Limited sampling hampers “big data” estimation of species richness in a tropical biodiversity hotspot

Macro‐scale species richness studies often use museum specimens as their main source of information. However, such datasets are often strongly biased due to variation in sampling effort in space and time. These biases may strongly affect diversity estimates and may, thereby, obstruct solid inference on the underlying diversity drivers, as well as mislead conservation prioritization. In recent years, this has resulted in an increased focus on developing methods to correct for sampling bias. In this study, we use sample‐size‐correcting methods to examine patterns of tropical plant diversity in Ecuador, one of the most species‐rich and climatically heterogeneous biodiversity hotspots. Species richness estimates were calculated based on 205,735 georeferenced specimens of 15,788 species using the Margalef diversity index, the Chao estimator, the second‐order Jackknife and Bootstrapping resampling methods, and Hill numbers and rarefaction. Species richness was heavily correlated with sampling effort, and only rarefaction was able to remove this effect, and we recommend this method for estimation of species richness with “big data” collections.     

Elevation‐dependent effects of forest fragmentation on plant–bird interaction networks in the tropical Andes

Tropical forests harbor diverse ecological communities of plants and animals that are organized in complex interaction networks. The diversity and structure of plant–animal interaction networks may change along elevational gradients and in response to human‐induced habitat fragmentation. While previous studies have analyzed the effects of elevation and forest fragmentation on species interaction networks in isolation, to our knowledge no study has investigated whether the effects of forest fragmentation on species interactions may differ along elevational gradients. In this study, we analyzed main and interaction effects of elevation and forest fragmentation on plant–frugivore interaction networks at plant and bird species level. Over a period spanning two years, we recorded plant–frugivore interactions at three elevations (1000, 2000 and 3000 m a.s.l.) and in two habitat types (continuous and fragmented forest) in tropical montane forests in southern Ecuador. We found a consistent effect of elevation on the structure of plant–frugivore networks. We observed a decrease in the number of effective bird partners of plants and, thus, a decline in the redundancy of bird species with increasing elevation. Furthermore, bird specialization on specific plant partners increased towards high elevations. Fragmentation had a relatively weak effect on the interaction networks for both plant and bird species, but resulted in a significant increase in bird specialization in fragmented forests at high elevations. Our results indicate that forest fragmentation may have stronger effects on plant–frugivore interaction networks at high compared to low elevations because bird species richness declined more steeply towards high elevations than plant species richness. We conclude that conservation efforts should prioritize the maintenance of consumer diversity, for instance by maintaining stretches of continuous forest. This applies in particular to species‐poor communities, such as those at high elevations, as the ecological processes in these communities seem most sensitive towards forest fragmentation.     

Functional diversity and trait–environment relationships of stream fish assemblages in a large tropical catchment

1. The species composition of stream fish assemblages changes across the longitudinal fluvial gradient of large river basins. These changes may reflect both zonation in species distributions and environmental filtering of fish traits as stream environments change from the uplands to the lowlands of large catchments. Previous research has shown that taxonomic diversity generally increases in larger, lowland streams, and the River Continuum Concept, the River Habitat Template and other frameworks have provided expectations for what functional groups of fishes should predominate in certain stream types. However, studies addressing the functional trait composition of fish assemblages across large regions are lacking, particularly in tropical river basins. 2. We examined functional trait–environment relationships and functional diversity of stream fish assemblages in the Río Grijalva Basin in southern Mexico. Traits linked to feeding, locomotion and life history strategy were measured in fishes from streams throughout the catchment, from highland headwaters to broad, lowland streams. Relationships between functional traits and environmental variables at local and landscape scales were examined using multivariate ordination, and the convex hull volume of trait space occupied by fish assemblages was calculated as a measure of functional diversity. 3. Although there were a few exceptions, functional diversity of assemblages increased with species richness along the gradient from uplands to lowlands within the Grijalva Basin. Traits related to swimming, habitat preference and food resource use were associated with both local (e.g. substratum type, pool availability) and landscape‐scale (e.g. forest cover) environmental variables. 4. Along with taxonomic structure and diversity, the functional composition of fish assemblages changed across the longitudinal fluvial gradient of the basin. Trait–environment relationships documented in this study partially confirmed theoretical expectations and revealed patterns that may help in developing a better understanding of general functional responses of fish assemblages to environmental change.     

