DOI: 10.5061/dryad.547d7wmm4
title: Parasites perform poorly at high host densities: An experimental test in the salmon louse <em>Lepeophtheirus salmonis</em>

description: The link between host density and parasite population size is
 well-established. However, while high host density facilitates parasite
 transmission, it may negatively impact parasites through more intense
 competition and/or more intense host immune defense. We assessed the
 performance of individually tagged female salmon lice (Lepeophtheirus
 salmonis), an ectoparasite of Atlantic salmon (Salmo salar), under
 experimental low and high host density conditions, the latter mimicking
 salmon aquaculture conditions. Lice at high density exhibit greater
 pre-reproductive mortality, reduced growth, delayed maturation, smaller
 adult sizes, and lower fecundity. Adult size in salmon lice correlates
 negatively with age at maturity and positively with early fecundity,
 lifetime fecundity, and lifespan. Thus, lice in high-density host
 populations perform poorly across all life-history traits, likely due to
 stronger immune responses of hosts initially exposed to higher parasite
 doses. This study suggests density-dependent regulation of parasites in
 intensive agriculture, where hosts are farmed at high densities. Our
 results further suggest that salmon lice in aquaculture may be selected
 for greater resistance to host immune defense. As host populations now
 consist overwhelmingly of farmed fish, continued research is essential to
 understand the implications for wild salmonids, which are frequently
 infected by lice originating from farms.
description: # Parasites perform poorly at high host densities: An experimental test in
 the salmon louse *Lepeophtheirus salmonis* Dataset DOI:
 [10.5061/dryad.547d7wmm4](10.5061/dryad.547d7wmm4) ## Description of the
 data and file structure ### Files and variables Metrics * File count: 5 *
 File formats: .csv, .R Table of contents * FILE 1:
 data_MS2_combined_f1_tidy_v2.1.csv * FILE 2: data_MS2_f1_clutch2_temp.csv
 * FILE 3: data_MS2_f1_summary_v1.1.csv * FILE 4:
 data_MS2_fish_f1_period.csv * R script: Rscript_submitted_revised_B.r ####
 File: Rscript_submitted_revised_B.r **Description:** annotated R code with
 descriptions of the data files and required packages #### File:
 data_MS2_f1_clutch2_temp.csv **Description:**  ##### Variables * ID: chip
 number of the louse * clutch_number: 2 = second clutch *
 recent_temp_cl2hatch: mean water temperature in the tank in the last 7
 days prior to second clutch hatching, in degrees Celsius *
 mean_temp_cl2hatch: mean water temperature from infection to hatching of
 the second clutch, in degrees Celsius #### File:
 data_MS2_f1_summary_v1.1.csv **Description:**  ##### Variables * ID: louse
 chip number * origin: parent geographical origin * treatment: either high
 or low host density * generation: F1 = first generation after sampling of
 parents * longevity: time from infection to loss from the population, in
 days * lifespan_degreedays: time from infection to loss from the
 population, in degree-days * loss_ID: how the individual was assessed as
 lost from the population (either from scanning the chip when found in the
 tank outlet, or IDed from a photo using color patterns, or the first day
 it was noted as absent) * survival_status: 2 = lost 'naturally',
 1 = censored (lost following manual host change) * dpi_1st_observed: time
 from infection to first record, in days * degreeday_to_1st_obs: time from
 infection to first record, in degree-days * mean_temp_to_1st_obs: mean
 water temperature in the tank from infection to first record, in degrees
 Celsius * recent_temp_1st_obs: mean water temperature in tank in past 7
 days prior to first record, in degrees Celsius * nr_females_initial:
 female parasite load on fish at first record * nr_males_initial: male
 parasite load on fish at first record * nr_all_lice_initial: total
 parasite load (both sexes) at first record * host_id_1st_obs: tag number
 of the initial host the louse was recorded on * fish_mass_1st_obs: mass
 (in g) of the initial host at first record * fish_TL_1st_obs: length (in
 cm) of the initial host at first record * glue_exclude_entire: Y = exclude
 this louse from the analysis due to a glue accident possibly affecting
 data * lost_after_hostchange_tf: whether the louse was lost following a
 manual host change * dpi_for_60ish_dpi: time (in days post-infection) at
 the sampling falling around 60 days post-infection (for some tanks, an
 earlier sampling was done the previous week) * nr_females_60ish_dpi:
 female parasite load at the sampling around 60 days post infection *
 fish_mass_60ish_dpi: host mass (in g) that day * fish_TL_60ish_dpi: host
 length (in cm) that day * ddpi_for_60ish_dpi: time at the sampling falling
 around 60 days post-infection, in degree-days post-infection *
 max_degreeday_observed: last time the louse was observed, in degree-days
 post-infection * max_dpi_observed_live: last time the louse was observed,
 in days post-infection * last_ceph_length: last measure of live
 cephalothorax length (in mm) * last_genital_length: last measure of live
 genital segment length (in mm) * last_GC_ratio: last
 genital-to-cephalothorax length ratio * degreeday_54dpi: degree-day value
