Mobile receivers: releasing the mooring to ‘see’ where fish go

Much has been learned from the large scale deployment of acoustic tags on aquatic species and associated networks of riverine and marine receivers. While effective in the linear environment of river systems, marine systems limit the ability to provide spatial information on fish movements and distributions due to a combination of costs, logistics, and lack of off-shore technology. At the same time, each year millions of dollars worth of tags are being released into the aquatic environment with extended battery/transmission life, yet detections are limited to coastal arrays. Here we explore new methods of tracking acoustically tagged species in the marine environment. A new miniaturized acoustic receiver, the Vemco Mobile Transceiver (VMT) can be carried by large marine organisms. In combination with satellite and archival tag technology, VMTs were deployed on northern elephant seals to monitor acoustic tags encountered during their migrations across the Northeast Pacific. Early results include acoustic detections of tagged great white sharks, salmon sharks, Chinook salmon, steelhead, lingcod, green sturgeon and other elephant seals. We also propose several alternative directions for future effort: 1) analyzing the growing number of passive acoustic survey recordings made from hydrophone arrays for acoustic tag detections, 2) working with acoustic technology providers to develop hull-mounted receiver systems for the thousands of ocean going vessels around the world and 3) integrating acoustic receiver technology into the thousands of moored and drifting oceanographic buoy arrays.     

Herbivorous fishes,ecosystem function and mobile links on coral reefs

Understanding large-scale movement of ecologically important taxa is key to both species and ecosystem management. Those species responsible for maintaining functional connectivity between habitats are often called mobile links and are regarded as essential elements of resilience. By providing connectivity, they support resilience across spatial scales. Most marine organisms, including fishes, have long-term, biogeographic-scale connectivity through larval movement. Although most reef species are highly site attached after larval settlement, some taxa may also be able to provide rapid, reef-scale connectivity as adults. On coral reefs, the identity of such taxa and the extent of their mobility are not yet known. We use acoustic telemetry to monitor the movements of Kyphosus vaigiensis, one of the few reef fishes that feeds on adult brown macroalgae. Unlike other benthic herbivorous fish species, it also exhibits large-scale (>2 km) movements. Individual K. vaigiensis cover, on average, a 2.5 km length of reef (11 km maximum) each day. These large-scale movements suggest that this species may act as a mobile link, providing functional connectivity, should the need arise, and helping to support functional processes across habitats and spatial scales. An analysis of published studies of home ranges in reef fishes found a consistent relationship between home range size and body length. K. vaigiensis is the sole herbivore to depart significantly from the expected home range–body size relationship, with home range sizes more comparable to exceptionally mobile large pelagic predators rather than other reef herbivores. While the large-scale movements of K. vaigiensis reveal its potential capacity to enhance resilience over large areas, it also emphasizes the potential limitations of small marine reserves to protect some herbivore populations.     

Thresholds for impaired species recovery

Studies on small and declining populations dominate research in conservation biology. This emphasis reflects two overarching frameworks: the small-population paradigm focuses on correlates of increased extinction probability; the declining-population paradigm directs attention to the causes and consequences of depletion. Neither, however, particularly informs research on the determinants, rate or uncertainty of population increase. By contrast, Allee effects (positive associations between population size and realized per capita population growth rate, r_realized, a metric of average individual fitness) offer a theoretical and empirical basis for identifying numerical and temporal thresholds at which recovery is unlikely or uncertain. Following a critique of studies on Allee effects, I quantify population-size minima and subsequent trajectories of marine fishes that have and have not recovered following threat mitigation. The data suggest that threat amelioration, albeit necessary, can be insufficient to effect recovery for populations depleted to less than 10% of maximum abundance (N_max), especially when they remain depleted for lengthy periods of time. Comparing terrestrial and aquatic vertebrates, life-history analyses suggest that population-size thresholds for impaired recovery are likely to be comparatively low for marine fishes but high for marine mammals. Articulation of a ‘recovering population paradigm’ would seem warranted. It might stimulate concerted efforts to identify generic impaired recovery thresholds across species. It might also serve to reduce the confusion of terminology, and the conflation of causes and consequences with patterns currently evident in the literature on Allee effects, thus strengthening communication among researchers and enhancing the practical utility of recovery-oriented research to conservation practitioners and resource managers.     

