Ecological Data Research Articles

Metabolomics-Guided Discovery of New Dimeric Xanthones from Co-Cultures of Mangrove Endophytic Fungi Phomopsis asparagi DHS-48 and Phomopsis sp. DHS-11.

The co-culture strategy, which mimics natural ecology by constructing an artificial microbial community, is a useful tool for the activation of biosynthetic gene clusters (BGCs) to generate new metabolites, as well as to increase the yield of respective target metabolites. As part of our project aiming at the discovery of structurally novel and biologically active natural products from mangrove endophytic fungi, we selected the co-culture of a strain of Phomopsis asparagi DHS-48 with another Phomopsis genus fungus DHS-11, both endophyted in mangrove Rhizophora mangle considering the impart of the taxonomic criteria and ecological data. The competition interaction of the two strains was investigated through morphology observation and scanning electron microscopy (SEM), and it was found that the mycelia of the DHS-48 and DHS-11 compacted and tangled with each other with an interwoven pattern in the co-culture system. A new approach that integrates HPLC chromatogram, 1HNMR spectroscopy, UPLC-MS-PCA, and molecular networking enabled the targeted isolation of the induced metabolites, including three new dimeric xanthones phomoxanthones L-N (1-3), along with six known analogs (4-9). Their planar structures were elucidated by an analysis of their HRMS, MS/MS, and NMR spectroscopic data and the absolute configurations based on ECD calculations. These metabolites showed broad cytotoxic activity against the cancer cells assessed, of which compounds 7-9 displayed significant cytotoxicity towards human liver cells HepG-2 with IC50 values ranging from 4.83 μM to 12.06 μM. Compounds 1-6 exhibited weak immunosuppressive activity against the proliferation of ConA-induced (T-cell) and LPS-induced (B-cell) murine splenic lymphocytes. Therefore, combining co-cultivation with a metabolomics-guided strategy as a discovery tool will be implemented as a systematic strategy for the quick discovery of target bioactive compounds.

Confirmation of the recognition of Culiseta (Culiseta) indica Edwards, 1920 as a distinct species based on integrated morphological and molecular data.

Theobaldia indica Edwards, 1920, classified as a subspecies of Culiseta (Culiseta) alaskaensis (Ludlow, 1906), was recently restored to its original species status, as Culiseta (Culiseta) indica (Edwards), based on comprehensive assessments of morphological, ecological and distributional data. Predating the recognition of indica as a separate species, we collected specimens of this nominal taxon in the Western Himalayan region of India during 20152017, and used morphological and molecular studies to assess its taxonomic status. Our detailed examination of adult morphology, male genitalia and larval characteristics revealed significant distinctions between putative Cs. alaskaensis alaskaensis and Cs. alaskaensis indica, and sequencing of the barcode region of the mitochondrial COI gene yielded a Kimura 2 parameter genetic distance of 5.9% between them, well above the standard 23% commonly accepted to indicate separate species. These results strongly support the formal recognition of Cs. indica as a separate species. Furthermore, the geographical distribution of Cs. indica provides additional evidence in support of its species status.

EKOLOJİK AYAK İZİ VE TİCARI AÇIKLIK BAĞLANTISI: G7 ÜLKELERİ ÖRNEĞİ

The ecological footprint basically aims to measure the impact of humans on the ecosystem. The measurements made include the area required to produce the materials consumed in terms of the consumption footprint and the area required to absorb the carbon dioxide emissions. No distinction is made between domestic and foreign producers in the production by the countries. The countries with the most developed industry and the highest impact on the ecosystem in this sense appear as the countries with the highest footprint in the ecosystem. This study, based on the ecological footprint data of seven industrialized countries (G7) and these countries between 1984 and 2019, aims to reveal the effect of ecological footprints on trade openness. Panel data analysis and ARDL Boundary Test / PMG (Pooled Average Group) method was used to obtain the results. DOLS and FMOLS methods were also used to compare both economic and empirical results and for consistency. As a result of the analysis, as the impact of industrialized countries on the ecosystem increases, their trade openness also increases in the short and long term. This effect could be seen most clearly in the United States (USA), which has the most developed industry. This research paper will be pointed out these important issues.