Tree community structure and stem mortality along a water availability gradient in a Mexican tropical dry forest

We document spatial changes in species diversity, composition, community structure, and mortality of trees across a gradient of water availability in a tropical dry forest in western Mexico. This gradient occurs along the main stream of a small watershed of less than 1 km in length. Four 30 × 80 m plots were established systematically to include the driest (ridge top of the watershed) to the wettest sites (watershed bottom) within this watershed. All stems larger than 5 cm were identified, and measured for diameter and height. Dead stems larger than 5 cm were measured and classified as: a) found on live or dead trees, and b) standing (“snags”) or lying (“downlogs”) on the ground. The number of recorded species per plot declined from 73 to 44 species as water availability decreased. A decline in estimated total richness, and in Shannon-Wiener and Simpson diversity indices was also observed in the drier plots. Species composition strongly changed along the gradient, with the two ends of the gradient sharing only 11% of the species. Stem density and percentage of dead stems and trees increased in abundance and basal area from the wetter to the drier sites. Tree and stem size (basal area, height and stem diameter) showed the opposite trend. Nonetheless, total basal area of live trees was largest at the two end gradient locations and oscillated between 12.22 m² ha⁻¹ and 7.93 m² ha⁻¹. Proportion of snags increased towards the driest site (from 46 to 72%), while that of down logs decreased. Overall, our results suggest that small-scale gradients of water availability play a paramount role in the spatial organization of tree communities in seasonal tropical environments. This revised version was published online in June 2006 with corrections to the Cover Date.     

Spider diversity in a tropical habitat gradient in Chiapas, Mexico

This paper presents an assessment of spider diversity in a complex landscape of southern Mexico. Eighteen different habitats were identified, measured and mapped across this fragmented landscape. Habitat types were characterized by measuring various features, including number of plant forms, tree cover and litter depth. Each month from February to April (dry season) and from June to August 2002 (wet season), spiders were sampled on each habitat by using pitfall traps and direct collection. Correlations between spider diversity and habitat characteristics were carried out to explore the relative contribution of each habitat variable as related to changes in spider composition and richness. In total, 115 spider species were recorded in 18 habitat types, and the mean number and density of species per habitat were 21 (± 3, standard error of mean) and 57 (± 9), respectively. The species recorded represent 41% of the fauna recorded in the Mexican state of Chiapas and 4% of the fauna recorded in Mexico. Relatively pristine habitats (e.g. deciduous forest) contained an important proportion of spider diversity in this fragmented landscape. Epigean spider diversity was significantly correlated with tree cover and with the diversity of plant forms during the rainy season. No correlation was detected between soil spider diversity and the habitat variables measured for any season. The results of this work suggest that in highly fragmented tropical landscapes, some habitat types (e.g. coffee plantations, hedgerows) might play an important role for the persistence of spider populations. The prevalence of relatively stable conditions in some of these habitats can allow spiders species (e.g. Nephila clavipes ) to overcome adverse conditions such as a decrease in humidity and dramatic changes in temperature and wind exposure, allowing them to recolonize when favourable conditions return.     

Temperature effects on “overwintering” phenology of a polyphagous,tropical fruit fly (Tephritidae) at the subtropical/temperate interface

Around the world, several pest tephritids are extending their ranges from warm tropical or Mediterranean climates into cooler temperate regions. The ability to tolerate climatic diversity is uncommon among insects, and understanding the population phenology drivers of such species across different parts of their range will be critical for their management. Here, we determined the role of temperature versus fruit availability on the population phenology of Queensland fruit fly, Bactrocera tryoni. Using a field site located at the subtropical/temperate interface, with host fruits continuously available, we monitored the development times and abundance of B. tryoni, a species which has invaded temperate Australia from the tropics. From fruit samples held at ambient and controlled conditions, the abundance of emerging flies was highly variable among collection dates, but the variance did not reflect the observed changes in temperature. For most samples, the survival rate of flies in a field site was lower than predicted by a day‐degree population model fitted with mean daily field temperatures. The development time of the immature stage in the field was prolonged, presumably due to cooler ambient conditions, but the fitted day‐degree population model consistently over‐predicted estimated development times. Our results indicate that at the subtropical/temperate interface, the decline in B. tryoni populations during winter is only partly driven by temperature and host availability. We classify B. tryoni as a climate generalist, which likely employs physiological as well as behavioural mechanisms to achieve broad climatic tolerance ranges.     

