Insights on Species Richness and Turnover from Long-Term Ecological Research: Fishes in North Temperate Lakes

SYNOPSIS. We examined eleven years of annual survey data onfish assemblages in seven lakes. Expectations based on biogeographicliterature were that, owing to the isolation of lakes, fishspecies structure should be relatively stable and species turnoverlow. Our original objective was to determine whether lakes houserelatively stable fish assemblages or ones with high rates ofspecies turnover. Methodological issues became apparent thatcaused us to consider issues of rare species and sample sufficiency.Ourdata were from samples rather than complete counts and rarespecies could have been missed. In our results mean annual richnesswas considerably lower than cumulative richness. In addition,species turnover was overestimated and decreased exponentiallyas the number of yearsbetween observation increased. Samplingvariability might explain these results; however, given thesame number of survey years, cumulative richness increased withthe number of years between observations. Apparently extinctionsand invasions occurred even within eleven years, but uncertaintyremains because rare taxa can be missed and their appearancesand disappearances in the record influence estimates of richnessand turnover. To compensate for this problem we removed raretaxa and corrected turnover rates by removing an estimate ofsampling error (the turnover rate between adjacent years). Evenusing these conservative approaches, estimates of turnover amonglakes ranged from 0.36% to 0.50% per year. Because the thresholdfor species detection by most sampling regimes is greater thanzero, survey data are expected to underestimate species richnessand overestimate species turnover even with standardized methods.Conservation biologists should evaluate claims of decline inspecies richness against such considerations     

Staying close to home: Ecological constraints on space use and range fidelity in a mountain ungulate

Understanding patterns of animal space use and range fidelity has important implications for species and habitat conservation. For species that live in highly seasonal environments, such as mountain goats (Oreamnos americanus), spatial use patterns are expected to vary in relation to seasonal changes in environmental conditions and sex‐ or age‐specific selection pressures. To address hypotheses about sex, age, and seasonality influence on space‐use ecology, we collected GPS location data from 263 radio‐collared mountain goats (males, n = 140; females, n = 123) in coastal Alaska during 2005–2016. Location data were analyzed to derive seasonal and sex‐specific fixed‐kernel home range estimates and to quantify the degree of seasonal range and utilization distribution overlap. Overall, we determined that home range size was smallest during winter, expanded coincident with the onset of green‐up and parturition, and was largest during summer. Home range size of males and females did not differ significantly during winter, but females had larger home ranges than males during summer, a relationship that was switched during the mating season. Pairwise comparisons involving individual females across subsequent years indicated home ranges were significantly smaller during years when they gave birth to offspring. Mountain goats exhibited a strong degree of range fidelity, and 99% (n = 138) of individual animals returned to their previous year''s seasonal range with an average annual Bhattacharyya''s affinity utilization distribution overlap index of 68%. Similarity of seasonal home range utilization distributions varied in relation to sex and season in some respects. Home range overlap was highest during the summer vegetation growing season, particularly among females. These findings advance our understanding about how environmental variation and sex‐ and age‐related reproductive constraints influence space use and range fidelity among alpine ungulates. Documentation of the high degree of range fidelity among mountain goats has important conservation implications in landscapes increasingly altered by anthropogenic activities.     

Paleogenomics in a Temperate Environment: Shotgun Sequencing from an Extinct Mediterranean Caprine

Background

Numerous endemic mammals, including dwarf elephants, goats, hippos and deers, evolved in isolation in the Mediterranean islands during the Pliocene and Pleistocene. Most of them subsequently became extinct during the Holocene. Recently developed high-throughput sequencing technologies could provide a unique tool for retrieving genomic data from these extinct species, making it possible to study their evolutionary history and the genetic bases underlying their particular, sometimes unique, adaptations.

Methodology/Principals Findings

A DNA extraction of a ∼6,000 year-old bone sample from an extinct caprine (Myotragus balearicus) from the Balearic Islands in the Western Mediterranean, has been subjected to shotgun sequencing with the GS FLX 454 platform. Only 0.27% of the resulting sequences, identified from alignments with the cow genome and comprising 15,832 nucleotides, with an average length of 60 nucleotides, proved to be endogenous.

