger beetle (Cicindela marginipennis) along the upper Genesee River in western New York for development of a monitoring strategy. We used occupancy surveys and distance sampling to examine two types of detectability. The first type was site-level detectability: the probability of detecting a single cobblestone tiger beetle on an occupied cobble bar, calculated using program PRESENCE. The second type was individual-level detectability: the probability of detecting an individual cobblestone tiger beetle in a population on a single cobble bar, calculated using program DISTANCE. Our occupancy surveys consisted of collecting presence and absence data on cobble bars along the Genesee River; these showed a relatively narrow range of site-level detection probabilities (0.60?C0.68) for cobblestone tiger beetles in 2008 and 2009. Three visits were necessary to detect cobblestone tiger beetles on 90% of occupied cobble bars. Individual cobblestone tiger beetles were detectable one-half of the time (0.50) in our surveys. It is important for ecologists to distinguish between the two kinds of detectability, as monitoring implications could differ substantially depending on which is calculated. Our monitoring recommendations include (1) continuing occupancy surveys with at least three visits to each cobble bar; (2) conducting occupancy surveys between 10:00 and 17:00 on warm sunny days in mid-July and mid-August; and (3) conducting surveys at three- to five-year intervals depending on the study objective.     

Extinction risks in metapopulations of a beetle inhabiting hollow trees predicted from time series

Ancient and dead trees are declining habitats harbouring many threatened species. These habitats are naturally patchy, and inhabiting species might exhibit metapopulation dynamics at a small spatial scale. In this study, the demography and metapopulation dynamics was analysed for Osmoderma eremita , which is an endangered beetle species associated with tree hollows in Europe. Extinction risks of O. eremita populations were predicted using Monte Carlo simulations based on time series of population assessments. Predicted occurrence patterns were consistent with field observations from an area with many small stands in which the populations are believed to have been more or less isolated from each other during the last 150–200 yr. Population growth was found to be density dependent. Carrying capacity was proportional to the volume of wood mould (i.e. loose material of dead wood in the tree hollows), which varied widely between hollow trees. This generates large differences in local extinction risks between hollow trees. The predicted metapopulation extinction risk was much higher if the habitat dynamics (formation, gradual increase and deterioration of tree hollows) were taken into consideration than in predictions yielded by models in which the amount of wood mould was assumed to be constant over time. Thus, this system has features from both mainland-island metapopulations and habitat-tracking metapopulations, and is rather far from a classic metapopulation. For the long-term persistence of the species in hollow trees, the habitat dynamics seem to be more important than demographic processes. Since the formation and deterioration of suitable tree are partly stochastic processes, there is a considerable extinction risk for many O. eremita populations, because they mainly rely on only one or a few trees with large amounts of wood mould.     

Habitat of Osmoderma eremita Scop. (Coleoptera: Scarabaeidae), a beetle living in hollow trees

The habitat of Osmoderma eremita, a vulnerable species in Europe restricted to tree cavities, was examined in southeastern Sweden. The occurrence of O. eremita larvae and fragments, larval frass and imagines were investigated in 135, 72 and 21 living oak trees with wood mould cavities, respectively. Living individuals and fragments were only found in hollows with frass. The correlation between different characteristics of the oaks and the occurrence of the beetle were examined by building multi-variate models with logistic regression. The frequency of O. eremita is higher in hollows with openings directed towards the sun (S or W) and in cavities with large amounts of wood mould. In one area the frequency was higher in trees which stand in an open or half open surrounding. The tendency to prefer sun exposed sites implies that the forestation of oak meadows, caused by cessation of traditional management, might be detrimental to the species.     

Application of detectability in the use of indicator species: A case study with birds

The use of indicator species is popular in ecological monitoring and management. In recent years, new methods to improve the quality and application of indicator data have been proposed and developed. Here we propose the use of detection probability in the selection and application of indicator species. We evaluated environmental and observer factors believed to affect detection of potential species. Observer effects were the most evident factor and may necessitate the greatest consideration in the use of indicator species. Our results call attention to the fact that raw counts are far from accurate and that the use of detection probability can and should be incorporated into sampling protocols, species selection, and the allocation of effort for projects that use indicator species as part of monitoring and management programs.     