 from infection to 54 days post-infection * mean_7day_temp_54dpi: mean
 water temperature in the tank in the last 7 days prior to 54 days
 post-infection, in degrees Celsius * dpi_of_ref_measure: time at the body
 size measures used in analysis, in days post-infection *
 size_is_adult_mean: whether the size measure used in analysis is the mean
 of all size measurements from the second clutch and onwards, or the size
 measure taken prior to the second clutch (for lice having died early) *
 ref_ceph_length: cephalothorax length used in analysis (in mm) *
 ref_genital_length: genital segment length used in analysis (in mm) *
 ref_GC_ratio: genital-to-cephalothorax length used in analysis *
 dpi_1st_repro_observation: time at sampling of first clutch, in days
 post-infection * degreeday_1st_repro_observation: time at sampling of
 first clutch, in degree-days post-infection * age_1st_repro: time at
 hatching of first clutch, in days post-infection *
 degreeday_age_1st_repro: time at hatching of first clutch, in degree-days
 post-infection * recent_temp_clutch1: mean water temperature in tank in 7
 days prior to hatching of first clutch, in degrees Celsius *
 nr_females_1st_repro: female parasite load at sampling of first clutch *
 host_id_1st_repro: tag number of the host the louse was on at first clutch
 * fish_mass_1st_repro: mass (in g) of the host the louse was on at first
 clutch * fish_TL_1st_repro: length (in cm) of the host the louse was on at
 first clutch * ceph_length_1st_repro: cephalothorax length of the louse at
 first clutch * genital_length_1st_repro: genital segment length of the
 louse at first clutch * GC_ratio_1st_repro: genital-to-cephalothorax ratio
 of the louse at first clutch * n_eggs_total_cl1: egg count for first
 clutch * glue_exclude_cl1: whether the louse data for the first clutch
 needs to be excluded due to a glue accident * nr_eggstrings_cl1: number of
 egg strings produced at first clutch * ES_missing_reason_cl1: if fewer
 than 2 egg strings are produced in the first clutch, assumed that this is
 the reason for the missing egg string * dpi_2nd_repro_observation: time at
 sampling of second clutch, in days post-infection *
 degreeday_2nd_repro_observation: time at sampling of second clutch, in
 degree-days post-infection * age_2nd_repro: time at hatching of second
 clutch, in days post-infection * degreeday_age_2nd_repro: time at hatching
 of second clutch, in degree-days post-infection * recent_temp_clutch2:
 mean water temperature in tank in 7 days prior to hatching of second
 clutch, in degrees Celsius * host_id_2nd_repro: tag number of the host the
 louse was on at the second clutch * ceph_length_2nd_repro: cephalothorax
 length of the louse at second clutch (in mm) * genital_length_2nd_repro:
 genital segment length of the louse at second clutch (in mm) *
 GC_ratio_2nd_repro: genital-to-cephalothorax length ratio at second clutch
 * n_eggs_total_cl2: egg count for second clutch * glue_exclude_cl2:
 whether the louse data for the second clutch needs to be excluded due to a
 glue accident * nr_eggstrings_cl2: number of egg strings produced at
 second clutch * ES_missing_reason_cl2: if fewer than 2 egg strings are
 produced in the second clutch, assumed that this is the reason for the
 missing egg string * sum_eggs_life_all: sum of all egg counts during
 lifetime, including first clutch * sum_egglength_life_all: sum of all egg
 string lengths during lifetime, including first clutch *
 sum_eggs_life_nocl1: sum of all egg counts during lifetime, excluding
 first clutch * sum_egglength_life_nocl1: sum of all egg string lengths
 during lifetime, excluding first clutch * min_clutch_number: 1 = the louse
 records start at first clutch, 2 = they start at second clutch *
 max_clutch_number: number of clutches the louse produced during the study
 * time_last_clutch_observed_dpi: time of sampling of the last clutch
 produced by that louse, in days post-infection *
 time_last_clutch_observed_ddpi: time of sampling of the last clutch
 produced by that louse, in degree-days post-infection *
 age_last_clutch_hatch_dpi: time of hatching of the last clutch produced by
 that louse, in days post-infection * age_last_clutch_hatch_degreeday: time
 of hatching of the last clutch produced by that louse, in degree-days
 post-infection * n_egglength_missing: number of egg length estimates
 missing for the louse (due to missing picture) * n_eggcount_missing_all:
 number of egg counts missing * n_eggcount_missing_nocl1: number of egg
 counts missing in lifetime fecundity estimate * cl1_egg_estimate_missing:
 whether the first clutch estimates are missing * n_hosts_life: number of
 different hosts the louse was recorded on during its lifetime *
 mean_females_life: mean female parasite load experienced by the louse
 during lifetime * mean_males_life: mean male parasite load experienced by
 the louse during lifetime * n_hosts_before_first_manual: number of
 different hosts the louse was recorded on prior to first manual host
 change * n_manual_host_change: number of manual host changes experienced
 by the louse during its lifetime * n_host_change_other: number of other
 host changes during lifetime (other than manual) * last_obs_host_id: tag
 number of the last host the louse was recorded on *
