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opencc-zeroJul 2020View details →

Data from: Kokanee–sockeye salmon hybridization leads to intermediate morphology and resident life history: implications for fisheries management

Stocking programs designed to return extirpated species to their historical range have become increasingly prevalent, punctuating the need to better understand the risks posed to recipient ecosystems. Here, we investigated the genetic and biological consequences of an anadromous sockeye salmon (Oncorhynchus nerka) stocking program in Skaha Lake, British Columbia, where substantial levels of hybridization/introgression with the native freshwater resident ecotype (kokanee) have been detected. We genetically-assigned 543 individuals (adult spawners, age-0 juveniles) to estimate stock proportions (pure-stock sockeye/kokanee or hybrid) between 2010 and 2017, with a subset undergoing otolith microchemistry analysis to determine migratory life history and maternal ancestry. Proportion of hybrid spawners varied from 5-20% across sampling years, while hybrid age-0 juveniles remained relatively constant (~11%). Hybrid spawners exhibited intermediate size relative to pure-stocks, with the vast majority being non-anadromous (92%) and of resident maternal ancestry (76%). Our results provide empirical support for previously hypothesized mechanisms of hybridization between O. nerka life-history forms, and underscore the importance of continued monitoring of stocking programs to quantify long-term fitness impacts of introgression and refine management strategies.

opencc-zeroAug 2020View details →

Reconciling seascape genetics and fisheries science in three co-distributed flatfishes

<p>Uncertainty hampers innovative mixed-fisheries management by the scales at which connectivity dynamics are relevant to management objectives. The spatial scale of sustainable stock management is species-specific and depends on ecology, life history and population connectivity. One valuable approach to understand these spatial scales is to determine to what extent population genetic structure correlates with the oceanographic environment. Here we compare the level of genetic connectivity in three co-distributed and commercially exploited demersal flatfish species living in the North East Atlantic Ocean. Population genetic structure was analysed based on 14, 14 and 10 neutral DNA microsatellite markers for turbot, brill and sole respectively. We then used redundancy analysis (RDA) to attribute the genetic variation to spatial (geographic location), temporal (sampling year) and oceanographic (water column characteristics) components.</p>

opencc-zeroNov 2020View details →

Data from: All is fish that comes to the net: metabarcoding for rapid fisheries catch assessment

AbstractMonitoring marine resource exploitation is a key activity in fisheries science and biodiversity conservation. Since research surveys are time-consuming and costly, fishery-dependent data (i.e. derived directly from fishing vessels) are increasingly credited with a key role in expanding the reach of ocean monitoring. Fishing vessels may be seen as widely ranging data-collecting platforms, which could act as a fleet of sentinels for monitoring marine life, in particular exploited stocks. Here, we investigate the possibility of assessing catch composition of single hauls carried out by trawlers by applying DNA metabarcoding to the "slush" collected from fishing nets just after the end of hauling operations. We assess the performance of this approach in portraying β-diversity and examining the quantitative relationship between species abundances in the catch and DNA amount in the slush (reads counts generated by amplicon sequencing). We demonstrate that the assemblages identified using DNA in the slush mirror those returned by visual inspection of net content and detect a strong relationship between read counts and species abundances in the catch. We therefore argue that this approach could be upscaled to serve as a powerful source of information on the structure of demersal assemblages and the impact of fisheries.

FIGURE 6 in The distributionof fourspeciesof thegenus Macrourus (Gadiformes:Macrouridae) from the Southern Ocean based on samples from the toothfish longline fishery

FIGURE 6. Scatter chart of the 4-scale series length in species of Macrourus in the Southern Hemisphere.

FIGURE 3 in The distributionof fourspeciesof thegenus Macrourus (Gadiformes:Macrouridae) from the Southern Ocean based on samples from the toothfish longline fishery

FIGURE 3. Barcoding tree for species of Macrourus collected by longline vessels in the Indian Ocean Sector of the Southern Ocean in 2015–16. Sequence labels of Macrourus species include the tissue sample number (001–174) followed by GenBank number (MN729502–MN729550) and capture locality.

