NEFSC Ref Doc 09-03

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CONTENTS

Introduction

The Fishery

Stock Abundance and Biomass Indices

Estimation of Fishing Mortality Rates and Stock Size

Biological Reference Points

Conclusions

Acknowledgements

Literature Cited

Northeast Fisheries Science Center Reference Document 09-03

The 2008 Assessment of the Gulf of Maine
Atlantic Cod (Gadus morhua) Stock

by R.K. Mayo, G. Shepherd, L. O’Brien, L.A. Col, and M. Traver

NOAA National Marine Fisheries Service, Northeast Fisheries Science Center, 166 Water Street, Woods Hole MA 02543

Print publication date February 2009; web version posted March 25, 2009

Citation: Mayo RK, Shepherd G, O’Brien L, Col LA, Traver, M. 2009. The 2008 assessment of the Gulf of Maine Atlantic cod (Gadus morhua) stock. US Dept Commer, Northeast Fish Sci Cent Ref Doc. 09-03; 128 p.

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ABSTRACT
The status of the Gulf of Maine Atlantic cod (Gadus morhua) stock is reviewed, and terminal year VPA estimates of 2007 fishing mortality and spawning stock biomass, and the survivors in 2008 are presented. Precision estimates of the 2007 fishing mortality and spawning stock biomass estimates for Gulf of Maine cod are also provided. The 2008 assessment is based on several sources of information including: the age composition of USA commercial and recreational landings, commercial fishing vessel trip reports (VTR), Northeast Fisheries Science Center (NEFSC) Fishery Observer Program data, MRFSS estimates of recreational harvest, NEFSC and Massachusetts Division of Marine Fisheries (DMF) spring and autumn research vessel survey data, and standardized USA commercial fishing effort data. This assessment represents a major revision to the analyses presented in the 2001 assessment of the Gulf of Maine cod stock reviewed at SAW 33 (NEFSC 2001a, b, Mayo et al. 2002) and those reviewed in 2002 at the first Groundfish Assessment Review Meeting (GARM) (NEFSC 2002b) and in 2005 at the 2^nd Groundfish Assessment Review Meeting (GARM II) (NEFSC 2005, Mayo and Col 2006). The analyses presented herein were recently reviewed in 2008 at the 3rd Groundfish Assessment Review Meeting (GARM III) (NEFSC 2008).

Input data and the assessment formulation were revised in the present assessment as follows. Landings data from 1994 forward were revised based on a preferred allocation of trips to statistical area. Discard estimates were revised from 1989 forward based on SBRM methodology and recreational catches were revised from 1981 forward based on revised MRFSS data and a revised approach to allocate catches to stock. The assessment formulation now employs an age 11+ group vs. age 7+, and includes survey indices out to age 8 for calibration.

Biological reference points are estimated using a non-parametric approach incorporating an SSB per recruit analysis and a stochastic equilibrium projection of MSY and SSB_msy.

Total catches (commercial and recreational landings and commercial discards) of Gulf of Maine cod decreased from 21,650 metric tons (mt) in 1991 to 4,700 – 4,800 mt in 1998 and 1999, increased to 7,600 mt in 2003 and have since declined to 5,500 mt in 2007. Commercial discards increased sharply from 97 mt in 1998 to 2,624 mt in 1999, likely due to the imposition of very low trip limits during 1999, but declined thereafter as trip limits were relaxed in early 2000.

Fishery-independent spring and autumn bottom trawl surveys conducted by the NEFSC have documented a steady decline in total stock biomass since the 1960s; the largest decreases occurred during the 1980s. Although the most recent indices suggest a modest increase since the early 1990s, the Gulf of Maine cod stock biomass remains low compared to the 1960s and 1970s. Except for the 1998 year class, recruitment during the 1990s has been well below the long-term mean. The 1999 and 2000 year classes are weak but the 2003 and 2005 year classes well above average. Spawning stock biomass (SSB) declined from over 29,600 mt in 1990 to a low of 9,900 mt in 1997; SSB increased to 28,700 mt in 2002 but declined to 11,000 mt in 2005 due to very low abundance of the poor 1999 and 2000 year classes. SSB has since increased to 33,877 mt in 2007 due to the maturation of the above-average 2003 year class. Fully recruited instantaneous fishing mortality (F, ages 5-7) remained close to or above 1.0 between 1983 and 1997, but declined to 0.32 by 2000, increased to greater than 0.5 from 2002 - 2007, and declined to 0.46 in 2007. SSB_msy is estimated to be 58,248 mt with a corresponding F_msy of 0.237, (fully recruited, ages 5+). With respect to the age-structured MSY-based reference points, 2007 spawning stock biomass is above ½ SSB_msy, and 2007 F is 1.9 times F_msy.

INTRODUCTION
Atlantic cod (Gadus morhua) in the Gulf of Maine region (Figure 1) have been commercially exploited since the 17th century, and landings statistics are available since 1893. Historically, the Gulf of Maine fishery can be separated into four periods (Figure 2): (1) an early era from 1893-1915 in which record-high landings (> 17,000 mt) in 1895 and 1906 were followed by about 10 years of sharply-reduced catches; (2) a later period from 1916-1940 in which annual landings were relatively stable, fluctuating between 5,000 and 11,500 mt, and averaging 8,300 mt per year; (3) a period from 1941-1963 when landings sharply increased (1945: 14,500 mt) and then rapidly decreased, reaching a record-low of 2,600 mt in 1957; and (4) the most recent period from 1964 onward during which Gulf of Maine landings have generally increased but have declined steadily since the early 1990s. Total commercial landings doubled between 1964 and 1968, doubled again between 1968 and 1977, and averaged 12,200 mt per year during 1976-1985 (Table 1). Gulf of Maine cod landings subsequently increased, reaching 17,800 mt in 1991, the highest level since the early 1900s. Total landings declined sharply in 1992 to 10,891 mt, and have since decreased steadily to 1,636 mt in 1999 before increasing to 3,730 mt in 2000. Total commercial landings have since fluctuated between 3,800 and 4,400 mt. Landed cod from the recreational sector have represented between 6 and 39 percent of the combined commercial and recreational harvest.

This report presents an updated and revised analytical assessment of the Gulf of Maine cod stock (NAFO Division 5Y) for the period 1982-2007 based on analyses of commercial and recreational data through 2007 and research vessel survey data through spring 2008. From the early 1960s through 1993, information on the catch quantity by market category was derived from reports of landings transactions submitted voluntarily by processors and dealers. More detailed data on fishing effort and location of fishing activity were obtained for a subset of trips from personal interviews of fishing captains conducted by port agents in the major ports of the Northeast. Information acquired during the course of these interviews was used to augment the total landings information obtained from the dealers. Procedures for collecting and processing commercial fishery data in the Northeast were revised after 1993.

Beginning in 1994, data on number of hauls, average haul time, and catch locale were obtained from logbooks submitted to the National Marine Fisheries Service (NMFS) by operators fishing for groundfish in the Northeast under a mandatory reporting program. Landings were allocated to statistical area based on dealer trip reports and species landings records matched to fishing vessel logbooks (VTRs). Thus, commercial landings data utilized in the present assessment from 1994 to present were revised from those reported in previous assessments using a more comprehensive approach to allocate fishing trips and landings of all species among statistical areas (Wigley et al. 2008). This approach represents a substantial improvement over the previous method (Wigley et al. 1998) that addressed the spatial proration of landings on an aggregate trip basis at the quarter – stock level.