Conclusions

A phylogenetic tree generated with Myotragus sequences and those from other artiodactyls displays an identical topology to that generated from mitochondrial DNA data. Despite being in an unfavourable thermal environment, which explains the low yield of endogenous sequences, our study demonstrates that it is possible to obtain genomic data from extinct species from temperate regions.     

Ecological Thresholds in the Savanna Landscape: Developing a Protocol for Monitoring the Change in Composition and Utilisation of Large Trees

Background

Acquiring greater understanding of the factors causing changes in vegetation structure - particularly with the potential to cause regime shifts - is important in adaptively managed conservation areas. Large trees (≥5 m in height) play an important ecosystem function, and are associated with a stable ecological state in the African savanna. There is concern that large tree densities are declining in a number of protected areas, including the Kruger National Park, South Africa. In this paper the results of a field study designed to monitor change in a savanna system are presented and discussed.

Methodology/Principal Findings

Developing the first phase of a monitoring protocol to measure the change in tree species composition, density and size distribution, whilst also identifying factors driving change. A central issue is the discrete spatial distribution of large trees in the landscape, making point sampling approaches relatively ineffective. Accordingly, fourteen 10 m wide transects were aligned perpendicular to large rivers (3.0–6.6 km in length) and eight transects were located at fixed-point photographic locations (1.0–1.6 km in length). Using accumulation curves, we established that the majority of tree species were sampled within 3 km. Furthermore, the key ecological drivers (e.g. fire, herbivory, drought and disease) which influence large tree use and impact were also recorded within 3 km.

Conclusions/Significance

The technique presented provides an effective method for monitoring changes in large tree abundance, size distribution and use by the main ecological drivers across the savanna landscape. However, the monitoring of rare tree species would require individual marking approaches due to their low densities and specific habitat requirements. Repeat sampling intervals would vary depending on the factor of concern and proposed management mitigation. Once a monitoring protocol has been identified and evaluated, the next stage is to integrate that protocol into a decision-making system, which highlights potential leading indicators of change. Frequent monitoring would be required to establish the rate and direction of change. This approach may be useful in generating monitoring protocols for other dynamic systems.     

Seasonal Dynamics of Phytoplankton and Planktonic Protozoan Communities in a Northern Temperate Humic Lake: Diversity in a Dinoflagellate Dominated System

Species diversity and richness, and seasonal population dynamics of phytoplankton, planktonic protozoa, and bacterioplankton sampled from the epilimnion of Crystal Bog in 2000, were examined in order to test the hypothesis that these groups diversity and abundance patterns might be linked. Crystal Bog, a humic lake in Vilas County, Wisconsin, is part of the North Temperate Lakes Long-Term Ecological Research Site. Phytoplankton and planktonic protozoa were identified and enumerated in a settling chamber with an inverted microscope. Bacterial cells were enumerated with the use of fluorescence 4, 6-diamidino-2-phenylindole (DAPI)-staining procedures, and automated ribosomal intergenic spacer analysis (ARISA) was used to assess bacterioplankton diversity. Bacterial cell counts showed little seasonal variation and averaged 2.6 × 10⁶ cells/mL over the ice-free season. Phytoplankton and planktonic protozoan numbers varied by up to two orders of magnitude and were most numerous in late spring and summer. Dinoflagellates largely dominated Crystal Bog throughout the ice-free period, specifically Peridiniopsis quadridens in the spring, Peridinium limbatum in summer, and Gymnodinium fuscum and P. quadridens in fall. Brief blooms of Cryptomonas, Dinobryon, and Synura occurred between periods of dinoflagellate domination. The dominant dinoflagellate, Peridinium limbatum, was calculated to have a growth rate of 0.065 day^–1 and a doubling time of 10.7 days. Heterotrophic nanoflagellates (HNFs) were a consistent component of the planktonic protozoa; seasonal patterns were determined for three genera of HNFs (Monosiga, Bicosoeca, and Desmarella moniliformis). Three genera of ciliates (Coleps, Strobilidium, and Strombidium) comprised the greater part of the planktonic protozoa in Crystal Bog. The number of species of planktonic protozoa was too low to calculate a diversity index. Shannon–Weaver diversity indices for phytoplankton and bacterioplankton in the epilimnion followed very similar seasonal patterns in this lake, supporting the hypothesis that in freshwaters, diversity patterns of these groups are linked.     