The genetic basis of dispersal in a vertebrate metapopulation.

Dispersal affects evolutionary processes by changing population size and genetic composition, influencing the viability and persistence of populations. Investigating which mechanisms underlie variation in dispersal phenotypes and whether populations harbour adaptive potential for dispersal is crucial to understanding the eco-evolutionary dynamics of this important trait. Here, we investigate the genetic architecture of dispersal among successfully recruited individuals in an insular metapopulation of house sparrows. We use an extensive long-term individual-based ecological data set and high-density single-nucleotide polymorphism (SNP) genotypes for over 2500 individuals. We conducted a genome-wide association study (GWAS), and found a relationship between dispersal probability and a SNP located near genes known to regulate circadian rhythm, glycogenesis and exercise performance, among other functions. However, this SNP only explained 3.8% of variance, suggesting that dispersal is a polygenic trait. We then used an animal model to estimate heritable genetic variation (σA 2 ), which composes 10% of the total variation in dispersal probability. Finally, we investigated differences in σA 2 across populations occupying ecologically relevant habitat types (farm vs. non-farm) using a genetic groups animal model. We found different adaptive potentials across habitats, with higher mean breeding value, σA 2 , and heritability for the habitat presenting lower dispersal rates, suggesting also different roles of environmental variation. Our results suggest a complex genetic architecture of dispersal and demonstrate that adaptive potential may be environment dependent in key eco-evolutionary traits. The eco-evolutionary implications of such environment dependence and consequent spatial variation are likely to become ever more important with the increased fragmentation and loss of suitable habitats for many natural populations.

Bayesian multi-proxy reconstruction of early Eocene latitudinal temperature gradients

Abstract. Accurately reconstructing large-scale palaeoclimatic patterns from sparse local records is critical for understanding the evolution of Earth's climate. Particular challenges arise from the patchiness, uneven spatial distribution, and disparate nature of palaeoclimatic proxy records. Geochemical data typically provide temperature estimates via transfer functions derived from experiments. Similarly, transfer functions based on the climatic requirements of modern taxa exist for some fossil groups, such as pollen assemblages. In contrast, most ecological and lithological data (e.g. coral reefs and evaporites) only convey information on broad climatic requirements. Historically, most large-scale proxy-based reconstructions have used either geochemical or ecological data, but few studies have combined multiple proxy types into a single quantitative reconstruction. Large spatial gaps in existing proxy records have often been bridged by simple averaging, without taking into account the spatial distribution of samples, leading to biased temperature reconstructions. Here, we present a Bayesian hierarchical model to integrate ecological data with established geochemical proxies into a unified quantitative framework, bridging gaps in the latitudinal coverage of proxy data. We apply this approach to the early Eocene climatic optimum (EECO), the interval with the warmest sustained temperatures of the Cenozoic. Assuming the conservation of thermal tolerances of modern coral reefs and mangrove taxa, we establish broad sea surface temperature ranges for EECO coral reef and mangrove sites. We integrate these temperature estimates with the EECO geochemical shallow marine proxy record to model the latitudinal sea surface temperature gradient and global average temperatures of the EECO. Our results confirm the presence of a flattened latitudinal temperature gradient and unusually high polar temperatures during the EECO, which is supported by high-latitude ecological data. We show that integrating multiple types of proxy data, and adequate prior information, has the potential to enhance quantitative palaeoclimatic reconstructions, improving temperature estimates from datasets with limited spatial sampling.

