Data from: Geography and past climate changes have shaped the evolution of a widespread lizard from the Chilean hotspot

The complex orogenic history and structure of Southern South America,
coupled with Pleistocene glacial cycles, have generated paleoclimatic and
environmental changes that influenced the spatial distribution and genetic
composition of natural populations. Despite the increased number of
phylogeographic studies in this region and given the frequent
idiosyncratic phylogeographic patterns, there is still the need to focus
research especially on species that are currently distributed within a
wide range of bioclimatic regimes, and that historically have been subject
to contrasting scenarios. Liolaemus tenuis is a widely distributed lizard
species inhabiting latitudinally in almost 1,000 km through central and
southern Chile. Here we describe the geographical patterns of genetic
variation and lineage diversification within L. tenuis, and their
association with geography and Pleistocene glaciations, using sequences
from one mitochondrial and two nuclear genes, and five microsatellite
loci, and covering most of the species distributional range. Our results
revealed a high diversity both within and among populations, as well as
two phylogeographic breaks, which are consistent with two of the larger
rivers of central Chile, the Maipo and Biobío Rivers. Liolaemus tenuis is
characterized by several allopatric lineages, especially in its north and
central range, which suggest a history of multiple vicariance processes.
Conversely, populations found in the southern range, south of the Biobío
River, show signatures of recent decreases in effective population sizes,
coupled with recent range expansions and secondary contact. Niche
“envelope” data are consistent with patterns of genetic variation; both
suggest a history of discontinuous areas of relatively stable populations
throughout all of the distribution of L. tenuis. These data are also
consistent with higher probabilities of habitat suitability north of the
Maipo River (ca. 33°S), in both coastal areas and the “Intermediate
Depression” between 34° - 37°S, as well as in the southern Coastal
Cordillera between the Biobío and Araucanía regions. Interestingly, both
molecular and niche envelope modelling data suggest that some populations
may have persisted in fragmented refugia in Andean valleys, within the
limits of the ice sheet. Finally, our results suggest that several
populations of L. tenuis colonized glaciated regions from refugial areas
in lowlands and coastal regions, and in the southern distribution,
historic migration events would have occurred from refugial areas within
the limits of the ice sheet.