Loss of Resilience, Crisis, and Institutional Change: Lessons from an Intensive Agricultural System in Southeastern Australia

Linked social-ecological systems in which surprise and crisis are interspersed with periods of stability and predictability are inherently difficult to manage. This condition, coupled with the legacies of past management actions, typically leaves policy and decision makers few options other than to incrementally adapt and reinforce the current trajectory of the system. Decision making becomes increasingly reactive and incremental as the system moves from one crisis to another. Eventually the system loses its capacity to cope with perturbations and surprise. Using a combination of dynamical-systems modeling and historical analysis, we studied a process of this kind as it developed in the Goulburn Broken Catchment in southeastern Australia over the past 150 years. Using the model to simulate trajectories of the biohydrological system, we correlate the state of the physical system to historical events and management action. We show how sequential management decisions have eroded the resilience of the system (its ability to cope with shocks and surprises) and reduced options for future change. Using the model in a forward-looking mode, we explore future management options and their implications for the resilience of the system.     

Nitrogen Uptake by Trees and Mycorrhizal Fungi in a Successional Northern Temperate Forest: Insights from Multiple Isotopic Methods

Forest succession may cause changes in nitrogen (N) availability, vegetation and fungal community composition that affect N uptake by trees and their mycorrhizal symbionts. Understanding how these changes affect the functioning of the mycorrhizal symbiosis is of interest to ecosystem ecology because of the fundamental roles mycorrhizae play in providing nutrition to trees and structuring forest ecosystems. We investigated changes in tree and mycorrhizal fungal community composition, the availability and uptake of N by trees and mycorrhizal fungi in a forest undergoing a successional transition (age-related loss of early successional tree taxa). In this system, 82–96% of mycorrhizal hyphae were ectomycorrhizal (EM). As biomass production of arbuscular mycorrhizal (AM) trees increased, AM hyphae comprised a significantly greater proportion of total fungal hyphae, and the EM contribution to the N requirement of EM-associated tree taxa declined from greater than 75% to less than 60%. Increasing N availability was associated with lower EM hyphal foraging and ¹⁵N tracer uptake, yet the EM-associated later-successional species Quercus rubra was nonetheless a stronger competitor for ¹⁵N than AM-associated Acer rubrum, likely due to the more extensive nature of the persistent EM hyphal network. These results indicate that successional increases in N availability and co-dominance by AM-associated trees have increased the importance of AM fungi in the mycorrhizal community, while down-regulating EM N acquisition and transfer processes. This work advances understanding of linkages between tree and fungal community composition, and indicates that successional changes in N availability may affect competition between tree taxa with divergent resource acquisition strategies.     

Reduced Diversity and High Sponge Abundance on a Sedimented Indo-Pacific Reef System: Implications for Future Changes in Environmental Quality

Although coral reef health across the globe is declining as a result of anthropogenic impacts, relatively little is known of how environmental variability influences reef organisms other than corals and fish. Sponges are an important component of coral reef fauna that perform many important functional roles and changes in their abundance and diversity as a result of environmental change has the potential to affect overall reef ecosystem functioning. In this study, we examined patterns of sponge biodiversity and abundance across a range of environments to assess the potential key drivers of differences in benthic community structure. We found that sponge assemblages were significantly different across the study sites, but were dominated by one species Lamellodysidea herbacea (42% of all sponges patches recorded) and that the differential rate of sediment deposition was the most important variable driving differences in abundance patterns. Lamellodysidea herbacea abundance was positively associated with sedimentation rates, while total sponge abundance excluding Lamellodysidea herbacea was negatively associated with rates of sedimentation. Overall variation in sponge assemblage composition was correlated with a number of variables although each variable explained only a small amount of the overall variation. Although sponge abundance remained similar across environments, diversity was negatively affected by sedimentation, with the most sedimented sites being dominated by a single sponge species. Our study shows how some sponge species are able to tolerate high levels of sediment and that any transition of coral reefs to more sedimented states may result in a shift to a low diversity sponge dominated system, which is likely to have subsequent effects on ecosystem functioning.     