Description of the helminth community structure from two populations of Plains Viscacha (Rodentia: Chinchillidae) in semi-captive and wild conditions

Lagostomus maximus is a native rodent of South America that presents economic and biological importance. However, few studies on parasites of this rodent are available throughout its geographic distribution. The aim of this study was to explore, describe and compare the structure of helminth communities from 2 populations of L. maximus in semi-captive (SCHP) and wild (WHP) conditions in Buenos Aires Province, Argentina. The structure of helminth communities was studied considering ecological data at different levels. Seven helminth taxa were collected. Graphidioides spp. and Lagostonema ecasiense were the most prevalent species in SCHP, and Viannella viscaciae in WHP. This last species showed the highest values of mean intensity and mean abundance in both host populations. Helminths from SCHP showed higher values of abundance, mean intensity, mean abundance, diversity, and evenness, and lower values of specific richness and dominance than WHP. Specific richness, evenness and dominance allowed separating the 2 host populations. The abundances of V. viscaciae and Graphidioides spp. distinguished both host populations, suggesting possible influences of human intervention and/or environmental characteristics, as consequence of semi-captive and wild conditions.

Polyphasic description of Ciimarium marinum gen. et sp. nov. (Prochlorococcaceae, Synechococcales): a new picocyanobacterial taxon from the Portuguese coastal ecosystem

In this paper, we describe Ciimarium marinum gen. et sp. nov. (Prochlorococcaceae, Synechococcales) based on 16S rRNA gene phylogenies, 16S-23S ITS secondary structures, ultrastructure (TEM), morphological, pigments and ecological data of “Synechococcus” sp. LEGE 11466. The strain was isolated from a sample collected at Leixões Harbour, Portugal (41°11’08.1”N 8°43’08.8”W) on September 26th, 2011, by scraping an epilithic biofilm under 10-13m depth, less than 1km offshore. Bayesian Inference and Maximum Likelihood phylogenies demonstrate that the Ciimarium sequence is placed in a monophyletic clade with strong phylogenetic support (BI=1, ML=100), within the Prochlorococcaceae cluster. The type strain LEGE 11466 is phylogenetically distant from other reference strains of Cyanobacteria and is grouped with Uncultured “Synechococcus” MLS1228cl3 , “Synechococcus” MLCB, “Cyanobium” ATX 6A2 ATX-6A2-C45 and “Synechococcus” MBIC10613.. The secondary structures of 16S-23S ITS corroborate with the separation of Ciimarium from all the Prochlorococcaceae genera. Also, they show that MLCB and ATX 6A2 ATX-6A2-C45 may be different species from the type LEGE 11466. The ultrastructure analysis shows parietal thylakoids, in agreement with the family description. Morphologically the genus is indistinguishable from other Prochlorococcaceae genera. The pigments analysis shows Zeaxanthin and β-carotene as the main pigments, and also a low concentration of phycocyanin. Finally, our phylogenies indicate that a revision of the Prochlorococcaceae family is necessary, as there are still many Synechococcus-like Cyanobacteria strains that should be described as new genera in the future.

Nature-Based Management of Lawns—Enhancing Biodiversity in Urban Green Infrastructure

Urban green areas have multifunctional benefits that may mitigate unfavorable health and ecological effects. Green areas represent important biodiversity hideouts in anthropogenic regions. Lawns are the most common elements of urban greenery, covering a considerable number of green areas in cities. The aim of this analysis was to gain knowledge on urban greenery and elaborate recommendations related to management that favors grass lawn biodiversity. The established working hypothesis is that the limited intensity of management in urban grass areas is reflected in the modification of their species composition, as well as their potential ecological functions. An experiment on the management of city lawns was conducted in 2010 (still ongoing). There are three lawn variants under different management methods: ornamental, city, and permaculture lawns. Vegetation was assessed using the method of phytocoenological relevés. The coverage values of the individual plant species were processed using multidimensional analysis of ecological data. The results showed that human decisions and activities affected the species composition of these grassy areas. There were 46 plant taxa found during the monitoring: 12 in ornamental lawn variants, 24 in city lawn variants, and 31 in permaculture lawn variants. Permaculture lawns with extensive management represent the most environmentally friendly variant with respect to biodiversity and soil moisture content. However, changes in species composition have raised questions regarding the extent to which they may perform other ecosystem functions. Increasing the intensity of lawn management has resulted in lower plant diversity. Extensive management alters the aesthetic value of lawns and creates spaces for species that may spread in urban environments.

