Species delimitation in the symphyotrichum subulatum group (Asteraceae) reveals a new species in central Mexico
Data files
Mar 21, 2024 version files 58.77 KB
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Caribbean_clade.xlsx
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README.md
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Symphyotrichum_morphometrics_final.csv
Abstract
Symphyotrichum (Asteraceae) is a well-circumscribed genus on the basis of morphological and molecular data, but species boundaries remain poorly understood. Here, the species delimitation of the contentious Symphyotrichum subulatum group (Symphyotrichum subg. Astropolium) is illuminated using morphometric, phylogenomic, and geographical analyses. Symphyotrichum mexicanum sp. nov., a new species endemic to central Mexico, is described and distinguished from Symphyotrichum expansum based on its morphometric attributes, phylogenetic placement, geographic range, and ecological specialization.
README: Symphyotrichum Mexicanum Description
Morphometrics:
This includes the R script that uses a .csv file to create ggplot, boxplots, perform MANOVA and PairWise significance.
- /PCA_MANOVA.r: R script for analysis.
- Symphyotrichum_morphometrics_final.csv: CSV file that contains the morphometric data required for the analysis
Phylogenomics:
This includes the shell scripts to clean the sequencing data, doing the alignments, getting ASTRAL and RaxML tree
- Caribbean_clade.xlsx: Excel file for running the analysis
- 1_astropolium_project_selector.sh: Shell script to check all sequences, remove bad sequences, and detect duplicates
- 2_process_align_astropolium.sh: Shell script to do the alignments and get the gene trees for ASTRAL, concatenate alignments and get the concanated tree
- astral.astropolium.renamed 2.tre: ASTRAL result
- astropolium.raxml.support.renamed 2.tre: RAxML result
- symphyo_add_county_state.sh: Shell script to add county and state to each species
Code/Software
- RStudio, Bash