An initial analytical assessment of this stock (Serchuk and Wigley 1986) was presented at the Seventh NEFC Stock Assessment Workshop in November 1988 (NEFC 1989) and subsequent assessments were reviewed at the 12^th, 15^th, 19^th, 24^th and 27^th Northeast Regional Stock Assessment Workshops in June 1991, December 1992, December 1994, June 1997 and June 1998 (NEFSC 1991, 1993, 1995, 1997, 1998; Mayo 1995, 1998; Mayo et al. 1993, 1998).   Interim assessments were reviewed by the Northern Demersal Working Group in July 1999 (NEFSC 2000) and August 2000 (NEFSC 2001a). A peer review of this assessment (Mayo et al. 2002) occurred at the 33^rd Northeast Regional Stock Assessment Workshop in June 2001 (NEFSC 2001b). An updated assessment through 2001 was reviewed at the Groundfish Assessment Review Meeting in October 2002 (NEFSC 2002b, Mayo and Col 2002) and a further update through 2004 was reviewed at the second Groundfish Assessment Review Meeting in August 2005 (NEFSC 2005, Mayo and Col 2006). The present assessment was reviewed at the third Groundfish Assessment Review Meeting in August 2008 (NEFSC 2008, Mayo et al. 2008).

THE FISHERY
Management History

Fishing for Gulf of Maine cod has been managed under international treaty prior to 1977 and by domestic management authority since 1977 (Appendix A). Annual Total Allowable Catches (TACs) were first established under the International Commission for the Northwest Atlantic Fisheries (ICNAF) for Division 5Y (i.e., the Gulf of Maine) cod in 1973 (Serchuk et al. 1994).   The TAC remained at 10,000 mt from 1973-1975; the 1976 TAC was reduced to 8,000 mt and the TAC proposed for 1977 was reduced further to 5,000 mt.

Following implementation of the Magnuson Fishery Conservation and Management Act (FCMA) in 1977, management of this stock fell under the auspices of the New England Fishery Management Council. TACs were carried forward for the first few years under the Fishery Management Plan for Atlantic Groundfish, and were distributed among vessel tonnage classes and quarters of the years until 1982 when the “Interim” Plan for Atlantic groundfish was implemented. This plan eliminated all direct catch controls (quotas) and established mesh size and minimum landing size regulations as the primary regulatory measures for cod, haddock and yellowtail flounder.

Management of the Gulf of Maine cod fishery has been carried out since 1985 under the Northeast Multispecies Fishery Management Plan (FMP). This plan and its Amendments 1 through 4 essentially carried forward the regulatory measures originally implemented in 1982 under the “Interim” Plan (Appendix A). Beginning in 1994 with the implementation of Amendment 5, the primary goal of the FMP became a reduction in fishing mortality for 5 key monitoring stocks.   This was to be achieved through a combination of reductions in days at sea (DAS) usage and, under Amendment 7, an additional series of seasonal and year-round area closures oriented primarily towards Gulf of Maine stocks. Amendment 13, implemented in May 2004, added additional restrictions on Days at Sea (DAS) usage and further defined the use of A DAS and B DAS to allow fishing on stocks in relatively good condition while still restricting effort on stocks of concern (including Gulf of Maine cod). Framework 42, implemented in 2006, established Bmsy targets and Fmsy thresholds for 18 groundfish stocks reviewed at GARMII in August 2005. This framework also established formal rebuilding plans for stocks that were classified as overfished, i.e., where the 2004 stock biomass was estimated to be less than ½ B_msy.
Commercial Landings Total commercial landings
Annual commercial landings data for Gulf of Maine cod in years prior to 1994 were obtained from trip-level detailed landings records maintained by the Northeast Fisheries Science Center (NEFSC), Woods Hole, Massachusetts (1963-1993) and from summary reports of the Bureau of Commercial Fisheries and its predecessor the U.S. Fish Commission (1895-1962). More detailed data on fishing effort and location of fishing activity were obtained for a subset of trips from personal interviews of fishing captains conducted by port agents in the major ports of the Northeast. Information acquired during the course of these interviews was used to augment the total landings information obtained from the dealers.

Beginning in 1994, data on number of hauls, average haul time, and catch locale were obtained from logbooks submitted to the National Marine Fisheries Service (NMFS) by operators fishing for groundfish in the Northeast under a mandatory reporting program that replaced the earlier interview system. Thus, an interim, species-based scheme was developed in 1997 to allocate landings by market category to stock based on a matched subset of trips between the dealer and logbook databases. Data in both databases were stratified by calendar quarter, port group, and gear group to form a pool of observations from which proportions of landings by stock could be allocated to market category within the matched subset. The cross-products of the market category by stock proportions derived from the matched subset were employed to compute the total landings by stock, market category, calendar quarter, port group, and gear group on an annual basis. A full description of the proration methodology and an evaluation of the 1994-1996 logbook data is given in Wigley et al. (1998) and DeLong et al. (MS 1997). This scheme was used in all assessments conducted between 1994 and 2005.

Commercial landings data used in the present assessment represent a substantial departure from those used in previous assessments. The quantity of each species landed on every trip since 1994 has now been allocated to statistical area based on dealer trip reports and species-market category landings records matched to logbooks (fishing vessel trip reports or VTRs) under a four tiered scheme. This allocation scheme produces comprehensive annual data sets that are virtually identical to the data sets produced prior to 1994. Thus, commercial landings data from 1994 to present utilized in the present assessment were revised from those reported in previous assessments using this comprehensive approach to allocate fishing trips and landings of all species among statistical areas (Wigley et al. 2008). This approach represents a substantial improvement over the previous method (Wigley et al. 1998) that addressed the spatial proration of landings on an aggregate trip basis at the quarter – stock level.

Annual commercial landings declined from 17,781 mt in 1991 to a low of 1,380 mt in 1999 Landings remained relatively stable between 2000 and 2007, varying between 3,000 and 4,300 mt. Total landings in 2007 were 3,989 mt, slightly below those from 2002-2006 (Table 1, Figure 2). Since 1977, the USA fishery has accounted for all of the commercial landings. Canadian landings reported as Gulf of Maine catch after 1977 are believed by Canadian scientists to have been misreported catches from the Scotian Shelf stock (Campana and Simon 1985; Campana and Hamel 1990) and have thus been excluded.
Landings by market category
Since 1964 market cod have generally dominated the landings with percentages ranging from 40 – 60% in most years (Table 2, Figure 3). The percentage of large cod has fluctuated over time, accounting for over 50% during the early 1970s and then declining to a low of 13% in 1996. Large cod have since accounted for a higher percentage of the total landings, reaching 52% in 2004 before declining once again. Scrod cod have generally represented about 20% of the total, but this share has declined to less than 10% since 2000, likely due to recent increases in minimum mesh size regulations. In 2007, the percentages by market category were: Large – 24%, Market – 65%, and Scrod – 5%. Approximately 1% of the landings were classified as Mixed.
Landings by gear type
Although otter trawl catches account for most of the landings (averaging 62% between 1965 and 2007), the otter trawl percentage has declined considerably since 1993 compared to the period prior to 1993 from an average of 68% to 51% (Table 3, Figure 4). Most of this change can be attributed to an increase in the percentage of cod taken by sink gillnets from an average of 25% prior to1993, to an average of 41% since 1993. The percentage from combined handline and line trawls also increased substantially during the 1990s, but still remains below levels observed during the 1970s.   In 2007, the percentages by gear type were: Otter Trawl – 37.5%, Sink Gill Net – 53.2%, and combined Line Trawl and Handline – 5.7%.
Commercial Sampling Intensity
A summary of USA length frequency and age sampling of Gulf of Maine cod landings during 1982-2007 is presented in Table 4. Most of the USA samples have been taken from otter trawl landings, but sampling and the estimation of length composition is stratified by market category (large, market, and scrod). Although the length composition of cod differs among gear types (primarily between otter trawl and gillnet), the length composition of cod landings within each market category is virtually identical among gear types.

