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Stock assessment of yellowfin tuna in the Indian Ocean using MULTIFAN-CL (IOTC-2011-WPTT13-36). Adam Langley, Miguel Herrera and Julien Million. Introduction. Preliminary assessment using MFCL in 2008; refined during WPTT 10.

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Stock assessment of yellowfin tuna in the Indian Ocean using MULTIFAN-CL (IOTC-2011-WPTT13-36).

Adam Langley, Miguel Herrera and Julien Million



  • Preliminary assessment using MFCL in 2008; refined during WPTT 10.
  • Assessment updated and revised during WPTT-11 and WPTT-12 (2009 & 2010).
  • Starting point for WPTT-13 assessment.

MFCL model dynamics

  • Regional structure. Spatially disaggregated, age structure population model.
  • Model fitting to catch, size data (length freq), and tag release/recovery data.
  • Fishery data (catch, effort, lf) by time step.
  • Movement between regions (can be age specific).
  • Tag dynamic similar to overall population dynamics. Reporting rates, mixing phase.

WPTT-12 assessment

  • Commence model 1972.
  • Fixed growth (Fonteneau 2008).
  • Longline selectivity cubic spline.
  • Down-wt LF data (Sample size 10).
  • PS 2 fisheries: three time blocks. Different selectivity.
  • Low age-specific natural mortality (M).
  • SSR steepness options 0.60, 0.70, 0.80, 0.90.
  • Additional spatial aggregated model (one-region).

WPTT-13 revisions

  • Additional year of data – all fisheries.
  • LL CPUE indices: JP updated (CPUE2010) and alternative indices with lat*long (R2-5); revised TW indices (R1).
  • Revised catch data. Major revision to TR 5 and OT 5 catch history.
  • Segregated distant-water (LL 5) and fresh tuna longline fleets (LF 5) in R5. 25 fisheries.
  • Range of steepness values (consistent with BET) 0.55,0.65,0.75,0.85, 0.95.
  • Single region, region 2 models.

Spatial stratification

Relatively homogeneous areas wrt species population dynamics (size, fishing mortality, fishery distribution).

Consistent with spatial distribution of tag releases.


Catch distribution

Most of catch within regions 1, 2 and 5. PS and GN dominate total catch.

Purse-seine catch largely restricted to region 2. Gillnet R1 and R5. Handline R1.

LL fresh R5.

High catches 2004/2005. PS free schools sets. Log sets dominate last few yrs.

2010 catch 294,000 t.


Model structure

  • 5 regions. 28 age classes. 1972-2010.
  • LL CPUE index (1972 onwards) – shared (constant) catchability and selectivity among regions (LL 1-5).
  • Age-specific natural mortality (fixed).
  • Growth (fixed).
  • Common biol pars for male and female.
  • Movement dynamics (estimated).
  • Recruitment: overall regional proportion, temporal trend, regional deviates.
  • SRR steepness fixed (0.55,0.65, 0.75, 0.85,0.95).

Key inputs – biol. parameters

M-at-age fixed.

Growth parameters.

Maturity at age.

Fonteneau & Hallier (IOTC-2010-WPTT-27).



Fonteneau 2008

Variation of length at age.


Key inputs – catch data

Catch data complete to 2010.

Expressed in tonnage for all fisheries, except LL.

Recent drop in LL2 catch. Drop in LL 4 and 5 catches.

High PS FS 2 catch in 2004/05.

Increasing TR, GI, HD catches.


Key inputs – effort data

CPUE plotted for each fishery.

Effort data not available for several fisheries (“missing”).

Standardised CPUE indices for JP LL fleet (in regions 2-5). TW CPUE index in region 1.

PS effort not separated by set type. Effort data for many fisheries considered unreliable.


Key inputs – LL CPUE

GLM standardised CPUE index of JP and TW LL data. JP indices incl. lat*long.

Regional scaling (0.21, 1.00, 0.55, 0.15, and 0.85).

Standardised effort series (effort = catch/CPUE).

Sharp decline in LL2 from 2005. Steady decline in LL5.

LL IO for single region model.


Key inputs – size data

Length frequency data from most of the key fisheries.

No/limited data for some minor fisheries.

