Computational protocol: Yolked Oocyte Dynamics Support Agreement between Determinate- and Indeterminate-Method Estimates of Annual Fecundity for a Northeastern United States Population of American Shad

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Protocol publication

[…] A determinate-method PAF was estimated by counting the standing crop of the advanced cohort of oocytes. Based on the examination of whole oocytes (see ), this advanced cohort was defined as transitional and secondary oocytes (C1, C2, V1, V2, NM1; ). These fish were classified macroscopically as developing (Class A), and presence of these oocyte stages, and not more advanced stages, was confirmed by examining gonad histology. Samples without POFs were categorized as pre-spawning and those with POFs were categorized as spawning females.Determinate PAF was estimated for 45 pre-spawning females: 25 collected in the lower river by gillnet (4/30–5/6) and 20 collected early in the run at Hadley Falls (5/12). Annual fecundity was also estimated from 21 spawning females: 11 collected early in the run at Hadley Falls and Cabot Power Stations (5/12–5/13), and 10 collected at Hadley Falls and Vernon Power Stations one week later (5/19–5/20). Estimates of PAF from pre-spawning and spawning females were compared with analysis of covariance (ANCOVA) to confirm that the standing crop of oocytes declined with spawning, which would be predicted if fecundity was determinate at the beginning of the spawning run. All fish ranged in size from 396 to 528 mm LF (1023.8g–2011.3 g MT), with IG between 8.5 and 22.6.Determinate PAF was estimated gravimetrically (PAF = [CS / MS] * MO), excising one subsample of tissue (0.1975–0.5564 g [MS]), which produced cell counts between 138 and 532 (CS). A macro (ImageJ software: v1.48v, ObjectJ software: 1.03p) automatically measured a majority of the oocytes, which was followed by inspection to ensure accuracy (e.g., when cells were touching).Initially, the counts of transitional growth phase cells were kept separate from both the other primary growth phase cells and the secondary growth phase cells. After analyzing the oocyte length frequencies, it was decided that the transitional growth phase observed at the beginning of the spawning run recruit fully and are spawned in the current year. Their numbers are both included in and omitted from the determinate PAF estimate, to show that even when they are present, they are typically a small percentage of annual fecundity. The percentage of transitional growth oocytes, among transitional and secondary oocytes combined, is referred to later as “gap uncertainty,” where higher values indicate higher uncertainty in group synchrony of yolk oocyte development and potential for bias in the annual fecundity estimate when using a determinate method. […]

Pipeline specifications

Software tools ImageJ, ObjectJ
Application Microscopic phenotype analysis
Diseases Pulmonary Atresia