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Research Article
Molecular and acoustic evidence for large-scale underestimation of frog species diversity on New Guinea
expand article infoFlavien Ferreira, Paul Oliver§|, Fred Kraus, Rainer Günther#, Stephen Richards¤, Burhan Tjaturadi«, Evy Arida», Amir Hamidy˄, Awal Riyanto˄, Wahyu Trilaksono˄, Christophe Thébaud, Antoine Fouquet
‡ Université Paul Sabatier, Toulouse, France
§ Biodiversity and Geosciences, Queensland Museum, South Brisbane, Australia
| Griffith University, Brisbane, Australia
¶ University of Michigan, Ann Arbor, United States of America
# Museum für Naturkunde, Berlin, Germany
¤ South Australian Museum, Adelaide, Australia
« Sanata Dharma University, Yogyakarta, Indonesia
» National Research and Innovation Agency (BRIN), Cibinong, Indonesia
˄ Museum Zoologicum Bogoriense, Research Center for Biosystematics and Evolution, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
Open Access

Abstract

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.

Highlights

  • 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.

Keywords

Amphibians, 16S, integrative approach, IUCN, Linnean shortfall, Microhylidae, New Guinea, taxonomy

Introduction

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 (Myers et al. 2000; Wilson et al. 2016; Guedes et al. 2020; Robertson et al. 2023). Knowledge gaps in species richness and distribution (“Linnean” and “Wallacean” shortfalls, respectively; Brown and Lomolino (1998); Lomolino (2004)) represent major obstacles to research and conservation (Nori et al. 2022; Baranzelli et al. 2023; Serrano et al. 2023) and their effect combined with the lack of resources allocated to taxonomy is referred to as the “taxonomic impediment” (Engel et al. 2021). This impediment is of particular concern in amphibians (Giam et al. 2012; Moura and Jetz 2021; Carné and Vieites 2024) because many new species are being described every year, especially in the Tropics, and yet they represent the most threatened group of vertebrates worldwide (Cordier et al. 2021; Luedtke et al. 2023).

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 (Monaghan et al. 2009; Puillandre et al. 2012, 2021; Zhang et al. 2013; Yang 2015). Although these methods are fraught with potential pitfalls (Goldstein and DeSalle 2011; Sukumaran and Knowles 2017), they still provide an efficient way of flagging populations that may represent species unrecognised by current taxonomy (candidate species) and that should be the focus of further taxonomic investigation. Studies following this approach have recently estimated that some focal clades of tropical amphibians could be 2–6 times more diverse than recognised by current taxonomy (Fouquet et al. 2021, 2022; Ferreira et al. 2023; Carné and Vieites 2024).

The region comprising New Guinea and its neighbouring islands is both megadiverse and one of the least biologically studied of the world (Di Marco et al. 2017; Cámara-Leret et al. 2020; Oliver et al. 2022; Slavenko et al. 2023). It spans from the islands immediately west of New Guinea, the world’s largest and highest tropical island, to northern Melanesia and represents a distinct zoogeographical region for amphibians (Holt et al. 2013). The resident amphibian fauna is currently the least threatened (Oliver et al. 2022) and species-richest globally for an insular region, with 560 recognised species, all of which are frogs (Frost 2024). Based on candidate species known to taxonomists working in the region, Oliver et al. (2022) suggested that frog diversity likely exceeds 700 species, a figure similar to current estimates in Madagascar (Carné and Vieites 2024). However, several factors suggest this figure may be conservative: 1) many large or isolated areas remain unsurveyed on New Guinea; 2) taxonomic effort is very limited relative to the geographic area of the region (since 2000, most species have been described by the same six authors; Rodrigues et al. (2010); Frost (2024)); and 3) efforts to investigate frog diversity in the region integrating molecular data only started a decade ago (Oliver et al. 2013; Oliver et al. 2017; Arida et al. 2021; Hill et al. 2022; Ferreira et al. 2023).

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 (Frodin 2007). Known frog species richness as well as projected number of extant species are currently far lower in the western half than in the eastern half of New Guinea (215 vs. 416 resident species, respectively) (IUCN 2024). In a first attempt to fill these knowledge gaps, Arida et al. (2021) conducted a DNA-based inventory of aquatic and terrestrial vertebrate communities in the westernmost peninsula of New Guinea, a region known as the Vogelkop Peninsula or Bird’s Head. These analyses highlighted extensive frog lineage diversity, but no attempt was made to include taxonomically significant characters, such as morphology or calls nor to assess the extent to which lineages matched species recognised by taxonomy. Hence, the extent of unrecognised frog diversity in western New Guinea remains virtually untested.

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 (Vences et al. 2005; Fouquet et al. 2007). We then validated some of these MOTUs using bioacoustic data as additional lines of evidence (i.e. integrative taxonomy approach; Dayrat (2005); Padial et al. (2010)) because advertisement vocalisations are sensitive inherent species-isolating mechanisms and, therefore, highly relevant in delimiting frog species (Köhler et al. 2017). Finally, we derived estimates of species diversity that may remain to be described and provided a perspective on the magnitude of the taxonomic impediment for amphibians in the region.

Methods

Sampling

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 Arida et al. (2021) from the Barcoding of Life Database (BOLD) in order to increase geographic sampling. A summary of the genetic dataset is presented in Table 1 and the full list of sequences is available in the Suppl. material 2. Sequences were retrieved from GenBank using the filter tool, specifying genera occurring in our study region (based on the distributional data of the International Union for Conservation of Nature, IUCN, https://www.iucnredlist.org) and targeted loci. These data were further filtered to remove species that do not occur in the study region. Coordinates for sampling localities were directly retrieved from publications by contacting the authors or were georeferenced with a ~ 10 km precision using Google Earth and Mapcarta (https://mapcarta.com/) when only locality names were available.

Species delimitation

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 1: appendix S1) from specimens collected in western New Guinea during field work undertaken over the last 20 years, including 160 (out of the 167) specimens that were included in Arida et al. (2021). The sequences were aligned using MAFFT (version 7) (Katoh et al. 2019) following the E-INS-i method. MOTUs were delimited using three complementary single-locus methods: Automatic Barcode Gap Discovery (ABGD; Puillandre et al. (2012)); 2) single-rate Poisson Tree Processes (PTP; Zhang et al. (2013)); and 3) the Generalised Mixed Yule Coalescent approach (GMYC; Pons et al. (2006); Monaghan et al. (2009)); Briefly, 1) ABGD infers an intra- and interspecific threshold based on genetic distances, 2) PTP infers species boundaries from the number of substitutions on the branches of a Maximum-Likelihood phylogenetic tree and 3) GMYC uses an ultrametric tree to infer a temporal threshold delimiting species (each partitioning method is detailed in Suppl. material 1: appendix S2). For all methods, four species were used as outgroups: Heleophryne purcelli, Leiopelma hochstetteri, Pipa pipa and Rhinophrynus dorsalis. The final delimitation was based on a majority-rule consensus across the three partitions obtained (Dellicour and Flot 2018), i.e. defining as an MOTU any lineage supported by at least two of the three methods (Fig. 1; see the Suppl. material 2 for all delimitations’ results). We followed the nomenclature of Frost (2024) and assigned taxon names to MOTUs represented by type specimens or to those geographically closest to the type locality in case of conflicting initial identifications.

