Report on fisheries invertebrate survey of the Groove Beck,Thornsgill Beck,Troutbeck system

This is the Report on fisheries invertebrate survey of the Groove Beck, Thornsgill Beck and Troutbeck system produced by the Environment Agency North West in 1997. In 1996 the National Rivers Authority (NRA) report on the 1992 strategic stock assessment for the Upper Derwent catchment Jane Atkins recommended that should subsequent electrofishing show continued low densities, a survey of the invertebrate fauna should be undertaken to assess the food availability for salmonids, in order that lack of food could be ruled out as a contributory factor in their poor breeding success. Additionally the survey looked at the substrate to try to determine whether the bed type might actually be unsuitable for spawning, especially in view of the previously mentioned silt inputs.

River Lemon (Teign catchment) fisheries survey

This is the River Lemon (Teign catchment) fisheries survey report produced by South West Water Authority in 1979. This report aims to determine the penetration of Salmon into the River Lemon System and to a lesser degree estimate the population of resident salmonids. Five sections were surveyed being easily accessible and fishable by electro fishing methods.

River Avon (including Glazebrook) fisheries survey 1978

This is the River Avon (including Glazebrook) fisheries survey 1978 report produced by South West Water Authority in 1978. This report aims to determine the penetration of Salmon into the River Avon system and to a lesser degree estimate the population of resident salmonids and other indigenous species. Six sections were electro fished at accessible points as detailed below. All fish were identified and measured. Each section was fished through three times to take the majority of the resident species. Small specimens of salmonid fry, eels and lamprey were common in almost all River Avon sections with the exception of Shipley bridge and Avon Dam but due to the mesh size of the standard dip nets used, many slipped through making accurate number estimation impossible.

Age and length composition of Columbia Basin chinook, sockeye, and coho salmon at Bonneville Dam in 2001

In 2001, representative samples of adult Columbia Basin chinook (Oncorhynchus tshawytscha), sockeye (O. nerka), and coho salmon (O. kisutch) populations at Bonneville Dam were collected. Fish were trapped, anesthetized, sampled for scales and biological data, revived, and then released adult migrating salmonids. Scales were examined to estimate age composition; the results contributed to an ongoing database for age class structure of Columbia Basin salmon populations. Based on scale analysis of chinook salmon, four-year-old fish (from brood year [BY] 1997) comprised 88% of the spring chinook, 67% of the summer chinook, and 42% of the Bright fall chinook salmon population. Five-year-old fish (BY 1996) comprised 9% of the spring chinook, 14% of the summer chinook, and 9% of the fall chinook salmon population. The sockeye salmon population at Bonneville was predominantly four-year-old fish (81%), with 18% returning as five-year-olds in 2001. The coho salmon population was 96% three-year-old fish (Age 1.1). Length analysis of the 2001 returns indicated that chinook salmon with a stream-type life history are larger (mean length) than the chinook salmon with an ocean-type life history. Trends in mean length over the sampling period for returning 2001 chinook salmon were analyzed. Chinook salmon of age classes 0.2 and 1.3 show a significant increase in mean length over time. Age classes 0.1, 0.3, 0.4, 1.1, 1.2, and 1.4 show no significant change over time. A year class regression over the past 12 years of data was used to predict spring, summer, and Bright fall chinook salmon population sizes for 2002. Based on three-year-old returns, the relationship predicts four-year-old returns of 132,600 (± 46,300, 90% predictive interval [PI]) spring chinook and 44,200 (± 11,700, 90% PI) summer chinook salmon for the 2002 runs. Based on four-year-old returns, the relationship predicts five-year-old returns of 87,800 (± 54,500, 90% PI) spring, 33,500 (± 11,500, 90% PI) summer, and 77,100 (± 25,800, 90% PI) Bright fall chinook salmon for the 2002 runs. The 2002 run size predictions should be used with caution; some of these predictions are well beyond the range of previously observed data.

Fish consumption by harbor seals (Phoca vitulina) in the San Juan Islands, Washington

The harbor seal (Phoca vitulina) is a large-bodied and abundant predator in the Salish Sea ecosystem, and its population has recovered since the 1970s after passage of the Marine Mammal Protection Act and the cessation of bounties. Little is known about how this large predator population may affect the recovery of fish stocks in the Salish Sea, where candidate marine protected areas are being proposed. We used a bioenergetics model to calculate baseline consumption rates in the San Juan Islands, Washington. Salmonids (Oncorhynchus spp.) and herring (Clupeidae) were the 2 most energetically important prey groups for biomass consumed by harbor seals. Estimated consumption of salmonids was 783 (±380 standard deviation [SD]) metric tons (t) in the breeding season and 675 (±388 SD t in the nonbreeding season. Estimated consumption of herring was 646 (±303 SD) t in the breeding season and 2151 (±706 SD) t in the nonbreeding season. Rockfish, a depressed fish stock currently in need of population recovery, composed one of the minor prey groups consumed by harbor seals (84 [±26 SD] t in the nonbreeding season). The variables of seal body mass and proportion of prey in seal diet explained >80% of the total variation in model outputs. Prey groups, such as rockfish, that are targeted for recovery may still be affected by even low levels of predation. This study highlights the importance of salmonids and herring for the seal population and provides a framework for refining consumption estimates and their confidence intervals with future data.