Estuarine recruitment of a marine goby reconstructed with an isotopic clock

Information on movement patterns of marine fishes between estuarine populations and stocks at sea is fundamental to understanding their population dynamics, life history tactics and behavior. Furthermore, understanding estuarine habitat use by marine fishes is crucial for their effective conservation and integrated estuarine management. Although large numbers of young marine fish make use of temperate estuaries in highly predictable abundance patterns, very little is known about how estuarine populations interact with the populations at sea. Recruitment of sand goby Pomatoschistus minutus (Pallas, 1770) into the low salinity zone of the Scheldt estuary (Belgium) was reconstructed over an entire year by means of an isotopic clock. These results were combined with a growth model to yield age and length at immigration. Sand gobies entered the upper Scheldt estuary almost continuously from May onwards, except in July when they appeared to avoid the estuary due to warm summer temperatures. About 70% of the fish caught in the upper estuary resided there for less than 1 month, which indicates a strong temporal overlap of immigration and emigration. This complex migration pattern suggests that estuarine residence is caused by trade-offs made at the individual level, whereby migration is probably triggered by temperature. The high turnover of individuals in the estuarine population leads us to question the functional role of the estuary for marine fishes. Sand gobies entering the upper estuary had a wide range of ages and body sizes, although they were at least 2 months old and had a minimum standard length of approximately 20 mm. This study shows that the use of an isotopic clock strongly complements catch data and is useful to describe the connectivity between populations.     

Fossil fish otoliths from the Chibanian Miyata Formation,Kanagawa Prefecture,Japan, with comments on the paleoenvironment

The Paleo-Tokyo Bay (Kanto Plateau) that persisted during the transgression periods in the Middle-Late Pleistocene is known for its rich marine fauna that accommodated both the warm and cold water taxa brought by the Kuroshio and Oyashio Currents, respectively. However, little is known on the paleoichthyofauna in this area and the processes shaping the marine ichthyofauna of modern southern Kanto. We used fossil fish otoliths and teeth discovered in the Sha’ana Tuffaceous Sand Member belonging to the Chibanian Miyata Formation, exposed at Sha’ana-dai, Miura City, Kanagawa Prefecture, Japan, to reconstruct the paleoichthyofauna and its associated paleoenvironment and explore the content of fish assemblages during this period. The Sha’ana Tuffaceous Sand Member was composed of upper sandy mud and lower muddy sand horizons at the exposure. A total of 1,675 fish remains were collected from this site, of which 1,389 were assigned to 62 distinct taxa (20 orders, 31 families). The taxonomic composition revealed taxa from various environments, including shallow continental shelf, epi- to meso-pelagic settings, and the majority were from a generally temperate climatic zone. Paleoenvironmental analyses suggested that the fish assemblages were from the continental shelf (approximate depth of 100–200 m) in a temperate sea where both warm Kuroshio and cold Oyashio Currents had an influence on the biota. The analysis also showed that two boreal fishes, namely Clupea pallasii and Theragra chalcogramma, once had a wider distribution that extended to the southwestern areas of the Paleo-Tokyo Bay. This study provides a more complete view of the related paleobiogeography of marine fishes during the Chibanian and is essential for reconstructing the evolutionary processes of the rich ichthyofauna in the southern Kanto.     

Measuring marine fishes biodiversity: temporal changes in abundance, life history and demography

Patterns in marine fishes biodiversity can be assessed by quantifying temporal variation in rate of population change, abundance, life history and demography concomitant with long-term reductions in abundance. Based on data for 178 populations (62 species) from four north-temperate oceanic regions (Northeast Atlantic and Pacific, Northwest Atlantic, North mid-Atlantic), 81% of the populations in decline prior to 1992 experienced reductions in their rate of loss thereafter; species whose rate of population decline accelerated after 1992 were predominantly top predators such as Atlantic cod (Gadus morhua), sole (Solea solea) and pelagic sharks. Combining population data across regions and species, marine fishes have declined 35% since 1978 and are currently less than 70% of recorded maxima; demersal species are generally at historic lows, pelagic species are generally stable or increasing in abundance. Declines by demersal species have been associated with substantive increases in pelagic species, a pattern consistent with the hypothesis that increases in the latter may be largely attributable to reduced predation mortality. There is a need to determine the consequences to population growth effected by the reductions in age and size at maturity, and in mean age and size of spawners, concomitant with population decline. We conclude that reductions in the rate of population decline, in the absence of targets for population increase, will be insufficient to effect a recovery of marine fishes biodiversity, and that great care must be exercised when interpreting multi-species patterns in abundance. Of fundamental importance is the need to explain the geographical, species-specific and habitat biases that pervade patterns of marine fishes recovery and biodiversity.     

