Geographic and host factors shape the evolution of a newly recognized subgroup within the U genogroup of the fish rhabdovirus IHNV

Thesis (Master's)--University of Washington, 2015

Resource abundance and Survival of indigenous ornamental fishes of central Kerala with emphasis on handling and packing stress in Puntius filamentosus(VALENCIENNES)

This thesis Entitled Resource abundance and survival of indigenous ornamental fishes of central kerala with emphasis on handling and packing stress in puntius filamentosus (valenciennes).Kerala state is endowed with 41 west flowing and three east flowing rivers originating in the Western Ghats. These rivers and their vast network of tributaries and distributaries harbour rich and diversified fish fauna. Most of the freshwater fishes available in Kerala are highly appreciated as ornamental fishes in the national and international markets.Today the ornamental fish industry is one of the largest industries all over the world. The demand for ornamental fishes has been increasing steadily with the enlargement of the industry, such that the current demand for indigenous ornamental fishes have exceeded the supply. This has led to serious concern about the resources available in the country that can be utilised judiciously for the economic benefit of the state. With an aim to fill up the lacuna, a database of freshwater ornamental fishes of Kerala was created as part of the present study. Ornamental fishes destined for export marketing should thrive well in the aquarium conditions.The study reiterates fishes caught from different environmental conditions and feeding habits have a greater ability to adapt and acclimatise to an entirely new environment and food habits. Marketing studies based on the statistics available with Marine Products Export Development Authority show that these species are not being exported at the required level over the past 6 years, when compared to the availability in the water bodies of Kerala. Sustainable utilisation of these resources from the wild using modern management principles and code of conduct for responsible fishing are advisable until captive breeding technology is popularised.

Systematics, Germplasm evaluation and pattern of distribution and abundance of freshwater fishes of Kerala (lndia)

The overall focus of the thesis involves the systematics,germplasm evaluation and pattern of distribution and abundance of freshwater fishes of kerala (india).Biodiversity is the measure of variety of Life.With the signing on the convention on biodiversity, the countries become privileged with absolute rights and responsibility to conserve and utilize their diverse resources for the betterment of mankind in a sustainable way. South-east Asia along with Africa and South America were considered to be the most biodiversity rich areas in the world .The tremendous potential associated with the sustainable utilization of fish germplasm resources of various river systems of Kerala for food, aquaculture and ornamental purposes have to be fully tapped for economic upliftment of fisherman community and also for equitable sharing of benefits among the mankind without compromising the conservation of the rare and unique fish germplasm resources for the future generations.The study was carried during April 2000 to December 2004. 25 major river systems of Kerala were surveyed for fish fauna for delineating the pattern of distribution and abundance of fishes both seasonally and geographically.The results of germplasm inventory and evaluation of fish species were presented both for the state and also river wise. The results of evaluation of fish species for their commercial utilization revealed that, of the 145, 76 are ornamental, 47 food and 22 cultivable. 21 species are strictly endemic to Kerala rivers. The revalidation on biodiversity status of the fishes assessed based on IUCN is so alarming that a high percentage of fishes (59spp.) belong to threatened category which is inclusive of 8 critically ndangered (CR), 36 endangered and 15 species under vulnerable (VU) category.The river wise fish germplasm inventory surveys were conducted in 25 major river systems of Kerala.The results of the present study is indicative of existence of several new fish species in the streams and rivulets located in remote areas of the forests and therefore, new exclusive surveys are required to surface fish species new to science, new distributional records etc, for the river systems.The results of fish germplasm evaluation revealed that there exist many potential endemic ornamental and cultivable fishes in Kerala. It is found imperative to utilize these species sustainably for improving the aquaculture production and aquarium trade of the country which would definitely fetch more income and generate employment.

