Research Article |
Corresponding author: Flavien Ferreira ( flavienferreira1@gmail.com ) Academic editor: Christopher Burridge
© 2025 Flavien Ferreira, Paul Oliver, Fred Kraus, Rainer Günther, Stephen Richards, Burhan Tjaturadi, Evy Arida, Amir Hamidy, Awal Riyanto, Wahyu Trilaksono, Christophe Thébaud, Antoine Fouquet.
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Ferreira F, Oliver P, Kraus F, Günther R, Richards S, Tjaturadi B, Arida E, Hamidy A, Riyanto A, Trilaksono W, Thébaud C, Fouquet A (2025) Molecular and acoustic evidence for large-scale underestimation of frog species diversity on New Guinea. Frontiers of Biogeography 18: e137988. https://doi.org/10.21425/fob.18.137988
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Species are fundamental units in biology; however, information on species diversity and distribution remain scarce for most taxonomic groups, especially in tropical rainforests. Such knowledge gaps are particularly acute in amphibians, the most threatened group of vertebrates, in which new species continue to be described at a high rate. Herein, using molecular-based approaches, we provide estimates for species diversity of frogs (Anura) in New Guinea and nearby islands, one of the biologically most diverse regions of the world. We first characterised taxonomic and geographic sampling for all available mitochondrial DNA sequences from native frog species. This led us to identify important molecular sampling gaps in the western half of New Guinea that we partially filled by adding 534 new sequences (16S rRNA). Large territories remain uncharted, particularly in the westernmost part of the central cordillera of New Guinea. Using our 16S rRNA dataset, we then delimited Molecular Operational Taxonomic Units (MOTUs), a subset of which was bioacoustically analysed. From a total of 369 delimited MOTUs, we found that 190 could not be assigned to any taxon. Amongst these, 123 are represented by specimens collected in the western half of New Guinea and 19 were supported as distinct by bioacoustics, confirming that this portion of the island is home to many unrecognised species. Based on the estimated level of undescribed diversity in taxa and areas for which data are available, we extrapolate that New Guinea and neighbouring islands could host 800–1,200 frog species, with only 560 species described to date.
We assembled the most comprehensive molecular dataset to date (16S rRNA) for frogs from New Guinea and neighbouring islands.
We delimited 190 candidate species, of which 19 are supported by available bioacoustic data.
We estimated the actual number of frog species on New Guinea and neighbouring islands to be between 800 and 1,200.
Parts of New Guinea exhibit species-diversity levels comparable to similarly sized regions in Amazonia and Madagascar.
Most unrecognised frog taxa in the region are likely confined to restricted geographical areas and, thus, likely sensitive to both land use and climate change.
Amphibians, 16S, integrative approach, IUCN, Linnean shortfall, Microhylidae, New Guinea, taxonomy
In the face of accelerating rates of global biodiversity loss, documenting and describing species remains a crucial challenge (Scheffers et al. 2012; Ceballos et al. 2017, 2020), especially in tropical regions where incomplete biodiversity knowledge and rapid biodiversity loss are most marked (
DNA-based species-delimitation methods have been proposed as one strategy to mitigate the taxonomic impediment and they have become widely used for that purpose (
The region comprising New Guinea and its neighbouring islands is both megadiverse and one of the least biologically studied of the world (
Gaps in the knowledge of frog diversity on New Guinea are thought to be particularly substantial in the western half of the island, partly because of the paucity of field surveys in this area since the mid-20th century (
Here, to better estimate frog species diversity on New Guinea and neighbouring islands, we first aimed to characterise the taxonomic and geographic sampling bias of existing molecular data (mitochondrial DNA from public databases) for frogs from the region. We complemented these data with additional sequences obtained from specimens collected recently in the western half of New Guinea. We re-evaluated species diversity estimates by delimiting Molecular Operational Taxonomic Units (MOTUs) using the 16S rRNA locus that has been advocated as useful to delimit amphibian candidate species (
We focused on the region spanning from the islands in the northern and central Moluccas, across New Guinea to the Bismarck and Solomon Archipelago and refer to it as “the New Guinea region”. We downloaded GenBank-deposited mitochondrial DNA (mtDNA) sequences of frog species native to this region and compared the taxonomic and geographic distribution of the most commonly sequenced loci (COI, cytb, 12S and two non-overlapping regions of 16S rRNA, here referred as “16Sa” and “16Sb”). In addition, we downloaded the data of
Given the unevenness of taxonomic and geographic sampling across loci, we delimited MOTUs using the 16Sb locus only. To expand our sampling, we produced 534 new 16Sb sequences (DNA extraction and sequencing protocol in Suppl. material
The robustness of the delimitations was further assessed for 38 MOTUs (i.e. 19 pairs) by searching for concordant patterns of acoustic differentiation (e.g. Fig.