Integration of bioacoustic data

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. 1) using both published and newly acquired audio recordings (see Suppl. material 1: appendix S3 for data availability). These focal species complexes provided an overall evaluation of the robustness of the delimitation otherwise based on mtDNA only.

We investigated call variation following a note-centred approach (Köhler et al. 2017) with particular focus on: 1) note duration; 2) inter-note duration; 3) note repetition rate per second; 4) number of notes per call; 5) number of pulses per note; 6) amplitude modulation (i.e. increasing or decreasing amplitude within a note); 7) dominant frequency; and 8) note frequency modulation (absence, upward or downward). We conservatively considered slight variations in dominant frequency (7), note and inter-note duration (1 and 2) between allopatric MOTUs to be non-diagnostic, due to potential variation inherent to specimens’ body size and recording environment temperature (Gerhardt and Huber 2002). On the other hand, non-overlapping numbers of notes per call (4), note amplitude modulation (6) and note frequency modulation (8) were considered as supporting the delimitations regardless of whether the MOTUs occurred in sympatry or allopatry. All comparisons are summarised in Suppl. material 1: table S1 and individually presented in Suppl. material 1: figs S1–S6.

Figure 1. 

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 1: appendix S3. Call data for O. cf. roedeli 1. and O. cf. roedeli 3 were unavailable.

Spatial inferences

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. 2) that are representative of the geographic and environmental diversity within our study region (justifications in Suppl. material 1: appendix S4). MOTU richness and endemism per subregion were compared to estimates of species richness derived from IUCN species-distributional data (IUCN, https://www.iucnredlist.org). These distributional data are based on minimum-convex polygons defined for each MOTU/species (i.e. linking all outermost occurrence points), regardless of the potential non-suitability of habitat within polygons. Richness was defined as the number of polygons intersecting each subregion or as simple presence in the case of MOTUs with fewer than two occurrences. Endemism was defined as the proportion of MOTUs/species uniquely found in each subregion. All maps were generated on QGIS v.3.20 (QGIS Development Team 2020).

Figure 2. 

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.

Results

Taxonomic and spatial distribution

The complete dataset of mitochondrial data comprised 2301 DNA sequences (1767 from online repositories and 534 newly generated) (Table 1, Fig. 2, Suppl. material 1: fig. S7), representing 1537 specimens (out of which 1380 were georeferenced) distributed across 226 unique sampling localities (i.e. within a 10 km radius) and including six families: Microhylidae, Hylidae, Ceratobatrachidae, Ranidae, Myobatrachidae and Dicroglossidae. When considering all families and online data only, more sequences were available for the 12S locus, but we chose to focus on the 16Sb locus for the rest of our study because it had the most comprehensive taxonomic and geographic sampling (Table 1; Suppl. material 1: fig. S7A). Combining GenBank and newly acquired sequences, 16Sb is the best-sampled locus for all families (35% of all sequences), followed by 12S (21%), 16Sa (20%) and cytb (16%). Microhylidae was the most-represented family with 1523 sequences, followed by Hylidae (353) and Ceratobatrachidae (298). It is noteworthy that more than half of the Microhylidae sequences corresponded to three genera only (Mantophryne, Hylophorbus and Choerophryne) that have been the focus of specific studies using 12S, 16S (a and b) and cytb (Oliver et al. 2013; Oliver et al. 2017; Ferreira et al. 2023).

The majority of the georeferenced sequences are from the eastern half of New Guinea (1177 sequences; Fig. 2), mainly from the Papuan Peninsula (367 sequences, 32 unique localities) and the eastern central range (CRE) (274 sequences, 37 unique localities). Conversely, in the western half of New Guinea and its surrounding islands (963 sequences), most sequences were from specimens collected in the Bird’s Neck and Bird’s Head subregions (393 and 312 sequences from 27 and 11 unique localities, respectively). Across subregions, microhylids are best represented in the dataset (175, 342, 259 and 145 sequences in the eastern central range, Papuan Peninsula, Bird’s Neck and Bird’s Head, respectively).

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 1). With the exception of Aphantophryne and Callulops, species-poor genera (sensu Frost (2024)) tend to have the highest taxonomic coverage: Mantophryne, Paedophryne, Barygenys and Hylophorbus (78–100%).

Table 1.

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 Frost (2024)) represented by molecular data. Details on which species are represented by molecular data are given in the Suppl. material 1. Abbreviation: GB, GenBank.

Taxa 12S 16Sa 16Sb cytb COI Total sequences Taxonomic completion (%)
GB GB GB This study Total GB GB Arida et al. (2021)
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

Species delimitation

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 1), all 16Sb sequences (Fig. 3A), MOTU counts and proportion of candidate species (Fig. 3B).

Acoustic data were available for 38 MOTUs (Suppl. material 1: appendix S3, table S1), amongst which 30 were supported as distinct species, with 11 recognised and 19 (63%) unrecognised species. The mean p-distance between the MOTUs confirmed as valid species by acoustic data is 4.0% (1.0–13.0%) for Microhylidae and 2.7% (2.0–3.0%) for Ceratobatrachidae; limited bioacoustic data prevented comparisons between related MOTUs in other families.

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. 3B), we can extrapolate the total number of species remaining to be described from the number of recognised species (560) if we assume: 1) that all candidate species are confirmed; 2) that we have evenly sampled total taxonomic diversity; and 3) that taxonomic gaps are evenly distributed across the region. Extrapolated to all groups, there would be a total of 1176 frog species across New Guinea and its neighbouring islands (Fig. 3C), of which 616 would be unrecognised at present (560*1.1 = 616). However, candidate species richness is unbalanced across families, being mostly driven by Microhylidae, with 1.5 times more candidate species than recognised species (97 vs. 68). The same extrapolation in this family alone would lead to 501 unrecognised species in addition to the current 334 recognised species.

The Bird’s Head and Bird’s Neck subregions contain the highest number of MOTUs (75 and 61 respectively; Fig. 3D), MOTUs assigned to recognised species (24 and 34, respectively), 16Sb sequences (223 and 175, Suppl. material 1: fig. S7) and are occupied by species of all families, except Dicroglossidae. By contrast, the western central range is represented by no 16Sb sequences at all, but one 12S, two 16Sa and three cytb sequences (Suppl. material 1: fig. S7A).

Figure 3. 

