Colony Size Distribution Research Articles

A time-resolved clonogenic assay for improved cell survival and RBE measurements.

The in vitro clonogenic assay (IVCA) is the mainstay of quantitative radiobiology. Here, we investigate the benefit of a time-resolved IVCA version (trIVCA) to improve the quantification of clonogenic survival and relative biological effectiveness (RBE) by analyzing cell colony growth behavior. In the IVCA, clonogenicity classification of cell colonies is performed based on a fixed colony size threshold after incubation. In contrast, using trIVCA, we acquire time-lapse microscopy images during incubation and track the growth of each colony using neural-net-based image segmentation. Attributes of the resulting growth curves are then used as predictors for a decision tree classifier to determine clonogenicity of each colony. The method was applied to three cell lines, each irradiated with 250kV X-rays in the range 0-8Gy and carbon ions of high LET (100keV/μm, dose-averaged) in the range 0-2Gy. We compared the cell survival curves determined by trIVCA to those from the classical IVCA across different size thresholds and incubation times. Further, we investigated the impact of the assaying method on RBE determination. Size distributions of abortive and clonogenic colonies overlap consistently, rendering perfect separation via size threshold unfeasible at any readout time. This effect is dose-dependent, systematically inflating the steepness and curvature of cell survival curves. Consequently, resulting cell survival estimates show variability between 3% and 105%. This uncertainty propagates into RBE calculation with variability between 8% and 25% at 2Gy.Determining clonogenicity based on growth curves has an accuracy of 95% on average. The IVCA suffers from substantial uncertainty caused by the overlap of size distributions of delayed abortive and clonogenic colonies. This impairs precise quantification of cell survival and RBE. By considering colony growth over time, our method improves assaying clonogenicity.

Bottom-contact fisheries disturbance and signs of recovery of precious corals in the Northwestern Hawaiian Islands and Emperor Seamount Chain

Deep-sea precious corals in the octocoral family Coralliidae are among the dominant benthic megafauna at depths of 300–600 m on seamounts of the Northwestern Hawaiian Islands and lower Emperor Seamount Chain. Pleurocorallium secundum and Hemicorallium laauense were once abundant enough on these seamounts to support a targeted coral fishery in the 1960s and 1970s. Significant trawl finfish fisheries were also occurring in the same time frame on the same seamounts. Because they had high enough abundance to support a targeted fishery for two decades, these two coralliid species must have been a key component of the baseline community on these seamounts. Therefore, they provide an ideal indicator species for testing effects of large-scale disturbance and potential for recovery in deep-sea coral and seamount communities. Using AUVs and submersibles, we explored seamounts outside the US EEZ that are still actively fished by trawl, seamounts within the US EEZ that were historically trawled but have been protected since the establishment of the EEZ, and seamounts that have never been trawled, to determine population distributions and colony sizes for the targeted coral species. P. secundum had only one individual on actively trawled seamounts and occurred in low abundance on most Recovering seamounts. H. laauense was present in a few areas in Recovering and Still Trawled seamounts. Colony size distributions for H. laauense showed a smaller median size on Recovering and Still Trawled seamounts compared to the Never Trawled sites. P. secundum had a slightly smaller median colony size on the Recovering Seamounts than on the Never Trawled seamounts. These results indicate a reduction in abundance for both species in disturbed areas with some unexpected potential for recovery on protected seamounts. Recovery was uneven among sites and species with SE Hancock and Koko showing the largest populations of H. laauense among the Recovering and Still Trawled seamounts, respectively. P. secundum showed much less recovery, with its largest population on Bank 11 in the Recovering seamounts. Kammu, one of the primary seamounts of the coral fishery, had only a single coralliid observed. The other primary target, Yuryaku, had a small number of coralliids in a steeply sloped area. These two Still Trawled seamounts do not appear to be able to recover under the current levels of fishing pressure.

