scholarly journals The use of species-specific TaqMan probes for identifying early stage gadoid eggs following formaldehyde fixation

2008 ◽  
Vol 65 (9) ◽  
pp. 1573-1577 ◽  
Author(s):  
Freya Goodsir ◽  
Michael J. Armstrong ◽  
Peter R. Witthames ◽  
David L. Maxwell ◽  
Clive J. Fox
Keyword(s):  
Gadus Morhua ◽  
Atlantic Cod ◽  
Early Stage ◽  
Melanogrammus Aeglefinus ◽  
Fish Eggs ◽  
Important Species ◽  
Taqman Probes ◽  
Positive Rate ◽  
Identification Technique ◽  
Species Specific

Abstract Goodsir, F., Armstrong, M. J., Witthames, P. R., Maxwell, D. L., and Fox, C. J. 2008. The use of species-specific TaqMan probes for identifying early stage gadoid eggs following formaldehyde fixation. – ICES Journal of Marine Science, 65: 1573–1577. Surveys of fish eggs are increasingly being used to monitor the spawning areas and stock status of commercially important species such as Atlantic cod (Gadus morhua), but early stage cod eggs are visually indistinguishable from those of several other common co-occurring species, including haddock (Melanogrammus aeglefinus) and whiting (Merlangius merlangus). In recent surveys in the Irish and North Seas, a molecular identification technique (TaqMan multiplex real-time polymerase chain-reaction) assay has been used to overcome this problem. The method needs high-quality DNA, so the current protocol requires that individual “cod-like” eggs are “presorted” from plankton hauls on board ship and immediately preserved in ethanol. This increases seagoing staff costs, can be a difficult process at sea, and means that plankton sampling cannot be undertaken from non-specialized vessels such as fishing boats. Successful application of TaqMan probes to DNA from eggs preserved in formalin would overcome these problems, but previous attempts have resulted in poor success. In this study, batches of hatchery-sourced cod, haddock, and whiting eggs were fixed in 4% buffered formalin for up to 3 weeks, then transferred to a formaldehyde-free solution for 1, 2, or 3 months. After these periods they were assessed visually for fixation quality and analysed using species-specific TaqMan probes. Eggs, which had been fixed for up to 3 weeks in formalin, were identified successfully, although the positive rate (84–96%) was slightly lower than samples preserved throughout in ethanol (92–99%). There was no increase in the percentage of eggs misidentified comparing formalin-fixed and ethanol-preserved material. These results suggest that TaqMan probes can be applied successfully to fish eggs fixed in 4% buffered formalin for up to 3 weeks.

Stage Dependent Vertical Distribution of Haddock (Melanogrammus aeglefinus) Eggs in a Stratified Water Column: Observations and Model

1989 ◽  
Vol 46 (S1) ◽  
pp. s55-s67 ◽  
Author(s):  
Fred H. Page ◽  
Kenneth T. Frank ◽  
Keith R. Thompson
Keyword(s):  
Water Column ◽  
Gadus Morhua ◽  
Atlantic Cod ◽  
Early Stage ◽  
Surface Wind ◽  
Melanogrammus Aeglefinus ◽  
Near Surface ◽  
Egg Transport ◽  
Haddock Melanogrammus Aeglefinus ◽  
Surface Drift

The depth distribution of four development stages of haddock (Melanogrammus aeglefinus) eggs was measured during May 1984 in a continuously stratified water column over Browns Bank. The egg profile varied with development. Early stage eggs were most concentrated near the sea surface whereas late stage eggs were distributed uniformly over depth or had a subsurface maximum. In order to explain the shape of these profiles a one-dimensional (vertical) advection–diffusion model including density stratification was used. Model egg profiles compared favourably with observed profiles and indicate that a large proportion (>30%) of haddock eggs are below the Ekman depth (δe. This proportion increases as the eggs develop. For example more than 50% of the stage III and IV eggs are below δe. Surface drift bottles and other indicators of the very near surface wind-driven transport would appear to be poor indicators of egg transport in haddock and possibly several other species, such as Atlantic cod (Gadus morhua) and mackerel (Scomber scombrus).