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 1: fig. S8; B) Final number of recognised species and candidate species amongst MOTUs across families; C) Global number of recognised species, candidate species from this study and extrapolation of unrecognised species per family. The extrapolation is based on the proportion of putative candidate species in B (details in Results: Species delimitation); D) Total number of MOTUs per subregion (grey shading). Pie charts indicate the proportion of each family in the final MOTUs delimitation (colours presented in A), for the eight richest subregions. Abbreviations: Mic, Microhylidae; Hyl, Hylidae; Cer, Ceratobatrachidae; Ran, Ranidae; Myo, Myobatrachidae; Dic, Dicroglossidae.

Species diversity and endemism

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. 4A), revealed that the Papuan Peninsula and eastern central range were the most deficient, with 151 and 126 recognised species missing in the MOTU dataset, respectively (Fig. 4B). This deficit was less pronounced in the Solomon Islands, Seram and Halmahera (two, four and eight recognised species missing) and the Bird’s Neck and Bird’s Head (21 and 25 recognised species missing). When comparing species richness between IUCN data and all MOTUs regardless of their correspondence to recognised or candidate species, the molecular dataset missed species the most in eastern New Guinea (Fig. 4C). In contrast, the westernmost peninsula of New Guinea and the Island of Halmahera displayed levels of species diversity higher than those published by IUCN, with the Bird’s Head in particular having an excess of 18 MOTUs over the number of taxonomically known species (Fig. 4C).

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 1: fig. S9). However, estimates of endemism rates for MOTUs were much more homogeneous across subregions and higher on average (85%) than those obtained for species in the IUCN dataset (35%).

Figure 4. 

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.

Discussion

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 (Giller and O’Donovan 2002; Utami et al. 2022). As these gaps alter our perception of diversity patterns, they also hamper our capacity to address the ongoing extinction crisis (Baranzelli et al. 2023). This particularly applies to tropical rainforest areas such as the New Guinea region, which possibly host the least-studied fauna and flora of all terrestrial biomes (Dinerstein and Wikramanayake 1993; Di Marco et al. 2017; Cámara-Leret et al. 2020). Molecular-based inventories represent a fast and efficient way to estimate species diversity and they can foster subsequent taxonomic efforts (Padial et al. 2010). Here, we used this approach by collating data from existing repositories and new data to improve our current understanding of species diversity in frogs in the New Guinea region, a fauna for which the taxonomic impediment is expected to be very high. We provided 534 new DNA sequences of specimens mainly collected from the Bird’s Head and the Bird’s Neck, two of the most poorly studied regions on New Guinea. Using our dataset, we delimited MOTUs to assess geographic variation in species diversity across the region and to compare our diversity estimates with IUCN counts that are based on recognised species. Our results show that frog species richness in the New Guinea region is vastly underestimated, with the strongest taxonomic impediment located in the western half of New Guinea, where large areas still remain unsurveyed by biologists.

Sampling gaps and geographic bias

Although DNA sequencing has been increasingly accessible, with the rate of publication of new sequences rocketing over the last two decades (Smith 2016), the New Guinea region still remains poorly represented in DNA sequence repositories. Our georeferenced dataset highlighted that most (81%) of the mtDNA sequences from New Guinean amphibians published before this study (GenBank) originate from the eastern half of the island, in the country of Papua New Guinea (Fig. 2). This sampling bias is also apparent in other taxa (e.g. ants; Kass et al. (2022)). We partially filled this gap by providing newly acquired sequences from specimens recently collected in western New Guinea and we encourage others to pursue efforts to document species diversity in this part of the island by combining field surveys and molecular identification protocols (Arida et al. 2021).

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 1). Missing data are most prevalent in Microhylidae and Hylidae and especially in species having narrow ranges (Suppl. material 1: table S3). Studies focusing on specific genera have already started to fill these gaps (e.g. Oliver et al. (2017); Ferreira et al. (2023)) and work on the Hylidae is in progress (S.C. Donnellan, pers. comm.).

Barcoding and the amphibian Linnean shortfall

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 1: table S4), while PTP tended to be more conservative, except for Microhylidae. A similar pattern between delimitation methods was also found by Arida et al. (2021), who analysed variation at the COI locus in a subset of samples included in our study (Suppl. material 1: table S5). The MOTU consensus in Arida et al. (2021) only partially overlaps with ours (Suppl. material 1: table S5), highlighting the benefits of integrating additional data (e.g. bioacoustics, morphometrics) to define robust candidate species hypotheses (Padial et al. 2010).

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 (Vences et al. 2005; Fouquet et al. 2007). Hence, a 3% threshold would be relatively conservative with our 16S dataset, since 69, 56 and 26 pairs of MOTUs in Microhylidae, Hylidae and Ceratobatrachidae display p-distances below 3% (including eight that were supported by acoustic data). Yet, because mtDNA-based approaches can lead to either species-oversplitting or lumping (Sukumaran and Knowles 2017; Dellicour and Flot 2018), the true extent of unrecognised diversity remains uncertain in the absence of bioacoustic data and the lack of morphological data prevents further characterisation that could strengthen the candidate species hypotheses. Nevertheless, because Microhylidae and Ceratobatrachidae are direct-developing frogs that often have narrow distributions and climatic niches (Oliver et al. 2022), we consider it likely that a very large portion of allopatric MOTUs in these groups correspond to distinct species. Conversely, we advise caution regarding Hylidae, for which species diversity remains ambiguous in our dataset due to sampling gaps and because numerous species complexes have been documented (e.g. Sulaeman et al. (2021); Günther et al. (2023)).

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%; Frost (2024)) and supports the idea that our sampling is representative of actual species diversity in the region. Following this assumption and assuming that the ratio between candidate and recognised species within our MOTU dataset is representative of the whole region (see Results), we obtained an estimate of 1,200 frog species in the New Guinea region. This estimate is subject to uncertainty and could well be an overestimate due to the nature of mtDNA (cf. paragraph above) and also because unsurveyed or poorly surveyed areas could be home to higher proportions of previously-known species (i.e. low beta diversity). On the other hand, our estimate could also be an underestimate if our dataset contains false negatives (species undelimited by mtDNA) or there is overlooked high beta diversity, as suggested by recent work in eastern New Guinea (Kraus 2021; Dahl et al. 2024).

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. 5). However, major uncertainties persist in areas where data remain substantially lacking, such as the western portion of the central range, which is thought to be highly biodiverse (Fig. 4A). This part of the island is the least sampled of all New Guinea both for molecular data and for most taxa, except perhaps some arthropod groups and birds (Toussaint et al. 2021; Kennedy et al. 2022; Letsch et al. 2023).