Recovery trends of reef carbonate budgets at remote coral atolls 6 years post‐bleaching

AbstractCoral bleaching events and resultant changes in benthic community composition and population size structure can diminish the important geo‐ecological functions reefs provide, including habitat provision and carbonate production to support reef accretion. Net reef carbonate budgets, the balance between carbonate production and erosion processes, are thus important functional indicators of reef health. This study quantifies changes in coral community composition and colony size structures, and the resultant reef carbonate budget trajectories after the 2015/2016 bleaching event in the remote Chagos Archipelago, Indian Ocean. ReefBudget surveys were conducted at 12 sites across three atolls in 2015, 2018, and 2021, with calculations of biological carbonate production and erosion supported by locally obtained calcification and bioerosion rates. Carbonate budgets (in G = kg CaCO3 m−2 yr−1) shifted from net positive states in 2015 (mean ± SD: 3.8 ± 2.6 G) to net negative states in 2018 (−2.4 ± 1.4 G) in response to bleaching‐driven mass coral mortality. By 2021, all sites were on a trajectory of recovery, but net budgets differed significantly between atolls (−2.0 ± 1.7 to 2.2 ± 1.4 G). At Salomon atoll, the threefold faster recovery of carbonate production and return to positive reef budget states only 6 yr post‐bleaching was associated with the persistence of high structural complexity and the rapid recovery of fast growing tabular Acropora spp. Inter‐atoll differences in colony size distributions furthermore illustrate that coral identity and size class are more important predictors of reef functions and post‐disturbance recovery speed than coral cover alone.

Measuring Up to the Challenge: Enhancing the Capacity of ARAICoBeH System by Enabling Coral Colony Size Measurement

The health of many coral reefs around the globe is being threatened by a variety of local and global stressors, which makes it even more important to assess and monitor them. While the coral cover is one of the easiest and used quantifiers of reef health, the addition of coral colony sizes provides deeper insights into reef recruitment potential, fecundity, and possible environmental conditions for survivability. The use of the ARAICoBeH (A Rapid Assessment Instrument for Coastal Benthic Habitats) System can already provide similar coral cover and composition results as common methods in coral reef monitoring yet are faster and cheaper. The capacity of the ARAICoBeH System was expanded to coral measurements by adding paired lasers, and results were compared with tape measurement and photoquadrat methods. The time and cost to conduct this study were also compared for the three methods. The results illustrate that the ARAICoBeH System with paired laser attachment was able to provide digital reference points that can be used as a scale to accurately measure coral colonies. Colony sizes across different coral lifeforms derived from the system correlated well overall with the two commonly used methods. The colony size distributions from ARAICoBeH more closely resembled the distribution from the photoquadrat data than from the tape measure method. While the varying resolution of images from the ARAICoBeH System took longer to process, the overall time and cost to conduct this study were faster and cheaper, respectively. From these findings, the addition of paired lasers proved to enhance the capability of the ARAICoBeH System as a viable, low-cost, and rapid coral reef assessment method.

A framework for automated time-resolved analysis of cell colony growth after irradiation

Understanding dose-dependent survival of irradiated cells is a pivotal goal in radiotherapy and radiobiology. To this end, the clonogenic assay is the standard in vitro method, classifying colonies into either clonogenic or non-clonogenic based on a size threshold at a fixed time. Here we developed a methodological framework for the automated analysis of time course live-cell image data to examine in detail the growth dynamics of large numbers of colonies that occur during such an experiment. We developed a segmentation procedure that exploits the characteristic composition of phase-contrast images to identify individual colonies. Colony tracking allowed us to characterize colony growth dynamics as a function of dose by extracting essential information: (a) colony size distributions across time; (b) fractions of differential growth behavior; and (c) distributions of colony growth rates across all tested doses. We analyzed three data sets from two cell lines (H3122 and RENCA) and made consistent observations in line with already published results: (i) colony growth rates are normally distributed with a large variance; (ii) with increasing dose, the fraction of exponentially growing colonies decreases, whereas the fraction of delayed abortive colonies increases; as a novel finding, we observed that (iii) mean exponential growth rates decrease linearly with increasing dose across the tested range (0–10 Gy). The presented method is a powerful tool to examine live colony growth on a large scale and will help to deepen our understanding of the dynamic, stochastic processes underlying the radiation response in vitro.