scholarly journals Linking spawning ground extent to environmental factors — patterns and dispersal during the egg phase of four North Sea fishes

2018 ◽  
Vol 75 (3) ◽  
pp. 357-374 ◽  
Author(s):  
Hannes Höffle ◽  
Cindy J.G. Van Damme ◽  
Clive Fox ◽  
Stéphanie Lelièvre ◽  
Christophe Loots ◽  
...  
Keyword(s):  
North Sea ◽  
Gadus Morhua ◽  
Atlantic Cod ◽  
Early Stage ◽  
Distribution Patterns ◽  
Melanogrammus Aeglefinus ◽  
Spawning Grounds ◽  
The North ◽  
Generalized Additive Mixed Models ◽  
Additive Mixed Models

Previous studies have shown that four commercially important demersal species, namely Atlantic cod (Gadus morhua), haddock (Melanogrammus aeglefinus), whiting (Merlangius merlangus), and European plaice (Pleuronectes platessa), spawn in distinct areas across the North Sea. Based on two comprehensive ichthyoplankton surveys in 2004 and 2009, the present study uses generalized additive mixed models to delimit these spawning grounds using the distribution of recently spawned eggs, investigates their relationship to specific environmental conditions, and examines egg dispersal during their development. Results indicate that presence–absence of early stage eggs is more related to temporal and topographic variables, while egg densities are closely linked with hydrography. Egg distribution patterns were relatively consistent during development and only changed near hatching. Compared with historic observations, the location of the spawning grounds appeared stable on the broad scale but centres of egg abundance varied between the surveyed years. Potential effects of long-term climate change and anthropogenic short-term disturbances, such as seismic surveys, on fish reproduction are discussed, pointing out the demand for multispecies studies on these issues.

Discarding practices for commercial gadoids in the North Sea

1998 ◽  
Vol 55 (7) ◽  
pp. 1632-1644 ◽  
Author(s):  
Yorgos Stratoudakis ◽  
Robert J Fryer ◽  
Robin M Cook
Keyword(s):  
North Sea ◽  
Gadus Morhua ◽  
Atlantic Cod ◽  
Melanogrammus Aeglefinus ◽  
The North ◽  
The North Sea ◽  
Merlangius Merlangus ◽  
Using Data ◽  
Species Specific ◽  
Catch Composition

Understanding fishers' discarding behaviour, and anticipating their reactions to changes in the biological or regulatory characteristics of a fishery, are important for dealing with the problem of discarding. In this paper, we investigate the discarding of haddock (Melanogrammus aeglefinus), whiting (Merlangius merlangus), and Atlantic cod (Gadus morhua) in the North Sea, using data collected by scientific observers onboard Scottish demersal vessels. We describe discarding on each trip by species-specific discard curves and explore how these curves depend on biological and regulatory variables. There are large differences in the size of discarded fish between inshore and offshore areas, with offshore-operating vessels discarding larger fish (high-grading). Increases in legal landing size correspond to immediate increases in the size of discarded fish, particularly for haddock and cod in inshore areas. In general, discarding practices for haddock and cod are similar over time and consistent across gears, whereas decisions for the lesser valued whiting are more variable and can be affected by the catch composition.

