Implications of movement for species distribution models - Rethinking environmental data tools

Individual based models for the simulation of fish movement near barriers: Current work and future directions

River fragmentation is an increasing issue for water managers and conservationists. Barriers such as dams interfere with freshwater fish migration, leading to drastic population declines. While there are a range of widely implemented mitigation approaches, e.g. fish passes, such measures are often inefficient due to suboptimal operation and design. There is increasing need to be able to assess mitigation options prior to implementation. Individual based models (IBMs) are a promising option. IBMs can simulate the fine-scale movement of individual fish within a population as they attempt to find a fish pass, incorporating movement processes themselves. Moreover, IBMs have high transferability to other sites or conditions (e.g. changing mitigation, change in flow conditions), making them potentially valuable for freshwater fish conservation yet their application to the fine-scale movement of fish past barriers is still novel. Here, we present an overview of existing IBMs for fine-scale freshwater fish movement, with emphasis on study species and the parameters driving movement in the models. In this review, we focus on IBMs suitable for the simulation of fish tracks as they approach or pass a single barrier. The selected IBMs for modelling fine-scale freshwater fish movement largely focus on salmonids and cyprinid species. IBMs have many applications in the context of fish passage, such as testing different mitigation options or understanding processes behind movement. Existing IBMs include movement processes such as attraction and rejection behaviours, as reported in literature. Yet some factors affecting fish movement e.g. biotic interactions are not covered by existing IBMs. As the technology available for fine scale data collection continues to advance, such as increasing data linking fish behaviour to hydraulics, IBMs could become a more common tool in the design and implementation of fish bypass structures.

Sampling errors and variability in video transects for assessment of reef fish assemblage structure and diversity

Video monitoring is a rapidly evolving tool in aquatic ecological research because of its non-destructive ability to assess fish assemblages. Nevertheless, methodological considerations of video monitoring techniques are often overlooked, especially in more complex sampling designs, causing inefficient data collection, processing, and interpretation. In this study, we discuss how video transect sampling designs could be assessed and how the inter-observer variability, design errors and sampling variability should be quantified and accounted for. The study took place in the coastal areas of the Galapagos archipelago and consisted of a hierarchical repeated-observations sampling design with multiple observers. Although observer bias was negligible for the assessment of fish assemblage structure, diversity and counts of individual species, sampling variability caused by simple counting/detection errors, observer effects and instantaneous fish displacement was often important. Especially for the counts of individual species, sampling variability most often exceeded the variability of the transects and sites. An extensive part of the variability in the fish assemblage structure was explained by the different transects (13%), suggesting that a sufficiently high number of transects is required to account for the within-location variability. Longer transect lengths allowed a better representation of the fish assemblages as sampling variability decreased by 33% if transect length was increased from 10 to 50 meters. However, to increase precision, including more repeats was typically more efficient than using longer transect lengths. The results confirm the suitability of the technique to study reef fish assemblages, but also highlight the importance of a sound methodological assessment since different biological responses and sampling designs are associated with different levels of sampling variability, precision and ecological relevance. Therefore, besides the direct usefulness of the results, the procedures to establish them may be just as valuable for researchers aiming to optimize their own sampling technique and design.

Conserved fatty acid profiles and lipid metabolic pathways in a tropical reef fish exposed to ocean warming - An adaptation mechanism of tolerant species?

Climate warming is causing rapid spatial expansion of ocean warm pools from equatorial latitudes towards the subtropics. Sedentary coral reef inhabitants in affected areas will thus be trapped in high temperature regimes, which may become the "new normal". In this study, we used clownfish Amphiprion ocellaris as model organism to study reef fish mechanisms of thermal adaptation and determine how high temperature affects multiple lipid aspects that influence physiology and thermal tolerance. We exposed juvenile fish to two different experimental conditions, implemented over 28 days: average tropical water temperatures (26 °C, control) or average warm pool temperatures (30 °C). We then performed several analyses on fish muscle and liver tissues: i) total lipid content (%), ii) lipid peroxides, iii) fatty acid profiles, iv) lipid metabolic pathways, and v) weight as body condition metric. Results showed that lipid storage capacity in A. ocellaris was not affected by elevated temperature, even in the presence of lipid peroxides in both tissues assessed. Additionally, fatty acid profiles were unresponsive to elevated temperature, and lipid metabolic networks were consequently well conserved. Consistent with these results, we did not observe changes in fish weight at elevated temperature. There were, however, differences in fatty acid profiles between tissue types and over time. Liver showed enhanced α-linolenic and linoleic acid metabolism, which is an important pathway in stress response signaling and modulation on environmental changes. Temporal oscillations in fatty acid profiles are most likely related to intrinsic factors such as growth, which leads to the mobilization of energetic reserves between different tissues throughout time according to organism needs. Based on these results, we propose that the stability of fatty acid profiles and lipid metabolic pathways may be an important thermal adaptation feature of fish exposed to warming environments.

