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ATLANTIC COD

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Title: ATLANTIC COD


1
BI3063 H10 J. Mork
ATLANTIC COD
Both with respect to potential harmful genetic
effects on fish stocks from human activities, and
the available management tools for remedying the
situation, Hallerman mostly use examples from
salmonids, and in particular anadromous Pacific
salmonids. Among the targeted human activities,
the fish farming industry and its effects has
atracted particular attention. The Danish
population geneticist Dorte Bekkevold and
collegues (Bekkevold et al. 2005) argue that the
problems encountered in salmonid farming apply to
cod farming as well (cf next slide).
Web site for downloading Bekkevold et al.
(2005) http//icesjms.oxfordjournals.org/cgi/repr
int/63/2/198
2
BI3063 H10 J. Mork
ATLANTIC COD
3
BI3063 H10 J. Mork
ATLANTIC COD
4
BI3063 H10 J. Mork
ATLANTIC COD
In the following, we shall explore various
aspects of cod and gadoid genetics which have a
bearing on whether these species are vulnerable
to various human activities (wild stock
exploitation, introgression by escaped farmed
fish) in a way similar to the salmon.
5
BI3063 H10 J. Mork
ATLANTIC COD
  • Genetic effects from ranching lessons come
    mainly from salmonid farming/ranching
  • Changes in genetic composition of farmed stock
    over time
  • Agents
  • Random genetic drift
  • Domestication selection (no predators, excess
    food, vaccines)
  • Selection for performance traits reduces genetic
    variability
  • Mating of close relatives
  • Effects
  • Reduced genetic variability
  • Reduced shyness
  • Loss of natural adaptivity
  • Harmful inbreeding effects

6
BI3063 H10 J. Mork
ATLANTIC COD
Knowledge on gadoid population structure exists
for Cod (Gadus morhua L.) Haddock
(Melanogrammus aeglefinus) Whiting (Merlangus
merlangius) Saithe (Pollachius virens) Norway
pout (Trisopterus esmarkii) Poor cod
(Trisopterus minutus) Blue whiting
(Micromesistius poutassou) Hake (Merluccius
merluccius)
7
BI3063 H10 J. Mork
ATLANTIC COD
(Source Smith Mork unpublished)
8
BI3063 H10 J. Mork
ATLANTIC COD
Milestone studies on the genetic population
structure of the Atlantic cod are Schmidt
(1930) Meristics used in cod study throughout
range Tåning (1946) Showed meristics are
affected by selection (temperature) Sick (1961)
Cod and whiting haemoglobin polymorphism Sick
(1965 a,b) Cod HbI allele frequencies throughout
range Frydenberg et al. (1965) Cod HbI allele
frequencies Norwegian waters Møller (1968) Cod
HbI, Tf and blood type Norwegian waters Karpov
Novikov (1980) Cod HbI affected by natural
selection (temperature) Mork et al. (1985) Cod
tissue allozymes througout range Dahle
(1992) Cod (NEAC NCC) mtDNA RFLP Pogson
(1995) Cod allozyme and PanI cDNA RFLP)
throughout range Arnason Palsson (1996) Cod
(NEAC NCC) mt Cyt b sequences Arnason
(1998) Cod mtDNA Cyt b sequences throughout
range Karlson Mork (2001) Showed PanI heavily
affected by natural selection Karlsson Mork
(2005) Showed microsat loci affected by natural
selection Nielsen et al. (2005) Microsat
hitchhike selection create false impression of
isolation Are 3rd codon position silent
substitutions (e.g. at mtDNA Cyt b) the great
white hope?
9
BI3063 H10 J. Mork
ATLANTIC COD
Cod genetics literature
Arnason, E., Palsson, S. 1996. Mitochondrial
cytochrome b DNA sequence variation of Atlantic
cod (Gadus morhua) from Norway. Molecular Ecology
5 715-724. Arnason, E. 1998. Mitochondrial
cytochrome b DNA sequence variation of Atlantic
cod Gadus morhua. In The implications of
localized fishery stocks (Ed.) von Herbing, I.H.,
Kornfield, I., Tupper, M., Wilson, J. Natural
Resource Agriculture and Engineering Service New
York. pp 129-137. Frydenberg, O., Møller, D.,
Nævdal, G., Sick, K. 1965. Haemoglobin
polymorphism in Norwegian cod populations.
Hereditas 53 257-272. Godø, O.R., Moksness, E.
