scholarly journals Genomic testing of landlocked Kildin cod (Gadus morhua kildinensis) for its ancestral state: stationary or migratory ecotype?

2016 ◽  
Author(s):  
Anastasia A Teterina ◽  
Lev A Zhivotovsky
Keyword(s):  
Gadus Morhua ◽  
Atlantic Cod ◽  
Habitat Preferences ◽  
Genomic Testing ◽  
Ancestral State ◽  
Genome Diversity ◽  
Effective Population ◽  
Marine Population ◽  
Genomic Regions ◽  
Kildin Cod

Kildin cod is a small landlocked population of Atlantic cod reproductively isolated from marine counterparts for around 1500-2000 years. The Kildin cod lives in a shallow meromictic lake in the five-meter intermediate layer of water with sharp gradients of oxygen and salinity. The cod had an effective population size of around one hundred individuals and evolved unique physiological, morphological and behavioral features. The marine Atlantic cod has two ecologically distinct forms: the stationary (coastal) and migratory (deep-water) ecotypes that differ in migratory behavior and habitat preferences (the depth, oxygen content, salinity and temperature). To understand the origin and genetic properties of Kildin cod, we scrutinized genomic regions associated with the cod ecotypes differentiation (LG1, LG2, and LG7) and found out that Kildin cod’s regions LG2 and LG7 were fixed with the migratory variants, whereas polymorphic LG1 had a higher frequency of the stationary variant, that could be explained by the possible strong genetic drift. The lake cod investigated had four times lesser genome diversity than marine population. Our finding suggests that Kildin cod originated from the migratory ecotype of the marine cod.

scholarly journals Genomic testing of landlocked Kildin cod (Gadus morhua kildinensis) for its ancestral state: stationary or migratory ecotype?

2016 ◽  
Author(s):  
Anastasia A Teterina ◽  
Lev A Zhivotovsky
Keyword(s):  
Gadus Morhua ◽  
Atlantic Cod ◽  
Habitat Preferences ◽  
Genomic Testing ◽  
Ancestral State ◽  
Genome Diversity ◽  
Effective Population ◽  
Marine Population ◽  
Genomic Regions ◽  
Kildin Cod

Kildin cod is a small landlocked population of Atlantic cod reproductively isolated from marine counterparts for around 1500-2000 years. The Kildin cod lives in a shallow meromictic lake in the five-meter intermediate layer of water with sharp gradients of oxygen and salinity. The cod had an effective population size of around one hundred individuals and evolved unique physiological, morphological and behavioral features. The marine Atlantic cod has two ecologically distinct forms: the stationary (coastal) and migratory (deep-water) ecotypes that differ in migratory behavior and habitat preferences (the depth, oxygen content, salinity and temperature). To understand the origin and genetic properties of Kildin cod, we scrutinized genomic regions associated with the cod ecotypes differentiation (LG1, LG2, and LG7) and found out that Kildin cod’s regions LG2 and LG7 were fixed with the migratory variants, whereas polymorphic LG1 had a higher frequency of the stationary variant, that could be explained by the possible strong genetic drift. The lake cod investigated had four times lesser genome diversity than marine population. Our finding suggests that Kildin cod originated from the migratory ecotype of the marine cod.

The effects of isolation and colonization history on the genetic structure of marine-relict populations of Atlantic cod (Gadus morhua) in the Canadian Arctic

2006 ◽  
Vol 63 (8) ◽  
pp. 1830-1839 ◽  
Author(s):  
David C Hardie ◽  
Roxanne M Gillett ◽  
Jeffrey A Hutchings
Keyword(s):  
Gadus Morhua ◽  
Atlantic Cod ◽  
Allelic Diversity ◽  
Canadian Arctic ◽  
Environmental Stochasticity ◽  
Arctic Lakes ◽  
The Arctic ◽  
Effective Population ◽  
Eastern Canada ◽  
High Allelic Diversity