 last_obs_host_nr_females: female parasite load on the last host the louse
 was recorded on * last_obs_host_mass: male parasite load on the last host
 the louse was recorded on * dpi_last_host_changed: time when the louse
 last changed host during lifetime, in days post-infection *
 dpi_first_host_changed: time when the louse first changed host, in days
 post-infection #### File: data_MS2_fish_f1_period.csv **Description:** 
 ##### Variables * Fish_code: tank and sampling rank for the fish on that
 sampling day * Tank: tank number * Origin: geographical origin of the lice
 in the tank * n_fish_tank: number of fish in the tank on that sampling day
 * Treatment: either high or low host density * Fish_Tag: tag number of the
 fish * CheckDate: date of sampling * Days_since_1st_infection: time at
 sampling, in days post-infection * Females: number of adult female lice on
 the fish * Males: number of adult male lice on the fish * Length: length
 of the fish, in cm * Weight: weight of the fish, in g * Fate: either
 blank, or fish euthanised * Comment: additional info on the fish ####
 File: data_MS2_combined_f1_tidy_v2.1.csv **Description:**  ##### Variables
 * ID: chip number of the louse * lousename: tank and fish number the louse
 was sampled on, and left-to-right rank in the picture * treatment: high or
 low host density treatment * origin: parent geographical origin *
 observe_date: date sampled * generation: F1 = first generation after
 sampling of parents * infect_date: date of infection with F1 copepodids *
 loss_date: date the louse was lost from the population * days_post_infect:
 date sampled, in days post-infection * lifespan_degreedays: lifespan of
 the louse in degree-days post-infection * chip_glued: 'glued' if
 the chip was glued that day, or 'NA' if not * clutch_number: 1 =
 first clutch, 2 = second clutch etc. * clutch1_tf: whether clutch 1 is
 available for this louse * Leggstring: length of left side egg string, in
 mm * Reggstring: length of right side egg string, in mm *
 real_L_eggstring: same as previous measures, except for some pictures that
 needed rescaling * real_R_eggstring: same as previous measures, except for
 some pictures that needed rescaling * sum_egglength: sum of both egg
 string lengths * nr_eggstrings: whether 0, 1, or 2 egg strings were
 collected from the louse * ES_missing_reason: reason why one or both egg
 strings were missing (e.g., dysfunctional louse) * ceph_length:
 cephalothorax length, in mm * genital_length: genital segment length, in
 mm * GC_ratio: genital-to-cephalothorax length ratio *
 degreeday_hatch_interval: interval between current and previous clutch, in
 degree-days * degreeday_to_hatch: time from infection to hatching of the
 clutch, in degree-days * hatch_interval: interval between current and
 previous clutch, in days * hatch_since_infect: time from infection to
 hatching of the clutch, in days * hatch_date: date of hatching of the
 clutch * macro_photo_missing: indicates whether the photo of the louse is
 missing for this sampling * egg_estimate_missing: whether egg count is
 available or not for this record * ES1_L_or_R: which side of the louse
 photo egg string 1 was * egg_length_1_mm: mean egg length for egg string
 1 (in mm) * egg_width_1_mm: mean egg width for egg string 1 (in mm) *
 egg_length_2_mm: mean egg length for egg string 2 (in mm) *
 egg_width_2_mm: mean egg width for egg string 2 (in mm) * n_eggs_total:
 estimated total egg count in the clutch * host_id: tag number of the
 salmon host the louse was sampled on * fish_total_length: length (in cm)
 of the host the louse was sampled on * fish_mass: mass (in g) of the host
 the louse was sampled on * nr_females_on_host: female parasite load on the
 host * nr_males_on_host: male parasite load on the host *
 host_manually_changed: whether the host was replaced on sampling day *
 new_host_manual: if the host was replaced, tag number of the new host *
 new_host_mass: mass (in g) of the new host * glue_exclude: whether the
 louse was accidentally affected by gluing this day * glue_exclude_entire:
 whether the louse needs to be excluded, definitely due to a gluing
 accident * tank_temp: water temperature in the tank this day, in degrees
 Celsius * mean_temp_to_present: mean water temperature in the tank from
 infection to current sampling, in degrees Celsius * mean_temp_between:
 mean water temperature in the tank between the last and current sampling,
 in degrees Celsius * recent_tank_temp: mean water temperature in the tank
 in the past 7 days, in degrees Celsius * degree_day_to_present: time from
 infection to sampling, in degree-days * degree_day_between: time since
 last sampling, in degree-days * degree_day_recent: degree-day value for
 past 7 days * min_since_start: minutes from the start of the sampling
 session until the collection of the clutch * est_minutes_eggs_out:
 estimated duration (in minutes) between collection of eggs and arrival in
 incubation room (water flow restored) * scan_time_or_estimated: info from
 the chip reading * lost_after_hostchange_tf: whether the louse was lost
 within one week of manual host change * host_id_1st_obs: tag number of the
 host the louse was initially on (at first repro) ## Code/software R
 software, see annotations in the file