FIGURE 4 in The distributionof fourspeciesof thegenus Macrourus (Gadiformes:Macrouridae) from the Southern Ocean based on samples from the toothfish longline fishery

FIGURE 4. Scanning electron microscope images of body scales of species of Macrourus species taken from the body area between the first dorsal fin and the lateral line. (a) and (b) M. caml SAIAB 203945, 131.2 (sample PEI15-M077) and 125.0 (sample PEI15-M085) mm HL, respectively. (c) M. whitsoni, 117.7 mm HL (sample PEI15-M088). (d) M. carinatus, SAIAB 209621, 126.9 mm HL (sample PEI15-M014). (e) and (f) M. holotrachys, SAIAB 209622, 158.2 (sample PEI15-M012) and 122.7 (sample PEI15-M013) mm HL, respectively.

FIGURE 7 in The distributionof fourspeciesof thegenus Macrourus (Gadiformes:Macrouridae) from the Southern Ocean based on samples from the toothfish longline fishery

FIGURE 7. Graph of the annual catch of Dissostichus spp. and Macrourus spp. for the period 2000–2016 (data source: CCAM- LR).

FIGURE 1 in The distributionof fourspeciesof thegenus Macrourus (Gadiformes:Macrouridae) from the Southern Ocean based on samples from the toothfish longline fishery

FIGURE 1. Diagram of scale rows depicting a 4-scale series used for the 'four scale series length' measurement (indicated by red arrows) and a diagonal scale row counted between anal-fin origin and lateral line (adapted from McMillan et al. 2012).

FIGURE 2 in The distributionof fourspeciesof thegenus Macrourus (Gadiformes:Macrouridae) from the Southern Ocean based on samples from the toothfish longline fishery

FIGURE 2. Distribution maps for southern hemisphere species of Macrourus based on specimens examined in this study (red stars, 2015–16), plotted along with the records (black shapes) from McMillan et al. (2012). (a) Macrourus caml; (b) M. whitsoni; (c) M. carinatus; (d) M. holotrachys. The Polar Front (PF) and the sub-Antarctic Front (SAF) are shown, and each map indicates the three main areas referred to in the text. Prepared by Susan Jane Baird, NIWA, Wellington.

FIGURE 5 in The distributionof fourspeciesof thegenus Macrourus (Gadiformes:Macrouridae) from the Southern Ocean based on samples from the toothfish longline fishery

FIGURE 5. Scanning electron microscope images of lateral line scales of species of Macrourus taken from below the first dorsal fin. (a) and (b) M. caml SAIAB 203945, 131.2 (tissue sample PEI15-M077) and 125.0 mm HL (tissue sample PEI15-M085) respectively. (c) M. whitsoni, 117.7 mm HL (tissue sample PEI15-M 088). (d) M. carinatus, 159.5 mm HL (tissue sample PEI15- M076). (e) and (f) M. holotrachys, SAIAB 209622, 158.2 (tissue sample PEI15-M012) and 122.7 (tissue sample PEI15-M013) mm HL, respectively.

FIGURE 8 in The distributionof fourspeciesof thegenus Macrourus (Gadiformes:Macrouridae) from the Southern Ocean based on samples from the toothfish longline fishery

FIGURE 8. Presence/absence of scales on underside of head in Macrourus spp. (a) M. caml, 123.1 mm HL (tissue sample PEI15- M168). (b) M. caml NMNZ P.047809, 123 mm HL. (c) M. whitsoni, 92.8 mm HL (tissue sample PEI15-M129). (d) M. whitsoni NMNZ P.036150, 137 mm HL. (e) M. carinatus, SAIAB 209621, 127.2 mm HL (tissue sample PEI15-M003). (f) M. carinatus NMNZ P.042354, 133 mm HL. (g) M. holotrachys, SAIAB 209622, 145.1 mm HL (tissue sample PEI15-M009). (h) M. holotrachys NMNZ P.039922, 166 mm HL.