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. 5). Amongst those, only six overlap with the ~ 200 candidate species identified by Oliver et al. (2022) from the New Guinea region. This gap derives from the differing sources of data used: mtDNA data in this study vs. expert surveys in Oliver et al. (2022). We can further highlight the geographic unbalance across datasets, i.e. most candidate species of Oliver et al. (2022) are from eastern New Guinea and many candidates from western New Guinea were not considered. These two largely non-overlapping datasets illustrate the scale of the Linnean shortfall for frogs in this region; while estimating a total of 700 species, Oliver et al. (2022) did not include at least 117 species identified here. Combining these two candidate species datasets, both incomplete and patchy in different ways, generates a minimum estimate of 800 species (~ 240 currently undescribed).

Figure 5. 

Examples of candidate species from the Bird’s Head and Bird’s Neck subregions (West Papua, Indonesia). The full list of candidate species is presented in the Suppl. material 2.

Investigating the amphibian Wallacean shortfall

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. 1) and the most species-rich according to the IUCN (Fig. 4A), but one of the least sampled and least diverse in our MOTUs dataset (Fig. 3D and Suppl. material 1: fig. S7). This discrepancy derives from the positive correlation between the number of available 16Sb sequences per subregion and the number of delimited MOTUs (Figs 3D, 4B, 7B). How the correlation between species richness and geographic area varies across the study region remains to be tested with more data. However, we suspect that most areas of New Guinea show high levels of species richness, as suggested by the similar areal extents and species diversity of: 1) the Papuan Peninsula (85,000 km²) where 162 species are resident according to the IUCN and 2) the combined Bird’s Head and Bird’s Neck (90,000 km²) that are our best 16Sb-sampled subregions and have 110 delimited MOTUs in our analyses. Such diversity levels in western New Guinea are in line with recent studies that uncovered high levels of undocumented diversity in numerous taxa in this part of the island (Kadarusman et al. 2012; Cámara-Leret et al. 2020; Natusch et al. 2020; Arida et al. 2021; Milá et al. 2021; Ferreira et al. 2023; Oliver et al. 2025).

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 (Duellman et al. 1999; Bickford 2004). Endemism is generally high for amphibians in tropical mountains that act as habitat islands, which ultimately favours biological diversification (Anthelme et al. 2014; Stein et al. 2014). This pattern has been reported for frogs in eastern New Guinea (Oliver et al. 2017; Tallowin et al. 2017; Dahl et al. 2024) and undoubtedly occurs in western New Guinea, which harbours similar topographic heterogeneity (Oliver et al. 2022; Ferreira et al. 2023).

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) (Vacher et al. 2020) and Madagascar (Central plateau) (Brown et al. 2016). However, the diversification of the Amazonian and Malagasy amphibian fauna has a long history throughout the Cenozoic, whereas terrestrial ecosystems of New Guinea may only date back to the early Oligocene (e.g. Jønsson et al. (2011)). These differences of context are clearly exemplified when comparing the crown age of Microhylidae from these regions; ~ 60 vs. 20 Ma (Feng et al. 2017; Hime et al. 2021; Portik et al. 2023). The New Guinean clade of Microhylidae (at least 14 genera and more than 300 species; Frost (2024)) would then have rapidly diversified during the island’s recent orogenic development and adapted to fossorial, terrestrial, scansorial and arboreal habitats (Rivera et al. 2017; Hill et al. 2023), a pattern typical of an adaptive radiation (Moen et al. 2021).

Phylogenetic insights on New Guinean amphibians

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 1: fig. S8). Since our phylogenetic inferences are based on a single mtDNA locus only, we refrain from discussing node age estimates or interrelationships further than for the most external branches. We note, however, that our tree topologies are largely congruent with recent phylogenetic hypotheses that focused on Ranidae and Ceratobatrachidae (Brown et al. 2015; Chan et al. 2020). Interestingly, the addition of new Cornufer lineages revealed overlooked diversity in western New Guinea that could be very important for understanding the evolutionary history of that group (Suppl. material 1: fig. S8).

Most incongruences between our trees and previously published phylogenies occur within Hylidae and especially within Litoria (sensu Frost (2024)). Most discrepancies concern weakly supported clades that are also unresolved in literature (Portik et al. 2023). On the other hand, microhylid phylogenetic relationships are difficult to evaluate herein due to insufficient sequence data and limited species sampling. This echoes the long-standing challenge of resolving microhylid phylogenetic relationships in the region (Rivera et al. 2017; Hill et al. 2022).

Amphibian conservation in the New Guinea region

New Guinea’s forests are still relatively extensive compared to many other tropical areas (Vancutsem et al. 2021) and their amphibian faunas remains substantially intact (Oliver et al. 2022). The region has been considered a “wilderness area” (Mittermeier et al. 2003); consequently, it has received little conservation attention compared to other regions that face much more extensive and imminent threats (e.g. Madagascar; Ralimanana et al. (2022)). Yet, a quarter of recognised amphibians from the New Guinea region still awaits an IUCN conservation status assessment and might already be subject to some threats (Oliver et al. 2022). In addition, we showed here that the region hosts an important and undocumented cryptic amphibian diversity, a large portion of which may consist of species confined to restricted geographical areas and, therefore, likely to be more sensitive to both land-use and climate changes. At a minimum, this indicates that the conservation status of many species will need to be re-assessed as distributions become better known, as highlighted by Kraus (2021) for the south-easternmost part of New Guinea and its archipelagos. More generally, there is a crucial need to hasten formal species descriptions in the New Guinea region (best achieved using integrative approaches), in order to facilitate conservation while also providing a more robust foundation for future research. The significant extent of the Linnean and Wallacean shortfalls of this region should also emphasise the importance of taking early conservation measures for amphibians to mitigate the risks of destructive land-use change (Cordier et al. 2021) and potential biotic invasions (e.g. chytrid fungus; Bower et al. (2019)) and to address the vulnerability and resilience of locally endemic upland species to threats from climate change (Lenoir et al. 2020). This rationale also applies to other tropical regions that are subject to significant amphibian Linnean shortfalls (e.g. Neotropics and Madagascar) (Vacher et al. 2020; Carné and Vieites 2024) and already face massive threats to biodiversity (Luedtke et al. 2023).

Acknowledgements

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.

Funding

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.

Conflicts of interest

The authors declare they have no conflict of interest.

Author contributions

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).

Data accessibility statement

Molecular data used in the analyses are available in online repositories: GenBank (newly generated sequences are available under the accessions PQ334073PQ334606) 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 1, 2 are available upon request to the corresponding author and have been uploaded on iNaturalist.

