Artificial intelligence enables unified analysis of historical and landscape influences on genetic diversity

While genetic variation in any species is potentially shaped by a range of processes, phylogeography and landscape genetics are largely concerned with inferring how environmental conditions and landscape features impact neutral intraspecific diversity. However, even as both disciplines have come to utilize SNP data over the last decades, analytical approaches have remained for the most part focused on either broad-scale inferences of historical processes (phylogeography) or on more localized inferences about environmental and/or landscape features (landscape genetics). Here we demonstrate that an artificial intelligence model-based analytical framework can consider both deeper historical factors and landscape-level processes in an integrated analysis. We implement this framework using data collected from two Brazilian anurans, the Brazilian sibilator frog (Leptodactylus troglodytes) and granular toad (Rhinella granulosa). Our results indicate that historical demographic processes shape most the genetic variation in the sibulator frog, while landscape processes primarily influence variation in the granular toad. The machine learning framework used here allows both historical and landscape processes to be considered equally, rather than requiring researchers to make an a priori decision about which factors are important.

Exploring Paleogene Tibet's warm temperate environments through target enrichment and phylogenetic niche modelling of Himalayan spiny frogs (Paini, Dicroglossidae)

The Cenozoic topographic development of the Himalaya-Tibet orogen (HTO) substantially affected the paleoenvironment and biodiversity patterns of High Asia. However, concepts on the evolution and paleoenvironmental history of the HTO differ massively in timing, elevational increase and sequence of surface uplift of the different elements of the orogen. Using target enrichment of a large set of transcriptome-derived markers, ancestral range estimation and paleoclimatic niche modelling, we assess a recently proposed concept of a warm temperate paleo-Tibet in Asian spiny frogs of the tribe Paini and reconstruct their historical biogeography. That concept was previously developed in invertebrates. Because of their early evolutionary origin, low dispersal capacity, high degree of local endemism, and strict dependence on temperature and humidity, the cladogenesis of spiny frogs may echo the evolution of the HTO paleoenvironment. We show that diversification of main lineages occurred during the early to Mid-Miocene, while the evolution of alpine taxa started during the late Miocene/early Pliocene. Our distribution and niche modelling results indicate range shifts and niche stability that may explain the modern disjunct distributions of spiny frogs. They probably maintained their (sub)tropical or (warm)temperate preferences and moved out of the ancestral paleo-Tibetan area into the Himalaya as the climate shifted, as opposed to adapting in situ. Based on ancestral range estimation, we assume the existence of low-elevation, climatically suitable corridors across paleo-Tibet during the Miocene along the Kunlun, Qiangtang and/or Gangdese Shan. Our results contribute to a deeper understanding of the mechanisms and processes of faunal evolution in the HTO.

Testing the efficiency of passive acoustic monitoring and active monitoring in anuran community in lotic environments in Itinguçu State Park, Peruíbe-SP

The following work presents the first study applying the passive acoustic monitoring of anurans at lotic environments for a long time. This study aims to test the efficiency of the passive acoustic monitoring method and active monitoring in detecting anurans in lotic environments of Itinguçu State Park. Specifically, we tested whether species richness differs when comparing active and passive monitoring surveys. Therefore, this study aims to test the efficiency of the passive acoustic monitoring method and active monitoring in detecting anurans in lotic environments of the Itinguçu State Park. The passive acoustic monitoring period was 72 uninterrupted hours at each collection point with intervals of 45 days. Finally, species richness was calculated, and the efficiency of the methods was compared in different scenarios. Our results demonstrated that the park has species that vocalize day and night, but most at night, there is overlapping acoustic niche; waterfall environments harm the quality of recordings; and in lotic environments the active monitoring method was more efficient than the passive acoustic monitoring in all sampling scales. Although the passive acoustic monitoring was not as efficient in a low temporal scale, it tends to increase in efficiency with longer sampling duration.

Populating a Continent: Phylogenomics Reveal the Timing of Australian Frog Diversification

The Australian continent's size and isolation make it an ideal place for studying the accumulation and evolution of biodiversity. Long separated from the ancient supercontinent Gondwana, most of Australia's plants and animals are unique and endemic, including the continent's frogs. Australian frogs comprise a remarkable ecological and morphological diversity categorized into a small number of distantly related radiations. We present a phylogenomic hypothesis based on an exon-capture dataset that spans the main clades of Australian myobatrachoid, pelodryadid hyloid, and microhylid frogs. Our time-calibrated phylogenomic-scale phylogeny identifies great disparity in the relative ages of these groups that vary from Gondwanan relics to recent immigrants from Asia and include arguably the continent's oldest living vertebrate radiation. This age stratification provides insight into the colonization of, and diversification on, the Australian continent through deep time, during periods of dramatic climatic and community changes. Contemporary Australian frog diversity highlights the adaptive capacity of anurans, particularly in response to heat and aridity, and explains why they are one of the continent's most visible faunas. [Anuran; adaptive radiation; Gondwana; phylogenetics].