FIGURE 15. Zagrammosoma fisheri n in Read between the lineata: A revision of the tattooed wasps, Zagrammosoma Ashmead (Hymenoptera: Eulophidae), with descriptions of eleven new species

FIGURE 15. Zagrammosoma fisheri n. sp., ♀: (A) head, frontolateral, (B) lateral habitus, (C) fore wing, dorsal, (D) dorsal habitus; (E) ♁ dorsal habitus. Scale bar = 0.2 mm (A), 0.5 mm (B–E).

opencc-zeroDec 2015View details →

Data from: Catch reconstructions reveal that global marine fisheries catches are higher than reported and declining

Fisheries data assembled by the Food and Agriculture Organization (FAO) suggest that global marine fisheries catches increased to 86 million tonnes in 1996, then slightly declined. Here, using a decade-long multinational 'catch reconstruction' project covering the Exclusive Economic Zones of the world's maritime countries and the High Seas from 1950 to 2010, and accounting for all fisheries, we identify catch trajectories differing considerably from the national data submitted to the FAO. We suggest that catch actually peaked at 130 million tonnes, and has been declining much more strongly since. This decline in reconstructed catches reflects declines in industrial catches and to a smaller extent declining discards, despite industrial fishing having expanded from industrialized countries to the waters of developing countries. The differing trajectories documented here suggest a need for improved monitoring of all fisheries, including often neglected small-scale fisheries, and illegal and other problematic fisheries, as well as discarded bycatch.

Data from: A function-valued trait approach to estimating the genetic basis of size at age and its potential role in fisheries induced evolution

Natural selection is inherently a multivariate phenomenon. The selection pressure on size (natural and artificial) and the age at which selection occurs is likely to induce evolutionary changes in growth rates across the entire life history. However, the covariance structure that will determine the path of evolution for size-at-age has been studied in only a few fish species. We therefore estimated the genetic covariance function for size throughout ontogeny using Atlantic silversides (Menidia menidia) as the model system. Over a 3-year period, a total of 542 families were used to estimate the genetic covariance in length at age from hatch through maturity. The function-valued trait approach was employed to estimate the genetic covariance functions. A Bayesian hierarchical model was used to account for the unbalanced design, unequal measurement intervals, unequal sample sizes, and family-aggregated data. To improve mixing, we developed a two-stage sampler using a Gibbs sampler to generate the posterior of a well-mixing approximate model followed by an importance sampler to draw samples from posterior of the completely specified model. We found that heritability of length is age-specific and there are strong genetic correlations in length across ages that last 30d or more. We used these estimates in a hypothetical model predicting the evolutionary response to harvesting following a single generation of selection under both sigmoidal and unimodal patterns of gear selectivity to illustrate the potential outcomes of ignoring the genetic correlations. In these scenarios genetic correlations were found to have a strong effect on both the direction and magnitude of the response to harvest selection.

opencc-zeroDec 2016View details →

Data from: A parallel population genomic and hydrodynamic approach to fishery management of highly-dispersive marine invertebrates: the case of the Fijian black-lip pearl oyster Pinctada margaritifera

Fishery management and conservation of marine species increasingly relies on genetic data to delineate biologically relevant stock boundaries. Unfortunately for high gene flow species which may display low, but statistically significant population structure, there is no clear consensus on the level of differentiation required to resolve distinct stocks. The use of fine-scale neutral and adaptive variation, considered together with environmental data can offer additional insights to this problem. Genome-wide genetic data (4,123 SNPs), together with an independent hydrodynamic particle dispersal model were used to inform farm and fishery management in the Fijian black-lip pearl oyster Pinctada margaritifera, where comprehensive fishery management is lacking, and the sustainability of exploitation uncertain. Weak fine-scale patterns of population structure were detected, indicative of broad-scale panmixia among wild oysters, while a hatchery-sourced farmed population exhibited a higher degree of genetic divergence (Fst = 0.0850–0.102). This hatchery-produced population had also experienced a bottleneck (NeLD = 5.1; 95% C.I. = [5.1–5.3]); compared to infinite NeLD estimates for all wild oysters. Simulation of larval transport pathways confirmed the existence of broad-scale mixture by surface ocean currents, correlating well with fine-scale patterns of population structuring. Fst outlier tests failed to detect large numbers of loci supportive of selection, with 2–5 directional outlier SNPs identified (average Fst = 0.116). The lack of biologically significant population genetic structure, absence of evidence for local adaptation and larval dispersal simulation, all indicate the existence of a single genetic stock of P. margaritifera in the Fiji Islands. This approach using independent genomic and oceanographic tools has allowed fundamental insights into stock structure in this species, with transferability to other highly-dispersive marine taxa for their conservation and management.

