Deciphering the enigma of undetected species, phylogenetic, and functional diversity based on Good-Turing theory

Estimating the species, phylogenetic, and functional diversity of a community is challenging because rare species are often undetected, even with intensive sampling. The Good-Turing frequency formula, originally developed for cryptography, estimates in an ecological context the true frequencies of rare species in a single assemblage based on an incomplete sample of individuals. Until now, this formula has never been used to estimate undetected species, phylogenetic, and functional diversity. Here, we first generalize the Good-Turing formula to incomplete sampling of two assemblages. The original formula and its two-assemblage generalization provide a novel and unified approach to notation, terminology, and estimation of undetected biological diversity. For species richness, the Good-Turing framework offers an intuitive way to derive the non-parametric estimators of the undetected species richness in a single assemblage, and of the undetected species shared between two assemblages. For phylogenetic diversity, the unified approach leads to an estimator of the undetected Faith\u27s phylogenetic diversity (PD, the total length of undetected branches of a phylogenetic tree connecting all species), as well as a new estimator of undetected PD shared between two phylogenetic trees. For functional diversity based on species traits, the unified approach yields a new estimator of undetected Walker et al.\u27s functional attribute diversity (FAD, the total species-pairwise functional distance) in a single assemblage, as well as a new estimator of undetected FAD shared between two assemblages. Although some of the resulting estimators have been previously published (but derived with traditional mathematical inequalities), all taxonomic, phylogenetic, and functional diversity estimators are now derived under the same framework. All the derived estimators are theoretically lower bounds of the corresponding undetected diversities; our approach reveals the sufficient conditions under which the estimators are nearly unbiased, thus offering new insights. Simulation results are reported to numerically verify the performance of the derived estimators. We illustrate all estimators and assess their sampling uncertainty with an empirical dataset for Brazilian rain forest trees. These estimators should be widely applicable to many current problems in ecology, such as the effects of climate change on spatial and temporal beta diversity and the contribution of trait diversity to ecosystem multi-functionality

Habitat filtering determines spatial variation of macroinvertebrate community traits in northern headwater streams

Although our knowledge of the spatial distribution of stream organisms has been increasing rapidly in the last decades, there is still little consensus about trait-based variability of macroinvertebrate communities within and between catchments in near-pristine systems. Our aim was to examine the taxonomic and trait based stability vs. variability of stream macroinvertebrates in three high-latitude catchments in Finland. The collected taxa were assigned to unique trait combinations (UTCs) using biological traits. We found that only a single or a highly limited number of taxa formed a single UTC, suggesting a low degree of redundancy. Our analyses revealed significant differences in the environmental conditions of the streams among the three catchments. Linear models, rarefaction curves and beta-diversity measures showed that the catchments differed in both alpha and beta diversity. Taxon- and trait-based multivariate analyses also indicated that the three catchments were significantly different in terms of macroinvertebrate communities. All these findings suggest that habitat filtering, i.e., environmental differences among catchments, determines the variability of macroinvertebrate communities, thereby contributing to the significant biological differences among the catchments. The main implications of our study is that the sensitivity of trait-based analyses to natural environmental variation should be carefully incorporated in the assessment of environmental degradation, and that further studies are needed for a deeper understanding of trait-based community patterns across near-pristine streams

Identifying foundation species in North American forests using long‐term data on ant assemblage structure

