Corresponding author: Miguel Vences (
Academic editor Raffael Ernst
The small arboreal frog
Koppetsch T, Pabijan M, Hutter CR, Köhler J, Gehring P-S, Rakotoarison A, Ratsoavina FM, Scherz MD, Vieites DR, Glaw F, Vences M (2023) An initial molecular resolution of the mantellid frogs of the
Madagascar is renowned for the high proportion of microendemism of its biota (
The dichotomy between microendemic vs. widespread species also characterizes
Across its range,
In the present study we provide data on the phylogeography and systematics of the
Samples for this study were collected during various field campaigns in Madagascar between 2000–2016. Frogs were caught either during nocturnal searches, typically by locating calling males and breeding individuals in swamps, or during the day by searching in
Morphometric measurements were taken by TK and MV at an accuracy of 0.1 millimeter with a manual caliper. The following measurements were taken: snout–vent length (
We recorded vocalizations in the field using different types of tape recorders (Tensai RCR-3222, Sony WM-D6C) with external microphones (Sennheiser Me-80, Vivanco EM 238), and with a digital recorder with built-in microphones (Edirol R-09). Recordings were sampled or re-sampled at 22.05 kHz and 32-bit resolution and computer-analyzed using the software Cool Edit Pro 2.0. We obtained frequency information through Fast Fourier Transformation (
To examine the phylogeography and genetic differentiation within the
(1) For an initial screening of genetic variation in all available samples, we used a fragment of the mitochondrial cytochrome
(2) To understand the concordance between the variation in mitochondrial and nuclear-encoded genes, we amplified fragments of four nuclear-encoded, protein-coding genes: recombination-activating gene 1 (
(3) To infer the phylogenetic position of lineages in the
(4) For an additional phylogenomic verification of lineage relationships and resolution of deep nodes in the tree, we applied the FrogCap sequence capture strategy to sequence 12,951 nuclear-encoded markers from a set of selected samples, using methods described below.
PCR products of datasets 1–3 were purified with Exonuclease I and Shrimp Alkaline Phosphatase digestion. The mitochondrial gene fragments were sequenced with the forward primer only, nuclear genes were sequenced on both strands and combined after careful inspection of reads to ensure correct identification of double peaks indicative of heterozygous nucleotide positions. Multiple heterozygous sites in two of the nuclear genes impeded accurate computational haplotype inference. We therefore selected a set of representative samples (7 samples for
The sequence capture probe set used for assembling dataset 4 of this study is the FrogCap
Genomic DNA was extracted from selected tissue samples using a PROMEGA Maxwell bead extraction robot, quantified, and used for library preparation by Arbor Biosciences library preparation service (Ann Arbor, Michigan, USA) using Illumina Truseq-style sticky-end library preparation. Following enrichment using the MYbaits v. 3.1 protocol, library pools were amplified for 10 cycles using universal primers and sequenced on an Illumina HiSeq X Ten with 150 bp paired-end reads. Raw reads can be found on the NCBI SRA: BioProject: PRJNA924698; BioSamples: SAMN32767203–SAMN32767214). The bioinformatics pipeline used for filtering adapter contamination, assembling markers, and exporting alignments has been described previously (
(1) To obtain a first understanding of mitochondrial differentiation among all available samples of
(2) The nuclear-encoded genes (
(3) The multigene dataset of a representative number of samples was first analyzed with PartitionFinder v. 2.1.1 (
(4) Phylogenomic (FrogCap sequence capture) data were analyzed under maximum-likelihood in IQ-Tree v. 1.6.7 (