USA length frequency sampling averaged one sample per 155-200 mt landed during 1983-1987 but the sampling intensity was reduced in 1990 (1 sample per 387 mt) and 1993 (1 sample per 360 mt), and the absolute level of sampling was extremely low in 1993. Overall, sampling improved slightly in 1994 and 1995, but the seasonal distribution was uneven and poorly matched to the landings. Sampling improved substantially in 1996 and remained equally high in 1997, reaching all-time highs in terms of both absolute number of samples and samples per ton landed in both years.

The quality of commercial port sampling for Gulf of Maine cod began to decline again in 1998. The total number of samples taken declined sharply in 1998 and again in 1999, a possible outcome of the very low trip limits imposed in 1999. Although the number of samples collected increased in 2000, the distribution by market category was out of phase with actual landings. In particular, the number of ‘Large’ market category cod samples had diminished to the point that the representation of the older age groups may have been somewhat compromised. As well, the seasonal distribution of samples remained skewed for several years such that, although there appears to have been sufficient numbers of samples taken, there had been insufficient sampling in some quarters and half-years, requiring pooling of samples on an annual basis.

Sampling improved considerably in 2001, especially in the case of large market category cod as a result of augmented sampling effort, and has remained high (less than 50 mt landed per sample). This increase has allowed quarterly pooling since 2003. However, in many cases large samples comprise less than 10 fish; thus, number of fish sampled is a better representation of sampling intensity.

Of the 10,702 cod measured in 2007, 4,782 were large (45%), 4,781 were market (45%), and 1,073 were scrod (10%). Compared with the 2007 market category landings distribution by weight (large: 24%, market: 65%, scrod: 5%) (Table 2), large cod were over-sampled and market cod were under-sampled. The average sample sizes in 2007 were: Large - 17, Market – 85, and. Scrod – 31.
Commercial Landings Age Composition
The age composition of landings during 1982-1993 was estimated, by market category, from length frequency and age samples, pooled by calendar quarter. Quarterly mean weights, by market category, were obtained by applying the NEFSC research vessel survey length-weight equation for cod:

ln Weight _{(kg,
live)} = -11.7231 + 3.0521 ln Length _(cm)

to the quarterly market category sample length frequencies. Computed mean weights were then divided into quarterly market category landed weight to derive estimated numbers landed by quarter, by market category. Quarterly age/length keys were applied to the quarterly market category numbers at length distributions to provide numbers at age. These results were summed over market categories and quarters to derive the annual landings-at-age matrix (Table 5a).

Age composition of landings from 1994 through 2002 was estimated in a manner similar to that employed for the 1982-1993 estimates except that samples and landings were, at times, pooled to semi-annual or annual resolution because of the uneven distribution of length and age samples by quarter (Table 4). Semi-annual pooling was required for the 1st and 2nd quarters of 1994 because of incomplete sampling coverage of scrod and large cod landings; in 1995, samples were pooled in both semi-annual periods due to the absence of large cod samples and the sparse coverage of market cod in quarters 1 and 3. Quarterly allocation of samples to landings was achieved for all market categories in 1996 and 1997, but semi-annual and annual pooling was required in 1998 and annual pooling was required in 1999 and 2000. Quarterly stratification resumed in 2003 and continued through 2007.

Gulf of Maine cod commercial landings have generally been dominated by age 3 and 4 fish in numbers (Table 5a, Figure 5) and by ages 3, 4, and 5 in weight. Representation of age 2 cod was relatively high in the early 1980s but, in response to a series of minimum mesh size increases during the 1990s, age 2 fish have gradually all but disappeared from the landings. Cod from the strong 1987 year class predominated from 1990 through 1992 but, by 1993, fish from the 1990 year class accounted for the greatest proportion of the total number landed. In terms of weight, the 1993 landings were equally distributed between the 1987 and 1990 year classes. In 1993 these two year classes accounted for approximately 70% of the total number and weight landed. From 1994 through 1996, landings were dominated by age 4 cod in both number and weight. In 1997 age 5 fish were dominant in terms of both number and weight, reflecting the higher abundance of the 1992 year class. More recently, the 1998 year class has dominated the landings at ages 3 through 6 in 2001 through 2004, respectively. In 2005 and 2006, the below average 2001 year class predominated at ages 4 and 5, respectively. However, in 2007, the above average 2003 year class dominated the landings at age 4.

Although traditionally low in terms of their contribution to the total landings, age 10 and 11+ fish were absent for several years during the 1990s, and numbers of age 8 and 9 fish were also unusually low (Table 5a, Figure 5). In recent years, however, the contribution of these older fish has steadily increased. Although this pattern may be partly a result of the poor sampling of ‘Large' category cod, especially during the mid- to late 1990s, the trend towards fewer older fish in the landings began in 1991 before sampling had begun to decline. The proportion of cod older than age 7 has been increasing since 2001 (Table 5a, Figure 5). In 2004 - 2006 ages 8 and older represented 13 -16% of the landed weight, more than the 7-13% contribution during 1982-1984 and the very low 1% contribution in 2000. Although the percentage of ages 8 and older fish in the landings decreased to 7.7% in 2007, this value remained greater than any of the percentages observed between 1991 and 2003. Unlike previous assessments that carried out ages to only 7+, representation of these older ages now allows us to carry out the age composition to age 11+ and explore the age structure of the age 7+ group used since the 1995 assessment.
Commercial Landings Mean Weights at Age
Mean weights at age in the landings during 1982-2007 are presented in Table 5b for ages 1-11+. These are considered mid-year values based on seasonal patterns of the fishery. Mean weights of age 2 and 3 cod have increased since about 1992 and mean weights of age 4 cod have increased since 2000, likely reflecting reduced partial recruitment to the fishery of the slower-growing, smaller fish at these ages, while the average weights for age 5 and 6 cod have fluctuated without trend. Mean weights for ages 7-10 fluctuate considerably and are particularly sensitive to sampling variability. However, a marked decline is evident in mean weights of these older ages during the 1990s. The generally higher mean weights of age 2 and 3 cod since the mid - 1990s may be related to an increase in minimum codend mesh size from 140 mm (5.5 in.) to 152 mm (6 in.) in 1994, while the increase in mean weights of age 4 cod occurred after an increase in the minimum codend square mesh to 165 mm (6.5 in.) in May, 1999.
Commercial Discards
In past assessments, discard rates were routinely calculated for Gulf of Maine cod by quarter and gear from NEFSC Observer Program data collected since 1989 (e.g., Mayo and Col 2006). Discard and kept components of the catch were summed for all observed tows within each gear type occurring in Division 5Y, and the ratio of the discarded- to-kept quantity was applied to landings for the corresponding quarter and gear type within each year. Data were available for otter trawls, shrimp trawls (through 1993 only), and sink gillnets.

Previous assessments (e.g., Mayo and Col 2006) also evaluated Vessel Trip Report (VTR) data from trips reporting some catch of cod in the Gulf of Maine to further evaluate the extent of discards. The discard estimates of Gulf of Maine cod derived from the two data sets have been reasonably close to each other, with annual differences of 3 -18 percent on the estimates of total commercial catch. Given that they saw no objective basis to select the results obtained from either data set, the SAW 33 SARC Panel (NEFSC 2001b) concluded that both estimates could be used to derive annual estimates to the nearest 500 mt increment. This approach was adopted in assessments that were accepted by the SAW33 SARC Panel and the 2 meetings of the GARM in 2002 (NEFSC 2002b) and 2005 (NEFSC 2005).

