Parentage Analysis Reveals Unequal Family Sizes during Hatchery Production
Round 1
Reviewer 1 Report
Akers et al. compared the paternal representation and genetic diversity of two stocking strategies: artificially bred fish from a partial factorial design versus naturally spawned individuals. The authors discovered that none of the hatchery-produced family groups had equal paternal representation when compared to the wild-produced offspring, which had equal paternal representation. However, there was no statistically significant difference in genetic diversity between wild-caught larvae and representative hatchery-produced offspring. Their research yields actionable results for improving hatchery-breeding design in terms of broodstock selection and assessment.
###### QUIBBLES #######
Some of the fish used in the breeding programme may be physiologically unprepared to spawn and, as a result, deposit low-quality gametes, resulting in a skew in parental contribution. In this case, hatchery-produced family groups can under evident fecundity and viability selections. Furthermore, because the broodstock is made up of randomly selected fish each year, the effects of genetic erosion can be hidden, which is otherwise impossible to assess without temporal sampling to monitor genetic diversity in the wild. It is important that authors note the latter in their discussion of the results in Lines 300-303.
Lines 93-94: Putting one’s fish eggs in one ‘basket’. Why was randomization not carried out to ensure that variation in family size was not due to different environmental (cage-specific) conditions? There is no information on how the statistical test for the results reported in Table 1 was performed. It is not clear if random effects were accounted for or not in the model.
Lines 183-185: It is not clear why ARLEQUIN was used to calculate heterozygosity values when FSTAT and CERVUS can computes these stats. Please clean up your analytical pipeline.
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In all, the manuscript is very well written and the flow of logic is impeccable, as side from a few generalization regarding the results of genetic diversity. However, more detail is needed in the Methods sections of how statistical test for the variance in paternal contribution were performed to assess if these were done in accurately and robustly. I recommend minor revisions.
Author Response
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Author Response File: 
Author Response.pdf
Reviewer 2 Report
Dear Authors,
your manuscript ID 2223388 entitled “Parentage analysis reveals unequal family sizes during hatchery production” is original and interesting. Stocking represents an important tool for managing sturgeon recovery and microsatellites are useful to guide stocking decisions.
I have just a few minor concerns and suggestions reported below:
· Fin clipping was used for biological material sampling but ethical statement is not reported. I suggest the Authors to consider, for future study, buccal swabbing.
· At line 65 is reported Figure 1, but figure 1 is not available
· I suggest using a graphical representation to explain partial factorial mating schemes.
· Point 2.2 described microsatellites analysis but the fluorophores used are not reported; please add fluorophores, size range foreseen for each microsatellites
Author Response
Please see attachment.
Author Response File: Author Response.pdf