Foundation species are locally abundant and uniquely control associated biodiversity, whereas dominant species are locally abundant but are thought to be replaceable in ecological systems. It is important to distinguish foundation from dominant species to direct conservation efforts. Long‐term studies that remove abundant species while measuring community dynamics have the potential to (1) aid in the identification of foundation vs. dominant species and, (2) once a foundation species is identified, determine how long its effects persist within a community after its loss. Long‐term data on ant assemblages within two canopy‐manipulation experiments—the Harvard Forest Hemlock Removal Experiment (HF‐HeRE) and the Black Rock Future of Oak Forests Experiment (BRF‐FOFE)—provide insights into how ant assemblages change and reassemble following the loss of Tsuga canadensis or Quercus spp. Previous research documented foundation species effects on ants in the HF‐HeRE for up to four years after T. canadensis loss. Six additional years of data at HF‐HeRE presented for the first time here show that removal of T. canadensis resulted in taxonomic and some measures of functional shifts in ant assemblages that persisted for ten years, further supporting the hypothesis that T. canadensis is a foundation species at Harvard Forest. In contrast, ant assemblages at BRF‐FOFE varied little regardless of whether oaks or other tree species were removed from the canopy, suggesting that Quercusspecies do not act as foundation species at Black Rock Forest. Deer and moose exclosures within each experiment also allowed for comparisons between effects on ants of foundation or dominant tree species relative to effects of large herbivores. At HF‐HeRE, effects of T. canadensis were stronger than effects of large herbivores on taxonomic and functional diversity of ant assemblages. At BRF‐FOFE, in contrast, effects of Quercus species were weaker than effects of large herbivores on ant taxonomic diversity and some measures of ant functional diversity. These findings illustrate the importance of distinguishing between the roles of irreplaceable foundation species and replaceable dominant ones in forested ecosystems along with other drivers of biodiversity (e.g., herbivory)

Subtidal macrozoobenthos communities from northern Chile during and post El Niño 1997–1998

Despite a large amount of climatic and oceanographic information dealing with the recurring climate phenomenon El Niño (EN) and its well known impact on diversity of marine benthic communities, most published data are rather descriptive and consequently our understanding of the underlying mechanisms and processes that drive community structure during EN are still very scarce. In this study, we address two questions on the effects of EN on macrozoobenthic communities: (1) how does EN affect species diversity of the communities in northern Chile? and (2) is EN a phenomenon that restarts community assembling processes by affecting species interactions in northern Chile? To answer these questions, we compared species diversity and co-occurrence patterns of soft-bottoms macrozoobenthos communities from the continental shelf off northern Chile during (March 1998) and after (September 1998) the strong EN event 1997–1998. The methods used varied from species diversity and species co-occurrence analyses to multivariate ordination methods. Our results indicate that EN positively affects diversity of macrozoobenthos communities in the study area, increasing the species richness and diversity and decreasing the species dominance. EN represents a strong disturbance that affects species interactions that rule the species assembling processes in shallow-water, sea-bottom environments

Specialized Learning in Antlions (Neuroptera: Myrmeleontidae), Pit-Digging Predators, Shortens Vulnerable Larval Stage

Unique in the insect world for their extremely sedentary predatory behavior, pit-dwelling larval antlions dig pits, and then sit at the bottom and wait, sometimes for months, for prey to fall inside. This sedentary predation strategy, combined with their seemingly innate ability to detect approaching prey, make antlions unlikely candidates for learning. That is, although scientists have demonstrated that many species of insects possess the capacity to learn, each of these species, which together represent multiple families from every major insect order, utilizes this ability as a means of navigating the environment, using learned cues to guide an active search for food and hosts, or to avoid noxious events. Nonetheless, we demonstrate not only that sedentary antlions can learn, but also, more importantly, that learning provides an important fitness benefit, namely decreasing the time to pupate, a benefit not yet demonstrated in any other species. Compared to a control group in which an environmental cue was presented randomly vis-à-vis daily prey arrival, antlions given the opportunity to associate the cue with prey were able to make more efficient use of prey and pupate significantly sooner, thus shortening their long, highly vulnerable larval stage. Whereas “median survival time,” the point at which half of the animals in each group had pupated, was 46 days for antlions receiving the Learning treatment, that point never was reached in antlions receiving the Random treatment, even by the end of the experiment on Day 70. In addition, we demonstrate a novel manifestation of antlions' learned response to cues predicting prey arrival, behavior that does not match the typical “learning curve” but which is well-adapted to their sedentary predation strategy. Finally, we suggest that what has long appeared to be instinctive predatory behavior is likely to be highly modified and shaped by learning