Patch dynamics and metapopulation theory: the case of successional species

We present a mathematical framework that combines extinction-colonization dynamics with the dynamics of patch succession. We draw an analogy between the epidemiological categorization of individuals (infected, susceptible, latent and resistant) and the patch structure of a spatially heterogeneous landscape (occupied-suitable, empty-suitable, occupied-unsuitable and empty-unsuitable). This approach allows one to consider life-history attributes that influence persistence in patchy environments (e.g., longevity, colonization ability) in concert with extrinsic processes (e.g., disturbances, succession) that lead to spatial heterogeneity in patch suitability. It also allows the incorporation of seed banks and other dormant life forms, thus broadening patch occupancy dynamics to include sink habitats. We use the model to investigate how equilibrium patch occupancy is influenced by four critical parameters: colonization rate, extinction rate, disturbance frequency and the rate of habitat succession. This analysis leads to general predictions about how the temporal scaling of patch succession and extinction-colonization dynamics influences long-term persistence. We apply the model to herbaceous, early-successional species that inhabit open patches created by periodic disturbances. We predict the minimum disturbance frequency required for viable management of such species in the Florida scrub ecosystem.     

Modelling hollow organs for impact conditions: a simplified case study

This study compares the performances of three numerical approaches [Lagrangian (LAG), arbitrary Lagrangian–Eulerian (ALE) and control volume (CV)] for modelling the response of a short cylindrical pipe representing a portion of the intestines subjected to large and rapid compressions. While not being able to simulate sustained fluid flow, the LAG approach provided similar results as the ALE for moderate levels of compression. However, it was the stiffest approach for larger levels and had numerical issues for extreme compressions. While the ALE did not have these issues, its computing cost was very high, which would be problematic for large models. The CV approach had the lowest computing cost and seemed promising for larger compressions. However, its response was the softest and further investigations are needed to define its dependency to modelling parameters.     

Air sampling of its pheromone to monitor the occurrence of Osmoderma eremita, a threatened beetle inhabiting hollow trees

Osmoderma eremita is a threatened scarab beetle living in the hollows of old deciduous trees and is regarded as an umbrella species of the beetle fauna associated with this habitat. Several methods like pitfall trapping and wood mould sampling have been used to monitor the occurrence of O. eremita, but these methods cannot be applied for trees with certain characteristics. Recently, (R)-(+)--decalactone was identified as a male-produced sex pheromone of the species. Here, we show that -decalactone can be detected in hollow trees by air sampling and that the presence of the compound is strongly correlated with the occurrence of living male beetles in the same trees. Air was sampled from tree cavities and extracts analysed using gas chromatography–and mass spectrometry. There was a 89% match between the detection of -decalactone in extracts and the occurrence of male O. eremita±2 days from the sampling event. In the absence of males, samples never contained -decalactone, and the presence of this compound in a tree cavity appears to be a good predictor of O. eremita occupancy. Air sampling can be a useful complement to other methods when trying to detect as many trees housing this beetle as possible, which is crucial when estimating populations sizes and developing conservation strategies for this species.     

Ambrosia beetle (Coleoptera: Scolytidae) species, flight, and attack on living eastern cottonwood trees

