Workshop on Stock Identification and Allocation of Catches of Herring to Stocks

99 Pages·2017·3.03 MB·English

ICES WKSIDAC REPORT 2017
ICES ADVISORY COMMITTEE
ICES CM 2017/ACOM:37
Workshop on Stock Identification and Alloca-
tion of Catches of Herring to Stocks (WKSIDAC)
20–24 November 2017
Galway, Ireland
International Council for the Exploration of the Sea
Conseil International pour l’Exploration de la Mer
H. C. Andersens Boulevard 44–46
DK-1553 Copenhagen V
Denmark
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Recommended format for purposes of citation:
ICES. 2017. Workshop on Stock Identification and Allocation of Catches of Herring to
Stocks (WKSIDAC). ICES WKSIDAC Report 2017 20-24 November 2017. Galway, Ire-
land. ICES CM 2017/ACOM:37. 99 pp.
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This document is the product of an Expert Group under the auspices of the International
Council for the Exploration of the Sea and does not necessarily represent the view of the
Council.
© 2017 International Council for the Exploration of the Sea
Contents
Executive summary ................................................................................................................ 3
1 Introduction .................................................................................................................... 1
1.1 Terms of reference ............................................................................................... 1
1.2 General background ............................................................................................ 1
1.3 Regional herring overviews ............................................................................... 2
1.3.1 Herring in the North Sea ......................................................................... 2
1.3.2 Herring in the western waters ................................................................ 3
1.3.3 Herring in the Western Baltic and Baltic Sea ........................................ 5
1.3.4 Herring in the Norwegian Sea, Icelandic waters and Faroe
waters ......................................................................................................... 5
1.4 Structure of the report ......................................................................................... 6
2 Review information on stock identification and validation work done so
far (Tor a) ......................................................................................................................... 7
2.1 WKSIDAC – the assessment perspective ......................................................... 7
2.2 Otolith shape analysis ......................................................................................... 7
2.2.1 Matlab approach ....................................................................................... 7
2.2.2 ShapeR approach ...................................................................................... 8
2.2.3 ImageJ approach ....................................................................................... 9
2.3 Otolith microstructure ...................................................................................... 10
2.3.1 Smartdots ................................................................................................. 13
2.4 Otolith growth macrostructures ...................................................................... 14
2.5 Separation function approach as applied for the separation of Central
Baltic herring and Western Baltic Spring Spawners ..................................... 14
2.6 Vertebrae Series count....................................................................................... 16
2.7 Genetic separation techniques (as applied to e.g. boarfish, horse
mackerel and 6.a herring) ................................................................................. 16
2.7.1 Danish approach ..................................................................................... 16
2.7.2 Irish approach ......................................................................................... 16
2.7.3 Faroese approach .................................................................................... 19
2.8 Morphometrics ................................................................................................... 20
2.9 Parasites .............................................................................................................. 20
2.10 Quality assurance .............................................................................................. 22
3 Review available material for the workshop by method (Table 1) (ToR b)
......................................................................................................................................... 25
3.1 Review of methods and materials ................................................................... 25
3.2 Otolith shape analysis trial ............................................................................... 26
4 Analysis of the potential or preferred allocation methods for stock
assessment purposes by area (ToR c) ....................................................................... 28
4.1 Norwegian Sea: NSSH, NASH, NSAS, ISS .................................................... 28
4.2 North Sea and 3.a: WBSS, NSAS, NSSH ......................................................... 28
4.3 Western Baltic: WBSS, CBH ............................................................................. 28
4.4 West of British Isles (6.a, 7.b-c): ....................................................................... 29
5 Outline a manual by method (a – e) for stock identification of herring for
implementation in individual laboratories (ToR d) .............................................. 30
6 Provide guidance on a retrospective correction of herring survey time-
series where necessary (ToR e) .................................................................................. 31
7 Conclusions and recommendations ......................................................................... 32
8 References ..................................................................................................................... 34
Annex 1: List of participants ............................................................................................... 39
Annex 2: Recommendations ............................................................................................... 42
Annex 3: Working documents ............................................................................................ 43
Annex 4: Rapporteurs’ reports ........................................................................................... 60
Annex 5: Standard Operating Procedures (SOP) ............................................................ 78
Workshop on Stock Identification and Allocation of Catches of Herring to Stocks (WKSIDAC)
Executive summary
The Workshop on stock identification and allocation of catches of herring to stocks
(WKSIDAC) met on 20–24th November 2017 in Galway, Ireland. The workshop had
several objectives; improve the accuracy and precision of the methods currently ap-
plied across laboratories by area; compare alternative available methods; outline a
common generic approach in terms of methods; and draft guidelines for conducting
stock-splits for assessment purposes. The meeting was co-chaired by Richard D.M.