Medical Misadventures as Errors and Mistakes and Motor Vehicular Accidents in the Disproportionate Burden of Childhood Mortality among Blacks/African Americans in the United States: CDC Dataset, 1968-2015.

Racial disparities in infant mortality in the United States persist after adjustment for known confounders of race and mortality association, as well as heterogeneity assessment. Epidemiologic and clinical data continue to show the survival disadvantages of Black/AA children: when Black/AAs are compared to whites, they are three times as likely to die from all-cause mortality. The persistent inability to remove the variance in race-mortality association is partly due to unobserved, unmeasured, and residual confounding, as well as implicit biases in public health and clinical medicine in health equity transformation. This current epidemiologic-perspective explanatory model study aimed to examine the possible explanation of racial differences in U.S. infant mortality using medical misadventures as errors and mistakes, and infants' involvement in motor vehicular traffic accidents. Using CDC WONDER ecologic data from 1968 to 2015, we assessed the infant mortality-rate ratio and percent change associated with medical misadventures as well as motor vehicular accidents or trauma. The rate ratio and percent change were estimated using stratification analysis and trend homogeneity, respectively. There was a Black-white racial difference in medical misadventures during the study period. Relative to the years 1968-1978 (rate ratio [RR], 1.43), there was a steady increase in the mortality-rate ratio in 1979-1998 (52%, RR = 1.52), and mortality was more than two times as likely in 1999-2015 (RR = 2.37). However, with respect to motor vehicular accident/trauma mortality, the mortality ratio, although lower among Blacks in 1968-1978 (RR, 0.92), increased in 1979-1998 by 27% (RR = 1.27) but decreased in 1999-2015 (RR, 1.17), though there was still an excess of 17% mortality among Black/AAs. The percent change for medical misadventures indicated an increasing trend from 9.3% in 1998 to 52% in 2015. However, motor vehicular-related mortality indicated a positive trend in 1998 (38.5%) but a negative trend in 2015 (-8.4%). There were substantial race differentials or variances in infant mortality associated with medical misadventures compared to traffic accidents, and Black/AA children relative to whites experienced a survival disadvantage. These comparative findings are suggestive of medical misadventures and motor vehicular trauma as potential explanations for some of the persistent Black-white disparities in overall infant mortality in the U.S. From these findings, we recommend a national effort to address these issues, thus narrowing the observed disparities in the U.S. infant mortality burden among Black/AAs.

A unified framework for time‐to‐detection occupancy and abundance models

Abstract Time‐to‐detection (TTD) occupancy models are increasingly used to study site occupancy of organisms. Occupancy is a reduced representation of abundance (distinguishing only between and individuals), which is also often a quantity of interest. In this paper, we present a novel framework for TTD occupancy models that address limitations of existing approaches. Our approach incorporates factors that accommodate detection heterogeneity among sites/visits and inter‐visit dependency, allowing for the relaxation of some restrictive assumptions inherent in previous models. As a result, our framework offers a robust and versatile tool for analysing various ecological data sets. We employ a maximum likelihood approach to estimate model parameters and conduct inference for the proposed TTD occupancy models. A key feature of these models is the introduction of a community parameter. This parameter characterizes the similarity of detectabilities, ranging from complete independence to complete identity, across multiple site visits. This framework disentangles the detection rate, abundance and occupancy, similar to the popular N‐mixture model. For situations where abundance estimation is not the primary goal, a family of mixed gamma exponential TTD models is developed, which generally exhibit more stable numerical properties compared to N‐mixture type TTD models. The performance of the proposed models and some reduced models is evaluated through simulation studies. The results indicate that the N‐mixture TTD model tends to considerably overestimate the occupancy probability when the community parameter is less than one, a condition necessary to satisfy the strict closure population assumption. On the other hand, the standard exponential TTD occupancy model underestimates the occupancy probability in the presence of unobserved detection heterogeneity and inter‐visit dependency. An analysis of bird species in the Karoo region of South Africa demonstrates the enhanced flexibility of the proposed TTD occupancy models for data fitting. This paper demonstrates the importance of employing more flexible and general models to accurately capture the complexities of ecological systems or survey data. We provide R‐code to fit all considered models to data. The proposed TTD model framework contributes to enhancing our understanding of species occupancy distributions.