High species richness of early stages of fish in a locality of the Mesoamerican Barrier Reef System: a small-scale survey using different sampling gears

The Mesoamerican Barrier Reef System (MBRS) contains a diverse array of coastal habitats that are critical for the survival of the early stages of reef fish; however, the knowledge on the abundance and distribution of the early stages of coastal fishes is still limited in this region. This study investigated the species richness of larval and juvenile fishes using a combination of a sled net, standard plankton net, and a nightlight lift-net; these were deployed simultaneously at Bacalar Chico, a site on the MBRS within the protected “Parque Nacional Arrecifes de Xcalak” (PNAX). We collected 53 families and 118 species of larval and juvenile fishes in a small area of about 3 km². This species diversity of early life-history stages is greater than previously found in surveys on the MBRS. Each gear caught a number of species exclusively, so combined sampling with the three methods provided a much fuller picture of the local larval and juvenile fish assemblage. A species-accumulation model estimated that the samples likely represented 84% of the total assemblage. Many species caught were represented predominantly by newly settled juveniles, underscoring the importance of this coastal habitat for settlement of many ecologically and economically important fish species. This information is expected to improve the conservation and management strategies in the fragile PNAX coastal zones by providing additional information based on original field data to raise awareness among managers about the ecological relevance of these coastal habitats. This study provides encouraging evidence that the PNAX is a well-suited natural protected area to preserve a critical fish habitat in a hotspot of marine biodiversity.     

Complex Life Cycles in a Variable Environment: Predicting When the Timing of Metamorphosis Shifts from Resource Dependent to Developmentally Fixed

To test models of the timing of and size at metamorphosis, researchers manipulate food at several times during the larval phase of an animal's complex life cycle. Data from diverse taxa show that the age at metamorphosis becomes resource independent (i.e., fixed) at some point during the larval phase. Although existing models have been modified to incorporate a fixed rate of development, none predicts when phenotypic plasticity in metamorphic timing is lost. A graphical model is presented that extends knowledge of a genotype's optimal age and size at metamorphosis in different environments in which resources remain constant throughout the larval phase (i.e., the genotype's reaction norm) to predict when development rate becomes fixed in response to resource variability during the larval phase. Model predictions concur with data from food-switching experiments on anuran tadpoles and barnacle nauplii. As interest in the timing of and size at metamorphosis expands from well-studied taxa (e.g., amphibians) to the many others that have complex life cycles, the predictive model provides a useful tool to design and improve experiments.     

Comparative Genomic Study Reveals a Transition from TA Richness in Invertebrates to GC Richness in Vertebrates at CpG Flanking Sites： An Indication for Context-Dependent Mutagenicity of Methylated CpG Sites

Vertebrate genomes are characterized with CpG deficiency, particularly for GCpoor regions. The GC content-related CpG deficiency is probably caused by context-dependent deamination of methylated CpG sites. This hypothesis was examined in this study by comparing nucleotide frequencies at CpG flanking positions among invertebrate and vertebrate genomes. The finding is a transition of nucleotide preference of 5＇ T to 5＇ A at the invertebrate-vertebrate boundary, indicating that a large number of CpG sites with 5＇ Ts were depleted because of global DNA methylation developed in vertebrates. At genome level, we investigated CpG observed/expected （obs/exp） values in 500 bp fragments, and found that higher CpG obs/exp value is shown in GC-poor regions of invertebrate genomes （except sea urchin） but in GC-rich sequences of vertebrate genomes. We next compared GC content at CpG flanking positions with genomic average, showing that the GC content is lower than the average in invertebrate genomes, but higher than that in vertebrate genomes. These results indicate that although 5＇ T and 5＇ A are different in inducing deamination of methylated CpG sites, GC content is even more important in affecting the deamination rate. In all the tests, the results of sea urchin are similar to vertebrates perhaps due to its fractional DNA methylation. CpG deficiency is therefore suggested to be mainly a result of high mutation rates of methylated CpG sites in GC-poor regions.     

