Marine intrusion and freshwater discharge as opposite forces driving fish guilds distribution along coastal plain streams

This work investigated variations in fish guilds along marine surf zone to freshwater reaches of coastal plain streams and their relationships with environmental factors. Fish and abiotic data were collected monthly during 1 year and an automatic image-recording system was used to monitor marine intrusion events. Aside ephemeral salinity gradients produced by storm surges, freshwater conditions prevailed inside streams. Despite of that, fish habitat use guilds were spatially distributed according to their salinity tolerance, with marine species occurring mainly in the stream site near the adjacent surf zone and non-salinity tolerant freshwater fish in the upstream site. Marine intrusion was the main factor correlated with the entrance of marine-related fish into streams during summer. In contrast, higher rainfall during colder months prevented the dominance of marine species. This work highlighted that spatial segregation in fish habitat use guild could occur even in the absence of long-lasting salinity gradients, since active colonization by euryhaline fish and sporadic marine intrusions can lead to the occurrence of marine-related fish in coastal plain streams. Future studies should evaluate if this marine intrusion role on fish of coastal plain streams would be affected by changes in sea level and rainfall in a global warming scenario.     

Automatic detection of fish and tracking of movement for ecology

1. 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.
2. 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.
3. 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%.
4. 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.

     

The influence of watershed land use cover on stream fish diversity and size-at-age of a generalist fish

Changes in land use have manifold effects on stream ecosystems. Consequently, the degradation of watersheds can cause extreme responses if the resilience of the stream is exceeded, triggering changes in fish communities and a reorganization of the ecosystem. Fish community surveys are frequently used to evaluate the impact of anthropogenic pressures on freshwater streams. Dynamic indices such as individual growth are also interesting because they integrate the effects of environmental conditions through time, providing an assessment in the long term. In this study we have investigated the ecological implications of watershed land use cover on fish diversity and growth of the generalist species Umbra limi (central mudminnow) in six streams in Southern Ontario (Canada). In detail, the growth of U. limi has been explored using a Dynamic Energy Budget (DEB) model, which pursues a mechanistic explanation of the bioenergetics of an individual under different environmental conditions. Given the mechanistic approach, the outcomes of the DEB model can provide a solid foundation for extrapolating the conclusions of this study to a broader spatial scale. The results of this study reveal that the proportion of modified land use of the watershed (agricultural and urban land) can reach a tipping point beyond which the functioning of the stream abruptly changes. Consequently, land use cover may be used as a precautionary indicator for watershed management. The results also demonstrate that U. limi could be used as a sentinel species to identify potential impacts on fish diversity and size-at-age as a cost-effective indicator for stream monitoring programs.     

Applications of deep convolutional neural networks to predict length,circumference, and weight from mostly dewatered images of fish

Simple biometric data of fish aid fishery management tasks such as monitoring the structure of fish populations and regulating recreational harvest. While these data are foundational to fishery research and management, the collection of length and weight data through physical handling of the fish is challenging as it is time consuming for personnel and can be stressful for the fish. Recent advances in imaging technology and machine learning now offer alternatives for capturing biometric data. To investigate the potential of deep convolutional neural networks to predict biometric data, several regressors were trained and evaluated on data stemming from the FishL? Recognition System and manual measurements of length, girth, and weight. The dataset consisted of 694 fish from 22 different species common to Laurentian Great Lakes. Even with such a diverse dataset and variety of presentations by the fish, the regressors proved to be robust and achieved competitive mean percent errors in the range of 5.5 to 7.6% for length and girth on an evaluation dataset. Potential applications of this work could increase the efficiency and accuracy of routine survey work by fishery professionals and provide a means for longer‐term automated collection of fish biometric data.     

