Linking occupancy surveys with habitat characteristics to estimate abundance and distribution in an endangered cryptic bird

Accurate estimates of the distribution and abundance of endangered species are crucial to determine their status and plan recovery options, but such estimates are often difficult to obtain for species with low detection probabilities or that occur in inaccessible habitats. The Puaiohi (Myadestes palmeri) is a cryptic species endemic to Kaua?i, Hawai‘i, and restricted to high elevation ravines that are largely inaccessible. To improve current population estimates, we developed an approach to model distribution and abundance of Puaiohi across their range by linking occupancy surveys to habitat characteristics, territory density, and landscape attributes. Occupancy per station ranged from 0.17 to 0.82, and was best predicted by the number and vertical extent of cliffs, cliff slope, stream width, and elevation. To link occupancy estimates with abundance, we used territory mapping data to estimate the average number of territories per survey station (0.44 and 0.66 territories per station in low and high occupancy streams, respectively), and the average number of individuals per territory (1.9). We then modeled Puaiohi occupancy as a function of two remote-sensed measures of habitat (stream sinuosity and elevation) to predict occupancy across its entire range. We combined predicted occupancy with estimates of birds per station to produce a global population estimate of 494 (95% CI 414–580) individuals. Our approach is a model for using multiple independent sources of information to accurately track population trends, and we discuss future directions for modeling abundance of this, and other, rare species.     

Multiyear fate of a 15N tracer in a mixed deciduous forest: retention,redistribution, and differences by mycorrhizal association

The impact of atmospheric nitrogen deposition on forest ecosystems depends in large part on its fate. Past tracer studies show that litter and soils dominate the short‐term fate of added ¹⁵N, yet few have examined its longer term dynamics or differences among forest types. This study examined the fate of a ¹⁵N‐ tracer over 5–6 years in a mixed deciduous stand that was evenly composed of trees with ectomycorrhizal and arbuscular mycorrhizal associations. The tracer was expected to slowly mineralize from its main initial fate in litter and surface soil, with some ¹⁵N moving to trees, some to deeper soil, and some net losses. Recovery of added ¹⁵N in trees and litterfall totaled 11.3% both 1 and 5–6 years after the tracer addition, as ¹⁵N redistributed from fine and especially coarse roots into cumulative litterfall and small accumulations in woody tissues. Estimates of potential carbon sequestration from tree ¹⁵N recovery amounted to 12–14 kg C per kg of N deposition. Tree ¹⁵N acquisition occurred within the first year after the tracer addition, with no subsequent additional net transfer of ¹⁵N from detrital to plant pools. In both years, ectomycorrhizal trees gained 50% more of the tracer than did trees with arbuscular mycorrhizae. Much of the ¹⁵N recovered in wood occurred in tree rings formed prior to the ¹⁵N addition, demonstrating the mobility of N in wood. Tracer recovery rapidly decreased over time in surface litter material and accumulated in both shallow and deep soil, perhaps through mixing by earthworms. Overall, results showed redistribution of tracer ¹⁵N through trees and surface soils without any losses, as whole‐ecosystem recovery remained constant between 1 and 5–6 years at 70% of the ¹⁵N addition. These results demonstrate the persistent ecosystem retention of N deposition even as it redistributes, without additional plant uptake over this timescale.     

Generation interval contraction and epidemic data analysis

The generation interval is the time between the infection time of an infected person and the infection time of his or her infector. Probability density functions for generation intervals have been an important input for epidemic models and epidemic data analysis. In this paper, we specify a general stochastic SIR epidemic model and prove that the mean generation interval decreases when susceptible persons are at risk of infectious contact from multiple sources. The intuition behind this is that when a susceptible person has multiple potential infectors, there is a "race" to infect him or her in which only the first infectious contact leads to infection. In an epidemic, the mean generation interval contracts as the prevalence of infection increases. We call this global competition among potential infectors. When there is rapid transmission within clusters of contacts, generation interval contraction can be caused by a high local prevalence of infection even when the global prevalence is low. We call this local competition among potential infectors. Using simulations, we illustrate both types of competition. Finally, we show that hazards of infectious contact can be used instead of generation intervals to estimate the time course of the effective reproductive number in an epidemic. This approach leads naturally to partial likelihoods for epidemic data that are very similar to those that arise in survival analysis, opening a promising avenue of methodological research in infectious disease epidemiology.     

Prevalence and differential host-specificity of two avian blood parasite genera in the Australo-Papuan region

The degree to which widespread avian blood parasites in the genera Plasmodium and Haemoproteus pose a threat to novel hosts depends in part on the degree to which they are constrained to a particular host or host family. We examined the host distribution and host-specificity of these parasites in birds from two relatively understudied and isolated locations: Australia and Papua New Guinea. Using polymerase chain reaction (PCR), we detected infection in 69 of 105 species, representing 44% of individuals surveyed (n = 428). Across host families, prevalence of Haemoproteus ranged from 13% (Acanthizidae) to 56% (Petroicidae) while prevalence of Plasmodium ranged from 3% (Petroicidae) to 47% (Ptilonorhynchidae). We recovered 78 unique mitochondrial lineages from 155 sequences. Related lineages of Haemoproteus were more likely to derive from the same host family than predicted by chance at shallow (average LogDet genetic distance = 0, n = 12, P = 0.001) and greater depths (average distance = 0.014, n = 11, P < 0.001) within the parasite phylogeny. Within two major Haemoproteus subclades identified in a maximum likelihood phylogeny, host-specificity was evident up to parasite genetic distances of 0.029 and 0.007 based on logistic regression. We found no significant host relationship among lineages of Plasmodium by any method of analysis. These results support previous evidence of strong host-family specificity in Haemoproteus and suggest that lineages of Plasmodium are more likely to form evolutionarily-stable associations with novel hosts.     