Stay or go? Geographic variation in risks due to climate change for fishing fleets that adapt in-place or adapt on-the-move

From fishers to farmers, people across the planet who rely directly upon natural resources for their livelihoods and well-being face extensive impacts from climate change. However, local- and regional-scale impacts and associated risks can vary geographically, and the implications for development of adaptation pathways that will be most effective for specific communities are underexplored. To improve this understanding at relevant local scales, we developed a coupled social-ecological approach to assess the risk posed to fishing fleets by climate change, applying it to a case study of groundfish fleets that are a cornerstone of fisheries along the U.S. West Coast. Based on the mean of three high-resolution climate projections, we found that more poleward fleets may experience twice as much local temperature change as equatorward fleets, and 3–4 times as much depth displacement of historical environmental conditions in their fishing grounds. Not only are they more highly exposed to climate change, but some poleward fleets are >10x more economically-dependent on groundfish. While we show clear regional differences in fleets’ flexibility to shift to new fisheries via fisheries diversification (‘adapt in-place’) or shift their fishing grounds in response to future change through greater mobility (‘adapt on-the-move’), these differences do not completely mitigate the greater exposure and economic dependence of more poleward fleets. Therefore, on the U.S. West Coast more poleward fishing fleets may be at greater overall risk due to climate change, in contrast to expectations for greater equatorward risk in other parts of the world. Through integration of climatic, ecological, and socio-economic data, this case study illustrates the potential for widespread implementation of risk assessment at scales relevant to fishers, communities, and decision makers. Such applications will help identify the greatest opportunities to mitigate climate risks through pathways that enhance flexibility and other dimensions of adaptive capacity.

Reproducible WiSDM: a workflow for reproducible invasive alien species risk maps under climate change scenarios using standardized open data

IntroductionSpecies distribution models (SDMs) are often used to produce risk maps to guide conservation management and decision-making with regard to invasive alien species (IAS). However, gathering and harmonizing the required species occurrence and other spatial data, as well as identifying and coding a robust modeling framework for reproducible SDMs, requires expertise in both ecological data science and statistics.MethodsWe developed WiSDM, a semi-automated workflow to democratize the creation of open, reproducible, transparent, invasive alien species risk maps. To facilitate the production of IAS risk maps using WiSDM, we harmonized and openly published climate and land cover data to a 1 km2 resolution with coverage for Europe. Our workflow mitigates spatial sampling bias, identifies highly correlated predictors, creates ensemble models to predict risk, and quantifies spatial autocorrelation. In addition, we present a novel application for assessing the transferability of the model by quantifying and visualizing the confidence of its predictions. All modeling steps, parameters, evaluation statistics, and other outputs are also automatically generated and are saved in a R markdown notebook file.ResultsOur workflow requires minimal input from the user to generate reproducible maps at 1 km2 resolution for standard Intergovernmental Panel on Climate Change (IPCC) greenhouse gas emission representative concentration pathway (RCP) scenarios. The confidence associated with the predicted risk for each 1km2 pixel is also mapped, enabling the intuitive visualization and understanding of how the confidence of the model varies across space and RCP scenarios.DiscussionOur workflow can readily be applied by end users with a basic knowledge of R, does not require expertise in species distribution modeling, and only requires an understanding of the ecological theory underlying species distributions. The risk maps generated by our repeatable workflow can be used to support IAS risk assessment and surveillance.