Distribution and diversification of Adelphobates, emblematic poison frogs from Brazilian Amazonia

Adelphobates contains three species, and the inaccurate identification of A. quinquevittatus and the scarcity of records of A. castaneoticus complicate inference of their distributions; the latter species occurs in sympatry with A. galactonotus. Our objective was to revise the distributions of Adelphobates by compiling data and modeling habitat suitability, as range limits may be shaped by landscape features and biotic interactions. We initially analyzed the existence of operational taxonomic units within the nominal species and subsequently inferred the observed and potential distributions, taking into account the possible independent lineages for the three species, and we also generated a molecular timetree to understand the chronology of interspecific diversification events. Adelphobates quinquevittatus was found to have a more easterly distribution than previously described, and specimens with phenotypic variation were found to occur in areas inconsistent with the modeling, and A. castaneoticus was concentrated in the Tapajós-Xingu interfluve, surrounded by A. galactonotus. Models indicated that the right bank of the Xingu River is suitable for both species, indeed, both were found there. Despite Adelphobates species having their distributions delimited by major Amazonian rivers, estimated divergence times predate the formation of the modern river network, suggesting that other mechanisms were involved in their diversification.

Marine introgressions and Andean uplift have driven diversification in neotropical Monkey tree frogs (Anura, Phyllomedusinae)

The species richness in the Neotropics has been linked to environmental heterogeneity and a complex geological history. We evaluated which biogeographic processes were associated with the diversification of Monkey tree frogs, an endemic clade from the Neotropics. We tested two competing hypotheses: the diversification of Phyllomedusinae occurred either in a "south-north" or a "north-south" direction in the Neotropics. We also hypothesized that marine introgressions and Andean uplift had a crucial role in promoting their diversification. We used 13 molecular markers in a Bayesian analysis to infer phylogenetic relationships among 57 species of Phyllomedusinae and to estimate their divergence times. We estimated ancestral ranges based on 12 biogeographic units considering the landscape modifications of the Neotropical region. We found that the Phyllomedusinae hypothetical ancestor range was probably widespread throughout South America, from Western Amazon to Southern Atlantic Forest, at 29.5 Mya. The Phyllomedusines' ancestor must have initially diverged through vicariance, generally followed by jump-dispersals and sympatric speciation. Dispersal among areas occurred mostly from Western Amazonia towards Northern Andes and the South American diagonal of dry landscapes, a divergent pattern from both "south-north" and "north-south" diversification hypotheses. Our results revealed a complex diversification process of Monkey tree frogs, occurring simultaneously with the orogeny of Northern Andes and the South American marine introgressions in the last 30 million years.

Repetitive DNA Mapping in Five Genera of Tree Frogs (Amphibia: Anura) from the Atlantic Forest: New Highlights on Genomic Organization in Hylidae

INTRODUCTION

The tribes Cophomantini, Scinaxini, and Dendropsophini are anurans that belong to Hylidae, with wide distribution in tropical and subtropical regions around the world. The taxonomy and systematics of this family remain in a state of ongoing revision. Previous cytogenetic analyses of genera Boana, Bokermannohyla, Ololygon, Scinax, and Dendropsophus described some karyotypic characters such as conventional staining, C-banding and NORs, and FISH with specific probes.

METHODS

This study describes for the first time the karyotypes of four species: Bokermannohyla ibitipoca, Ololygon luizotavioi, Dendropsophus bipunctatus, and Dendropsophus ruschii. Furthermore, we map CA(15) and CAT(10) microsatellite sites for the aforementioned species and six more species from the same genera for insight into the chromosomal evolution within the subfamily Hyalinae.

RESULTS

B. ibitipoca and O. luizotavioi had 2n = 24 and karyotypic formulas 18m + 4sm + 2st and 8m + 12sm + 4st, while D. bipunctatus and D. ruschii showed 2n = 30 and karyotypic formulas 12m + 12sm + 4st + 2t and 10m + 10sm + 6st + 4t, respectively. The diploid numbers and karyotypic formulas revealed here follow the previously reported trend for Hylidae, except B. ibitipoca has a particularity of eight metacentric chromosomes, more than what is commonly found in species of this genus. The microsatellites probes CA(15) and CAT(10) had markings accumulated in blocks in the centromeric, pericentromeric, and terminal regions that were more specific for some species, as well as markings scattered along the chromosomes. We present a comprehensive review table of current data on cytogenetics of these genera.

CONCLUSION

Our findings showed that the karyotypes of the hylids studied here majority fit the postulated conserved diploid number (2n = 24) and morphological chromosome patterns, while the mapping of the microsatellites enabled us to detect differences between species that share similar chromosomal morphologies.