Abstract IA20: Novel cell microarray technologies for studies of DNA damage and cell survival and applications for studies of microbe-induced DNA damage

Abstract Genotoxicity testing is critical for predicting adverse effects of pharmaceutical, industrial, and environmental chemicals. The comet assay is a commonly used approach for detecting DNA damage that is based on the underlying principle that damaged DNA migrates more readily than undamaged DNA when electrophoresed in agarose. We previously developed a higher-throughput version of the comet assay (Wood DK, PNAS 2010). For the “CometChip” assay, cells are loaded into an array of agarose microwells to create a cell microarray. The CometChip can be fully automated, making the assay more than 1000X faster, while improving reproducibility. While effective for detecting single-strand breaks, abasic sites, and alkali-sensitive sites, the alkaline comet assay is not effective for detection of carcinogenic bulky DNA lesions that do not impact DNA mobility and that require metabolic activation. To overcome this, we use DNA replication inhibitors (hydroxyurea and 1-β-d-arabinofuranosyl cytosine) shown to trap single-strand breaks that are formed during nucleotide excision repair, which normally removes bulky lesions. Thus, comet-undetectable bulky lesions are converted into comet-detectable single-strand breaks. Together with HepaRG™ cells that recapitulate in vivo metabolic capacity, we have thus created the “HepaCometChip,” which provides a more broadly effective approach for detection of DNA damage. In addition to genotoxicity testing, the microwell array has also been harnessed for use in a cell survival assay. For the “MicroColonyChip” (Ngo LP, Cell Reports 2019), cells are loaded into the agarose microwell array and allowed to grow to form microcolonies. Differences in cell survival can be detected by changes in the distribution of colony sizes, a novel metric for cell survival quantitation. The assay is as sensitive as the traditional “gold standard” colony-forming assay, yet it takes days instead of weeks to complete. Parallel studies of genotoxicity and cytotoxicity can thus be performed using a shared microwell platform. These tools have broad utility, including studies of microbe-induced DNA damage. Examples of S. pneumoniae and E. coli microbial product-induced double-strand breaks and interstrand crosslinks contribute to an emerging paradigm wherein pathogen-induced DNA damage has the potential to promote disease. Citation Format: Le P. Ngo, Prashant Rai, Matthew R. Wilson, Carole Swartz, John Winters, Yang Su, Jing Ge, Tze-Khee Chan, Emily P. Balskus, Vincent Chow, Les Recio, Leona D. Samson, Bevin P. Engelward. Novel cell microarray technologies for studies of DNA damage and cell survival and applications for studies of microbe-induced DNA damage [abstract]. In: Proceedings of the AACR Special Conference on Environmental Carcinogenesis: Potential Pathway to Cancer Prevention; 2019 Jun 22-24; Charlotte, NC. Philadelphia (PA): AACR; Can Prev Res 2020;13(7 Suppl): Abstract nr IA20.

Size-frequency distribution of coral assemblages in insular shallow reefs of the Mexican Caribbean using underwater photogrammetry.