Effective sample size 10 (n = 1000/100.


Key inputs – size data

LL2 length data, recent period.

Contraction of the LF distribution.

Uncertainty in the comparability of data over entire time period.


Key inputs – tag data

Tag release/recoveries IO RT.

54,393 releases, 9961 recoveries (corrected). Not including recent small scale tag releases.

Reporting rate information for PS fishery from tag seeding. Used to correct recoveries.

Overall RR for PS fishery fixed at 0.81 (retention 90%, PS catch sampled = Seychelles landings 90%).

PS recoveries aggregated within region.


Key inputs – tag data

Tag recoveries by release/recovery region.

Mostly within region 2.

Some movement of tags

1 > 2, 2 > 1, 2 > 5

(3 > 2, 2 > 3)


Model runs

  • Approximate final 2010 model (WPTT 12) (CPUE2010).
  • New JP CPUE indices (CPUElatlong) (BASE).
  • New LL R5 structure and new JP CPUE indices (newLL).
  • Single region model (IOregion).
  • Region 2 model (region2).
  • 5 values of steepness.
  • Sensitivity. Tag mixing period (1-4 Q).

Model diagnostics - catch

Good fit to the catch data for all fisheries.

High catch penalty.


Model diagnostics – CPUE indices

Effort deviates.

Principal LL fisheries – no strong trend in edevs with the exception of LL1.

High penalty assoc with LL edevs (cv 10%).


Model diagnostics – CPUE indices

Principal LL fisheries.

Good fit to CPUE data.

Strong recent decline in LL 2 CPUE.


Model diagnostics – size data

Selectivity functions (cubic spline ).

Shared between LL fisheries.

Shared between fisheries where size data not available.

PS 2 – temporal split esp. LS.


Model diagnostics – length data

Overall fit to the length data (aggregated over time).

Related to fixed-growth assumption?


Model diagnostics – length data

Overall fit to the length data (aggregated over time).


Model diagnostics – length data

Some lack of fit for some fishery/periods:

HD 1 recent Maldives data.

LL 2 and 5. Smaller fish in 1990s.


Model diagnostics – length data

Sampling error in some fisheries e.g. PS FS 3, TR 5.


Model diagnostics – tag data

Fixed tag reporting rate for PS fishery.

PS grouped for tag returns.

All other fisheries have uninformative priors on RR.

LL in R2 reporting rate about 15%.


Model diagnostics – tag data

Recoveries by period at liberty.

First 4 quarters not in LL (mixing period).

Reflects size of fish tagged, fishery selectivity, fishery RR.


Model diagnostics – tag data

Tag recoveries by fishery and by quarter.

Good fit to the PS tag recoveries, except for a couple of quarters.

Reasonable fit to some of the other main fisheries recovering tags (except OT2).


Improved fit with longer mixing rate (Q4).

Figure includes mixing period.


PS 2 fishery recoveries by age class.

Figure excludes mixing period.


Model pars/outputs – movement

Max. 12.8% per quarter, 4 > 5 in Q2.


Model pars/outputs – catchability

Constant LL catchability.

Dependent on effort data series.

Increasing PS q ??

Free temporal q for fisheries with missing effort.


Model pars/outputs – recruitment

R2 and R5 account for most of the recruitment.

Temporal trends in recruitment (initial and long-term).

Low recruitment in R2 during 2000s.

Recent recruitment 80% of long-term average.


Model pars/outputs – biomass

Total and adult biomass.

R2 and R5 (and 3) account for most of the biomass.


Model pars/outputs – biomass

Comparison of runs REGION2.


Comparison with 2010

Differences in LL CPUE data set, LL5 fishery configuration and catch history for some key fisheries.

Reconciliation of differences.


Comparison with 2010


2010 tag, LL CPUE 2010 approach, old LL 5 fishery, new catch/effort.


2010 fishery catch/effort, 2010 year.


Ex 2010 year


Model pars/outputs – fishing mortality

F for the “current” (2006-2009) period.

F highest in R1, R2 and R5.


Model pars/outputs – fishery impact

Main fishery impact occurring within R1, 2 and 5.

Fishery impact lower in region 4.

Overall, 45% reduction in biomass.