In the present assessment, commercial discards were re-estimated for the 1989-2007 period on a gear-quarter basis from NEFSC Observer Program data using SBRM methods (Wigley et al. 2007) incorporating cod discard/cod kept ratios (Table 6). The revised estimates compare favorably with those presented at GARMII using the approach used in past assessments based on the observer data (Table 6). Both approaches indicate a substantial increase in the overall discard/kept ratio in 1999 compared to previous years. Ratios calculated for years after 1999 were lower, but still remain substantially greater than the 1991-1998 ratios. Discards re-estimated from the Observer Program data have ranged from 97 mt in 1998 to 3,092 in 1990.   These discard estimates were then used to generate the discards at age from 1999 to present (Table 7).

For otter trawl gear, discard-to-kept ratios (d/k) and absolute quantities of discarded cod declined from relatively high values in 1989 and 1990 to relatively low levels from 1991 through 1998 as the overall d/k ratios generally fluctuated between 0.02 and 0.06. Discards from the sink gill net fishery remained relatively low between 1989 and 1998, at less than 200 mt. In 1999, discard ratios increased sharply for otter trawl and sink gill nets during the second and third quarters, declined from these peak levels in the fourth quarter, but continued to remain relatively high from 2000 to early 2004 compared to pre-1999 ratios. Ratios declined in 2004 after trip limits were further relaxed in the second quarter.

The relatively high discards calculated for otter trawl and shrimp trawl gear during 1989-1991 (Table 6) coincide with recruitment of the strong 1987 year class to the small mesh shrimp trawl gear and then to the large mesh general otter trawl gear. Available length composition data for these gear types suggest that most of the discarded cod were about 30-50 cm with a mode around 40 cm. Discards emanating from these two gears are the likely result of minimum size regulations. In contrast, the relatively low, but persistent, discards of cod in the gillnet fishery comprised fish of all lengths, up to 125 cm. The larger size range reflects discarding resulting from minimum size regulations as well as poor fish quality (in the case of the larger, marketable cod). Discards in 1999 were estimated to be 2,624 mt, one of the highest in the data series, likely due to the imposition of very low trip limits. Estimated discards declined to 998 mt in 2000 as trip limits were relaxed to 400 lbs/day in early 2000, and fluctuated between 1,200 and 1,500 mt between 2001 and 2003 before declining to less than 500 mt from 2004 – 2006 (Table 6) as trip limits were further relaxed to 800 lbs/day. In 2007, the estimated discards were 516 mt.
Adjustment of the 1999 - 2007 Commercial Landings at Age
The fishery for Gulf of Maine cod was affected by specific management actions that began in 1999 and have continued into 2007. The implementation of extremely low trip limits in 1999 likely precipitated a substantial increase in the amount of cod discarded compared to previous years, as noted above. While these trip limits were relaxed to some extent in subsequent years, a substantial portion of the total catch continues to be discarded. Consequently, the 1999-2007 estimated commercial landings at age presented in Table 5a do not reflect the full extent of removals from the stock by the commercial fishery. Therefore, prior to inclusion in the VPA, the 1999-2007 estimates of numbers landed at age had to be adjusted upwards by the ratio of total estimated catch biomass (landings + discard) to the landed catch biomass.

This approach assumes that the age composition of the discarded component of the catch is the same as the landed component. In cases where discards occur because the mesh selectivity in the fishery is not consistent with minimum landing size regulations, it is necessary to estimate the size and age composition of the discarded component separate from the landed component. In general, discards comprise the smaller, younger fish compared to those that are landed. However, where regulatory discards are generated as a result of low trip limits (as occurred during 1999-2007), it is presumed that cod of all sizes and ages are discarded without prejudice. Examination of the 1998, 1999 and 2000 kept and discarded length composition samples from the NEFSC Observer Program database support this assumption. The sizes of discarded cod in 1998, when trip limits were considerably higher, were primarily below the 48 cm minimum landing size, and the sizes of retained cod were approximately the same as those observed in the commercial port samples. In 1999 and 2000, however, the sizes of discarded and retained cod were generally the same, well above the minimum landing size and similar to those observed in the commercial port samples. Therefore, the 1999 -2007 commercial landings at age estimates in Table 5a were multiplied by the discard to kept ratios in Table 6 to derive the discarded numbers at age in Table 7, and commercial landings mean weights at age were used to estimate the discarded weight at age (Table 7).
Recreational Catches
Estimates of the recreational cod catch were obtained from the Marine Recreational Fishery Statistics Survey (MRFSS), which has been conducted annually since 1979. For this assessment, recreational catches (Table 8) were re-estimated and partitioned by Gulf of Maine and Georges Bank stocks for the 1981-2007 period using revised MRFSS data and a revised site register (Steinbak and Thunberg, pers. comm.). Further information on the details of the allocation scheme and sampling intensity are given in NEFSC (1992). Estimates of the total Gulf of Maine cod recreational catch as well as the retained portion of the catch (i.e., excluding those caught and released) are provided in Table 8. The estimated recreational catch of Gulf of Maine cod (retained component only) has varied considerably over the past decades, ranging from 337 mt in 1997 to 4,218 mt in 1981 (Table 8).

The quantity of cod retained generally exceeded 80% of the total recreational catch during 1981 through 1988, but has been steadily declining, averaging less than 40% since 1994 and less than 30% in 2006 and 2007. The estimated total cod catch (including those caught and released) declined from over 4,500 mt in 1981 to about 2,000 mt between 1983 and 1986, increased to over 3,500 mt in 1990 and 1991, and fluctuated between 1,200 and 3,300 mt between 1992 and 1999. The total catch increased sharply beginning in 2000, reaching 7,100 mt in 2003 before declining to between 3,600 and 4,500 mt in 2006 and 2007. Trends in the weight of retained cod were similar to the total catch, but the magnitude of the removals has been considerably less, especially since 1992.
Recreational Sampling Intensity
Information on the length frequency sampling levels of Gulf of Maine cod taken in the recreational fishery is also provided in Table 8. Overall, sampling of cod taken by recreational gear is poor, ranging from less than 1 ton retained per fish measured annually to over 40 tons retained per fish measured, averaging about 5 tons retained per fish measured. Sampling of the recreational fishery improved during the 1990s, declined between 1999 and 2003 and has improved again in recent years. The age composition of the 1982-1996 recreational landings was estimated for the 1997 assessment (Mayo 1998) but, given the highly variable sampling, these estimates were not formally included in the VPA conducted in 1997 (NEFSC 1997; Mayo 1998).   However, the retained recreational catch became a substantial portion of the combined commercial and recreational landings beginning in 1999. Therefore, the age composition of the recreational landings from 1997 through 2000 was estimated for the 2001 assessment, and the 1982-2000 recreational landings at age estimates were incorporated into the total catch at age (Mayo et al. 2002) despite the noted sampling variability.

In the present assessment, the recreational fishery landings age composition was re-estimated from 1982 to 2007 using available length measurements from the MRFSS database allocated to the Gulf of Maine area and a combination of commercial, survey (NEFSC and MADMF) and the cod industry-based survey (2004 and 2005 only) age/length keys.
Recreational Landings Age Composition
Given the limited length sampling coverage in the recreational sector of the fishery, the estimation of the number of Gulf of Maine cod caught by length and age required that samples be pooled on an annual basis. The low inter-seasonal variability displayed by the sample length composition data supported this approach. Differences between the party/charter and private/rental fishing modes are also minimal. Therefore, estimates of the age composition of cod retained by the recreational sector were derived from the length composition data applied to the retained numbers of cod based on pooled annual length frequency samples from Gulf of Maine trips. Only the retained numbers of cod were included because the intercept sampling is not likely to accurately reflect the size composition of the released cod. Age-length keys obtained from sampling the commercial landings, augmented by age samples from trawl surveys for cod less than 40 cm, were applied to the numbers retained at length on an annual basis to derive the numbers retained at age (Table 9a).