Bumble Bees (Bombus spp) along a Gradient of Increasing Urbanization

BACKGROUND: Bumble bees and other wild bees are important pollinators of wild flowers and several cultivated crop plants, and have declined in diversity and abundance during the last decades. The main cause of the decline is believed to be habitat destruction and fragmentation associated with urbanization and agricultural intensification. Urbanization is a process that involves dramatic and persistent changes of the landscape, increasing the amount of built-up areas while decreasing the amount of green areas. However, urban green areas can also provide suitable alternative habitats for wild bees. METHODOLOGY/PRINCIPAL FINDINGS: We studied bumble bees in allotment gardens, i.e. intensively managed flower rich green areas, along a gradient of urbanization from the inner city of Stockholm towards more rural (periurban) areas. Keeping habitat quality similar along the urbanization gradient allowed us to separate the effect of landscape change (e.g. proportion impervious surface) from variation in habitat quality. Bumble bee diversity (after rarefaction to 25 individuals) decreased with increasing urbanization, from around eight species on sites in more rural areas to between five and six species in urban allotment gardens. Bumble bee abundance and species composition were most affected by qualities related to the management of the allotment areas, such as local flower abundance. The variability in bumble bee visits between allotment gardens was higher in an urban than in a periurban context, particularly among small and long-tongued bumble bee species. CONCLUSIONS/SIGNIFICANCE: Our results suggest that allotment gardens and other urban green areas can serve as important alternatives to natural habitats for many bumble bee species, but that the surrounding urban landscape influences how many species that will be present. The higher variability in abundance of certain species in the most urban areas may indicate a weaker reliability of the ecosystem service pollination in areas strongly influenced by human activity

Shelters and Their Use by Fishes on Fringing Coral Reefs

Coral reef fish density and species richness are often higher at sites with more structural complexity. This association may be due to greater availability of shelters, but surprisingly little is known about the size and density of shelters and their use by coral reef fishes. We quantified shelter availability and use by fishes for the first time on a Caribbean coral reef by counting all holes and overhangs with a minimum entrance diameter ≥3 cm in 30 quadrats (25 m2) on two fringing reefs in Barbados. Shelter size was highly variable, ranging from 42 cm3 to over 4,000,000 cm3, with many more small than large shelters. On average, there were 3.8 shelters m−2, with a median volume of 1,200 cm3 and a total volume of 52,000 cm3m−2. The number of fish per occupied shelter ranged from 1 to 35 individual fishes belonging to 66 species, with a median of 1. The proportion of shelters occupied and the number of occupants increased strongly with shelter size. Shelter density and total volume increased with substrate complexity, and this relationship varied among reef zones. The density of shelter-using fish was much more strongly predicted by shelter density and median size than by substrate complexity and increased linearly with shelter density, indicating that shelter availability is a limiting resource for some coral reef fishes. The results demonstrate the importance of large shelters for fish density and support the hypothesis that structural complexity is associated with fish abundance, at least in part, due to its association with shelter availability. This information can help identify critical habitat for coral reef fishes, predict the effects of reductions in structural complexity of natural reefs and improve the design of artificial reefs

An Experimental Field Study of Delayed Density Dependence in Natural Populations of Aedes albopictus

Aedes albopictus, a species known to transmit dengue and chikungunya viruses, is primarily a container-inhabiting mosquito. The potential for pathogen transmission by Ae. albopictus has increased our need to understand its ecology and population dynamics. Two parameters that we know little about are the impact of direct density-dependence and delayed density-dependence in the larval stage. The present study uses a manipulative experimental design, under field conditions, to understand the impact of delayed density dependence in a natural population of Ae. albopictus in Raleigh, North Carolina. Twenty liter buckets, divided in half prior to experimentation, placed in the field accumulated rainwater and detritus, providing oviposition and larval production sites for natural populations of Ae. albopictus. Two treatments, a larvae present and larvae absent treatment, were produced in each bucket. After five weeks all larvae were removed from both treatments and the buckets were covered with fine mesh cloth. Equal numbers of first instars were added to both treatments in every bucket. Pupae were collected daily and adults were frozen as they emerged. We found a significant impact of delayed density-dependence on larval survival, development time and adult body size in containers with high larval densities. Our results indicate that delayed density-dependence will have negative impacts on the mosquito population when larval densities are high enough to deplete accessible nutrients faster than the rate of natural food accumulation