Nash, Norway and Martin Pastoors, The Netherlands. In total there were 26 partici-
pants in the meeting, of which two were present remotely, for their presentations. Par-
ticipants were from 11 countries (representing 14 different institutes and three industry
related organisations).
A series of five ToRs were addressed which are summarized as follows:
At the outset of the meeting the key issues relating to stock mixes in each of the man-
agement areas (2, 3, 5, 6 and 7) were outlined along with why the stock identification
was important for the assessments of each of these stocks.
During the review of information on stock identification and validation work done so
far it was apparent that there was no consistency between areas and in most either
there was no validation or the validation needed to be updated. Only a few areas cur-
rently utilise herring stock identification methodology for the assessments, namely ar-
eas 3.a and 4 for separation of WBSS from NSAS although the methodology was not
ideal, Icelandic waters for separation of ISS from NSS and in Faroese waters for sepa-
rating autumn from spring spawners.
The concept of this workshop was more on potential methods rather than a hands-on
approach and as such the only material available to work on was the shape analyses
approach. The attendees were able to capture images and the initial shape outlines un-
dertaken with three different analytical techniques giving stable results. The rest of the
workshop provided information on the available genetic, otolith-shape, -microstruc-
ture, - chemistry (including stable isotopes), morphometrics, and growth. The necessity
of validation and Standard protocols or operating procedures was highlighted.
The optimal allocation method for stock assessment purposes (as perceived by the
Workshop members) varied by area. Otolith shape analyses appeared the most widely
recommended, however, other techniques such as genetics and otolith microstructure
and micro-chemistry would be necessary for validating the shape analyses results. In
the Baltic separation based on the growth, through length-at-age was favoured and in
Area 6.a a combined approach using genetics and morphology is preferred. Baselines
would also need to be updated on a regular basis.
The Workshop was not able to provide an outline of a manual by method for stock
identification of herring for implementation in individual laboratories nor provide
guidance on retrospective corrections of herring survey time-series. These topics need
to be taken up in some future Workshop/Meeting.
Workshop on Stock Identification and Allocation of Catches of Herring to Stocks (WKSIDAC) | 1

1 Introduction
1.1 Terms of reference
2016/2/ACOM38 A Workshop on Stock Identification and allocation of catches of her-
ring to stocks (WKSIDAC) will be established and Chaired by Richard Nash, Norway,
and Martin Pastoors, The Netherlands and will meet in Galway, Ireland from Monday
20 November 2017 (13:00) until Friday 24 November 2017 (13:00), to:
a) Review information on stock identification and validation work done so far;
i. Otolith shape (at least two methods: Danish [MATLAB] and Icelandic
[ShapeR]);
ii. Otolith microstructure;
iii. Otolith growth macrostructures
iv. Separation function approach as applied for the separation of Central
Baltic herring and Western Baltic Spring Spawners;
v. Vertebrae Series count;
vi. Genetic separation techniques (as applied to e.g. boarfish, horse
mackerel and 6.a herring)
b) Review available material for the workshop by method (Table 1)
c) Analysis of the optimal allocation method for stock assessment purposes by
area;
i. Norwegian Sea: NSSH, NASH, NSAS
ii. North Sea and 3.a: WBSS, NSAS, NSSH
iii. Western Baltic: WBSS, CBH
iv. West of British Isles (6.a, 7.b and 7.c)
v. WBIH (genetic multi-marker approach pending its availability)
d) Outline a manual by method (a – e) for stock identification of herring for im-
plementation in individual laboratories;
e) Provide guidance on a retrospective correction of herring survey time-series
where necessary
1.2 General background
Most herring populations are migratory and often congregate on feeding and winter-
ing grounds where aggregations may consist of mixtures of individuals from several
populations, thus the standard concept of ‘a herring stock’ within a geographical area
such as a management unit is not straight-forward to assume.
Morphometric analysis, analysis of calcified structures, and analysis of the genetic
composition are among the most widespread tools available for stock identification of
bony fish and a wide variety of methods have been used to separate herring into pop-
ulations or stocks.
A prevailing method is to relate population affiliation to spawning time of the indi-
vidual herring and the current stock splitting procedure for NSAS and WBSS applied
in the herring assessment working group in ICES (HAWG) assigns individual herring
to stock based on spawning time based on either otolith microstructure, otolith shape
or vertebrae count. These methods rely on updated baselines and inter-calibration be-
tween assigning laboratories in order to be as accurate and precise as possible. The last
workshop was held between Sweden and Denmark in 1989. Since then, the methods
have been implemented in several other countries and new methods have been de-
veloped.