Plant ecology of tropical and subtropical karst ecosystems

Substantial areas of tropical forests, including those within nine tropical biodiversity hotspots, contain karst landscapes that have developed on soluble carbonate rocks. Here, we review how the ecology of karst forest trees is influenced by hydrological, edaphic, and topographic factors that exhibit fine spatial heterogeneity. Comparative analysis of drought tolerance traits including wood density contributes to the assessment of whether karst tree species are more drought‐tolerant compared to non‐karst trees. Although karst ecosystems are generally considered to have low phosphorus availability, foliar nitrogen‐to‐phosphorus ratios exhibit wide variation across karst regions without a clear difference from non‐karst ecosystems. According to the analyses of leaf phenology, stem water storage, and isotopic signatures from xylem sap, water use strategies of karst trees can be classified into five types: (a) soil water dependent, (b) epikarst water dependent (mainly use water stored in fine pores and gaps within the epikarst rock during the dry season), (c) groundwater dependent, (d) fog water dependent, and (e) drought‐deciduous (shed leaves during the dry season). Overall, published data suggest that only a subset of karst tree species are exclusively distributed within karst hilltops where water availability is limited. The diverse resource acquisition and utilization strategies of karst plants across edaphic habitats must be considered when developing effective strategies to conserve and restore biodiversity in karst landscapes, which are under increasing anthropogenic pressure.     

Fine scale heterogeneity of soil properties causes seedling spatial niche separation in a tropical rainforest

Plant and Soil - In tropical rainforests, seedling performance at fine ecological scales has traditionally been explained by seed dispersal limitation and negative density dependence. Soil...     

Niches in the Anthropocene: passerine assemblages show niche expansion from natural to urban habitats

Human‐mediated habitat transformation is increasingly evident around the world. Yet, how this transformation influences species’ niche width and overlap remains unclear. On the one hand, human‐mediated habitat transformation promotes increased species similarity through trait‐based filtering, and an increased prevalence of generalist species with broad niches, resulting in functional homogenization. On the other hand, species that colonize transformed habitats could use empty niches, resulting in decreased species similarity and an expansion of assemblage‐level niche space. Here we explore these two alternatives in eight highly diverse passerine assembles in natural, rural and urban habitats in south and southwest China, a rapidly developing region of the world. Based on stable isotopes, we found that species’ niche width increased from natural to human‐made habitats, but there were no differences in niche overlap among habitats. Therefore, we found evidence for niche expansion, with generalists appearing to use empty niches created by human habitat modification, and with assemblages being comprised of complementary species. Further research is needed to determine whether increased between‐ or within‐individual niche variation is the main driver of niche expansion in transformed habitats.     

Effects of climate warming on carbon fluxes in grasslands— A global meta‐analysis

Climate warming will affect terrestrial ecosystems in many ways, and warming‐induced changes in terrestrial carbon (C) cycling could accelerate or slow future warming. So far, warming experiments have shown a wide range of C flux responses, across and within biome types. However, past meta‐analyses of C flux responses have lacked sufficient sample size to discern relative responses for a given biome type. For instance grasslands contribute greatly to global terrestrial C fluxes, and to date grassland warming experiments provide the opportunity to evaluate concurrent responses of both plant and soil C fluxes. Here, we compiled data from 70 sites (in total 622 observations) to evaluate the response of C fluxes to experimental warming across three grassland types (cold, temperate, and semi‐arid), warming methods, and short (≤3 years) and longer‐term (>3 years) experiment lengths. Overall, our meta‐analysis revealed that experimental warming stimulated C fluxes in grassland ecosystems with regard to both plant production (e.g., net primary productivity (NPP) 15.4%; aboveground NPP (ANPP) by 7.6%, belowground NPP (BNPP) by 11.6%) and soil respiration (Rs) (9.5%). However, the magnitude of C flux stimulation varied significantly across cold, temperate and semi‐arid grasslands, in that responses for most C fluxes were larger in cold than temperate or semi‐arid ecosystems. In semi‐arid and temperate grasslands, ecosystem respiration (Reco) was more sensitive to warming than gross primary productivity (GPP), while the opposite was observed for cold grasslands, where warming produced a net increase in whole‐ecosystem C storage. However, the stimulatory effect of warming on ANPP and Rs observed in short‐term studies (≤3 years) in both cold and temperate grasslands disappeared in longer‐term experiments (>3 years). These results highlight the importance of conducting long‐term warming experiments, and in examining responses across a wide range of climate.     

Action insight: the role of the dorsal stream in the perception of grasping

In this issue of Neuron, Shmuelof and Zohary use functional magnetic resonance imaging (fMRI) to demonstrate differential sensitivity of the ventral and dorsal cortical streams of visual processing to images of objects and grasping hands, respectively.