Social-ecological vulnerability to environmental extremes and adaptation pathways in small-scale fisheries of the southern California Current

Coastal ecosystems and human communities are threatened worldwide by climate change, and shocks from social, market and political change. There is an urgent global need to promote resilient food production and livelihoods in the face of these shocks. Small-scale fisheries (SSF) in rural settings can be particularly vulnerable as they frequently lack the resources, rights and infrastructure to respond to shocks originating outside the focal systems. We examined ecological and social outcomes of environmental extremes in a SSF socio-ecological system (SES) by using long-term oceanographic (between 2010-2019) and ecological (2006-2018) data tracking change in a kelp forest ecosystem of Baja California, Mexico, and concurrent documentation of proactive and reactive actions of a fishing community organized in a cooperative. Results indicate a complex landscape of ‘winners’ and ‘losers’ among species and fisheries exposed to unprecedented environmental extremes, including marine heat waves and prolonged hypoxia, and a suite of adaptive actions by the local fishing cooperative, and others in the region, that have helped confront these rapid and drastic changes. Cooperatives have established voluntary marine reserves to promote recovery of affected populations and have invested in diversification of activities enabled by access rights, collective decision-making, and participatory science programs. Results indicate that local actions can support social and ecological resilience in the face of shocks, and that enabling locally-driven adaptation pathways is critical to resilience. This case study highlights the crucial importance of strengthening and supporting rights, governance, capacity, flexibility, learning, and agency for coastal communities to respond to change and sustain their livelihoods and ecosystems in the long run.

Excess Deaths During the COVID-19 Pandemic in Southern Iran: Estimating the Absolute Count and Relative Risk Using Ecological Data.

The coronavirus disease 2019 (COVID-19) pandemic led to increased mortality rates. To assess this impact, this ecological study aimed to estimate the excess death counts in southern Iran. The study obtained weekly death counts by linking the National Death Registry and Medical Care Monitoring Center repositories. The P-score was initially estimated using a simple method that involved calculating the difference between the observed and expected death counts. The interrupted time series analysis was then used to calculate the mean relative risk (RR) of death during the first year of the pandemic. Our study found that there were 5571 excess deaths from all causes (P-score=33.29%) during the first year of the COVID-19 pandemic, with 48.03% of these deaths directly related to COVID-19. The pandemic was found to increase the risk of death from all causes (RR, 1.26; 95% confidence interval [CI], 1.19 to 1.33), as well as in specific age groups such as those aged 35-49 (RR, 1.21; 95% CI, 1.12 to 1.32), 50-64 (RR, 1.38; 95% CI, 1.28 to 1.49), and ≥65 (RR, 1.29; 95% CI, 1.12 to 1.32) years old. Furthermore, there was an increased risk of death from cardiovascular diseases (RR, 1.17; 95% CI, 1.11 to 1.22). There was a 26% increase in the death count in southern Iran during the COVID-19 pandemic. More than half of these excess deaths were not directly related to COVID-19, but rather other causes, with cardiovascular diseases being a major contributor.

Similarity visualization of soundscapes in ecology and music

The concept of a soundscape is found in both ecology and music studies. Nature soundscapes and soundscape compositions are analyzed by both disciplines, respectively, to understand their biological diversity and ecosystem functioning and to interpret their compositional structure. A major challenge for both disciplines is visualizing the information embedded in a large variety of soundscapes and to share it with different audiences, from non-professionals to experts. To analyze soundscapes, both disciplines have independently developed similarity visualizations. However, no attempt has been made yet to combine these two fields of research to improve our ecological and musical perception of environmental sounds through shared similarity analysis methods. In this paper, we introduce a new visualization tool, the soundscape chord diagram (SCD), a circular similarity representation method that can be applied to any type of soundscape, either in ecoacoustics or electroacoustic studies. Our approach consists of visualizing spectral similarities between predefined sound segments based on the computation of a β-diversity acoustic index and on automatic clustering. SCDs were tested on two ecoacoustic forest databases and two electroacoustic soundscape compositions. SCDs were performant for the identification of specific acoustic events and highlighted known diel periods for nature soundscapes and written parts for soundscape compositions. This new visualization tool allows us to easily decipher the structure of musical and ecological acoustic data. SCDs could be applied to a large variety of soundscapes and promote their knowledge and preservation. This study opens a new way of investigating soundscapes at the interface between ecology and music, bringing together science and the arts.

