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Edward A Trippel - One of the best experts on this subject based on the ideXlab platform.
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fecundity estimation of atlantic cod gadus morhua and haddock Melanogrammus aeglefinus of georges bank application of the autodiametric method
Fisheries Research, 2009Co-Authors: Alexandre Alonsofernandez, Ann Carole Vallejo, Fran Saboridorey, Hilario Murua, Edward A TrippelAbstract:Abstract Haddock, Melanogrammus aeglefinus (L.), and Atlantic cod, Gadus morhua (L.), are species of major commercial interest in the Northwest Atlantic and their spawning strategy is characterized by group-synchronous oocyte development and determinate fecundity. Recent advances in image analysis systems and the development of the autodiametric method have led to rapid assessment and accurate estimation of the annual egg production of an individual or its potential fecundity. In this study we estimated the corresponding autodiametric calibration curves for Atlantic cod and haddock of Georges Bank and used these to estimate potential fecundity of these two species near the southern limits of their geographic distribution. In addition, we explored the relationships between potential fecundity and different condition indices for these populations and found the hepatosomatic index to significantly increase the explanatory power of the fecundity–length relationship which is in agreement with previous studies on the influence of nutritional state on egg production.
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parental effects on early life history traits of haddock Melanogrammus aeglefinus
Ices Journal of Marine Science, 2006Co-Authors: Nikolaus W Probst, Gerd Kraus, Rick M Rideout, Edward A TrippelAbstract:Gametes from five male and three female haddock ( Melanogrammus aeglefinus ) were crossed to produce 15 half-sibling families that were used to evaluate potential parental contributions to early life history variability. Larval morphology at 0 and 5 days post-hatch (dph) and time to starvation in the absence of food were examined. Maternal influences on larval standard length and yolk area were significant at 0 and 5 dph. Paternal effects on larval standard length were significant at 0 and 5 dph, whereas paternal effects on yolk area were only significant at 5 dph. Larval eye diameter was influenced by maternity at day 0 post-hatch and by both maternity and paternity at 5 dph. Myotome height of larvae was subject to maternal and paternal influences at 0 and 5 dph. Growth rate was significantly influenced by both paternity and maternity. Yolk utilization efficiency was significantly influenced by parental interaction, while the time taken for larvae to die in the absence of food was affected only by maternity. Results of this study not only confirm the importance of female contributions to larval development but also indicate a paternal influence on the development and the early life history success of marine fish.
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effects of egg size food supply and spawning time on early life history success of haddock Melanogrammus aeglefinus
Marine Ecology Progress Series, 2005Co-Authors: Rick M Rideout, Edward A Trippel, Matthew K LitvakAbstract:Eggs and larvae produced by pairs of spawning haddock Melanogrammus aeglefinus were monitored between 2001 and 2003 to determine the effects of spawning time, egg size and food supply on early life history success. Females usually released eggs at 3 d intervals. All females exhibited a continuous decrease in egg diameter and dry weight with consecutive batches, but the decrease in size did not influence fertilization or hatching success. Larval size (standard length and dry weight), yolk area, eye diameter, myotome height, and finfold area were all positively related to egg size and therefore decreased between early- and late-season larvae produced by the same spawning pairs. Differences in larval morphology persisted for at least the first 5 d after hatching. Jaws were not developed at hatching (5°C), but jaw length did show a strong positive relationship with egg size at 5 d post-hatch (dph). The ability of newly hatched larvae to withstand periods of starvation was directly related to initial egg size. Under high prey abundance (5000 l-1) larval survival to 20 dph was highly variable (1.8 to 50.7%) with no differences in survivorship or specific growth rate (0.818 to 0.936% d-1 in standard length) for larvae from early-, middle- and late-season egg batches. With low prey density (1000 l-1) survival of larvae from late-season egg batches was significantly lower (0.4%) than those from early egg batches (1.8%). No differences in larval specific growth rate existed between early and late batches, but growth rate was reduced in both cases with low food abundance (0.683 to 0.690 d-1 in standard length). Results suggest that smaller larvae produced late in the spawning season have reduced feeding capabilities and may experience lower survivorship in the ocean than larger, early-season larvae.
