LpictusSeqNoGapAIS

Input file for the software Alleles In Spac

Data from: Lizards on ice: evidence for multiple refugia in Liolaemus pictus (Liolaemidae) during the Last Glacial Maximum in the southern Andean beech forests

Historical climate changes and orogenesis are two important factors that have shaped intraspecific biodiversity patterns worldwide. Although southern South America has experienced such complex events, there is a paucity of studies examining the effects on intraspecific diversification in this part of the world. Liolaemus pictus is the southernmost distributed lizard in the Chilean temperate forest, whose genetic structure has likely been influenced by Pleistocene glaciations. We conducted a phylogeographic study of L. pictus in Chile and Argentina based on one mitochondrial and two nuclear genes, and recovered two strongly divergent groups, Northern and Southern clades, the former distributed from the northernmost limit of the species to the Araucanía region, and the latter being distributed throughout the Andes and the Chiloé archipelago in Southern Chile. Our results suggest that L. pictus originated 751 Kya, with divergence between the two clades occurring in the late Pleistocene. Demographic reconstructions for the Northern and Southern clades indicate a decrease in effective population sizes likely associated with Pleistocene glaciations. Surprisingly, patterns of genetic variation, clades ages and historical gene flow in populations distributed within the limits of the Last Glacial Maximum (LGM) are not explained by recent colonization. We propose an “intra-Andean multiple refuge” hypothesis, along with the classical refuge hypothesis previously proposed for the biota of the Chilean Coastal range and Eastern Andean Cordillera. Our hypothesis is supported by niche modeling analysis suggesting the persistence of fragments of suitable habitat for the species within the limits of the LGM ice shield. This type of refuge hypothesis is proposed for the first time for an ectothermic species

SecuenciasEXPH5GenBank_oK

Sequences for the nuclear gene EXPH5. Alleles at heterozygous sites were inferred with PHASE 2.

Lpictus con 2OG

Fasta file of all the mtDNA sequences used to run phylogeographic analyses on JModeltest, Bayes Phylogenies, TCS, Mega and DNAsp

SecuenciasLDB5B_GenBank

Sequences from the nuclear gene LDB5B. Alleles at heterozygous sites were inferred with PHASE 2.

Lizards on Ice: Evidence for Multiple Refugia in <em>Liolaemus pictus</em> (Liolaemidae) during the Last Glacial Maximum in the Southern Andean Beech Forests

<div><p>Historical climate changes and orogenesis are two important factors that have shaped intraspecific biodiversity patterns worldwide. Although southern South America has experienced such complex events, there is a paucity of studies examining the effects on intraspecific diversification in this part of the world. <em>Liolaemus pictus</em> is the southernmost distributed lizard in the Chilean temperate forest, whose genetic structure has likely been influenced by Pleistocene glaciations. We conducted a phylogeographic study of <em>L. pictus</em> in Chile and Argentina based on one mitochondrial and two nuclear genes recovering two strongly divergent groups, Northern and Southern clades. The first group is distributed from the northernmost limit of the species to the Araucanía region while the second group is distributed throughout the Andes and the Chiloé archipelago in Southern Chile. Our results suggest that <em>L. pictus</em> originated 751 Kya, with divergence between the two clades occurring in the late Pleistocene. Demographic reconstructions for the Northern and Southern clades indicate a decrease in effective population sizes likely associated with Pleistocene glaciations. Surprisingly, patterns of genetic variation, clades age and historical gene flow in populations distributed within the limits of the Last Glacial Maximum (LGM) are not explained by recent colonization. We propose an “intra-Andean multiple refuge” hypothesis, along with the classical refuge hypothesis previously proposed for the biota of the Chilean Coastal range and Eastern Andean Cordillera. Our hypothesis is supported by niche modelling analysis suggesting the persistence of fragments of suitable habitat for the species within the limits of the LGM ice shield. This type of refuge hypothesis is proposed for the first time for an ectothermic species.</p> </div

Geneland

Data used to run Geneland. The file includes coordinates and sequences. Nucleobases were changed by numbers (1-4) in order to be able to run Geneland

Results of Θ and migration rate between clusters of population of <i>L. pictus</i>. Clusters correspond to the same already defined by Geneland.

<p>Θ = 2Neµ. N = number of individuals in each sample. Migration rate values are in Nm. _r = receiving population.</p

Prediction of the historical effective population size in <i>L. pictus</i>.

<p>Bayesian skyline plots and mismatch analysis for the two major mtDNA clades of <i>L. pictus</i>. The black line is the temporal trend of the mean of effective population size. Vertical light blue band corresponds to the LGM.</p

Present and LGM potential distribution for <i>L. pictus</i> estimated from Ecological Niche Modeling (ENM).

<p>The color scale corresponds to the probability for suitable habitat; red and light blue indicate highest and lowest suitability values respectively. The heavy blue line delimits the maximum extension of ice shield during LGM according to Heusser <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0048358#pone.0048358-Heusser1" target="_blank">[11]</a>.</p