The genetic consequences of extended periods at low population size are fundamental to the conservation of depleted species such as the Atlantic cod (Gadus morhua). We compared microsatellite genetic variability among cod populations in Canadian Arctic lakes with that of Gilbert Bay resident and inshore cod from eastern Canada. The Arctic populations had the lowest genetic diversity and were the most strongly genetically structured and distinct. By contrast, eastern Canadian samples expressed high allelic diversity and were not significantly genetically structured or distinct relative to each other, whereas Gilbert Bay resident cod were intermediate to the Arctic and eastern Canadian groups. Our results are consistent with the hypothesis that the Arctic populations were colonized between 8000 and 5000 years ago and have experienced little or no gene flow since that time. Despite isolation at the extreme of the species' range, the Arctic populations have retained relatively high heterozygosities and high genetic effective population sizes relative to census sizes (Ne–Nc ratios). Potential explanations for this include the absence of fishing pressure, allowing for the persistence of large, highly fecund individuals, as well as biotic (e.g., absence of planktivores) and abiotic (e.g., low environmental stochasticity) factors in the Arctic lakes that minimize individual variance in reproductive success.

Large effective population size and temporal genetic stability in Atlantic cod (Gadus morhua) in the southern Gulf of St. Lawrence

2010 ◽  
Vol 67 (10) ◽  
pp. 1585-1595 ◽  
Author(s):  
Nina Overgaard Therkildsen ◽  
Einar Eg Nielsen ◽  
Douglas P. Swain ◽  
Jes Søe Pedersen
Keyword(s):  
Genetic Variability ◽  
Population Size ◽  
Effective Population Size ◽  
Gadus Morhua ◽  
Atlantic Cod ◽  
Population Decline ◽  
Allelic Diversity ◽  
Estimation Methods ◽  
Effective Population ◽  
Commercial Fish

Worldwide, many commercial fish stocks have experienced dramatic declines due to overfishing. Such fisheries-induced population reductions could potentially erode the genetic diversity of marine fish populations. Based on analyses of DNA extracted from archived and contemporary samples, this paper compares the genetic variability at nine microsatellite loci in a Canadian population of Atlantic cod ( Gadus morhua ) over 80 years, spanning from before the fishery intensified to now when the population is at historically low abundance. Extensively validated genetic data from the temporally spaced samples were used to estimate the effective population size. Over the period, we observed no loss of either heterozygosity or allelic diversity. Several of the estimation methods applied could not distinguish the effective population size from infinity, and the lower 95% confidence limit on estimates was generally >500, suggesting that the effective population size is probably considerably larger than this. Hence, it appears that the southern Gulf of St. Lawrence cod stock has maintained genetic variability to sustain future evolution despite a dramatic population decline.

scholarly journals Depensation, probability of fertilization, and the mating system of Atlantic cod (Gadus morhua L.)

2004 ◽  
Vol 61 (7) ◽  
pp. 1144-1150 ◽  
Author(s):  
Sherrylynn Rowe ◽  
Jeffrey A. Hutchings ◽  
Dorte Bekkevold ◽  
Ana Rakitin
Keyword(s):  
Population Size ◽  
Gadus Morhua ◽  
Atlantic Cod ◽  
Fertilization Rate ◽  
Effective Population ◽  
Broadcast Spawning ◽  
The North ◽  
Research Programmes ◽  
The North Sea ◽  
Census Population Size

Abstract Atlantic cod (Gadus morhua L.) have been severely overexploited and are currently at historic population lows, having declined 90% in the North Sea and 99% off northeast Newfoundland in recent decades. Slow rates of recovery and continuing declines may be attributable to depensation, defined as a reduction in per capita growth rate concomitant with reduced population size. Several potential causes of depensation relate to low mating success and consequent reduced production of offspring. We explore the empirical basis of one of these in Atlantic cod using egg fertilization and male abundance data obtained from 21 experimental populations generated by three independent research programmes. We find support for the hypotheses that (a) fertilization rate declines with abundance and (b) variance in fertilization rate increases as population size declines. The former identifies one potential mechanism underlying depensation in Atlantic cod. The latter has negative genetic consequences for effective population size (Ne), resulting in a decline in the ratio of Ne to census population size (Ne/Nc) with declining abundance. Our results may have general implications for the conservation biology of broadcast-spawning marine fish, particularly those with mating systems similar to that of Atlantic cod.

