A diverse assemblage and putative microendemic radiation of Stumpffia frogs (Microhylidae: Cophylinae) on Montagne d'Ambre in North Madagascar

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' sequences
AlignmentB_16S_5.fas - FASTA file of 16S 5' sequences
AlignmentC_16S_5_3.fas - FASTA file of concatenated 16S 5' and 3' sequences
AlignmentD_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.wav
Stumpffia_angeluci_ZCMV13608.wav
Stumpffia_bishopi_MSZC0730.wav
Stumpffia_huwei_MSZC0660.wav
Stumpffia_huwei_MSZC0744.wav
Stumpffia_huwei_MSZC0769_part1.wav
Stumpffia_huwei_MSZC0769_part2.wav
Stumpffia_huwei_ZCMV13618.wav
Stumpffia_huwei_ZCMV13619.wav
Stumpffia_madagascariensis_MSZC0707.wav
Stumpffia_madagascariensis_ZCMV12185.wav
Stumpffia_maledicta_MSZC0666_part1.wav
Stumpffia_maledicta_MSZC0666_part2.wav
Stumpffia_maledicta_MSZC0666_part4.wav
Stumpffia_maledicta_MSZC0724_part1.wav
Stumpffia_maledicta_MSZC0724_part2.wav
Stumpffia_maledicta_ZCMV13504_L.wav
Stumpffia_mamitika_MSZC0793_part1.wav
Stumpffia_mamitika_MSZC0793_part2.wav
Stumpffia_mamitika_not_collected_Andapa.wav
Stumpffia_mamitika_ZCMV13616.wav
Stumpffia_megsoni_MSZC0545.wav
Stumpffia_megsoni_MSZC0764.wav
Stumpffia_megsoni_MSZC0765.wav
Stumpffia_megsoni_MSZC0768_part1.wav
Stumpffia_megsoni_MSZC0768_part2.wav
Stumpffia_megsoni_MSZC0777_part1.wav
Stumpffia_megsoni_MSZC0777_part2.wav
Stumpffia_megsoni_MSZC0777_part3.wav
Stumpffia_megsoni_MSZC0777_part4.wav
Stumpffia_megsoni_MSZC0777_part5.wav

Supplementary 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 ACCEPTANCE
Supplementary 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).