1987. Growth and maturation of Norwegian coastal
cod and northeast Arctic cod under different
conditions. Fisheries Research 5 235-242. Godø,
O.R. 1995. Transplantation-tagging experiments in
preliminary studies of migration of cod off
Norway. ICES Journal of Marine Science 52
955-962. Karlsson, S., Mork, J. 2001. Evidence
for natural selection at the synaptophysin locus
(Syp1) in a natural population of cod (Gadus
morhua L.). ICES C.M.2001/L11 Karpov, A.K.,
Novikov, G.G. 1980. Hemoglobin alloforms in cod,
Gadus morhua (gadiformes, gadidae), their
functional characteristics and occurrence in
populations. Journal of Ichthyology (In Russian)
20(6) 45-50. Mork, J., Ryman, N., Ståhl, G.,
Utter, F., Sundnes, G. 1985. Genetic variation in
Atlantic cod (Gadus morhua) throughout its range.
Canadian Journal of Fisheries Aquatic Sciences
42 1580-1587.
10
BI3063 H10 J. Mork
ATLANTIC COD
Cod genetics literature cont'd
Møller, D., 1968. Genetic diversity in spawning
cod along the Norwegian coast. Hereditas60
132.Møller, D., 1969. The relationship between
arctic and coastal cod in their immature stages
illustrated by frequencies of genetic characters.
FiskDir. Skr. (Havunders.)15 220233.  Nielsen,
E.E., Hansen, M.M. Meldrup, D. 2006. Evidence
of microsatellite hitch-hiking selection in
Atlantic cod (Gadus morhua L.) implications for
inferring population structure in nonmodel
organisms.Molecular Ecology 15 (11)
3219-3229. Nielsen, E. MacKenzies, B.,
Magnussen, E. and Meldrup, D. 2007. Historical
analysis of Pan I in Atlantic cod (Gadus morhua)
temporal stability of allele frequencies in the
southeastern part of the species
distribution. Can. J. Fish. Aquat. Sci. 64(10)
1448-1455. Pogson, G.H., Mesa, K.A., Boutilier,
R.G. 1995. Genetic population structure and gene
flow in the Atlantic cod Gadus morhua a
comparison of allozyme and nuclear RFLP loci.
Genetics 139 375-385. Pogson, G.H. 2001.
Nucleotide polymorphism and natural selection at
the Panthophysine (Pan I) locus in the Atlantic
cod, Gadus morhua (L.). Genetics 157
317-330. Sick, K., 1961. Haemoglobin
polymorphism in fishes. Nature, Lond.192
894896. Sick, K. 1965a. Haemoglobin
polymorphism of cod in the Baltic and Danish Belt
Sea. Hereditas 54 19-48. Sick, K. 1965b.
Haemoglobin polymorphism of cod in the North Sea
and the North Atlantic Ocean. Hereditas 54
49-69. Rollefsen, G., 1933. The otoliths of the
cod. FiskDir. Skr. (Havunders.)4 (3), 114.
Wilkins, N. P., 1971. Haemoglobin polymorphism
in cod, whiting and pollack in Scottish waters.
Rapp. P.-v. Réun. Cons. perm. int. Explor. Mer161
6064. Tåning, A.V. 1946 Stage of
determination of vertebrae in teleostean fishes.
Nature 157 594-595.
11
BI3063 H10 J. Mork
ATLANTIC COD
Cod genetics literature cont'd
Cod population genetic studies at Trondhjem
Biological Station Mork. J., Giskeødegard, R.,
Sundnes, G. 1983. Haemoglobin polymorphism in
Gadus morhua genotypic differences in maturing
age and within-season gonad maturation.
Helgolander Meerescuntersuchungen 36
313-322. Mork, J., Ryman, N., Ståhl, G., Utter,
F., Sundnes, G. 1985. Genetic variation in
Atlantic cod (Gadus morhua) throughout its range.
Canadian Journal of Fisheries Aquatic Sciences
42 1580-1587. Mork. J., Sundnes, G. 1985a.
0-Group cod (Gadus morhua) in captivity
differential survival of certain genotypes.
Helgolander Meerescuntersuchungen 39
63-70. Mork. J., Sundnes, G. 1985b. The
haemoglobin polymorphism in cod (Gadus morhua)
allele frequency variation between year classes
in a Norwegian fjord stock. Helgolander
Meerescuntersuchungen 39 55-62. Mork, J.,
Giæver, M. 1999. Genetic structure of cod along
the coast of Norway results from isozyme
studies. Sarsia 84 157-168. Karlsson, S., and
Mork, J. 2003. Selection-induced variation at
the. pantophysin locus (PanI) in a Norwegian
fjord population of. cod (Gadus morhua L.).
