Data and code for NPRB 1807: Experimental infections of age-4 herring with Ichthyophonus at the Marrowstone Lab (2018) and surveillance of Ichthyophonus in wild adult herring from Sitka Sound and Prince William Sound (2007-2019)

Data and code beginning with 18-2 refer to an infection trial (described in chapter 2 of the final report). This was an experiment to investigate and quantify the effects of host response and pathogen load on mortality in age-4 Pacific Herring, as well as results of yearly surveys for Ichthyophonus in Pacific herring from Sitka Sound and Prince William Sound. There are two csv files and one R file. The csv files contain data on (1) fish fork length, mass, survival and infection status of the fish (using a culture method) (Master data), and (2) results from an image analysis conducted on histological preps of ventricle tissue of herring infected with Ichthyophonus. Data include the area of tissue with host response, parasite stages and the total area of the ventricle. The 18-2 code includes an analysis of these data. Additional data and code collected are in reference to fish health surveys of wild herring conducted in late March and early April (e.g., around spawning) in Sitka Sound and Prince William Sound. Fish health data were collected in conjunction with the EVOSTC Herring Research and Monitoring Program disease program. The csv file, 'AK samples for R', includes the date, location, age, length, sex and infection status (IchFinal), for the fish sampled. Approximately, 180 herring were sampled per site in each year that surveys were conducted (2007-2019). The csv file 'historical measurements for R', consists of results of an image analysis of histological preps of ventricle tissue of Ichthyophonus infected herring. Data include the area of tissue containing Ichthyophonus parasite stages and the total area of the ventricle. Fixed ventricle tissue were not available for all years that surveys were conducted, but include most years between 2009-2019 for both sites. Age length analyses and age-length keys for Sitka and Cordova include code to calculate the keys and the resulting age-length keys for herring in Sitka and PWS respectively for 2007-2019. The age-length keys are unique for each year and were made using age-length data collected by ADFG use a combination of cast-net and purse seine collected fish, caught before, during and after spawning, at the respective locations.