We investigated call variation following a note-centred approach (
Species delimitation combining molecular and acoustic data, exemplified in an Oreophryne species complex. In this example, the species delimitation between O. roedeli and O. cf. roedeli 2 is confirmed by their difference in note repetition rate and mean number of pulses per note. The subtree was extracted from the ultrametric tree used for the GMYC analysis. Mean genetic p-distance (%) between lineages is indicated at the nodes. Dots above tree branches indicate posterior probabilities > 0.95. All detailed comparisons and specimen vouchers are presented in Suppl. material
We undertook additional analyses in order to better characterise potential geographic bias in the distribution of: 1) genetic sampling and 2) MOTUs across the fifteen subregions (Fig.
Distribution of sampled localities for all compiled georeferenced mtDNA sequences (12S, 16Sa, 16Sb, COI, cytb) of amphibians across the focal area, with the number of sequences per subregion indicated by grey shading. The vertical white-dashed line represents the international border between the western half (Indonesia) and the eastern half (Papua New Guinea) of the island of New Guinea. Abbreviations: CRW, western central range; CRC, central central range; CRE, eastern central range.
The complete dataset of mitochondrial data comprised 2301 DNA sequences (1767 from online repositories and 534 newly generated) (Table
The majority of the georeferenced sequences are from the eastern half of New Guinea (1177 sequences; Fig.
Most recognised species of Ceratobatrachidae and Ranidae in our study region are represented by molecular data (69% and 86% of 58 and 15 recognised species, respectively). By contrast, molecular data are available for only half of the recognised species in Microhylidae and Hylidae (Table
Details of compiled sequences for all Melanesian amphibians, by family and genus, on commonly sequenced mitochondrial loci. The column “taxonomic completion” indicates the proportion of recognised species (as per
Taxa | 12S | 16Sa | 16Sb | cytb | COI | Total sequences | Taxonomic completion (%) | |||
---|---|---|---|---|---|---|---|---|---|---|
GB | GB | GB | This study | Total | GB | GB |
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Microhylidae | 346 | 365 | 126 | 218 | 344 | 366 | 4 | 98 | 1523 | 49 |
Mantophryne | 119 | 120 | 2 | 2 | 121 | 1 | 363 | 100 | ||
Hylophorbus | 81 | 84 | 70 | 1 | 71 | 52 | 1 | 18 | 307 | 94 |
Choerophryne | 91 | 95 | 6 | 13 | 19 | 20 | 225 | 67 | ||
Oreophryne | 9 | 48 | 57 | 46 | 15 | 118 | 45 | |||
Xenorhina | 19 | 22 | 8 | 35 | 43 | 10 | 1 | 9 | 104 | 29 |
Asterophrys | 17 | 18 | 3 | 34 | 37 | 7 | 15 | 94 | 87 | |
Cophixalus | 6 | 28 | 34 | 35 | 13 | 82 | 39 | |||
Callulops | 15 | 16 | 4 | 19 | 23 | 17 | 10 | 81 | 39 | |
Austrochaperina | 17 | 17 | 12 | 11 | 40 | 28 | ||||
Sphenophryne | 1 | 7 | 9 | 16 | 13 | 7 | 37 | 53 | ||
Copiula | 7 | 14 | 21 | 11 | 32 | 53 | ||||
Barygenys | 1 | 5 | 3 | 3 | 7 | 1 | 17 | 78 | ||
Paedophryne | 3 | 4 | 8 | 15 | 86 | |||||
Aphantophryne | 1 | 1 | 7 | 8 | 20 | |||||
Hylidae | 87 | 19 | 79 | 147 | 226 | 4 | 3 | 15 | 354 | 42 |
Litoria | 58 | 7 | 37 | 71 | 110 | 3 | 2 | 180 | 40 | |
Nyctimystes | 18 | 12 | 18 | 42 | 60 | 4 | 7 | 101 | 40 | |
Ranoidea | 11 | 24 | 34 | 58 | 6 | 75 | 45 | |||
Ceratobatrachidae | 44 | 54 | 33 | 122 | 155 | 5 | 1 | 39 | 298 | 69 |
Cornufer | 44 | 54 | 33 | 122 | 155 | 5 | 1 | 39 | 298 | 69 |
Ranidae | 7 | 28 | 27 | 39 | 66 | 14 | 115 | 86 | ||
Papurana | 7 | 28 | 27 | 39 | 66 | 14 | 115 | 86 | ||
Myobatrachidae | 2 | 4 | 6 | 1 | 7 | 67 | ||||
Platyplectrum | 2 | 4 | 6 | 1 | 7 | 67 | ||||
Dicroglossidae | 4 | 4 | 4 | 100 | ||||||
Limnonectes | 4 | 4 | 4 | 100 | ||||||
Total | 484 | 466 | 267 | 534 | 801 | 375 | 8 | 167 | 2301 | 51 |
The number of “species” delimited by the different methods ranged from 263 (PTP) to nearly 400 (386 (ABGD), 371 (GMYC)), with a majority-rule consensus of 372 MOTUs in our focal area. This count was reduced to 369 with our integrative approach, comprising 179 species recognised by current taxonomy and 190 MOTUs that could not be assigned to any taxon (i.e., unidentified or undescribed candidate species). Microhylidae are dominant in our dataset in every measure: total number of sequences (Table
Acoustic data were available for 38 MOTUs (Suppl. material
Adding the 560 recognised species known to be resident in our study region to our 190 candidate species suggests that a minimum of 750 species inhabit the region. Most candidate species (123) originate from the western half of New Guinea where 215 species are currently recognised. Based on the ratio between the candidate species (190) and the recognised species included in our dataset (179; thus ratio = 1.1) (Fig.