In spring 2002, ambrosia beetles (Coleoptera: Scolytidae) infested an intensively managed 22-ha tree plantation on the upper coastal plain of South Carolina. Nearly 3,500 scolytids representing 28 species were captured in ethanol-baited traps from 18 June 2002 to 18 April 2004. More than 88% of total captures were exotic species. Five species [Dryoxylon onoharaensum (Murayama), Euwallacea validus (Eichhoff), Pseudopityophthorus minutissimus (Zimmermann), Xyleborus atratus Eichhoff, and Xyleborus impressus Eichhoff]) were collected in South Carolina for the first time. Of four tree species in the plantation, eastern cottonwood, Populus deltoides Bartram, was the only one attacked, with nearly 40% of the trees sustaining ambrosia beetle damage. Clone ST66 sustained more damage than clone S7C15. ST66 trees receiving fertilization were attacked more frequently than trees receiving irrigation, irrigation + fertilization, or controls, although the number of S7C15 trees attacked did not differ among treatments. The study location is near major shipping ports; our results demonstrate the necessity for intensive monitoring programs to determine the arrival, spread, ecology, and impact of exotic scolytids.     

Effects of exotic invasive trees on nitrogen cycling: a case study in Central Spain

We assess the hypothesis that rates of nitrogen transformations in the soil are altered upon replacement of native by exotic trees, differing in litter properties. Ailanthus altissima and Robinia pseudoacacia, two common exotic trees naturalized in the Iberian Peninsula, were compared with the native trees Ulmus minor and Fraxinus angustifolia, respectively. Naturally senesced leaves of each species were collected and C:N ratio, N and lignin content assessed. We prepared 64 litter bags per species and left them to decompose, below the canopy of the same species and below the canopy of the paired species. Dry mass, N concentration and N pool of the remaining litter were assessed after 5 and 7 months. Soil samples were collected three times during the experiment to assess soil moisture, organic matter, pH, potential mineralization rates and mineral N pools. Mineral N availability was assessed three times in the field by using ion-exchange resin-impregnated membranes. Ailanthus litter decomposed faster than Ulmus litter, probably due to the higher toughness of the latter. In spite of its high N content, Robinia litter decomposed slower than Fraxinus one, probably due to its high lignin content. In both cases, litter decomposition was faster below the exotic than the native canopies. The release of N per unit of initial litter mass was higher under both invaded situations (Ailanthus below Ailanthus and Robinia below Robinia) than under the native ones. However, soils collected below native and exotic trees neither differed in potential N mineralization rate nor in mineral N. This may be attributed to a quick plant uptake of released N and/or to a high organic matter accumulation in the soil previous to invasion that can exert a tighter control on soil N transformations than the current exotic litter.     

Modelling floristic species richness on a regional scale: a case study in Switzerland

In this paper a multivariate linear regression model is proposed for predicting and mapping regional species richness in areas below the timberline according to environmental variables. The data used in setting up the model were derived from a floristic inventory. Using a stepwise regression technique, five environmental variables were found to explain 48.9% of the variability in the total number of plant species: namely temperature range, proximity to a big river or lake, threshold of minimum annual precipitation, amount of calcareous rock outcrops and number of soil types. A considerable part of the unexplained variability is thought to have been influenced by variations in the quality of the botanical inventory. These results show the importance of systematic floristic sampling in addition to conventional inventories when using floristic data as a basis in nature conservation. Nevertheless it is still possible to interpret the resulting diversity patterns ecologically. Regional species richness in Switzerland appears to be a function of: (i) environmental heterogeneity; (ii) threshold values of minimum precipitation; and (iii) presence of calcareous rock outcrops. According to similar studies, environmental heterogeneity was the strongest determinant of total species richness. In contrast to some studies, high productivity decreased the number of species. Furthermore, the implications of this work for climate change scenarios are discussed.     