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maternal and seasonal differences in egg sizes and spawning activity of northwest atlantic haddock Melanogrammus aeglefinus in relation to body size and condition
Canadian Journal of Fisheries and Aquatic Sciences, 2004Co-Authors: Edward A Trippel, Steven R E NeilAbstract:Egg and larval production of 22 captive spawning pairs of northwest Atlantic haddock (Melanogrammus aeglefinus) were monitored. Females spawned an average of nine egg batches (range 316) with a mean batch fecundity of 60 000 eggs and mean total fecundity of 535 000 eggs. Mean spawning duration was 37 days with a mean batch interval of 5.4 days. In multiple linear regression, male Fulton's condition factor (range 1.101.55) and mean batch interval explained 56% of variation in fertilization rate (33% and 23%, respectively). Seasonal composite egg diameter spanned 1.371.53 mm among females. Mean egg diameter within females declined seasonally by an average of 10.4% (37% by volume). Females produced 46 larvae per gram body weight. Body weight was the single best predictor of fecundity (r2 = 0.57), with Fulton's condition factor (range 1.041.76) explaining no significant additional variation over length or weight. Length and condition explained 39% of variation in seasonal composite egg diameter (22% and 1...
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effects of photoperiod and light intensity on growth and activity of juvenile haddock Melanogrammus aeglefinus
Aquaculture, 2003Co-Authors: Edward A Trippel, Steven R E NeilAbstract:Abstract Enhancement of growth of juvenile haddock ( Melanogrammus aeglefinus ) was achieved through photomanipulation. After 24 weeks (August–January), hatchery-reared haddock under 24 h light were 53–60% heavier than those under natural photoperiod. In a second 24-week experiment, haddock were grown under five photoperiod regimes (natural photoperiod, 12, 16, 20 and 24 h light) with two light intensities (30 and 100 lx) at 24 h. Continuous light (and 20 h light) resulted in the greatest growth response, though other seasonally unchanging photoperiods (12 and 16 h light) also resulted in faster growth than natural photoperiod. Reduced light intensity, from 100 to 30 lx, at 24 h, led to a further 11% improvement in body mass. The effects of photomanipulation declined as temperatures decreased in late autumn and winter. Locomotor activity was the greatest under natural photoperiod (100 lx), less at 24 h (100 lx) and lowest at 24 h (30 lx). Lower swimming activity under continuous dim light may translate into metabolic savings and increased body mass. Integrating these findings with research on larval haddock suggests a period in the ontogeny exists during which bright light should be dimmed to maximize growth and this perhaps coincides with changes in body morphology and behaviour associated with benthic foraging.
Lawrence J Buckley - One of the best experts on this subject based on the ideXlab platform.
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The effects of temperature, body size and growth rate on energy losses due to metabolism in early life stages of haddock (Melanogrammus aeglefinus)
Marine Biology, 2008Co-Authors: Kate F. Lankin, Lawrence J Buckley, Myron A Peck, David A BengtsonAbstract:Rates of routine respiration ( R _R, μl O_2 fish^−1 h^−1) and total ammonia nitrogen excretion ( E _R, μg NH_4–N + NH_3–N fish^−1 h^−1) were measured on larval and juvenile haddock ( Melanogrammus aeglefinus ) to ascertain how energy losses due to metabolism were influenced by temperature ( T ), dry body mass ( M _D, mg) and specific growth rate (SGR, % per day). R _R and E _R increased with M _D according to y = a · M _D^ b with b -values of 0.96, 0.98, 1.14, and 0.89, 0.78, 0.74, respectively, at 10, 7, and 4°C, respectively. Multiple regressions explained 98% of the variability in the combined effects of M _D and T on R _R and E _R in larval haddock: R _R = 0.97 · M _D^0.98 · e^0.092 · T ; E _R = 0.06 · M _D^0.79 · e^0.092 · T . In young juvenile (24–30 mm standard length) haddock, R _R tended to decline ( P = 0.06) and E _R significantly declined ( P = 0.02) with increasing SGR. O:N ratios significantly increased with increasing SGR suggesting that N was spared in relatively fast-growing individuals. Our results for young larval and juvenile haddock suggest: (1) nearly isometric scaling of R _R with increasing body size, (2) allometric scaling of E _R with increasing body size, (3) Q _10 values of 2.5 for both R _R and E _R, (4) metabolic differences in substrate utilization between relatively fast- and slow-growing individuals, and (5) that rates of routine energy loss and growth were not positively related. The measurements in this study will provide robust parameter estimates for individual-based models that are currently being utilized to investigate how variability in climatic forcing influences the vital rates of early life stages of haddock. Our results also stress that inter-individual differences in rates of energy loss should not be overlooked as a factor influencing growth variability among individuals.