opencc-zeroDec 2016View details →

Data from: Temperate marine protected area provides recruitment subsidies to local fisheries

The utility of marine protected areas (MPAs) as a means of protecting exploited species and conserving biodiversity within MPA boundaries is supported by strong empirical evidence. However, the potential contribution of MPAs to fished populations beyond their boundaries is still highly controversial; empirical measures are scarce and modelling studies have produced a range of predictions, including both positive and negative effects. Using a combination of genetic parentage and relatedness analysis, we measured larval subsidies to local fisheries replenishment for Australasian snapper (Chrysophrys auratus: Sparidae) from a small (5.2 km2), well-established, temperate, coastal MPA in northern New Zealand. Adult snapper within the MPA contributed an estimated 10.6% (95% CI: 5.5-18.1%) of newly settled juveniles to surrounding areas (approx. 400 km2), with no decreasing trend in contributions up to 40 km away. Biophysical modelling of larval dispersal matched experimental data, showing larvae produced inside the MPA dispersed over a comparable distance. These results demonstrate that temperate MPAs have the potential to provide recruitment subsidies at magnitudes and spatial scales relevant to fisheries management. The validated biophysical model provides a cost-efficient opportunity to generalize these findings to other locations and climate conditions, and potentially informs the design of MPA networks for enhancing fisheries management.

Data from: A low-cost solution for documenting distribution and abundance of endangered marine fauna and impacts from fisheries

Fisheries bycatch is a widespread and serious issue that leads to declines of many important and threatened marine species. However, documenting the distribution, abundance, population trends and threats to sparse populations of marine species is often beyond the capacity of developing countries because such work is complex, time consuming and often extremely expensive. We have developed a flexible tool to document spatial distribution and population trends for dugongs and other marine species in the form of an interview questionnaire supported by a structured data upload sheet and a comprehensive project manual. Recognising the effort invested in getting interviewers to remote locations, the questionnaire is comprehensive, but low cost. The questionnaire has already been deployed in 18 countries across the Indo-Pacific region. Project teams spent an average of USD 5,000 per country and obtained large data sets on dugong distribution, trends, catch and bycatch, and threat overlaps. Findings indicated that >50% of respondents had never seen dugongs and that 20% had seen a single dugong in their lifetimes despite living and fishing in areas of known or suspected dugong habitat, suggesting that dugongs occured in low numbers. Only 3% of respondents had seen mother and calf pairs, indicative of low reproductive output. Dugong hunting was still common in several countries. Gillnets and hook and line were the most common fishing gears, with the greatest mortality caused by gillnets. The questionnaire has also been used to study manatees in the Caribbean, coastal cetaceans along the eastern Gulf of Thailand and western Peninsular Malaysia, and river dolphins in Peru. This questionnaire is a powerful tool for studying distribution and relative abundance for marine species and fishery pressures, and determining potential conservation hotspot areas. We provide the questionnaire and supporting documents for open-access use by the scientific and conservation communities.

