Comments from curator
Phenotyping data comes from
Table S1 of the
Supporting Information of the paper (ece32552-sup-0001, file ECE3-6-8460-s001.docx;
journal page, also in the
PMC full text and the
Europe PMC supplementary files): median egg-to-adult development time (DT) of males and females and egg-to-adult viability (EAV), each ± standard error, for 31 DGRP lines at three larval densities. No per-vial or per-fly data were published, so the study has a summary dataset only, with the values exactly as in Table S1.
Design: eggs from a 1-h collection of age-synchronised population cages of each DGRP line (Bloomington stocks) were seeded together with the same number of eggs of a white-eyed reference strain (
w1118), a standard competitor, in 20-mm vials with about 8 mL of molasses/soy-corn flour/agar food, at 25 °C:
low density (LowDens: 20 + 20 eggs per vial, 5 replicate vials),
medium density (MedDens: 50 + 50 eggs, 3 vials) and
high density (HighDens: 175 + 175 eggs, 3 vials). Red-eyed (DGRP) and white-eyed adults were counted daily at 2 pm from day 9 until no more flies eclosed. The
w1118 competitor flies are not reported. DGRP_555 was measured only at medium and high density (NA at low density).
The summary dataset has:
-
md_DevTime_LowDens,
md_DevTime_MedDens,
md_DevTime_HighDens and their standard errors
se_DevTime_* (days): DT is the time from the day of egg collection to adult emergence, scored separately for males and females; the replicate value is the mean DT of the flies of a vial, and Table S1 gives the median over the replicate vials, uploaded with sex M and F.
-
mn_Viab_LowDens,
mn_Viab_MedDens,
mn_Viab_HighDens and their standard errors
se_Viab_* (proportion, 0-1): EAV is the proportion of the DGRP eggs seeded in a vial that emerged as adults, sexes pooled (sex NA). Table S1 calls these values medians, but they are
means over the replicate vials: for all 92 line × density rows, EAV × eggs per vial × number of vials equals the number of DGRP flies scored (column N), and 25 of the 30 low-density values cannot be the median of five vials of 20 eggs (they are not multiples of 0.05). Table 1 of the paper also says that replicate averages were used for EAV. They are therefore uploaded as means (mn_).
The DT values are uploaded as medians, as labelled in Table S1 and in the Figure 2 legend; this cannot be checked without the per-vial data.
Not uploaded: the
N column of Table S1 (number of DGRP flies scored per line and density, both sexes; it equals EAV × eggs per vial × number of vials, so it duplicates the viability); Table S2 (per-line Levene test statistics and P-values comparing the among-fly DT variance between densities: test results, not phenotypes); the follow-up experiment at six densities (10 + 10 to 250 + 250 eggs) on DGRP_301, DGRP_307 and DGRP_555 (Table 3 gives only the averages of the three lines, and the per-line values are only shown in Figure S1); the sex ratios (Figure S4) and the larval viabilities of Figure S5 (figures only).
Checks against the paper: the sums of N over the lines equal the N of Table 1 at medium (2,637) and high density (5,957); at low density the sum is 1,684 vs 1,685 in Table 1, because DGRP_380 has N = 75 in Table S1 (consistent with its EAV of 0.75) but 76 in Table S2. The means over the lines of the uploaded viabilities (0.561, 0.567 and 0.366 at low, medium and high density) are close to the overall means of Table 1 (0.562, 0.561 and 0.366). Three standard errors are 0 in Table S1 and were kept as published (female DT of DGRP_360 and DGRP_774 at low density, 10.000 ± 0.00; viability of DGRP_852 at high density, 0.189 ± 0.00). A few DT values have two decimals instead of three in Table S1 (e.g. 10.62 for DGRP_181 females at medium density); they were kept as published.
The authors found strong genotype-by-density interactions for both traits, and higher among-line variance of DT at high density. They published no per-line plasticity index; the response to crowding of a line can be derived from the uploaded phenotypes (e.g. md_DevTime_HighDens - md_DevTime_LowDens). The 31 lines are all among the 43 DGRP lines of
DGRPool study 50 (Horváth et al. 2016, duration of embryogenesis), by the same group.