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does the fall phytoplankton bloom control recruitment of georges bank haddock Melanogrammus aeglefinus through parental condition
Canadian Journal of Fisheries and Aquatic Sciences, 2008Co-Authors: Kevin D Friedland, Lawrence J Buckley, Gregory R Lough, Jonathan A Hare, Grayson Woodg B B Wood, Laurel A Col, David G Mountain, Joseph Kane, Jon K T Brodziak, Cynthia H PilskalnAbstract:In 2003, the Georges Bank stock of haddock (Melanogrammus aeglefinus) experienced the largest recruitment event recorded during its assessed history. Several hypotheses have been advanced to explain recruitment variability in this much-scrutinized stock, including variability in the retention of eggs and larvae on Georges Bank, the timing of haddock spawning, and variability in the spring bloom, which influences larval growth and survival. Although these processes may contribute to the formation of successful year classes, none of the factors associated with these previous hypotheses provides an adequate explanation of the 2003 recruitment event. We analyzed data on the dynamics of the fall phytoplankton bloom the year prior to spawning and show it to be highly correlated with subsequent recruitment. We suggest that the fall bloom affects recruitment through enhanced condition of adults and by increasing the quantity and quality of their reproductive output, which in turn leads to a higher probability of ...
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effect of acclimation temperature on the acute stress response in juvenile atlantic cod gadus morhua l and haddock Melanogrammus aeglefinus l
Aquaculture Research, 2006Co-Authors: William King, Lawrence J Buckley, David L BerlinskyAbstract:Juvenile Atlantic cod (Gadus morhua L.) and haddock (Melanogrammus aeglefinus L.) were subjected to 30 s air exposure stressors following acclimation to 4, 10 and 14 and 4, 8 and 14°C respectively. Both species responded to the stressor with increases in plasma cortisol at all temperatures tested. At 14°C cortisol levels peaked within 1 h post-stressor, and returned to pre-stressor levels within 24 h. In contrast, at 4°C, peak cortisol levels were not attained until 6 h post-stressor in haddock and remained elevated beyond 24 h in both species. The rate of plasma glucose accumulation was greater at higher temperatures in both species and no increase was seen at 4°C. Lysozyme activity in cod, in response to the stressor, was lower than the values reported for some other species and increased slightly at 14°C. The results show that cod and haddock acclimated to different temperatures respond to common, acute stressors in a manner similar to other teleosts.
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hatch date distributions of young of year haddock Melanogrammus aeglefinus in the gulf of maine georges bank region implications for recruitment
Marine Ecology Progress Series, 2005Co-Authors: Amy Lapolla, Lawrence J BuckleyAbstract:We determined the hatch dates of young-of-year (YOY) juveniles from the 1995 to 1999 year-classes of haddock Melanogrammus aeglefinus collected in the Northeast Fisheries Science Center fall groundfish surveys in the Gulf of Maine/Georges Bank region. Hatch dates were based on age estimates made by counting otolith daily rings. The average YOY haddock was >200 d old at the time of capture, with estimated hatch dates ranging from mid November to early June. Haddock collected in the Gulf of Maine had mean hatch dates about 1 mo later than fish collected on Georges Bank. Each year on Georges Bank, hatch date frequencies (HDF) of survivors peaked between Feb- ruary and mid March, considerably earlier than the peak in HDF estimated from late-stage eggs. The ratio of the relative HDF of survivors collected in the fall to the relative HDF estimated from late-stage eggs was used to calculate relative survivorship of different cohorts. These data suggest that haddock hatched early in the season had a survival advantage over those hatched later in the year. The 1998 year-class, the largest produced on Georges Bank in the past 20 yr, had one of the latest peaks in HDF of juveniles among the 5 years examined. More survivors were produced in each month of 1998 com- pared to the monthly averages of the remaining years. In particular, the 1998 year-class benefited from enhanced survival of individuals hatched in the mid and latter portions of the hatch curve, although survival was still highest for individuals originating from the early portion of the hatching curve.
