DOI: 10.5061/dryad.c5271
title: Data from: Climatic niche evolution in the Andean genus Menonvillea (Cremolobeae: Brassicaceae)

description: The study of how climatic niches change over evolutionary time has
 recently attracted the interest of many researchers. Different
 methodologies have been employed principally to analyze the temporal
 dynamics of the niche and specially to test for the presence of
 phylogenetic niche conservatism. Menonvillea, a genus of Brassicaceae
 including 24 species, is distributed primarily along the Andes of
 Argentina and Chile, with some taxa growing in southern Patagonia and
 others in the Atacama Desert and the Chilean Matorral. The genus is highly
 diversified morphologically but also presents a remarkably wide ecological
 range, growing from the high Andean elevations, to the dry coastal deserts
 in Chile, or the Patagonia Steppe in Argentina. In this study, we used
 molecular phylogenies together with climatic data to study climatic niche
 evolution in the genus. The results show that the main climatic niche
 shifts in Menonvillea occurred between the sections Cuneata-Scapigera and
 sect. Menonvillea throughout the Mid-Late Miocene, and associated with the
 two main geographical distribution centers of the genus: the highlands of
 the central-southern Andes and the Atacama Desert-Chilean Matorral,
 respectively. Climatic niches in these lineages were mainly differentiated
 by the aridity and potential evapotranspiration, the minimum temperatures
 of the coldest month, and the temperature annual range and seasonality.
 Niche evolution in Menonvillea deviated from a Brownian motion process,
 with most of the climatic dimension best-fitting to an Ornstein-Uhlenbeck
 model of multiple adaptive peaks. Our results also indicated that higher
 aridity levels and lower annual temperature ranges were associated with
 the evolution of the annual habit, as exemplified by the distribution of
 sect. Menonvillea. Finally, the results suggested that climatic niche
 evolution in Menonvillea exhibited some degree of phylogenetic niche
 conservatism, fundamentally within the two main lineages (sect.
 Menonvillea and sects. Cuneata-Scapigera).
description: ITS
 alignmentNuclear ribosomal ITS
 aligned matrixITS_BEAST.nextrnL-F alignmentChloroplast trnL-F aligned matrixtrnLF_BEAST.nextrnH-psbA alignmentChloroplast trnH-psbA intergenic spacer aligned matrixtrnH_BEAST.nexrps16 intron alignmentchloroplast rps16 intron aligned matrixrps16_BEAST.nexBEAST species tree analysesxml file for species tree analyses in BEAST v2.3.0 under the coalescent-based method implemented in *BEAST extension, using ribosomal ITS and three chloroplast DNA regions(trnL-F, trnH-psbA, rps16 intron), uncorrelated lognormal relaxed clock models, and two secondary calibrations under normal prior distributions.MEN_coalescent-based_method.xmlMCCT from species tree analysesMaximum clade credibility species tree (MCCT) estimated in BEAST v2.3.0 from nuclear ribosomal ITS and three chloroplast DNA regions(trnL-F, trnH-psbA, rps16 intron) using the multispecies coalescent method implemented in *BEAST, uncorrelated lognormal relaxed clock models, and two secondary calibrations under normal prior distributions.MCCT_species_tree_analyses.tre1000 trees from species tree analyses1000 randomly subsampled posterior trees from the Bayesian species tree analyses in BEAST v2.3.0 using ribosomal ITS and three chloroplast DNA regions(trnL-F, trnH-psbA, rps16 intron), the multispecies coalescent method implemented in *BEAST, uncorrelated lognormal relaxed clock models, and two secondary calibrations under normal prior distributions.1000_trees_species_tree_analyses.treBEAST concatenated analysesxml file for concatenated analyses in BEAST v2.3.0 under the concatenated method implemented in BEAST, using nuclear ribosomal ITS and three chloroplast DNA regions (trnL-F, trnH-psbA, rps16 intron), uncorrelated lognormal relaxed clock models, and two secondary calibrations under normal prior distributions.MEN_concatenated-based_method.xmlMCCT from concatenated analysesMaximum clade credibility tree (MCCT) estimated in BEAST v2.3.0 from nuclear ribosomal ITS and three chloroplast DNA regions (trnL-F, trnH-psbA, rps16 intron) using the concatenated method, uncorrelated lognormal relaxed clock models, and two secondary calibrations under normal prior distributions.MCCT_concatenated_analyses.treMaterials and Methods for phylogenetic analysesDescriptions for all phylogenetic analyses conducted in this studyphylogenetic_analyses.docxSpecies occurrenceSpecies ocurrence data used in the niche analysesSpecies_Ocurrence.xlsx