Systematics, Life history traits, abundance andstock assessment of cobia, Rachycentron canadum ( Linnaeus, 1766) occurring in Indian waters with special reference to the north west coast in India

This thesis entitled Systematics,life history traits ,abundance and stock assessment of cobia rachycentron canadum (linnaeus ,1766) occurring in indian waters with special reference to the northwest coast of india.Cobia, Rachycentron canadum is a fast growing pelagic fish belonging to the monotypic family Rachycentridae. They show worldwide distribution in tropical and sub tropical waters. Cobia is exploited commercially in various countries like Taiwan, Pakistan, India, United State of America, Australia, Gulf of Mexico and the Caribbean. Recreational fishery of Cobia exists in different parts of the world. In India Cobia is caught as bycatch of trawlers, gillnet and hook and line fishery.This study also focuses on to bring out the distribution pattern and also to assess the biomass and estimate sustainable yield of Cobia inhabiting in Indian EEZ. In addition to above, present study standardised live collection methods and also reviewed culture prospects.Results of osteological study and morphological studies indicate its close resemblance to Remora and support the view that Cobia was evolved from Dolphin fishes and remoras followed it. Study also confirmed that Cobia does not have any relative or similar species and is a monotypic species belonging to the family Rachycentridae. Re description of the species was done based on the characters identified. In this study, feeding intensity was also assessed following methods like Gastrosomatic index, Mean index of feeding intensity and Index of fullness. Sex wise, month wise and length group wise fluctuations in the feeding intensity also were studied. Cobia actively fed during post monsoon period. In general, adult fed actively than the juveniles. Trophic level value estimated (4.36) indicates that Cobia occupy top level position in the food chain.

Studies on some fish larvae of the arabian sea and bay of bengal

Though several scientific expeditions surveyed tha Indian ocean. their findings on larval fishes were fragmentory and incomplete. During the International Indian ocean expedition (1960-1965) zooplankton samples were collected from vast area at the lndian ocean adopting standard procedures by participating vessels. These planktons provided an opportunity for a general study of the zooplanltton as well as their anotomy. abundance and distribution.. Realising the imortance of the analysis and classification of fish larvae at the family level being one of the most important information required then for the Indian Ocean region the fish larval portion sorted out from the above zooplankton samples was allocated to the author by the UNESCO consultative committee for the Indian Ocean Biological centre. In spite of the emhasis laid on The study of the family scombridae. owing to the paucity of the scombridae material in tne collection. much could not be done about it.However the record and description of the very early stages of morakel larvae made in 1967 as part of this study was the first of its kind. The present study on the distribution aspects o fish larva of such large area in the Indian ocean is also unique and first of its kind

Do dietary changes of Australasian gannets (Morus serrator) reflect variability in pelagic fish stocks?

The relationship between changes in the diet of Australasian gannets (Morus serrator) and commercial fisheries landings was investigated. The contribution of pilchard (Sardinops sagax) to the diet of gannets was significantly related to the commercial catch of that species, suggesting that changes in the relative proportion of pilchard in the diet of gannets may be a useful index of pilchard abundance and availability. Equivalent relationships, however, were not found for other common prey species in the gannet diet. It is considered that the abundance of important prey items in the gannet diet, such as pilchards, and commercial landings are proportional to stock abundance. The implications of this relationship for fisheries management are examined.

Heterologous microarray experiments used to identify the early gene response to heat stress in a coral reef fish

Coral reef fishes are expected to experience rising sea surface temperatures due to climate change. How well tropical reef fishes will respond to these increased temperatures and which genes are important in the response to elevated temperatures is not known. Microarray technology provides a powerful tool for gene discovery studies, but the development of microarrays for individual species can be expensive and time-consuming. In this study, we tested the suitability of a Danio rerio oligonucleotide microarray for application in a species with few genomic resources, the coral reef fish Pomacentrus moluccensis. Results from a comparative genomic hybridization experiment and direct sequence comparisons indicate that for most genes there is considerable sequence similarity between the two species, suggesting that the D. rerio array is useful for genomic studies of P. moluccensis. We employed this heterologous microarray approach to characterize the early transcriptional response to heat stress in P. moluccensis. A total of 111 gene loci, many of which are involved in protein processing, transcription, and cell growth, showed significant changes in transcript abundance following exposure to elevated temperatures. Changes in transcript abundance were validated for a selection of candidate genes using quantitative real-time polymerase chain reaction. This study demonstrates that heterologous microarrays can be successfully employed to study species for which specific microarrays have not yet been developed, and so have the potential to greatly enhance the utility of microarray technology to the field of environmental and functional genomics.