Species-specific residence times in the aft part of a pelagic survey trawl: implications for inference of pre-capture spatial distribution using the Deep Vision system

2018 ◽  
Vol 75 (4) ◽  
pp. 1393-1404 ◽  
Author(s):  
Melanie J Underwood ◽  
Shale Rosen ◽  
Arill Engås ◽  
Terje Jørgensen ◽  
Anders Fernö
Keyword(s):  
Spatial Distribution ◽  
Residence Time ◽  
Gadus Morhua ◽  
Atlantic Cod ◽  
Vision System ◽  
Ground Truth ◽  
Clupea Harengus ◽  
Melanogrammus Aeglefinus ◽  
Camera System ◽  
Species Specific

Abstract In-trawl camera systems promise to improve the resolution of trawl sampling used to ground-truth the interpretation of acoustic survey data. In this study, the residence time of fish in front of the Deep Vision camera system, used to identify, measure and count fish inside the trawl, was analysed to determine the reliability of spatial distribution recorded by the system. Although Atlantic herring (Clupea harengus), haddock (Melanogrammus aeglefinus), and most Atlantic cod (Gadus morhua) moved quickly back through the aft part of the pelagic trawl, saithe (Pollachius virens) spent up to 4 min in front of the system. The residence time increased for saithe and cod when other individuals were present, and cod swimming in the low water flow close to the trawl netting spent longer there than cod at the centre of the trawl. Surprisingly, residence time was not related to the size of the fish, which may be explained by the collective behaviour of shoaling fish. Our findings suggest that while in-trawl images can be used to identify, measure and count most species, when sampling fast-swimming species such as saithe the position inferred from when they were imaged may not reflect the actual spatial distribution prior to capture.

Distribution of Early-Stage Atlantic Cod (Gadus morhua), Haddock (Melanogrammus aeglefinus), and Witch Flounder (Glyptocephalus cynoglossus) Eggs on the Scotian Shelf: A Reappraisal of Evidence on the Coupling of Cod Spawning and Plankton Production

1992 ◽  
Vol 49 (2) ◽  
pp. 238-251 ◽  
Author(s):  
Keith Brander ◽  
Peter C. F. Hurley
Keyword(s):  
Gadus Morhua ◽  
Atlantic Cod ◽  
Early Stage ◽  
Calanus Finmarchicus ◽  
Melanogrammus Aeglefinus ◽  
Scotian Shelf ◽  
Plankton Production ◽  
Peak Abundance ◽  
Haddock Melanogrammus Aeglefinus ◽  
Timing Of Spawning

In spring, Atlantic cod (Gadus morhua) spawned progressively later from southwest to northeast along the Scotian Shelf and matched the variation in peak abundance of Calanus finmarchicus. In fall, cod spawned in some, but not all, areas where Calanus were abundant. This is consistent with the hypothesis that cod spawning is coupled to copepod production, which is a part of the "match–mismatch" hypothesis proposed by D. H. Cushing. The timing of spawning was estimated from the distributions of early- and late-stage eggs of cod, haddock (Melanogrammus aeglefinus), and witch flounder (Glyptocephalus cynoglossus) collected during Scotian Shelf Ichthyoplankton Survey (SSIP) cruises in 1979–81.

Species specific behaviour and catchability of gadoid fish to floated and bottom set pots

2016 ◽  
Vol 74 (3) ◽  
pp. 769-779 ◽  
Author(s):  
Neil Anders ◽  
Anders Fernö ◽  
Odd-Børre Humborstad ◽  
Svein Løkkeborg ◽  
Anne Christine Utne-Palm
Keyword(s):  
Water Column ◽  
Gadus Morhua ◽  
Capture Efficiency ◽  
Escape Rate ◽  
Melanogrammus Aeglefinus ◽  
Encounter Rate ◽  
Specific Behaviour ◽  
Upstream Direction ◽  
Species Specific ◽  
Specific Food

To increase our understanding of the interaction between fish and baited fishing gear we quantitatively described the behaviour of cod (Gadus morhua), saithe (Pollachius virens), and haddock (Melanogrammus aeglefinus) to baited pots in a fjord in northern Norway. Detailed video analyses were made to describe species specific responses and examine the effect of lifting the pot off the bottom. The majority of both cod and saithe approached the pots in an upstream direction, and fish approached floated pots higher in the water column than bottom set pots. Cod tended to approach a pot along the seabed and were more likely to encounter the bottom set pot than the floated pot, whereas saithe more often approached in the water column. The capture efficiency was low for all species, but cod were more likely to be caught than saithe and haddock. Cod showed a high encounter rate, low entrance rate and high escape rate. For saithe, a low encounter rate was the chief factor limiting capture efficiency. The observed differences between cod and saithe were explained by species-specific food-search strategies. No difference in entrance rate, escape rate or catch efficiency between the two pot types were found.