References

  • Anthelme F, Jacobsen D, Macek P, Meneses RI, Moret P, Beck S, Dangles O (2014) Biodiversity Patterns and Continental Insularity in the Tropical High Andes. Arctic, Antarctic, and Alpine Research 46: 811–828. https://doi.org/10.1657/1938-4246-46.4.811
  • Arida E, Ashari H, Dahruddin H, Fitriana YS, Hamidy A, Irham M, Kadarusman Riyanto A, Wiantoro S, Zein MSA, Hadiaty RK, Apandi Krey F, Kurnianingsih Melmambessy EHP, Mulyadi Ohee HL, Saidin Salamuk A, Sauri S, Suparno Supriatna N, Suruwaky AM, Laksono WT, Warikar EL, Wikanta H, Yohanita AM, Slembrouck J, Legendre M, Gaucher P, Cochet C, Delrieu-Trottin E, Thébaud C, Mila B, Fouquet A, Borisenko A, Steinke D, Hocdé R, Semiadi G, Pouyaud L, Hubert N (2021) Exploring the vertebrate fauna of the Bird’s Head Peninsula (Indonesia, West Papua) through DNA barcodes. Molecular Ecology Resources 21: 2369–2387. https://doi.org/10.1111/1755-0998.13411
  • Baranzelli MC, Villalobos F, Cordier JM, Nori J (2023) Knowledge shortfalls’ interactions shadow our perception of species’ exposure to human threats. Biological Conservation 282: 110069. https://doi.org/10.1016/j.biocon.2023.110069
  • Bickford DP (2004) Differential parental care behaviors of arboreal and terrestrial microhylid frogs from Papua New Guinea. Behavioral Ecology and Sociobiology 55: 402–409. https://doi.org/10.1007/s00265-003-0717-x
  • Bower DS, Lips KR, Amepou Y, Richards S, Dahl C, Nagombi E, Supuma M, Dabek L, Alford RA, Schwarzkopf L, Ziembicki M, Noro JN, Hamidy A, Gillespie GR, Berger L, Eisemberg C, Li Y, Liu X, Jennings CK, Tjaturadi B, Peters A, Krockenberger AK, Nason D, Kusrini MD, Webb RJ, Skerratt LF, Banks C (2019) Island of opportunity. Ecology and the Environment 17: 348–354. https://doi.org/10.1002/fee.2057
  • Brown RM, Siler CD, Richards SJ, Diesmos AC, Cannatella DC (2015) Multilocus phylogeny and a new classification for Southeast Asian and Melanesian forest frogs (family Ceratobatrachidae). Zoological Journal of the Linnean Society 174: 130–168. https://doi.org/10.1111/zoj.12232
  • Cámara-Leret R, Frodin DG, Adema F, Anderson C, Appelhans MS, Argent G, Arias Guerrero S, Ashton P, Baker WJ, Barfod AS, Barrington D, Borosova R, Bramley GLC, Briggs M, Buerki S, Cahen D, Callmander MW, Cheek M, Chen CW, Conn BJ, Coode MJE, Darbyshire I, Dawson S, Dransfield J, Drinkell C, Duyfjes B, Ebihara A, Ezedin Z, Fu LF, Gideon O, Girmansyah D, Govaerts R, Fortune-Hopkins H, Hassemer G, Hay A, Heatubun CD, Hind DJN, Hoch P, Homot P, Hovenkamp P, Hughes M, Jebb M, Jennings L, Jimbo T, Kessler M, Kiew R, Knapp S, Lamei P, Lehnert M, Lewis GP, Linder HP, Lindsay S, Low YW, Lucas E, Mancera JP, Monro AK, Moore A, Middleton DJ, Nagamasu H, Newman MF, Nic Lughadha E, Melo PHA, Ohlsen DJ, Pannell CM, Parris B, Pearce L, Penneys DS, Perrie LR, Petoe P, Poulsen AD, Prance GT, Quakenbush JP, Raes N, Rodda M, Rogers ZS, Schuiteman A, Schwartsburd P, Scotland RW, Simmons MP, Simpson DA, Stevens P, Sundue M, Testo W, Trias-Blasi A, Turner I, Utteridge T, Walsingham L, Webber BL, Wei R, Weiblen GD, Weigend M, Weston P, de Wilde W, Wilkie P, Wilmot-Dear CM, Wilson HP, Wood JRI, Zhang LB, van Welzen PC (2020) New Guinea has the world’s richest island flora. Nature 584: 579–583. https://doi.org/10.1038/s41586-020-2549-5
  • Carné A, Vieites DR (2024) A race against extinction: The challenge to overcome the Linnean amphibian shortfall in tropical biodiversity hotspots. Diversity and Distributions 30: e13912. https://doi.org/10.1111/ddi.13912
  • Chan KO, Hutter CR, Wood PL, Grismer LL, Brown RM (2020) Larger, unfiltered datasets are more effective at resolving phylogenetic conflict: Introns, exons, and UCEs resolve ambiguities in Golden-backed frogs (Anura: Ranidae; genus Hylarana). Mole­cular Phylogenetics and Evolution 151: 106899. https://doi.org/10.1016/j.ympev.2020.106899
  • Cordier JM, Aguilar R, Lescano JN, Leynaud GC, Bonino A, Miloch D, Loyola R, Nori J (2021) A global assessment of amphibian and reptile responses to land-use changes. Biological Conservation 253: 108863. https://doi.org/10.1016/j.biocon.2020.108863
  • Dahl C, Richards SJ, Basien I, Mungkaje AJ, Novotny V (2024) Local and regional diversity of frog communities along an extensive rainforest elevation gradient in Papua New Guinea. Biotropica 56: 90–97. https://doi.org/10.1111/btp.13283
  • Duellman WE, Borkin LJ, Campbell JA, Hedges SB, Inger RF, Poynton JC, Sweet SS, Tyler MJ, Er-Mi Z (1999) Patterns of Distribution of Amphibians. A Global Perspective. Duellman WE (Ed.). The Johns Hopkins University Press, Baltimore. https://doi.org/10.56021/9780801861154
  • Engel MS, P Ceríaco LM, Daniel GM, Dellapé PM, Löbl I, Marinov M, Reis RE, Young MT, Dubois A, Agarwal I, Lehmann PA, Alvarado M, Alvarez N, Andreone F, Araujo-vieira K, Ascher JS, Baêta D, Baldo D, Bandeira SA, Barden P, Barrasso DA, Bendifallah L, Bockmann FA, Böhme W, Borkent A, Brandão CRF, Busack SD, Bybee SM, Channing A, Chatzimanolis S, M Christenhusz MJ, Crisci JV, Da Costa LM, Davis SR, Alberto De Lucena CS, Deuve T, Fernandes Elizalde S, Faivovich J, Farooq H, Ferguson AW, Gippoliti S, Gonçalves FMP, Gonzalez VH, Greenbaum E, Hinojosa-Díaz IA, Ineich I, Jiang J, Kahono S, Kury AB, F Lucinda PH, Lynch JD, Malécot V, Marques MP, M Marris JW, Mckellar RC, Mendes LF, Nihei SS, Nishikawa K, Ohler A, Orrico VGD, Ota H, Paiva J, Parrinha D, Pauwels OSG, Pereyra MO, Pestana LB, Pinheiro PDP, Prendini L, Prokop J, Rasmussen C, Rödel M, Trefaut Rodrigues M, Rodríguez SM, Salatnaya H, Sampaio Í, Sánchez-garcía A, Shebl MA, Santos BS, Solórzano-kraemer MM, Sousa ACA, Stoev P, Teta P, Trape J, Van-dúnem Dos Santos C, Vasudevan K, Vink CJ, Vogel G, Wagner P, Wappler T, Ware JL, Wedmann S, Kusamba Zacharie C (2021) The taxonomic impediment: a shortage of taxonomists, not the lack of technical approaches. Zoological Journal of the Linnean Society 193: 381–387. https://doi.org/10.1093/zoolinnean/zlab072