Pinniped diet composition: a comparison of estimation models

Along the west coast of the United States, the potential impact of increasing pinniped populations on declining salmonid (Oncorhynchus spp.) stocks has become an issue of concern. Fisheries managers need species-specific estimates of consumption by pinnipeds to evaluate their impact on salmonid stocks. To estimate consumption, we developed a model that estimates diet composition by reconstructing prey biomass from fecal samples. We applied the model to data collected from harbor seals (Phoca vitulina) that are present year-round in the lower Columbia River where endangered stocks of salmonids pass as returning adults and as seaward-migrating smolts. Using the same data, we applied the split-sample frequency of occurrence model, which avoids reconstructing biomass by assuming that each fecal sample represents an equal volume of consumption and that within each sample each prey item represents an equal proportion of the volume. The two models for estimating diet composition yielded size-specific differences in consumption estimates that were as large as tenfold for the smallest and largest prey. Conclusions about the impact of harbor seal predation on adult salmonids, some of their largest prey species, remain uncertain without some appropriate rationale or further information (e.g. empirical captive studies) to discriminate between these models.

Identification of an additional two-cysteine containing type I interferon in rainbow trout Oncorhynchus mykiss provides evidence of a major gene duplication event within this gene family in teleosts

Multiple type I interferons (IFNs) have recently been identified in salmonids, containing two or four conserved cysteines. In this work, a novel two-cysteine containing (2C) IFN gene was identified in rainbow trout. This novel trout IFN gene (termed IFN5) formed a phylogenetic group that is distinct from the other three salmonid IFN groups sequenced to date and had a close evolutionary relationship with IFNs from advanced fish species. Our data demonstrate that two subgroups are apparent within each of the 2C and 4C type I IFNs, an evolutionary outcome possibly due to two rounds of genome duplication events that have occurred within teleosts. We have examined gene expression of the trout 2C type I IFN in cultured cells following stimulation with lipopolysaccharide, phytohaemagglutinin, polyI:C or recombinant IFN, or after transfection with polyI:C. The kinetics of gene expression was also studied after viral infection. Analysis of the regulatory elements in the IFN promoter region predicted several binding sites for key transcription factors that potentially play an important role in mediating IFN5 gene expression.

Two cathelicidin genes are present in both rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar)

Further to the previous finding of the rainbow trout rtCATH_1 gene, this paper describes three more cathelicidin genes found in salmonids: two in Atlantic salmon, named asCATH_1 and asCATH_2, and one in rainbow trout, named rtCATH_2. All the three new salmonid cathelicidin genes share the common characteristics of mammalian cathelicidin genes, such as consisting of four exons and possessing a highly conserved preproregion and four invariant cysteines clustered in the C-terminal region of the cathelin-like domain. The asCATH_1 gene is homologous to the rainbow trout rtCATH_1 gene, in that it possesses three repeat motifs of TGGGGGTGGC in exon IV and two cysteine residues in the predicted mature peptide, while the asCATH_2 gene and rtCATH_2 gene are homologues of each other, with 96% nucleotide identity. Salmonid cathelicidins possess the same elastase-sensitive residue, threonine, as hagfish cathelicidins and the rabbit CAP18 molecule. The cleavage site of the four salmonid cathelicidins is within a conserved amino acid motif of QKIRTRR, which is at the beginning of the sequence encoded by exon W. Two 36-residue peptides corresponding to the core part of rtCATH_1 and rtCATH_2 were chemically synthesized and shown to exhibit potent antimicrobial activity. rtCATH_2 was expressed constitutively in gill, head kidney, intestine, skin and spleen, while the expression of rtCATH_1 was inducible in gill, head kidney, and spleen after bacterial challenge. Four cathelicidin genes have now been characterized in salmonids and two were identified in hagfish, confirming that cathelicidin genes evolved early and are likely present in all vertebrates.

