CPUE time series for Atlantic blue and white marlin are believed to be compromised by changes in fishing tactics by the Japanese longline fleet that cannot be completely removed by standardization methods. The highest catches for both species come from the early part of the Japanese longline fishery, before it shifted from shallow to deep sets. The consequences of limiting analyses to the most recent period were evaluated with simulated fisheries data generated by a computer program constructed around life history characteristics of Atlantic blue marlin. The population simulation generated sample time series of simulated catches and population abundance histories using several alternative assumptions about natural and fishing mortalities, stock-recruitment slopes, and measurement error. Within this framework the highest simulated catches came from the early part of the fishery and the trend in CPUE was constrained to approximate observed 1986-2005 CPUE trends. The resulting time series of simulated catches and abundances were fitted to a logistic surplus-production model with the full time series (1956-2005), the last 20 years, and the last 16 years. Overall, truncation of the 1956-2005 time series to only include the last 16 years of data resulted in MSY being overestimated by more than 50%, and the ratios of final-year stock biomass to biomass at MSY being overestimated by over 100%. However, the results varied substantially among the assumed population parameters and further research is indicated.
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