Relative changes in krill abundance inferred from Antarctic fur seal

Antarctic krill Euphausia superba is a predominant species in the Southern Ocean, it is very sensitive to climate change, and it supports large stocks of fishes, seabirds, seals and whales in Antarctic marine ecosystems. Modern krill stocks have been estimated directly by net hauls and acoustic surveys; the historical krill density especially the long-term one in the Southern Ocean, however, is unknown. Here we inferred the relative krill population changes along the West Antarctic Peninsula (WAP) over the 20th century from the trophic level change of Antarctic fur seal Arctocephalus gazella using stable carbon (δ(13)C) and nitrogen (δ(15)N) isotopes of archival seal hairs. Since Antarctic fur seals feed preferentially on krill, the variation of δ(15)N in seal hair indicates a change in the proportion of krill in the seal's diets and thus the krill availability in local seawater. For the past century, enriching fur seal δ(15)N values indicated decreasing krill availability. This is agreement with direct observation for the past ～30 years and suggests that the recently documented decline in krill populations began in the early parts of the 20th century. This novel method makes it possible to infer past krill population changes from ancient tissues of krill predators.     

海洋动物档案式标志及其定位方法研究进展

档案式标志是一种可存储数据档案的电子标志,应用于水生动物尤其是大洋高度洄游性鱼类的研究,是获取海洋动物长时间、大空间尺度的活动信息和环境数据的有力工具.自20世纪90年代以来,档案式标志被大量用于海洋动物研究,取得了一系列成果,其不足之处在于需要回收标志来获取采样数据.90年代末,分离式卫星档案标志的问世解决了数据回收的问题,不再依赖于渔业捕捞,扩展了海洋动物研究的广度和深度.基于光亮度定位是研究海洋动物洄游路线的关键,其重点在于匹配光亮度与特定天顶角(如日出、日落),有3种方法：固定参照法、可变参照法和映射法.在过去的20年内,光亮度定位方法有所发展,并取得了一定的成果,但纬度向的定位还不够精确,有继续发展的空间.本文还总结了档案式标志定位的现存问题,展望了档案式标志及其定位方法的研究方向,并认为存在档案式标志小型化和传感器集成化、定位方法由单一光亮度反演向多因子反演的趋势.     

Using passive acoustic telemetry to infer mortality events in adult herbivorous coral reef fishes

Mortality is considered to be an important factor shaping the structure of coral reef fish communities, but data on the rate and nature of mortality of adult coral reef fishes are sparse. Mortality on coral reefs is intrinsically linked with predation, with most evidence suggesting that predation is highest during crepuscular periods. We tested this hypothesis using passive acoustic telemetry data to determine the time of day of potential mortality events (PMEs) of adult herbivorous reef fishes. A total of 94 fishes were tagged with acoustic transmitters, of which 43 exhibited a PME. Furthermore, we identified five categories of PMEs based on the nature of change in acoustic signal detections from tagged fishes. The majority of PMEs were characterised by an abrupt stop in detections, possibly as a result of a large, mobile predator. Overall, mortality rates were estimated to be approximately 59 % per year using passive acoustic telemetry. The time of day of PMEs suggests that predation was highest during the day and crepuscular periods and lowest at night, offering only partial support for the crepuscular predation hypothesis. Visually oriented, diurnal and crepuscular predators appear to be more important than their nocturnal counterparts in terms of predation on adult reef fishes. By timing PMEs, passive acoustic telemetry may offer an important new tool for investigating the nature of predation on coral reefs.     

Animal-Borne Acoustic Transceivers Reveal Patterns of at-Sea Associations in an Upper-Trophic Level Predator

Satellite telemetry data have substantially increased our understanding of habitat use and foraging behaviour of upper-trophic marine predators, but fall short of providing an understanding of their social behaviour. We sought to determine whether novel acoustic and archival GPS data could be used to examine at-sea associations among grey seals (Halichoerus grypus) during the fall foraging period. Fifteen grey seals from Sable Island, Canada were deployed with Vemco Mobile Transceivers and Satellite-GPS transmitters in October 2009, 13 of which were recaptured and units retrieved 79±2.3 days later during the following breeding season, December 2009–January 2010. An association between two individuals was defined as a cluster of acoustic detections where the time between detections was <30 min. Bathymetry, travel rate, and behavioural state (slow and fast movement) were determined for each GPS archival point (3.7±0.1 locations recorded per hour). Behavioural state was estimated using a hidden Markov model. All seals had been involved in associations with other instrumented seals while at sea, with a total of 1,872 acoustic detections recorded in 201 associations. The median number of detections per association was 3 (range: 1–151) and the median duration of an association was 0.17 h (range: <0.1–11.3 h). Linear mixed-effects models showed that associations occurred when seals were exhibiting slow movement (0.24±0.01 ms⁻¹) on shallow (53.4±3.7 m) offshore banks where dominant prey is known to occur. These results suggest the occurrence of short-term associations among multiple individuals at foraging grounds and provide new insights into the foraging ecology of this upper-trophic marine predator.     

