Additional file 1: Table S1. of Molecular phylogenetic analyses reveal the importance of taxon sampling in cryptic diversity: Liolaemus nigroviridis and L. monticola (Liolaeminae) as focal species

List of species and museum or scientific collection codes used in the phylogeny, locality, haplotype number and map locality. SSUC: Colección flora y fauna, Profesor Patricio Sánchez Reyes; CFFPUCV: Colección flora y fauna de la Pontificia Universidad Católica de Valparaíso. MNHNCL: Museo Nacional de Historia Natural de Chile; MZUC: Museo de Zoología de la Universidad de Concepción; CUCH: Colección de la Universidad de Chile. (PDF 86 kb

Neighbornet of HVI haplotypes.

<p>Labels for haplotypes represent the following groups: red = Mediterranean ecoregion, green = Temperate Forest ecoregion, blue = Patagonian ecoregion.</p

BI and ML haplotype trees based on the combined D-LOOP-FGB sequences for <i>P</i>. <i>darwini</i> and <i>A</i>. <i>olivacea</i>.

<p>The haplotype trees represent the intraspecific relationships of <i>P</i>. <i>darwini</i> and <i>A</i>. <i>olivacea</i> from central Chile mountaintop and lowland areas (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0180231#pone.0180231.s002" target="_blank">S2</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0180231#pone.0180231.s003" target="_blank">S3</a> Tables for the geographic location of haplotypes of <i>A</i>. <i>olivacea</i> and <i>P</i>. <i>darwini</i>, respectively). Numbers on the nodes represent the posterior probability and 1,000 bootstrap support values. Color labels on the trees represent mountaintop and/or lowland haplotypes as specified inside the figure. For <i>P</i>. <i>darwini</i> A = lineage A (coastal and Andean), B = lineage B (coastal and Andean); For <i>A</i>. <i>olivacea</i> = A = lineage A (Andean), B = lineage B (lowlands-Andean and lowlands).</p

Mountaintops phylogeography: A case study using small mammals from the Andes and the coast of central Chile

<div><p>We evaluated if two sigmodontine rodent taxa (<i>Abrothrix olivacea</i> and <i>Phyllotis darwini</i>) from the Andes and Coastal mountaintops of central Chile, experienced distributional shifts due to altitudinal movements of habitat and climate change during and after the Last Glacial Maximum (LGM). We tested the hypothesis that during LGM populations of both species experienced altitudinal shifts from the Andes to the lowlands and the coastal Cordillera, and then range retractions during interglacial towards higher elevations in the Andes. These distributional shifts may have left remnants populations on the mountaintops. We evaluated the occurrence of intraspecific lineages for each species, to construct distribution models at LGM and at present, as extreme climatic conditions for each lineage. Differences in distribution between extreme climatic conditions were interpreted as post-glacial distributional shifts. <i>Abrothrix olivacea</i> displayed a lineage with shared sequences between both mountain systems, whereas a second lineage was restricted to the Andes. A similar scenario of panmictic unit in the past was recovered for <i>A</i>. <i>olivacea</i> in the Andes, along with an additional unit that included localities from the rest of its distribution. For <i>P</i>. <i>darwini</i>, both lineages recovered were distributed in coastal and Andean mountain ranges at present as well, and structuring analyses for this species recovered coastal and Andean localities as panmictic units in the past. Niche modeling depicted differential postglacial expansions in the recovered lineages. Results suggest that historical events such as LGM triggered the descending of populations to Andean refuge areas (one of the <i>A</i>. <i>olivacea</i>’s lineages), to the lowlands, and to the coastal Cordillera. Backward movements of populations after glacial retreats may have left isolates on mountaintops of the coastal Cordillera, suggesting that current species distribution would be the outcome of climate change and habitat reconfiguration after LGM.</p></div

GENELAND analyses with posterior probability isoclines denoting the extent of genetic landscapes.

<p>The Mediterranean (2a), the Temperate Forests (2b) and Patagonia (2c) ecoregions are recovered in the figure. To facilitate interpretation, GENELAND output has been cropped, re-scaled and superimposed over the map of Chile and Argentina where <i>O. longicaudatus</i> ranges. Black dots represent localities analyzed in this study and the limit of the LGM is also shown. Regions with the greatest probability of inclusion are indicated by white, whereas diminishing probabilities of inclusion are proportional to the degree of coloring.</p

General description of hypothesized distribution for each lineage with latitudinal extension and orographic characteristics of the suitable areas.

<p>Columns are intraspecific lineages and rows represent climatic models for present and LGM conditions (CCSM and MIROC). The last row indicates if a lineage has a stable distribution since LGM until present day, or if its distribution range has changed.</p

Neighbor-Net of D-LOOP sequence haplotypes of <i>P</i>. <i>darwini</i> and <i>A</i>. <i>olivacea</i>.

<p>Labels for haplotypes on the network are explained inside the figure.</p

D-LOOP sequence variability data for the Coast, Valley and the Andes in <i>Abrothrix olivacea</i> and the Coast and the Andes for <i>Phyllotis darwini</i>.

<p>Abreviations mean Nh = number of haplotypes, Hd = haplotype diversity, S = polymorphic sites and pi = nucleotide diversity.</p

Area under the curve (AUC) average values for each distribution model.

<p>These values represent the Area under the “receiving operating characteristic” curve. AUC value measures the performance of a distribution model, which ranges from 0.5 for a random prediction to 1 for perfect prediction.</p

Descriptive statistics of genetic variation and Fu-<i>Fs</i>, Tajima's D and Ramos-Onsis & Rozas' R₂ neutrality tests of <i>O. longicaudatus</i> sequences in Chile and Argentina.

<p><i>N</i>: Number of individuals; S: Number of segregating sites; Hd: Haplotype diversity; pi: Nucleotide diversity; Θ_G = a compound parameter representing the effective population size and substitution rate estimated under the model of growing population; g: Growth parameter (<i>t</i> = 1/μ); SD: Standard deviation.</p