Previous bio- and phylogeographic studies in the northern hemisphere
revealed the major role of the Quaternary in the evolution of
biodiversity. Important climatic fluctuations resulted in alternations
of glacial and interglacial periods that profoundly influenced the
distribution of habitats, dispersal and isolation among populations
[e.g. [1-4]]. In South America, climate fluctuation periods were equivalent to those known for the northern hemisphere [5,6].
During the glacial periods, glacier boundaries descended hundreds of
meters, and advanced dramatically in the southern part of the continent
In the central Andes, although late Quaternary glaciations eliminated
the material evidence of glacier advances older than 200 000 years ,
research has shown that the distribution of plant species and habitats
cycled with climatic changes, descending to lower elevations during
periods of reduced temperature [9,10].
However, studies on the influence of the Quaternary on current
South-American biodiversity are scarce and have usually focused on
lowland regions [11,12].
Species with broad ranges of distribution can be informative regarding glacial refugia, dispersal pathways and contact zones [13,14] and, then, provide useful insights about the role of climatic changes on biodiversity. The pampas cat (Leopardus colocolo) displays a large distribution in South America, from Central Ecuador to Patagonia, in a variety of habitats [15,16]. Based on morphological characteristics, between 8 and 11 subspecies are currently recognized [15,17,18] and the scission of this taxon into three different species was proposed by García-Perea : L. colocolo for populations distributed on the western slope of the southern Andes; L. pajeros distributed along the Andes; and L. braccatus found to the east of the Andes, in Brazil, Uruguay and Paraguay. Previous studies performed on mitochondrial genome [19,20]
also revealed that the Andean pampas cat populations are genetically
structured and may have experienced significant and lengthy periods of
isolation and reduced gene flow.
In spite of its wide distribution, the pampas cat is one of the less known felids 
and its status is affected by a variety of threats, comprising habitat
loss and fragmentation, hunting for traditional reasons and decline of
prey populations [22,23]. Lack of evaluation of its conservation status through its range causes the pampas cat to be considered as vulnerable  and to be included in the IUCN Near Threatened (NT) category .
The aim of the present study was to link the genetic diversity of
the pampas cat throughout the central Andes to ancient climate
fluctuations. To address this objective, the genetic structure of the
pampas cat in 19 localities over a distance of more than 4000 km was
inferred with both mitochondrial and nuclear genomes, using