Contrasting levels of β-diversity and underlying phylogenetic trends indicate different paths to chemical diversity in highland and lowland willow species
Authors/Creators
- 1. Biology Centre of the Czech Academy of Sciences, 37005 Ceske Budejovice, CZ; 2 Faculty of Science, University of South Bohemia
- 2. Biology Centre of the Czech Academy of Sciences, 37005 Ceske Budejovice, CZ; 3 Department of Biology, Aarhus University, 8000 Aarhus, DK
- 3. Biology Centre of the Czech Academy of Sciences, 37005 Ceske Budejovice, CZ
- 4. Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Goettingen, Göttingen, Germany
- 5. Natural Chemistry Research Group, Department of Chemistry, University of Turku, FI- 20500 Turku, FI
- 6. Agriculture and Environment Department, Harper Adams University, Newport, UK
- 7. Department of Integrative Biology, University of Texas at Austin, Austin, TX, US; Smithsonian Tropical Research Institute, Apartado 0843–03092, Ancón, PA
Description
Diverse specialized metabolites contributed to the success of vascular plants in colonizing most terrestrial habitats. Understanding how distinct aspects of chemical diversity arise through heterogeneous environmental pressures can help us understand the effects of abiotic and biotic stress on plant evolution and community assembly. Here we examine highland and lowland willow species within a phylogenetic framework to test for trends in their chemical α-diversity (richness) and β-diversity (variation among species sympatric in elevation). We show that differences in chemistry among willows growing at different elevations occur mainly through shifts in chemical β-diversity and convergence or divergence among species sharing their elevation level. We also detect contrasting phylogenetic trends in concentration and α-diversity of metabolites in highland and lowland willow species. The resulting elevational patterns contribute to the chemical diversity of Salix and suggest that variable selective pressure across ecological gradients may, more generally, underpin complex changes in plant chemistry.
In this repository, you will find all the data related to our paper:
1) Phylogenetic_trees.zip: Zip file comprising the phylogenetic trees before prunning. Specifically, there are two folders:
- Concatenation_iqtree: this folder comprises the phylogenetic tree inferred from the maximum likelihood analysis in IQTREE.
- Speciestree_astral: this folder comprises two subfolders: 1) final_species_tree, it comprises the results from the species tree analysis inferred in ASTRAL-III; 2) gene_trees; it comprises a phylogenetic tree for each 7,636 locus that were used as an input to compute the species tree.
2) Reference_targets.zip: Zip file comprising the fasta files used in the mapping step. Specifically, there are two folders:
- First_approach: the reference fasta file here comprises the consensus sequence for each locus identified in a previous RADseq study (Wagner et al. 2020).
- Second_approach: the reference fasta here is based on our second mapping step where trimmed multiple sequence alignments were used to generate a consensus sequence for each locus by using the reference-based function in SECAPR.
3) Multiple_sequence_alignments.zip: Zip file comprising a fasta file for 7,636 multiple sequence alignments used to infer the phylogenetic trees.
4) Traits_data.zip: Traits_data.zip: Zip file comprising the trait data. Specifically, there are:
- CSCS_matrices_metadata.txt - this file contains metadata for all CSCS matrices.
- CSCS_matrix_all_metabolites.txt - this file contains the CSCS matrix showing structural dissimilarity in all metabolites among the studied plant species.
- CSCS_matrix_flavonoids.txt - this file contains the CSCS matrix showing structural dissimilarity in flavonoids among the studied plant species.
- CSCS_matrix_salicinoids.txt - this file contains the CSCS matrix showing structural dissimilarity in salicinoids among the studied plant species.
- Trait_metadata.txt - this file contains metadata for Trait_data.txt that shows individual level traits and environmental variables for the studied plants.
- Trait_data.txt - this file contains individual level traits and environmental variables for the studied plants.