The use of fish in ecological assessments

Abstract Fish provide powerful tools for assessing aquatic environments. Three attributes are especially significant: the sensitivity of fish to most forms of human disturbance, their usefulness at all levels of biological organization and the favourable benefit-to-cost ratio offish assessment programmes. Fish can be used as indicators over wide temporal and spatial ranges. Because they cover all trophic levels of consumer ecology, fish can effectively integrate the whole range of ecological processes in waterways. Fish have been used in many different roles for assessing river health and monitoring responses to remedial management. Three of these applications appear to have particular value for management of Australian rivers: (i) automated systems monitoring fish ventilation can provide sensitive, broad-spectrum and continuous sensing of water quality to protect receiving waters or water-supply intakes; (ii) programmes collecting routine data on commercial or recreational fisheries can be designed and analysed so as to isolate confounding effects due to fishery-specific factors and, hence, used to detect and monitor environmental change on large scales; (iii) the Index of Biotic Integrity (IBI) can be modified to suit Australian conditions and fish communities to meet the important need for a predictive model of aquatic environmental quality. The IBI is a quantitative biological tool with a strong ecological foundation that integrates attributes from several levels of ecosystem organization. Examples of the use of IBI elsewhere suggest its robustness, flexibility and sensitivity can cope effectively with the low diversity of the Australian fish fauna and the dominance of ecological generalists. A provisional structure is suggested for a test of the IBI in four riverine regions of New South Wales.     

Biomass size distributions as a tool for characterizing lake fish communities

Biomass size distributions (BSDs) can be useful tools to (1) summarize complex information about fish community structure in a condensed graphical form, facilitating the characterization of freshwater fish communities, (2) compare the position of fish communities along environmental gradients and (3) elucidate major trophic interactions in freshwater fish communities. Biomass size distributions are presented by taxonomic and trophic group, for a selection of fish communities from 35 Scandinavian and eight Dutch lakes. They were used for the analysis of taxonomic and trophic shifts in the fish communities along a large environmental gradient, with productivity (expressed as total phosphorus concentration, TP) as its most important component. Regression analysis of fish community variables (such as proportion of cyprinids, or biomass of benthivores) were consistent with the semi‐quantitative conclusions drawn from BSDs, regarding taxonomic and trophic shifts with changes in TP in both Scandinavian and Dutch lakes, especially an increase in the amount and size of benthivorous fishes with increasing TP‐levels. In addition, differences in mortality and growth rates were shown to partly explain differences in BSDs. Biomass size distributions thus provide an integrative tool for qualitative and quantitative comparisons among fish communities.     

Surveillance of fish species composition using environmental DNA

Prompt and accurate methods for assessing the species composition of given areas are indispensable in addressing the rapid loss of biodiversity. Here, we propose a method for the surveillance of fish species composition in freshwater using environmental DNA as species markers. First, the applicability of the method was demonstrated through aquarium experiments. DNA was extracted from 120?ml aquarium water, and the degenerated primers targeting the fish mitochondrial cytochrome b gene were used for amplification. PCR-amplified fragments were analysed by random cloning, and all species reared in the aquarium were detected. Next, this method was applied to natural freshwater environments. Water samples were collected from three sites in the Yura River, Japan; DNA was concentrated from 2?l of environmental water, and then amplified and cloned. Up to four species of fish were detected by sequencing 47 randomly selected clones from a single water sample. Overall, the results were consistent with previous knowledge of fish habitat utilisation. Using this method, the surveillance of fish species composition can be conducted less laboriously than with traditional methods.     

淡水鱼类功能生态学研究进展

在全球变化和人类活动的影响下,生物多样性正以前所未有的速度丧失,全球生物正经受第六次生物多样性危机。淡水生态系统是最脆弱的生态系统之一。淡水鱼类作为淡水生态系统的重要组成部分,承受着日趋严重的气候变化、栖息地退化、生物入侵和过度捕捞等压力,面临巨大的威胁。在此背景下,如何准确评估鱼类种群和群落对环境变化的响应,以及鱼类群落结构和功能的变化对生态系统功能的影响是淡水鱼类多样性和淡水生态系统保护的关键问题。近年来,淡水鱼类功能生态学的快速发展为解答这一问题提供了一个框架。系统地介绍了淡水鱼类功能生态学主要研究内容、方法、进展及其应用,并着重介绍了淡水鱼类功能特征及其与环境的关系、环境变化下的功能生态学响应研究。据此提出了淡水鱼类功能生态学未来的重点研究方向,指出了其在鱼类多样性保护和资源利用等领域的应用前景。     