Because some of the species distinguished herein according to available data cannot be reliably diagnosed based on morphology, we provide a molecular diagnosis to satisfy the requirements of the Code for diagnostic traits that purport to distinguish each new species from all previously described species. For molecular diagnosis we used the tool DNAdiagnoser implemented in iTaxoTools (
As in previous studies, we follow the general lineage concept (
The cytochrome
Maximum likelihood phylogeny based on DNA sequences of the mitochondrial cytochrome
Map of Madagascar showing the confirmed localities of the assigned lineages of the
The minimum and maximum pairwise uncorrected cytochrome
Substantial genetic divergence was also observed between the northern and central/southern lineages, e.g., when comparing
Genetic distances in a fragment of the 16S rRNA gene that has often been used for DNA barcoding of Malagasy frogs (e.g.,
The alignments of the four nuclear-encoded genes, not counting the outgroup sequences, consisted of 257 sequences of the
Haplotype network reconstructed from 257 phased DNA sequences of the
Haplotype network reconstructed from 244 phased DNA sequences of the
Haplotype network reconstructed from 245 phased DNA sequences of the
Haplotype network reconstructed from 153 phased DNA sequences of the
The ML tree inferred from the cytochrome
Partitioned Bayesian phylogenetic inference of the combined mitochondrial and nuclear-encoded gene fragments (
Majority-rule consensus tree from a partitioned Bayesian phylogenetic inference based on the combined mitochondrial and nuclear-encoded gene fragments (
The FrogCap procedure carried out on 11 representative samples of
Maximum likelihood tree based on a partitioned analysis of 12,951 nuclear-encoded markers obtained via the FrogCap strategy for representative samples of the main lineages of the
All specimens of the
Preserved name-bearing holotype specimens of
Specimens of
Specimens of
Specimens of
Measurements of specimens of the
Field Number | Status | Locality | Lineage | Sex |
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ZCMV 12515 ( |
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Bemanevika |
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male | 28.0 | 9.3 | 10.7 | 3.1 | 4.4 | 2.8 | 1.7 | 2.5 | 8.7 | 17.4 | 43.3 | 13.6 | 20.2 | 14.0 | |
ZCMV 12532 |
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Bemanevika |
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male | 30.2 | 9.7 | 11.4 | 3.1 | 4.2 | 2.8 | 2.0 | 2.5 | 9.4 | 17.9 | 49.0 | 14.4 | 21.4 | 15.2 | |
ZCMV 12516 |
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Bemanevika |
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male | 26.5 | 8.3 | 10.2 | 2.1 | 4.0 | 2.6 | 1.4 | 2.6 | 8.2 | 15.5 | 43.0 | 13.3 | 19.6 | 14.5 | |
ZCMV 12531 |
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Bemanevika |
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male | 31.5 | 10.0 | 12.0 | 2.8 | 4.4 | 3.0 | 2.3 | 2.4 | 9.2 | 19.6 | 49.2 | 15.5 | 22.2 | 16.0 | |
ZCMV 12523 |
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Bemanevika |
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male | 29.8 | 10.0 | 11.0 | 2.5 | 4.6 | 2.9 | 1.9 | 2.2 | 9.0 | 17.3 | 45.5 | 13.4 | 19.8 | 14.5 | |
FG/MV 2002-0874 |
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M. d’Ambre |
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male | 32.4 | 10.8 | 11.6 | 3.0 | 4.3 | 2.7 | 2.2 | 2.4 | 10.0 | 20.4 | 51.4 | 15.5 | 22.7 | 15.7 | |
FG/MV 2002-0875 |
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M. d’Ambre |
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male | 33.9 | 11.2 | 12.7 | 2.8 | 4.4 | 4.0 | 2.2 | 2.3 | 10.3 | 22.6 | 51.8 | 16.1 | 23.0 | 16.5 | |
MSZC 0520 |