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optimum temperature and food limited growth of larval atlantic cod gadus morhua and haddock Melanogrammus aeglefinus on georges bank
Fisheries Oceanography, 2004Co-Authors: Lawrence J Buckley, Elaine M Caldarone, Gregory R LoughAbstract:We estimated recent growth of Atlantic cod (Gadus morhua) and haddock (Melanogrammus aeglefinus) larvae collected on the southern flank of Georges Bank in May 1992–94 from the ratio of RNA to DNA (R/D) and water temperature. Growth of both species increased with water temperature to about 7°C and then decreased. The highest growth rates were observed in May 1993 at water temperatures around 7°C. These data confirm an earlier observation of comparable temperature optima for growth of Atlantic cod and haddock larvae in the north-west Atlantic. Comparisons of field growth rates and temperature optima with data for larvae cultured at high temperatures and prey densities in the laboratory suggest that growth may have been food-limited at higher temperatures on Georges Bank. Given that 7°C is the long-term mean water temperature on the southern flank in May and that climate models predict a possible 2–4°C rise in water temperatures for the western North Atlantic, our findings point to a possible adverse effect of global warming on Atlantic cod and haddock.
Richard D M Nash - One of the best experts on this subject based on the ideXlab platform.
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skipped spawning in northeast arctic haddock Melanogrammus aeglefinus
Marine Ecology Progress Series, 2015Co-Authors: Jon Egil Skjaeraasen, Knut Korsbrekke, Trygve Nilsen, Merete Fonn, Olav Sigurd Kjesbu, Gjert Endre Dingsor, Richard D M NashAbstract:Large interannual fluctuations in the numbers of offspring joining a teleost popula- tion are common, yet factors affecting offspring production, a key driver of fish population size and demography, are often poorly understood. For some iteroparous teleosts, spawning omission ('skipping') following sexual maturation may occur, but this is typically difficult to verify. Through the detection of post-ovulatory follicles, i.e. evidence of past spawning activity, in gonads of females not spawning in the current year, we demonstrate skipping in Northeast Arctic (NEA) haddock Melanogrammus aeglefinus. Based on samples obtained just prior to the main spawning season in the Barents Sea from February to April in 2009 to 2012, the estimated population fre- quency of skippers ranged from 23 (2009) to 64% (2011) for females ≥35 cm in total length found in this area at this time. Skipping was associated with limited energy reserves and persisted with age, although it appeared to be most common in 5 yr old females. This suggests that skipping is linked to a combination of feeding condition and demography of the fish population. While previ- ously virtually undocumented in this species, this phenomenon appears to be an integral life his- tory feature for NEA haddock and may have a major impact on the annual realised egg production in this population. Finally, given the similarity between the results reported here and those recently published for NEA cod, we postulate that skipping may be a common occurrence in gadoids undertaking long, energetically demanding spawning migrations.