Environmental heterogeneity shapes physiological traits in tropical direct‐developing frogs

1. Tropical ectotherm species tend to have narrower physiological limits than species from temperate areas. As a consequence, tropical species are considered highly vulnerable to climate change since minor temperature increases can push them beyond their physiological thermal tolerance. Differences in physiological tolerances can also be seen at finer evolutionary scales, such as among populations of ectotherm species along elevation gradients, highlighting the physiological sensitivity of such organisms.
2. Here, we analyze the influence of elevation and bioclimatic domains, defined by temperature and precipitation, on thermal sensitivities of a terrestrial direct‐developing frog (Craugastor loki) in a tropical gradient. We address the following questions: (a) Does preferred temperature vary with elevation and among bioclimatic domains? (b) Do thermal tolerance limits, that is, critical thermal maximum and critical thermal minimum vary with elevation and bioclimatic domains? and (c) Are populations from high elevations more vulnerable to climate warming?
3. We found that along an elevation gradient body temperature decreases as environmental temperature increases. The preferred temperature tends to moderately increase with elevation within the sampled bioclimatic domains. Our results indicate that the ideal thermal landscape for this species is located at midelevations, where the thermal accuracy (d_b) and thermal quality of the environment (d_e) are suitable. The critical thermal maximum is variable across elevations and among the bioclimatic domains, decreasing as elevation increases. Conversely, the critical thermal minimum is not as variable as the critical thermal maximum.
4. Populations from the lowlands may be more vulnerable to future increases in temperature. We highlight that the critical thermal maximum is related to high temperatures exhibited across the elevation gradient and within each bioclimatic domain; therefore, it is a response to high environmental temperatures.

     

Tumor microenvironment as the “regulator” and “target” for gene therapy

In this review, we focus on strategies for designing functional nano gene carriers, as well as choosing therapeutic genes targeting the tumor microenvironment. Gene mutations have a great impact on the occurrence of cancer. Thus, gene therapy plays a major role in cancer therapy and has the potential to cure cancer. Well‐designed gene therapy largely relies on effective gene carriers, which can be divided into viral carriers and non‐viral carriers. A gene carrier delivers functional genes to their intracellular target and avoids nucleic acids being degraded by nucleases in the serum. Most conventional cancer gene therapies only target cancer cells and do not appear to be sufficintly efficient to pass clinical trials. Accumulating evidence has shown that extending the therapeutic strategies to the tumor microenvironment, rather than the tumor cell itself, can allow more options for achieving robust anti‐cancer efficiency. In addition, unusual features between tumor microenvironment and normal tissues, such as a lower pH, higher glutathione and reactive oxygen species concentrations, and overexpression of some enzymes, facilitate the design of smart stimuli‐responsive gene carriers regulated by the tumor microenvironment. These carriers interact with nucleic acids and then form stable nanoparticles under physiological conditions. By regulation of the tumor microenvironment, stimuli‐responsive gene carriers are able to change their properties and achieve high gene delivery efficiency. Considering the tumor microenvironment as the “regulator” and “target” when designing gene carriers and choosing therapeutic genes shows significant benefit with respect to improving the accuracy and efficiency of cancer gene therapy.     