Distribution and abundance of seabirds in Western Port, Victoria

The distribution, abundance and biomass of seabirds in Western Port, Victoria, were surveyed between April 1991 and August 1994. Individuals were counted along an 81-km series of transects from a boat at approximately monthly intervals. A total of 25 seabird taxa were recorded, of which 18 and 15 were common to those recorded by an earlier study in Port Phillip Bay and waters south of Phillip Island, respectively. The most numerous species by far was the Short-tailed Shearwater (Puffinus tenuirostris) followed by the Silver Gull (Larus novaehollandiae), Little Penguin (Eudyptula minor) and Crested Tern (Sterna bergii). Distribution within Western Port was not uniform, with pursuit divers such as cormorant and grebe species being recorded mostly in the shallow Eastern Arm. In contrast, surface-seizing (e.g. albatrosses), surface-plunging (e.g. Crested Terns), shallow-plunging (Australasian Gannet, Morus serrator) and pursuit-plunging (e.g. shearwaters) species predominated in the deeper Western Arm of Western Port. These species were also seasonally abundant, with peak numbers for most occurring in late summer–early autumn, which coincides with the reported influx of juvenile clupeoid fish into Western Port. Average biomass (686 ± 395 kg) comprised mostly Short-tailed Shearwaters, Little Penguins and Pied Cormorants (Phalacrocorax varius). Biomass density (8.5 kg km^–2) was similar to that reported for Port Phillip Bay (8.1 kg km^–2) but lower than off the southern coast of Phillip Island (9.9 kg km^–2).

Physical environmental conditions, spawning and early-life stages of an estuarine fish : climate change implications for recruitment in intermittently open estuaries

Significant variation in the egg and larval survival and juvenile recruitment of estuarine fishes has been linked to fluctuating environmental conditions. This present study compared the distribution and abundance of black bream (Acanthopagrus butcheri) eggs and yolk-sac larvae between two microtidal estuaries of different flow regimes, where the riverine flow into the Glenelg estuary was around eight times the flow volume into the Hopkins estuary. Samples were collected monthly from September to November at sites along each estuary where vertical profiles of temperature, salinity and dissolved oxygen (DO) were measured, and vertically stratified sampling of black bream eggs and yolk-sac larvae was conducted using a Schindler sampler. Salt wedge formation was apparent in both estuaries, with significant de-oxygenation of deeper, saline waters. Eggs occurred in a wide range of DO levels but yolk-sac larvae were less common at the lowest levels. Most eggs and yolk-sac larvae were collected in salinities greater than 10. Results suggested that egg mortality was higher in the Hopkins than the Glenelg estuary, which may be associated with the hypoxic conditions characteristic of low-flow conditions. The results have significant implications in terms of climate change that is predicted to lead to warmer, drier conditions in south-eastern Australia, potentially increasing stratification and subsequent hypoxic zones.

Fish assemblage response to rehabilitation of a sand-slugged lowland river

The impact of excessive sediment supply on river channels has been  described in many areas of the world. Sediment deposition disturbance alters habitat  structure by decreasing channel depth, changing substrate composition and burying woody debris. River rehabilitation is occurring worldwide, but information is scant on fish assemblage responses to rehabilitation in sedimentdisturbed lowland rivers. Sediment removal and large woody debris (LWD) replacement  were used to experimentally rehabilitate habitat along a 1500m stretch of the Glenelg River in western Victoria, Australia. Using an asymmetrical before-after control-impact (BACI) design, fish were captured before and after the reach was rehabilitated, from two control reaches and from a ‘higher quality’ reference reach. After two years post-rehabilitation monitoring, the fish assemblage at the rehabilitated reach did not differ from control reaches. Temporal changes in taxa richness and the abundance of Philypnodon grandiceps, Nannoperca spp. and three angling taxa occurred after rehabilitation (winter 2003) compared with the before period (winter 2002), but these effects did not differ between rehabilitated and control locations. Highest taxa richness and abundances occurred at the reference location. High salinity coincided with the timing of rehabilitation works, associated with low river discharges due to drought. The negative effects of other large-scale disturbances may have impaired the effectiveness of reachscale rehabilitation or the effects of rehabilitation may take longer than two years to develop in a lowland river subjected to multiple environmental disturbances.

