DOI: 10.5061/dryad.z34tmpggw
title: Rapid brain development and reduced neuromodulator titres correlate with host shifts in Rhagoletis pomonella

description: Host shifts are considered a key generator of insect biodiversity. For
 insects, adaptation to new host plants often requires changes in
 larval/pupal development and behavioural preference towards new hosts.
 Neurochemicals play key roles in both development and behaviour, and
 therefore provide a potential source for such synchronization. Here, we
 correlated life history timing, brain development, and corresponding
 levels of 14 neurochemicals in Rhagoletis pomonella (Diptera:
 Tephritidae), a species undergoing ecological speciation through an
 ongoing host shift from hawthorn to apple fruit. These races exhibit
 differences in pupal diapause timing as well as adult behavioural
 preference with respect to their hosts. This difference in behavioural
 preference is coupled with differences in neurophysiological response to
 host volatiles. We found that apple race pupae exhibited adult brain
 morphogenesis three weeks faster after an identical simulated winter than
 the hawthorn race, which correlated with significantly lower titres of
 several neurochemicals. In some cases, particularly biogenic amines,
 differences in titres were reflected in the mature adult stage, when host
 preference is exhibited. In summary, life history timing, neurochemical
 titre, and brain development can be coupled in this speciating system,
 providing new hypotheses for the origins of new species through host
 shifts.
description: Uploaded as part of this dataset are raw files collected in
 pursuit of results figure 1, s2, part 3.1 (brain development and brain
 morphology of apple and hawthorn race through developmental stage 1-8),
 figure s1(respiration data), figure 2, part 3.2 (brain morphology analysis
 post winter collection),  figure 3, part 3.3 (quantification of
 neuromodulators through the developmental stages) and figure 4, part 3.4
 (Correlation between day post winter and quantification of neuromodulators
 from adult brain differentiation stage 4) of our manuscript.
 The data for figure 1, s2, part 3.1, brain morphology of apple
 and hawthorn race, confocal images are divided into each stage, seven
 folders. The ".oib" files, labelled with "host race-each
 stage-magnification used-number given to brain sample", for
 example,apple-stage1-10x-B1”.  They are the raw stacks of images obtained
 via confocal microscopy, consisting of one channel capturing the neuropil
 marker at the 647 wavelength. Magnification was 10x, and 20x objective.
 Files can by opened in FIJI (Fiji: an open-source platform for
 biological-image analysis. <em>Nat.
 Methods</em> <strong>9</strong>, 676–82). These files
 are raw files, before all processing. To replicate the results shown in
 the manuscript in Figure 1 and Supplementary Figure S2, one should consult
 the methods and supplementary methods of the manuscript, or the uploaded
 ReadMe file. The
 data for figure s2 consists of 21 .xlsx files of raw data of respiration.
 Each file is labelled as “date of experiment-host race-cohort day-cohort
 date-age of pupae res”. File 22 has compiled data after classifying pupae
 into diapausing or non-diapausing groups. There are also two .pdf files.
 File 1, code1 (r script) of respiration data-classification of diapausing
 and non-diapausing pupae. File 2, code 2(r script) of respiration mixed
 effect analysis. For
 details on processing and analysis, one should consult the methods and
 supplementary methods of the manuscript or the uploaded ReadMe
 file. The data for figure 2, part 3.2
 brain morphology analysis post winter collection consists of two .xslx
 files with raw data and fit data calculation. This folder also contains
 code used to explain the proportion of individuals transitioning from
 stage 3 to stage 4 of brain development between apple and hawthorn flies,
 as well as to estimate 95% CIs around the logistic estimates.
 The data for figure 3, part 3.3. quantification of
 neuromodulators using mass spectrometry. The folder for figure 3-mass raw
 data and analysis contains two main folders and one pdf file of code used
 to analyse the dataset. The individual PDF file contains Code (r script)
 for linear mixed model effect for neurotansmitter.pdf. One can replicate
 this analysis using R (V4.0.2, R Core Team. R: A Language and Environment
 for Statistical Computing. 2017.). Folder A-raw mass
 spec files contain 15 .xlsx files for each mass spec run. This folder has
 detail about each mass spec batch with retention time detail, area ratio
 for each sample, standard curve, and calculated amount for each standard
 and sample run on that particular date. The file has been labelled the
 date of run, batch number and with developmental stage details. Folder
 B-outlier calculation contains 3 .xlsx files for stages 1-8 with compiled
 data from all the batches of mass spec run. Each file has all the details
 about host race, developmental stage, neurochemicals, amount in ng, batch
 number and outlier calculation. The data for figure
 3.4, to compare how these precursor neurochemicals titres changed over
 time between the developing hawthorn and apple race pupae, we compared
 neurochemical titres of Stage 4 brains against the day they were sampled
 after winter. The folder for figure 4-datasheets of stage 4 contains two
 datasheets used for analysis in SPSS software. File 1 contains stage 4
 data for day 0-day 70. It also indicated host race, chemicals their amount
 and file detail used for univariate analysis. File 2 contains similar
 details as file 1 except excluding early time point data from day0-day
 20.
description: Uploaded with these files is a master README file (Read Me
 file_kharva et al_2022) that describes all the main experimental parts
 included in this publication: Figure 1-4 and figure s1. This file also
 includes all methods from the manuscript, pulled from both the main paper
 and the supplementary methods, which were used to collect and analyze the
 data, as well as a listing of each associated file name.