Shifting from Right to Left: The Combined Effect of Elevated CO2 and Temperature on Behavioural Lateralization in a Coral Reef Fish

Recent studies have shown that elevated CO₂ can affect the behaviour of larval and juvenile fishes. In particular, behavioural lateralization, an expression of brain functional asymmetries, is affected by elevated CO₂ in both coral reef and temperate fishes. However, the potentially interacting effects of rising temperatures and CO₂ on lateralization are unknown. Here, we tested the combined effect of near-future elevated-CO₂ concentrations (930 µatm) and temperature variation on behavioural lateralization of a marine damselfish, Pomacentrus wardi. Individuals exposed to one of four treatments (two CO₂ levels and two temperatures) were observed in a detour test where they made repeated decisions about turning left or right. Individuals exposed to current CO₂ and ambient temperature levels showed a significant right-turning bias at the population level. This biased was reversed (i.e. to the left side) in fish exposed to the elevated-CO₂ treatment. Increased temperature attenuated this effect, resulting in lower values of relative lateralization. Consequently, rising temperature and elevated CO₂ may have different and interactive effects on behavioural lateralization and therefore future studies on the effect of climate change on brain functions need to consider both these critical variables in order to assess the potential consequences for the ecological interactions of marine fishes.     

Impact of a Dengue Outbreak Experience in the Preventive Perceptions of the Community from a Temperate Region: Madeira Island, Portugal

The ability to effectively modify behaviours is increasingly relevant to attain and maintain a good health status. Current behaviour-change models and theories present two main approaches for (healthier) decision-making: one analytical/logical, and one experiential/emotional/intuitive. Therefore, to achieve an integral and dynamic understanding of the public perceptions both approaches should be considered: community surveys should measure cognitive understanding of health-risk contexts, and also explore how past experiences affect this understanding. In 2011, community perceptions regarding domestic source reduction were assessed in Madeira Island. After Madeira’s first dengue outbreak (2012) a unique opportunity to compare perceptions before and after the outbreak-experience occurred. This was the aim of this study, which constituted the first report on the effect of an outbreak experience on community perceptions regarding a specific vector-borne disease. A cross-sectional survey was performed within female residents at the most aegypti-infested areas. Perceptions regarding domestic source reduction were assessed according to the Essential Perception (EP)-analysis tool. A matching process paired individuals from studies performed before and after the outbreak, ensuring homogeneity in six determinant variables. After the outbreak, there were more female residents who assimilated the concepts considered to be essential to understand the proposed behaviour. Nevertheless, no significant difference was observed in the number of female residents who achieved the defined ‘minimal understanding’’. Moreover, most of the population (95.5%) still believed at least in one of the identified myths. After the outbreak some myths disappeared and others appeared. The present study quantified and explored how the experience of an outbreak influenced the perception regarding a dengue-preventive behaviour. The outbreak experience surprisingly led to the appearance of new myths within the population, apart from the expected increase of relevant concepts’ assimilation. Monitoring public perceptions is therefore crucial to make preventing dengue campaigns updated and worthy.     

A Self-microemulsifying Drug Delivery System (SMEDDS) for a Novel Medicative Compound Against Depression: a Preparation and Bioavailability Study in Rats

AJS is the code name of an untitled novel medicative compound synthesized by the Tasly Holding Group Company (Tianjin, China) based on the structure of cinnamamide, which is one of the Biopharmaceutics Classification System (BCS) class II drugs. The drug has better antidepressant effect, achieved by acting on the 5-hydroxytryptamine receptor. However, the therapeutic effects of the drug are compromised due to its poor water solubility and lower bioavailability. Herein, a self-microemulsifying drug delivery system (SMEDDS) was developed to improve its solubility and oral bioavailability. AJS-SMEDDS formulation was optimized in terms of drug solubility in the excipients, droplet size, stability, and drug precipitation using a pseudo-ternary diagram. The pharmacokinetic study was performed in rats, and the drug concentration in plasma samples was assayed using the high-performance liquid chromatography-electrospray tandem mass spectrometry (HPLC-MS/MS) method. The optimized formulation for SMEDDS has a composition of castor oil 24.5%, Labrasol 28.6%, Cremphor EL 40.8%, and Transcutol HP 2.7% (co-surfactant). No drug precipitation or phase separation was observed from the optimized formulation after 3 months of storing at 25°C. The droplet size of microemulsion formed by the optimized formulation was 26.08 ± 1.68 nm, and the zeta potential was −2.76 mV. The oral bioavailability of AJS-SMEDDS was increased by 3.4- and 35.9-fold, respectively, compared with the solid dispersion and cyclodextrin inclusion; meanwhile, the C_max of AJS-SMEDDS was about 2- and 40-fold as great as the two controls, respectively. In summary, the present SMEDDS enhanced oral bioavailability of AJS and was a promising strategy to orally deliver the drug.KEY WORDS: bioavailability, HPLC-MS/MS, self-microemulsifying drug delivery system, solubilization, stability     