Discordance of species trees with their most likely gene trees: the case of five taxa

Under a coalescent model for within-species evolution, gene trees may differ from species trees to such an extent that the gene tree topology most likely to evolve along the branches of a species tree can disagree with the species tree topology. Gene tree topologies that are more likely to be produced than the topology that matches that of the species tree are termed anomalous, and the region of branch-length space that gives rise to anomalous gene trees (AGTs) is the anomaly zone. We examine the occurrence of anomalous gene trees for the case of five taxa, the smallest number of taxa for which every species tree topology has a nonempty anomaly zone. Considering all sets of branch lengths that give rise to anomalous gene trees, the largest value possible for the smallest branch length in the species tree is greater in the five-taxon case (0.1934 coalescent time units) than in the previously studied case of four taxa (0.1568). The five-taxon case demonstrates the existence of three phenomena that do not occur in the four-taxon case. First, anomalous gene trees can have the same unlabeled topology as the species tree. Second, the anomaly zone does not necessarily enclose a ball centered at the origin in branch-length space, in which all branches are short. Third, as a branch length increases, it is possible for the number of AGTs to increase rather than decrease or remain constant. These results, which help to describe how the properties of anomalous gene trees increase in complexity as the number of taxa increases, will be useful in formulating strategies for evading the problem of anomalous gene trees during species tree inference from multilocus data.     

The maintenance of nucleocytoplasmic polymorphism in a metapopulation: the case of gynodioecy

In gynodioecious species, gender is generally determined by epistatic interactions between cytoplasmic and nuclear loci. However, theoretical studies suggest that, for a joint polymorphism at both cytoplasmic and nuclear loci to be maintained in a panmictic population, selection must act differently on the various genotypes that determine the same gender. Here we show that, in a metapopulation with local extinction and restricted gene flow, nucleocytoplasmic polymorphism can be maintained without these differences. We use deterministic simulations. We assume that gene flow occurred only at recolonization. Founder effects create genetic variance between populations in the metapopulation, and local population growth is faster when the local frequency of females is high. Group selection phenomena are involved in the maintenance of the joint polymorphism in the metapopulation. The frequency of females in the metapopulation at equilibrium is higher than in a panmictic population with the same genetic system. However, these conclusions hold only if nuclear alleles restoring male fertility are dominant.     

Heterozygosity-fitness correlations in a bottlenecked island species: a case study on the Seychelles warbler

We used capture-mark-recapture models to investigate the effects of both individual and parental heterozygosity, measured at microsatellite loci on the survival of Seychelles warblers (Acrocephalus sechellensis), an endemic island species which went through a severe population bottleneck in the middle of the last century. We found that an individual's survival was not correlated with multilocus heterozygosity, or with heterozygosity at any specific locus. However, maternal, but not paternal, multilocus heterozygosity was positively associated with offspring survival, but only in years with low survival probabilities. A nestling cross-fostering experiment showed that this was a direct maternal effect as there was an effect of the genetic mother's, but not of the social mother's, heterozygosity. Heterozygosity-fitness correlations at microsatellite markers were generally assumed to reflect genome-wide effects. Although this might be true in partially inbred populations, such correlations may also arise as a result of local effects with specific markers being closely linked to genes which determine fitness. However, heterozygosity at the individual microsatellite loci was not correlated and therefore does not seem to reflect genome-wide heterozygosity. This suggests that even in a small bottlenecked population, heterozygosity-fitness correlations may not be caused by genome-wide effects. Support for the local effects hypothesis was also equivocal; although three specific loci were associated with offspring survival, including all single-locus heterozygosities as independent predictors for the variation in survival was not supported by the data. Furthermore, in contrast to the local effects hypothesis, the loci which contributed most to the heterozygosity-survival relationship were not more polymorphic than the other loci. This study highlights the difficulties in distinguishing between the two hypotheses.     

Sampling effort and species richness assessment: a case study on Brazilian spiders

The knowledge on the geographical distribution of species is essential for building biogeographical and macroecological hypotheses. However, information on this regard is not distributed uniformly in space and usually come from biased sampling. The aim of this study is to quantify the influence of spatial distribution of sampling effort on the assessment of spider species richness in Brazil. We used a database of spider distribution records in Brazil, based on the taxonomic and biodiversity survey literature. The results show that the Atlantic Forest was better sampled and had the highest spider species richness among the Brazilian biomes. The Amazon, though having large collecting gaps and high concentration of records around major cities and rivers, showed the second highest number of species. The Pampa had a large number of records, but these are concentrated near a major city in the transition zone with the Atlantic Forest. The Cerrado, Caatinga and Pantanal had shown to be poorly sampled and, consequently, were among the lesser known biomes regarding the spider fauna. A linear regression analysis showed that the spider species richness in Brazil is strongly correlated to the number of records. However, we have identified areas potentially richest in species, which strongly deviate from the predicted by our analyses. Our results show that it is possible to access the spatial variation in species richness, as long as the variation in sampling effort is taken into account.     