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M. d’Ambre |
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male | 33.6 | 11.4 | 12.2 | 2.4 | 4.1 | 4.0 | 2.2 | 2.8 | 9.7 | 21.7 | 51.9 | 15.1 | 22.6 | 15.9 | |
FG/MV 2002-0898 |
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M. d’Ambre |
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male | 29.3 | 9.7 | 10.9 | 2.4 | 4.1 | 2.6 | 1.9 | 1.8 | 9.0 | 19.8 | 43.8 | 13.1 | 20.8 | 14.5 | |
ZCMV 12539 |
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Bemanevika |
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female | 31.7 | 9.6 | 11.4 | 2.6 | 4.4 | 3.0 | 1.8 | 2.4 | 9.8 | 19.6 | 47.5 | 14.4 | 20.8 | 15.7 | |
ZCMV 12514 |
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Bemanevika |
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female | 29.8 | 9.7 | 11.2 | 3.0 | 4.4 | 2.5 | 1.7 | 2.3 | 8.8 | 17.6 | 45.5 | 13.8 | 20.3 | 14.7 | |
FG/MV 2002-0899 |
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M. d’Ambre |
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female | 32.8 | 10.8 | 12.0 | 2.4 | 4.0 | 3.2 | 2.0 | 2.9 | 10.9 | 21.0 | 45.2 | 15.0 | 22.3 | 15.2 | |
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ZCMV 0791 | — | Andasibe |
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male | 28.9 | 9.3 | 10.8 | 2.4 | 4.0 | 2.5 | 2.0 | 2.4 | 8.5 | 18.3 | 43.9 | 13.3 | 20.0 | 13.4 | |
ZCMV 8066 | — | Ambodisakoa |
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male | 27.0 | 8.9 | 10.6 | 2.2 | 3.7 | 2.6 | 2.0 | 2.2 | 8.6 | 16.8 | 41.1 | 12.3 | 17.9 | 13.5 | |
ZCMV 8076 | — | Ambodisakoa |
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male | 26.4 | 8.0 | 9.7 | 2.2 | 3.3 | 2.5 | 1.6 | 2.0 | 7.2 | 15.0 | 41.0 | 10.8 | 17.9 | 13.3 | |
ZCMV 8088 | — | Ambodisakoa |
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male | 23.7 | 7.3 | 8.8 | 2.0 | 3.8 | 2.5 | 1.8 | 2.9 | 6.2 | 13.2 | 36.9 | 11.3 | 15.3 | 12.0 | |
ZCMV 3199 | — | Ranomafana |
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male | 27.1 | 8.4 | 9.3 | 2.4 | 3.3 | 2.3 | 1.7 | 2.2 | 8.9 | 18.4 | 42.0 | 13.3 | 18.5 | 13.0 | |
ZCMV 3028 | — | Ranomafana |
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male | 24.2 | 7.9 | 8.7 | 2.1 | 3.5 | 2.4 | 1.7 | 2.3 | 8.0 | 17.5 | 38.4 | 11.5 | 17.4 | 12.0 | |
ZCMV 3041 | — | Ranomafana |
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male | 26.3 | 8.9 | 9.9 | 2.4 | 3.6 | 3.2 | 1.8 | 2.5 | 8.0 | 18.0 | 39.9 | 12.1 | 17.7 | 12.3 | |
ZCMV 3018 | — | Ranomafana |
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male | 25.2 | 8.0 | 10.0 | 2.1 | 3.5 | 3.2 | 1.7 | 2.9 | 8.4 | 17.5 | 36.5 | 12.2 | 18.1 | 12.4 | |
ZCMV 5833 | — | Manombo |
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male | 27.8 | 9.3 | 10.7 | 2.7 | 4.2 | 2.6 | 2.0 | 2.4 | 8.0 | 18.5 | 40.6 | 12.5 | 18.2 | 13.0 | |
ZCMV 5830 | — | Manombo |
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male | 25.7 | 8.1 | 9.8 | 2.1 | 3.4 | 2.9 | 1.1 | 2.1 | 6.9 | 16.0 | 40.7 | 11.8 | 17.9 | 12.3 | |
FGZC 4452 | — | Anosibe An’Ala |
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female | 24.4 | 8.3 | 10.0 | 2.7 | 4.0 | 2.6 | 1.7 | 2.3 | 8.0 | 16.2 | 40.6 | 12.9 | 18.8 | 13.0 | |
ZCMV 0786 | — | Andasibe |
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female | 30.7 | 10.3 | 10.9 | 2.9 | 4.5 | 2.8 | 2.0 | 2.2 | 8.4 | 18.0 | 44.4 | 13.8 | 19.5 | 14.0 | |
ZCMV 1074 | — | Andasibe |
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female | 26.8 | 8.5 | 9.7 | 2.6 | 3.7 | 2.8 | 2.0 | 2.3 | 8.2 | 18.3 | 43.9 | 13.4 | 19.2 | 13.5 | |
ZCMV 5675 | — | Ambohitantely |
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female | 33.3 | 11.7 | 13.1 | 2.3 | 4.6 | 3.7 | 2.4 | 2.7 | 10.5 | 21.3 | 51.2 | 15.7 | 23.4 | 17.0 | |
ZCMV 5672 | — | Ambohitantely |