During the 1980s, Gulf of Maine cod recreational landings in numbers were dominated by age 3 fish with age 2 fish next in importance (Table 9a, Figure 6). Following the increases in minimum retention size in 1989 and again in 1996, the proportion of age 2 cod declined, and the age composition of the recreational landings now resembles that of the commercial fishery with ages 3, 4 and 5 predominant (Table 5a and Table 9a, Figure 6). The strong 1987 year class dominated the recreational catch in 1990, 1991 and 1992. The 1992 year class can also be tracked in the estimated catch at age between 1995 and 1999 and the 1998 year class predominates after 2000. Ages 3 and 4 cod generally predominate in terms of weight caught, although the 1987, 1992, and 1998 year classes predominated at age 5 in 1992, 1997 and 2003 respectively. The 2001 year class was predominant in 2004, 2005 and 2006, and the 2003 year class dominated the recreational fishery landings in 2007.
Recreational Landings Mean Weights at Age
Mean weights at age were obtained by applying the NEFSC research vessel survey length-weight equation for cod to the numbers retained at age on an annual basis:

ln Weight _{(kg,
live)} = -11.7231 + 3.0521 ln Length _(cm)

Mean lengths and weights at age of cod landed by the recreational sector (Table 9b) are consistently lower than those taken in the commercial fishery. This pattern persists through age 5 but, for ages 6 and older, mean weights are highly variable due to the relatively poor sampling of fish at the larger sizes combined with the lack of market category stratification. Despite this variability, patterns present in the commercial landings mean weights are also evident in the recreational landings, i.e., an increase in the mean weight of age 2 and 3 cod beginning in the mid-to-late 1990s, apparent stability of mean weights of age 4, 5 and 6 cod, and an indication of a similar decline in the mean weight of age 7 -10 fish.
Components of the Total Catch
Commercial landings account for the greatest share of the total catch of Gulf of Maine cod (Figure 7), generally exceeding 75% of the total. However, beginning in 1999, when commercial discards and recreational landings began to consistently account for a substantial share of the total catch, commercial landings have generally represented between 50 and 60% of the total catch (Table 10, Figure 7). Commercial discards were relatively low, generally representing less than 10% of the total commercial catch (landings and discards) between 1989 and 1998. The percentage of discards increased sharply in 1999 to 65.5% and remained between 20 and 30% between 2000 and 2003. Since 2004, discards have accounted for 7.1 -13.0% of the total commercial catch.

The fraction of the total landings (commercial and recreational) taken by the recreational sector (retained cod) has ranged from 5.5 to 39.6% since 1981 (Table 10, Figure 7). The proportion taken by the recreational sector fluctuated between 11.3% and 20% between 1981 and 1989, then remained relatively low, ranging from 5% to 15% between 1990 and 1998. Recreational landings equaled or exceeded 30% of the combined landings between 1999 and 2004, but declined somewhat in 2006 and 2007.
Total Catch Age Composition
Estimates of the age composition of total cod catch (Table 11a) were derived by combining the separate age composition estimates obtained for the commercial landings (Table 5a) and discards (Table 7) and recreational landings (Table 9a). Given the general similarities between the age compositions estimated for the commercial and recreational sectors, the total age composition reflects the same dominant year classes and age structure over time. The total catch at age in numbers was dominated by age 3 and 4 fish through 2001, with ages 4-6 predominating during the past 6 years (Table 11a, Figure 8) and the total catch at age in weight is dominated by ages 3, 4, and 5 (Table 11a, Figure 9). Representation of age 2 cod was relatively high in the early 1980s but age 2 fish have gradually all but disappeared from the total catch. The 1987 year class dominated the total catch in 1990, 1991 and 1992 and the 1992 year class can also be tracked between 1995 and 1999. The 1998 year class dominated the period between 2001 and 2003, while the above average 2003 year class predominated in 2007. When viewed over time, the age composition of the total catch (Figure 8 and Figure 9) displays a strong contraction and subsequent expansion of the age range. The maximum age seen in the catch was reduced to ages 7 or 8 during the mid-to-late 1990s. Since then, the age structure has begun to resemble the pattern of the early 1980s. In 2004-2006, the proportion of cod ages 8 and older was equal to or greater than that observed during 1982-1984.
Total Catch Mean Weights at Age
Estimates of the mean length and weight at age of the total cod catch (Table 11b, Figure 10) were derived as an average of the separate mean weights at age of the commercial (Table 5b and Table 7) and recreational sectors (Table 9b) weighted by the corresponding numbers at age (Tables 5a, 7 and 9a). Mean lengths and weights at age of cod taken by the combined commercial and recreational sectors (Table 11b) are intermediate to those obtained from the individual sectors. Mean weights at age are highly variable for the older ages due to the relatively low sampling of fish at the larger sizes

Mean weights at age for the total catch show persistent increases over time at ages 2 and 3, a moderate increase at age 4, no apparent trend at age 5, a moderate decline at age 6, and persistent declines at ages 7 and older (Table 11b, Figure 10). The increase in mean weights at the younger ages primarily reflects the trends in the recreational landings. Ages that constitute the majority of the catch (ages 3, 4 and 5) show only minor trends in mean weight over time. The declines at the older ages may reflect changes in the spatial distribution pattern and/or selectivity of the fishery.
Stock Mean Weights at Age
Mean weights at age used in the estimation of spawning stock biomass and January 1 biomass were derived from the total catch mean weights at age using methods described by Rivard (1980, 1982). This method adjusts the catch mean weights at age, which are considered to represent mid-year mean weights, to the beginning of the year. The mean weights at the beginning of a given year for a specific age are calculated as the geometric mean of the mean weight of that age in the same year and of the previous age in the previous year. The marginal calculations for the initial and final years and ages are also described by Rivard (1980, 1982).

Trends in stock mean weights at age over time (Table 12, Figure 11) reflect the trends exhibited by the catch mean weights but with slightly less variability, likely due to the smoothing effect of the geometric mean calculations.

STOCK ABUNDANCE and BIOMASS INDICES

Commercial Catch Rates

Trends in commercial landings per unit effort (LPUE) and fishing effort for the period 1965-1993 and 1994-1996 were reported by Mayo (1998). The 1982-1993 age composition of the landings corresponding to the effort sub-fleet as presented by Mayo et al. (1994) was used with the standardized effort estimates through 1996 to calculate updated LPUE-at-age indices. Numbers landed at age were estimated by applying quarterly commercial age-length keys to quarterly commercial numbers landed at length by market category. The LPUE-at-age indices were derived by dividing the estimated numbers landed at age by corresponding 1982 through 1996 standardized fishing effort. Further details regarding data selection, preparation and estimation procedures are provided in Mayo et al. (1994).

Given the uncertainty in reported fishing effort since 1994, LPUE data after 1993 were not formally included in the VPA conducted in 1998 (NEFSC 1998; Mayo et al.1998). Recent management actions, including imposition of trip limits and rolling closures, continue to make interpretation of 1994-2007 LPUE inconsistent with previous years.

Research Vessel Surveys

Background

The Northeast Fisheries Science Center (NEFSC) has conducted research vessel bottom trawl surveys in offshore waters (> 27 m) off the northeast coast of the United States since 1963 (autumn) and 1968 (spring). Inshore areas of the Gulf of Maine (< 27 m) have also been sampled during spring and autumn since 1978. Gear and door changes have occurred during the survey period. Details on the NEFSC survey sampling design and procedures are provided in Azarovitz (1981) and Clark (1981). The Commonwealth of Massachusetts Division of Marine Fisheries (MADMF) has conducted research vessel bottom trawl surveys during spring and autumn primarily in state waters in the southwest portion of the Gulf of Maine since 1978. These surveys are conducted in relatively shallow water and, as such do not provide an abundance index of the stock as a whole. However they do provide an abundance index of recruiting year classes. The MADMF inshore bottom trawl sampling program is described in Howe et al. (1981).

