The end of the Last Glacial Maximum (LGM) dramatically reshaped temperate ecosystems, with many species moving poleward as temperatures rose and ice receded. Whereas reinvading terrestrial taxa tracked melting glaciers, marine biota recolonized ocean habitats freed by retreating sea ice. The extent of sea ice in the Southern Hemisphere during the LGM has, however, yet to be fully resolved, with most palaeogeographic studies suggesting only minimal or patchy ice cover in subantarctic waters. Here, through population genetic analyses of the widespread Southern Bull Kelp ( Durvillaea antarctica ), we present evidence for persistent ice scour affecting subantarctic islands during the LGM. Using mitochondrial and chloroplast genetic markers (COI; rbc L) to genetically characterize some 300 kelp samples from 45 Southern Ocean localities, we reveal a remarkable pattern of recent recolonization in the subantarctic. Specifically, in contrast to the marked phylogeographic structure observed across coastal New Zealand and Chile (10- to 100-km scales), subantarctic samples show striking genetic homogeneity over vast distances (10,000-km scales), with a single widespread haplotype observed for each marker. From these results, we suggest that sea ice expanded further and ice scour during the LGM impacted shallow-water subantarctic marine ecosystems more extensively than previously suggested.

Knowledge of DNA evolution is central to our understanding of biological history, but how fast does DNA change? Previously, pedigree and ancient DNA studies—focusing on evolution in the short term—have yielded molecular rate estimates substantially faster than those based on deeper phylogenies. It has recently been suggested that short-term, elevated molecular rates decay exponentially over 1–2 Myr to long-term, phylogenetic rates, termed “time dependency of molecular rates.” This transition has potential to confound molecular inferences of demographic parameters and dating of many important evolutionary events. Here, we employ a novel approach—geologically dated changes in river drainages and isolation of fish populations—to document rates of mitochondrial DNA change over a range of temporal scales. This method utilizes precise spatiotemporal disruptions of linear freshwater systems and hence avoids many of the limitations associated with typical DNA calibration methods involving fossil data or island formation. Studies of freshwater-limited fishes across the South Island of New Zealand have revealed that genetic relationships reflect past, rather than present, drainage connections. Here, we use this link between drainage geology and genetics to calibrate rates of molecular evolution across nine events ranging in age from 0.007 Myr (Holocene) to 5.0 Myr (Pliocene). Molecular rates of change in galaxiid fishes from calibration points younger than 200 kyr were faster than those based on older calibration points. This study provides conclusive evidence of time dependency in molecular rates as it is based on a robust calibration system that was applied to closely related taxa, and analyzed using a consistent and rigorous methodology. The time dependency observed here appears short-lived relative to previous suggestions (1–2 Myr), which has bearing on the accuracy of molecular inferences drawn from processes operating within the Quaternary and mechanisms invoked to explain the decay of rates with time.