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female | 32.1 | 9.9 | 12.2 | 2.4 | 4.0 | 3.4 | 2.0 | 2.3 | 9.7 | 20.8 | 49.4 | 15.1 | 22.4 | 15.8 | |
ZCMV 3021 | — | Ranomafana |
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female | 27.0 | 8.0 | 10.0 | 2.2 | 3.5 | 3.5 | 1.9 | 2.4 | 8.9 | 18.0 | 41.4 | 13.3 | 19.0 | 13.1 | |
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FGZC 2851 ( |
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Marojejy, Camp Simpona | NE1 | male | 25.6 | 8.3 | 9.7 | 2.7 | 3.9 | 2.7 | 1.6 | 2.7 | 7.8 | 18.0 | 42.1 | 12.5 | 19.9 | 13.6 | |
FGZC 2865 |
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Marojejy, Camp Simpona | NE1 | male | 25.9 | 9.0 | 10.2 | 2.2 | 4.0 | 2.9 | 1.6 | 2.5 | 8.4 | 18.4 | 42.0 | 13.0 | 20.4 | 14.0 | |
FGZC 2867 |
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Marojejy, Camp Simpona | NE1 | male | 24.4 | 7.8 | 9.2 | 2.0 | 3.9 | 2.6 | 1.4 | 2.6 | 8.2 | 16.5 | 41.0 | 12.5 | 18.3 | 12.7 | |
ZCMV 15176 |
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Marojejy, Camp Simpona | NE1 | male | 27.4 | 8.7 | 10.3 | 2.2 | 3.7 | 2.6 | 1.5 | 2.4 | 8.6 | 18.9 | 44.2 | 12.5 | 18.2 | 13.6 | |
ZCMV 12570 |
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Bemanevika | NE1 | male? | 21.8 | 6.7 | 8.8 | 2.1 | 3.0 | 1.8 | 1.2 | 1.6 | 6.6 | 14.0 | 36.4 | 10.1 | 16.9 | 11.4 | |
ZCMV 12584 |
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Bemanevika | NE1 | male? | 22.7 | 7.2 | 9.0 | 2.8 | 3.4 | 2.2 | 1.5 | 2.2 | 7.0 | 14.0 | 33.2 | 10.1 | 16.3 | 10.8 | |
ZCMV 12578 |
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Bemanevika | NE1 | male? | 24.3 | 7.2 | 9.0 | 2.5 | 3.8 | 2.2 | 1.8 | 2.7 | 6.8 | 14.1 | 35.6 | 10.7 | 16.1 | 11.7 | |
ZCMV 12579 |
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Bemanevika | NE1 | male? | 23.8 | 7.2 | 9.0 | 3.0 | 3.3 | 2.3 | 1.4 | 2.8 | 6.4 | 13.9 | 36.9 | 11.4 | 16.4 | 11.4 | |
ZCMV 12580 |
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Bemanevika | NE1 | male? | 22.2 | 6.8 | 8.1 | 2.5 | 3.5 | 2.1 | 1.6 | 1.8 | 6.8 | 13.5 | 34.7 | 11.3 | 16.3 | 10.8 | |
ZCMV 12581 |
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Bemanevika | NE1 | male? | 23.1 | 7.3 | 8.5 | 2.6 | 3.7 | 2.0 | 1.7 | 2.4 | 6.9 | 14.8 | 35.6 | 10.7 | 16.2 | 11.0 | |
ZCMV 12583 |
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Bemanevika | NE1 | male? | 22.9 | 7.3 | 8.8 | 2.8 | 3.1 | 1.8 | 1.6 | 1.5 | 6.4 | 14.4 | 34.5 | 11.4 | 16.6 | 10.6 | |
ZCMV 11218 |
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Makira | NE1 | female | 22.8 | 7.2 | 8.4 | 2.2 | 3.3 | 2.3 | 1.7 | 2.6 | 6.8 | 14.0 | 35.6 | 10.2 | 15.6 | 11.6 | |
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FGZC 2781 |
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Marojejy, Camp |
NE2 | male | 25.5 | 8.2 | 10.0 | 2.4 | 4.0 | 2.8 | 2.2 | 19.0 | 7.5 | 15.6 | 42.5 | 12.1 | 18.5 | 12.6 | |
FGZC 2722 |
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Andrakata-Andapa | NE2 | male | 25.9 | 8.4 | 10.2 | 2.5 | 3.4 | 2.7 | 1.7 | 2.2 | 8.3 | 15.8 | 38.1 | 12.0 | 18.0 | 11.1 | |
FGZC 2721 |
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Andrakata-Andapa | NE2 | male | 26.0 | 7.9 | 9.4 | 2.0 | 3.8 | 3.2 | 1.7 | 2.2 | 7.7 | 14.6 | 39.3 | 11.7 | 18.1 | 12.4 | |
FGZC 2780 |
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Marojejy, Camp |
NE2 | male | 25.1 | 8.3 | 9.7 | 2.7 | 4.0 | 2.9 | 1.7 | 2.3 | 7.5 | 15.7 | 40.5 | 11.6 | 18.2 | 12.7 |
Some differences among lineages seem to exist in body size: When comparing male specimens (for female specimens see Table
Vocalizations in the
Breeding assemblages of
As observed in many other groups of frogs, we may assume that the different note types recognized in the
Among the lineages with calls analyzed, some rather clear differences in temporal structure and spectral character are evident, as summarized in the following. For detailed call descriptions, see the accounts of new species below, and Appendix