The characterisation of changes in coral communities depends heavily on systematic monitoring programs and the collection of necessary metrics to assess reef health. Coral cover is the most used metric to determine reef health. The current organizational shift in coral requires the evaluation of complementary metrics, such as colony size and frequency distributions, which help to infer the responses of the coral populations to local stress or larger scale environmental changes. In this study, underwater digital photogrammetry techniques were used to assess the live cover of all coral colonies ≥3 cm2 and determine the size-frequency distribution of the dominant species in the shallow reefs of the Cozumel Reefs National Park (CRNP). In addition, the minimum sampling area (m2) needed to obtain a representative sample of the local species pool was estimated. Areas between 550 and 825 m2 per reef were photographed to generate high-resolution digital ortho-mosaics. The live area of the colonies was digitised to generate community matrices of species and abundance. EstimateS software was used to generate accumulation curves and diversity (Shannon H′) at increasing area intervals. Chi-Square tests (χ2, p = 0.05) were used to compare the observed vs estimated species richness. Spearman’s coefficients (rs), were calculated to correlate the increase in sampling area (m2) vs H′, and the Clench’s function was used to validate the observed richness (R2 = 1 and R > 90%). SIMPER analysis was performed to identify dominant species. Comparisons in terms of abundance, coral cover and size-frequencies were performed with Kruskal-Wallis (H test, p = 0.05), and paired Mann-Whitney (U test, p = 0.05). In order to obtain 90% of the species richness, a minimum sampling area of 374 m2is needed. This sampling area could be used in shallow Caribbean reefs with similar characteristics. Twelve (mainly non-massive) species: Agaricia agaricites, A humilis, A. tenuifolia, Eusmilia fastigiata, Meandrina meandrites, Montastrea cavernosa, Orbicella annularis, Porites astreoides, P. porites, Pseudodiploria strigosa, Siderastrea radians andS. siderea, were dominant in terms of abundance and coral cover. A significant increase (p < 0.05) in the number of colonies and live coral (m2) was observed from north to south of the study area. Furthermore, a wide intraspecific variation of size-frequency, even between adjacent reefs, was also observed. The size-frequency distributions presented positive skewness and negative kurtosis, which are related to stable populations, with a greater number of young colonies and a constant input of recruits. Considering the increase in disturbances in the Caribbean and the appearance of a new coral disease, digital photogrammetry techniques allow coral community characteristics to be assessed at high spatial resolutions and over large scales, which would be complementary to conventional monitoring programs.

Recovery of Microcystis surface scum following a mixing event: Insights from a tank experiment

Cyanobacteria of the genus Microcystis produces surface scum that negatively affects water quality in inland waters. This scum layer can be disintegrated and vertically dispersed by external forces (e.g., wind mixing), followed by reformation of surface scum as buoyant Microcystis colonies migrate upward. However, the recovery dynamics of Microcystis surface scum following a strong mixing event have rarely been studied. Here, we used a tank experiment to investigate the process of Microcystis surface scum recovery after a mixing event with focus on dynamics of colonies of different size classes and their contribution to that process. Microcystis colony size distribution and colony volume concentration was measured using a laser in-situ scattering and transmissometry instrument. The dynamics of Microcystis in the water column and upward colony migration velocity were strongly dependent on colony size. Larger colonies (>180 μm) with fast upward migration rates contributed the most to surface scum formation shortly after turbulence subsided. The contribution of slowly migrating smaller colonies to scum formation was observed over notably longer time. The estimated floating velocities of large colonies ranged 0.15 to 0.46 m h−1 depending on colony size and were 5–15 times higher than those of smaller colonies (~0.03 m h−1). The changes in colony size distribution of Microcystis in the water column reflect the dynamics of surface scum. Analysis of size distribution of Microcystis colonies can be used for better understanding and prediction of Microcystis surface scum development in water bodies.

Study of the transport modeling by diffusion of pollutants through porous materials

This paper presents how distance function dispersal produces diffusion range expansion of the contamination. We construct a stratified diffusion model, which describes the dynamics of the size distribution of colonies created by distance migrants of metal ions. The model consists of a Fick's equation combined with a Navier-stokes. The model provides an estimate of range expansion in terms of the rate adsorption due to neighborhood diffusion, the leap time and the geometric form. The results explain various types of nonlinear range expansion observed in materials or biomaterials.