Distinct responses of sympatric migrant and resident Atlantic cod phenotypes to substrate and temperature at a remote Gulf of Maine seamount

2017 ◽  
Vol 75 (1) ◽  
pp. 122-134 ◽  
Author(s):  
Christian W Conroy ◽  
Jay Calvert ◽  
Graham D Sherwood ◽  
Jonathan H Grabowski
Keyword(s):  
Life History ◽  
Gadus Morhua ◽  
Gulf Of Maine ◽  
Atlantic Cod ◽  
Habitat Preferences ◽  
Kelp Forest ◽  
Thermal Conditions ◽  
Life History Strategies ◽  
Benthic Habitat ◽  
Shallow Habitat

Abstract Life-history strategies often vary within motile marine species, affecting morphometry, growth, diet, and fecundity. Atlantic cod (Gadus morhua) in the Gulf of Maine display marked variation in a number of life-history traits, exemplified by differences in body colour. Migratory behaviours are suspected to differ among these colour types, but have yet to be shown definitively. Here, we used the combination of an acoustic telemetry system and fine-scale benthic habitat maps to reveal that the red phenotype cod adhered to an isolated kelp forest covering <2 km2 of a seamount in the central Gulf of Maine. Meanwhile, the olive phenotype cod adopted diel vertical migratory behaviour, possibly in response to a temperature gradient. Use of shallow, structured habitat was influenced by temperature and may be enabled by dynamic conditions related to internal waves that persist throughout the summer and early fall. Detections decreased in response to changing thermal conditions, although phenotypes reacted to these changes in distinct ways: the olive phenotype abandoned shallow habitat prior to peak summer temperatures, while the red phenotype remained until mid-fall when temperatures and temperature variability declined. Our findings support a link between morphometry, colour, behavioural strategies, and habitat preferences that may be widespread in Atlantic cod.

Genomic tools for management and conservation of Atlantic cod in a coastal marine protected area

2018 ◽  
Vol 75 (11) ◽  
pp. 1915-1925 ◽  
Author(s):  
Marion Sinclair-Waters ◽  
Paul Bentzen ◽  
Corey J. Morris ◽  
Daniel E. Ruzzante ◽  
Matthew P. Kent ◽  
...  
Keyword(s):  
Gadus Morhua ◽  
Marine Protected Area ◽  
Atlantic Cod ◽  
Marine Species ◽  
Effective Population ◽  
Coastal Marine ◽  
Genomic Tools ◽  
Snp Panel ◽  
Surrounding Areas ◽  
Management And Conservation

Marine protected areas (MPAs) can serve as effective tools for the management and conservation of exploited marine species. The Gilbert Bay MPA in coastal Labrador was created to protect a genetically distinct population of Atlantic cod (Gadus morhua); however, decreases in abundance continue to occur potentially due to exploitation outside the MPA. We developed a single-nucleotide polymorphism (SNP) panel to identify Gilbert Bay cod in areas outside MPA boundaries where mixing with offshore cod occurs. In total, 361 individuals from Gilbert Bay, surrounding areas, and offshore were genotyped for 10 913 SNPs. Using FST rankings and guided regularized random forest, we selected 23 SNPs that together generate 100% accuracy in individual assignment and accurately estimate the proportion of Gilbert Bay cod in fishery samples from sites outside MPA boundaries: on average, fishery samples included 17.3% Gilbert Bay cod. Estimates of effective population size for the Gilbert Bay population ranged from 655 to 1114. Our findings demonstrate the power of using genomic approaches for management of an exploited marine species and enhancing the design of MPAs.

