Reviewer 1's Review

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In this manuscript, a matrix population model is parameterized to explore the effects of habitat fragmentation on the persistence of brook trout populations, and the mechanisms (demographic) by which extinction (local and meta-population) can be prevented. Modelling is based on an unusually (at least for freshwater fish species) high quality data set of growth, survival, fecundity and dispersal of brook trout in small brook systems of eastern US. The main limitation with the data set is the lack of information on survival from egg to 0+ fish in the autumn (when the fish are large enough for pit-tagging). In my opinion, this deficiency is not critical, the authors take a simulation approach to overcome the problem, and results are nevertheless interesting. In my opinion, the most interesting results were the links between local extinction due to fragmentation and the potential for system-wide extinction.

The current study, alongside several other, once again emphasise the need to study and estimate the rate of local adaptation, as real life extinctions (in contrast to the modelled) will depend upon "the race between adaptation and reduced survival in response to fragmentation" (line 49). As such, it should stimulate new lines of studies necessary for the protection of animal populations under strong anthropogenic influence.

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N.B. These are the general comments made by the reviewer when reviewing this paper in light of which the manuscript was revised. Specific points addressed during revision of the paper are not shown.