Ecology of fish inhabiting the inter-tidal zone of Swan Bay, Victoria, Australia

Swan Bay is a shallow marine embayment of Port Phillip Bay, just north of Queenscliff, Victoria. It has been part of the Harold Holt Marine Reserves since 1977 and is a seagrass habitat. This study investigated the species of fish present in the inter-tidal zone of Swan Bay, collected information on their ecology, investigated the importance of Swan Bay compared to Port Phillip Bay as a nursery and/or breeding area and compared these results with those of similar seagrsss habitats. Field work was carried out monthly over a two year period, from April 1981 to April 1983, using beach seine nets at Swan Bay and Portarlington. Forty four species of fish were identified from Swan Bay and nineteen from Portarlington. Fish were most abundant during the summer and autumn months when seagrass growth was at a maximum and least abundant during winter due to the absence of seasonal residents and decreased numbers of permanent residents. Swan Bay was found to be an important nursery ground for two commercially-caught species: the Yellow-eye Mullet and the King George Whiting. Juvenile Yellow-eye Mullet were more numerous in Swan Bay than at Portarlington. Smell juvenile King George Whiting were more abundant at Portarlington than in Swan Bay where older juveniles were more numerous. The fish fauna of Swan Bay was found to be similar to western Port but the abundance of species varied. Atherinosome microstoma was the dominant species in terms of abundance and biomass. Diet was found to be different from that reported by Robertson (1979) at Western Port due to the different range of prey items.