Data from: Genotyping-by-sequencing of genome-wide microsatellite loci reveals fine-scale harvest composition in a coastal Atlantic salmon fishery

Individual assignment and genetic mixture analysis are commonly utilized in contemporary wildlife and fisheries management. Although microsatellite loci provide unparalleled numbers of alleles per locus, their use in assignment applications is increasingly limited. However, next-generation sequencing, in conjunction with novel bioinformatic tools allows large numbers of microsatellite loci to be simultaneously genotyped, presenting new opportunities for individual assignment and genetic mixture analysis. Here we scanned the published Atlantic salmon genome to identify 706 microsatellite loci, from which we developed a final panel of 101 microsatellites distributed across the genome (average 3.4 loci per chromosome). Using samples from 35 Atlantic salmon populations (n=1485 individuals) from coastal Labrador, Canada, a region characterized by low levels of differentiation in this species, this panel identified 844 alleles (average of 8.4 alleles per locus). Simulation-based evaluations of assignment and mixture identification accuracy revealed unprecedented resolution, clearly identifying 26 rivers or groups of rivers spanning 500 km of coastline. This baseline was used to examine the stock composition of 696 individuals harvested in the Labrador Atlantic salmon fishery and revealed that coastal fisheries largely targeted regional groups (<300km). This work suggests that the development and application of large sequenced microsatellite panels presents great potential for stock resolution in Atlantic salmon and more broadly in other exploited anadromous and marine species.

opencc-zeroDec 2018View details →

Data from: Maiden voyage into death: are fisheries affecting seabird juvenile survival during the first days at sea?

The study of juvenile migration behavior of seabird species has been limited so far by the inability to track their movements during long time periods. Foraging and flying skills of young individuals are assumed to be inferior to those of adults, making them more vulnerable during long-distance migrations. In addition to natural oceanographic effects and intrinsic conditions, incidental seabird harvest by human fisheries is one of the main causes for worldwide seabird population declines, and it has been hypothesized that juveniles are particularly vulnerable to bycatch during their first weeks at sea after leaving the nest. We used solar powered satellite tags to track the at sea movements of adults and juveniles of Scopoli's shearwater (Calonectris diomedea) after the autumn departure from their breeding colony in Chafarinas Islands (southwestern Mediterranean Sea). Eighty percent of juvenile tags stopped transmitting during the first week at sea, within 50 km of their natal colony, in an area with one of the highest concentrations of fishing activities in the Mediterranean Sea. All adult birds tagged and only twenty per cent of juveniles migrated into the Atlantic and southwards along the coast of West Africa. The two age groups showed different habitat preferences, with juveniles travelling farther from the coast, in windier and less productive waters than adults. We conclude that Scopoli's shearwater juveniles are particularly vulnerable to mortality events, and we highlight that fisheries, along with differential age-related behavior skills between adults and juveniles, are likely causes of this mortality. Overall, our study highlights the importance of conducting tracking studies during the first stages of juvenile migration.

Data from: Integrating complementary methods to improve diet analysis in fishery-targeted species

Developing efficient, reliable, cost-effective ways to identify diet is required to understand trophic ecology in complex ecosystems and improve food web models. A combination of techniques, each varying in their ability to provide robust, spatially and temporally explicit information can be applied to clarify diet data for ecological research. This study applied an integrative analysis of a fishery-targeted species group - Plectropomus spp.in the central Great Barrier Reef, Australia by comparing three diet-identification approaches. Visual stomach content analysis provided poor identification with ~14% of stomachs sampled resulting in identification to family or lower. A molecular approach was successful with prey from ~80% of stomachs identified to genus or species, often with several unique prey in a stomach. Stable isotope mixing models utilising experimentally-derived assimilation data, identified similar prey as the molecular technique but at broader temporal scales, particularly when prior diet information was incorporated. Overall, Caesionidae and Pomacentridae were the most abundant prey families (>50% prey contribution) for all Plectropomus spp., highlighting the importance of planktivorous prey. Less abundant prey categories differed among species/colour phases indicating possible niche segregation. This study is one of the first to demonstrate the extent of taxonomic resolution provided by molecular techniques, and, like other studies, illustrates that temporal investigations of dietary patterns are more accessible in combination with stable isotopes. The consumption of mainly planktivorous prey within this species group has important implications within coral reef foodwebs and provides cautionary information regarding the effects that changing resources could have in reef ecosystems.