Limited Functional Redundancy in a High Diversity System: Single Species Dominates Key Ecological Process on Coral Reefs

Herbivory is a key process structuring plant communities in both terrestrial and aquatic ecosystems, with variation in herbivory often being related to shifts between alternate states. On coral reefs, regional reductions in herbivores have underpinned shifts from coral to dominance by leathery macroalgae. These shifts appear difficult to reverse as these macroalgae are unpalatable to the majority of herbivores, and the macroalgae suppress the recruitment and growth of corals. The removal of macroalgae is, therefore, viewed as a key ecological process on coral reefs. On the Great Barrier Reef, Sargassum is a dominant macroalgal species following experimentally induced coral–macroalgal phase-shifts. We, therefore, used Sargassum assays and remote video cameras to directly quantify the species responsible for removing macroalgae across a range of coral reef habitats on Lizard Island, northern Great Barrier Reef. Despite supporting over 50 herbivorous fish species and six macroalgal browsing species, the video footage revealed that a single species, Naso unicornis, was almost solely responsible for the removal of Sargassum biomass across all habitats. Of the 42,246 bites taken from the Sargassum across all habitats, N. unicornis accounted for 89.8% (37,982) of the total bites, and 94.6% of the total mass standardized bites. This limited redundancy, both within and across local scales, underscores the need to assess the functional roles of individual species. Management and conservation strategies may need to look beyond the preservation of species diversity and focus on the maintenance of ecological processes and the protection of key species in critical functional groups.     

Shifts in frog size and phenology: Testing predictions of climate change on a widespread anuran using data from prior to rapid climate warming

Changes in body size and breeding phenology have been identified as two major ecological consequences of climate change, yet it remains unclear whether climate acts directly or indirectly on these variables. To better understand the relationship between climate and ecological changes, it is necessary to determine environmental predictors of both size and phenology using data from prior to the onset of rapid climate warming, and then to examine spatially explicit changes in climate, size, and phenology, not just general spatial and temporal trends. We used 100 years of natural history collection data for the wood frog, Lithobates sylvaticus with a range >9 million km², and spatially explicit environmental data to determine the best predictors of size and phenology prior to rapid climate warming (1901–1960). We then tested how closely size and phenology changes predicted by those environmental variables reflected actual changes from 1961 to 2000. Size, phenology, and climate all changed as expected (smaller, earlier, and warmer, respectively) at broad spatial scales across the entire study range. However, while spatially explicit changes in climate variables accurately predicted changes in phenology, they did not accurately predict size changes during recent climate change (1961–2000), contrary to expectations from numerous recent studies. Our results suggest that changes in climate are directly linked to observed phenological shifts. However, the mechanisms driving observed body size changes are yet to be determined, given the less straightforward relationship between size and climate factors examined in this study. We recommend that caution be used in “space‐for‐time” studies where measures of a species’ traits at lower latitudes or elevations are considered representative of those under future projected climate conditions. Future studies should aim to determine mechanisms driving trends in phenology and body size, as well as the impact of climate on population density, which may influence body size.     

Building the contractile ring from the ground up: a lesson in perseverance and scientific creativity

This contribution to the Festschrift for Professor Thomas (Tom) D. Pollard focuses on his work on the elucidation of the protein organization within the cytokinetic nodes, protein assemblies, precursors to the contractile ring. In particular, this work highlights recent discoveries in the molecular organization of the proteins that make the contractile machine in fission yeast using advanced microscopy techniques. One of the main aspects of Tom’s research philosophy that marked my career as one of his trainees is his embrace of interdisciplinary approaches to research. The cost of interdisciplinary research is to be willing to step out of our technical comfort zone to learn a new set of tools. The payoff of interdisciplinary research is the expansion our realm of possibilities by bringing new creative tools and ideas to push our research program forward. The rewarding outcomes of this work under Tom’s mentorship were the molecular model of the cytokinetic node and the development of new techniques to unravel the structure of multi-protein complexes in live cells. Together, these findings open a new set of questions about the mechanism of cytokinesis and provide creative tools to address them.