The Bird’s Head and Bird’s Neck subregions contain the highest number of MOTUs (75 and 61 respectively; Fig.
A) Ultrametric tree used for the GMYC analysis, based on all 16Sb sequences. Numbers in parentheses indicate the number of sequences. The detailed tree is presented in Suppl. material
Out of the 369 delimited MOTUs, 294 are represented by one or two occurrence points and 75 by three or more occurrence points. The evaluation of our taxonomic sampling across subregions, based on the richness of MOTUs assigned to recognised species vs. richness derived from IUCN data (Fig.
When looking at the degree of endemism per subregion, distributional data for both MOTUs and IUCN range maps suggested higher levels of endemism in archipelagos (e.g. Bismarck and Solomon Isl.) and in the eastern half of New Guinea (Suppl. material
A) Regional species richness based on IUCN data; B) Number of missing recognised species in the MOTU dataset based on the difference between the count of MOTUs assigned to recognised species and IUCN data presented in A; C) Difference in species richness, between the total MOTUs dataset and IUCN data. Negative values indicate a species-deficit in the DNA-based dataset, as compared to IUCN data.
Gaps in knowledge of species diversity and distribution hinder our understanding of the ecological and evolutionary processes driving species diversification and geographic variation in species diversity (
Although DNA sequencing has been increasingly accessible, with the rate of publication of new sequences rocketing over the last two decades (
Despite relatively intensive frog sampling in the eastern half of New Guinea, where 75% of all recognised species from our study region occur, 49% of these are not yet represented by molecular data (Table
Using 16S mtDNA, we delimited 369 MOTUs in the study region and a significant fraction of these (179) are named and considered taxonomically valid. Overall, the ABGD and GMYC delimitations were congruent with one another and mainly drove our final consensus (Suppl. material
Thirty of the 38 MOTUs, for which acoustic data were available, displayed notable differences in call features and we consider 19 of these to represent confirmed candidate species. MOTUs supported by acoustic data display mean p-distances at the 16S locus of 2.75–4% (minimum of 1% between Asterophrys pullifer and Asterophrys cf. pullifer), broadly overlapping with the 3–5% distances that have been advocated as useful thresholds to flag “candidate species” in amphibians (
Microhylidae
, Hylidae and Ceratobatrachidae together include 93% of all our MOTUs and 91% of the MOTUs assigned to recognised species. This proportion mirrors the proportion of taxonomically known species from these families (94%;
Although the validity of our estimate of frog species richness across all of the New Guinea region remains to be confirmed, we argue that a two-fold increase in species diversity seems reasonable in the western half of New Guinea where most of our candidate species occur (Fig.
We delimited a total of 190 candidate species, of which 123 occur in western New Guinea (mainly in the Bird’s Head and Bird’s Neck subregions; Fig.
Due to large geographic and taxon sampling gaps for the 16Sb locus in several regions on New Guinea (e.g. Microhylidae in the central range, Hylidae in southern New Guinea and Ceratobatrachidae in the central portion of northern New Guinea), assessments of species distribution and endemism are necessarily limited. The Papuan Peninsula stands out as being the most sampled subregion when considering all mtDNA sequences (Fig.