Spatio-temporal changes in habitat potential of endangered freshwater fish in Japan

In recent years, biodiversity conservation and ecosystem restoration have been key issues of watershed management in many countries. To maintain or restore the environmental quality of watersheds, we need to assess the impact of anthropogenic changes on stream ecosystems with accuracy. In addition, watershed conservation planners have to make strategic plans and determine priorities of each conservation activity.

A new monitoring methodology to evaluate the change of habitat condition for freshwater fish based on a predictive habitat model using logistic regression was developed and applied to the whole of Japan. The main contributions of our approach were 1) the construction of a Geographical Information System (GIS) database that integrates many types of data, including freshwater fish species, water quality, habitat fragmentation by damming, geology, and climate; 2) spatial analysis for quantitative assessment and predictive habitat modeling using logistic regression to combine fish survey data and environmental habitat factors to determine critical and major habitat variables for each target fish; and 3) digital mapping and changes detection of fish habitat potential for targeted endangered fish species to show habitat distribution and spatio-temporal changes of habitat potential over a 25-year period (from 1977 to 2002). We found that predicted suitable habitat and actual fish habitat showed high overlap, and that habitat conditions and distribution patterns of target freshwater fish had been affected by major habitat variables to target species respectively.     

Monitoring fish passes using infrared beaming: a case study in an Iberian river

An application of a new automated fish counting device – the Riverwatcher System (RW) – was used to monitor upstream fish movements in a pool‐and‐weir fish pass in the River Zêzere, Portugal, for 141 days from June 2002 to May 2003. Fish populations were also collected downstream using multimesh gillnets (5 different mesh sizes ranging from 30 mm to 85 mm knot to knot; ratio between mesh sizes of about 1.30) and electrofishing for comparison with fish records produced by the RW. More than 3000 individual Iberian nase Chondrostoma polylepis ascended the fish pass and moved through the RW during the study period. However, only 18% of the records produced by the RW contained silhouettes similar to fish; no individual smaller than 15 cm TL was recorded by the counter. Most seasonal movements (73.9%) occurred in spring and were associated with reproduction. Displacements seemed to occur independently of time of day. Water temperature (range: 12–22°C) was the only significant environmental variable (P < 0.01) influencing upstream movements of this species. Further development of hardware and software will be necessary to improve performance of the counter, particularly in Mediterranean rivers, where more turbid waters and a greater proportion of small‐size species are present.     

Ocean acidification alters temperature and salinity preferences in larval fish

Ocean acidification alters the way in which animals perceive and respond to their world by affecting a variety of senses such as audition, olfaction, vision and pH sensing. Marine species rely on other senses as well, but we know little of how these might be affected by ocean acidification. We tested whether ocean acidification can alter the preference for physicochemical cues used for dispersal between ocean and estuarine environments. We experimentally assessed the behavioural response of a larval fish (Lates calcarifer) to elevated temperature and reduced salinity, including estuarine water of multiple cues for detecting settlement habitat. Larval fish raised under elevated CO₂ concentrations were attracted by warmer water, but temperature had no effect on fish raised in contemporary CO₂ concentrations. In contrast, contemporary larvae were deterred by lower salinity water, where CO₂-treated fish showed no such response. Natural estuarine water—of higher temperature, lower salinity, and containing estuarine olfactory cues—was only preferred by fish treated under forecasted high CO₂ conditions. We show for the first time that attraction by larval fish towards physicochemical cues can be altered by ocean acidification. Such alterations to perception and evaluation of environmental cues during the critical process of dispersal can potentially have implications for ensuing recruitment and population replenishment. Our study not only shows that freshwater species that spend part of their life cycle in the ocean might also be affected by ocean acidification, but that behavioural responses towards key physicochemical cues can also be negated through elevated CO₂ from human emissions.     