The NOAA research vessels Albatross IV and Delaware II have been used exclusively during the NEFSC surveys. For the NEFSC surveys, a "36 Yankee" trawl has been the standard sampling gear except during spring 1973-1981 when a modified "41 Yankee" trawl was used. Prior to 1985, BMV oval doors (550 kg) were used in all NEFSC surveys; since 1985, Portuguese polyvalent doors (450 kg) have been used. No adjustments in the survey catch-per-tow data for cod have been made for any of the trawl differences, but vessel and door coefficients have been applied to adjust the stratified means (number and weight per tow) as described in Table 13.

Indices of cod abundance (stratified mean catch per tow in numbers) and biomass (stratified mean weight per tow in kilograms) developed from the NEFSC and MADMF trawl survey data, have been used to monitor changes and assess trends in population size and recruitment of cod populations off New England. Standardized stratified mean catch-per-tow-at-age (number) indices from NEFSC spring and autumn surveys are listed in Appendix B: Tables 1 and 2, and catch-per-tow-at-age indices from MADMF spring and autumn surveys are listed in Appendix B: Tables 3 and 4. The entire series of NEFSC spring and autumn abundance and biomass indices was re-estimated for the 2005 assessment (Mayo and Col 2006) to better account for vessel effects between RV Albatross IV and RV Delaware II. Although the only major difference during the 1982-2007 assessment period occurred in 1987, minor changes to the indices occurred in most years. In the present assessment, the MADMF survey indices were recalculated over the entire time period beginning in 1978 to account for minor changes to the strata boundaries. Therefore, the indices listed in Table 13, Table 14, and Appendix B: Tables 1, 2, 3 and 4 may differ slightly from those provided in previous assessments.
Trends in Relative Abundance and Biomass
NEFSC spring and autumn offshore stratified mean catch per tow indices for Gulf of Maine cod have generally exhibited similar trends throughout the survey time series (Table 13, Figure 12). Biomass indices declined during the mid- and late 1960s, but between 1972 and 1985 they fluctuated as a result of a series of recruitment pulses. Biomass declined again between the mid-1980s and early 1990s, and then remained relatively low throughout the 1990s. Both spring and autumn indices began to show modest increases after 2000 but the large value in autumn 2002 is the result of a single very large tow that unduly influenced the calculation of the mean. Although the autumn biomass indices have returned to the relatively low levels of the 1990s, the spring indices have shown some increases in 2007 and 2008 (Table 13, Figure 12).

Spring NEFSC number-per-tow indices have remained relatively low since 1985, below the 1981-1984 average (Table 13), but the index increased temporarily in 1988 due to a large contribution from the 1987 year class (Appendix B: Table 1). The index declined thereafter and fluctuated until 2002 and 2003 based in part on contributions from the 1998 year class. The sharp increases in 2007 and 2008 reflect the appearance of the large 2003 and 2005 year classes (Appendix B: Table 1, Figure 13).

Sharp increases in the autumn number per tow indices reflect above-average recruitment of the 1971, 1973, 1977-1980, and 1985-1987 year classes at ages 1 and 2 (Appendix B: Table 2, Figure 14). The sequential dominance of these cohorts at older ages is evident from number-per-tow-at-age values in both spring and autumn NEFSC surveys (Appendix B: Tables 1 and 2). Increases in the autumn 1994-1995 and spring 1996-1997 biomass indices may be attributed to somatic growth of fish from the 1992 year class which was the largest within a series of poor year classes. The 1998 year class is equivalent to the 1992 year class, and the 2003 and 2005 year classes appear to be the strongest since the 1987 year class.

Overall, the 1987 year class appears to have been one of the strongest ever produced; catch-per-tow indices for this cohort at ages 1-3 in the NEFSC autumn surveys (Appendix B: Table 2) and at ages 0 and 1 in the MADMF autumn inshore surveys (Appendix B: Table 3) were nearly all high values. Based on MADMF and NEFSC survey catch per tow indices, the 1992, 1998, 2003 and 2005 year classes of Gulf of Maine cod appear to be moderate to large, and the intervening year classes, particularly the 1993, 1994, 1995, 1997, 1999 and 2000 year classes, have been well below average (Figure 13 and Figure 14).
Maturity at Age Estimates
Observations of external gonadal characteristics, classified according to the maturity stages described by Burnett et al. (1989) and recorded during NEFSC spring bottom trawl surveys, were also analyzed in order to construct a series of maturity at age moving window ogives over the assessment time period using probit analysis. A series of annual 3-year moving windows was employed in order to achieve a smooth transition across years. O’Brien et al. (2008) developed the following procedure for deriving the annual moving window ogives. To calculate an ogive for year t, the data for year t-1 and year t+1 were combined with the data for year t in order to estimate a single ogive for year t. Ogives for subsequent years were estimated in a similar manner by advancing the years by 1. Two years of data were used for the first year and 2008 was included in the last year of the time series (2007). Ninety-five percent confidence limits for proportion mature at age were estimated using the approximate variance for large samples (Ashton 1972, O’Brien et al. 1993). Inverse 95% confidence limits for A₅₀ (median age at maturity) were estimated within the SAS PROBIT procedure. This was accomplished to provide a smoother transition in the maturity schedule used to determine spawning stock biomass. Annual female maturity ogives are presented in Table 15, and trends in female and male A50 with 95% confidence limits are illustrated in Figure 15.

The maturity ogives reveal two cycles where full maturation occurs as early as age 4 alternating with two cycles where full maturation is delayed to ages 5 or 6. Earliest maturation occurred during the mid -1980s and mid -1990s whereas delayed maturation occurred during the early 1980s and early 1990s and since 2000. Trends in A50 for both females and males (Figure 15) are consistent with the changes in the maturity ogives with the lowest values occurring during the mid -1980s and mid -1990s.
Total Mortality Estimates
In recent assessments (e.g., Mayo and Col 2006) instantaneous total mortality (Z) estimates were calculated annually. Total mortality was calculated from NEFSC survey mean number per tow at age data (Appendix B: Tables 1 and 2) by the log_e ratio of the pooled age 3+/age 4+ indices in the autumn surveys, and the pooled age 4+/age 5+ indices in the spring surveys. For example, the 1983 estimates were derived from:

Spring:   ln ( E ages 4+ for 1983/ E ages 5+ for 1984)
Autumn:ln ( E ages 3+ for 1982/ E ages 4+ for 1983)

Different age groups were used in the spring and autumn analyses so that Z could be evaluated over the same year classes within each year. Given recent increases in codend mesh sizes, the ages were increased by one year so that total mortality is calculated for the pooled age 4+/age 5+ indices in the autumn surveys, and the pooled age 5+/age 6+ indices in the spring surveys. In this example, the 1983 estimates were derived from:

Spring:   ln ( E ages 5+ for 1983/ E ages 6+ for 1984)
Autumn:ln ( E ages 4+ for 1982/ E ages 5+ for 1983)

Values of Z derived from the spring surveys are generally comparable to those calculated from the autumn data (Figure 16). These values of Z exhibit considerable inter-annual variability due primarily to year effects in the surveys. When smoothed with a 3-year moving average, however, the annual estimates suggest a pattern of increasing mortality during the1980s, with total mortality remaining in the range of 1-1.5 from the mid-1980s through the mid 1990s, depending on the age ranges used in the calculations. Total mortality declined during the late 1990s, but the most recent estimates suggest an increase.