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In addition, Next Generation Sequencing (NGS) and Genotyping by Sequencing
(GBS) based approaches have recently been developed and applied to e.g. cod (Gadus
morhua), boarfish (Capros aper) and horse mackerel (Trachurus trachurus) for marker
development and screening of spawning samples. Given all these developments, it
was now highly appropriate to have this comprehensive workshop for herring stock
identification methods.
The workshop covered herring in the areas 2.a, 6.a+7.b-c, 4.a-c+7.d, 3.a, SD 22+23+24 and
the most common methods used to separate herring in those areas.
1.3 Regional herring overviews
1.3.1 Herring in the North Sea
There are a number of fishery independent surveys for the North Sea herring stock,
two targeting the larvae stages (International Herring Larvae Survey (IHLS) and the
MIK sampling which is imbedded into the Q1 IBTS) and three targeting older ages
(bottom trawl surveys in the Q1 and Q3 International Bottom Trawl Survey (IBTS) and
an acoustic survey (HERAS)). The ICES Coordinated Acoustic Survey covers the Skag-
errak and Kattegat, the North Sea, plus now includes the West of Scotland and the
Malin Shelf. This survey started in 1989 with North Sea and has been extended to in-
clude 3.a since 1991. In the same year the west of the British Isles was added. The sur-
vey provides indices of numbers at age, mean weight at age and maturity ogive for
assessments of NSAS, WBSS and herring in 6.a, 7.b-c.
The HERAS survey is carried out annually from end of June to end of July. The timing
coincide with herring aggregating on summer feeding grounds prior to spawning mi-
grations. Autumn spawning herring distributed in ICES Subarea 4, divisions 3.a and
7.d. They migrate between spawning, feeding and over wintering areas as well as
nursery areas. The stock consists of four major spawning components; contributions of
these individual components to the total stock differ over time and mixing occurs out-
side of spawning time. Spawning of the main North Sea herring population begins in
the north of the North Sea in August /September. Spawning progresses southwards
with time, finishing in Dec/Jan with the Downs component in the eastern English
Channel.
Post spawning the adults then migrate to overwintering grounds in the North. The
larvae drift south and east on prevailing wind-induced flows. Juvenile 0-group fish are
found mainly in the southern and eastern North Sea (German Bight and Skagerrak).
Juveniles remain until they are ~2 years old (mixed with Western Baltic Spring Spawn-
ers in 3.a). Recruitment to the adult population is through active migration to the feed-
ing grounds in April–June.
The Western Baltic Spring Spawners (WBSS) spawn in spring in Baltic Sea. They mi-
grate out of Baltic to summer feeding grounds (June/July). Extent of migrations
age/size dependent with older fish migrate further out in to the north-eastern North
Sea. At the end of summer, they aggregate in Kattegat and eastern Skagerrak prior to
retuning in to the Baltic.
At the time the HERAS Survey is carried out in summer when herring is on the feeding
grounds. mixing between stocks occurs, especially in Division 3.a and eastern part of
4.a (NSAS and WBSS). Juveniles from NSAS and WBSS mix in the Skagerrak and east-
ern North Sea. Some adult WBSS (generally the older fish) migrate out into the North
Sea to feed and appear in Q3 catches and survey indices.
Workshop on Stock Identification and Allocation of Catches of Herring to Stocks (WKSIDAC) | 3

Currently, Geographic in the areas between 4oW and 2oE and then south of 56oN are all
considered to be NSAS. Identification and allocation between NSAS and WBSS is only
undertaken east of 2oE in the Norwegian and Danish Sectors. In the Norwegian area
allocation is based on vertebrate counts (percentage assignment) and in the Danish area
it is undertaken based on a combination of otolith shape and otolith micro structure
(individual assignment).
There is a need for a change in identification methodology so it is standardised for the
survey, and the catches. Within the survey we need a standardised method that can
provide stock assignment at the individual level to allow a split to be performed di-
rectly within the acoustic analysis tool used (StoX) based assignment of individuals to
stocks. There is a need to consider a method that can potentially be applied across the
survey area where WBSS and NSAS could be encountered (presently 2oE is a geograph-
ical border). The methods need to be validated and calibrated for a retrospective up-
date of the historical data.