  • Feng Y-J, Blackburn DC, Liang D, Hillis DM, Wake DB, Cannatella DC, Zhang P (2017) Phylogenomics reveals rapid, simultaneous diversification of three major clades of Gondwanan frogs at the Cretaceous–Paleogene boundary. Proceedings of the National Academy of Sciences of the USA 114: E5864–E5870. https://doi.org/10.1073/pnas.1704632114
  • Ferreira F, Kraus F, Richards S, Oliver P, Günther R, Trilaksono W, Arida EA, Hamidy A, Riyanto A, Tjaturadi B, Thébaud C, Gaucher P, Fouquet A (2023) Species delimitation and phylogenetic analyses of a New Guinean frog genus (Microhylidae: Hylophorbus) reveal many undescribed species and a complex diversification history driven by late Miocene events. Zoological Journal of the Linnean Society 202: zlad168. https://doi.org/10.1093/zoolinnean/zlad168
  • Fouquet A, Leblanc K, Framit M, Réjaud A, Rodrigues MT, Castroviejo-Fisher S, Peloso PL V, Prates I, Manzi S, Suescun U, Baroni S, Moraes LJCL, Recoder R, De Souza SM, Dal Vecchio F, Camacho A, Ghellere JM, Rojas-Runjaic FJM, Gagliardi-Urrutia G, Tadeu V, Carvalho DE, Gordo M, Menin M, Kok PJR, Hrbek T, Werneck FP, Crawford AJ, Ron SR, Mueses-Cisneros JJ, Zamora RRR, Pavan D, Simões PI, Ernst R, Fabre A-C (2021) Species diversity and biogeography of an ancient frog clade from the Guiana Shield (Anura: Microhylidae: Adelastes, Otophryne, Synapturanus) exhibiting spectacular phenotypic diversification. Biological Journal of the Linnean Society 132: 233–256. https://doi.org/10.1093/biolinnean/blaa204
  • Fouquet A, Cornuault J, Rodrigues MT, Werneck FP, Hrbek T, Acosta-Galvis AR, Massemin D, Kok PJR, Ernst R (2022) Diversity, biogeography, and reproductive evolution in the genus Pipa (Amphibia: Anura: Pipidae). Molecular Phylogenetics and Evolution 170: 107442. https://doi.org/10.1016/j.ympev.2022.107442
  • Frodin DG (2007) Biological exploration of New Guinea. In: Marshall AJ, Beehler BM (Eds) Ecology of Papua, part One. Singapore, 14–107.
  • Gerhardt HC, Huber F (2002) Acoustic Communication in Insects and Anurans Common Problems and Diverse Solutions. The University of Chicago Press, Chicago.
  • Giam X, Scheffers BR, Sodhi NS, Wilcove DS, Ceballos G, Ehrlich PR (2012) Reservoirs of richness: least disturbed tropical forests are centres of undescribed species diversity. Proceedings of the Royal Society B: Biological Sciences 279: 67–76. https://doi.org/10.1098/rspb.2011.0433
  • Giller PS, O’Donovan G (2002) Biodiversity and Ecosystem Function: Do Species Matter? Biology and Environment: Proceedings of the Royal Irish Academy 102B: 129–139. https://doi.org/10.1353/bae.2002.0004
  • Goldstein PZ, DeSalle R (2011) Integrating DNA barcode data and taxonomic practice: Determination, discovery, and description. BioEssays 33: 135–147. https://doi.org/10.1002/bies.201000036
  • Guedes JJM, Feio RN, Meiri S, Moura MR (2020) Identifying factors that boost species discoveries of global reptiles. Zoological Journal of the Linnean Society 190: 1274–1284. https://doi.org/10.1093/zoolinnean/zlaa029
  • Günther R, Richards SJ, Hamidy A, Trilaksono W, Sulaeman TN, Oliver PM (2023) A new large green treefrog (Litoria: Pelodryadidae) from western New Guinea, with the description of a new diagnostic character for the Litoria graminea group. Raffles Bulletin of Zoology 71: 417–429. https://doi.org/10.26107/RBZ-2023-0031
  • Hill EC, Fraser CJ, Gao DF, Jarman MJ, Henry ER, Iova B, Allison A, Butler MA (2022) Resolving the deep phylogeny: Implications for early adaptive radiation, cryptic, and present-day ecological diversity of Papuan microhylid frogs. Molecular Phylogenetics and Evolution 177: 107618. https://doi.org/10.1016/j.ympev.2022.107618
  • Hill EC, Gao DF, Polhemus DA, Fraser CJ, Iova B, Allison A, Butler MA (2023) Testing geology with biology: Plate tectonics and the diversification of Microhylid frogs in the Papuan Region. Integrative Organismal Biology 5: obad028. https://doi.org/10.1093/iob/obad028
  • Hime PM, Lemmon AR, Lemmon ECM, Prendini E, Brown JM, Thomson RC, Kratovil JD, Noonan BP, Pyron RA, Peloso PLV, Kortyna ML, Keogh JS, Donnellan SC, Mueller RL, Raxworthy CJ, Kunte K, Ron SR, Das S, Gaitonde N, Green DM, Labisko J, Che J, Weisrock DW (2021) Phylogenomics reveals ancient gene tree discordance in the amphibian Tree of Life. Systematic Biology 70: 49–66. https://doi.org/10.1093/sysbio/syaa034
  • Holt BG, Lessard J-P, Borregaard MK, Fritz SA, Araújo MB, Dimitrov D, Fabre P-H, Graham CH, Graves GR, Jønsson KA, Nogués-Bravo D, Wang Z, Whittaker RJ, Fjeldså J, Rahbek C (2013) An update of Wallace’s Zoogeographic regions of the world. Science 339: 74–78. https://doi.org/10.1126/science.1228282
  • Jønsson KA, Fabre P-H, Ricklefs RE, Fjeldså J (2011) Major global radiation of corvoid birds originated in the proto-Papuan archipelago. Proceedings of the National Academy of Sciences of the USA 108: 2328–2333. https://doi.org/10.1073/pnas.1018956108
  • Kadarusman Hubert N, Hadiaty RK, Sudarto Paradis E, Pouyaud L (2012) Cryptic diversity in Indo-Australian rainbowfishes revealed by DNA barcoding: Implications for Conservation in a biodiversity hotspot candidate. PLOS ONE 7: e40627. https://doi.org/10.1371/journal.pone.0040627