Biology of extinction risk in marine fishes

We review interactions between extrinsic threats to marine fishes and intrinsic aspects of their biology that determine how populations and species respond to those threats. Information is available on the status of less than 5% of the world's approximately 15500 marine fish species, most of which are of commercial importance. By 2001, based on data from 98 North Atlantic and northeast Pacific populations, marine fishes had declined by a median 65% in breeding biomass from known historic levels; 28 populations had declined by more than 80%. Most of these declines would be sufficient to warrant a status of threatened with extinction under international threat criteria. However, this interpretation is highly controversial, in part because of a perception that marine fishes have a suite of life history characteristics, including high fecundity and large geographical ranges, which might confer greater resilience than that shown by terrestrial vertebrates. We review 15 comparative analyses that have tested for these and other life history correlates of vulnerability in marine fishes. The empirical evidence suggests that large body size and late maturity are the best predictors of vulnerability to fishing, regardless of whether differences among taxa in fishing mortality are controlled; there is no evidence that high fecundity confers increased resilience. The evidence reviewed here is of direct relevance to the diverse criteria used at global and national levels by various bodies to assess threat status of fishes. Simple life history traits can be incorporated directly into quantitative assessment criteria, or used to modify the conclusions of quantitative assessments, or used as preliminary screening criteria for assessment of the approximately 95% of marine fish species whose status has yet to be evaluated either by conservationists or fisheries scientists.     

Pseudomonas putida and Pseudomonas fluorescens Species Group Recovery from Human Homes Varies Seasonally and by Environment

By shedding light on variation in time as well as in space, long-term biogeographic studies can help us define organisms’ distribution patterns and understand their underlying drivers. Here we examine distributions of Pseudomonas in and around 15 human homes, focusing on the P. putida and P. fluorescens species groups. We describe recovery from 10,941 samples collected during up to 8 visits per home, occurring on average 2.6 times per year. We collected a mean of 141 samples per visit, from sites in most rooms of the house, from the surrounding yards, and from human and pet occupants. We recovered Pseudomonas in 9.7% of samples, with the majority of isolates being from the P. putida and P. fluorescens species groups (approximately 62% and 23% of Pseudomonas samples recovered respectively). Although representatives of both groups were recovered from every season, every house, and every type of environment sampled, recovery was highly variable across houses and samplings. Whereas recovery of P. putida group was higher in summer and fall than in winter and spring, P. fluorescens group isolates were most often recovered in spring. P. putida group recovery from soils was substantially higher than its recovery from all other environment types, while higher P. fluorescens group recovery from soils than from other sites was much less pronounced. Both species groups were recovered from skin and upper respiratory tract samples from healthy humans and pets, although this occurred infrequently. This study indicates that even species that are able to survive under a broad range of conditions can be rare and variable in their distributions in space and in time. For such groups, determining patterns and causes of stochastic and seasonal variability may be more important for understanding the processes driving their biogeography than the identity of the types of environments in which they can be found.     

Changes in the trade of bycatch species corresponding to CITES regulations: the case of dried seahorse trade in Thailand

Exploitation for trade is one of the biggest threats to many species, especially for marine fishes. Trade regulations should, therefore, be effective in helping conserve marine fish populations. The Convention of International Trade in Endangered Species of Wild Fauna and Flora (CITES), one of the few multilateral environmental agreements with enforcement capacity, has embraced a number of marine fishes in recent years. However, the impacts of such measures on wildlife trade have rarely been assessed. We conducted a case study of the dried seahorse (Hippocampus spp.) trade in Thailand to understand the trade of these species under CITES regulations. We carried out 203 semi-structured interviews with traders to estimate the economic scale of Thai seahorse trade, and compared perceived changes with official trade datasets. Even though most seahorses were incidentally caught, we estimated that dried seahorses could be worth US$26.5 million per year for Thai fishers. However, the total declared annual export value was only around US$5.5 million, and had decreased to US$1 million in 2013. Considering the economic value of seahorses, the large discrepancy between declared export volumes and catch estimates suggested that trade may be underreported. While official data shows the export volume decreased after the implementation of CITES listing in 2005, our respondents did not report a similar trend. In contrast, the prices of seahorses were reported to be increasing. Our study highlights the economic importance of marine fishes captured as bycatch and the importance of international and domestic management measures for the trade of bycatch species.     