ESTIMATION of FISHING MORTALITY RATES and STOCK SIZE

Natural Mortality

Instantaneous natural mortality (M) for Gulf of Maine cod is assumed to be 0.20, the conventional value of M used for all Northwest Atlantic cod stocks (Paloheimo and Koehler 1968, Pinhorn 1975, Minet 1978).

Assessment

Input Data and Model Formulation

The present assessment represents more than a three-year update to the previous assessment (Mayo and Col 2006). As noted above, each component of the total catch at age has changed since the 2005 GARMII assessment. This required re-estimation of the landings at age from 1994 to present, the recreational landings at age from 1981 to present and the observer based discards at age since 1989.

The VPA formulation used in the previous assessment was evaluated and, based on an observed shift in the age of full recruitment from age 4 to age 5, the age 7 plus group formulation was discontinued in favor of an extended age range out to age 11+. This effectively reverses the decision reported by Mayo (1995) to restrict the age range to ages 7+ due to high coefficients of variation (CV) on the terminal year stock size estimates and variable estimates of F on ages 7-9 in most years prior to the terminal year.

Catch at age data were revised or updated over the 1982 to 2007 assessment time period to account for the data changes described above. NEFSC survey abundance indices (stratified mean number per tow at age) were updated through spring 2008. The MADMF spring and autumn survey indices were recalculated over the entire period since 1978 due to slight changes in the strata boundaries that affected the stratified mean calculations. Differences were minor in most cases.
Virtual Population Analysis Calibration
The ADAPT calibration method (Parrack 1986, Gavaris 1988, Conser and Powers 1990) was used to derive estimates of terminal fishing mortality (F) in 2007 and stock sizes in 2008. The formulation in the present assessment is: catch at age from 1982-2007 out to age 11+, estimation of age 2-10 stock sizes in terminal year+1. Calibration included NEFSC spring and autumn age 2-8 indices, and MADMF spring age 2-4 and autumn age 2 indices. The NEFSC and MADMF autumn indices were lagged forward by one age and one year whereby age 1-7 indices were related to age 2-8 stock sizes in the subsequent year for corresponding cohorts. All NEFSC and MADMF indices were related to January 1 stock sizes, and USA commercial LPUE indices were related to mid-year stock sizes. As in recent assessments (e.g., Mayo and Col 2006), commercial LPUE indices, derived from the catch at age corresponding to the effort sub-fleet used in the estimation of standardized fishing effort as described by Mayo et al. (1994), were included only through 1993. This change effectively removed the influence of the LPUE indices on the terminal year outcome of the calibration, while preserving the historic relationship employed in previous assessments.

This formulation provided direct stock size estimates for ages 2 through 10 in 2008 and estimates of F for corresponding cohorts on ages 1 through 9 in 2007. Since the age at full recruitment was defined as 5 years in the input partial recruitment vector, the terminal year F on age 10 was estimated as the mean of the age 5 through 9 Fs; age 10 is also the oldest true age in the terminal year. In all years prior to the terminal year, F on the oldest true age (age 10) was determined from weighted estimates (by age group abundance, in numbers) of Z for ages 5 through 9. In all years, the age 10 F was applied to the age 11+ group. Spawning stock biomass (SSB) was calculated at spawning time (March 1) by applying a series of annual maturity ogives calculated on a 3 – year moving average basis as presented in Table 15. Because there is a moderate dome in the partial recruitment beginning at age 8, the average fully recruited F in each year is calculated as the unweighted average of the Fs on ages 5 through 7.

Precision and bias of the 2008 stock size estimates and 2007 spawning stock biomass and fishing mortality estimates was calculated from 1,000 bootstrap replicates (Efron 1982) of the VPA. Retrospective analyses of terminal year estimates of stock sizes, fully recruited fishing mortality and SSB were also carried out. Residuals of the observed and predicted indices derived from VPA calibration are also provided.

This formulation of the present assessment addresses the recommendations of the GARMIII Model Selection Panel and the GARMIII Biological Reference Point Panel, and was accepted by the GARMIII Assessment Review Panel (NEFSC 2008) as the final assessment.
Virtual Population Analysis Results
Fully recruited fishing mortality (unweighted average of ages 5-7) is estimated at 0.46 in 2007, a moderate decrease since 2004 and 2005 (Table 17; Figure 17). The 2004 year class is estimated to be equivalent to the 1998 year class (approximately 7-8 million fish), the 2003 year class (11 million fish) is about twice the long term average and the 2005 year class (24 million fish) is equivalent to the strong 1987 year class (Table 16a, Figure 18). The 2000 year class (1.2 million fish) is by far the weakest in the entire VPA series and the 2002 year class (1.7 million fish) is the second weakest.

Spawning stock biomass increased to 18,000 mt in 2001, but declined to 11,000 mt in 2005 as a result of the above average 1998 year class being removed from the population, followed by subsequent poor recruiting year classes of 2000 and 2002 (Tables 16a and 16c; Figure 18).   Spawning stock biomass increased substantially to 19,000 mt in 2006 on the strength of the 2003 year class becoming partially mature, and further to 34,000 mt in 2007 on the combined strength of the 2003 year class (95% mature) and the partially mature 2005 year class (34% mature). A complete listing of the final ADAPT VPA results, and bootstrap and retrospective analyses is given in Appendix C, and key results, including age-specific estimates of stock size, instantaneous fishing mortality (F), and spawning stock biomass, are presented in Table 16. Annual estimates of fully recruited (ages 5-7) average fishing mortality are also given in Table 17.
VPA Diagnostics and Uncertainty
Extension of the age range out to 11+ resulted in a partial recruitment pattern that peaked at ages 5-7, followed by a reduction at ages 8 and 9 to about 70-80 percent of the maximum. Estimates of F at ages 8 and 9 were highly variable, however, especially during the 1990s. The calculation of F on the oldest true age (age 10) was evaluated over a range of ages ranging from ages 5-6 to ages 5-9. There were only minor differences in the estimates of F on age 10, no discernable differences in the age 5-7 average F estimates, and no appreciable differences in the estimates of SSB over time. An additional trial using ages 8 and 9 to estimate F on age 10 produced similar trends in SSB but highly variable estimates of F on age 10. Taking account of these results we elected to include as many ages as possible (ages 5-9) to calculate F on age 10. Further details and graphics of this analysis can be found in Appendix D.

The 2008 NLLS stock size estimates were relatively precise for ages less than 8, with Coefficients of Variation (CVs) on these ages ranging from 26% (ages 4 and 5) to 44% (ages 2 and 7) (Table 18). However the CVs on ages 8-10 were considerably higher, ranging from 55% (age 8) to 72% (age 10). The bootstrapped estimates of bias were relatively low for intermediate ages ranging from 3% (ages 4 and 5) to 6-7% (ages 3, 6 and 7). Bias was higher on other ages, ranging from 13% on age 8 to about 21% on ages 2, 9 and 10 (Table 19a). Coefficients of Variation on the NEFSC survey Qs varied between 10% and 17% for ages 2-6, increasing to between 20% and 28% on ages 7 and 8. The CVs on the MADMF spring survey Qs ranged from 9% to15% while the Q on the MADMF autumn survey was estimated to be about 30% (Table 18).

An analysis was also carried out to determine the magnitude and trends in survey Qs by raising the Qs estimated by the VPA using survey swept area calculations. For Gulf of Maine cod, these raised values of Q ranged from about 10% at age 2, increasing to about 50-60% at age 5, and leveling off at about 70-90% at ages 7-8. Further details and graphics of this analysis can be found in Appendix E.

