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Hierarchical population structure can result from range-wide geographic subdivision under conditions of environmental heterogeneity and weak gene flow. While a lower level of structure can be formed by local populations within eco-geographic regions, an upper level can be characterized by variation between populations from different regions, and thus, be represented by evolutionarily significant units (ESUs) defined by environmental, ecological and genetic variation. Selection of ESUs may depend on the sequence of using these three sources of variation. We propose to determine ESUs by first using non-genetic, ecological and geographical gradients for defining preliminary population groups (eco-geographic units, EGUs) and then testing whether the boundaries of these units are genetically coherent and thus represent ESUs or warrant their further modification. We evaluate this approach using Sakhalin taimen, an East Asian endangered endemic fish. Forty-one samples (473 fish) were drawn from thirty populations across the species range and genotyped at microsatellite DNA markers. We assign the populations into ESUs based on geographic and life history criteria and subsequent application of genetic diversity analyses. The ESUs appeared to be greatly diverged genetically. Within ESUs, local populations are genetically differentiated, have low effective sizes, show signatures of demographic decline and extremely restricted gene flow. Conservation plans aimed to restore or maintain a specific threatened population should take into account such hierarchical structure, and in particular be based on the genetic resources drawn from each population or using ecologically and genetically similar populations from the same ESU as donors for restoration of the population.

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