Harvesting colonial Microcystis flos-aquae using two-stage filtration: Influence of pre-filtration on harvesting performance

The harvesting of bloom-forming colonial Microcystis flos-aquae using filtration helps with bloom control, the acquisition of a biomass resource and nutrient removal from eutrophic lakes. In this study, two-stage filtration of three combinations for M. flos-aquae harvesting was investigated, and the main factors affecting two-stage filtration performance were analysed. The results showed that compared with filtration with a 5 μm membrane alone, pre-filtration with a 20 μm screen improved biomass harvesting rate by 25.03% while 200 μm and 550 μm screens pre-filtrations resulted in decreases of 26.90% and 42.20%, respectively. The influences of colony size distribution and cellular concentration on filtration performance were predicted well using a multiple linear regression model (MLR). According to the model analysis, filtrate with larger colony size and narrower size distribution resulted higher harvesting performance. As the cellular concentration increased, the averaged flux decreased, while biomass harvesting rate increased initially, reached the highest value and then decreased. These results could be applied for the development of efficient filtration harvesting strategies for Microcystis bloom control.

Ritualized aggressive behavior reveals distinct social structures in native and introduced range tawny crazy ants.

How workers within an ant colony perceive and enforce colony boundaries is a defining biological feature of an ant species. Ants fall along a spectrum of social organizations ranging from single-queen, single nest societies to species with multi-queen societies in which workers exhibit colony-specific, altruistic behaviors towards non-nestmate workers from distant locations. Defining where an ant species falls along this spectrum is critical for understanding its basic ecology. Herein we quantify queen numbers, describe intraspecific aggression, and characterize the distribution of colony sizes for tawny crazy ant (Nylanderia fulva) populations in native range areas in South America as well as in their introduced range in the Southeastern United States. In both ranges, multi-queen nests are common. In the introduced range, aggressive behaviors are absent at all spatial scales tested, indicating that within the population in the Southeastern United States N. fulva is unicolonial. However, this contrasts strongly with intraspecific aggression in its South American native range. In the native range, intraspecific aggression between ants from different nests is common and ritualized. Aggression is typically one-sided and follows a stereotyped sequence of escalating behaviors that stops before actual fighting occurs. Spatial patterns of non-aggressive nest aggregation and the transitivity of non-aggressive interactions demonstrate that results of neutral arena assays usefully delineate colony boundaries. In the native range, both the spatial extent of colonies and the average number of queens encountered per nest differ between sites. This intercontinental comparison presents the first description of intraspecific aggressive behavior for this invasive ant and characterizes the variation in colony organization in the native-range, a pre-requisite to a full understanding of the origins of unicoloniality in its introduced range.

Individual and Population Level Variation in the Reproductive Potential of Deep-Sea Corals From Different Regions Within the Gulf of Maine

Deep-sea corals are of conservation concern in the North Atlantic due to prolonged disturbances associated with the exploitation of natural resources and a changing environment. As a result, two research cruises in the Gulf of Maine region during 2014 and 2017 collected samples of two locally dominant coral species, Primnoa resedaeformis and Paramuricea placomus, at six locations to investigate reproductive ecology. Remotely operated vehicles (ROVs) were used to collect specimens that were examined via paraffin histology, and coincident video surveys were used to determine size class distributions. Both species were identified as gonochoristic, and sampled locations exhibited dissimilarities in spermatocyst development and oocyte size except for those in close geographic proximity. Fecundities exhibited substantial ranges across sample locations and average oocyte sizes ( SD) were 140  117 m for P. resedaeformis and 64  46 m for P. placomus. In addition, colony size distributions were also significantly different across sampling locations. Notably, the Outer Schoodic Ridge sample location, with larger colony and oocyte sizes, was identified as a potential key source population of reproductive material in the Gulf of Maine. These data were used to calculate differences in reproductive potential based on relationships between colony morphology and reproductive output using height as a predictive proxy. Furthermore, calculated age at first reproduction, 7.6-19.8 years for P. resedaeformis and 20.7-37 years for P. placomus, which may be dependent on sex of the colony, provides a metric for estimating the amount of time these coral habitats will take to recover. This investigation, in response to historical population impacts and environmental change, links reproductive and morphometric relationships to inform population scale reproductive models, while also establishing an understanding of regional scale gametogenic variability within the Gulf of Maine region.