Rearing juvenile Australian native percichthyid fish in fertilised earthen ponds

The post-larvae and fry of Australian native species, including those of species belonging to the family Percichthyidae, are routinely reared to a fingerling size (35-55 mm in length) in fertilised earthen fry rearing ponds. The juveniles of Murray cod (Maccullochella peelii peelii\ trout cod (Maccullochella macquariensis) and Macquarie perch (Macquaria australasicd) (Percichthyidae) are grown in fry rearing ponds at the Marine and Freshwater Resources Institute, Snobs Creek (Vie. Australia) for production of fingerlings for stock enhancement and aquaculture purposes. However, no detailed studies have been undertaken of the productivity of these ponds and factors that influence fish production. An ecologically based study was undertaken to increase the knowledge of pond ecology and dynamics, particularly in relation to the rearing of juvenile Murray cod, trout cod and Macquarie perch in ponds. Over nine consecutive seasons commencing in 1991, water chemistry, plankton, macrobenthos (2 seasons only) and fish were monitored and studied in five ponds located at Snobs Creek. A total of 80 pond fillings were undertaken during the study period. Additional data collected from another 24 pond fillings undertaken at Snobs Creek collected prior to this study were included in some analyses. Water chemistry parameters monitored in the ponds included, temperature, dissolved oxygen pH, ammonia, nitrite, nitrate, orthophosphate and alkalinity. Water chemistry varied spatially (within and between ponds) and temporally (diurnally, daily and seasonally). Liming of ponds increased the total alkalinity to levels that were considered to be suitable for enhancing plankton communities and fish production. Water quality within the ponds for the most part was suitable for the rearing of juvenile Murray cod, trout cod and Macquarie perch, as reflected in overall production (growth, survival and yield) from the ponds. However, at times some parameters reached levels which may have stressed fish and reduced growth and survival, in particular, low dissolved oxygen concentrations (minimum 1.18 mg/L), high temperatures (maximum 34°C), high pH (maximum 10.38) and high unionised ammonia (maximum 0.58 mg/L). Species belonging to 37 phytoplankton, 45 zooplankton and 17 chironomid taxa were identified from the ponds during the study. In addition, an extensive checklist of aquatic flora and fauna, recorded from aquaculture ponds in south-eastern Australia, was compiled. However, plankton and benthos samples were usually numerically dominated by a few species only. Rotifers (especially Filinia, Brachionus, Polyarthra, and Asplanchnd), cladocerans (Moina and Daphnid) and copepods (Mesocyclops and Boeckelld) were most abundant and common in the plankton, while chironomids (Chironomus, Polypedilum, and Prodadius) and oligochaetes were most common and abundant in the benthos. Both abundance and species composition of the plankton and macrobenthos varied spatially (within and between ponds) and temporally (diurnally, daily and seasonally). Chlorophyll a concentrations, which ranged from 1.8 to 184 \ig/L (mean 29.37 ng/L), initially peaked within two weeks of filling and fertilising the ponds. Zooplankton peaked in abundance 2-4 weeks after filling the ponds. The maximum zooplankton density recorded in the ponds was 6,621 ind./L (mean 721 ind./L). Typically, amongst the zooplankton, rotifers were first to develop high densities (2nd-3rd week after filling), followed by cladocerans (2nd-4th week after filling) then copepods (2nd-5th week after filling). Chironomid abundance on average peaked later (during the 5th week after filling). The maximum chironomid density recorded in the ponds was 27,470 ind./m2 (mean 4,379 ind./m2). Length-weight, age-weight and age-length relationships were determined for juvenile Murray cod, trout cod and Macquarie perch reared in ponds. These relationships were most similar for Murray cod and trout cod, which are more closely related phylogenetically and similar morphologically than Macquarie perch. Growth of fish was negatively correlated with both size at stocking and stocking biomass. Stocking density experiments showed that, at higher densities, growth offish was significantly reduced, but survival was not affected. The diets of juvenile Murray cod trout cod and Macquarie perch reared in fry ponds were similar. The cladocerans Moina and Daphnia, adult calanoid and cyclopoid copepods and the chironomids, Chironomus, Polypedilum and Procladius were the most commonly occurring and abundant prey. Selection for rotifers and copepod nauplii was strongly negative for all three species of fish. Size range of prey consumed was positively correlated with fish size for trout cod and Macquarie perch, but not for Murray cod. Diet composition changed as the fish grew. Early after stocking the fish into the ponds, Moina was generally the more common prey consumed, while in latter weeks, copepods and chironomids became more abundant and common in the diet. On a dry weight basis, chironomid larvae were the most important component in the diets of these fish species. Selective feeding by fish on larger planktonic species such as adult copepods and cladocerans, may have influenced the plankton community structure as proposed by the trophic cascade or top -down hypothesis. The proximate composition and energy content of Murray cod, trout cod and Macquarie perch, reared in the ponds did not vary significantly between the species, and few significant changes were observed as the fish grew. These results suggested that the nutrient requirements of these species might not vary over the size range of fish examined. Significant differences in the proximate composition of prey were observed between species, size of species and time of season. The energy content of prey (cladocerans, copepods and chironomids) on a pond basis, was closely related to the abundance of these taxa in the ponds. Data collected from all pond fillings during the present study, along with historical data from pond fillings undertaken prior to this study, were combined in a data matrix and analysed for interactions between pairs of parameters. In particular, interactions between selected water chemistry parameters, zooplankton and chironomid abundance indicators were analysed to identify key factors that influence fish production (growth, survival, condition and yield). Significant correlations were detected between fish production indicators and several water chemistry and biota (zooplankton and chironomids) parameters. However, these were not consistent across all three species of fish. These results indicated that the interactions between water chemistry, biota and fish were complex, and that combinations of these parameters, along with other factors not included in the present study, may influence fish production in these ponds. The present study, showed that more stringent monitoring of fry rearing ponds, especially water quality, zooplankton and benthos communities and fish, combined with an associated increase in understanding of the pond ecosystem, can lead to substantial improvements in pond productivity and associated fish production. In the present study this has resulted in a general increase in fish survival rates, which became less variable or more predictable in nature. The value of such knowledge can provide managers with a more predicative capacity to estimate production of ponds in support of stock enhancement programs and provision of juvenile for aquaculture grow-out.

Density-dependent mortality is mediated by foraging activity for prey fish in whole-lake experiments

1. Whereas the effects of density-dependent growth and survival on population dynamics are well-known, mechanisms that give rise to density dependence in animal populations are not well understood. We tested the hypothesis that the trade-off between growth and mortality rates is mediated by foraging activity and habitat use. Thus, if depletion of food by prey is density-dependent, and leads to greater foraging activity and risky habitat use, then visibility and encounter rates with predators must also increase.