三种海水经济鱼类早期发育生物学的研究

海水经济鱼类的养殖在我国已经形成第四次海水养殖浪潮，经济效益显著，有力地推动了我国海水养殖的产业结构调整和可持续发展。然而在海水养殖发展过程中也存在着诸多问题，尤其是早期发育阶段的高死亡率，严重制约了我国海水养殖产业的稳定和健康发展。 海水鱼类养殖的关键为高质量，高存活率苗种的生产和培育，由于鱼类种类繁多，生物多样性丰富，对应实际的繁育技术，尤其是新品种的开发，必须要做出相应的调整。这就要求我们必须对每一种鱼类早期发育有所了解，并将形态和组织上的数据用于指导生产。 本文通过显微观察和组织学研究，主要描述和研究了我国北方三种重要的海水经济鱼类(条斑星鲽、杂交鲆、条石鲷)的早期发育生物学，并结合实际生产进一步阐明关键期的产生原因，机理以及采用相应的对策。具体结果如下： 1.条斑星鲽：作为冷温性鲆鲽鱼类，条斑星鲽早期发育过程的特征主要有： ① 条斑星鲽受精卵无油球，卵子呈半浮性；不同步卵裂现象提前，发生在第三次卵裂；卵裂期裂球大小差异大。孵化过程较长，在水温8 ± 0.3℃，盐度33的条件下，经9 d孵化。条斑星鲽胚胎发育的不同时期对温度的敏感性不同，其中原肠期对温度比较敏感。 ②在8-10℃，盐度33的条件下，8-9 dph开口摄食。且开口时，其吻前端出现有一点状黑褐色素，构成了条斑星鲽仔鱼“开口期”的重要标志。卵黄囊于消失。在后期仔鱼末期，背鳍和臀鳍上形成特有的黑褐色条斑带。 ③杯状细胞首先出现在咽腔后部和食道前段，胃腺和幽门盲囊出现于29 dph，变态期始于30dph。在条斑星鲽早期发育过程中，观察到其直肠粘膜层细胞质出现大量嗜伊红颗粒，为仔鱼肠道上皮吸收的蛋白质。 ④首先淋巴化的免疫器官是头肾，然后是胸腺和脾脏，这与大部分硬骨鱼类不同。条斑星鲽除头肾和脾脏外，胸腺实质也形成MMCs。其中以脾脏形成MMCs最为丰富，形态多样。 2. 杂交鲆：为同属的牙鲆和夏鲆间的远缘杂交种，其发育过程的特点为： ① 在温度为15.4～16.0℃，杂交鲆胚胎从受精到孵化所需的时间为76 h左右，胚孔关闭前期，胚胎先出现视囊及克氏囊，而后形成体节。孵出前胚体在卵膜内环绕不到1周。 ② 孵化后消失。杂交鲆群体变态间隔长(34-60 dph)，且变态高峰期出现的冠状幼鳍不明显(与母本牙鲆相比)，数量为7-8根。 ③组织学观察发现，其消化系统中胃腺出现较晚，且胃腺发育过程缓慢(与母本牙鲆相比)。甲状腺滤泡增生不明显，颜色较浅，数量较少。杂交鲆在早期发育过程中，并没有出现鳔原基。 3. 条石鲷作为岩礁性的暖水性鱼类，早期发育过程也较为特殊，包括外形以及内部的器官结构。主要特点有： ① 受精卵：受精卵卵黄上具有龟裂结构，为鱼卵的分类特征之一。 ② 初孵仔鱼：初孵仔鱼背鳍膜上的黑色素，从体背面向背鳍膜边缘移动，到3dph仔鱼基本消失，此为本种仔鱼发育所特有的特点。 ③ 后期仔鱼和稚鱼：肠道肌肉层加厚明显，仔稚鱼胃肠排空率急剧上升，死亡率增加，通过改善常规的投饵方式部分解决了这个死亡高峰的问题。在幼鱼初期，牙齿融合为骨喙，为石鲷科鱼类的特征。 ④胸腺上皮分泌细胞：类似的现象同样在虹鳟鱼中发现，但是虹鳟鱼胸腺上皮分泌细胞不如条石鲷的丰富，同样也不如条石鲷的排列整齐，而是零星分布在胸腺上皮与咽腔接触的表面。除了正常的造血器官—脾脏和头肾外，肝脏、胰腺和鳔等多种组织等也出现MMCs，此现象在硬骨鱼类不多见，一般发生在软骨鱼类。

Osmoregulatory actions of growth hormone in juvenile tilapia (Oreochromis niloticus)