Molecular Ecology 12 3265-3274. Karlsson, S.
Mork, J. 2005. Deviation from HardyWeinberg
equilibrium, and temporal instability in allele
frequencies at microsatellite loci in a local
population of Atlantic cod. ICES Journal of
Marine Science Journal du Conseil 2005
62(8)1588-1596.
12
BI3063 H10 J. Mork
Case studies in cod
ATLANTIC COD
13
BI3063 H10 J. Mork
Case studies in cod
ATLANTIC COD
Deviation from HardyWeinberg equilibrium, and
temporal instability in allele frequencies at
microsatellite loci in a local population of
Atlantic cod S. Karlsson J. Mork
Abstract A total of 1455 spawning cod,
sampled from a local spawning area in
Trondheimsfjord (Norway) between 1985 and 2002,
was screened at the microsatellite loci Gmo132
and Gmo2. Samples from 15 spawning years
comprising 29 consecutive cohorts were analysed.
At the Gmo132 locus, but not at Gmo2, allele
frequencies varied significantly among sampling
years as well as cohorts, corresponding to
FST-values of 0.004 and 0.006, respectively. Both
loci showed examples of significant deviations
from HardyWeinberg expectation within sampling
years as well as cohorts, manifested as
deficiencies of heterozygotes. Combining the
p-values from the single tests (Fisher's method)
revealed an overall significant p-value for
deviation from the HardyWeinberg expectations at
Gmo132 but not at Gmo2. Trend tests showed
significant HW deficiencies at both loci for
annual samples but not for cohorts. Possible
reasons for the deficiencies were discussed
inter alia the existence of null alleles, or a
form of pseudo Wahlund effect due to a patchy
distribution of habitats for settling O-group cod
in the Trondheimsfjord. It was noted that there
might be a relationship between the relatively
high temporal within-population variability of
allele frequencies at Gmo132 and the fact that
among microsatellite loci studied so far, Gmo132
is the one that usually shows the highest genetic
differentiation geographically in cod.
14
BI3063 H10 J. Mork
Case studies in cod
ATLANTIC COD
Evidence of microsatellite hitch-hiking selection
in Atlantic cod (Gadus morhua L.) implications
for inferring population structure in nonmodel
organisms Nielsen, E.E., Hansen, M.M. Meldrup,
D.
Abstract Microsatellites have gained wide
application for elucidating population structure
in nonmodel organisms. Since they are generally
noncoding, neutrality is assumed but rarely
tested. In Atlantic cod (Gadus morhua L.),
microsatellite studies have revealed highly
heterogeneous estimates of genetic
differentiation among loci. In particular one
locus, Gmo 132, has demonstrated elevated genetic
differentiation. We investigated possible
hitch-hiking selection at this and other
microsatellite loci in Atlantic cod. We employed
11 loci for analysing samples from the Baltic
Sea, North Sea, Barents Sea and Newfoundland
covering a large part of the species'
distributional range. The 'classical'
LewontinKrakauer test for selection based on
variance in estimates of FST and (standardized
genetic differentiation) revealed only one
significant pairwise test (North SeaBarents
Sea), and the source of the elevated variance
could not be ascribed exclusively to Gmo 132. In
contrast, different variants of the recently
developed ln R? test for selective sweeps at
microsatellite loci revealed a high number of
significant outcomes of pair-wise tests for Gmo
132. Further, the presence of selection was
indicated in at least one other locus. The
results suggest that many previous estimates of
genetic differentiation in cod based on
microsatellites are inflated, and in some cases
relationships among populations are obscured by
one or more loci being the subject to
hitch-hiking selection. Likewise, temporal
estimates of effective population sizes in
Atlantic cod may be flawed. We recommend,
generally, to use a higher number of
microsatellite loci to elucidate population
structure in marine fishes and other nonmodel
species to allow for identification of outlier
loci that are subject to selection.
15
BI3063 H10 J. Mork
Case studies in cod
ATLANTIC COD
Historical analysis of Pan I in Atlantic cod
(Gadus morhua) temporal stability of allele
frequencies in the southeastern part of the
species distribution Nielsen, E.