Jinks E, Buelow CA, Brown CJ, Wang D, Kusy B, M. Ditria E, Connolly RM. Automatic detection of fish and tracking of movement for ecology

Animal movement studies are conducted to monitor ecosystem health, understand ecological dynamics, and address management and conservation questions. In marine environments, traditional sampling and monitoring methods to measure animal movement are invasive, labor intensive, costly, and limited in the number of individuals that can be feasibly tracked. Automated detection and tracking of small-scale movements of many animals through cameras are possible but are largely untested in field conditions, hampering applications to ecological questions.Here, we aimed to test the ability of an automated object detection and object tracking pipeline to track small-scale movement of many individuals in videos. We applied the pipeline to track fish movement in the field and characterize movement behavior. We automated the detection of a common fisheries species (yellowfin bream, Acanthopagrus australis) along a known movement passageway from underwater videos. We then tracked fish movement with three types of tracking algorithms (MOSSE, Seq-NMS, and SiamMask) and evaluated their accuracy at characterizing movement.We successfully detected yellowfin bream in a multispecies assemblage (F1 score =91%). At least 120 of the 169 individual bream present in videos were correctly identified and tracked. The accuracies among the three tracking architectures varied, with MOSSE and SiamMask achieving an accuracy of 78% and Seq-NMS 84%.By employing this integrated object detection and tracking pipeline, we demonstrated a noninvasive and reliable approach to studying fish behavior by tracking their movement under field conditions. These cost-effective technologies provide a means for future studies to scale-up the analysis of movement across many visual monitoring systems.

Assessing the Drivers behind the Structure and Diversity of Fish Assemblages Associated with Rocky Shores in the Galapagos Archipelago

Oceanic islands harbor unique yet fragile marine ecosystems that require evidence-based environmental management. Among these islands, the Galapagos archipelago is well known for its fish diversity, but the factors that structure communities within and between its islands remain poorly understood. In this study, water quality, physical habitats and geographical distance were assessed as potential predictors for the diversity and structure of fish assemblages. Differences in the structure of fish assemblages of the two studied islands (Santa Cruz and Floreana) were most likely driven by temperature and nutrient concentrations. In the relatively highly populated island Santa Cruz, the structure of fish assemblages was more affected by water conditions than physical habitats while the contrary was true for the more pristine area of Floreana. A wide variety of species with different geographical origins were distributed over the different islands, which indicates that most fish species are able to reach the islands of the archipelago. However, temperature gradients and elevated nutrient levels cause large differences in the structure of local fish assemblages. In addition, in Santa Cruz nutrient concentrations were negatively correlated with α diversity. Since pollution is a clear pressure on the fish assemblages of oceanic islands, environmental management of the coastal areas is of paramount importance.

Does weighting presence records improve the performance of species distribution models? A test using fish larval stages in the Yangtze Estuary

To obtain realistic forecasts of the impacts of climate change on species habitat suitability, novel approaches based on species distribution models (SDMs) are being developed and scrutinized. We argue here that, when dealing with data from long-term monitoring programmes, incorporating a temporal weight on the occurrence points may result in a more realistic prediction of a species' potential distribution. Using larval fish presence records collected from 1999 to 2013 in the Yangtze Estuary, China, we compared the performance of ensembles of standard SDMs versus SDMs constructed with weighted time-series presence records in predicting the present and future distributions of the larval stages of two dominant fish. The results of the ensemble SDMs showed that weighted presence records can significantly improve SDM performance, as measured through standard validation metrics. The SDM projections suggest that suitable habitat for both species will decrease under future climate scenarios, with one species (Stolephorus commersonnii) predicted to be more susceptible to climate change than the other (Engraulis japonicus). In addition to range contraction, model projections suggest that the future habitats of both species will shift northward-an implication of climate change that should be considered in future management and conservation strategies for the Yangtze Estuary.