Growth hormone (GH) effectively promotes seawater (SW) adaptation in salmonids, but little is known of its effect in tilapias. Experiments were performed to investigate the effects of recombinant eel GH (reGH) on osmoregulatory actions and ultrastructural features of gill chloride cells in juvenile tilapia, Oreochromis niloticus. Tilapia showed a markedly improved SW survival, when directly transferred from freshwater (FW) to 62.5% SW 24h after a single reGH injection (0.25 or 2.5 mu g g(-1)) or 3 reGH injections (0.25 mu g g(-1) every other day). Plasma Na+ and Mg2+ levels were significantly reduced by reGH (0.25 and 2.5 mu g g(-1)) compared with saline injections; Ca2+ concentrations were reduced significantly by high dose of reGH (2.5 mu g g(-1)) after SW transfer. However, fish failed to survive more than 24h when directly transferred to 70 % SW, although the fish treated with reGH could survive longer than the controls. When examined by electron microscopy, the chloride cells were identified as mitochondrion-rich and an extensive tubular system was induced by GH treatment. The results of the present study suggest that, similar to its effect on salmonids, GH also exerts acute osmoregulatory actions and enhances SW adaptation in juvenile tilapia. GH also stimulates the differentiation of chloride cells toward SW adaptation.

The study of molecular variation in Atlantic salmon (Salmo salar L.) and brown trout (Salmo trutta L.)

Polymorphic microsatellite DNA loci were used here in three studies, one on Salmo salar and two on S. trutta. In the case of S. salar, the survival of native fish and non-natives from a nearby catchment, and their hybrids, were compared in a freshwater common garden experiment and subsequently in ocean ranching, with parental assignment utilising microsatellites. Overall survival of non-natives was 35% of natives. This differential survival was mainly in the oceanic phase. These results imply a genetic basis and suggest local adaptation can occur in salmonids across relatively small geographic distances which may have important implications for the management of salmon populations. In the first case study with S trutta, the species was investigated throughout its spread as an invasive in Newfoundland, eastern Canada. Genetic investigation confirmed historical records that the majority of introductions were from a Scottish hatchery and provided a clear example of the structure of two expanding waves of spread along coasts, probably by natural straying of anadromous individuals, to the north and south of the point of human introduction. This study showed a clearer example of the genetic anatomy of an invasion than in previous studies with brown trout, and may have implications for the management of invasive species in general. Finally, the genetics of anadromous S. trutta from the Waterville catchment in south western Ireland were studied. Two significantly different population groupings, from tributaries in geographically distinct locations entering the largest lake in the catchment, were identified. These results were then used to assign very large rod caught sea trout individuals (so called “specimen” sea trout) back to region of origin, in a Genetic Stock Identification exercise. This suggested that the majority of these large sea trout originated from one of the two tributary groups. These results are relevant for the understanding of sea trout population dynamics and for the future management of this and other sea trout producing catchments. This thesis has demonstrated new insights into the population structuring of salmonids both between and within catchments. While these chapters look at the existence and scale of genetic variation from different angles, it might be concluded that the overarching message from this thesis should be to highlight the importance of maintaining genetic diversity in salmonid populations as vital for their long-term productivity and resilience.

Temporal and spatial variation in otter Lutra lutra diet in Northern Ireland

The European otter (Lutra lutra L.) has a highly specialised diet that is composed predominantly of fish. The current study investigates the percentage composition of food items in otter spraints collected in six river catchments in Northern Ireland in 1980 and again from the same locations in 2003. Spraints contained significantly more salmonids than any other prey item. The composition of spraints differed among catchments. More salmonids and three-spined stickleback (Gasterosteus aculeatus L.) were found in spraints from the Glens of Antrim, while spraints from the Lagan catchment had significantly more eel (Anguilla anguilla L.). There were significantly more spraints containing non-fish food items in 2003 compared with 1980. These non-fish items were insects, amphipods, birds, rats (Rattus norvegicus Berkenhout) and lagomorphs. Increased consumption of non-fish items was apparent in all but one of the river catchments. The mean diversity of spraint composition was significantly greater in 2003 than in 1980. Therefore, our findings indicate that otters have diversified their diet since 1980 and now eat more non-fish prey.

