Akhund-Zade et al., 2021
Genetic basis of offspring number–body weight tradeoff in Drosophila melanogaster
[10.1093/g3journal/jkab129]

Description

Offspring number and mean offspring wet weight (daughters and sons) were measured per vial for 143 DGRP lines, and six lines were also tested at five parental densities. An offspring index (first principal component of the four traits) captured a tradeoff between offspring number and weight.

Comments from curator

Phenotyping data come from the authors' companion data page (de Bivort lab), also archived on Zenodo (DGRP_Offspring_DataCode_Upload_v2.zip):
- DGRP_Screen_Data.csv: daily eclosion records of the DGRP screen (number and weight of the females and males eclosed per vial and day), used for raw dataset 1.
- Line_Effects_Data.csv and pca_phenotype.csv: per-line values modelled by the authors and the offspring index used for their GWAS, used for the summary dataset.
- Density_Data_Records.csv: daily records of the parental density experiment, used for raw dataset 2.

Raw dataset 1 (screen, 143 lines): one row per vial and offspring sex. For each line, 10 females and 5 males (2-5 days old) laid eggs for 2 days at 23 °C in each of 3 vials; the adult offspring were counted and weighed every day for 10 days from the start of eclosion. The sex column is the sex of the offspring. OffspringNum is the total number of offspring of that sex eclosed from the vial, and OffspringWt their mean wet weight in mg, computed as in the authors' script ModelingPhenotypes.R (mean of the daily mean weights; the male weight is the total weight minus the female weight). Following the authors, vials with fewer than 5 females or 5 males (or a zero weight) were excluded, then lines left with a single vial: 32 of the 452 vials and 11 of the 154 lines tested (DGRP_048, 142, 317, 502, 642, 790, 852, 861, 884, 890 and 908) are therefore not included. The remaining 420 vials match the authors' Raw_Line_Phenotypes.csv exactly (values recomputed at full precision from the daily records).

The lines were tested in two batches (Batch and Vial are kept as obsolete design phenotypes): after the filters above, 134 lines have vials in batch 1 (September 2015) and 44 in batch 2 (October 2015), 35 of them in both, as in the paper (batch 2 repeated the lines without three completed vials in batch 1). The raw values are not batch-corrected. The authors corrected batch 2 by subtracting from all its vials the mean difference between the two batches over the 35 shared lines (-17.4 females, -22.3 males, +0.134 mg female weight, +0.119 mg male weight), which reproduces their Batch_Adjusted_Line_Phenotypes.csv.

Summary dataset: mn_OffspringNumAuth and mn_OffspringWtAuth are the authors' per-line values (Line_Effects_Data.csv): values fitted by random-intercept mixed models on the batch-corrected vials (linear model for the counts, gamma model with log link for the weights), averaged per line; they are the values the authors submitted to the DGRP2 webtool for their single-trait GWAS. They differ from the means computed by DGRPool from raw dataset 1 (batch correction and shrinkage; r = 0.93-0.97, differences up to 28 flies or 0.25 mg), which is why both are provided. mn_OffspringIndex (sex NA) is the offspring index used for the GWAS (pca_phenotype.csv): the score of each line on the first principal component (71% of the variance) of these four scaled values. It is negatively loaded for the offspring numbers and positively for the weights: a negative index means many light offspring, a positive index few heavy offspring.

Raw dataset 2 (parental density, 6 lines): six lines chosen for their offspring index (DGRP_176, 237, 350, 049, 812 and 894) laid eggs at five parental densities: 1 female + 1 male (Dens1), 5 + 1 (Dens2), 10 + 5 (Dens3), 25 + 10 (Dens4) and 50 + 20 (Dens5); the offspring were counted and weighed every day for 25 days. One row per replicate vial and offspring sex; the replicates of the different densities are independent and are placed side by side (row k holds the k-th replicate of each density). There are 2 to 7 replicates per line and density, and none for DGRP_894 at density 5. OffspringWt is NA when no offspring of that sex eclosed. The authors' file codes the lines 1 to 6; they were mapped with the authors' script DensityAnalysis.R (1 = RAL 176, 2 = RAL 237, 3 = RAL 350, 4 = RAL 49, 5 = RAL 812, 6 = RAL 894), which follows the order of their offspring index as described in the paper. The paper's methods name RAL 327 instead of RAL 237, which is a typo: RAL 327 was not screened, and RAL 237 has the index of -2.9 given in the paper.

