Current molecular genetic methods allow the understanding of the genetic structure underlying different populations of a species with previously unforeseen resolution [e.g. [1–3]]. As a result, it is possible to undertake fundamental investigations in ecology and evolution, like the study of the influence of past and current environmental conditions, together with ecological barriers, in shaping the population structure of wild animal species. These studies provide a unique opportunity to understand how species have evolved and how they are organised across landscapes . The constraints that heterogeneous landscapes (e.g. barriers, resource distribution) and environmental conditions (e.g. climate) impose on the ability of animals to colonise new habitats have genetic implications affecting the structure, dynamics and persistence of populations [e.g. [5–9]]. Thus, significant genetic structuring can be expected among populations where gene flow is restricted [e.g. [5, 10]].
However, when contact between divergent populations is re-established, hybrid zones can form with resultant consequences for the evolutionary trajectories of the interbreeding populations [e.g. ]. Two scenarios could potentially occur: if hybrid fitness is high, introgression will be widespread and hybridising populations may become panmictic over time, replacing the original populations ; but if interbreeding is limited in geographical range, hybridising populations may experience genetic exchange without panmixia [e.g. ]. Under such circumstances hybrid zones may persist over time and function as channels for genetic exchange between the populations, increasing overall levels of genetic and phenotypic diversity [e.g. [14–17]].
Although Pleistocene climate conditions played an important role in initiating major phylogeographical structuring in today's fauna , very little is known about their effects on southern South American terrestrial vertebrates. Phylogeographic studies in this region are scarce and have been conducted on rodents [19–21], lizards [22–24], amphibians [9, 25], and a bird species . Several of these studies suggested that the phylogeographic patterns observed, such as past fragmentation, range expansion, and secondary contact, could in part be understood in light of Pleistocene climate conditions. There is evidence of several cycles of more arid conditions intercalated with moist periods during the Pleistocene and Holocene of Southern South America [e.g. [27–30]], which were related to glaciation events , influencing the vegetation distribution  and the fauna depending on it.
One species that may allow hypotheses about gene flow both across a heterogeneous distribution, and into hybrid zones to be tested is the burrowing parrot (Cyanoliseus patagonus) (Aves, Psittaciformes). This species is distributed in a particularly heterogeneous arid to semi-arid landscape, across an extensive ~1,000,000 km2 range in Chile and Argentina. A previous study  suggested that precipitation and temperature restrict burrowing parrot distribution in Argentina. According to this study , burrowing parrots are restricted to an area with median annual precipitation up to 600 mm, and annual average temperatures of no less than 8°C. However, this topic merits further research, as the study  was based on outdated distributional data and on the plain interpretation of maps, without detailed statistical analyses. The most dominant feature of this region is the high Andes, a mountain range that attains an altitude of up to 6,900 m and appears to separate burrowing parrot populations in Chile from those in Argentina. The predominant ecosystem on the Chilean side of this region is the 'Matorral', where vegetation is adapted to the generally dry conditions of a Mediterranean climate zone [34–36]. On the Argentinean side the semi-desert scrubland known as the 'Monte' is predominant, and this occurs from Patagonia to the North-west of Argentina [ and references therein]. Even though there are no extrinsic barriers to parrot dispersal in Argentina, more than 2,300 km separate the southernmost and northernmost burrowing parrot populations there. In addition, burrowing parrots breed in sandstone, limestone or earthen cliffs or "barrancas" (gorges or ravines), where they excavate nest burrows and form colonies [e.g. ]. These cliffs are heterogeneously located in the driest parts of the burrowing parrots range, being commonly found along permanent or temporary rivers, lakeshores, and the seacoast. Given the dryness of this environment, burrowing parrot colonies are never far from freshwater on which they are completely dependent, as they need to drink several times per day [37, 38] (Figure S1). These specific requirements for nest sites, which are spread over thousands of square kilometres, and water, together with the colossal barrier of the Andes, may favour the isolation of burrowing parrot breeding sites and a complex population structure driven by genetic drift.
Due to the heterogeneity of habitats within this species' range, four burrowing parrot sub-species have been proposed, three of which are found in Argentina: C. p. patagonus in Patagonia, C. p. andinus in the Cuyo region to the west and north-west, and C. p. conlara ranging in the San Luis region between the former two (hereafter patagonus, andinus, conlara) [34, 39, 40]. The sub-species C. p. bloxami (hereafter bloxami) is found on the Andean foothills of Central Chile [34, 41]. Three of the sub-species, namely andinus, patagonus and bloxami, are clearly morphologically distinct (size and plumage coloration) , while some authors [34, 40, 42] considered conlara a hybrid, owing to its intermediate geographic location and phenotype, between patagonus and andinus. Little is known about the genetic structure of burrowing parrots and how this corresponds to the morphological sub-species described above. A previous study  attempted to address this using seven microsatellite markers and suggested moderate differentiation between bloxami and all other subspecies, but differentiation within Argentinean samples was not detected. Analysis of a larger sample using a uniparental marker such a mitochondrial DNA may increase the resolution of genetic structure in this species.
Burrowing parrots are currently threatened by intense collection of birds for the pet trade , unjustified persecution as a crop pest [41, 44] and strong habitat loss and degradation, particularly in the Monte ecosystem . The latter could strongly reduce connectivity among the populations, enhancing isolation. As key species in the Monte, any negative impact on burrowing parrots could potentially affect other species since their abandoned and semi-collapsed nests provide breeding space to many other cavity nesters (such as insects, reptiles, birds and small mammals) .
Given the marked phenotypic differences between the populations on both sides of the Andes we hypothesise that gene flow across this high mountain range, the largest barrier in the region, must be severely restricted. We tested this hypothesis using three mtDNA loci, in a large scale sampling effort covering almost the entire species range. We also aimed to uncover the underlying population structure of this species, determine their geographic origins and suggest possible routes of colonisation. We also used these data to determine if an andinus-patagonus hybrid zone exists. Lastly, considering the conservation value of this key species, its potentially restricted distribution with respect to climatic factors, and the unchecked degradation of their preferred habitats, we aim to ascertain the extent to which ecological and climatic factors influence their population structure.