This README document presents the two datasets made available here: "qPCR" and "ReproductionTraits"

qPCR - summary

The 7 datasheets made available here result from two campaigns of data collection and have been adjusted to be used into the R script script_analysis_of_qPCR_results.R available in the same archive.
This script can be launched using R version 4.2.3 and R studio and by installing the packages associated with the library used in the script (see ### packages and library ###).
All datasheets can be extracted in the same folder from the archive qPCR.zip and used directly in the script after adding the path of the folder in the script.

Data are issued from qPCR performed on soft ticks Ornithodoros moubata (first nymphs or adults) treated or not with antibiotics and/or B vitamins to eliminate their microbiota.

Quantitative PCRs were performed to amplify target genes: RpoB gene marker of the presence of Francisella; GltA gene marker of the presence of Rickettsia; Actin gene of Ornithodoros moubata to assess the success of the extraction and qPCR, and to standardize for the tick size.

qPCR - Description of the Data and file structure

Data were collected over two series of qPCR performed by two different experimenters due to material constraints. Indeed, shortage of laboratory supply during COVID19 pandemics led to first analyze a small part of the samples (first experimenter): Nymphs from day0, day1, day3 and day10 from the treatment groups (control, gentamycin, and rifampicin) which were not treated with vitamins. All other nymph groups and adults were analyzed later by a second experimenter.
For qPCR cycle threshold, a threshold >38 was considered negative. If the threshold was negative for actin, the qPCR result for the sample was considered a false negative and was launched a second time.

The file names indicate which individual are concerned (nymphs or adults) and which genes are studied.

Here is the detail of how the information were collected/registered/transformed for each variable:
groupe_antibiotique: Antibiotic treatment group of the tick (Rifampicin R, Gentamycin G or Control T).
groupe_vitamine: Vitamin supplementation group of the tick (Vitamin Vit or NoVitamin NoVit).
gene: Gene that was targeted by qPCR (GltA or RpoB)
jour and jour_num: For nymphs, day after bloodmeal at which the tick was collected for DNA extraction.
groupe_Day: Compilation of antibiotic group and day group in the same variable.
num_tique: For adults, individual number associated with the tick.
experimenter: Experimenter which performed the qPCR (experimenter1 or experimenter2)
Ct_GltA and Ct_RpoB: cycle threshold at which the qPCR turned positive for GltA or RpoB gene
Ct_Actin: cycle threshold at which the qPCR turned positive for actin gene
Ratio_Ct_GltA_Ct_Actin and Ratio_Ct_RpoB_Ct_Actin: Ratio of GltA or RpoB threshold / Actin threshold to normalize for the tick size.
Concentration_GltA and Concentration_RpoB: Conversion of GltA or RpoB threshold into GltA or RpoB concentration using standard curves performed in the same qPCR.
Concentration_Actin: Conversion of actin threshold into actin concentration using standard curves performed in the same qPCR.
Ratio_des_concentrations: Ratio of GltA or RpoB concentration / Actin concentration to normalize for the tick size.
ConversionLog: Log conversion of the ratio of concentration for statistical analyses: =log(1+ratio)

ReproductionTraits - summary

The 15 datasheets made available here result from two campaigns of data collection and have been adjusted to be used into the R script script_analysis_of_tick_reproduction.R available in the same archive.
This script can be launched using R version 4.2.3 and R studio and by installing the packages associated with the library used in the script (see ### packages and library ###).
All datasheets can be extracted in the same folder from the archive ReproductionTraits.zip and used directly in the script after adding the path of the folder in the script.

Data are issued from the monitoring of life history traits of soft ticks Ornithodoros moubata (female adults) treated or not with antibiotics and/or B vitamins to eliminate their microbiota.

After blood feeding with treatments, female ticks were monitored during 2 periods of 50 days. We registered survival and traits associated with reproduction: laying success, laying date, number of eggs laid (standardized with the female tick weight as big ticks tend to lay more eggs), egg mass, date of hatching, hatching rate, date of molting into first nymphal stage, and molting rate.

ReproductionTraits - Description of the Data and file structure

Data were collected over two successive periods of 50 days following blood meal of the ticks.
The file names indicate which period X is concerned: first 50-day period (1), second 50-day period (2) or both (1and2). For instance, Bloodmeal_1_complete contains all the data for the first period of 50 days.

