Data from: Cold origins limit the establishment of northern temperate plants in the Southern Hemisphere
Data files
May 19, 2026 version files 103.79 MB
-
240611_FA_IRb_Poregonus_trimmed.fasta
25.41 MB
-
240611_FA_IRb_Poregonus_trimmed.phylip
25.42 MB
-
240903_Glatispicea_Alignment_IRb_trimmed.phylip
948.18 KB
-
240916_combined.tree
14.34 MB
-
BioGeoBEARS.zip
11.60 KB
-
chloroplast_dated_tree.nex
22.52 KB
-
chloroplast_ML_tree.nex
22 KB
-
Final_alignments.zip
29.71 MB
-
Meliceae_biogeo.csv
12.76 KB
-
ML_coalescent_tree.nex
37.72 KB
-
Occurrence.zip
7.85 MB
-
README.md
3.88 KB
Abstract
Plants with amphitropical distributions have closely related populations in both Northern and Southern Hemispheres, but are absent from the intervening tropics. They provide a unique opportunity to study the constraints shaping the distribution of temperate lineages through time. Using grasses from the ecologically diverse supertribe Melicodae, an emerging study system with species distributed throughout the temperate regions, we test the hypothesis that geography and/or environmental niche constrain which lineages successfully cross the tropics to establish in the opposite hemisphere. Biogeographic and evolutionary modelling was conducted on well resolved plastid and nuclear phylogenies constructed from whole-genome sequencing of 178 Melicodae grasses. Results show that species from areas with cold winters are much less likely to successfully cross the tropics, with lineages that establish amphitropical distributions all sharing warmer niches that evolved prior to establishment in the opposite hemisphere. Evidence suggests that this result is explained both by the greater distances that high latitude, cold origin lineages must disperse to cross the tropics, and inherent limitations associated with colder thermal niches. In particular, our results are consistent with the hypothesis that trade-offs between cold-tolerance and competitive ability contribute to the limited success of cold origin species in successfully crossing the tropics. These results provide insight into the drivers of the distribution and diversity of plants, and the challenges facing cold origin lineages in a rapidly warming world. If cold origin species occupy a smaller proportion of their potential range, and are unlikely to establish in new areas with suitable climates, their ability to track preferred habitat as climates warm may be worse than currently expected.
https://doi.org/10.5061/dryad.dz08kps7q
Description of the data and file structure
Phylogenetic, biogeographic, geospatial, and environmental niche data for grasses in the supertribe Melicodae. Data used to test hypotheses regarding the biogeographic and environmental niche evolution of the group.
Files and variables
File: 240903_Glatispicea_Alignment_IRb_trimmed.phylip
Description: final trimmed chloroplast alignment for supplementary phylogenetic analyses of Glyceria latispicea
File: 240611_FA_IRb_Poregonus_trimmed.phylip
Description: final trimmed chloroplast alignment in phylip format
File: chloroplast_ML_tree.nex
Description: Maximum likelihood bootstrap consensus tree constructed from chloroplast sequence data
File: chloroplast_dated_tree.nex
Description: Dated maximum clade credibility tree from diverge time analysis using chloroplast sequence data
File: Meliceae_biogeo.csv
Description: biogeographic classification for sampled species
Variables
- species: species name
- range: description of species biogeographic range
- class.i: biogeographic classification of range using 6 areas -- africa, atlantic.island, australia, north.america, palearctic (incl. North Africa), and south.america; cases consisting of multiple areas are separated by commas (e.g., north.america,palearctic)
- tips: corresponding tip names in dated chloroplast phylogeny, blanks entered for species not sampled in our phylogenetic tree
- notes: notes about biogeographic descriptions and classification
File: BioGeoBEARS.zip
Description: compressed folder including files formatted for running DEC analyses in the R package BioGeoBEARS, additional READ ME inside
File: 240916_combined.tree
Description: final nuclear gene trees used in coalescent analyses
File: ML_coalescent_tree.nex
Description: Coalescent tree computed from 2837 nuclear gene trees
File: 240611_FA_IRb_Poregonus_trimmed.fasta
Description: final trimmed chloroplast alignment in fasta format
File: Final_alignments.zip
Description: compressed folder containing all 2837 final nuclear gene alignments
File: Occurrence.zip
Description: compressed folder including vetted occurrence records and files used in vetting of occurrence records, additional READ ME inside
Code/software
Most of the data should be viewable in typical spreadsheet software (e.g., excel), although occurrence record and climate datasets will likely need to be opened in R or an equivalent program.
Alignments and tree files can be viewed in text editors or alignment software such as Geneious. Trees may also be visualized in R using a variety of packages (e.g., ape).
The following code files are available in association with these data (Zenodo):
## BioGeoBEARS.r - R code used to fit all primary DEC models in BioGeoBEARS
## BioGeoBEARS optim.r - R code used to run model optimization given a saved model object (see BioGeoBEARS.r)
## BioGeoBEARS stochastic mapping.r - R code used to run biogeographic stochastic mapping given a saved model object (see BioGeoBEARS.r)
## GIS data.r - R code used to vet raw GBIF occurrence records and extract climate data from WorldClim rasters
## threshold models.r - R code used to fit Bayesian threshold models
## OUwie models.r - R code used to fit evolutionary models using OUwie
## Genome and Marker Assembly.zip - compressed folder including code for assembling chloroplast genomes & nuclear markers and running phylogenetic analyses
Access information
Other publicly accessible locations of the data:
- N/A
Data was derived from the following sources:
- N/A
