Cryptic diversity in Amazonian frogs: Integrative taxonomy of the genus Anomaloglossus (Amphibia: Anura: Aromobatidae) reveals a unique case of diversification within the Guiana Shield

Diversification of the terrestrial frog genus Anomaloglossus (Anura, Aromobatidae) in the Guiana Shield proceeded from highlands to lowlands, with successive loss and reacquisition of endotrophy

Two main landscapes emerge from the Guiana Shield: the highlands to the west called the Pantepui region and the Amazonian lowlands to the east, both harbouring numerous endemic species. With 32 currently recognized species, the genus Anomaloglossus stands out among Neotropical frogs as one that diversified only within the Guiana Shield both in the highlands and the lowlands. We present a time-calibrated phylogeny obtained by using combined mitogenomic and nuclear DNA, which suggests that the genus originates from Pantepui where extant lineages started diversifying around 21 Ma, and subsequently (ca. 17 Ma) dispersed during the Miocene Climatic Optimum to the lowlands of the eastern Guiana Shield where the ability to produce endotrophic tadpoles evolved. Further diversification within the lowlands in the A. stepheni group notably led to an evolutionary reversal toward exotrophy in one species group during the late Miocene, followed by reacquisition of endotrophy during the Pleistocene. These successive shifts of reproductive mode seem to have accompanied climatic oscillations. Long dry periods might have triggered evolution of exotrophy, whereas wetter climates favoured endotrophic forms, enabling colonization of terrestrial habitats distant from water. Acquisition, loss, and reacquisition of endotrophy makes Anomaloglossus unique among frogs and may largely explain the current species diversity. The micro evolutionary processes involved in these rapid shifts of reproductive mode remain to be revealed.

A new species of rain frog (Anura: Strabomantidae: Pristimantis) from the Guiana Shield and amended diagnosis of P. ockendeni (Boulenger, 1912)

Pristimantis is already the most speciose genus among vertebrates, yet the current number of species remains largely underestimated. A member of the P. unistrigatus species group from the Guiana Shield has been historically misidentified as P. ockendeni, a species described from southern Peru. We combined mitochondrial (16S and COI) and nuclear (RAG1) loci, external morphology, skull osteology (μ-CT scan), vocalization (advertisement and courtship calls), geographic distribution and natural history data to differentiate the Guiana Shield populations from P. ockendeni, and describe them as a new species. The new species is crepuscular and nocturnal and inhabits the understory of unflooded (terra firme) forests in Brazil, Guyana and Suriname. It is phylogenetically related to P. arda­lonychus, P. martiae and undescribed species from Brazilian Amazonia. The new species notably differs from P. ockendeni and its congeners in the P. unistrigatus species group occurring in the Guiana Shield by the combination of the following characters: absence of dentigerous processes of vomers, presence of vocal slits in males, body size (SVL 16.2–20.7 mm in males and 21.4–25.7 mm in females), advertisement call (call with 4–6 notes, call duration of 158–371 ms and dominant frequency of 3,466–4,521 Hz) and translucent groin coloration in life. To facilitate the recognition and description of cryptic species previously hidden under the name P. ockendeni, we provide an amended diagnosis of this taxon based on external morphology and advertisement call of specimens recently collected nearby the type locality and additional localities in southwestern Amazonia.

Identity signaling, identity reception, and the evolution of social recognition in a Neotropical frog

Animals recognize familiar individuals to perform a variety of important social behaviors. Social recognition is often mediated by communication between signalers who produce signals that contain identity information and receivers who categorize these signals based on previous experience. We tested two hypotheses about adaptations in signalers and receivers that enable the evolution of social recognition using two species of closely related territorial poison frogs. Male golden rocket frogs (Anomaloglossus beebei) recognize the advertisement calls of conspecific territory neighbors and display a "dear enemy effect" by responding less aggressively to neighbors than strangers, whereas male Kai rocket frogs (Anomaloglossus kaiei) do not. Our results did not support the identity signaling hypothesis: both species produced advertisement calls that contain similar amounts of identity information. Our results did support the identity reception hypothesis: both species exhibited habituation of aggression to playbacks simulating the arrival of a new neighbor, but only golden rocket frogs showed renewed aggression when they subsequently heard calls from a different male. These results suggest that an ancestral mechanism of plasticity in aggression common among frogs has been modified through natural selection to be specific to calls of individual males in golden rocket frogs, enabling a social recognition system.