遮荫对13种盆栽棕榈植物生长的影响

研究13种盆栽棕榈植物在不同遮荫处理条件下的生长、叶片叶绿素含量、含水量及比叶重的变化,并通过系统聚类分析及主分量分析,将13种棕榈植物的耐阴性分为三类,其中缨络椰子、散尾葵和小琼棕较耐阴,国王椰子、假槟榔、金帝葵和美丽针葵耐阴性较差,短穗鱼尾葵、袖珍椰子、雪佛里椰子、穗花轴榈、蒲葵和棕竹等棕榈植物耐阴性居中.     

Rooting phylogenetic trees with distant outgroups: a case study from the commelinoid monocots

Phylogenetic rooting experiments demonstrate that two chloroplast genes from commelinoid monocot taxa that represent the closest living relatives of the pickerelweed family, Pontederiaceae, retain measurable signals regarding the position of that family's root. The rooting preferences of the chloroplast sequences were compared with those for artificial sequences that correspond to outgroups so divergent that their signal has been lost completely. These random sequences prefer the three longest branches in the unrooted ingroup topology and do not preferentially root on the branches favored by real outgroup sequences. However, the rooting behavior of the artificial sequences is not a simple function of branch length. The random outgroups preferentially root on long terminal ingroup branches, but many ingroup branches comparable in length to those favored by random sequences attract no or few hits. Nonterminal ingroup branches are generally avoided, regardless of their length. Comparisons of the ease of forcing sequences onto suboptimal roots indicate that real outgroups require a substantially greater rooting penalty than random outgroups for around half of the least-parsimonious candidate roots. Although this supports the existence of nonrandomized signal in the real outgroups, it also indicates that there is little power to choose among the optimal and nearly optimal rooting possibilities. A likelihood-based test rejects the hypothesis that all rootings of the subtree using real outgroup sequences are equally good explanations of the data and also eliminates around half of the least optimal candidate roots. Adding genes or outgroups can improve the ability to discriminate among different root locations. Rooting discriminatory power is shown to be stronger, in general, for more closely related outgroups and is highly correlated among different real outgroups, genes, and optimality criteria.     

Positive and negative density-dependence and boom-bust dynamics in enemy-victim populations: a mountain pine beetle case study

Negative density-dependent population regulation in exploitative species is well studied. Positive density-dependence can arise if exploiters must cooperate to obtain access to well-defended resources. Most studies, however, focus on the first type of density-dependence at the expense of the other. Using a parasitoid-host model, we explored how positive density-dependence driven by host defenses in combination with negative density-dependence due to competition for resources impact transient population dynamics. Inspired by interactions between the mountain pine beetle and its pine hosts, we formulated a model of enemy-victim interactions in discrete-time in which the victim is capable of deadly self-defense against exploitation. We fitted the model to data and then analyzed its non-equilibrium dynamics to determine what conditions promote boom-bust dynamics. When present together, strong Allee effects and overcompensating competition for resources among exploiters can cause their populations to irrupt and then crash even though many exploitable resources remain. Accelerating population irruptions followed by precipitous collapse occur for realistic parameter values of our model of mountain pine beetle dynamics. Insect dynamics are often dominated by sudden irruptions and collapses on short time scales. Population crashes in exploitative species often happen enigmatically even when exploitable resources are not depleted. Herein, we argue that strong Allee effects in combination with overcompensation provide a plausible explanation for these boom-bust dynamics in some species.