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Throughout the Quaternary, the continental‐based Antarctic ice sheets expanded and contracted repeatedly. Evidence suggests that during glacial maxima, grounded ice eliminated most benthic (bottom‐dwelling) fauna across the Antarctic continental shelf. However, paleontological and molecular evidence indicates most extant Antarctica benthic taxa have persisted in situ throughout the Quaternary. Where and how the Antarctic benthic fauna survived throughout repeated glacial maxima remain mostly hypothesised. If understood, this would provide valuable insights into the ecology and evolution of Southern Ocean biota over geological timescales. Here we synthesised and appraised recent studies and presented an approach to demonstrate how genetic data can be effective in identifying where and how Antarctic benthic fauna survived glacial periods. We first examined the geological and ecological evidence for how glacial periods influenced past species demography in order to provide testable frameworks for future studies. We outlined past ice‐free areas from Antarctic ice sheet reconstructions that could serve as glacial refugia and discussed how benthic fauna with pelagic or non‐pelagic dispersal strategies moved into and out of glacial refugia. We also reviewed current molecular studies and collated proposed locations of Southern Ocean glacial refugia on the continental shelf around Antarctica, in the deep sea, and around sub‐Antarctic islands. Interestingly, the proposed glacial refugia based on molecular data generally do not correspond to the ice‐free areas identified by Antarctic ice sheet reconstructions. The potential biases in sampling and in the choice of molecular markers in current literature are discussed, along with the future directions for employing testable frameworks and genomic methods in Southern Ocean molecular studies. Continued data syntheses will elucidate greater understanding of where and how Southern Ocean benthic fauna persisted throughout glacial periods and provide insights into their resilience against climate changes in the future.

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Understanding the processes responsible for shaping the spatial genetic patterns of species is critical for predicting evolutionary dynamics and defining significant evolutionary and/or management units. Here, we investigated the potential role of environmental factors in shaping the genetic structure of the endemic New Zealand scallop Pecten novaezelandiae using a seascape genetics approach. For this, we assayed genetic variation at 12 microsatellite markers in 952 individuals collected from 14 sites throughout New Zealand, and used data for 9 site-specific environmental variables (3 geospatial and 6 environmental variables). Our results indicate that a combination of environmental factors may be contributing to the observed patterns of genetic differentiation, but in particular, freshwater discharge and suspended particulate matter concentration were identified as being important. Environmental variation in these parameters may be acting as a barrier to gene flow. In terms of their ecophysiology, scallops are not particularly tolerant of high concentrations of either freshwater input or suspended sediment, making the identification of an association between these environmental variables and genetic variation particularly relevant across the full distributional range of this species. Although geographic distance between populations was also an important variable explaining the genetic variation among populations, it appears that levels of genetic differentiation are not a simple function of interpopulation distance. This study has identified previously unknown environmental factors that may be acting on the genetic structure of the New Zealand scallop and highlights the utility of seascape genetic studies to better understand the processes shaping the genetic structure of organisms.