Taxonomic revision of the native Magnolia (Magnoliaceae) species of Brazil

The genus Magnolia (Magnoliaceae) has a wide and disjunct geographic distribution ranging from Eastern and South Asia to Malaysia, extending across the Neartics and reaching into the Neotropics. Regarding its infrageneric classification, the genus is divided into three subgenera: Yulania, Gynopodium and Magnolia, the latter including the section Talauma in which the native Brazilian taxa are classified. The species of Magnolia sect. Talauma can be recognized by two parallel longitudinal scars on the petiole formed by the shedding of the stipules, in addition to a woody syncarp that breaks into irregular plates at dehiscence. Currently, in Brazil, species recognition is not clear on national platforms that are widely used by the Brazilian botanical community (e.g. Flora do Brasil), with only two native Magnolia species being accepted: M. amazonica and M. ovata. The lack of knowledge about the species and their respective characteristics has resulted in many identification errors in Brazilian herbaria, which contributes to the lack of knowledge about their current conservation status. We conducted a complete taxonomic revision based on extensive fieldwork, a herbarium survey, along with literature study. Based on this, we propose to recognize three previously described species, supporting the acceptance of five native Magnolias occurring in Brazil, namely: M. amazonica, M. brasiliensis, M. irwiniana, M. ovata and M. sellowiana. However, we follow the Flora do Brasil in maintaining M. paranaensis as a synonym of M. ovata. Additionally, we designate a lectotype for M. sellowiana. We present morphological descriptions and the geographic distribution for each species, in addition to an identification key to all of these plus the two introduced ornamental species from Asia and North America, illustrations, photographs, ecological data, updated conservation status and taxonomic notes.

Stelfi: An R package for fitting Hawkes and log-Gaussian Cox point process models.

Modelling spatial and temporal patterns in ecology is imperative to understand the complex processes inherent in ecological phenomena. Log-Gaussian Cox processes are a popular choice among ecologists to describe the spatiotemporal distribution of point-referenced data. In addition, point pattern models where events instigate others nearby (i.e., self-exciting behaviour) are becoming increasingly popular to infer the contagious nature of events (e.g., animal sightings). While there are existing R packages that facilitate fitting spatiotemporal point processes and, separately, self-exciting models, none incorporate both. We present an R package, stelfi, that fits spatiotemporal self-exciting and log-Gaussian Cox process models using Template Model Builder through a range of custom-written C++ templates. We illustrate the use of stelfi's functions fitting models to Sasquatch (bigfoot) sightings data within the USA. The structure of these data is typical of many seen in ecology studies. We show, from a temporal Hawkes process to a spatiotemporal self-exciting model, how the models offered by the package enable additional insights into the temporal and spatial progression of point pattern data. We present extensions to these well-known models that include spatiotemporal self-excitation and joint likelihood models, which are better suited to capture the complex mechanisms inherent in many ecological data. The package stelfi offers user-friendly functionality, is open source, and is available from CRAN. It offers the implementation of complex spatiotemporal point process models in R for applications even beyond the field of ecology.

Among-individual behavioural variation in the ornamental red cherry shrimp, Neocaridina heteropoda.

