Molecular phylogenetics and dating of the problematic New Guinea microhylid frogs (Amphibia: Anura) reveals elevated speciation rates and need for taxonomic reclassification

Testing Geology with Biology: Plate Tectonics and the Diversification of Microhylid Frogs in the Papuan Region

Studies of the Papuan region have provided fundamental insights into the evolutionary processes generating its exceptional biodiversity, but the influence of geological processes merits further study. Lying at the junction of five tectonic plates, this region has experienced a turbulent geological history that has not only produced towering mountains allowing elevational specialization and island archipelagos with varying degrees of isolation promoting vicariance, but also active margins where land masses have collided and been subsequently rifted apart creating a mosaic of intermixed terranes with vastly different geological histories. Asterophryine frogs are a hyperdiverse clade representing half the world's microhylid diversity (over 360 species) centered on New Guinea and its satellite islands. We show that vicariance facilitated by geological history explains this far and wide distribution of a clade that should have poor dispersal abilities. We recovered a mainland tectonic unit, the East Papua Composite Terrane (EPCT), as the center of origin for Asterophryinae and no fewer than 71 instances of what appear to be long-distance dispersal events, 29 of which are between mainland regions, with 42 from the mainland to the islands, some presently as far as 200 km away from source populations over open ocean. Furthermore, we find strong support for a "Slow and Steady" hypothesis for the formation of the northern margin of New Guinea by many separate accretion events during the Miocene, over other major geological alternatives, consistent with the 20 M year age of the clade and arrival via the EPCT. In addition, the historical biogeography of our frogs strongly supports an affiliation of the Louisiade Archipelago and Woodlark Island with the Owen Stanley Range on the EPCT, and the recent proximity of the large New Britain Island. Our results show that Asterophryinae did not have to repeatedly and independently disperse across large ocean barriers to the offshore islands, against the predictions of island biogeography theory, but that the current distribution can be explained through vicariance and short-distance oceanic dispersal as historical land connections disappeared and islands slowly became separated from each other. We show that islands have a life history, changing in distance from other land masses, with consequent opportunities for dispersal, isolation, and cladogenesis of their biotas. More broadly, we can begin to see how the geological history of the Papuan region can result in the rapid accumulation and staggering number of extant species.

Molecular and phylogenetic datasets for the Asterophryinae frogs of New Guinea with additional data on lifestyle, geography, and elevation

The data provided here are related to the article "Resolving the Deep Phylogeny: Implications for Early Adaptive Radiation, Cryptic, and Present-day Ecological Diversity of Papuan Microhylid Frogs" [1]. The dataset is based on 233 tissue samples of the subfamily Asteroprhyinae, with representatives from all recognized genera, in addition to three outgroup taxa. The sequence dataset contains over 2400 characters per sample for five genes: three nuclear (Seventh in Absentia (SIA), Brain Derived Neurotrophic Factor (BDNF), Sodium Calcium Exchange subunit-1 (NXC-1)), and two mitochondrial loci (Cytochrome oxidase b (CYTB), and NADH dehydrogenase subunit 4 (ND4)); and is 99% complete. New primers were designed for all loci and accession numbers for the raw sequence data are provided. The sequences are used with geological time calibrations to produce time-calibrated Bayesian inference (BI) and Maximum Likelihood (ML) phylogenetic reconstructions using BEAST2 and IQ-TREE. Lifestyle data (arboreal, scansorial, terrestrial, fossorial, semi-aquatic) were collected from the literature and field notes and used to infer ancestral character states for each lineage. Collection location and elevation data were used to verify sites where multiple species or candidate species co-occur. All sequence data, alignments, and associated metadata (voucher specimen number, species identification, type locality status, global positioning system [GPS] coordinates, elevation, site with species list, and lifestyle) as well as the code to produce all analyses and figures are provided.

Another giant species of the microhylid frog genus Cophixalus Boettger, 1892 from the mountains of Papua New Guinea and first records of procoracoids in the genus