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size energy and stage dependent fecundity and the occurrence of atresia in the northeast arctic haddock Melanogrammus aeglefinus
Fisheries Research, 2013Co-Authors: Jon Egil Skjaeraasen, Knut Korsbrekke, Trygve Nilsen, Merete Fonn, Olav Sigurd Kjesbu, Richard D M NashAbstract:Abstract The Northeast Arctic (NEA) haddock ( Melanogrammus aeglefinus ) population size has fluctuated greatly over the last few decades. Such fluctuations may be influenced by changes in reproductive investment, yet no fecundity study on this population has been undertaken since 1974 with which to address such a concept. We therefore estimated potential fecundity of >350 NEA haddock caught in February–March 2009–2011 and correlated this with potential fecundity proxies, i.e. female age, length, relative liver size and somatic condition and leading oocyte cohort development (diameter) ( LC 20 ). We also examined the incidence (prevalence) and intensity of atresia in histological ovary sections. Finally, we estimated population (total) egg production (TEP) for NEA haddock in 2010 and 2011. Fecundity was mainly determined by length, although it was also positively associated with our metric of liver size and somatic condition. Fecundity decreased with LC 20 , indicating atresia, confirmed by the direct observation of atresia in histological sections ( n = 185). Although 45% of the females possessed atretic oocytes, the intensity of atresia was low, typically only 1–5% of the oocytes with yolk granules were atretic, complete reabsorption of all vitellogenic oocytes was not observed. Our proxies give no indication of any change in reproductive investment for NEA haddock in the last few decades. The present study confirms the importance of liver and white muscle energy for oocyte recruitment and shows atretic down-regulation in NEA haddock. Further, NEA haddock females whose oocytes reach the yolk granule stage will likely spawn. NEA haddock TEP for females aged 4–8 years was estimated to be 4.5 × 10 13 and 2.9 × 10 13 in 2010 and 2011, respectively.
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comment on does the fall phytoplankton bloom control recruitment of georges bank haddock Melanogrammus aeglefinus through parental condition
Canadian Journal of Fisheries and Aquatic Sciences, 2009Co-Authors: Mark R Payne, Mark Dickeycollas, Richard D M NashAbstract:In the paper “Does the fall phytoplankton bloom control recruitment of Georges Bank haddock, Melanogrammus aeglefinus, through parental condition?”, Friedland et al. (Can. J. Fish. Aquat. Sci. 65(6...
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gape morphology of cod gadus morhua l haddock Melanogrammus aeglefinus l and whiting merlangius merlangus l through metamorphosis from larvae to juveniles in the western irish sea
Journal of Fish Biology, 2006Co-Authors: Ll W Rowlands, Mark Dickeycollas, Audrey J Geffen, Richard D M NashAbstract:Variations in standard length (LS), gape size (SG) and jaw length (LJ) were studied in larval and juvenile gadoids (cod Gadus morhua, haddock Melanogrammus aeglefinus and whiting Merlangius merlangus) from 4 to 70 mm. The increase in SG and LJ was not linear with respect to LS. The relationship was best described by segmented regression lines in all three species, with an inflection point at c. 10·5 mm. The SG and LJ increased more rapidly in relation to larval LS for individuals smaller than this inflection point size. The rates of increase slowed significantly post-inflection, an effect more noticeable in SG data compared to LJ data. In each case, the inflection point fell in the intermediate period of development between the larval and juvenile stages, which could be considered as metamorphosis. Published equations that have been used to predict SG from LJ lead to the overestimation of gape. New relationships are presented, which may be used to predict SG from measurements of either LS or upper jaw length in cod, haddock and whiting.
Sonnich Meier - One of the best experts on this subject based on the ideXlab platform.
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embryonic exposure to produced water can cause cardiac toxicity and deformations in atlantic cod gadus morhua and haddock Melanogrammus aeglefinus larvae
Marine Environmental Research, 2019Co-Authors: Bjorn Henrik Hansen, Sonnich Meier, Lisbet Sorensen, Trond Rovik Storseth, Raymond Nepstad, Dag Altin, Daniel Franklin Krause, Trond NordtugAbstract:Regular discharges of produced water from the oil and gas industry represents the largest direct discharge of effluent into the marine environment worldwide. Organic compound classes typically reported in produced water include saturated hydrocarbons, monoaromatic and polyaromatic hydrocarbons (MAHs, PAHs) as well as oxygenated compounds, such as phenols, acids and ketones. This forms a cocktail of known and suspect toxicants, but limited knowledge is yet available on the sub-lethal toxicity of produced water to cold-water marine fish species. In the present work, we conducted a 4-day exposure of embryos of Atlantic cod (Gadus morhua) and haddock (Melanogrammus aeglefinus) to produced water extracts equivalent to 1:50, 1:500 and 1:5000 times dilutions of raw effluent. No significant reduction in survival or hatching success was observed, however, for cod, hatching was initiated earlier for exposed embryos in a concentration-dependent manner. During recovery, significantly reduced embryonic heart rate was observed for both species. After hatch, larvae subjected to embryonic exposure to produced water extracts were smaller, and displayed signs of cardiotoxicity, jaw and craniofacial deformations. In order to improve risk assessment and regulation of produced water discharges, it is important to identify which produced water components contribute to these effects.