Freeware tool for analysing numbers and sizes of cell colonies

The clonogenic cell survival assay is a basic method to study the cytotoxic effect of radiation and chemical toxins. In large experimental setups, counting of colonies by eye is tiresome and prone to bias. Moreover, it is often interesting to quantify the size of individual colonies. Such analyses are largely facilitated by computerised image analysis systems. Although a number of such systems exist, they all focus on enumerating colonies and not on analysing the colony size. We have developed a new software package for both counting colonies and plotting their size distributions. The software called count and Plot HIstograms of Colony Size (countPHICS) consists of two parts: (1) a macro written for ImageJ which analyses computerised images of cell culture dishes or 6-well plates, counts colonies, estimates their size and saves the results in a text file; (2) a program written with QT Creator which reads the text file, plots histograms of colony size distribution and fits the best function. The full program is freely available at: http://www.fuw.edu.pl/~bbrzozow/FizMed/countPHICS.html. In conclusion, our new publically available software will facilitate colony counting and provide additional information on the colony growth rate, which is relevant especially for radiosensitisation studies.

A software tool for the quantification of metastatic colony growth dynamics and size distributions in vitro and in vivo.

The majority of cancer-related deaths are due to metastasis, hence improved methods to biologically and computationally model metastasis are required. Computational models rely on robust data that is machine-readable. The current methods used to model metastasis in mice involve generating primary tumors by injecting human cells into immune-compromised mice, or by examining genetically engineered mice that are pre-disposed to tumor development and that eventually metastasize. The degree of metastasis can be measured using flow cytometry, bioluminescence imaging, quantitative PCR, and/or by manually counting individual lesions from metastatic tissue sections. The aforementioned methods are time-consuming and do not provide information on size distribution or spatial localization of individual metastatic lesions. In this work, we describe and provide a MATLAB script for an image-processing based method designed to obtain quantitative data from tissue sections comprised of multiple subpopulations of disseminated cells localized at metastatic sites in vivo. We further show that this method can be easily adapted for high throughput imaging of live or fixed cells in vitro under a multitude of conditions in order to assess clonal fitness and evolution. The inherent variation in mouse studies, increasing complexity in experimental design which incorporate fate-mapping of individual cells, result in the need for a large cohort of mice to generate a robust dataset. High-throughput imaging techniques such as the one that we describe will enhance the data that can be used as input for the development of computational models aimed at modeling the metastatic process.

Coral disease prevalence estimation and sampling design.

In the last decades diseases have changed coral communities’ structure and function in reefs worldwide. Studies conducted to evaluate the effect of diseases on corals frequently use modified adaptations of sampling designs that were developed to study ecological aspects of coral reefs. Here we evaluate how efficient these sampling protocols are by generating virtual data for a coral population parameterized with mean coral density and disease prevalence estimates from the Caribbean scleractinian Orbicella faveolata at the Mexican Caribbean. Six scenarios were tested consisting of three patterns of coral colony distribution (random, randomly clustered and randomly over-dispersed) and two disease transmission modes (random and contagious). The virtual populations were sampled with the commonly used method of belt-transects with variable sample-unit sizes (10 × 1, 10 × 2, 25 × 2, 50 × 2 m). Results showed that the probability of obtaining a mean coral disease prevalence estimate of ±5% of the true prevalence value was low (range: 11–48%) and that two-sample comparisons achieved rather low power, unless very large effect sizes existed. Such results imply low statistical confidence to assess differences or changes in coral disease prevalence. The main problem identified was insufficient sample size because local mean colony size, density and spatial distribution of targeted coral species was not taken into consideration to properly adjust the sampling protocols.