The catch data are another issue that needs to be addressed. The majority of catches are
taken in Q2 and Q3, so they occur during the time of mixing when older WBSS are on
summer feeding grounds in 3.a and 4.a East. North Sea autumn spawners (NSAS) and
spring spawners (WBSS) occur in mixtures in fisheries operating in divisions 3.a and
4.a East. These are mainly 2+ ringers of the Western Baltic Spring Spawners (WBSS) on
their summer feeding areas (3.a and 4.aE). 0–2-ringers from the NSAS, including winter
spawning Downs herring (in 3.a). 4.a East is predominantly Norwegian catches and
splitting is done using vertebrate counts (south-eastern Norway). In Division 3.a the
Danish and Swedish catches only are split based on otolith shape and microstructure.
Further issues concerning the NSAS herring population that are not currently ad-
dressed include: the Downs herring component is targeted twice in the year, during
summer when the majority of NSAS is caught on pre-spawning feeding aggregations
(Downs is an unknown proportion of these catches) and in Q4 when Downs spawning
aggregations are directly targeted. With a separate quota assigned to this sub-stock
there is currently no way of knowing what fishing pressure is being exerted on this
section of the stock.
1.3.2 Herring in the western waters
In regard to the areas west of the British Isles, there are commercially important sea-
sonal fisheries for herring occurring there. The history of these western herring stocks,
their fisheries, assessment and management, is extensively reviewed in “The Herring
Fisheries of Ireland” (Molloy, 2006). The definition of these western stocks has changed
considerably over the last five decades (see ICES, 2015) and the putative stocks are
currently recognised as: 6.aN; 6.aS/7.b-c; Irish Sea; Celtic Sea and 7.j (see ICES, 2014).
This separation is largely based on information from fisheries and the recognition of
temporal and spatial differences in spawning season and grounds (ICES, 2015). A re-
view of the genetic research on these western herring stocks is compiled in Working
Document Farrell 2017.1 (see Annex 3). However, herring from separate stocks are
known to form mixed aggregations on common feeding grounds. Mixed stock fisheries
operate in these areas and the inability to assign catches to their stock of origin prevents
accurate assessment and has hampered the development and implementation of effec-
tive management strategies.
The mixing of herring stocks in the Irish Sea (7.aN) has received extensive research (see
review in ICES, 1994). This has been carried out over many decades and has high-
4 | ICES WKSIDAC REPORT 2017

lighted the links between these herring and the stocks surrounding them. The occur-
rence of juvenile Celtic Sea herring at Irish Sea nursery grounds is well documented
(Bowers, 1964; Molloy and Corten, 1975; Molloy, 1980). Tagging studies (Molloy et al.,
1993), otolith microstructure and shape (Brophy and Danilowicz, 2002, Beggs et al.,
2008, 2009, Burke et al., 2008a, 2008b) microchemistry; (Geffen et al., 2011), parasite
prevalence (Campbell et al., 2007) and genetics (King, 1985) are all tools that have been
used to investigate the mixing of herring populations in the area.
In particular otolith microstructure was used to demonstrate the presence of fast and
slow growth types in the Irish Sea, associated with winter and autumn spawning com-
ponents (Brophy and Danilowicz, 2002). Winter spawning is considered to be more
prevalent in the Celtic Sea, particularly in the eastern spawning areas (e.g. Dunmore
East) (Harma et al., 2012), while historically only low and infrequent levels of winter
spawning have been observed in the Irish Sea (Dickey-Collas et al., 2001).
Microstructure has subsequently been used to explore the dynamics of mixing between
these seasonal components of herring in the Irish Sea (Brophy and Danilowicz, 2002,
Brophy et al., 2006, Beggs et al., 2009, Burke et al., 2009). Analysis of mixing at age
showed that the proportions of “winter” type herring was greater in the younger age
classes (1 to 3-ringers), with relatively fewer “winter” spawned herring found at the
older age range (4+ ringers). At the age classes examined maturity stages 4+ were com-
monly dominated by “autumn” type fish. Therefore the “winter” type fish are gener-
ally at lower reproductive phases than the earlier spawning “autumn” type fish. Mix-
ing was found to be spatially dynamic with the majority of mixing occurring to the
west of the Isle of Man. The level of mixing to the east of the Isle of Man, in the area of
the Douglas bank spawning ground, was estimated to be much lower. This spatial pic-
ture of mixing is mirrored by the observation that the majority of juvenile fish (1–2
rings) are found to the west of the Isle of Man. The proportion of mixing varied annu-
ally in the survey (acoustic) and commercial catch samples. There is evidence that the
extent of mixing observed in the commercial landings is influenced by local spawning
area closures, the spatial and temporal dynamics of the fleet and the timing of the her-
ring spawning migration (Beggs et al., 2010).
These results have implications for the assessment of Irish Sea herring and in particular
the calculation of population parameters such as maturity, total biomass and spawning
stock biomass (SSB).