2. We tested this hypothesis by experimentally manipulating the density of young rainbow trout (Oncorhynchus mykiss) at risk of cannibalism, in a replicated single-factor experiment using eight small lakes, during an entire growing season.

3. We found no evidence for density-dependent depletion of daphnid food in the near-shore refuge where most age-0 trout resided. Nonetheless, the proportion of time spent moving by individual age-0 trout, the proportion of individuals continuously active, and use of deeper habitats was greater in high density populations than in low density populations. Differences in food abundance among lakes had no effect on measures of activity or habitat use.

4. Mortality of age-0 trout over the growing season was higher in high density populations, and in lakes with lower daphnid food abundance. Therefore, population-level mortality of age-0 trout is linked to greater activity and use of risky habitats by individuals at high densities. We suspect that food resources were depleted at small spatial and temporal scales not detected by our plankton sampling in the high density treatment, because food-dependent activity and habitat use by age-0 trout occurs in our lakes when food abundance is experimentally manipulated

Seagrass patch size affects fish responses to edges

1. Patch area and proximity of patch edge can influence ecological processes across patchy landscapes and may interact with each other. Different patch sizes have different amounts of core habitat, potentially affecting animal abundances at the edge and middle of patches. In this study, we tested if edge effects varied with patch size.

2. Fish were sampled in 10 various-sized seagrass patches (114–5934 m²) using a small (0·5 m²) push net in three positions within each patch: the seagrass edge, 2 m into a patch and in the middle of a patch.

3. The two most common species showed an interaction between patch size and the edge–interior difference in abundance. In the smallest patches, pipefish (Stigmatopora nigra) were at similar densities at the edge and interior, but with increasing patch size, the density at the edge habitat increased. For gobies (Nesogobius maccullochi), the pattern was exactly the opposite.

4. This is the first example from a marine system of how patch size can influence the magnitude and pattern of edge effects.

5. Both patch area and edge effects need to be considered in the development of conservation and management strategies for seagrass habitats.

Assessing effects of diel period, gear selectivity and predation on patterns of microhabitat use by fish in a mangrove dominated system in SE Australia

The relative value of temperate mangroves to fish, and the processes driving patterns of microhabitat use within this habitat, are unknown. There are 3 quickly identifiable microhabitats within temperate Australian mangroves: (1) forest (the area of mangroves with trees); (2) pneumatophores (the area directly seaward of the forest without trees but with pneumatophores [aerial roots]); and (3) channel (the area directly seaward of the pneumatophores without gross structural attributes such as trees or pneumatophores). Duplicate fyke and gill nets were both initially used to sample fish in the 3 microhabitats described above. Sampling took place across the seaward edge of mangroves on 10 sampling occasions (5 night and 5 day), in a large estuarine system in SE Australia. Fish assemblages (693 fish from 20 species and 15 families) varied significantly (p < 0.05) between the forest and the channel, and between diel periods for each gear (net type), but there was little difference in the assemblage structure of fish between forest–pneumatophore or pneumatophore–channel microhabitats. Juvenile lifestages (61% of all fish) and commercially important taxa (76%) were common. Abundance, biomass and species richness of fish were generally lower in the forest than the other microhabitats, but this pattern varied significantly (p < 0.05) between diel periods, among sampling occasions, and with water depth. Highly quantitative pop nets provided a preliminary assessment of whether differential gear selectivity caused patterns between microhabitats, but less rich fish assemblages were again recorded in forests than in pneumatophores. The importance of predation in structuring fish assemblages across microhabitats was assessed by measuring survival of juvenile fish tethered in 3 predation treatments (predator exclusion, cage control, and uncaged). Survival rates were high across the predator treatments and did not vary among microhabitats. The variation in fish assemblages across microhabitats within mangroves was not consistent with a model of mangrove structure providing a refuge for juvenile fish from predation, but instead could indicate differences in efficiency of gear types among microhabitats and/or other ‘edge effect’-driven processes such as the provision of food and/or shelter.