Demographics of the zooxanthellate coral Oculina patagonica along the Mediterranean Iberian coast in relation to environmental parameters

Marine ecosystems are threatened by cumulative human-related impacts that cause structural and functional alterations. In the Mediterranean Sea, the zooxanthellate coral Oculina patagonica (Scleractinia, Oculinidae) can turn algal forests into coral-dominated ecosystems and provides a case study for examining how zooxanthellate corals can affect the structure of algal-dominated shallow-water rocky ecosystems in temperate areas. Our goal was to provide a quantitative baseline assessment of O. patagonica demographics along ~1300km of the Mediterranean Iberian coast and relate them to environmental parameters. The highest coral success was in the South Balearic Sea zone, where the populations exhibited >6-fold higher mean living coral cover, lower partial colony mortality and colony size distributions indicating that the populations in this zone were growing faster than those in the peripheral south-west (North Alborán Sea) and north-east (Mid and North Balearic Sea, and West Gulf of Lyons) zones. The coral demographics (i.e., density, cover, and skewness and kurtosis coefficients of colony size distributions) were positively correlated with each other and the annual mean seawater temperature (ST), 10th-ST percentile (P10th-ST), 90th-ST percentile (P90th-ST) and photosynthetically active radiation at 3-m depth (PAR-3m), but they were negatively correlated with chlorophyll-a. Based on these results, we identified the following thresholds that may constrain the growth of O. patagonica colonies and populations: annual mean ST <19–20°C, P10th-ST <14°C, P90th-ST <25°C and >27°C, and PAR-3m <30molphotonsm−2day−1. The species abundance along the Iberian coast conforms to the abundant-center pattern of distribution. However, the coral demographics indicated that this pattern was not only related to the time of establishment but also to differences in coral population growth, which were correlated with key environmental parameters. Our results contribute understanding of the forces driving population growth of O. patagonica and support the hypothesis of an ongoing coral-mediated tropicalization of macroalgae-dominated temperate ecosystems.

Early-phase dynamics in coral recovery following cyclone disturbance on the inshore Great Barrier Reef, Australia

Coral recovery (the restoration of abundance and composition of coral communities) after disturbance is a key process that determines the resilience of reef ecosystems. To understand the mechanisms underlying the recovery process of coral communities, colony abundance and size distribution were followed on reefs around Pelorus Island, located in the inshore central region of the Great Barrier Reef, following a severe tropical cyclone in 2011 that caused dramatic loss of coral communities. Permanent quadrats (600 m2) were monitored biannually between 2012 and 2016, and individual coral colonies were counted, sized and categorized into morphological types. The abundance of coral recruits and coral cover were also examined using permanent quadrats and random line intercept transects, respectively. The number of colonies in the smallest size class (4–10 cm) increased substantially during the study period, driving the recovery of coral populations. The total number of coral colonies 5 yr post-cyclone reached between 73 and 122% of pre-cyclone levels though coral cover remained between 16 and 31% of pre-cyclone levels, due to the dominance of small coral colonies in the recovering communities. Temporal transitions of coral demography (i.e., colony-size distributions) illustrated that the number of recently established coral populations overtook communities of surviving colonies. Coral recruits (< 4 cm in size) also showed increasing patterns in abundance over the study period, underscoring the importance of larval supply in coral recovery. A shift in morphological composition of coral communities was also observed, with the relative abundance of encrusting corals reduced post-cyclone in contrast to their dominance prior to the disturbance. This study identifies the fine-scale processes involved in the initial recovery of coral reefs, providing insights into the dynamics of coral demography that are essential for determining coral reef resilience following major disturbance.

The ecology of the Mediterranean stony coral Cladocora caespitosa (Linnaeus, 1767) in the Gulf of Trieste (northern Adriatic Sea): a 30-year long story