Species richness and functional structure of fish assemblages in three freshwater habitats: effects of environmental factors and management

In this study, the inverted trophic hypothesis was tested in the freshwater fish communities of a reservoir. The distribution of fish species in three freshwater habitats in the Jurumirim Reservoir, Brazil, was examined using both species richness and the relative proportions of different trophic groups. These groups were used as a proxy for functional structure in an attempt to test the ability of these measures to assess fish diversity. Assemblage structures were first described using non-metric multidimensional scaling (NMDS). The influence of environmental conditions for multiple fish assemblage response variables (richness, total abundance and abundance per trophic group) was tested using generalised linear mixed models (GLMM). The metric typically employed to describe diversity; that is, species richness, was not related to environmental conditions. However, absolute species abundance was relatively well explained with up to 54% of the variation in the observed data accounted for. Differences in the dominance of trophic groups were most apparent in response to the presence of introduced fish species: the iliophagous and piscivorous trophic groups were positively associated, while detritivores and herbivores were negatively associated, with the alien species. This suggests that monitoring functional diversity might be more valuable than species diversity for assessing effects of disturbances and managements policies on the fish community.     

Detection of invasive freshwater fish species using environmental DNA survey

Invasive species are one of the most significant problem in freshwater ecosystems. Most common non-native freshwater species in Turkish freshwater fish fauna are Prussian Carp (Carassius gibelio), North African Catfish (Clarias gariepinus), Nile Tilapia (Oreochromis niloticus) and Topmouth Gudgeon (Pseudorasbora parva).Recent studies showed that environmental DNA could be used to detect target species inhabiting the ecosystem with higher precision and less effort compared to traditional field surveys. In this study, eDNA approach was used to investigate non-native freshwater fish species from fifteen different locations of Upper Sakarya Basin. eDNA was successfully extracted from the water samples of locations where the species were visually observed. Mean amplification rate of eDNA was calculated as 77.03%.This study is the first environmental DNA study used in detection of four of the most common invasive freshwater fish species. Results clearly indicating that eDNA surveys could be used as an important molecular tool to monitor invasive fish species in freshwater ecosystems.     

Spatial isolation and fish communities in drainage lakes

Fifty-two drainage lakes, located in south-central Ontario, Canada, were examined to study the association of isolation- and environment-related factors with fish community composition. Eight quantitative measures of lake isolation were examined, each of which incorporated potential ecological "challenges" that a fish encounters when moving between lakes. A Procrustean approach was employed to assess the degree of concordance between fish assemblage structure, measures of lake isolation and environmental conditions (i.e., lake morphology and water chemistry). Our results revealed a high concordance between patterns in fish community composition and lake isolation and lake morphology at the watershed scale, suggesting that insular and habitat-related factors influence the structure of fish communities. At the scale of the individual lake, this relationship varied greatly, ranging from a strong match of community composition with both spatial and abiotic conditions to communities exhibiting weak association with these conditions. Furthermore, we showed that alternative measures of lake isolation provide additional insight into potential factors shaping patterns in fish community composition; information not provided using straight-line distances between lakes. Finally, the statistical methodology outlined in this paper provides a robust technique for assessing both the overall association between multivariate data matrices (i.e., landscape or regional scale), as well as facilitating the examination of smaller-scale relationships of individual observations (i.e., local scale).     

Fluctuations in pelagic fish density linked to ambient conditions

Animal behaviour has been broadly studied for its social or functional aspects but less often for understanding the interactions between organisms and their ambient conditions. A pilot observational study was performed by means of underwater camera to investigate the correlation between environmental factors and the density of fish in the epipelagic habitat of a European temperate reservoir. Explored factors confirmed a positive correlation between water temperature and all observed categories: nonpredatory, predatory, single nonpredatory and schooling fish, as well as freshwater bream and roach. On the other hand, de-trended solar irradiance was found to be negatively correlated with density of nonpredatory fish, freshwater bream and European perch. Sunshine duration was negatively correlated with the density of predatory fish. Precipitation a showed positive relationship with single nonpredatory fish and European perch, whereas wind strength had a negative relationship with density of schooling fish. Furthermore, density of predatory fish was positively correlated with density of single nonpredatory fish and counts of observed clusters. Altogether, findings indicate that fish density is correlated with abiotic factors and the occurrence of predators. This suggests that more ecologically complex studies should be encouraged for better understanding of ecological interactions that drive the structure of aquatic ecosystems.     

