DOI: 10.5061/dryad.fbg79cnsn
title: Evolutionary footprints of a cold relic in a rapidly warming world

description: With accelerating global warming, understanding the evolutionary dynamics
 of plant adaptation to environmental change is increasingly urgent. Here
 we reveal the enigmatic history of the genus Cochlearia (Brassicaceae), a
 Pleistocene relic that originated from a drought-adapted Mediterranean
 sister genus during the Miocene. Cochlearia rapidly diversified and
 adapted to circum-Arctic regions and other cold-characterized habitat
 types during the Pleistocene. This sudden change in ecological preferences
 was accompanied by a highly complex, reticulate polyploid evolution, which
 was apparently triggered by the impact of repeated Pleistocene glaciation
 cycles. Our results illustrate that two early diversified arctic-alpine
 diploid gene pools contributed differently to the evolution of this young
 polyploid genus now captured in a cold-adapted niche. Metabolomics
 revealed central carbon metabolism responses to cold in diverse species
 and ecotypes, likely due to continuous connections to cold habitats that
 may have facilitated widespread adaptation to alpine and subalpine
 habitats, and which we speculate were coopted from existing drought
 adaptations. Given the growing scientific interest in adaptive evolution
 of temperature-related traits, our results provide much-needed taxonomic
 and phylogenomic resolution of a model system as well as first insights
 into the origins of its adaptation to cold.
description: <b>The data supplements contain:</b><br>
   <b>a)
 Supplementary Data Set 1</b><br>
 SupplementaryDataSet1_CytogeneticDataSurvey.xlsx<br> <b>This
 file contains 575 georeferenced chromosome counts and/or genome sizes
 across the <i>Cochlearia</i> genus.</b> <b>b) Supplementary Data
 Set 2</b><br>
 SupplementaryDataSet2_AccessionDetailsNGSdata.xlsx<br> <b>This
 file contains detailed information on 65 <i>Cochlearia</i>
 samples and 3 <i>Ionopsidium</i> samples included in NGS data
 generation and analysis.</b> <b>c) Supplementary Data
 Set 3</b><br>
 SupplementaryDataSet3_MetabolicCompoundMatrix.xlsx<br> <b>This
 file contains raw and normalized tables of 40 metabolic compounds
 consistently detected in all analyzed samples.</b> <b>d) Supplementary Data
 Set 4</b><br>
 SupplementaryDataSet4_FlowCytometrySummaryTable.xlsx<br>
 <b>This file contains detailed flow cytometry
 results.</b> <b>d) Supplementary Data
 Set 5</b><br>
 SupplementaryDataSet5_PlastomeAlignment.txt<br> <b>This file
 provides the plastome alignment as used for RAxML and BEAST
 analyses.</b> <b>e) Supplementary Data
 Set 6</b><br>
 SupplementaryDataSet6_PlastomePartitionfileRaxmlBEAST.txt<br>
 <b>This file contains data partitioning schemes for plastome RAxML
 and BEAST analyses.</b> <b>f) Supplementary Data
 Set 7</b><br>
 SupplementaryDataSet7_MitochondrialContigs.zip<br> <b>This
 folder contains annotated mitochondrial de novo consensus sequences of
 sample Cmica_0979 (in Genbank Flat File Format (*.gb)), as used as
 reference sequences in reference-based mappings and named as
 follows:</b> 
 SupplementaryDataSet7a.gb
 SupplementaryDataSet7b.gb
 SupplementaryDataSet7c.gb
 SupplementaryDataSet7d.gb
 SupplementaryDataSet7e.gb
 SupplementaryDataSet7f.gb
 SupplementaryDataSet7g.gb SupplementaryDataSet7h.gb <b>g) Supplementary Data Set 8</b><br> SupplementaryDataSet8_MitochondrialGenomeAlignment.txt<br> <b>This file provides the alignment of mitochondrial genome sequences as inputted into RAxML analysis.</b> <b>h) Supplementary Data Set 9</b><br> SupplementaryDataSet9_nrSNPalignmentRAxML.phy<br> <b>This file provides the alignment of transcriptome-wide nuclear SNPs in phylip format as inputted into RAxML analysis.</b> <b>i) Supplementary Data Set 10</b><br> SupplementaryDataSet10_nrSNPsSplitstreeTreemix.vcf.zip<br> <b>This file provides hard-filtered biallelic transcriptome-wide nuclear SNPs in VCF format as used for SplitsTree and TreeMix analyses.</b> <b>j) Supplementary Data Set 11</b><br> SupplementaryDataSet11_nrSNPsStructure.txt<br> <b>This file provides the input for the STRUCTURE analysis of 62 <i>Cochlearia</i> samples.</b> <b>k) Supplementary Data Set 12</b><br> SupplementaryDataSet12_nrSNPsStructureBavarica.txt<br> <b>This file provides the input for the STRUCTURE analysis of <i>Cochlearia bavarica</i>.</b> <b>l) Supplementary Data Set 13</b><br> SupplementaryDataSet13_nrSNPsABC.vcf.gz<br> <b>This file provides the input for the ABC modelling in VCF format.</b>