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

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.

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

Science Advances ◽

10.1126/sciadv.aav2461 ◽

2019 ◽

Vol 5 (6) ◽

pp. eaav2461 ◽

Cited By ~ 12

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.

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Long-term persistence and evolutionary divergence of a marine fish population with a very small effective population size (Kildin cod Gadus morhua kildinensis)

Marine Biology ◽

10.1007/s00227-015-2642-8 ◽

2015 ◽

Vol 162 (5) ◽

pp. 979-992 ◽

Cited By ~ 2

Author(s):

Victor Andreev ◽

Mikhail Fokin ◽

Nikolai Mugue ◽

Petr Strelkov

Keyword(s):

Population Size ◽

Effective Population Size ◽

Marine Fish ◽

Gadus Morhua ◽

Fish Population ◽

Evolutionary Divergence ◽

Effective Population ◽

Kildin Cod ◽

Small Effective Population Size

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

ICES Journal of Marine Science ◽

10.1016/j.icesjms.2004.07.007 ◽

2004 ◽

Vol 61 (7) ◽

pp. 1144-1150 ◽

Cited By ~ 62

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.

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Increased accuracy of artificial selection by using the realized relationship matrix

Genetics Research ◽

10.1017/s0016672308009981 ◽

2009 ◽

Vol 91 (1) ◽

pp. 47-60 ◽

Cited By ~ 374

Author(s):

B. J. HAYES ◽

P. M. VISSCHER ◽

M. E. GODDARD

Keyword(s):

Population Size ◽

Effective Population Size ◽

Family Relationships ◽

Random Mating ◽

Family Relationship ◽

Relationship Matrix ◽

Effective Number ◽

Effective Population ◽

Breeding Values ◽

Selection Methodology

SummaryDense marker genotypes allow the construction of the realized relationship matrix between individuals, with elements the realized proportion of the genome that is identical by descent (IBD) between pairs of individuals. In this paper, we demonstrate that by replacing the average relationship matrix derived from pedigree with the realized relationship matrix in best linear unbiased prediction (BLUP) of breeding values, the accuracy of the breeding values can be substantially increased, especially for individuals with no phenotype of their own. We further demonstrate that this method of predicting breeding values is exactly equivalent to the genomic selection methodology where the effects of quantitative trait loci (QTLs) contributing to variation in the trait are assumed to be normally distributed. The accuracy of breeding values predicted using the realized relationship matrix in the BLUP equations can be deterministically predicted for known family relationships, for example half sibs. The deterministic method uses the effective number of independently segregating loci controlling the phenotype that depends on the type of family relationship and the length of the genome. The accuracy of predicted breeding values depends on this number of effective loci, the family relationship and the number of phenotypic records. The deterministic prediction demonstrates that the accuracy of breeding values can approach unity if enough relatives are genotyped and phenotyped. For example, when 1000 full sibs per family were genotyped and phenotyped, and the heritability of the trait was 0·5, the reliability of predicted genomic breeding values (GEBVs) for individuals in the same full sib family without phenotypes was 0·82. These results were verified by simulation. A deterministic prediction was also derived for random mating populations, where the effective population size is the key parameter determining the effective number of independently segregating loci. If the effective population size is large, a very large number of individuals must be genotyped and phenotyped in order to accurately predict breeding values for unphenotyped individuals from the same population. If the heritability of the trait is 0·3, and Ne=1000, approximately 5750 individuals with genotypes and phenotypes are required in order to predict GEBVs of un-phenotyped individuals in the same population with an accuracy of 0·7.

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Long-term stability and effective population size in North Sea and Baltic Sea cod (Gadus morhua)

Molecular Ecology ◽

10.1111/j.1365-294x.2005.02777.x ◽

2005 ◽

Vol 15 (2) ◽

pp. 321-331 ◽

Cited By ~ 93

Author(s):

NINA Aa. POULSEN ◽

EINAR E. NIELSEN ◽

MIKKEL H. SCHIERUP ◽

VOLKER LOESCHCKE ◽

PETER GRØNKJAER

Keyword(s):

Baltic Sea ◽

Population Size ◽

Effective Population Size ◽

North Sea ◽

Gadus Morhua ◽

Effective Population ◽

Term Stability ◽

Long Term Stability

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

10.1101/361691 ◽

2018 ◽

Author(s):

Tony Kess ◽

Paul Bentzen ◽

Sarah J. Lehnert ◽

Emma V.A. Sylvester ◽

Sigbjørn Lien ◽

...

Keyword(s):

Population Size ◽

Effective Population Size ◽

Phenotypic Variation ◽

Chromosomal Rearrangement ◽

Atlantic Cod ◽

Marine Species ◽

Genomic Variation ◽

Fine Scale ◽

Effective Population ◽

Northern Cod

AbstractIntraspecific phenotypic diversity is integral to ecological resilience and the provision of ecosystem services1. Chromosome structural variation may underpin intraspecific diversity and complex phenotypes2 by reducing recombination within supergenes containing linked, co-adapted alleles. Connecting ecologically-relevant phenotypes to genomic variation can enable more precise conservation of exploited marine species by protecting important genetic diversity3,4. Here, using genome-wide association analysis of a 12K single nucleotide polymorphism (SNP) array we confirm that an ancient, derived chromosomal rearrangement consisting of two adjacent inversions is strongly associated with migratory phenotype and individual-level genetic structure in Atlantic cod (Gadus morhua) across the Northwest Atlantic. The presence of all identified migration-associated loci within this rearrangement indicates that pervasive variation in migration phenotype is in part controlled by a recombination-resistant supergene, facilitating fine-scale individual phenotypic variation within Northern cod. Furthermore, we reconstruct trends in effective population size over the last century, and find genomic signatures of population collapse, and different patterns of population expansion and decline among individuals based on supergene alleles. We demonstrate declines in effective population size consistent with the onset of industrialized harvest (post 1950) and substantially reduced effective size of individuals homozygous for the derived chromosomal rearrangement relative to heterozygous individuals or those homozygous for the ancestral version of this chromosomal region. These results illustrate how chromosomal structural diversity can mediate fine-scale genetic and phenotypic variation in a highly connected marine species, and suggest a loss of biocomplexity from a migration-associated supergene within Northern cod by overfishing.

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