ABSTRACTCladocora caespitosa is an endemic coral of the Mediterranean Sea and an important carbonate bioconstructor that adds 3D complexity to the habitat, thus increasing marine biodiversity. Despite its important role in the ecosystem, the real status of the population along most of the Mediterranean coastline is still poorly investigated and very little is known about the resilience of the species. Using non-destructive visual surveys, colonies of C. caespitosa were investigated by SCUBA diving in 2013 and 2015 at seven sites of the northern Adriatic Sea (southern part of the Gulf of Trieste). Data about colony size, index of sphericity and corallite diameter were collected. Almost all biometrical parameters differed significantly among sampling sites, showing low occurrence of the larger size classes compared to the abundance of small-sized colonies. This pattern of distribution is typical of long-lived organisms. The positively skewed colony size distribution could be due to both a high mortality rate of small colonies unable to reach larger size classes, and to a high fragmentation rate of colonies, related to a strong hydrodynamic forces. The northern Adriatic population of C. caespitosa has previously been investigated by Schiller, who reported size and abundance data of colonies from one site, at a depth range of 2–5 m. We compared these data with our findings from the same sampling site, adding new information about the ecology of C. caespitosa. After a 30-year period, the comparison shows a change in the size distribution of colonies, with a decrease of the small class and an increase of the medium class of colonies. In view of these conclusions, further assessments are required in order to evaluate the trend of the northernmost C. caespitosa population in the Mediterranean Sea.

Evolution of the optimal reproductive schedule in the ant Camponotus (Colobopsis) nipponicus (wheeler): a demographic approach

1. Traits are hypothesised to optimise via natural selection. The schedule of reproduction is an important adaptive trait, but its evolution is difficult to study, as measuring parameters is usually difficult. However, the sufficient amounts of demographic data enable us to estimate these parameters.2. Here, it is shown that the reproductive schedule of the ant Camponotus (Colobopsis) nipponicus is tuned to maximise the lifetime production of alates.3. A colony started its reproduction 4 years after the colony founding, at which time they were far smaller than well‐developed colonies. This contradicts the prediction of the bang‐bang strategy theory. The size distribution of colonies in the study area showed that the mortality of small colonies is much higher than that of large colonies.4. A simulation analysis suggests that the colonies that are smaller than the threshold can still achieve significant improvement in colny survival to the following year by investing all resources in colony growth instead of reproduction. A sensitivity analysis for the starting year of reproduction showed that the observed schedule maximises lifetime alate production. The demographic data suggest a stable population, which is required for optimisation through this maximisation.5. The observed reproductive schedule must be optimised, and the breakdown of the bang‐bang theory is due to higher mortalities during the incipient stage of colonies. This study demonstrates that having enough demographic data creates a useful tool for studying the evolution of life‐history characteristics.

Why come back home? Breeding-site fidelity varies with group size and parasite load in a colonial bird

Fidelity to a past breeding site is widespread among animals and may confer both costs and benefits. Colonial species occur at specific sites that can accommodate multiple breeders, and the choice of whether to return to last year's site or disperse elsewhere can affect colony site use, the colony size distribution and individual fitness. For the colonial cliff swallow, Petrochelidon pyrrhonota, which occupies colonies of widely different sizes, we used a 30-year field study in western Nebraska to investigate how the extent of infestation by ectoparasites and colony size affected breeders' colony site fidelity between years. We compared philopatry at colonies where parasitic swallow bugs, Oeciacus vicarius, had been removed by fumigation with that at nonfumigated sites exposed to natural levels of ectoparasites. About 25% of birds at nonfumigated colonies returned to their previous year's site, whereas about 69% of birds at fumigated colonies did so. Site fidelity was greatest at nonfumigated sites that changed the least in size between years. Birds were less likely to return to a nonfumigated site as the colony there became increasingly larger. Individuals philopatric to both nonfumigated and fumigated sites resided in colonies more similar in size between years than did dispersing birds. Most cliff swallows settled within 6 km of their previous year's site, indicating that many nonphilopatric birds still may have had some familiarity with the local landscape surrounding the site to which they moved. Removal of ectoparasites at a site allows large colonies to persist there perennially, probably contributing to higher philopatry because such large colonies are rare and would have been difficult to find had the residents dispersed. Cliff swallows are likely to be sensitive to both colony size and general familiarity with a given site or landscape region, and probably integrate these with other cues to select breeding colonies.