DOI: 10.5281/zenodo.16385862
title: A diverse assemblage and putative microendemic radiation of Stumpffia frogs (Microhylidae: Cophylinae) on Montagne d'Ambre in North Madagascar

description: Supplementary files associated with the publication 'A diverse assemblage and putative microendemic radiation of Stumpffia frogs (Microhylidae: Cophylinae) on Montagne d’Ambre in North Madagascar'. 

Contains:

Alignments:

AlignmentA_16S_3.fas - FASTA file of 16S 3' sequencesAlignmentB_16S_5.fas - FASTA file of 16S 5' sequencesAlignmentC_16S_5_3.fas - FASTA file of concatenated 16S 5' and 3' sequencesAlignmentD_RAG1_Stumpffia.fas - FASTA file of RAG1 sequences for input into Hapsolutely

Parition file:

Rag1_partition.txt - partitions for the RAG1 alignment for input into Hapsolutely

Call recordings in the format Genus_species_Fieldnumber.wav:

Stumpffia_angeluci_MSZC0531.wavStumpffia_angeluci_ZCMV13608.wavStumpffia_bishopi_MSZC0730.wavStumpffia_huwei_MSZC0660.wavStumpffia_huwei_MSZC0744.wavStumpffia_huwei_MSZC0769_part1.wavStumpffia_huwei_MSZC0769_part2.wavStumpffia_huwei_ZCMV13618.wavStumpffia_huwei_ZCMV13619.wavStumpffia_madagascariensis_MSZC0707.wavStumpffia_madagascariensis_ZCMV12185.wavStumpffia_maledicta_MSZC0666_part1.wavStumpffia_maledicta_MSZC0666_part2.wavStumpffia_maledicta_MSZC0666_part4.wavStumpffia_maledicta_MSZC0724_part1.wavStumpffia_maledicta_MSZC0724_part2.wavStumpffia_maledicta_ZCMV13504_L.wavStumpffia_mamitika_MSZC0793_part1.wavStumpffia_mamitika_MSZC0793_part2.wavStumpffia_mamitika_not_collected_Andapa.wavStumpffia_mamitika_ZCMV13616.wavStumpffia_megsoni_MSZC0545.wavStumpffia_megsoni_MSZC0764.wavStumpffia_megsoni_MSZC0765.wavStumpffia_megsoni_MSZC0768_part1.wavStumpffia_megsoni_MSZC0768_part2.wavStumpffia_megsoni_MSZC0777_part1.wavStumpffia_megsoni_MSZC0777_part2.wavStumpffia_megsoni_MSZC0777_part3.wavStumpffia_megsoni_MSZC0777_part4.wavStumpffia_megsoni_MSZC0777_part5.wavSupplementary tables:

Flecketal_Supplementary_tables_Stumpffia_Montagne_d'Ambre_2025-04-20.xlsx

— this file contains the following tables as separate Sheets:

Supplementary Table S1. Approximate fragment sizes (bp), primer sequences and thermal cycling profiles used for the amplification of DNA fragments. Thermal cycling schemes start with temperature (in °C) of each step, followed by the time in seconds between parentheses; cycling repetitions are indicated within brackets. Direction is given as “F” for forward and “R” for reverse primer.Supplementary Table S2. GenBank accession numbers for all sequences used in Alignments A, B, and C. WILL BE COMPLETED UPON PAPER ACCEPTANCESupplementary Table S3. Pairwise uncorrected p-distances of the 16S 5’ phylogeny calculated from Alignment B, given as ‘mean (minimum – maximum)’ and in percent.Supplementary Table S4. Pairwise uncorrected p-distances of the 16S 3’ phylogeny calculated from Alignment A, given as ‘mean (minimum – maximum)’ and in percent.Supplementary Table S5. Morphometric data from Stumpffia species occurring on Montagne d’Ambre. For abbreviations see ‘Material and methods’ section. ‘Mea’ is measurer (AR=A. Rakotoarison; NJF=N. J. Fleck). This data is an alignment of own measurements as well as data from to Rakotoarison et al. (2017, 2022). Numbers are given in mm.Supplementary Table S6. Morphometric data from Stumpffia species occurring on Montagne d’Ambre. Specimens were collected on Montagne d’Ambre (‘d’Ambre’) or at a different location (‘not d’Ambre’). For abbreviations see Material and methods section. This data is a combination of our own measurements as well as data from Rakotoarison et al. (2017, 2022). Values are given in mm as ‘minimum – maximum (mean ± standard deviation, N=number of examined specimens)’. See Supplementary Table S2 for our raw measurement data.Supplementary Table S7. Pairwise uncorrected p-distances of the concatenated 16S 3’ and 5’ phylogeny calculated from Alignment C, given as ‘mean (minimum – maximum)’ and in percent.

Supplementary figures:

Suppl Fig 1 16S5_-Clade-A-phylogeny_2024-11-27.jpg – Supplementary Figure S1. Maximum Likelihood Phylogeny of Stumpffia based on Alignment B (5’ 16S). Node labels are given as bootstrap values, not displayed when below 50.

Suppl Fig 2 (full 16S5_ phylogeny) .pdf – Supplementary Figure S2. Maximum Likelihood Phylogeny of Stumpffia based on Alignment A (16S 3’). Node labels are given as bootstrap values, not displayed when below 50.

Suppl Fig 3 (full 16S3_ phylogeny) .pdf – Supplementary Figure S3. Bayesian Phylogeny of Stumpffia based on the concatenated Alignment C (3’+5’ 16S). Node labels are given as posterior probabilities. Bolded species and specimens indicate occurrence on Montagne d’Ambre.

Suppl Fig 4 (16S3_x5_ Bayesian phylogeny).pdf – Supplementary Figure S4. Maximum Likelihood Phylogenies of Stumpffia based on Alignment B (16S 5’). Only members of Clade A according to Rakotoarison et al. (2017) are shown; their position in the overall Stumpffia phylogeny is indicated by a grey rectangle. Specimens from Montagne d’Ambre are bolded. Node labels are given as bootstrap values, not displayed when below 50.

Suppl Fig 5 PC3vsPC4.pdf – Supplementary Figure S5. Third and fourth principal components of our principal component analysis (PCA) of morphometric data on Stumpffia that occur on Montagne d’Ambre (raw data in Supplementary Table S2).