DOI: 10.5061/dryad.05qfttfg3
title: <em>Brygophis coulangesi</em> (Domergue, 1988) (Serpentes: Pseudoxyrhophiidae) and its taxonomic relationship with respect to <em>Compsophis</em> (Günther, 1882)

description: 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. 
description: 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.
 <em>Systematic Biology</em>, 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.
description: # *Brygophis coulangesi* (Domergue, 1988) (Serpentes: Pseudoxyrhophiidae)
 and its taxonomic relationship with respect to *Compsophis* (Günther,
 1882) Dataset DOI: [10.5061/dryad.05qfttfg3](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](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](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](https://doi.org/10.5061/dryad.07h0n14)