Structure and evolution of the sexually dimorphic integumentary swelling on the hands of dendrobatid poison frogs and their relatives (Amphibia: Anura: Dendrobatoidea)

The hands of adult males of many dendrobatid poison frogs and their relatives possess swelling formed by glandular tissue hypothesized to secrete courtship pheromones delivered to the female during cephalic amplexus. Variation in the occurrence and external morphology of the swelling of finger IV has provided important evidence for dendrobatoid systematics for decades, but its underlying structure has not been investigated. We undertook a detailed comparative analysis of the integument of the hand, including both external morphology and histology, of 36 species representing the diversity of dendrobatoid frogs and several close relatives. The swelling is caused by four densely packed, hypertrophic, morpho-histochemical types of specialized mucous glands (SMGs). We observed type I SMGs on fingers II-V and the wrist, including areas that are not swollen, types II and IV exclusively on finger IV, and type III on finger IV and the wrist. Type I SMGs occur either in isolation or together with types II, III, or IV; types II, III, and IV never occur together or without type I. We delimited 15 characters to account for the variation in external morphology and the occurrence of SMGs. Our data suggest that type I SMGs are a new synapomorphy for Dendrobatoidea and that type II SMGs originated in either the most recent common ancestor (MRCA) of Dendrobatidae or independently in the MRCAs of Aromobatidae and Colostethinae, respectively, while types III and IV are restricted to Anomaloglossus. The discovery of these SMGs adds a new dimension to studies of poison frog reproductive biology, which have investigated acoustic, visual, and tactile cues in courtship, mating, and parental care across the diversity of Dendrobatoidea for decades but have almost entirely overlooked the possible role of chemical cues.

Species diversity and biogeography of an ancient frog clade from the Guiana Shield (Anura: Microhylidae: Adelastes, Otophryne, Synapturanus) exhibiting spectacular phenotypic diversification

The outstanding biodiversity of the Guiana Shield has raised many questions about its origins and evolution. Frogs of the genera Adelastes, Otophryne and Synapturanus form an ancient lineage distributed mostly across this region. These genera display strikingly disparate morphologies and life-history traits. Notably, Synapturanus is conspicuously adapted to fossoriality and is the only genus within this group to have dispersed further into Amazonia. Moreover, morphological differences among Synapturanus species suggest different degrees of fossoriality that might be linked to their biogeographical history. Through integrative analysis of genetic, morphometric and acoustic data, we delimited 25 species in this clade, representing a fourfold increase. We found that the entire clade started to diversify ~55 Mya and Synapturanus ~30 Mya. Members of this genus probably dispersed three times out of the Guiana Shield both before and after the Pebas system, a wetland ecosystem occupying most of Western Amazonia during the Miocene. Using a three-dimensional osteological dataset, we characterized a high morphological disparity across the three genera. Within Synapturanus, we further characterized distinct phenotypes that emerged concomitantly with dispersals during the Miocene and possibly represent adaptations to different habitats, such as soils with different physical properties.

ASAP: assemble species by automatic partitioning

Here, we describe Assemble Species by Automatic Partitioning (ASAP), a new method to build species partitions from single locus sequence alignments (i.e., barcode data sets). ASAP is efficient enough to split data sets as large 10⁴ sequences into putative species in several minutes. Although grounded in evolutionary theory, ASAP is the implementation of a hierarchical clustering algorithm that only uses pairwise genetic distances, avoiding the computational burden of phylogenetic reconstruction. Importantly, ASAP proposes species partitions ranked by a new scoring system that uses no biological prior insight of intraspecific diversity. ASAP is a stand-alone program that can be used either through a graphical web-interface or that can be downloaded and compiled for local usage. We have assessed its power along with three others programs (ABGD, PTP and GMYC) on 10 real COI barcode data sets representing various degrees of challenge (from small and easy cases to large and complicated data sets). We also used Monte-Carlo simulations of a multispecies coalescent framework to assess the strengths and weaknesses of ASAP and the other programs. Through these analyses, we demonstrate that ASAP has the potential to become a major tool for taxonomists as it proposes rapidly in a full graphical exploratory interface relevant species hypothesis as a first step of the integrative taxonomy process.