A new arboreal species of the microhylid genus Cophixalus Boettger, 1892 is described from montane rainforest on Papua New Guinea’s central cordillera. With a male SUL exceeding 44.0 mm, the new species is among the largest members of the genus; the only other Papuan species known to reach this size is C. riparius Zweifel, 1962. The new species differs from C. riparius in a small number of mensural characters and by its distinct advertisement call, a single explosive ‘bark’ uttered singly or in rapid series. In contrast, calls of C. riparius recorded near the type locality are a series of drawn out, rasping croaks. Calls of the two species are analysed and compared. The two species also appear to have different ecologies, with the new species found only high in trees, while C. riparius is often encountered in vegetation on or near the forest floor. Examination of osteological features revealed the presence of cartilaginous procoracoids in both species, representing the first records of procoracoids in the speciose genus Cophixalus. Lack of procoracoids is traditionally considered an important diagnostic character for defining Cophixalus but both species also lack clavicles, a character considered diagnostic for Cophixalus and a key feature distinguishing the genus from the closely related Oreophryne Boettger, 1895. Because preliminary published genetic data indicate that they are nested within Cophixalus, we retain both species in that genus until a comprehensive molecular phylogeny of Cophixalus and related genera, particularly Oreophryne, is completed.

Melanesia holds the world's most diverse and intact insular amphibian fauna

Identifying hotspots of biological diversity is a key step in conservation prioritisation. Melanesia-centred on the vast island of New Guinea-is increasingly recognised for its exceptionally species-rich and endemic biota. Here we show that Melanesia has the world's most diverse insular amphibian fauna, with over 7% of recognised global frog species in less than 0.7% of the world's land area, and over 97% of species endemic. We further estimate that nearly 200 additional candidate species have been discovered but remain unnamed, pointing to a total fauna in excess of 700 species. Nearly 60% of the Melanesian frog fauna is in a lineage of direct-developing microhylids characterised by smaller distributions than co-occurring frog families, suggesting lineage-specific high beta diversity is a key driver of Melanesian anuran megadiversity. A comprehensive conservation status assessment further highlights geographic concentrations of recently described range-restricted threatened taxa that warrant urgent conservation actions. Nonetheless, by world standards, the Melanesian frog fauna is relatively intact, with 6% of assessed species listed as threatened and no documented extinctions; and thus it provides an unparalleled opportunity to understand and conserve a megadiverse and relatively intact insular biota.

Resolving the deep phylogeny: Implications for early adaptive radiation, cryptic, and present-day ecological diversity of Papuan microhylid frogs

The microhylid frogs of the New Guinea region are the largest and most ecologically diverse subfamily (Asterophryinae) of one of the largest anuran families in the world and can live in communities of up to 20 species. While there has been recent progress in resolving the phylogenetic relationships of Asterophryinae, significant uncertainties remain, impeding further progress in understanding the evolution of microhabitat use, parental care, and life history variation in this group. In particular, the early divergences at the base of the tree remain unclear; as does the monophyly of some genera; and recent studies have discovered that species with wide geographic distribution are instead cryptic species complexes. In this study, we fortified geographic sampling of the largest previous phylogenetic effort by sequencing an additional 62 taxa and increased data quality and quantity by adding new layers of data vetting and by filling in previously incomplete loci to the five gene dataset (2 mitochondrial, 3 nuclear protein-coding genes) to obtain a dataset that is now 99% complete in over 2400 characters for 233 samples (205 taxa) of Asterophryinae and 3 outgroup taxa, and analyzed microhabitat use data for these taxa from field data and data collected from the literature. Importantly, our sampling includes complete community complements at 19 sites as well as representatives at over 80 sites across New Guinea and its offshore islands. We present a highly resolved molecular phylogeny which, for the first time, has over 95% of nodes supported (84% highly supported) whether using Maximum Likelihood or Bayesian Inference, allowing clarification of all genera (whether monophyletic or clearly not), their sister genera relationships, as well as an age estimate for the Asterophryinae at approximately 20MYA. Early generic diversification occurring between 17 and 12 MYA gave rise to a surprising diversity of about 18 genera as well as the 5 putative microhabitat types. Our tree reveals extensive cryptic diversity calling any widespread taxa into doubt, and clearly demonstrates that complex multispecies communities of Asterophryinae are ecologically diverse, are numerous, and of ancient origin across New Guinea. We discuss the implications of our phylogeny for explaining the explosive diversification of Asterophryinae as the result of adaptive radiation, niche conservatism, and non-adaptive radiation.