Our regional endemism rates for MOTU’s may be overestimates for some regions due to sparse sampling of species that may be more widely distributed. This is particularly true for Hylidae (also Ranidae, Dicroglossidae and Myobatrachidae) that tend to have wider ranges than microhylids and may occur throughout unsampled areas. This contrast in distribution patterns is probably tightly linked to reproductive features and habitat, i.e. between species breeding in waterbodies, which are abundant in the lowlands and the direct-developing Microhylidae that can breed virtually anywhere humidity is sufficient (
Estimated and recognised levels of regional frog species richness on New Guinea (e.g. 100–150 species in the Bird’s Head and the Papuan Peninsula) are similar to comparably sized areas in Amazonia (eastern Guiana Shield) (
The Maximum-Likelihood and ultrametric phylogenetic trees obtained from the analysis of 580 bp of 16S mtDNA are mostly congruent and revealed numerous lineages from western New Guinea that are new to science (Suppl. material
Most incongruences between our trees and previously published phylogenies occur within Hylidae and especially within Litoria (sensu
New Guinea’s forests are still relatively extensive compared to many other tropical areas (
We are grateful to Laurent Pouyaud, Gono Semiadi, Régis Hocdé, Jacques Slembrouck and Kadarusman who organised the Lengguru expedition in 2014, and Iqbal Setiadi and Philippe Gaucher for their contribution to the sampling in Maluku and west Papua, respectively. We thank the staff from the Museum Zoologicum Bogoriense (MZB) and the South Australian Museum (SAMA), Molly Hagemann from the Bernice Pauahi Bishop Museum (BPBM) and Frank Tillack from the Berlin Museum of Natural History (ZMB), who processed and shipped biological samples and showed great support over many years. We are also thankful to Uxue Suescun and Lucie Moreau from the Centre de la Recherche sur la Biodiversité et l’Environnement (CRBE) and Rachel Fourdin from the Génomique & Transcriptomique Plateforme Génotoul (GeT-PlaGe) for their help in generating molecular data. We thank Rafe Brown and Jimmy McGuire for their courtesy in providing Oreophryne anulata and O. variabilis call recordings. Finally, we thank Robert Whittaker, Christopher Burridge, Aurélien Miralles, David Vieites and an anonymous reviewer for their suggestions and support for this work.
The first author was supported by a PhD scholarship from the Ministère de l’Enseignement Supérieur et de la Recherche (FR) through SEVAB graduate school. Fieldwork in west Papua was conducted under the RISTEK research permit number 304/SIP/FRP/SM/X/2014, supported by the Lengguru Project conducted by the French Institut de Recherche pour le Développement (IRD), the Indonesian Institute of Sciences (LIPI), with the Research Center for Biology (RCB) and the Research Center for Oceanography (RCO), the University of Papua (UNIPA), the University of Cendrawasih (UNCEN), the University of Musamus (UNMUS) and the Polytechnic KP Sorong, with corporate sponsorship from COLAS and TIPCO groups, Veolia Water and the Total Foundation, and assistance from the Institut Français in Indonesia (IFI) and the French embassy in Jakarta. C.T. acknowledges support from the IRD.
The authors declare they have no conflict of interest.
Flavien Ferreira (Data curation and collection, Methodology, Formal analysis, Visualisation, Writing – Original draft and editing), Antoine Fouquet (Data curation and collection, Methodology, Writing – Review and editing), Paul Oliver (Writing – Review and editing), Stephen Richards (Data curation and collection, Writing – Review and editing), Fred Kraus (Data curation and collection, Writing – Review and editing), Rainer Günther (Data curation and collection, Writing – Review and editing), Burhan Tjaturadi (Data collection, Review), Evy Ayu Arida (Data collection, Review), Amir Hamidy (Data curation, Review), Awal Riyanto (Data curation, Review), Wahyu Trilaksono (Data collection, Review) and Christophe Thébaud (Data collection, Writing – Review and editing).
Molecular data used in the analyses are available in online repositories: GenBank (newly generated sequences are available under the accessions PQ334073–PQ334606) and OSF (the 16S sequences alignment used in the species delimitation are available at https://osf.io/ezg9y/). Unpublished call recordings analysed in Suppl. materials
appendix S1: DNA extraction and sequencing protocol. appendix S2: Species-delimitation method. appendix S3: Integrative delimitations: fig. S1. Integrative delimitations for an Oreophryne and Cornufer clade. fig. S2. Integrative delimitations for four Oreophryne clades. fig. S3. Integrative delimitations for a Xenorhina and Oreophryne clade. fig. S4. Integrative delimitations for two Cornufer clades. fig. S5. Integrative delimitations for a Hylophorbus and Nyctimystes clade. fig. S6. Integrative delimitations for a Choerophryne and Oreophryne clade. Appendix S4: Subregions choice. fig. S7. Distribution of GenBank mitochondrial DNA sequences, per locus. fig. S8. Ultrametric tree of amphibians from New Guinea and neighbouring islands (16S rRNA). fig. S9. Endemism rate of amphibian species based on the different datasets. table S1. Summary of the acoustic data analysed in appendix S3. table S2. Summary of the number of total mitochondrial DNA sequences, recognised species and candidate species. table S3. List of available mitochondrial DNA sequences for amphibians of the New Guinea region, per species. table S4. Congruence matrix between our different species-delimitation methods. table S5. Congruence matrix between different species-delimitation methods, for the 16S and COI locus. (.docx)
List of all samples and available molecular data, per specimen and species, with detailed results of the species-delimitation methods (.xlsx)