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vertebral column deformity in adult wild haddock Melanogrammus aeglefinus
Journal of Fish Diseases, 2018Co-Authors: Laith A Jawad, Sonnich Meier, Tom Johnny Hansen, Jon Egil Skjaeraasen, Per Gunnar FjelldalAbstract:This study describes radiological malformations in the vertebral column of adult sexually mature wild haddock, Melanogrammus aeglefinus collected from Masfjorden, Western Norway, in 2014 and 2015. There were seven deformed fish (33% of sampled fish), five with mild deformities and two with severe deformities. The deformity types discovered were lordosis, vertebra body asymmetry, compression, fusion (ankylosis), remodelling, and haemal spine hyperostosis. The two severely deformed fish were as follows: (a) one specimen with 29 deformed vertebrae within the region vertebrae nos. 1-30, including two sites of lordosis; (b) one specimen with 15 deformed vertebrae within the region vertebrae nos. 31-52 (most caudal vertebrae). The results of this study show that wild haddock can survive severe vertebra deformities, both in the trunk and tail region, and reach adulthood and sexual maturity. Whether normal nondeformed wild conspecifics would mate and spawn with these individuals and thereby complete the life cycle of the deformed individuals is, however, unknown. A possible link between bone fracture and fish hyperostosis is discussed.
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adhesion of mechanically and chemically dispersed crude oil droplets to eggs of atlantic cod gadus morhua and haddock Melanogrammus aeglefinus
Science of The Total Environment, 2018Co-Authors: Bjorn Henrik Hansen, Sonnich Meier, Lisbet Sorensen, Dag Altin, Patricia Almeira Carvalho, Andy M Booth, Julia Farkas, Trond NordtugAbstract:Crude oil accidentally spilled into the marine environment undergoes natural weathering processes that result in oil components being dissolved into the water column or present in particulate form as dispersed oil droplets. Oil components dissolved in seawater are typically considered as more bioavailable to pelagic marine organisms and the main driver of crude oil toxicity, however, recent studies indicate that oil droplets may also contribute. The adhesion of crude oil droplets onto the eggs of pelagic fish species may cause enhanced transfer of oil components via the egg surface causing toxicity during the sensitive embryonic developmental stage. In the current study, we utilized an oil droplet dispersion generator to generate defined oil droplets sizes/concentrations and exposed Atlantic cod (Gadus morhua) and haddock (Melanogrammus aeglefinus) to investigate if the potential for dispersed oil droplets to adhere onto the surface of eggs was species-dependent. The influence of a commercial chemical dispersant on the adhesion process was also studied. A key finding was that the adhesion of oil droplets was significantly higher for haddock than cod, highlighting key differences and exposure risks between the two species. Scanning electron microscopy indicates that the differences in oil droplet adhesion may be driven by the surface morphology of the eggs. Another important finding was that the adhesion capacity of oil droplets to fish eggs is significantly reduced (cod 37.3%, haddock 41.7%) in the presence of the chemical dispersant.