Distribution modelling of the Pudu deer (Pudu puda) in southern Chile

The Pudu deer (Pudu puda) is endemic to the temperate rainforest of Chile and Argentina and currently faces serious conservation problems related to habitat loss. However, studies undertaken on this species are not sufficient to identify suitable areas for conservation purposes across its distribution range. In order to estimate the current and future distribution of the Pudu deer in southern Chile, we modelled the potential distribution of this species, based on occurrence points taken from seven contiguous provinces of this area using the Maxent modelling method. The Pudu deer distribution covered an estimated area of 17,912 km2 (24.1% of the area analysed), using a probability of occurrence above 0.529, according to the threshold that maximises the sum of sensitivity and specificity. In contrast to the Andes mountain range, areas with higher probabilities of occurrence were distributed mainly on the eastern and western slopes of the Coastal Mountain Range, where extensive coverage of native forest persists, as occurs in the provinces of Ranco, Osorno and Llanquihue. Projections to 2070, with global warming scenarios of 2.6 and 8.5 rcp, revealed that large areas will conserve their habitability, especially in the Coastal mountain range. Our results reveal that the Coastal mountain range has a high current and future habitability condition for the Pudu deer, a fact which may have conservation implications for this species.

Mapping wild seafood potential, supply, flow and demand in Lithuania

While member states have made a great effort into mapping ecosystem services (ES) in Europe, much work is still needed, especially in the marine domain. Difficulties in understanding the ecological functioning of marine ecosystem services (MES), together with the lack of administrative and technical resources, calls for the development of new assessment approaches. Even for the well-studied MES, the provision of wild seafood, few studies focus on mapping and mostly in a qualitative way by applying expert-based methods. This study aims to quantitatively map MES by developing new methodological frameworks for each of the components of the cascade model for wild seafood provision. The results showed a high potential of wild seafood provision in coastal areas, contrasting with offshore areas of the Exclusive Economic Zone (EEZ). Wild seafood is mainly supplied in the central part of the EEZ and is influenced by biological (e.g. sediments) and anthropogenic (e.g. shipping) factors. The flow was mapped using the location of first buying companies, restaurants, hotels, and supermarkets showing that the highest values were located in the urban areas. The coastal zone has a high flow as a consequence of the high density of fish selling points. The demand was mapped using the population density, number of tourists, and the fish consumption per capita; showing a high demand for fish products in urban as coastal areas. A validation step for the developed potential and supply, the analysis of the limitations and methodological considerations for all components, highlights the future data needs; showing decision-makers where to direct efforts. Mapping all components of wild seafood provision is critical to understand dynamics, the trade-offs associated, and its role in the socio-economic dimensions of coastal communities. This information can then be integrated into decision-making by showing the advantages in achieving a sustainable provision of wild seafood.

Multi-objective optimisation of species distribution models for river management

Environmental and measure implementation costs are two key factors to be considered by river managers in decision making. To balance effects and costs of an action, practitioners can rely on diagnostic analysis of presence/absence freshwater species distribution models (SDMs) trained to over- or underestimating species presence. Prevalence-adjusted model training aims to balance under- and overestimation depending on study objectives and training data characteristics. The objective of minimising under- and overestimation is a typical example of multi-objective optimisation (MOO). The aim of this paper is to address, for the first time, the practice of MOO-based prevalence-adjusted SDM training for freshwater decision management. In a numerical experiment, the use of Pareto-based MOO, specifically the non-dominated sorting genetic algorithm II (NSGA-II), is compared to commonly-used single-objective optimisation. SDMs for 11 pollution-sensitive freshwater macroinvertebrate species are trained with a subset of the Limnodata, a large data set holding records in the Netherlands over 30 years at 20,000 locations. An increase of two to four times is observed for the ability to identify a large range distribution of the solutions in the Pareto space, when using NSGA-II counter to repeated single-objective optimisation, this by increasing the average runtime with only four percent for a single run. In addition, the use of NSGA-II is found to be effective to identify reliable SDMs useful for diagnostic analysis. By applying and comparing a broad range of MOO methodologies for prevalence-adjusted model training, we believe a closer collaboration between model developers and freshwater managers can be facilitated and environmental standard limits can be set on a more objective basis. In conclusion, the use of MOO for prevalence-adjusted model training is assessed as a valuable tool to support river - and potentially all environmental - decision making.