  • Katoh K, Rozewicki J, Yamada KD (2019) MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Briefings in Bioinformatics 20: 1160–1166. https://doi.org/10.1093/bib/bbx108
  • Kennedy JD, Marki PZ, Reeve AH, Blom MPK, Prawiradilaga DM, Haryoko T, Koane B, Kamminga P, Irestedt M, Jønsson KA (2022) Diversification and community assembly of the world’s largest tropical island. Global Ecology and Biogeography 31: 1078–1089. https://doi.org/10.1111/geb.13484
  • Köhler J, Jansen M, Rodríguez A, Kok PJR, Toledo LF, Emmrich M, Glaw F, Haddad CFB, Rödel MO, Vences M (2017) The use of bioacoustics in anuran taxonomy: Theory, terminology, methods and recommendations for best practice. Zootaxa 4251: 1–124. https://doi.org/10.11646/zootaxa.4251.1.1
  • Letsch H, Balke M, Kusy D, McKenna DD, Pramesa Narakusumo R, Sagata K, Toussaint EFA, White LT, Riedel A (2023) Beetle evolution illuminates the geological history of the World’s most diverse tropical archipelago. Ecography 2023: e06898. https://doi.org/10.1111/ecog.06898
  • Di Marco M, Chapman S, Althor G, Kearney S, Besancon C, Butt N, Maina JM, Possingham HP, von Bieberstein K, Venter O, Watson JEM (2017) Changing trends and persisting biases in three decades of conservation science. Global Ecology and Conservation 10: 32–42. https://doi.org/10.1016/j.gecco.2017.01.008
  • Milá B, Bruxaux J, Friis G, Sam K, Ashari H, Thébaud C (2021) A new, undescribed species of Melanocharis berrypecker from western New Guinea and the evolutionary history of the Melanocharitidae. Ibis 163: 1310–1329. https://doi.org/10.1111/ibi.12981
  • Mittermeier RA, Mittermeier CG, Brooks TM, Pilgrim JD, Konstant WR, da Fonseca GAB, Kormos C (2003) Wilderness and biodiversity conservation. Proceedings of the National Academy of Sciences of the USA 100: 10309–10313. https://doi.org/10.1073/pnas.1732458100
  • Moen DS, Ravelojaona RN, Hutter CR, Wiens JJ (2021) Testing for adaptive radiation: A new approach applied to Madagascar frogs. Evolution 75: 3008–3025. https://doi.org/10.1111/evo.14328
  • Monaghan MT, Wild R, Elliot M, Fujisawa T, Balke M, Inward DJG, Lees DC, Ranaivosolo R, Eggleton P, Barraclough TG, Vogler AP (2009) Accelerated species inventory on Madagascar using coalescent-based models of species delineation. Systematic Biology 58: 298–311. https://doi.org/10.1093/sysbio/syp027
  • Myers N, Mittermeier RA, Mittermeier CG, da Fonseca GAB, Kent J (2000) Biodiversity hotspots for conservation priorities. Nature 403: 853–858. https://doi.org/10.1038/35002501
  • Natusch DJD, Esquerré D, Lyons JA, Hamidy A, Lemmon AR, Moriarty Lemmon E, Riyanto A, Keogh JS, Donnellan S (2020) Species delimitation and systematics of the green pythons (Morelia viridis complex) of Melanesia and Australia. Molecular Phylogenetics and Evolution 142: 106640. https://doi.org/10.1016/j.ympev.2019.106640
  • Nori J, Semhan R, Simón Abdala C, Rojas-Soto O (2022) Filling Linnean shortfalls increases endemicity patterns: conservation and biogeographical implications for the extreme case of Liolaemus (Liolaemidae, Squamata) species. Zoological Journal of the Linnean Society 194: 592–600. https://doi.org/10.1093/zoolinnean/zlab012
  • Oliver LA, Rittmeyer EN, Kraus F, Richards SJ, Austin CC (2013) Phylo­geny and phylogeography of Mantophryne (Anura: Microhylidae) reveals cryptic diversity in New Guinea. Molecular Phylo­genetics and Evolution 67: 600–607. https://doi.org/10.1016/j.ympev.2013.02.023
  • Oliver PM, Iannella A, Richards SJ, Lee MSY (2017) Mountain colonisation, miniaturisation and ecological evolution in a radiation of direct-developing New Guinea Frogs (Choerophryne, Microhylidae). PeerJ: 23. https://doi.org/10.7717/peerj.3077
  • Oliver PM, Bower DS, McDonald PJ, Kraus F, Luedtke J, Neam K, Hobin L, Chauvenet ALM, Allison A, Arida E, Clulow S, Günther R, Nagombi E, Tjaturadi B, Travers SL, Richards SJ (2022) Melanesia holds the world’s most diverse and intact insular amphibian fauna. Communications Biology 5: 1182. https://doi.org/10.1038/s42003-022-04105-1
  • Oliver PM, Davie-Rieck A, Ramdani MI, Dashper J, Kusuma KI, Lee CC, Rittmeyer E, Clancy MJ, Hamidy A, Thompson JC, Fouquet A, Ferreira F, Richards SJ (2025) Can citizen science fill knowledge gaps for the world’s most speciose and poorly-known insular amphibian fauna? Pacific Conservation Biology 31: PC24063. https://doi.org/10.1071/PC24063
  • Pons J, Barraclough TG, Gomez-Zurita J, Cardoso A, Duran DP, Hazell S, Kamoun S, Sumlin WD, Vogler AP (2006) Sequence-based species delimitation for the DNA taxonomy of undescribed insects. Systematic Biology 55: 595–609. https://doi.org/10.1080/10635150600852011
  • Portik DM, Streicher JW, Wiens JJ (2023) Frog phylogeny: A time-calibrated, species-level tree based on hundreds of loci and 5,242 species. Molecular Phylogenetics and Evolution 188: 107907. https://doi.org/10.1016/j.ympev.2023.107907