Stock Status - SRR

Fixed steepness = 0.75 (intermediate value from range).

Uninformative about appropriate value for steepness.


Stock Status – equilibrium conditions

Fcurrent = F2006-2009

Steepness = 0.75

Fmult = 1.37

Ycurrent = 364,000 mt

Beq = 0.462 * B0

BMSY = 0.315 * B0



F/Fmsy = 0.73; B/Bmsy = 1.41; SB/SBmsy = 1.54

F2009/Fmsy = 0.79; B2009/Bmsy = 1.17; SB2009/SBmsy = 1.21


Stock Status – reference points

Based on current (2006-2009) conditions.

2009 and 2010 progressively more pessimistic.

Total catches in 2010 about 294,000 mt.

Lower recent recruitment.


Other model options

  • Higher/lower values of steepness; more/less optimistic stock status; higher/lower yields.
  • New LL5 fishery config slightly less optimistic.
  • New CPUE (lat*long) slightly more optimistic than old LL CPUE approach.
  • Region 2 stock status comparable to 5-region base case.
  • Single region IO model considerably more pessimistic.

5 Region

Single region


Comparison with 2010

Convergence problems with 2010 final model – local minima.

Differences in the selectivity of PS LS 2 fishery resulting in differences in F-at-age.

Degree of confounding between R0 and PS LS selectivity parameters.

Inclusion of 2010 data influential resulting in higher Fmult and MSY.

Differences in selectivity for PS FS 2 (2007-2010) and TR fisheries.


Stock status

  • Five values of steepness – stock status varies accordingly.
  • Stock status sensitive to regional structure.
  • Five region. F (2006-09) less than FMSY. B and SB (2006-09) well above BMSY and SBMSY. MSY 350-450 K mt.
  • Single region. F (2006-09) exceeds FMSY. B and SB (2006-09) approaching BMSY and SBMSY. MSY 250-350 k mt.
  • Current equilibrium yields comparable to MSY.
  • Stock status in 2009 and 2010 considerably more pessimistic than 2006-09 average.

Preliminary conclusions 1

  • Update and refinement of 2010 MFCL assessment. Complex model (spatial structure, fisheries).
  • Trends in SA model driven by CPUE indices (esp R2, 3, 5). Temporal trends in recruitment.
  • Fishing mortality at an historically high level.
  • Recent recruitment (last 10 years) lower (70%) than long term average.
  • High fishery impacts in most regions. Overall impact reducing biomass by 45%.

Preliminary conclusions 2

  • BRPs sensitive to SRR and conclusions on (MSY based) stock status dependent on steepness assumption and regional structure.
  • Stock biomass above or approaching BMSY (all options).
  • Exploitation rates above or below FMSY depending on regional structure.
  • Current catches at lower range of MSY estimates.
  • MSY dependent on equilibrium recruitment (recent low recruitment).
  • Management advice (projections, etc).

Keyissues 1

  • Longline CPUE indices, including temporal trends in LL catchability.
  • Spatial structure.
  • Reliability of most recent data (2010 year).
  • Growth (sex specific?), maturity, natural mortality.
  • SRR steepness (meta analysis).
  • Size data lacking for some important fisheries. Representativeness of size data.
  • LL length data; smaller fish 1990s.
  • LL selectivity – logistic, cubic spline.

Keyissues 2

  • Time blocks for PS 2 fisheries (pre 2003, 2003-06, post 2007). Later period sensitive to most recent data.
  • Possible temporal trends in selectivity for key fisheries.
  • Definition of effort. Limited effort data for many fisheries.
  • Express uncertainty of current stock status (probability surface on Kobe plot).

Stock projections

  • Kobe 2 strategy matrix.
  • The K2SM summarises potential management actions, for example TAC and time-area closures, that correspond to specific probabilities of reducing over fishing or rebuilding the stock within specific timeframes.


  • Deterministic or stochastic.
  • Uncertainty. MFCL recruitment only (other sources of uncertainty – numbers at age in terminal year, effort devs).
  • WCPFC advice.
  • Define base-line catch/effort for each fishery.
  • Recruitment – SRR, recent period.
  • Projection period.
  • Define probabilities.
  • Define period for defining MSY.