E. MacKenzie, B.R. Magnussen, E.  Meldrup,
D. Canadian Journal of Fisheries and Aquatic
Sciences, Volume 64, Number 10, 1 October 2007 ,
pp. 1448-1455(8)
Abstract We investigated temporal genetic
differentiation at the pantophysin (Pan I) locus
in four Atlantic cod (Gadus morhua) populations
from the southeastern part of the species
distribution the Baltic Sea, the North Sea, the
Faroe Plateau, and the Faroe Bank. Historical
otolith collections enabled investigation of
allele frequency variation over time periods up
to 69 years employing Pan I primers specifically
designed for partially degraded DNA. Small and
nonsignificant temporal changes in Pan I allele
frequencies were observed in the four
populations. Simultaneous microsatellite analysis
revealed similar temporal genetic stability with
temporal FST values ranging from 0 to 0.006,
suggesting limited demographic changes. Sea
surface temperature, which has been suggested as
the primary driver for the geographical
distribution of Pan I alleles in cod, showed no
long-term trend although temperature has
increased since the mid-1990s. Our study
demonstrates that populations in the southeastern
part of the species range has been characterized
by very high frequencies of the Pan IA allele for
many decades, and accordingly, Pan I serves as a
reliable marker for genetic stock identification
on a macrogeographical scale.
16
BI3063 H10 J. Mork
BLUE WHITING
17
BI3063 H10 J. Mork
Case studies in blue whiting
BLUE WHITING
Blue whiting population genetic studies at
Trondhjem Biological Station Mork, J.
Giæver, M. 1995. Genetic variation at isozyme
loci in blue whiting from the north-east
Atlantic. Journal of Fish Biology 46 462-468.
Giæver, M. Mork, J. 1995. Further studies on
the genetic population structure of the blue
whiting (Micromesistius poutassou) in the
north-east parts of the distribution range. ICES
C.M. 1995/H11. Mork, J. Giæver, M. 1993. The
genetic population structure of the blue whiting
(Micromesistius poutassou). ICES C.M. 1993/H5.
Giæver Stien, M. 1997. Population genetic
substructure in blue whiting based on allozyme
data. Journal of Fish Biology 52 782-795. Ryan,
A.W., Mattiangeli, V. Mork, J. 2005. Genetic
differentiation of blue whiting (Micromesistius
poutassou Risso) populations at the extremes of
the species range and at the Hebrides-Porcupine
Bank spawning grounds. ICES Journal of Marine
Sciences, 62 948-955).
18
BI3063 H10 J. Mork
Case studies in blue whiting
BLUE WHITING
Giæver Stien, M. 1997. Population genetic
substructure in blue whiting based on allozyme
data. Journal of Fish Biology 52 782-795.
19
BI3063 H10 J. Mork
HADDOCK
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BI3063 H10 J. Mork
Case study in haddock
HADDOCK
Material Haddock samples from the Russian boarer
to the west coast of Sweden. Methods Starch gel
electrophoresis and histochemical staining of 10
polymorphic tissues enzyme loci. Main result
No statistically significant genetic
differentiation in the investigated area.
21
BI3063 H10 J. Mork
SAITHE
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BI3063 H10 J. Mork
WHITING
23
BI3063 H10 J. Mork
Case study in saithe and whiting
SAITHE WHITING
24
BI3063 H10 J. Mork
NORWAY POUT
25
BI3063 H10 J. Mork
Case study in Norway pout
NORWAY POUT
26
BI3063 H10 J. Mork
HAKE
27
BI3063 H10 J. Mork
Case study in hake
HAKE
28
BI3063 H10 J. Mork
POOR COD
29
BI3063 H10 J. Mork
Case study in poor cod
POOR COD
VNTR variability in Atlantic poor cod
(Trisopterus minutus minutus) throughout its
range single locus minisatellite data suggest
reproductive isolation for the Faroe Bank
population Mattiangeli, V., Galvin, P., Ryan,
A., Mork, J., Cross, T. Abstract Nine samples
of Atlantic poor cod, Trisopterus minutus
minutus, collected from the Bay of Biscay to
Trondheimsfjord, Norway, were analysed using
three minisatellite DNA loci, amplified using PCR
and screened with an automated sequencer. One
locus was found to be polymorphic. FST analysis
using the polymorphic locus indicated that 2.2
of the total genetic diversity detected was due
to differences among samples (FST 0.022 P lt
0.001). The only significant pair-wise
heterogeneity was found between the Faroe Bank
and each of the other samples. This is consistent
with previous analyses of the same samples using
11 polymorphic allozyme loci. Journal
Fisheries research   ISSN 0165-7836   
30
BI3063 H10 J. Mork
Special case NEAC and NCC)
Norteast arctic cod (NEAC) and Norwegian
coastal cod (NCC)
31
BI3063 H10 J. Mork
Norteast arctic cod (NEAC)and Norwegian coastal
cod (NCC)
Allozymes
Cod sampling sites throughout the distribution
range
32
BI3063 H10 J. Mork
Norteast arctic cod (NEAC)and Norwegian coastal
cod (NCC)
Allozymes
Left UPGMA Dendrogram leaving out not
significant bifurcations. Right Comparison of
allele frequencies at polymorphic loci in all
localities.