Ecological and social drivers of neighbor recognition and the dear enemy effect in a poison frog

Navigating social relationships frequently rests on the ability to recognize familiar individuals using phenotypic characteristics. Across diverse taxa, animals vary in their capacities for social recognition, but the ecological and social sources of selection for recognition are often unclear. In a comparative study of two closely related species of poison frogs, we identified a species difference in social recognition of territory neighbors and investigated potential sources of selection underlying this difference. In response to acoustic playbacks, male golden rocket frogs (Anomaloglossus beebei) recognized the calls of neighbors and displayed a “dear enemy effect” by responding less aggressively to neighbors’ calls than strangers’ calls. In contrast, male Kai rocket frogs (Anomaloglossus kaiei) were equally aggressive to the calls of neighbors and strangers. This species difference in behavior is associated with key differences in reproductive ecology and characteristics of territories. Golden rocket frogs defend reproductive resources in the form of bromeliads, which is expected to create a threat asymmetry between neighbors and strangers favoring decreased aggression to neighbors. In contrast, Kai rocket frogs do not defend reproductive resources. Further, compared with Kai rocket frog territories, golden rocket frog territories occur at higher densities and are defended for longer periods of time, creating a more complex social environment with more opportunities for repeated but unnecessary aggression between neighbors, which should favor the ability to recognize and exhibit less aggression toward neighbors. These results suggest that differences in reproductive ecology can drive changes in social structure that select for social recognition.

A new tiny toad species of Amazophrynella (Anura: Bufonidae) from east of the Guiana Shield in Amazonia, Brazil

The combination of different approaches has successfully delimited new species within many Neotropical species complexes traditionally classified as a single nominal organism. Recent studies have shown that the Amazonian endemic genus Amazophrynella, currently composed of 12 small-sized species, could harbor several additional species. Based on morphology and molecular data, we describe a new species of Amazophrynella from east of the Guiana Shield, in Pará state, Brazil. The new species is characterized by having one of the biggest size of the genus (SVL of males 16.0–17.8 mm and females 22.9–24.4 mm), presence of a large palmar tubercle (occupying 2/4 of the palmar surface), 5.6–8.1% uncorrected p-distance from its sister clade (including A. teko, A. sp.1, and A. manaos) for the 16S mitochondrial gene, and 8.8% for the COI. The new species described here represents a newly discovered lineage. Of the 12 Amazophrynella species currently recognized, two were describe in the last century (A. bokermanni and A. minuta) and the remaining species were recently discovered and described (in the last six years), which underscores the degree to which species richness of Amazophrynella is underestimated.

Hidden diversity in Prochilodus nigricans: A new genetic lineage within the Tapajós River basin

Highly spread through the Amazon River basin, Prochilodus nigricans have had its taxonomic validity recently questioned, when genetic differences between Western and Eastern Amazon populations from the Brazilian shield were detected. This area has been seeing as a region of high ichthyofaunal diversity and endemism, in which the hybrid origin of the Tapajós River basin has been raised. In this paper, we report a new molecular lineage within P. nigricans of Tapajós River, highlighting this region still hides taxonomically significant diversity. Haplotype networks were reconstructed using the mitochondrial COI and ATP6/8 markers, which were also used to calculate genetic distances among clusters. We additionally conducted a delimiting species approach by employing a Generalized Mixed Yule-Coalescent model (GMYC) with COI sequences produced here, and previous ones published for individuals sampled across the Amazon River basin. In addition to the genetic differentiation within P. nigricans, our findings favor the hypothesis of hybrid origin of the Tapajós River basin and reaffirm the importance of studies aiming to investigate hidden diversity to address taxonomic and biogeographic issues, that certainly benefit better biodiversity conservation actions.

A morphometric assessment of species boundaries in a widespread anole lizard (Squamata: Dactyloidae)

Cryptic species – genetically distinct species that are morphologically difficult to distinguish – present challenges to systematists. Operationally, cryptic species are very difficult to identify and sole use of genetic data or morphological data can fail to recognize evolutionarily isolated lineages. We use morphometric data to test species boundaries hypothesized with genetic data in the North Caribbean bark anole (Anolis distichus), a suspected species complex. We use univariate and multivariate analyses to test if candidate species based on genetic data can be accurately diagnosed. We also test alternative species delimitation scenarios with a model fitting approach that evaluates normal mixture models capable of identifying morphological clusters. Our analyses reject the hypothesis that the candidate species are diagnosable. Neither uni- nor multivariate morphometric data distinguish candidate species. The best-supported model included two morphological clusters; however, these clusters were uneven and did not align with a plausible species divergence scenario. After removing two related traits driving this result, only one cluster was supported. Despite substantial differentiation revealed by genetic data, we recover no new evidence to delimit species and refrain from taxonomic revision. This study highlights the importance of considering other types of data along with molecular data when delimiting species.

