DOI: 10.5061/dryad.2rbnzs81c
title: Data from: When discrete characters are wanting: Continuous character integration under the phylospecies concept informs the revision of the Australian land snail <em>Thersites</em> (Eupulmonata, Camaenidae)

description: Species that are predominantly characterized by continuous instead of
 discrete morphological characters pose a challenge to species
 delimitation. Under the phylospecies concept, species are delimited by
 apomorphies, which are difficult to establish when characters are not
 discrete. In the present study, we address these challenges in the
 Australian land snail genus Thersites (family Camaenidae), where accepted
 species exhibit a scarcity of discrete distinguishing characters and
 differ in a limited range of continuous characters according to prior
 taxonomic studies. We integrate analyses of genome-scale molecular data
 with evaluations of several continuous, qualitative, and discrete
 morphological characters derived from landmarks to delineate species
 through detecting apomorphies. We found that the dimensions of the shell
 and genitals overlapped considerably among the currently accepted species.
 These overlaps may indicate morphospace saturation, which may affect
 species delineation through the gen-morph species concept. Statistical
 methods, such as Dunn’s test, failed to consistently delineate
 monophyletic taxa. Additionally, we could not derive apomorphies from the
 discretized landmarks due to the prevalence of outlier specimens. However,
 applying the Kruskal-Wallis test at certain nodes of the tree revealed
 significant differences in certain continuous characters. We propose that
 these inferred differences represent apomorphies. Ultimately, our results
 suggest that of the four species currently accepted, both T. mitchellae
 and T. novaehollandiae should be synonymized as T. novaehollandiae is
 paraphyletic with respect to T. mitchellae. In addition, T. darlingtoni
 nests within the T. richmondiana lineage, and both taxa are also
 considered synonyms. Distinct character states of the umbilicus support
 the existence of two independent lineages. One with an open (T. sp1 + T.
 sp2) and one with a closed umbilicus (T. novaehollandiae + T.
 richmondiana). The Kruskal-Wallis tests support the recognition of four
 distinct species, T. novaehollandiae and T. richmondiana, plus two new
 species.
description: # Data from: When discrete characters are wanting: Continuous character
 integration under the phylospecies concept informs the revision of the
 Australian land snail *Thersites* (Eupulmonata, Camaenidae) Dataset DOI:
 [10.5061/dryad.2rbnzs81c](10.5061/dryad.2rbnzs81c) ## Description of the
 data and file structure Folder structure of the *Thersites* project. This
 project provides an organized folder structure for the Thersites project,
 which is divided into four main modules: morphology, molecular, character,
 and GIS. Every folder was compressed into a single zip file. More README
 information can be found in every zip file, including corresponding
 software used for this dataset. ``` . ├── character │   ├── apomorphy │  
 ├── apomorphy_cont │   ├── apomorphy_lm │   ├── contmap │   ├── kmeans │  
 └── kruskal ├── GIS ├── molecular │   ├── BI │   ├── dartR │   ├──
 phylonet │   ├── ML │   ├── model │   └── MP │   ├── EIW │   ├── EW │  
 └── IW └── morphology ├── cont_phylogeny ├── genital │   ├──
 cont_phylogeny │   ├── flagellum │   ├── lm_phylogeny │   └── measurement
 ├── lm_phylogeny └── shell ``` ## Module descriptions ### morphology.zip
 The **morphology** module contains data related to the shapes and
 structures of snail shells and genitalia. Within this module, the `shell`
 folder holds data on shell morphology, while the `genital` folder is
 dedicated to genital morphology and is further subdivided into two
 folders: `flagellum`, which contains data on the flagellum, and
 `measurement`, which stores measurement data. `lm_phylogeny` contains
 phylogenetic data based on landmark analysis, and `cont_phylogeny`
 contains phylogenetic data based on continuous character analysis.
 Contains morphological measurements * **shell/** – Shell morphology
 analysis. Contains raw images (`.tif/.jpg/.png`) and processed landmark
 data (`.tps`). Analyses performed using tpsDig, tpsUtil, and MorphoJ. *
 **genital/** – Genital morphology. Subfolders: * **flagellum/** –
 Flagellum shape data processed using FIJI/ImageJ and Python scripts
 (`resample_point.py`, `draw_lines.py`) for landmark-based analysis. *
 **measurement/** – Raw measurements obtained using FIJI/ImageJ, scripts
 for plotting distributions, violin plots, and significance heatmaps
 (`gen_distribution.py`, `gen_violin_plot.py`, etc.). * **lm_phylogeny/** –
 Phylogenetic trees based on landmark analysis using TNT. Parallelized with
 `pvm`. * **cont_phylogeny/** – Phylogenetic trees based on continuous
 morphological characters using TNT. ### molecular.zip The **molecular**
 module focuses on molecular data optimization and phylogenetic analyses.