Of note, a few daily records of the screen have implausible mean weights (-0.08 mg for the males of DGRP_362 vial 2 on 2015-09-13, where the total weight is lower than the female weight; 0.27 mg for females and 2.37 mg for males of DGRP_235 vial 2 on 2015-09-15; 2.53 mg for males of DGRP_787 vial 1 of batch 2). They are kept, as in the authors' vial values.

143 DGRP lines 143 genotyped

DGRP_026 DGRP_038 DGRP_040 DGRP_045 DGRP_049 DGRP_057 DGRP_059 DGRP_069 DGRP_073 DGRP_083 DGRP_085 DGRP_088 DGRP_091 DGRP_093 DGRP_101 DGRP_105 DGRP_109 DGRP_129 DGRP_136 DGRP_138 DGRP_149 DGRP_153 DGRP_161 DGRP_176 DGRP_177 DGRP_181 DGRP_195 DGRP_217 DGRP_223 DGRP_229 DGRP_233 DGRP_235 DGRP_237 DGRP_256 DGRP_280 DGRP_287 DGRP_301 DGRP_304 DGRP_306 DGRP_307 DGRP_309 DGRP_310 DGRP_315 DGRP_318 DGRP_319 DGRP_320 DGRP_321 DGRP_324 DGRP_332 DGRP_335 DGRP_336 DGRP_338 DGRP_340 DGRP_350 DGRP_352 DGRP_356 DGRP_357 DGRP_358 DGRP_359 DGRP_360 DGRP_361 DGRP_362 DGRP_365 DGRP_367 DGRP_370 DGRP_373 DGRP_374 DGRP_377 DGRP_379 DGRP_380 DGRP_381 DGRP_382 DGRP_383 DGRP_385 DGRP_386 DGRP_391 DGRP_392 DGRP_399 DGRP_405 DGRP_406 DGRP_409 DGRP_426 DGRP_427 DGRP_437 DGRP_439 DGRP_440 DGRP_441 DGRP_443 DGRP_461 DGRP_486 DGRP_491 DGRP_492 DGRP_508 DGRP_513 DGRP_530 DGRP_535 DGRP_555 DGRP_563 DGRP_584 DGRP_589 DGRP_595 DGRP_646 DGRP_703 DGRP_707 DGRP_712 DGRP_714 DGRP_716 DGRP_721 DGRP_730 DGRP_732 DGRP_737 DGRP_738 DGRP_761 DGRP_765 DGRP_774 DGRP_776 DGRP_783 DGRP_786 DGRP_787 DGRP_796 DGRP_799 DGRP_802 DGRP_804 DGRP_805 DGRP_808 DGRP_812 DGRP_819 DGRP_821 DGRP_822 DGRP_837 DGRP_843 DGRP_849 DGRP_850 DGRP_855 DGRP_859 DGRP_879 DGRP_882 DGRP_892 DGRP_894 DGRP_897 DGRP_900 DGRP_907 DGRP_913