Implications of climate change for the fishes of the British Isles

Recent climatic change has been recorded across the globe. Although environmental change is a characteristic feature of life on Earth and has played a major role in the evolution and global distribution of biodiversity, predicted future rates of climatic change, especially in temperature, are such that they will exceed any that has occurred over recent geological time. Climate change is considered as a key threat to biodiversity and to the structure and function of ecosystems that may already be subject to significant anthropogenic stress. The current understanding of climate change and its likely consequences for the fishes of Britain and Ireland and the surrounding seas are reviewed through a series of case studies detailing the likely response of several marine, diadromous and freshwater fishes to climate change. Changes in climate, and in particular, temperature have and will continue to affect fish at all levels of biological organization: cellular, individual, population, species, community and ecosystem, influencing physiological and ecological processes in a number of direct, indirect and complex ways. The response of fishes and of other aquatic taxa will vary according to their tolerances and life stage and are complex and difficult to predict. Fishes may respond directly to climate-change-related shifts in environmental processes or indirectly to other influences, such as community-level interactions with other taxa. However, the ability to adapt to the predicted changes in climate will vary between species and between habitats and there will be winners and losers. In marine habitats, recent changes in fish community structure will continue as fishes shift their distributions relative to their temperature preferences. This may lead to the loss of some economically important cold-adapted species such as Gadus morhua and Clupea harengus from some areas around Britain and Ireland, and the establishment of some new, warm-adapted species. Increased temperatures are likely to favour cool-adapted (e.g. Perca fluviatilis) and warm-adapted freshwater fishes (e.g. roach Rutilus rutilus and other cyprinids) whose distribution and reproductive success may currently be constrained by temperature rather than by cold-adapted species (e.g. salmonids). Species that occur in Britain and Ireland that are at the edge of their distribution will be most affected, both negatively and positively. Populations of conservation importance (e.g. Salvelinus alpinus and Coregonus spp.) may decline irreversibly. However, changes in food-web dynamics and physiological adaptation, for example because of climate change, may obscure or alter predicted responses. The residual inertia in climate systems is such that even a complete cessation in emissions would still leave fishes exposed to continued climate change for at least half a century. Hence, regardless of the success or failure of programmes aimed at curbing climate change, major changes in fish communities can be expected over the next 50 years with a concomitant need to adapt management strategies accordingly.

Review and quantitative meta-analysis of diet suggests the Eurasian otter (Lutra lutra) is likely to be a poor bioindicator

The Eurasian otter (Lutra lutra L.) is a top predator in aquatic systems and plays an important role in ecosystem functioning. However, it has undergone dramatic declines throughout Europe as a result of environmental degradation. We examine the putative role of the otter as a bioindicator in Ireland which remains a stronghold for the species and affords a unique opportunity to examine variation in its ecological niche. We describe diet, using spraint contents, along rivers during 2010 and conduct a review and quantitative meta-analysis of the results of a further 21 studies. We aimed to assess variation in otter diet in relation to river productivity, a proxy for natural nutrification and anthropogenic eutrophication, and availability of salmonid prey (Salmo trutta and Salmo salar), to test the hypothesis that otter diet is related to environmental quality. Otter diet did not vary with levels of productivity or availability of salmonids whilst Compositional Analysis suggested there was no selection of salmonid over non-salmonid fish. There was a distinct niche separation between riverine and lacustrine systems, the latter being dominated by Atlantic eel (Anguilla anguilla). Otters are opportunistic and may take insects, freshwater mussels, birds, mammals and even fruit. Otters living along coasts have a greatest niche breath than those in freshwater systems which encompasses a wide variety of intertidal prey though pelagic fish are rarely taken. It is concluded that the ability of the otter to feed on a wide diversity of prey taxa and the strong influence of habitat type, renders it a poor bioindicator of environmental water quality. It seems likely that the plasticity of the habitat and dietary niche of otters, and the extent of suitable habitat, may have sustained populations in Ireland despite intensification of agriculture during the 20th century.

The signature of fine scale local adaptation in Atlantic salmon revealed from common garden experiments in nature

Understanding the extent, scale and genetic basis of local adaptation is important for conservation and management. Its relevance in salmonids at microgeographic scales, where dispersal (and hence potential gene flow) can be substantial, has however been questioned. Here we compare the fitness of communally-reared offspring of local and foreign Atlantic salmon Salmo salar from adjacent Irish rivers and reciprocal F1 hybrid crosses between them, in the wild ‘home’ environment of the local population. Experimental groups did not differ in wild smolt output but a catastrophic flood event may have limited our ability to detect freshwater performance differences, which were evident in a previous study. Foreign parr exhibited higher, and hybrids intermediate, emigration rates from the natal stream relative to local parr, consistent with genetically-based behavioural differences. Adult return rates were lower for the foreign compared to the local group. Overall lifetime success of foreigners and hybrids relative to locals was estimated at 31% and 40% (mean of both hybrid groups), respectively. The results imply a genetic basis to fitness differences among populations separated by only 50km, driven largely by variation in smolt to adult return rates. Hence even if supplementary stocking programs obtain broodstock from neighbouring rivers, the risk of extrinsic outbreeding depression may be high.