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genomic architecture of haddock Melanogrammus aeglefinus shows expansions of innate immune genes and short tandem repeats
BMC Genomics, 2018Co-Authors: Ole K Torresen, Marine S O Brieuc, Monica Hongro Solbakken, Elin Sorhus, Alexander J Nederbragt, Kjetill S Jakobsen, Sonnich Meier, Rolf B Edvardsen, Sissel JentoftAbstract:Increased availability of genome assemblies for non-model organisms has resulted in invaluable biological and genomic insight into numerous vertebrates, including teleosts. Sequencing of the Atlantic cod (Gadus morhua) genome and the genomes of many of its relatives (Gadiformes) demonstrated a shared loss of the major histocompatibility complex (MHC) II genes 100 million years ago. An improved version of the Atlantic cod genome assembly shows an extreme density of tandem repeats compared to other vertebrate genome assemblies. Highly contiguous assemblies are therefore needed to further investigate the unusual immune system of the Gadiformes, and whether the high density of tandem repeats found in Atlantic cod is a shared trait in this group. Here, we have sequenced and assembled the genome of haddock (Melanogrammus aeglefinus) – a relative of Atlantic cod – using a combination of PacBio and Illumina reads. Comparative analyses reveal that the haddock genome contains an even higher density of tandem repeats outside and within protein coding sequences than Atlantic cod. Further, both species show an elevated number of tandem repeats in genes mainly involved in signal transduction compared to other teleosts. A characterization of the immune gene repertoire demonstrates a substantial expansion of MCHI in Atlantic cod compared to haddock. In contrast, the Toll-like receptors show a similar pattern of gene losses and expansions. For the NOD-like receptors (NLRs), another gene family associated with the innate immune system, we find a large expansion common to all teleosts, with possible lineage-specific expansions in zebrafish, stickleback and the codfishes. The generation of a highly contiguous genome assembly of haddock revealed that the high density of short tandem repeats as well as expanded immune gene families is not unique to Atlantic cod – but possibly a feature common to all, or most, codfishes. A shared expansion of NLR genes in teleosts suggests that the NLRs have a more substantial role in the innate immunity of teleosts than other vertebrates. Moreover, we find that high copy number genes combined with variable genome assembly qualities may impede complete characterization of these genes, i.e. the number of NLRs in different teleost species might be underestimates.
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Genomic architecture of haddock (Melanogrammus aeglefinus) shows expansions of innate immune genes and short tandem repeats
BMC Genomics, 2018Co-Authors: Ole K Torresen, Marine S O Brieuc, Monica Hongro Solbakken, Elin Sorhus, Alexander J Nederbragt, Kjetill S Jakobsen, Sonnich Meier, Rolf B Edvardsen, Sissel JentoftAbstract:Background Increased availability of genome assemblies for non-model organisms has resulted in invaluable biological and genomic insight into numerous vertebrates, including teleosts. Sequencing of the Atlantic cod ( Gadus morhua ) genome and the genomes of many of its relatives (Gadiformes) demonstrated a shared loss of the major histocompatibility complex ( MHC ) II genes 100 million years ago. An improved version of the Atlantic cod genome assembly shows an extreme density of tandem repeats compared to other vertebrate genome assemblies. Highly contiguous assemblies are therefore needed to further investigate the unusual immune system of the Gadiformes, and whether the high density of tandem repeats found in Atlantic cod is a shared trait in this group. Results Here, we have sequenced and assembled the genome of haddock ( Melanogrammus aeglefinus) – a relative of Atlantic cod – using a combination of PacBio and Illumina reads. Comparative analyses reveal that the haddock genome contains an even higher density of tandem repeats outside and within protein coding sequences than Atlantic cod. Further, both species show an elevated number of tandem repeats in genes mainly involved in signal transduction compared to other teleosts. A characterization of the immune gene repertoire demonstrates a substantial expansion of MCHI in Atlantic cod compared to haddock. In contrast, the Toll-like receptors show a similar pattern of gene losses and expansions. For the NOD-like receptors ( NLRs ), another gene family associated with the innate immune system, we find a large expansion common to all teleosts, with possible lineage-specific expansions in zebrafish, stickleback and the codfishes. Conclusions The generation of a highly contiguous genome assembly of haddock revealed that the high density of short tandem repeats as well as expanded immune gene families is not unique to Atlantic cod – but possibly a feature common to all, or most, codfishes. A shared expansion of NLR genes in teleosts suggests that the NLRs have a more substantial role in the innate immunity of teleosts than other vertebrates. Moreover, we find that high copy number genes combined with variable genome assembly qualities may impede complete characterization of these genes, i.e. the number of NLRs in different teleost species might be underestimates.