Four new species of Pristimantis Jiménez de la Espada, 1870 (Anura: Craugastoridae) in the eastern Amazon

The Pristimantis genus (Anura: Craugastoridae) is the most diverse among all vertebrates with 531 described species. The highest diversity occurs in Ecuador (215 species), followed by Colombia (202), Peru (139), Venezuela (60), Brazil (30), Bolivia (17), Guyana (6) Suriname and French Guiana (5). The genus is divided into 11 species groups. Of these, the P. conspicillatus group (containing 34 species), distributed in extreme southeastern Costa Rica, Isla Taboga (Panama), northern South America (from Colombia to eastern Guyana), south Bolivia, and is the best represented in Brazil (16 species). The main characteristics of this group are the tympanic membrane and tympanic annulus distinct (except in P. johannesdei); dorsum smooth or shagreen; dorsal lateral fold present or absent; usually smooth belly, but may be weakly granular in some species; toe V slightly larger than the toe III. Most of the taxonomic inconsistencies in species of Pristimantis could be due to its much conserved morphology and the lack of comprehensive taxonomic evaluations. Thus, an ongoing challenge for taxonomists dealing with the Pristimantis genus is the ubiquitous abundance of cryptic species. In this context, accurate species delimitation should integrate evidences of morphological, molecular, bioacoustics and ecological data, among others. Based on an integrative taxonomy perspective, we utilize morphological, molecular (mtDNA) and bioacoustic evidence to describe four new species of the Pristimantis conspicillatus group from the eastern Amazon basin. Pristimantis giorgiisp. nov. is known from the Xingu/Tocantins interfluve and can be distinguished from the other Pristimantis species of the region by presenting discoidal fold, dorsolateral fold absent, vocalization composed of three to four notes and genetic distance of 7.7% (16S) and 14.8% (COI) from P. latro, the sister and sympatric species with respect P. giorgiisp. nov.. Pristimantis pictussp. nov. is known to the northern Mato Grosso state, Brazil, and can be distinguished from the other species of Pristimantis by presenting the posterior surface of the thigh with light yellow patches on a brown background, also extending to the inguinal region, vocalization consisting of four to five notes and a genetic distance of 11.6% (16S) and 19.7% (COI) from P. pluviansp. nov., which occurs in sympatry. Pristimantis pluviansp. nov. is known to the northern Mato Grosso state, Brazil, and may be distinguished from the other Pristimantis species by having a posterior surface of the thigh reddish and vocalization composed of two notes. Pristimantis moasp. nov. is known to the northern Tocantins state and southwestern Maranhão state. This species can be distinguished from the other Pristimantis species by possessing slightly perceptible canthal stripe, external thigh surface with dark yellow spots on brown background, vocalization consisting of three to five notes and genetic distance of 2.3–11.7 (16S) and 10.5–23.1 (COI) for the new Pristimantis species of this study.

Pristimantis in the Eastern Brazilian Amazon: DNA barcoding reveals underestimated diversity in a megadiverse genus

The genus Pristimantis has the highest species diversity among all terrestrial vertebrates, with most species observed in the Andean region and the Guiana Shield. Even with the recent description of a new species, only P. latro, P. dundeei and P. zimmermanae occur in the south of the Amazon River. The lack of taxonomists specialized in the field leads to the propagation of dubious terminologies (e.g. Pristimantis sp1, Pristimantis sp2, P. aff. Fenestratus and P. gr. conspicillatus) or even misidentification of species, resulting in erroneous species distributions. In this study, we applied the Automatic Barcode Gap Discovery (ABGD) algorithm for the delimitation of candidate species and values of genetic distances using the mitochondrial marker Cytochrome Oxidase Subunit I (COI), proposed in the barcode methodology, where values greater than 10% are considered as indicative of different species. We found large genetic distances between P. latro and Pristimantis sp1 Unconfirmed Candidate Species - UCS1 (21%), and between P. altamazonicus and Pristimantis sp2 UCS2 (14%). The ABGD method recognized UCS1 and UCS2 as distinct species. Pristimantis sp. UCS1 and UCS2 in the east of the Brazilian Amazon are indicated as candidate species. We suggest greater sampling of Pristimantis sp. UCS1 and UCS2, integrating morphology and bioacoustics to solve the taxonomic status in the east of the Brazilian Amazon.