33
BI3063 H10 J. Mork
Norteast arctic cod (NEAC)and Norwegian coastal
cod (NCC)
Allozymes
Relation between genetic distance and geographic
distance in Atlantic cod (based on same data as
in previous slides).
34
BI3063 H10 J. Mork
Norteast arctic cod (NEAC)and Norwegian coastal
cod (NCC)
Allozymes
Left Side-by-side comparison of allele
frequencies at the 11 most polymorphic allozyme
loci in NEAC and NCC. Right Small arrows point
at the level of genetic distances between cod
stocks compared to usual levels at the population
level.
35
BI3063 H10 J. Mork
Norteast arctic cod (NEAC)and Norwegian coastal
cod (NCC)
Allozymes
FST values for intra-specific groupings in cod
compared to other species From left to right
Atlantic cod, atlantic salmon, brown trout,
rainbow trout, house mouse, Drodophila, and
man. The hatched upper part of the bars
represent the FST vales.
36
BI3063 H10 J. Mork
Norteast arctic cod (NEAC)and Norwegian coastal
cod (NCC)
Haemoglobins
Karpov Novikov (1980) suggested that the
south-north HbI allele frequency cline observed
on both sides of the Atlantic can be explained by
a cline due to natural selection by temperatures.
This simultaneously suggested a new explanation
for the observed HbI allele frequency cline along
the Norwegian coast NCC) and into the Barents Sea
(NEAC). In the Trondheimsfjord cod, HbI
genotypic growth differences seem to concord with
the HbI genotypic differences in O2 affinity by
temperature (Figure to the left).
37
BI3063 H10 J. Mork
Gadoid phylogeny
38
NFFR project I 309.007 Phylogeny and genetic
structure in common benthic fish species of the
east Atlantic
Allozymes
39
BI3063 H10 J. Mork
Allozymes
Gadoid phylogeny
40
BI3063 H10 J. Mork
Allozymes
Gadoid phylogeny
NFFR project I 309.007 Phylogeny and genetic
structure in common benthic fish species of the
east Atlantic
41
BI3063 H10 J. Mork
Gadoid phylogeny
Allozymes
42
Genetic and biologic stock management
BI 3063 J. Mork H08
Gadoid phylogeny
(From Bakke Johansen)
mt DNA sequences
For comparison, the time since divergence
between Atlantic cod and Pacific cod is probably
around half a million years.
43
BI3063 H10 J. Mork
Gadoid phylogeny
Allozymes
44
BI3063 H10 J. Mork
Gadoid phylogeny
Allozymes
45
Gadoid phylogeny
BI3063 H10 J. Mork
Allozymes
Comparing measures of genetic variability in
gadoid species.
46
BI3063 H10 J. Mork
Gadoid phylogeny
Allozymes
47
BI3063 H10 J. Mork
Gadoid phylogeny
Allozymes
INTERPRETATION OF THE INTRA-SPECIFIC DENDROGRAMS
ON PREVIOUS SLIDE
48
BI3063 H10 J. Mork
Gadoid phylogeny
Allozymes
List of P-values from tests of intra-specific gene
tic differentiation between geographic areas in 5
gadoid species. Only P-values from the loci that
showed the largest genetic differences are shown,
and even they are all far from significance.
49
BI3063 H10 J. Mork
Gadoid phylogeny
Allozymes
Marianne Giæver at Trondhjem Biological Station
wrote her doctoral Thesis on the genetic
differentiation in three gadoid species cod,
haddock, and blue whiting. One of the main
conclusions was that in all the species, the
genetic differentiation appeares to be caused by
"Isolation by distance". Typically, it was the
populations at the fringes of the species' range
that were the genetically most divergent. This
is consistent with the meta-population concept.
50
BI3063 H10 J. Mork
Gadoid phylogeny
Summing up
With respect to genetic stock management, the
above treatment of genetic studies and
considerations suggest that the gadoids are more
resilient than anadromous salmonids to some human
activities (e.g. over-exploitation, genetic
introgression by farmed fish escapes, and disease
transfer from captive stocks). This is not to
say that gadoids are immune to effects from
over-exploitation and mis-management. Probably,
many species and populations are more vulnerable
in times of climate changes, like the situation
is today. There is still every reason to
conduct stock management by the pre-cautionary
principle, with respect to biological as well as
genetic and evolutionary hazards.
51
BI3063 H10 J. Mork
Gadoid phylogeny
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