Audiospectrogram and corresponding oscillogram of a series of advertisement calls (3 calls) of
Audiospectrogram and corresponding oscillogram of one advertisement call of
Audiospectrogram and corresponding oscillogram of a series of advertisement calls (5 calls) of
Audiospectrogram and corresponding oscillogram of a series of advertisement calls (3 calls) of
Audiospectrogram and corresponding oscillogram of a series of advertisement calls (5 calls) of
Calls assignable to the lineage
Calls from Ambodisakoa (near Mahasoa), assignable to lineage
Calls assigned to lineage
Calls from Montagne d’Ambre, assignable to lineage
Calls from Marojejy Camp Simpona (lineage NE1) mainly differ from calls of
In summary, even if not fully conclusive given the limitations mentioned above, bioacoustics provides additional evidence for the divergence of several of the genetic lineages in the
This is the oldest nomen in the
However, there is at present no reason to doubt that the lectotype designated by
This nomen is based on a holotype specimen, which according to the original description is an adult male of a purported
Although there is no precise type locality for
It is possible that the type material of
This nomen was coined by
Unfortunately, the labelling and identification of these syntypes in the
We examined the type material and associated specimens in the Paris museum in 2010. According to the original catalogue of the Paris museum, two catalogue numbers are considered to be types of
Upon examination of the specimens (stored in two separate jars), we found that the same jar containing
For each of the numbers given above (except for
Of these specimens,
Because currently no validly designated lectotype of
The combined evidence from mitochondrial and nuclear-encoded genes, geographical distribution, morphology and bioacoustics provides conclusive evidence that
(1) Based on geographic and morphological arguments, we conclude that the type material of
(2) Lineages NE1 and NE2 are most divergent within the
(3) The two northeastern lineages, NE1 and NE2, also occur sympatrically at Marojejy in very close geographical proximity but apparently separated by elevation. Due to this almost-sympatric occurrence without any signs of admixture, combined with divergence in mitochondrial genes (2.8–3.9% in 16S) and in nuclear encoded genes (long branches in the phylogenomic analysis) between NE1 and NE2, we consider each of them to be a distinct species.
(4) Lineage
(5) Among the lineages distributed in Madagascar’s Northern and Southern Central East (
Based on this rationale, we consider the current evidence to be sufficient to scientifically name lineages NE1, NE2 and
A total of 26 specimens:
This species corresponds to the mitochondrial lineage NE1 as defined herein, and to the candidate species
Adult male in excellent state of preservation (Fig.
After sixteen years in preservative (70% EtOH; Fig.
Based on photographs of holotype in life (Fig.
Specimens of
Males of
Advertisement calls recorded on 16 February 2005 at Marojejy National Park (air temperature unknown) consist of a single pulsatile note of somewhat variable duration. Calls (= notes) are usually emitted in short series at rather regular intervals (Fig.
The species is known from various sites in northern Madagascar, all at mid- to high-elevation: (1) the type locality Marojejy (Camp Simpona, at mid-elevation), (2) Bemanevika, (3) the southern slope of the Tsaratanana Massif, (4) the western slope of Makira Reserve, and (5) Anjanaharibe-Sud Reserve, based on specimen CRH1693 (
The name is derived from the Malagasy word
A total of 27 specimens:
This species corresponds to the mitochondrial lineages
Adult male in good state of preservation (Fig.
