Climatic changes are considered as one of the main factors regulating abundance, composition, and distribution of species at different temporal and spatial scales [1–3]. Direct historical evidence from fossil records indicates that many terrestrial species underwent rapid latitudinal shifts during the Quaternary glacial period and especially after the Last Glacial Maximum (LGM) around 23 to 18 ka [4–6]. Paleontological and palynological records from the Northern Hemisphere, along with biogeographic evidence, provided the empirical basis for the Expansion-Contraction (EC) model of Pleistocene biogeography  which describes the response of populations and species to climatic changes [3, 4, 6, 8, 9]. Under a basic EC model, cool-temperate species from the Northern Hemisphere survived the LGM at lower latitude refugia and then recolonized higher latitudes through range expansion [6, 7].
The application of molecular-based approaches in population genetics has provided new insights into the history of many species and helped us to further understand the impact of the Quaternary glacial cycles on patterns of genetic variation and structure [2, 3, 6, 7]. However, most examples come from studies of Northern Hemisphere biota mainly of terrestrial species [10, 11]. In marine ecosystems, interglacial period deposits are rich in fossils but glacial records are in most cases unavailable due to the Holocene rise in sea level . Phylogeographical studies in non-tropical areas of the Southern Hemisphere are scarce , but during the last decade more data has been accumulated in different southern South American groups [13–20]. Periodic global cooling during Quaternary glacial cycles (1.8 Ma – 10 ka) generated shifts in climate, landscape and sea level. For instance, during the LGM an ice sheet about 1800 km long covered the west slope of the Andes from 35°S to almost 56°S [21–24]. Much of the Atlantic side of Patagonia and northeastern Tierra del Fuego remained unglaciated through the late Pleistocene . These glacial changes in Patagonia led to regional isolations and local extinctions, shaping the current patterns of species diversity in temperate areas of southern South America [13, 16, 25, 26]. Genetic evidence of postglacial recolonization has been found in several Patagonian groups including galaxiid [16, 26, 27] and percichthyd fishes [13, 14, 28], lizards [29–31], amphibians , mammals [11, 20, 33–35] and plants [15, 18, 36]. These studies have provided conflicting results, indicating either postglacial colonization from restricted glacial refugia [26, 32, 36], recolonization from geographically distant ice-free regions [15, 34], or local persistence through glacial cycles [16, 28, 31, 33, 36]. Few genetic studies have examined the effect of the Quaternary glacial cycles in marine organisms of southern South America and most of these were restricted to Pacific sectors of Patagonia [15, 17, 37–39]. Moreover, due to logistic problems especially in the hard-to-access fiordal region of Chilean Patagonia, most of these studies present unbalanced sampling, only including localities from easy-access areas which represent the northern (Reloncaví Archipelago and Chiloé Island) and the southern extremes of Patagonian species distributions (Magellan Strait and Tierra del Fuego).
The true limpet genus Nacella (Patellogastropoda: Nacellidae) includes 15 nominal species distributed in different biogeographical provinces of the Southern Ocean . Along the Patagonian coast, Nacella represent a dominant group of benthic macro-invertebrates, especially in the marine rocky ecosystems [41–44]. Based on morphological characters, at least eight nominal species of the genus have been described in this region (Nacella chiloensis, N. deaurata, N. delicatissima, N. flammea, N. fuegiensis, N. magellanica, N. mytilina, and N. venosa; [40, 43]. On the basis of species richness, Powell  considered Patagonia as the center of origin and diversification of Nacella, from where it expanded eastward through the West Wind Drift (WWD). However, this assumption has been recently rejected by phylogenetic reconstructions showing that the Patagonian group of Nacella is the most derived one and diversified no more than 2.0 Ma . Molecular and morphological comparisons of Patagonian species suggest that the number of nominal species in Nacella was overestimated [17, 46]. For instance, González-Wevar et al. using COI sequences and geometric morphometrics in seven sympatric nominal species recognized only four units of Nacella in Patagonia. In spite of the absence of reciprocal monophyly , morphological, genetic and habitat preference differentiation among congeners are maintained even in sympatry. Considering these results, the diversification of Nacella in Patagonia includes four Evolutionarily Significant Units (ESUs): N. deaurata, N. flammea, N. mytilina and N. magellanica.
Nacella magellanica (Gmelin, 1791) exhibits the widest distribution in Patagonia, extending from Puerto Montt in the Pacific (42°S) to the Buenos Aires Province in the Atlantic (35°–40°S), including the Strait of Magellan, Cape Horn, Tierra del Fuego and the Falkland/Malvinas Islands [40, 43]. This species is the most abundant and conspicuous limpet in intertidal and shallow subtidal areas of Patagonia . It has been also reported in the Beagle Channel as an organism associated with holdfasts of the macroalga Macrocystis pyrifera. As in other nacellid limpets, N. magellanica is a broadcast spawner that reproduces during austral spring  but its free-living larval duration is still unknown. A recent phylogeographic study of the species in Atlantic Patagonia identified an absence of genetic structure and a very recent geographic-demographic expansion (~ 11 ka) . Nevertheless, there is still an absence of knowledge about the patterns of genetic diversity, structure and connectivity of the species in Pacific Patagonia.
The southern tip of South America constitutes an interesting system to evaluate the relative effects of habitat discontinuities, oceanography, and glaciological history in marine benthic organisms with limited autonomous motility that exhibit some degree of larval dispersal. The presence of an extensive ice sheet during the LGM in this region likely eradicated many populations of shallow-water marine benthic organisms. Considering the current distribution of N. magellanica, its narrow bathymetric range and its high abundance along both sides of Patagonia, this species constitutes a suitable model to infer how historical and contemporary climatic events shaped the patterns of population genetic diversity and structure. We analyzed samples from a total of 14 localities encompassing most of the species range in Pacific Patagonia and Tierra del Fuego, as well as two population from Atlantic Patagonia and individuals from the Falkland/Malvinas Islands. We aimed to test the hypothesis that (i) N. magellanica in the Pacific sector of Patagonia represents a post-glacial recolonization from restricted glacial refugia in the northern limit of its distribution, or alternatively, (ii) N. magellanica persisted unaffected through glacial cycles in this area. Also, we aimed to determine if glacial-interglacial periods promoted genetic differentiation or even divergence between Atlantic and Pacific populations. Finally, considering the glaciological history of Patagonia and the pattern of genetic diversity and structure in the species it will be possible to evaluate the role of the Falkland/Malvinas Islands in the phylogeography of the species as a source or sink area.