DOI: 10.6084/m9.figshare.25459135
title: The late rise of sky-island vegetation in the European Alps: Supplementary data

description: This README.txt file was generated 22.03.2024 by Lara Wootton

GENERAL INFORMATION
==========================

Title of Dataset
-------------------

Data from: 'Pleistocene climatic cycles, landscape dynamics and the late rise of sky-island vegetation in the European Alps' 

Author Information
-------------------

 Corresponding author
 Name: Lara Wootton
 Institution: Université Grenoble Alpes, Laboratoire d’Ecologie Alpine, FR-38000 Grenoble, France
 Email: larawootton@gmail.com
 
 Co-authors
 Names: Florian C Boucher, Charles Pouchon, Cristina Roquet, Eric Coissac, Inger G Alsos, Pierre Valla, Laurent Husson, Matthias Bernet, Christophe Perrier, Rolland Douzet, Maxime Rome, Jean-Gabriel Valay, Adriana Alberti, France Denoeud, Niklaus E. Zimmermann, Patrick Wincker, Wilfried Thuiller, Julien Renaud, PhyloNorway consortium, PhyloAlps consortium, Sébastien Lavergne




Methodological Information
==========================

* Methods of data collection/generation: see manuscript for details


Data Overview
======================

Setup
-------------------

* Unpacking instructions: Unzip folders before use

* Recommended software/tools: RStudio 2022.07.2; R version 4.1.2


Table of contents
-------------------

* Biogeographic_origins
* Data
* Scripts
* Tree_files
* TreePL


File/Folder Details
==========================


Folder: Tree_files
-------------------

Phylogenies inferred from 79 coding DNA sequences (CDS) and four noncoding rRNA genes. Tip labels contain taxon names (as identified by accession provider), NCBI number, project ID number and sequencing ID number.

* 230525_rooted_seedtree_families.tre
 -&gt; Phyloalps tree that has been rooted on Ginkgo biloba, and has been subset to include only seed plants and exclude duplicated accessions.

* 230525_rooted_seedtree_branch_x20.tre
 -&gt; As above, but branch lengths multiplied by 20 to improve dating outcomes. This is the input phylogeny to the TreePL analysis.
 
* 230601_treePLV2_final_run1_01.tre 
 -&gt; Fully dated seed plant tree. This is the output phylogeny from the TreePL analysis.
 
* 231108_pruned_phyloalps_tree.tre
 -&gt; Dated tree used for downstream analyses. This is "230601_treePLV2_final_run1_01.tre" filtered to include only angiosperms and a single accessions per species.
 
* Bootstraps.zip
 -&gt; Zip file containing 100 dated bootstrap phylogenies containing the same accessions as "230601_treePLV2_final_run1_01.tre".
 

Folder: TreePL 
-------------------

* 230525_treepl_opt_V2_final_run1_01.txt 
 -&gt; The TreePL optimisation file required to date the phylogeny
 
 
Folder: Biogeographic_origins 
-------------------

Results of a literature search to find the biogeographic origins of all EASI species

* 231206_biogeographic_origins.csv
 -&gt; Variables: Tip = Accession name in the phylogeny
 Taxon name = Name of the taxon (taxonomy following Euro+Med PlantBase (http://www.europlusmed.org))
 Assembly_process = The assembly process generating each sky-island species.
 Reference = Reference used to assign biogeographic origin
 Biogeographic_origin = The biogeographic origin as found in reference
 Broad_biogeo_category = Biogeographic assignation in this manuscript
 
 
Folder: Data 
------------------- 
All data needed to reconstruct assembly processes through time

* 240221_species_classified_by_process.csv
 -&gt; This file contains the ancestral and current elevational and geographic distributions of all species in this study. 
 -&gt; Variables: Tip = Accession name in the phylogeny
 EuroMedAcceptedName_formatted = Name of the taxon (taxonomy following Euro+Med PlantBase (http://www.europlusmed.org))
 naming_family = Taxon family
 Distribution = Distribution across the European Alpine System. EAS = core distribution of the taxon lies within the European Alpine System. Non_EAS = core distribution of the taxon does not lie within the European Alpine System.
 Status = Whether we considered the taxon to be a sky-island or non-sky-island taxon. Island = sky-island taxon. Mainland = non-sky-island taxon.
 Ancestor_EN = Ancestral distribution across the European Alpine System based on an ancestral state reconstruction. EAS = core distribution of the taxon lies within the European Alpine System. Non_EAS = core distribution of the taxon does not lie within the European Alpine System.
 Ancestor_IM = Whether that ancestral state of the is sky-island or non-sky-island based on a ancestral state reconstruction. Island = sky-island taxon. Mainland = non-sky-island taxon.
 Clade_name = Identifier to show which species are part of the same sky-island 'clade'.
 Notes = References or reasons to overrule reconstructed assembly process of taxon.
 Type = The reconstructed assembly process of each taxon.
 
* 240201_singletons0.5_bootstraps.RData 
 -&gt; Rate (species per lineage per 0.5 My) of single speciation through time for the 100 bootstrap trees.
 
* 240201_singletons0.5_OG.RData
 -&gt; Rate (species per lineage per 0.5 My) of single speciation through time for the ML tree.
 
* 240201_colonisation_bootstraps_500K.RData
 -&gt; Rate (species per lineage per 0.5 My) of colonisation through time for the 100 bootstrap trees.

* 240201_colonisation_rate_OG_500K
 &gt; Rate (species per lineage per 0.5 My) of colonisation through time for the ML tree.
 
* 240201_V2_clad_rate_boots0.5.RData
 -&gt; -&gt; Rate (species per lineage per 0.5 My) of cladogenetic speciation through time for the 100 bootstrap trees.

* 240201_V2_clad_rate_og0.5.RData 
 -&gt; Rate (species per lineage per 0.5 My) of cladogenetic through time for the ML tree.
 
* 240201_DAISE_df.csv
 -&gt; Input data required to replicate the DAISIE (Valente et al 2015) analysis
 
 

Folder: Scripts 
-------------------

* 240221_ancestral_state_reconstructions.R
 -&gt; Script to reconstruct sky-island/non-sky-island and EAS/non_EAS ancestral states.

* 240221_cladogenesis_rate.R
 -&gt; Script to calculate cladogenetic speciation rate through time.
 
* 240221_single_speciation_rate.R
 -&gt; Script to calculate single speciation rate through time.
 
* 240221_colonisation_rate.R
 -&gt; Script to calculate colonisation rate through time. 
 
* 240222_break_point_loop.R
 -&gt; Example script to test for the effects of geo-climatic events on assembly rates using a break point analysis.
 
* 240222_DAISIE.R
 -&gt; Example script to calculate average rates of assembly processes using DAISIE (Dynamic Assembly of Islands through Speciation, Immigration and Extinction).