Integrative taxonomic reassessment of Odontophrynus populations in Argentina and phylogenetic relationships within Odontophrynidae (Anura)

Amphibians are the most vulnerable vertebrates to biodiversity loss mediated by habitat destruction, climate change and diseases. Informed conservation management requires improving the taxonomy of anurans to assess reliably the species' geographic range. The genus Odontophrynus that is geographically refined to Argentina, Bolivia, Brazil, Uruguay and Paraguay includes currently 12 nominal species with many populations of uncertain taxonomic assignment and subsequently unclear geographic ranges. In this study, we applied integrative taxonomic methods combining molecular (mitochondrial 16S gene), allozyme, morphological and bioacoustic data to delimit species of the genus Odontophrynus sampled from throughout Argentina where most species occur. The combined evidence demonstrates one case of cryptic diversity and another of overestimation of species richness. The populations referred to as O. americanus comprise at least three species. In contrast, O. achalensis and O. barrioi represent junior synonyms of the phenotypically plastic species O. occidentalis. We conclude that each of the four species occurring in Argentina inhabits medium to large areas. The Red List classification is currently "Least Concern". We also propose a phylogenetic hypothesis for the genus and associated genera Macrogenioglottus and Proceratophrys (Odontophrynidae).

Anomaloglossus meansi sp. n., a new Pantepui species of the Anomaloglossus beebei group (Anura, Aromobatidae)

Recent extinctions and drastic population declines have been documented in the Guiana Shield endemic frog genus Anomaloglossus, hence the importance to resolve its alpha-taxonomy. Based on molecular phylogenies, the literature has long reported the occurrence of an undescribed species in the Pakaraima Mountains of Guyana in the Pantepui region. We here describe this new taxon and demonstrate that in addition to divergence at the molecular level the new species differs from congeners by a unique combination of morphological characters, notably a small size (maximum SVL in males 18.86 mm, maximum SVL in females 21.26 mm), Finger I = Finger II when fingers adpressed, Finger III swollen in breeding males, fringes on fingers absent, toes basally webbed but lacking fringes, in life presence of a thin dorsolateral stripe from tip of snout to tip of urostyle, and a black throat in preserved males (immaculate cream in females). Virtually nothing is known about the ecology of the new species. We suggest the new species to be considered as Data Deficient according to IUCN standards.

Variation in chromosome number and breeding systems: implications for diversification in Pachycereus pringlei (Cactaceae)

Polyploidy, the possession of more than two sets of chromosomes, is a major biological process affecting plant evolution and diversification. In the Cactaceae, genome doubling has also been associated with reproductive isolation, changes in breeding systems, colonization ability, and speciation. Pachycereus pringlei (S. Watson, 1885) Britton & Rose, 1909, is a columnar cactus that has long drawn the attention of ecologists, geneticists, and systematists due to its wide distribution range and remarkable assortment of breeding systems in the Mexican Sonoran Desert and the Baja California Peninsula (BCP). However, several important evolutionary questions, such as the distribution of chromosome numbers and whether the diploid condition is dominant over a potential polyploid condition driving the evolution and diversity in floral morphology and breeding systems in this cactus, are still unclear. In this study, we determined chromosome numbers in 11 localities encompassing virtually the entire geographic range of distribution of P. pringlei. Our data revealed the first diploid (2n = 22) count in this species restricted to the hermaphroditic populations of Catalana (ICA) and Cerralvo (ICE) Islands, whereas the tetraploid (2n = 44) condition is consistently distributed throughout the BCP and mainland Sonora populations distinguished by a non-hermaphroditic breeding system. These results validate a wider distribution of polyploid relative to diploid individuals and a shift in breeding systems coupled with polyploidisation. Considering that the diploid base number and hermaphroditism are the proposed ancestral conditions in Cactaceae, we suggest that ICE and ICA populations represent the relicts of a southern diploid ancestor from which both polyploidy and unisexuality evolved in mainland BCP, facilitating the northward expansion of this species. This cytogeographic distribution in conjunction with differences in floral attributes suggests the distinction of the diploid populations as a new taxonomic entity. We suggest that chromosome doubling in conjunction with allopatric distribution, differences in neutral genetic variation, floral traits, and breeding systems has driven the reproductive isolation, evolution, and diversification of this columnar cactus.