Here is the detail of how the information were collected/registered/transformed for each variable:
“num_tique“: Individual number associated with each tick (from F01 to F132) for randomization
“groupe_antibiotique“: Antibiotic treatment group of the tick (Rifampicin R, Gentamycin G or Control T). This information is added in the dataset after the collection of the data is over.
“groupe_vitamines“: Vitamin supplementation group of the tick (Vitamin Vit or NoVitamin NoVit) . This information is added in the dataset after the collection of the data is over.
“groupe_abvit“: Antibiotic treatment group and Vitamin supplementation group in the same variable. This information is added in the dataset after the collection of the data is over.
“poids_avant_gorgement“: Weight of the tick the day before bloodmeal in mg.
“poids_apres_gorgement“: Weight of the tick just after bloodmeal in mg.
“poids_apres_ponte”: Weight at the end of the 50-day period.
“poids_apres_gorgement_deux”: Weight of the tick just after second bloodmeal after the first 50-day period in mg.
“poids_fin_de_manip”: Weight of the tick at the end of the full experiment.
“date_de_la_mort“: Date at which the tick died. (Empty if it didn’t die)
“succes_gorgement“: If the tick fed properly during bloodmeal, i.e. gained at least 50mg of weight (1 if the tick fed succesfully, 0 if it did not)
“survie”: Survival (1 if the tick survived, 0 if it died during the 50-day period)
“succes_ponte”: Success of laying eggs (1 if the tick laid eggs successfully during the 50-day period, 0 if it did not)
“date_de_ponte“: Dates at which the tick laid eggs. The first date corresponds to the first time the tick laid eggs. The following dates correspond to all the dates which for eggs were laid by the tick.
“jours_avant_ponte“: Number of days between the date of the bloodmeal and the date of laying eggs. In days.
“nombre_d_oeufs“: Number of eggs laid in a patch of eggs laid the same day.
“poids_oeufs“: Weight of a patch of eggs laid the same day.
“poids_total_oeufs“: Weight of all eggs laid by a same tick.
“nombre_total_d_oeufs_avant_exclusion“: Total number of eggs that were laid by the tick during the 50-day period. Some eggs were collected for qPCR analyses and were then excluded from the rest of the study (hatching rate etc…). This is the number of eggs before exclusion.
“nombre_total_d_oeufs_apres_exclusion“: Total number of eggs that were laid by the tick during the 50-day period. Some eggs were collected for qPCR analyses and were then excluded from the rest of the study (hatching rate etc…). This is the number of eggs after exclusion.
“nombre_total_d_oeufs_avant_exclusion_div_par_poids“: Total number of eggs that were laid by the tick during the 50-day period divided by the weight of the tick mother (“poids_apres_gorgement“). Some eggs were collected for qPCR analyses and were then excluded from the rest of the study (hatching rate etc…). This is the number of eggs before exclusion divided by the tick weight.
“poids_moyen_oeuf“: Average weight of 1 egg for a tick (“poids_total_oeufs“ divided by “nombre_total_d_oeufs_avant_exclusion“).
“date_eclosion”: Date at which the eggs hatched. They can be several dates for a patch of eggs laid the same day if they didn’t hatch the same day.
“temps_incubation_oeufs“: Number of days between the date of hatching and the date of laying eggs. In days.
“nombre_de_larves_ecloses“: Number of eggs from a patch of eggs that hatched that day.
“oeufs_non_eclos“: Number of eggs from a patch of eggs that did not hatch at all.
“nb_total_de_larves“: Total number of larvae that hatched successfully by tick.
“taux_eclosion“: Hatching rate (“nombre_de_larves_ecloses“ divided by “nombre_total_d_oeufs_apres_exclusion“)
“date_de_mue“: Date at which the larvae molted. They can be several dates for a patch of larvae hatched the same day if they didn’t molt the same day.
“nb_de_mues“: Number of larvae that molted that day for each patch of larvae.
“nb_total_de_mues“: Total number of larvae that molted succesfully for a tick.
“mortalite_larves“: Number of larvae which died.
“temps_pour_mue“: Number of days between the date of hatching and the date of molting. In days.
“Survie“: Percentage of ticks that survived during the 50-day period, for a treatment condition.
“erreur_survie“: 95% confidence error on “Survie“
“ponte“: Percentage of ticks that laid at least one egg during the 50-day period, for a treatment condition.
“erreur_ponte“: 95% confidence error on “ponte“
“erreur_survie_old“: 95% confidence error for “Survie“ to add to graph without going under 0%
“erreur_ponte_old“: 95% confidence error on “ponte“ to add to graph without going under 0%
“erreur_survie_plus“: 95% confidence error for “Survie“ to add to graph without going over 100%
“erreur_ponte_plus“: 95% confidence error on “ponte“ to add to graph without going over 100%

Empty cells: Empty cells were not filled with "null," or "n/a," due to interference with the scripts.
Empty cells occur either after an adult tick died before laying eggs, a group of eggs didn't hatch, or a group of larvae didn't molt, which is taken into account by the following variables: “survie”, “taux_eclosion“, and “nb_total_de_mues“
In these cases, all the columns which are no longer relevant contain empty cells (example: for a tick which died before laying eggs, dates at which the tick laid eggs “date_de_ponte” is an empty cell).

Sharing/access Information

Authors: Florian Taraveau (florian.taraveau@cirad.fr or f.taraveau@gmail.com) with the help of Helene Jourdan (helene.jourdan@cirad.fr)
Affiliation of the authors: UMR ASTRE, CIRAD, INRAE, Campus de Baillarguet, F-34398 Montpellier, France
Feel free to contact the authors for any questions on this dataset.

DOI of the preprint which used these data: https://doi.org/10.1101/2023.05.09.539061