Datasets

Dataset	Phenotypes	DGRP lines
Summary dataset	3 phenotypes mn_OffspringIndex mn_OffspringNumAuth mn_OffspringWtAuth	143 DGRP lines DGRP_026 DGRP_038 DGRP_040 DGRP_045 DGRP_049 DGRP_057 DGRP_059 DGRP_069 DGRP_073 DGRP_083 DGRP_085 DGRP_088 DGRP_091 DGRP_093 DGRP_101 DGRP_105 DGRP_109 DGRP_129 DGRP_136 DGRP_138 DGRP_149 DGRP_153 DGRP_161 DGRP_176 DGRP_177 DGRP_181 DGRP_195 DGRP_217 DGRP_223 DGRP_229 DGRP_233 DGRP_235 DGRP_237 DGRP_256 DGRP_280 DGRP_287 DGRP_301 DGRP_304 DGRP_306 DGRP_307 DGRP_309 DGRP_310 DGRP_315 DGRP_318 DGRP_319 DGRP_320 DGRP_321 DGRP_324 DGRP_332 DGRP_335 DGRP_336 DGRP_338 DGRP_340 DGRP_350 DGRP_352 DGRP_356 DGRP_357 DGRP_358 DGRP_359 DGRP_360 DGRP_361 DGRP_362 DGRP_365 DGRP_367 DGRP_370 DGRP_373 DGRP_374 DGRP_377 DGRP_379 DGRP_380 DGRP_381 DGRP_382 DGRP_383 DGRP_385 DGRP_386 DGRP_391 DGRP_392 DGRP_399 DGRP_405 DGRP_406 DGRP_409 DGRP_426 DGRP_427 DGRP_437 DGRP_439 DGRP_440 DGRP_441 DGRP_443 DGRP_461 DGRP_486 DGRP_491 DGRP_492 DGRP_508 DGRP_513 DGRP_530 DGRP_535 DGRP_555 DGRP_563 DGRP_584 DGRP_589 DGRP_595 DGRP_646 DGRP_703 DGRP_707 DGRP_712 DGRP_714 DGRP_716 DGRP_721 DGRP_730 DGRP_732 DGRP_737 DGRP_738 DGRP_761 DGRP_765 DGRP_774 DGRP_776 DGRP_783 DGRP_786 DGRP_787 DGRP_796 DGRP_799 DGRP_802 DGRP_804 DGRP_805 DGRP_808 DGRP_812 DGRP_819 DGRP_821 DGRP_822 DGRP_837 DGRP_843 DGRP_849 DGRP_850 DGRP_855 DGRP_859 DGRP_879 DGRP_882 DGRP_892 DGRP_894 DGRP_897 DGRP_900 DGRP_907 DGRP_913	Download
Raw dataset #1	2 phenotypes OffspringNum OffspringWt	143 DGRP lines DGRP_026 DGRP_038 DGRP_040 DGRP_045 DGRP_049 DGRP_057 DGRP_059 DGRP_069 DGRP_073 DGRP_083 DGRP_085 DGRP_088 DGRP_091 DGRP_093 DGRP_101 DGRP_105 DGRP_109 DGRP_129 DGRP_136 DGRP_138 DGRP_149 DGRP_153 DGRP_161 DGRP_176 DGRP_177 DGRP_181 DGRP_195 DGRP_217 DGRP_223 DGRP_229 DGRP_233 DGRP_235 DGRP_237 DGRP_256 DGRP_280 DGRP_287 DGRP_301 DGRP_304 DGRP_306 DGRP_307 DGRP_309 DGRP_310 DGRP_315 DGRP_318 DGRP_319 DGRP_320 DGRP_321 DGRP_324 DGRP_332 DGRP_335 DGRP_336 DGRP_338 DGRP_340 DGRP_350 DGRP_352 DGRP_356 DGRP_357 DGRP_358 DGRP_359 DGRP_360 DGRP_361 DGRP_362 DGRP_365 DGRP_367 DGRP_370 DGRP_373 DGRP_374 DGRP_377 DGRP_379 DGRP_380 DGRP_381 DGRP_382 DGRP_383 DGRP_385 DGRP_386 DGRP_391 DGRP_392 DGRP_399 DGRP_405 DGRP_406 DGRP_409 DGRP_426 DGRP_427 DGRP_437 DGRP_439 DGRP_440 DGRP_441 DGRP_443 DGRP_461 DGRP_486 DGRP_491 DGRP_492 DGRP_508 DGRP_513 DGRP_530 DGRP_535 DGRP_555 DGRP_563 DGRP_584 DGRP_589 DGRP_595 DGRP_646 DGRP_703 DGRP_707 DGRP_712 DGRP_714 DGRP_716 DGRP_721 DGRP_730 DGRP_732 DGRP_737 DGRP_738 DGRP_761 DGRP_765 DGRP_774 DGRP_776 DGRP_783 DGRP_786 DGRP_787 DGRP_796 DGRP_799 DGRP_802 DGRP_804 DGRP_805 DGRP_808 DGRP_812 DGRP_819 DGRP_821 DGRP_822 DGRP_837 DGRP_843 DGRP_849 DGRP_850 DGRP_855 DGRP_859 DGRP_879 DGRP_882 DGRP_892 DGRP_894 DGRP_897 DGRP_900 DGRP_907 DGRP_913	Download
Raw dataset #2	10 phenotypes OffspringNum_Dens1 OffspringNum_Dens2 OffspringNum_Dens3 OffspringNum_Dens4 OffspringNum_Dens5 OffspringWt_Dens1 OffspringWt_Dens2 OffspringWt_Dens3 OffspringWt_Dens4 OffspringWt_Dens5	6 DGRP lines DGRP_049 DGRP_176 DGRP_237 DGRP_350 DGRP_812 DGRP_894	Download