Residual patterns from the NEFSC and MADMF survey data used to calibrate the VPA appear for the most part random, although there are some instances of 3 to 4 year blocks of positive and negative residuals (Figure 19).
Precision of 2007 F and SSB Estimates
The bootstrap procedure was also used to evaluate the precision of age-aggregated terminal year estimates, by generating 1000 estimates of the 2007 fully recruited fishing mortality rate and spawning stock biomass.   Summary statistics for these bootstrap analyses are provided in Table 19b and Appendix B, and the distributions of the bootstrap estimates and the corresponding cumulative probability curves are shown in Figure 20 and Figure 21. The cumulative probability expresses the likelihood that the fishing mortality rate was greater than a given level (Figure 20) or the likelihood that spawning stock biomass was less than a given level (Figure 21), when measurement error is considered.

The bootstrap analysis (Table 19b) provides an 80% CI about the 2007 fully recruited F estimate (0.46) of 0.36 – 0.67 (Figure 20) and an 80% CI about the 2007 SSB estimate (33,877 mt) of 29,133 mt – 41,747 mt (Figure 21). The average fully-recruited fishing mortality in 2007 for ages 5-7 was reasonably well estimated (CV = 0.27) and the mean bootstrap estimate of F (0.50) was slightly higher than the point estimate (0.46) from the NLLS solution. Spawning stock biomass in 2007 was also reasonably well estimated (CV = 0.14) and the mean bootstrap estimate of SSB (35,356 mt) was slightly higher than the point estimate (33,877 mt) from the NLLS solution.
Retrospective Analyses of Terminal Year Estimates of F, SSB and Recruitment
A weak retrospective pattern is evident in the estimates of the terminal year F whereby fully recruited F alternates between over- and under-estimation (Figure 22). The same pattern is evident for SSB (Figure 23). A retrospective pattern is also evident for age 1 recruitment estimates whereby recruitment was well overestimated for the 2001 and 2003 year classes (Figure 24). The estimate of the size of the 2005 year class appears to not suffer the same fate, as it is supported by an additional year of data in the present assessment (Figure 24). The degree of retrospective change in the estimates of average F (ages 5-7), SSB and age 1 recruitment was computed by calculating a Mohn’s average rho (Mohn 1999) based on the relative difference between terminal year estimates over the last 7 years of the assessment (2000 – 2006). The relative differences are as follows:

The relative differences are mostly positive during these years, although some negative values appear in each of the retrospective analyses. These results suggest a 16% positive relative difference for average F, a 19% positive difference for SSB, and a 71% positive relative difference for age 1 recruitment. The latter result is driven by very high values in 2002 and 2003. A complete listing of the retrospective analyses is given in Appendix B.
Spawning Stock and Recruitment
The relationship between spawning stock biomass and recruitment for Gulf of Maine cod was examined from two perspectives. First, a traditional spawning stock-recruitment scatterplot (Figure 25) was constructed over the period covering the 1981-2006 year classes. In addition, a survival ratio, expressed as age 1 recruits per unit of SSB (R/SSB) was also calculated for each year class (Figure 26). The two most prominent features in these graphs are the large 1987 (middle) and 2005 (left) year classes, each at over 20 million fish, produced by low to moderate spawning stock

Survival ratios of pre-recruits up to age 1 are highest for the 1987, 1992, 1998, 2003 and 2005 year classes. The 1987 and 2003 year classes were produced by about average SSB, and the 1998, 2003 and 2005 year class from relatively low SSB. Survival ratios were generally higher during the early-to-mid 1980s prior to the emergence of the large 1987 year class. Survival declined after the 1992 year class appeared, but increased in 1996, 1997 and 1998, declined thereafter and increased again with the appearance of the 2003 and 2005 year classes.

BIOLOGICAL REFERENCE POINTS
The following biological reference points first developed by the Working Group on Re-Evaluation of Biological Reference Points for New England Groundfish (NEFSC 2002a) have existed since 2002:

F_msy         0.225
SSB_msy82,830 mt
MSY       16,600 mt

Two approaches for estimating biological reference points have been evaluated for this stock. The existing reference points are based on a parametric approach whereby spawning biomass and age 1 recruitment results obtained from the VPA were included in a model (SRFIT) that also included life history and fishery parameters using the Sissenwine-Shepherd approach (see Brodziak and Legault 2005). This approach was employed by the Working Group on Re-Evaluation of Biological Reference Points for New England Groundfish (NEFSC 2002a). The GARMIII Biological Reference Point Panel recommended against this approach in favor of a non-parametric approach in order to provide consistency between reference point estimation and projection methodology.

Non-Parametric Approach

Yield and Spawning Stock Biomass per Recruit Analysis

In the non-parametric empirical approach, a yield and SSB per recruit analysis (Thompson and Bell 1934, Gabriel et al. 1989) was first conducted using catch and stock mean weights at age and maturity at age averaged over the 2003-2007 time period. Partial recruitment at age was derived from the average of the 2003-2007 time period Fs from the VPA results as:

Age 1: 0.0000, Age 2: 0.0021, Age 3: 0.1618, Age 4: 0.6821, Age 5: 0.9004,
Age 6: 1.0000, Age 7: 0.8260, Age 8: 0.7326, Age 9: 0.7705, Ages 10 and 11+: 0.7530.

Yield and SSB per recruit input and results are given in Table 20 and are illustrated in Figure 27. A proxy for F_msytaken from this analysis is F40% MSP = 0.237.
Stochastic Equilibrium Projections of MSY and SSB_msy
A stochastic projection program (AGEPRO, Brodziak et al. 1998) was then used to project 100 year scenarios to obtain equilibrium SSB_msy and MSY estimates. The initial conditions of 2008 stock sizes were based on the 1,000 bootstrap iterations performed by the VPA. Recruitment was derived by resampling the cumulative distribution function of age 1 cod from the 1981-2005 year classes estimated by the current VPA. Catch and stock mean weights at age, maturity at age and partial recruitment averaged over the 2003-2007 time period were the same as used in the yield and SSB per recruit analyses above. A constant F strategy was employed setting F at the F_msy proxy F40% MSP (0.237) obtained from the SSB per recruit analysis. Results from this approach provide the following estimates:

F_msy          0.237
SSB_msy   58,248 mt
MSY       10,014 mt

CONCLUSIONS
Gulf of Maine cod spawning stock biomass has increased from 10,974 mt in 2005 to 33,877 mt in 2007. Although the stock remains low relative to SSB_msy (58,248 mt), spawning stock biomass was above the ½ SSB_msy threshold in 2007. Fully recruited fishing mortality declined to about 0.46 in 2007, indicating that F continues to remain very high relative to fully recruited F reference points (F_40%F_msy proxy = 0.237). Thus, the stock is not overfished but overfishing continues to occur.

The 1987and 2005 year classes are the strongest in the VPA assessment period (1982-2007). The 1992, 1998, 2001 and 2003 cohorts have been above average and the 1993-1995, 1999-2000 and 2002 year classes are among the poorest in the VPA time series. Survival ratios (R/SSB) declined after 1998 but survival increased substantially with the appearance of the strong 2003 and 2005 year classes.

A retrospective pattern has existed in the VPA results for this stock, but the pattern has reversed several times over the past decade. At present, it appears that there is a slight tendency to over-estimate fully recruited F and spawning stock biomass in the terminal year and to over-estimate the magnitude of large incoming year classes in some years.

ACKNOWLEDGEMENTS
We are indebted to the Groundfish Assessment Review Meeting (GARM III) participants who provided a thorough, constructive review of this assessment. This assessment could not have been completed without the dedication of the age and growth staff in the Fishery Biology Program, the Fishery Independent Surveys Group staff, the Northeast Fishery Observer Program staff and the Data Management Systems staff.

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