scholarly journals A migration-associated supergene reveals loss of biocomplexity in Atlantic cod

2019 ◽  
Vol 5 (6) ◽  
pp. eaav2461 ◽  
Author(s):  
Tony Kess ◽  
Paul Bentzen ◽  
Sarah J. Lehnert ◽  
Emma V. A. Sylvester ◽  
Sigbjørn Lien ◽  
...  
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Chromosomal Rearrangement ◽  
Gadus Morhua ◽  
Atlantic Cod ◽  
Structural Diversity ◽  
Marine Species ◽  
Intraspecific Diversity ◽  
Effective Population ◽  
Demographic Trajectories

Chromosome structural variation may underpin ecologically important intraspecific diversity by reducing recombination within supergenes containing linked, coadapted alleles. Here, we confirm that an ancient chromosomal rearrangement is strongly associated with migratory phenotype and individual genetic structure in Atlantic cod (Gadus morhua) across the Northwest Atlantic. We reconstruct trends in effective population size over the last century and reveal declines in effective population size matching onset of industrialized harvest (after 1950). We find different demographic trajectories between individuals homozygous for the chromosomal rearrangement relative to heterozygous or homozygous individuals for the noninverted haplotype, suggesting different selective histories across the past 150 years. These results illustrate how chromosomal structural diversity can mediate fine-scale genetic, phenotypic, and demographic variation in a highly connected marine species and show how overfishing may have led to loss of biocomplexity within Northern cod stock.

Family relationships and effective population size in a natural cohort of Atlantic cod (Gadus morhua) larvae

1997 ◽  
Vol 54 (S1) ◽  
pp. 11-18 ◽  
Author(s):  
C M Herbinger ◽  
R W Doyle ◽  
C T Taggart ◽  
S E Lochmann ◽  
A L Brooker ◽  
...  
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Family Relationships ◽  
Gadus Morhua ◽  
Atlantic Cod ◽  
Effective Population

Who is fishing on what stock: population-of-origin of individual cod (Gadus morhua) in commercial and recreational fisheries

2018 ◽  
Vol 75 (6) ◽  
pp. 2153-2162 ◽  
Author(s):  
Per Erik Jorde ◽  
Alf Ring Kleiven ◽  
Marte Sodeland ◽  
Esben Moland Olsen ◽  
Keno Ferter ◽  
...  
Keyword(s):  
North Sea ◽  
Gadus Morhua ◽  
Atlantic Cod ◽  
Habitat Preferences ◽  
Large Set ◽  
Nucleotide Polymorphisms ◽  
Recreational Fisheries ◽  
The North ◽  
Recreational Angling ◽  
By Catch

Abstract Atlantic cod (Gadus morhua) in Skagerrak are structured into distinct ecotypes or stock components that have been severely depleted over the past decades. To improve our understanding of how local commercial and recreational fisheries influence cod stocks, we investigated whether these user groups target different stock components of cod. Cod were sampled from the recreational rod and line fishery and from commercial shrimp trawlers catching cod as by-catch. Based on a large set of single nucleotide polymorphisms (SNPs), we defined a subset of 27 semi-diagnostic SNPs designed to discriminate between two cod stock components: “inner fjord” cod and “North Sea” cod, designated by their dominant habitat preferences. Genetic assignments of fishery-caught cod indicated that 4% of individuals caught by shrimp trawlers belonged to the inner fjord cod component and 96% to the North Sea, whereas among cod caught by recreational fishers, the estimated percentages were 11.8 and 88.2%, respectively. Our findings confirm the existence of two sympatric cod stock components in coastal Skagerrak, indicating that existing management units are biologically inappropriate and should be reconsidered. Furthermore, more attention should be given to recreational angling to reduce fishing mortality on the depleted inner fjord cod component.

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