After eleven years in preservative (70% EtOH; Fig.
Based on photographs of the holotype specimen (Fig.
Specimens in the type series show differences in color pattern. For instance, in preservative two specimens of the
In November to December of 2017 we observed numerous congregations of calling males of
Advertisement calls recorded on 14 March 1994 at Montagne d’Ambre National Park (air temperature 21.2°C) consists of a single, click-like note of rather variable duration containing a low number of well-separated pulses (Fig.
Since many
The name is derived from the Malagasy word
Five specimens:
This species corresponds to the mitochondrial lineage NE2 as defined herein. It is assigned to the subgenus
Adult male in good state of preservation (Fig.
After sixteen years in preservative (70% EtOH; Fig.
The four available specimens (all males) are morphologically and morphometrically rather similar to each other (Table
No natural history observations on this species were made, but its habits and habitat are likely similar to those of other species of the
The species is reliably known from two sites in northern Madagascar: (1) the type locality Marojejy (Camp
The name is derived from the Malagasy words fotsy meaning white, and tenda meaning throat, referring to the white throat (vocal sac) typical for this and other species of the
In this study, we have presented evidence that
Since we observed several instances of syntopic occurrence of lineages without genetic admixture in northern Madagascar, and in part with maintenance of morphological differences, we became confident that multiple species were hidden under the name
However, resolution of the remaining lineages remains pending and will require a combination of new fieldwork to collect additional genetic, bioacoustic and morphological data, as well as increased scrutiny of the type material of the available names. Specifically, we identify the following research activities needed for a full comprehension of the taxonomy of the
While these new field data, in particular new material from Itremo and Andrangoloaka, would help to assign the three available names to lineages, a preferable course of action would be to genetically characterize their name-bearing types, as has been done by a DNA barcode fishing strategy in several other Malagasy anurans (e.g.,
One intriguing aspect of the molecular phylogenies inferred herein is the apparent paraphyly of the
We hypothesize that introgressive hybridization also explains the discordance of mitochondrial and nuclear signal for the two samples from Ambodivoangy. These samples, collected at a site near sea level, were grouped by multiple nuclear-encoded genes with the low-elevation species
According to our data, the
This work was carried out in framework of collaboration accords among the authors institutions, the Department of Animal Biology of the University of Antananarivo, and the Ministry of the Environment of the Republic of Madagascar. Field expeditions were supported, among other funders, by the Volkswagen Foundation, Deutsche Forschungsgemeinschaft, and Deutscher Akademischer Austauschdienst. A research stay of TK at TU Braunschweig was supported by a grant of the Alexander-Koenig-Gesellschaft. MP was supported by the Alexander von Humboldt Foundation. Fieldwork for CRH was supported by Global Wildlife Conservation Grant 5019-0096.
The samples used in this study have been assembled in numerous field campaigns, with the assistance of many colleagues, students and guides, of which we would like to particularly acknowledge L. Ball, M. C. Bletz, P. Bora, J. Borrell, E.Z. Lattenkamp, D.H. Nomenjanahary, J.L. and C. Patton, L. du Preez, J. Rabearivony, E. Rajeriarison, T. Rajoafiarison, M. Rakotondratisma, O. Randriamalala, R.D. Randrianiaina, S.M. Rasolonjavato, A. Razafimanantsoa, E. Razafimandimby, J.H. Razafindraibe, T. Starnes, and R.T. Rakotonindrina. We are grateful to O. Frank, S. Parlow and J. Weste who contributed substantially to the labwork, along with M. Kondermann and G. Keunecke.
In the following, we describe calls of different lineages assigned to
Advertisement calls recorded on 8 February 2000 at Mandraka (probably lineage
Advertisement calls recorded on 4 February 1994 at Andasibe (probably lineage
Advertisement calls recorded on 3 March 1996 at An’Ala (probably lineage
Advertisement calls recorded on 12 February 2008 at Ambodisakoa (clade
Advertisement calls recorded on 20 January 2004 near Vohiparara, Ranomafana region (lineage
For comparison, descriptions of the advertisement calls of
The following lists nucleotide positions in the mitochondrial gene (relative to the full cytochrome b sequence of
List of DNA sequences with metadata
Tables S1–S4, Figs S1–S4