Personality variation, defined as among-individual differences in behaviour that are repeatable across time and context, is widely reported across animal taxa. From an evolutionary perspective, characterising the amount and structure of this variation is useful since differences among individuals are the raw material for adaptive behavioural evolution. However, behavioural variation among individuals also has implications for more applied areas of evolution and ecology-from invasion biology to ecotoxicology and selective breeding in captive systems. Here, we investigate the structure of personality variation in the red cherry shrimp, Neocaridina heteropoda, a popular ornamental species that is readily kept and bred under laboratory conditions and is emerging as a decapod crustacean model across these fields, but for which basic biological, ecological and behavioural data are limited. Using two assays and a repeated measures approach, we quantify behaviours putatively indicative of shy-bold variation and test for sexual dimorphism and/or size-dependent behaviours (as predicted by some state-dependent models of personality). We find moderate-to-high behavioural repeatabilities in most traits. Although strong individual-level correlations across behaviours are consistent with a major personality axis underlying these observed traits, the multivariate structure of personality variation does not fully match a priori expectations of a shy-bold axis. This may reflect our ecological naivety with respect to what really constitutes bolder, more risk-prone, behaviour in this species. We find no evidence for sexual dimorphism and only weak support for size-dependent behaviour. Our study contributes to the growing literature describing behavioural variation in aquatic invertebrates. Furthermore, it lays a foundation for further studies harnessing the potential of this emerging model system. In particular, this existing behavioural variation could be functionally linked to life-history traits and invasive success and serve as a target of artificial selection or bioassays. It thus holds significant promise in applied research across ecotoxicology, aquaculture and invasion biology.

Climate Change: A bibliometric study of the Great Lakes Basin

The Great Lakes region of North America is experiencing climate-driven disturbances that threaten the safety and livelihoods of coastal communities and people. Limitations to the spatial and temporal coverage of research have the potential to hamper the ability to predict site-specific conditions and responses to climatic events. In this paper, we contextualize these spatial and temporal limitations of climate change research. Our summary reveals an uneven spatial distribution of research across the basin and publication outlets, with research focused on Lakes Superior, Michigan, and Huron, and the increasing availability of biological and ecological data to forecast future conditions. The spatial and temporal limitations related to historical data, region-wide monitoring efforts, research during the winter season, and the technological and methodological developments in natural resource management that can overcome these limitations are explored. Future research and emerging data needs are discussed, including the need for increased inclusion of the social sciences and improving relationships with Indigenous and First Nation communities in terms of research, data sharing, and governance.

Groundtruthing cumulative impact assessments with biodiversity data: Testing indicators and methods for marine ecosystem condition assessments in South Africa

Abstract Accurate assessments of ecosystem condition are needed to inform management processes such as systematic conservation planning and protected area expansion, marine spatial planning and other effective area‐based conservation measures. Yet measuring the condition of dynamic and often largely inaccessible marine ecosystems is extremely difficult and presents a global challenge. Broad‐scale cumulative impact assessments have been used in South Africa as a proxy for marine ecosystem condition in national assessments and reporting because the data are more readily available, and knowledge exists on the impacts of various human activities (or pressures) on marine ecosystems. While useful for national reporting, assessments based on in situ ecological data are also needed at finer scales relevant to management. Applying the HELCOM BEAT approach, this study used in situ ecological data to identify potential methods and indicators that can be applied in South Africa to conduct integrated ecosystem assessments and to assess the suitability of current cumulative impact assessments as a proxy for condition. Aggregated fish indicators demonstrated greater sensitivity to varying human pressures compared with benthic community indicators, with responsiveness differing by location. Notably, site‐level differences in empirical condition emerged that broad‐scale cumulative assessments often missed. The study thus highlighted the varying suitability of cumulative impact scores as proxies for condition, indicating their reliability for fish communities. However, this is also dependent on the pressure types included, the biotic indicators used and the area of focus. Conservation decisions based solely on cumulative impact scores could misrepresent the actual condition of the environment, which makes it difficult to make management decisions, especially at finer scales. As such, conservation initiatives need to be regionally adapted to effectively address the unique pressures and conditions of each area and should be tailored to account for fine‐scale variability, instead of adopting a one‐size‐fits‐all approach.