The intrinsic vulnerability to fishing of coral reef fishes and their differential recovery in fishery closures

Coral reef fishes differ in their intrinsic vulnerability to fishing and rates of population recovery after cessation of fishing. We reviewed life history-based predictions about the vulnerability of different groups of coral reef fish and examined the empirical evidence for different rates of population recovery inside no-take marine reserves to (1) determine if the empirical data agree with predictions about vulnerability and (2) show plausible scenarios of recovery within fully protected reserves and periodically-harvested fishery closures. In general, larger-bodied carnivorous reef fishes are predicted to be more vulnerable to fishing while smaller-bodied species lower in the food web (e.g., some herbivores) are predicted to be less vulnerable. However, this prediction does not always hold true because of the considerable diversity of life history strategies in reef fishes. Long-term trends in reef fish population recovery inside no-take reserves are consistent with broad predictions about vulnerability, suggesting that moderately to highly vulnerable species will require a significantly longer time (decades) to attain local carrying capacity than less vulnerable species. We recommend: (1) expanding age-based demographic studies of economically and ecologically important reef fishes to improve estimates of vulnerability; (2) long term (20–40 years), if not permanent, protection of no-take reserves to allow full population recovery and maximum biomass export; (3) strict compliance to no-take reserves to avoid considerable delays in recovery; (4) carefully controlling the timing and intensity of harvesting periodic closures to ensure long-term fishery benefits; (5) the use of periodically-harvested closures together with, rather than instead of, permanent no-take reserves.     

Ocean Heat Content Reveals Secrets of Fish Migrations

For centuries, the mechanisms surrounding spatially complex animal migrations have intrigued scientists and the public. We present a new methodology using ocean heat content (OHC), a habitat metric that is normally a fundamental part of hurricane intensity forecasting, to estimate movements and migration of satellite-tagged marine fishes. Previous satellite-tagging research of fishes using archival depth, temperature and light data for geolocations have been too coarse to resolve detailed ocean habitat utilization. We combined tag data with OHC estimated from ocean circulation and transport models in an optimization framework that substantially improved geolocation accuracy over SST-based tracks. The OHC-based movement track provided the first quantitative evidence that many of the tagged highly migratory fishes displayed affinities for ocean fronts and eddies. The OHC method provides a new quantitative tool for studying dynamic use of ocean habitats, migration processes and responses to environmental changes by fishes, and further, improves ocean animal tracking and extends satellite-based animal tracking data for other potential physical, ecological, and fisheries applications.     

Extinction, survival or recovery of large predatory fishes

Large predatory fishes have long played an important role in marine ecosystems and fisheries. Overexploitation, however, is gradually diminishing this role. Recent estimates indicate that exploitation has depleted large predatory fish communities worldwide by at least 90% over the past 50-100 years. We demonstrate that these declines are general, independent of methodology, and even higher for sensitive species such as sharks. We also attempt to predict the future prospects of large predatory fishes. (i) An analysis of maximum reproductive rates predicts the collapse and extinction of sensitive species under current levels of fishing mortality. Sensitive species occur in marine habitats worldwide and have to be considered in most management situations. (ii) We show that to ensure the survival of sensitive species in the northwest Atlantic fishing mortality has to be reduced by 40-80%. (iii) We show that rapid recovery of community biomass and diversity usually occurs when fishing mortality is reduced. However, recovery is more variable for single species, often because of the influence of species interactions. We conclude that management of multi-species fisheries needs to be tailored to the most sensitive, rather than the more robust species. This requires reductions in fishing effort, reduction in bycatch mortality and protection of key areas to initiate recovery of severely depleted communities.     