Kenneth T Frank - One of the best experts on this subject based on the ideXlab platform.
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size at age in haddock Melanogrammus aeglefinus application of the growing degree day gdd metric
Resiliency of Gadid Stocks to Fishing and Climate Change, 2008Co-Authors: Anna B Neuheimer, Christopher T Taggart, Kenneth T FrankAbstract:While growth variation in fishes is the result of a number of different factors (temperature, food consumption, genetic composition, etc.), temperature has been identified as one controlling factor on fish sizeat-age. Thus, variation in size-at-age due to variation in temperature should be explained before the other factors are explored. We argue that the relevant metric for explaining temperature-dependent size-at-age variation in most fishes is physiologically relevant temperature; i.e., the thermal integral parameterized as the growing degree-day (GDD, oC × d) metric. Accordingly, we employ GDD to examine the change in size-at-age (length-at-day, LaD) among eastern Scotian Shelf (Northwest Atlantic Fisheries Organization statistical divisions 4VW) haddock (Melanogrammus aeglefinus ) from 1970 through 2003. Significant varia tion in length-at-day (LaD) among year classes (decline in slopes and intercepts of LaD-at-GDD relations) remains after LaD variation due to GDD (temperature) is explained. The unexplained variation is postulated to be a result of temperature-independent factors such as condition or size-selective fishing or both.
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effects of condition on fecundity and total egg production of eastern scotian shelf haddock Melanogrammus aeglefinus
Canadian Journal of Fisheries and Aquatic Sciences, 2003Co-Authors: Julia L Blanchard, Kenneth T Frank, James E SimonAbstract:A fecundity study of the eastern Scotian Shelf haddock (Melanogrammus aeglefinus) stock during the 19971999 spawning seasons is reported. We developed a model that accounted for fecundity changes ...
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modelling the dispersal and mortality of browns bank egg and larval haddock Melanogrammus aeglefinus
Canadian Journal of Fisheries and Aquatic Sciences, 2000Co-Authors: David Brickman, Kenneth T FrankAbstract:An early life stage model is described with constant mortality for egg and larval stages. The model is used to simulate the stage 4 egg and larval data for haddock (Melanogrammus aeglefinus) in southwest Nova Scotia for the years 1983-1985. The model is initialized using published abundance and mortality estimates for these years, and its output is compared with field data. We find that the model does a systematically poor job of reproducing both the spatial-temporal and area-integrated versions of the data. To understand the discrepancy, we derive an integrated version of the model (integral model) and analyze its properties. This leads to a general method for determining whether sequential stage abundance data is consistent with a stage-dependent constant-mortality model. We use this method to show that a constant-mortality early life stage model is not consistent with the data. The integral model allows for year-day dependent mortality functions, which results in almost perfect fits to the abundance da...
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density dependent habitat selection by juvenile haddock Melanogrammus aeglefinus on the southwestern scotian shelf
Canadian Journal of Fisheries and Aquatic Sciences, 1995Co-Authors: Tara C Marshall, Kenneth T FrankAbstract:Positive correlations between total abundance and indices representing distributional area have been reported for several marine fish stocks. Different indices can produce different results for the same stock and many indices scale positively with total abundance. We describe an alternative approach to modelling the distributional response to variation in total abundance using data for juvenile haddock (Melanogrammus aeglefinus) from the southwestern Scotian Shelf. Annual bottom trawl surveys having a stratified random design were used to estimate the local density of haddock age 1 and 2 in each strata. Estimates of total abundance-at-age were obtained from sequential population analysis. The relationship between local density and total abundance-at-age was described for each strata using an exponential model with a Poisson error structure. Systematic variation among strata in the model parameters was indicative of density-dependent habitat selection and supported a previous study showing a positive corre...