Paradigm shifts in fish conservation: moving to the ecosystem services concept

Various factors constrain the existence and development of inland fishes and fisheries, such as pollution, habitat degradation, alien invasive species, local user conflicts, low social priority and inadequate research and funding. In many cases, however, degradation of the environment and loss of aquatic habitat are the predominant concerns for the conservation of freshwater aquatic biota. The need for concerted effort to prevent and reduce environmental degradation, as well as protection of freshwater fishes and fisheries as renewable common pool resources or entities in their own right, are the greatest challenges facing the conservation of fishes in inland waters. Unfortunately, traditional conservation practices such as regulation of exploitation, protected areas and habitat restoration have failed to arrest the alarming increase in number of threatened freshwater fish species worldwide. This paper examines the shifting paradigm of fisheries management from rule-based regulation, through fishery enhancement towards the ecosystem approach to fisheries, with reference to inland waters, and how the emerging concept of ecosystem services coupled with traditional fish conservation management practices, institutional restructuring and integrated management planning should provide a more sustainable thrust to formulation and promotion of fish conservation initiatives.     

A stereological method for estimating fish fecundity

This paper describes the application and evaluation of a stereological method for counting fish oocytes. The method has been applied to herring, Clupea harengus L., Dover sole, Solea solea L., and mackerel, Scomber scombrus L., and compared with existing volumetric and/or automated particle counter methods. The stereological method has been shown to given similar results and to have a number of distinct advantages over the other methods.     

基于环境DNA宏条形码技术的北京地区鱼类多样性调查和外来鱼种入侵风险评估

[目的]调查北京地区鱼类多样性和群落分布及评估外来鱼种的入侵风险.[方法]选取北京地区水库、湖泊和河流3种水体类型共33个采样点,于2020年6月10—17日开展水生态监测,利用环境DNA宏条形码技术对各样点的鱼类多样性和群落结构进行监测和分析,对目前北京地区水生态系统中本地鱼种和外来鱼种进行分类汇总,并评估典型外来入...     

Global imprint of historical connectivity on freshwater fish biodiversity

The relative importance of contemporary and historical processes is central for understanding biodiversity patterns. While several studies show that past conditions can partly explain the current biodiversity patterns, the role of history remains elusive. We reconstructed palaeo‐drainage basins under lower sea level conditions (Last Glacial Maximum) to test whether the historical connectivity between basins left an imprint on the global patterns of freshwater fish biodiversity. After controlling for contemporary and past environmental conditions, we found that palaeo‐connected basins displayed greater species richness but lower levels of endemism and beta diversity than did palaeo‐disconnected basins. Palaeo‐connected basins exhibited shallower distance decay of compositional similarity, suggesting that palaeo‐river connections favoured the exchange of fish species. Finally, we found that a longer period of palaeo‐connection resulted in lower levels of beta diversity. These findings reveal the first unambiguous results of the role played by history in explaining the global contemporary patterns of biodiversity.     

海洋鱼类肠道微生物研究进展及应用前景

肠道微生物在动物体内数量庞大、结构复杂,在宿主生长发育过程中发挥着重要作用.淡水鱼类肠道微生物的研究主要集中于其对鱼类生长代谢、营养吸收及免疫调节等方面的影响,海洋鱼类则研究相对较少,且多集中于肠道微生物多样性及其变动影响因素分析.本文在归纳总结鱼类肠道微生物功能及其研究方法的基础上,着重分析肠道微生物在海洋鱼类生长发...