In the past, Division 6.a was considered to have two separate stocks with their own
management advice. However, at present ICES is unable to distinguish between the
herring stocks in 6.aN and 6.aS/7.b-c in commercial catches or research surveys. This
means that ICES has to provide combined management advice for this area, leading to
a combined quota and management of the two putative stocks. However, ICES and the
scientific community agree that the two stocks are discrete, despite their being indis-
tinguishable with currently available and implemented stock discrimination tools.
Combined management of what amounts to an amalgam of separate stocks is a very
dangerous situation. Such management can only be precautionary if the two stocks are
of similar size and are homogeneously distributed together in commercial catches. If
these conditions are not met, the smaller stock will suffer a higher mortality than would
be sustainable and will eventually decline.
The only stock assessment tuning index currently available for the assessment of the
6.a/7.b-c herring stocks is the combined Malin Shelf Summer Herring Acoustic Survey
(MSHAS). Since 2008, this survey has covered non-spawning (feeding) aggregations of
Workshop on Stock Identification and Allocation of Catches of Herring to Stocks (WKSIDAC) | 5

herring mixing in the Hebrides, Malin shelf and Irish shelf areas (ICES, 2017). The sur-
vey straddles the 6.aN and 6.aS/7.b-c stock areas (ICES, 2017) and until recently herring
abundance was assigned to either stock based purely on the geographic position of the
observed herring acoustic echotraces in relation to the 56°N line of latitude. The results
of the WESTHER study (Anon, 2006; Hatfield et al., 2007) show herring in this area to
be a mixed stock or metapopulation. As this survey is known to include fish from a
number of spawning locations it is necessary to determine the level of mixing to obtain
meaningful tuning indices for the 6.aN and 6.aS/7.b-c assessments. Since 2010 otolith
and body morphometric samples have been collected during the combined MSHAS
survey to enable the discrimination and classification of herring from mixed aggrega-
tions to their natal origin based on comparison with baseline data from the WESTHER
project. However, based on the WESTHER baseline a reliable and consistent split has
not been possible to date (see WD Farrell 2017.1, Annex 3).
1.3.3 Herring in the Western Baltic and Baltic Sea
In the western Baltic, the distribution areas of two different herring stocks, the Western
Baltic Spring Spawning Herring (WBSSH) and the Central Baltic Herring (CBH) over-
lap. Stock assessment for Baltic herring so far is based on indices generated on a spatial
separation of both stocks according to ICES subdivisions. Generally, herring monitored
and sampled in ICES subdivisions 21–24 are allocated to the WBSSH stock. Overall, the
CBH stock is characterized by a lower weight at age and an overall “ailing” appearance
as compared to the WBSSH. The abundance and biomass index generated from the
German autumn acoustic herring survey (GERAS) data in 2010 showed an uncharac-
teristic decrease in weight with increasing age, together with lower mean weights at
age. Additionally, peak abundances in some age groups indicated strong previous year
classes, which had not been detected in previous surveys. This was mainly evident in
ICES SD 24. This indicated that in parts of the survey area, a stronger mixing and con-
tribution of CBH took place. To assess the degree of contribution of CBH to the abun-
dance and biomass index generated for WBSSH from catch data in the survey area, a
method was required to separate both stocks according to measures readily available
from survey data and to consecutively remove the CBH fraction from survey results.
As a separation according to e.g. genetic analyses etc. was not applicable due to a lack
of data and as other measures as e.g. eye diameter proved too inaccurate for a reliable
separation, another measure was required. Thus, a separation function (SF) based on
growth parameters was established. Generally, CBH show a lower weight at age than
WBSSH. Thus, based on Bertalanffy growth parameters of both WBSSH and CBH, a SF
was established and applied to survey data to identify and quantify the fraction of CBH
(Gröhsler et al., 2013, 2016).
1.3.4 Herring in the Norwegian Sea, Icelandic waters and Faroe waters
In the Norwegian Sea (2.a, 2.b), all monitored, sampled and caught herring are assessed
and managed as Norwegian spring spawners (NSS). No splitting or discrimination is
conducted between NSS and other stocks or populations occurring or migrating in the
Norwegian Sea. Nevertheless, the existence of other components like Norwegian au-
tumn spawners or local fjord populations is known (Husebø et al., 2005; Pampoulie et
al., 2015). These components are included in the management of NSS. Further, other
populations or stocks like the North Sea autumn spawners (NSAS) migrate into the
Norwegian Sea (North of 62°N) during their annual migrations. The occurrence of mi-
grating herring is completely neglected and in case of capture, they are registered as
NSS landings and consequently included in the assessment and management of NSS.
This might lead to on overestimation of the spawning stock biomass of NSS. During