  • Ralimanana H, Perrigo AL, Smith RJ, Borrell JS, Faurby S, Rajaonah MT, Randriamboavonjy T, Vorontsova MS, Cooke RSC, Phelps LN, Sayol F, Andela N, Andermann T, Andriamanohera AM, Andriambololonera S, Bachman SP, Bacon CD, Baker WJ, Belluardo F, Birkinshaw C, Cable S, Canales NA, Carrillo JD, Clegg R, Clubbe C, Crottini A, Damasco G, Dhanda S, Edler D, Farooq H, de Lima Ferreira P, Fisher BL, Forest F, Gardiner LM, Goodman SM, Grace OM, Guedes TB, Hackel J, Henniges MC, Hill R, Lehmann CER, Lowry PP, Marline L, Matos-Maraví P, Moat J, Neves B, Nogueira MGC, Onstein RE, Papadopulos AST, Perez-Escobar OA, Phillipson PB, Pironon S, Przelomska NAS, Rabarimanarivo M, Rabehevitra D, Raharimampionona J, Rajaonary F, Rajaovelona LR, Rakotoarinivo M, Rakotoarisoa AA, Rakotoarisoa SE, Rakotomalala HN, Rakotonasolo F, Ralaiveloarisoa BA, Ramirez-Herranz M, Randriamamonjy JEN, Randrianasolo V, Rasolohery A, Ratsifandrihamanana AN, Ravololomanana N, Razafiniary V, Razanajatovo H, Razanatsoa E, Rivers M, Silvestro D, Testo W, Torres Jiménez MF, Walker K, Walker BE, Wilkin P, Williams J, Ziegler T, Zizka A, Antonelli A (2022) Madagascar’s extraordinary biodiversity: Threats and opportunities. Science 378: eadf1466. https://doi.org/10.1126/science.adf1466
  • Rivera JA, Kraus F, Allison A, Butler MA (2017) Molecular phylogenetics and dating of the problematic New Guinea microhylid frogs (Amphibia: Anura) reveals elevated speciation rates and need for taxonomic reclassification. Molecular Phylogenetics and Evolution 112: 1–11. https://doi.org/10.1016/j.ympev.2017.04.008
  • Robertson RD, De Pinto A, Cenacchi N (2023) Assessing the future global distribution of land ecosystems as determined by climate change and cropland incursion. Climatic Change 176: 108. https://doi.org/10.1007/s10584-023-03584-3
  • Rodrigues ASL, Gray CL, Crowter BJ, Ewers RM, Stuart SN, Whitten T, Manica A (2010) A global assessment of amphibian taxonomic effort and expertise. BioScience 60: 798–806. https://doi.org/10.1525/bio.2010.60.10.6
  • Serrano FC, Vieira-Alencar JPdosS, Díaz-Ricaurte JC, Valdujo PH, Martins M, Nogueira CdeC (2023) The Wallacean Shortfall and the role of historical distribution records in the conservation assessment of an elusive Neotropical snake in a threatened landscape. Journal for Nature Conservation 72: 126350. https://doi.org/10.1016/j.jnc.2023.126350
  • Slavenko A, Allison A, Austin CC, Bauer AM, Brown RM, Fisher RN, Ineich I, Iova B, Karin BR, Kraus F, Mecke S, Meiri S, Morrison C, Oliver PM, O’Shea M, Richmond JQ, Shea GM, Tallowin OJS, Chapple DG (2023) Skinks of Oceania, New Guinea, and Eastern Wallacea: an underexplored biodiversity hotspot. Pacific Conservation Biology 29: 526–543. https://doi.org/10.1071/PC22034
  • Smith DR (2016) The past, present and future of mitochondrial genomics: Have we sequenced enough mtDNAs? Briefings in Functional Genomics 15: 47–54. https://doi.org/10.1093/bfgp/elv027
  • Stein A, Gerstner K, Kreft H (2014) Environmental heterogeneity as a universal driver of species richness across taxa, biomes and spatial scales. Ecology Letters 17: 866–880. https://doi.org/10.1111/ele.12277
  • Sukumaran J, Knowles LL (2017) Multispecies coalescent delimits structure, not species. Proceedings of the National Academy of Sciences of the USA 114: 1607–1612. https://doi.org/10.1073/pnas.1607921114
  • Sulaeman TN, Hamidy A, Farajallah A, Fouquet A, Riyanto A, Arida E, Mulyadi Trilaksono W, Munir M (2021) Mitochondrial DNA suggests the existence of two distinct species in Moluccas and New Guinea within Nyctimystes infrafrenatus (Günther, 1867). Biodiversitas 22: 3287–3297. https://doi.org/10.13057/biodiv/d220823
  • Tallowin O, Allison A, Algar AC, Kraus F, Meiri S (2017) Papua New Guinea terrestrial-vertebrate richness: elevation matters most for all except reptiles. Journal of Biogeography 44: 1734–1744. https://doi.org/10.1111/jbi.12949
  • Toussaint EFA, White LT, Shaverdo H, Lam A, Surbakti S, Panjaitan R, Sumoked B, von Rintelen T, Sagata K, Balke M (2021) New Guinean orogenic dynamics and biota evolution revealed using a custom geospatial analysis pipeline. BMC Ecology and Evolution 21: 51. https://doi.org/10.1186/s12862-021-01764-2
  • Utami CY, Sholihah A, Condamine FL, Thébaud C, Hubert N (2022) Cryptic diversity impacts model selection and macroevolutionary inferences in diversification analyses. Proceedings of the Royal Society B: Biological Sciences 289: 20221335. https://doi.org/10.1098/rspb.2022.1335
  • Vacher J, Chave J, Ficetola FG, Sommeria‐Klein G, Tao S, Thébaud C, Blanc M, Camacho A, Cassimiro J, Colston TJ, Dewynter M, Ernst R, Gaucher P, Gomes JO, Jairam R, Kok PJR, Lima JD, Martinez Q, Marty C, Noonan BP, Nunes PMS, Ouboter P, Recoder R, Rodrigues MT, Snyder A, Marques-Souza S, Fouquet A (2020) Large‐scale DNA‐based survey of frogs in Amazonia suggests a vast underestimation of species richness and endemism. Journal of Biogeography 47: 1781–1791. https://doi.org/10.1111/jbi.13847
  • Vancutsem C, Achard F, Pekel J-F, Vieilledent G, Carboni S, Simonetti D, Gallego J, Aragão LEOC, Nasi R (2021) Long-term (1990–2019) monitoring of forest cover changes in the humid tropics. Science Advances 7: eabe1603. https://doi.org/10.1126/sciadv.abe1603
  • Vences M, Thomas M, van der Meijden A, Chiari Y, Vieites DR (2005) Comparative performance of the 16S rRNA gene in DNA barcoding of amphibians. Frontiers in Zoology 2: 5. https://doi.org/10.1186/1742-9994-2-5
  • Wilson KA, Auerbach NA, Sam K, Magini AG, Moss ASL, Langhans SD, Budiharta S, Terzano D, Meijaard E (2016) Conservation research is not happening where it is most needed. PLOS Biology 14: e1002413. https://doi.org/10.1371/journal.pbio.1002413

Supplementary materials

Supplementary material 1 

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)

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Supplementary material 2 

List of all samples and available molecular data, per specimen and species, with detailed results of the species-delimitation methods (.xlsx)

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