Brygophis coulangesi (Domergue, 1988) (Serpentes: Pseudoxyrhophiidae) and its taxonomic relationship with respect to Compsophis (Günther, 1882)
Data files
Dec 12, 2025 version files 6.48 MB
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README.md
3.87 KB
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Supplemental_S1.zip
6.47 MB
Abstract
We sequenced the commonly used barcoding gene cytochrome oxidase subunit I to determine placement of two Brygophis coulangesi specimens within a tree, with respect to the similar and more well-known genus Compsophis.
Dataset DOI: 10.5061/dryad.05qfttfg3
Description of the data and file structure
SUPPLEMENTAL S1 ("Supplemental_S1.zip"):
These data represent all files referenced in text as "Supplemental S1" used to produce results for "Brygophis coulangesi (Domergue, 1988) (Serpentes: Pseudoxyrhophiidae) and its taxonomic relationship with respect to Compsophis (Günther, 1882)" including (1) the final multilocus alignment (phylip format), including new sequences (2) the partition file for this alignment, (3) outputs supporting the selection of this partition scheme following evaluated via the AIC (from Modeltest-NG, Darriba et al. 2020), and (4) the Maximum Likelihood raw consensus bootstrapped .tre file used in Figure 3 (from RAxML-NG 1.0.2, Kozlov et al. 2019) (5) all associated intermediate files associated with the final consensus tree (the RAxML log, the best tree, the best tree collapsed, the starting tree, the bootstrap file) and (6) the CO1 p-distance matrix for all described and putatively new Compsophis included in our analyses
Files and variables
SUPPLEMENTAL S1 Files ("Supplemental_S1.zip"): Data and directories provided below correspond to (1) the final multilocus alignment, (2) the partition file (3) partition justification and (4) raw consensus bootstrapped .tre file (5) intermediate RAxML files (Final RAxML log, best tree, best tree collapsed, starting tree, bootstrap file):
(1) "Concatenated_Sanger_Brygophis_alignment.phy": aligned multilocus sequences used to estimate (4)
(2) "Concatenated_Sanger_Brygophis_partition.txt": partition file used to estimate results in (4) as derived from (3)
(3) "Concatenated_Sanger_Brygophis.bestModel": results from Modeltest-NG as implemented in RAxML-NG to evaluate the best fit partition for the multilocus dataset in (1)
(4) "Concatenated_Sanger_Brygophis_RAXML_1000bs.support.tre": full concatenated maximum likelihood tree produced in RAxML-NG tree with input files (1) and (2); bootstrap support values included
(5) "Concatenated_Sanger_Brygophis_RAxML_supplemental.zip": individual alignments for each locus used in the multilocus dataset (1)
(6) "Compsophis_COI_Alignment_MEGA_pdistances.xls": uncorrected pairwise distances for all Compsophis seuquences included in this paper calculated from a subset of Compsophis-only data available in (1)
Code/software
FigTreev1.4.4 (https://github.com/rambaut/figtree/releases/tag/v1.4.4) was used to visualize the raw tree file; BBEdit was used to view and edit .txt files and final .phy alignment. RAxML-NG 1.0.2 (Kozlov et al. 2019) was used to infer the maximum likelihood tree, and Modeltest-NG (Darriba et al. 2020) was implemented in RAxML-NG to evaluate the best fit partition for our multilocus data. Geneious Prime 2025.0.3 (https://www.geneious.com) was used to assemble new sequences and examine these data for premature stop codons. MEGA 12 (Kumar et al. 2024) was used to calculate uncorrected pairwise distances among all Compsophis.
Access information
Newly derived COI sequences are publicly available on Genbank
- Compsophis coulangesi APR13404 (UADBA73004): PV976157
- Compsophis coulangesi APR14116 (UADBA73005): PV976158
Multilocus alignment data was downloaded from the following dryad repository:
- Burbrink, Frank; Ruane, Sara; Kuhn, Arianna et al. (2019). Data from: The origins and diversification of the exceptionally rich gemsnakes (Colubroidea: Lamprophiidae: Pseudoxyrhophiinae) in Madagascar [Dataset]. Dryad. https://doi.org/10.5061/dryad.07h0n14
We combined the two new samples with a previous dataset from Burbrink et al. 2019 (Burbrink, F.T., Ruane, S., Kuhn, A., Rabibisoa, N., Randriamahatantsoa, B., Raselimanana, A.P., Andrianarimalala, M.S., Cadle, J.E., Lemmon, A.R., Lemmon, E.M. & Nussbaum, R.A., (2019) The origins and diversification of the exceptionally rich gemsnakes (Colubroidea: Lamprophiidae: Pseudoxyrhophiinae) in Madagascar. Systematic Biology, 68, 918–936.); data available on Dryad as well here https://doi.org/10.5061/dryad.07h0n14) and we performed a maximum likelihood (ML) analysis using RAxML-NG 1.0.2.