Recent Growth, Biochemical Composition and Prey Field of Larval Haddock (Melanogrammus aeglefinus) and Atlantic Cod (Gadus morhua) on Georges Bank

1987 ◽  
Vol 44 (1) ◽  
pp. 14-25 ◽  
Author(s):  
L. J. Buckley ◽  
R. G. Lough
Keyword(s):  
Gadus Morhua ◽  
Atlantic Cod ◽  
Dry Weight ◽  
Melanogrammus Aeglefinus ◽  
Good Growth ◽  
Georges Bank ◽  
Larval Population ◽  
Prey Biomass ◽  
Recent Growth ◽  
Haddock Melanogrammus Aeglefinus

A transect across southern Georges Bank in May 1983 showed higher levels of available prey for haddock (Melanogrammus aeglefinus) and cod (Gadus morhua) larvae at two stratified sites than at a well-mixed site. At the stratified sites, prey biomass was high (30–300 μg dry wt∙L−1) near the surface above the thermocline; values were lower and more uniform with depth (10–30 μg dry wt∙L−1) at the well-mixed site. Larval population centers generally coincided with prey biomass vertically. Recent growth in dry weight of haddock larvae as estimated by RNA–DNA ratio analysis was higher at the stratified sites (8–13%∙d−1) than at the well-mixed site (7%∙d−1). Larvae appeared to be in excellent condition at the stratified sites, but up to 50% of haddock larvae from the well-mixed site had RNA–DNA ratios in the range observed for starved larvae in the laboratory. Cod collected at the same site were in better condition and growing faster than haddock. The data support the hypotheses that (1) stratified conditions in the spring favor good growth and survival of haddock larvae and (2) cod larvae are better adapted to grow and survive in well-mixed waters at lower levels of available food than haddock larvae.

Fish Catches and Long-Term Tidal Cycles in Northwest Atlantic Fisheries: A Nonlinear Regression Approach

1987 ◽  
Vol 44 (11) ◽  
pp. 1890-1897 ◽  
Author(s):  
Paul Cabilio ◽  
David L. DeWolfe ◽  
Graham R. Daborn
Keyword(s):  
New England ◽  
Nonlinear Regression ◽  
Gadus Morhua ◽  
Atlantic Cod ◽  
Significant Negative Correlation ◽  
Clupea Harengus ◽  
Atlantic Menhaden ◽  
Melanogrammus Aeglefinus ◽  
Grand Banks

Selected long-term fisheries catch data from the New England – Fundy area and the Grand Banks were examined for concordance between changes in fish catches and the 18.6-yr nodal cycle of the tides using a nonlinear regression model. Significant positive correlations were found for Atlantic cod (Gadus morhua), haddock (Melanogrammus aeglefinus), alewife (Alosa pseudoharengus), Atlantic herring (Clupea harengus harengus), and scallop (Placopecten magellanicus), with lag times that are biologically appropriate for the time from hatching to recruitment into the fishery. A significant negative correlation with the nodal cycle was evident for Atlantic menhaden (Brevoortia tyrannus), for which this area constitutes the most northerly part of its range. Cod catches on the Grand Banks showed no correlation with the nodal cycle. It is suggested that the correlations between the nodal cycle and the changes in fish catches are caused by correlated changes either in sea surface temperature or in productivity resulting from changes in the degree of vertical mixing.

Sign in / Sign up

Export Citation Format

Share Document