Evolution of the strikingly diverse submandibular muscles in Anura

The most ventral muscles of the head (the mm. submentalis, intermandibularis, and interhyoideus) provide support to the gular region and lift the buccal floor during ventilation and feeding. These muscles show limited variation in most gnathostomes, but in Anura they exhibit a surprising diversity. The few studies that have explored this character system highlighted its potential as a source of phylogenetic information. In this paper we explored the diversity of this character system studying specimens of 567 anuran species and reviewing published data to cover a total of 1321 species, belonging to 53 of the 54 currently recognized anuran families, as well as caudates and caecilians. We defined 27 discrete characters including the number of muscle bellies, supplementary layers, hypertrophy and diversity of elastic fibres, and pigmentation, among others, and optimized them on a comprehensive phylogenetic hypothesis. We recognized 223 unambiguously optimized synapomorphies for numerous clades on different scales, including three for Anura and many for suprafamiliar clades with poor phenotypic support. Finally, we discussed the evolution of this highly diverse character system, including homology, development, and its functional role in vocalization and feeding. Interestingly, the striking levels of variation in some structures contrast with the amount of phylogenetic inertia, allowing us to recognize several general patterns. Supplementary elements of the m. intermandibularis evolved first as broad layers occuring in more than half of extant anuran species and then concentrated forming discreet bellies in several clades. The anterior portion of the gular region is not sexually dimorphic, and is likely related to ventilation and tongue protraction. Conversely, the diversity of the m. interhyoideus is strongly linked to vocal sacs, which are present only in adult males, suggesting the presence of two independent modules.

Testing for adaptive radiation: A new approach applied to Madagascar frogs

Adaptive radiation is a key topic at the intersection of ecology and evolutionary biology. Yet the definition and identification of adaptive radiation both remain contentious. Here, we introduce a new approach for identifying adaptive radiations that combines key aspects of two widely used definitions. Our approach compares evolutionary rates in morphology, performance, and diversification between the candidate radiation and other clades. We then apply this approach to a putative adaptive radiation of frogs from Madagascar (Mantellidae). We present new data on morphology and performance from mantellid frogs, then compare rates of diversification and multivariate evolution of size, shape, and performance between mantellids and other frogs. We find that mantellids potentially pass our test for accelerated rates of evolution for shape, but not for size, performance, or diversification. Our results demonstrate that clades can have accelerated phenotypic evolution without rapid diversification (dubbed "adaptive non-radiation"). We also highlight general issues in testing for adaptive radiation, including taxon sampling and the problem of including another adaptive radiation among the comparison clades. Finally, we suggest that similar tests should be conducted on other putative adaptive radiations on Madagascar, comparing their evolutionary rates to those of related clades outside Madagascar. Based on our results, we speculate that older Madagascar clades may show evolutionary patterns more similar to those on a continent than an island.

Description of six new species of Xenorhina Peters, 1863 from southern Papua New Guinea (Amphibia, Anura, Microhylidae)

We describe six new species of the microhylid frog genus Xenorhina from the southern slopes of Papua New Guinea’s central cordillera and adjacent lowlands, based on a combination of morphological (including osteology) and bioacoustic features. All of the new species are fossorial or terrestrial inhabitants of tropical rainforest habitats and belong to a group of Xenorhina having a single, enlarged odontoid spike on each vomeropalatine bone. Advertisement calls and habitat preferences are described for each species, one of which is amongst the smallest hitherto members of the genus. Description of these six species brings the total number of Xenorhina known to 40 and emphasises the importance of the high-rainfall belt that extends along the southern flanks of New Guinea’s central cordillera as a hotspot of Melanesian amphibian diversity.

New Guinean orogenic dynamics and biota evolution revealed using a custom geospatial analysis pipeline

BACKGROUND

The New Guinean archipelago has been shaped by millions of years of plate tectonic activity combined with long-term fluctuations in climate and sea level. These processes combined with New Guinea's location at the tectonic junction between the Australian and Pacific plates are inherently linked to the evolution of its rich endemic biota. With the advent of molecular phylogenetics and an increasing amount of geological data, the field of New Guinean biogeography begins to be reinvigorated.

RESULTS

We inferred a comprehensive dated molecular phylogeny of endemic diving beetles to test historical hypotheses pertaining to the evolution of the New Guinean biota. We used geospatial analysis techniques to compare our phylogenetic results with a newly developed geological terrane map of New Guinea as well as the altitudinal and geographic range of species ( https://arcg.is/189zmz ). Our divergence time estimations indicate a crown age (early diversification) for New Guinea Exocelina beetles in the mid-Miocene ca. 17 Ma, when the New Guinean orogeny was at an early stage. Geographic and geological ancestral state reconstructions suggest an origin of Exocelina ancestors on the eastern part of the New Guinean central range on basement rocks (with a shared affinity with the Australian Plate). Our results do not support the hypothesis of ancestors migrating to the northern margin of the Australian Plate from Pacific terranes that incrementally accreted to New Guinea over time. However, our analyses support to some extent a scenario in which Exocelina ancestors would have been able to colonize back and forth between the amalgamated Australian and Pacific terranes from the Miocene onwards. Our reconstructions also do not support an origin on ultramafic or ophiolite rocks that have been colonized much later in the evolution of the radiation. Macroevolutionary analyses do not support the hypothesis of heterogeneous diversification rates throughout the evolution of this radiation, suggesting instead a continuous slowdown in speciation.