Assessing regulating and provisioning ecosystem services in a contrasting tropical forest landscape

Ecosystem services are the bridge between nature and society, and are essential elements of community well-being. The Wet Tropics Australia, is environmentally and biologically diverse, and supplies numerous ecosystem services. It contributes to the community well-being of this region, Australian national economy and global climate change mitigation efforts. However, the ecosystem services in the region have rarely been assessed undermining strategic landscape planning to sustain their future flow. In this study, we attempted to: (i) assess the quantity of five regulating ecosystem services – global climate regulation, air quality regulation, erosion regulation, nutrient regulation, and cyclone protection, and three provisioning ecosystem services – habitat provision, energy provision and timber provision across rainforests, sclerophyll forests and rehabilitated plantation forests; (ii) evaluate the variation of supply of those regulating and provisioning ecosystem services across environmental gradients, such as rainfall, temperature, and elevation; (iii) show the relationships among those ecosystem services; and (iv) identify the hotspots of single and multiple ecosystem services supply across the landscape. The results showed that rainforests possess a very high capacity to supply single and multiple ecosystem services, and the hotspots for most of the regulating and provisioning ecosystem services are found in upland rainforest followed by lowland rainforest, and upland sclerophyll forest. Elevation, rainfall and temperature gradients along with forest structure are the main determinant factors for the quantity of ecosystem services supplied across the three forest types. The correlation among ecosystem services may be positive or negative depending on the ecosystem service category and vegetation type. The rehabilitated plantation forests may provide some ecosystem services comparable to the rainforest. The results demonstrated disturbance regimes (such as tropical cyclones) may have influenced the usual spatial trend of ecosystem service values. This study will assist decision makers in incorporating ecosystem services into their natural resource management planning, and for practitioners to identify the areas with higher values of specific and multiple ecosystem services.     

Speciation and the “shifting balance” in a continuous population

Shifts between adaptive peaks, caused by sampling drift, are involved in both speciation and adaptation via Wright's “shifting balance.” We use techniques from statistical mechanics to calculate the rate of such transitions for a population in a single panmictic deme and for a population which is continuously distributed over one- and two-dimensional regions. This calculation applies in the limit where transitions are rare. Our results indicate that stochastic divergence is feasible despite free gene flow, provided that neighbourhood size is low enough. In two dimensions, the rate of transition depends primarily on neighbourhood size N and only weakly on selection pressure (≈s^k exp(− cN)), where k is a number determined by the local population structure, in contrast with the exponential dependence on selection pressure in one dimension (≈exp(− cN √s)) or in a single deme (≈exp(− cNs)). Our calculations agree with simulations of a single deme and a one-dimensional population.     

Beetle species’ responses suggest that microclimate mediates fragmentation effects in tropical Australian rainforest

Abstract Despite the enormous contribution of invertebrates to global biodiversity and ecosystem function, the patterns and causes of insect responses to tropical rainforest destruction and fragmentation remain poorly understood. We studied the responses of beetles to these factors in a fragmented upland rainforest landscape in north‐east Queensland, Australia. Beetles were sampled using flight interception traps from six replicate sites in rainforest interior, rainforest edge, small rainforest remnants and pasture, interspersed across about 600 km². Beetles from 10 family/subfamily groups were sorted to species. There were three major findings. First, converting rainforest into pasture has a very strong negative effect on beetle diversity and species composition. Very few beetle species were present in pasture and none of the most abundant species was more abundant in pasture than rainforest. Second, beetle assemblages appeared to respond to climate. Beetle species composition in drier rainforest habitats was different from that of moister rainforest and there were species unique to each rainforest type. Third, beetle species composition differed between small remnants and interior rainforest: drier‐associated species were more abundant in small remnants, whereas wetter‐associated species were more abundant in interiors. Edges tended to be intermediate. We argue that this pattern can be attributed to a fragmentation effect mediated by differences in microclimate rather than by floristic, structural, or area and isolation effects.     