Vertical Migrations of a Deep-Sea Fish and Its Prey

It has been speculated that some deep-sea fishes can display large vertical migrations and likely doing so to explore the full suite of benthopelagic food resources, especially the pelagic organisms of the deep scattering layer (DSL). This would help explain the success of fishes residing at seamounts and the increased biodiversity found in these features of the open ocean. We combined active plus passive acoustic telemetry of blackspot seabream with in situ environmental and biological (backscattering) data collection at a seamount to verify if its behaviour is dominated by vertical movements as a response to temporal changes in environmental conditions and pelagic prey availability. We found that seabream extensively migrate up and down the water column, that these patterns are cyclic both in short-term (tidal, diel) as well as long-term (seasonal) scales, and that they partially match the availability of potential DSL prey components. Furthermore, the emerging pattern points to a more complex spatial behaviour than previously anticipated, suggesting a seasonal switch in the diel behaviour mode (benthic vs. pelagic) of seabream, which may reflect an adaptation to differences in prey availability. This study is the first to document the fine scale three-dimensional behaviour of a deep-sea fish residing at seamounts.     

Changes in fish assemblages following 10 years of protection in Tasmanian marine protected areas

Most studies examining effects of marine protected areas (MPAs) on fish assemblages are potentially confounded, either because they are once off comparisons between fished and unfished locations, or because they are snapshot studies over a fixed period. Here we compare long-term changes within fully protected Tasmanian marine reserves with changes at external reference sites on an annual basis over the first ten years of protection. The results highlight the importance of long-term datasets for differentiating changes occurring over differing time scales. Notable results include a statistically significant increase in abundance of Latridopsis forsteri and large fish (> 300 mm) when examined across all reserves relative to controls, and a 10-fold increase in the abundance of large fish and a doubling of per site species richness of large fish within the Tinderbox Marine Reserve relative to controls. Short-term resident species that recruit sporadically show very different patterns in reserves compared to those that recruit regularly and have long-term age-class storage. While several recent reviews have suggested size of MPAs and duration of protection has little influence on the extent of recovery, our results suggest this is not the case and that responses can be slow, complex and species-specific. The extent of localised fishing pressure appeared to have a substantial influence on the degree of change detected, potentially confounding meta-analyses of recovery rates in MPAs if overlooked as a relevant parameter.     

Two new genera and species of cystidicolids (Nematoda,Cystidicolidae) from marine fishes off New Caledonia

Two new nematode species of the family Cystidicolidae, each representing a new genus, were recovered from marine perciform fishes off New Caledonia, South Pacific: Ascarophisnema tridentatum n. gen., n. sp. from the stomach of the Japanese large-eye bream, Gymnocranius euanus (Günther) (Lethrinidae) and Metabronemoides mirabilis n. gen., n. sp. from the stomach of the painted sweetlip, Diagramma pictum (Thunberg) (Haemulidae). Ascarophisnema is characterized mainly by its cephalic structures (presence of two tooth-like projections on either side of the base of each pseudolabium, dorsal and ventral inner extensions of each pseudolabium recurved laterally in apical view, and submedian sublabia fused together dorsally and ventrally) and the presence of trident-like deirids, and Metabronemoides by its unique cephalic structures (presence of one dorsal and one ventral labium and four large dorsolateral and ventrolateral labia, and absence of sublabia). Rhabdochona gymnocranius (considered a species inquirenda) is provisionally transferred to the former genus as Ascarophisnema gymnocranius (Yamaguti, 1935) n. comb. To date, a total of seven species of cystidicolids are reported from marine fishes off New Caledonia.     

The Digital Fish Library: using MRI to digitize, database, and document the morphological diversity of fish

Museum fish collections possess a wealth of anatomical and morphological data that are essential for documenting and understanding biodiversity. Obtaining access to specimens for research, however, is not always practical and frequently conflicts with the need to maintain the physical integrity of specimens and the collection as a whole. Non-invasive three-dimensional (3D) digital imaging therefore serves a critical role in facilitating the digitization of these specimens for anatomical and morphological analysis as well as facilitating an efficient method for online storage and sharing of this imaging data. Here we describe the development of the Digital Fish Library (DFL, http://www.digitalfishlibrary.org), an online digital archive of high-resolution, high-contrast, magnetic resonance imaging (MRI) scans of the soft tissue anatomy of an array of fishes preserved in the Marine Vertebrate Collection of Scripps Institution of Oceanography. We have imaged and uploaded MRI data for over 300 marine and freshwater species, developed a data archival and retrieval system with a web-based image analysis and visualization tool, and integrated these into the public DFL website to disseminate data and associated metadata freely over the web. We show that MRI is a rapid and powerful method for accurately depicting the in-situ soft-tissue anatomy of preserved fishes in sufficient detail for large-scale comparative digital morphology. However these 3D volumetric data require a sophisticated computational and archival infrastructure in order to be broadly accessible to researchers and educators.