CONCLUSIONS

Overall, our geospatial analysis approach to investigate the links between the location and evolution of New Guinea's biota with the underlying geology sheds a new light on the patterns and processes of lineage diversification in this exceedingly diverse region of the planet.

Analysis of ultraconserved elements supports African origins of narrow-mouthed frogs

Narrow-mouthed frogs (Anura: Microhylidae) are globally distributed and molecular data suggest the rapid evolution of multiple subfamilies shortly after their origin. Despite recent progress, several subfamilial relationships remain unexplored using phylogenomic data. We analysed 1,796 nuclear ultraconserved elements, a total matrix of 400,664 nucleotides, from representatives of most microhylid subfamilies. Summary method species-tree and maximum likelihood analyses unambiguously supported Hoplophryninae as the earliest diverging microhylid and confirm Chaperininae as a junior synonym of Microhylinae. Given the emerging consensus that subfamilies from mainland Africa diverged early, microhylids have likely occupied the continent for more than 66 million years.

A new genus and three new species of miniaturized microhylid frogs from Indochina (Amphibia: Anura: Microhylidae: Asterophryinae)

We report on the discovery of a new genus of microhylid subfamily Asterophryinae from northern and eastern Indochina, containing three new species. VietnamophryneGen. nov. are secretive miniaturized frogs (SVL<21 mm) with a mostly semi-fossorial lifestyle. To assess phylogenetic relationships, we studied 12S rRNA – 16S rRNA mtDNA fragments with a final alignment of 2 591 bp for 53 microhylid species. Morphological and osteological characters were analyzed using micro-CT scanning and used to describe the new genus. Results of phylogenetic analyses assigned the new genus into the mainly Australasian subfamily Asterophryinae as a sister taxon to the genus Siamophryne from southern Indochina. The three specimens collected from Gia Lai Province in central Vietnam, Cao Bang Province in northern Vietnam, and Chiang Rai Province in northern Thailand proved to be separate species, different both in morphology and genetics (genetic divergence 3.1%≤P≤5.1%). Our work provides further evidence for the “out of Indo-Eurasia” scenario for Asterophryinae, indicating that the initial cladogenesis and differentiation of this group of frogs occurred in the Indochina Peninsula. To date, each of the three new species of VietnamophryneGen. nov. is known only from a single specimen; thus, their distribution, life history, and conservation status require further study.

A striking new genus and species of cave-dwelling frog (Amphibia: Anura: Microhylidae: Asterophryinae) from Thailand

We report on a discovery of Siamophryne troglodytesGen. et sp. nov., a new troglophilous genus and species of microhylid frog from a limestone cave in the tropical forests of western Thailand. To assess its phylogenetic relationships we studied the 12S rRNA-16S rRNA mtDNA fragment with final alignment comprising up to 2,591 bp for 56 microhylid species. Morphological characterization of the new genus is based on examination of external morphology and analysis of osteological characteristics using microCT-scanning. Phylogenetic analyses place the new genus into the mainly Australasian subfamily Asterophryinae as a sister taxon to the genus Gastrophrynoides, the only member of the subfamily known from Sundaland. The new genus markedly differs from all other Asterophryinae members by a number of diagnostic morphological characters and demonstrates significant mtDNA sequence divergence. We provide a preliminary description of a tadpole of the new genus. Thus, it represents the only asterophryine taxon with documented free-living larval stage and troglophilous life style. Our work demonstrates that S. troglodytesGen. et sp. nov. represents an old lineage of the initial radiation of Asterophryinae which took place in the mainland Southeast Asia. Our results strongly support the "out of Indo-Eurasia" biogeographic scenario for this group of frogs. To date, the new frog is only known from a single limestone cave system in Sai Yok District of Kanchanaburi Province of Thailand; its habitat is affected by illegal bat guano mining and other human activities. As such, S. troglodytesGen. et sp. nov. is likely to be at high risk of habitat loss. Considering high ecological specialization and a small known range of the new taxon, we propose a IUCN Red List status of endangered for it.