 The `dartR` folder holds SNP call data generated using dartR. The `model`
 folder contains model selection files. It includes several subfolders that
 organize different analytical methods: the `BI` folder contains data from
 Bayesian Inference phylogenetics; the `ML` folder contains Maximum
 Likelihood phylogenetics data; and the `MP` folder contains Maximum
 Parsimony phylogenetics data. The `MP` folder is further divided into
 three subdirectories, `EIW` (Extended Implied Weighting), `EW` (Equal
 Weighting), and `IW` (Implied Weighting), each corresponding to a
 different weighting strategy. Contains molecular datasets and phylogenetic
 analyses. * **dartR/** – SNP calls processed with dartR. Input CSV
 obtained from DArT company. * **model/** – Model selection files. Uses
 `modeltest-ng`. * **BI/** – Bayesian Inference phylogenetics (MrBayes). *
 **ML/** – Maximum Likelihood phylogenetics (RAxML-NG). * **MP/** – Maximum
 Parsimony phylogenetics (TNT), subfolders: * **EIW/** – Extended Implied
 Weighting, subfolder `K` contains trees obtained from different K values.
 * **EW/** – Equal Weighting * **IW/** – Implied Weighting * **phylonet/**
 Results of PhyloNet. ### character.zip The **character** module includes
 files related to character optimization projects. This module is
 subdivided into four folders, each serving a specific analytical purpose:
 the `contmap` folder contains files for continuous character mapping; the
 `kmeans` folder holds data for k-means clustering analysis; the
 `apomorphy*` folder stores apomorphy analysis results generated by TNT and
 WinClada; and the `kruskal` folder includes results from the
 Kruskal-Wallis test based on phylogenetic lineages. Contains results for
 character optimization and clustering. * **apomorphy/** – Parsimony-based
 character optimization using TNT in `wincladtree` folder and WinClada in
 `winclada` folder. * **apomorphy_cont/** – Continuous character
 optimization (TNT scripts). * **apomorphy_lm/** – Landmark-based character
 optimization aligned to molecular phylogeny using TNT. Subfolder
 `rftra_align`, `tree_align` and `unalign` contain restulst under different
 alignment methods. * **contmap/** – Continuous character mapping onto
 phylogenies using R. * **kmeans/** – K-means clustering for landmark data.
 Scripts include `nts2csv.py`, `lm_tps.py`, `lm_nts.py`, `barchart.py`. *
 **kruskal/** – Kruskal-Wallis test for phylogenetic lineages. ### GIS.zip
 Lastly, the **GIS** module is dedicated to geographic information system
 (GIS) data, which records species occurrences and distribution
 information. ## File types & software | File type | Description |
 Recommended software | | ---------- |
 ------------------------------------------------------------- |
 --------------------------------------------------- | | `.R` | R scripts |
 R 4.x | | `.py` | Python scripts | Python 3.10+ | | `.sh` | Shell scripts
 | Unix shell (bash) | | `.run` | TNT run scripts | TNT | | `.csv` |
 Tabular data for morphometrics, SNP calls, or analysis output | Any
 spreadsheet software (Excel), text editor (vim) | | `.txt` | Plain text
 files | Any text editor (vim, Notepad) | | `.svg` | Scalable vector
 graphics | Web browser, Inkscape | | `.emf` | Enhanced metafile format |
 Inkscape, Adobe Illustrator | | `.ijm` | FIJI/ImageJ macros | FIJI/ImageJ
 | | `.tps` | Landmark and semi-landmark data | tpsDig, tpsUtil, MorphoJ |
 | `.morphoj` | MorphoJ project files | MorphoJ | | `.tnt` | TNT
 phylogenetic scripts and input files | TNT | | `.fasta` | DNA sequences |
 Any sequence viewer or analysis software | | `.ss` | WinClada files |
 WinClada | | `.nwk` | phylogenetic tree | FigTree, iTOL, R (ape) | |
 `.tre` | phylogenetic tree | FigTree, iTOL, R (ape) | | `.ctf` |
 phylogenetic tree for TNT | TNT | | `.Rdata` | R data | R | | `.qgz` |
 QGIS project file | QGIS | ## Abbreviations used in csv | Abbreviation |
 Meaning | | ------------ | ------------------------------ | | id |
 individual | | seq | sequence or specimen ID | | pop | population | | lat
 | latitude | | lon | longitude | | ph | phallus | | ep1 | epiphallus
 segment 1 | | ep2 | epiphallus segment 2 | | fl | flagellum | | lm | 7
 landmarks | | slm | 2 semi-landmark group | | slm1 | semi-landmark group 1
 | | slm2 | semi-landmark group 2 | | fl50 | 50% resampled flagellum points
 | | max | maximum number | | min | minimum number | | mean | mean value |
 | std | standard deviation | | NS | not significant | | S | significant |
 | dar | darlingtoni | | mit | mitchellae | | nov | novaehollandiae | | ric
 | richmondiana | | sp1 | species1=kaputarensis | | sp2 |
 species2=coolahensis | ## Usage examples ### Morphology ```bash # Shell
 processing for py in draw_shell_width_height.py gen_distribution.py
 gen_violin_plot.py ; do python "$py" done # Flagellum resampling
 python resample_point.py input.csv ``` ### Molecular ```bash # Convert SNP
 CSV to fasta nohup Rscript Thersites.R & # Maximum Likelihood tree
 raxml-ng --all --msa gl_output_rmq.fasta --model HKY+I+G16 --bs-trees 1000
 --threads 40 # Bayesian Inference nohup mpirun -np 4 mb -i mimi.nex &
 ``` ### Character optimization ```bash # Run TNT for parsimony apomorphy
 bash character/apomorphy/run.sh # Run continuous character mapping bash
 character/contmap/run.sh # K-means clustering bash character/kmeans/run.sh
 # Kruskal-Wallis phylogeny bash character/kruskal/run.sh ```