Role of environmental and spatial processes in structuring anuran communities across a tropical rain forest

This study aimed to evaluate if anuran species distributions in riparian and non‐riparian areas are influenced by environmental factors (i.e. niche) and/or by spatial factors (i.e. dispersal). The environmental variables analysed were altitude, distance from the stream and leaf litter depth. Spatial factors were represented by the eigenvectors extracted from geographical coordinates by eigenfunction analysis. The study was conducted in 24 km² of terra‐firme forest in Central Amazonia, Manaus – Amazonas, Brazil. Between November 2008 and May 2009, three samples were taken from 41 plots, 21 plots being placed at non‐riparian areas and another 20 placed in riparian areas. We submitted the assemblage dataset to a partial redundancy analysis to evaluate the contributions of environmental and spatial variables (selected with a forward selection procedure). In addition, we tested if communities differ from riparian and non‐riparian areas using a db‐MANOVA. Species richness and species composition differed between riparian and non‐riparian plots. Some species were restricted to riparian areas. Altitude was the only significant variable (P = 0.005) explaining 21% of the total variance. When analysing the data from all plots using the partial redundancy analysis, 27% of the variance was explained by spatial and environmental variables. The environmental variables explained exclusively 4% of the variance in assemblage composition, and 13% was explained by environmental variables that were also structured in space (i.e. the shared fraction), while 10% was explained exclusively by spatial variables. In conclusion, our results showed differences between the assemblages of riparian and non‐riparian areas which can be explained by the distribution of anuran species along environmental gradients altitude and distance to streams, with little evidence of dispersal limitation.     

Assessing invertebrate herbivory in human‐modified tropical forest canopies

1. Studies on the effects of human‐driven forest disturbance usually focus on either biodiversity or carbon dynamics but much less is known about ecosystem processes that span different trophic levels. Herbivory is a fundamental ecological process for ecosystem functioning, but it remains poorly quantified in human‐modified tropical rainforests.
2. Here, we present the results of the largest study to date on the impacts of human disturbances on herbivory. We quantified the incidence (percentage of leaves affected) and severity (the percentage of leaf area lost) of canopy insect herbivory caused by chewers, miners, and gall makers in leaves from 1,076 trees distributed across 20 undisturbed and human‐modified forest plots in the Amazon.
3. We found that chewers dominated herbivory incidence, yet were not a good predictor of the other forms of herbivory at either the stem or plot level. Chewing severity was higher in both logged and logged‐and‐burned primary forests when compared to undisturbed forests. We found no difference in herbivory severity between undisturbed primary forests and secondary forests. Despite evidence at the stem level, neither plot‐level incidence nor severity of the three forms of herbivory responded to disturbance.
4. Synthesis. Our large‐scale study of canopy herbivory confirms that chewers dominate the herbivory signal in tropical forests, but that their influence on leaf area lost cannot predict the incidence or severity of other forms. We found only limited evidence suggesting that human disturbance affects the severity of leaf herbivory, with higher values in logged and logged‐and‐burned forests than undisturbed and secondary forests. Additionally, we found no effect of human disturbance on the incidence of leaf herbivory.

     

Genetic consequences of fragmentation in “arbor vitae,” eastern white cedar (Thuja occidentalis L.), toward the northern limit of its distribution range

We tested the hypothesis that marginal fragmented populations of eastern white cedar (EWC) are genetically isolated due to reduced pollen and gene flow. In accordance with the central-marginal model, we predicted a decrease in population genetic diversity and an increase in differentiation along the latitudinal gradient from the boreal mixed-wood to northern coniferous forest. A total of 24 eastern white cedar populations were sampled along the north-south latitudinal gradient for microsatellite genotyping analysis. Positive F_is values and heterozygote deficiency were observed in populations from the marginal (F_is = 0.244; P_HW = 0.0042) and discontinuous zones (F_is = 0.166; P_HW = 0.0042). However, populations from the continuous zone were in HW equilibrium (F_is = −0.007; P_HW = 0.3625). There were no significant latitudinal effects on gene diversity (H_s), allelic richness (AR), or population differentiation (F_st). Bayesian and NJT (neighbor-joining tree) analyses demonstrated the presence of a population structure that was partly consistent with the geographic origins of the populations. The impact of population fragmentation on the genetic structure of EWC is to create a positive inbreeding coefficient, which was two to three times higher on average than that of a population from the continuous zone. This result indicated a higher occurrence of selfing within fragmented EWC populations coupled with a higher degree of gene exchange among near-neighbor relatives, thereby leading to significant inbreeding. Increased population isolation was apparently not correlated with a detectable effect on genetic diversity. Overall, the fragmented populations of EWC appear well-buffered against effects of inbreeding on genetic erosion.