Integrative overview of the herpetofauna from Serra da Mocidade, a granitic mountain range in northern Brazil

The Brazilian mountain ranges from the Guiana Shield highlands are largely unexplored, with an understudied herpetofauna. Here the amphibian and reptile species diversity of the remote Serra da Mocidade mountain range, located in extreme northern Brazil, is reported upon, and biogeographical affinities and taxonomic highlights are discussed. A 22-days expedition to this mountain range was undertaken during which specimens were sampled at four distinct altitudinal levels (600, 960, 1,060 and 1,365 m above sea level) using six complementary methods. Specimens were identified through an integrated approach that considered morphological, bioacoustical, and molecular analyses. Fifty-one species (23 amphibians and 28 reptiles) were found, a comparable richness to other mountain ranges in the region. The recorded assemblage showed a mixed compositional influence from assemblages typical of other mountain ranges and lowland forest habitats in the region. Most of the taxa occupying the Serra da Mocidade mountain range are typical of the Guiana Shield or widely distributed in the Amazon. Extensions of known distribution ranges and candidate undescribed taxa are also recorded. This is the first herpetofaunal expedition that accessed the higher altitudinal levels of this mountain range, contributing to the basic knowledge of these groups in remote areas.

Deciphering the origin of mito-nuclear discordance in two sibling caddisfly species

An increasing number of phylogenetic studies have reported discordances among nuclear and mitochondrial markers. These discrepancies are highly relevant to widely used biodiversity assessment approaches, such as DNA barcoding, that rely almost exclusively on mitochondrial markers. Although the theoretical causes of mito-nuclear discordances are well understood, it is often extremely challenging to determine the principal underlying factor in a given study system. In this study, we uncovered significant mito-nuclear discordances in a pair of sibling caddisfly species. Application of genome sequencing, ddRAD and DNA barcoding revealed ongoing hybridization, as well as historical hybridization in Pleistocene refugia, leading us to identify introgression as the ultimate cause of the observed discordance pattern. Our novel genomic data, the discovery of a European-wide hybrid zone and the availability of established techniques for laboratory breeding make this species pair an ideal model system for studying species boundaries with ongoing gene flow.

Induced parental care in a poison frog: a tadpole cross-fostering experiment

Understanding the external stimuli and natural contexts that elicit complex behaviours, such as parental care, is key in linking behavioural mechanisms to their real-life function. Poison frogs provide obligate parental care by shuttling their tadpoles from terrestrial clutches to aquatic nurseries, but little is known about the proximate mechanisms that control these behaviours. In this study, we used Allobates femoralis, a poison frog with predominantly male parental care, to investigate whether tadpole transport can be induced in both sexes by transferring unrelated tadpoles to the backs of adults in the field. Specifically, we asked whether the presence of tadpoles on an adult's back can override the decision-making rules preceding tadpole pick-up and induce the recall of spatial memory necessary for finding tadpole deposition sites. We used telemetry to facilitate accurate tracking of individual frogs and spatial analysis to compare movement trajectories. All tested individuals transported their foster-tadpoles to water pools outside their home area. Contrary to our expectation, we found no sex difference in the likelihood to transport or in the spatial accuracy of finding tadpole deposition sites. We reveal that a stereotypical cascade of parental behaviours that naturally involves sex-specific offspring recognition strategies and the use of spatial memory can be manipulated by experimental placement of unrelated tadpoles on adult frogs. As individuals remained inside their home area when only the jelly from tadpole-containing clutches was brushed on the back, we speculate that tactile rather than chemical stimuli trigger these parental behaviours.

Summary: Placement of unrelated tadpoles on adult poison frogs triggers a cascade of parental behaviours involving tadpole transport and spatial memory use in both sexes, despite the asymmetric parental sex roles.