Molecular species delimitation of shrub frogs of the genus Pseudophilautus (Anura, Rhacophoridae)

Sri Lanka is an amphibian hotspot of global significance. Its anuran fauna is dominated by the shrub frogs of the genus Pseudophilautus. Except for one small clade of four species in Peninsular India, these cool-wet adapted frogs, numbering some 59 extant species, are distributed mainly across the montane and lowland rain forests of the island. With species described primarily by morphological means, the diversification has never yet been subjected to a molecular species delimitation analysis, a procedure now routinely applied in taxonomy. Here we test the species boundaries of Pseudophilautus in the context of the phylogenetic species concept (PSC). We use all the putative species for which credible molecular data are available (nDNA-Rag-1; mt-DNA- 12S rRNA, 16S rRNA) to build a well resolved phylogeny, which is subjected to species delimitation analyses. The ABGD, bPTP, mPTP and bGMYC species delimitation methods applied to the 16S rRNA frog barcoding gene (for all species), 12S rRNA and Rag-1 nDNA grouped P. procax and P. abundus; P. hallidayi and P. fergusonianus; P. reticulatus and P. pappilosus; P. pleurotaenia and P. hoipolloi; P. hoffmani and P. asankai; P. silvaticus and P. limbus; P. dilmah and P. hankeni; P. fulvus and P. silus.. Surprisingly, all analyses recovered 14 unidentified potential new species as well. The geophylogeny affirms a distribution across the island's aseasonal 'wet zone' and its three principal hill ranges, suggestive of allopatric speciation playing a dominant role, especially between mountain masses. Among the species that are merged by the delimitation analyses, a pattern leading towards a model of parapatric speciation emerges-ongoing speciation in the presence of gene flow. This delimitation analysis reinforces the species hypotheses, paving the way to a reasonable understanding of Sri Lankan Pseudophilautus, enabling both deeper analyses and conservation efforts of this remarkable diversification. http://zoobank.org/urn:lsid:zoobank.org:pub:DA869B6B-870A-4ED3-BF5D-5AA3F69DDD27.

The Louisiana Amphibian Monitoring Program from 1997 to 2017: Results, analyses, and lessons learned

To determine trends in either frog distribution or abundance in the State of Louisiana, we reviewed and analyzed frog call data from the Louisiana Amphibian Monitoring Program (LAMP). The data were collected between 1997 and 2017 using North American Amphibian Monitoring Program protocols. Louisiana was divided into three survey regions for administration and analysis: the Florida Parishes, and 2 areas west of the Florida parishes called North and South. Fifty-four routes were surveyed with over 12,792 stops and 1,066 hours of observation. Observers heard 26 species of the 31 species reported to be in Louisiana. Three of the species not heard were natives with ranges that did not overlap with survey routes. The other two species were introduced species, the Rio Grande Chirping Frog (Eleutherodactylus cystignathoides) and the Cuban Treefrog (Osteopilus septentrionalis). Both seem to be limited to urban areas with little to no route coverage. The 15 most commonly occurring species were examined in detail using the percentage of stops at which they observed along a given survey and their call indices. Most species exhibited a multimodal, concave, or convex pattern of abundance over a 15-year period. Among LAMP survey regions, none of the species had synchronous population trends. Only one group of species, winter callers, regularly co-occur. Based on the species lists, the North region could be seen as a subset of the South. However, based on relative abundance, the North was more similar to Florida parishes for both the winter and summer survey runs. Our analyses demonstrate that long-term monitoring (10 years or more) may be necessary to determine population and occupancy trends, and that frog species may have different local demographic patterns across large geographic areas.

Toward an understanding of tree frog (Hyla japonica) for predator deterrence

Gene-encoded peptides with distinct potent bioactivities enable several animals to take advantage of fierce interspecific interaction, as seen in the skin secretion of amphibians. Unlike, most amphibian species that frequently switches terrestrial-aquatic habitats and hides easily from terrestrial predators, tree frogs of small body size are considered as the vulnerable prey in the arboreal habitat. Here, we show the structural and functional diversity of peptide families based on the skin transcriptome of Hyla japonica, which has evolved to be wrapped as an efficient chemical toolkit for defensive use in arboreal habitat. Generally, the presence of antimicrobial peptide and proteinase inhibitor families reveals the functional consistency of Hyla japonica skin compared to other amphibian species. Furthermore, we found that Anntoxin-like neurotoxins with high expression levels are species-specific in tree frogs. Interestingly, derivatives in the Anntoxin-like family exhibit multiple evolutionary traits in modifying the copy number, folding type, and three-dimensional architecture, which are considered essential for targeting the ion channels of terrestrial predators. Together, our study not only reveals the peptide diversity in the skin secretion of H. japonica, but also draws insights into the predator-deterring strategy for coping with arboreal habitat.

Hidden by the name: A new fluorescent pumpkin toadlet from the Brachycephalus ephippium group (Anura: Brachycephalidae)

Species of Brachycephalus has been having taxonomical issues due its morphological similarity and genetic conservatism. Herein, we describe a new species of Brachycephalus from the south Mantiqueira mountain range and semidecidual forests in the municipalities of Mogi das Cruzes, Campinas and Jundiaí, state of São Paulo, Brazil, based on an integrative approach. It can be distinguished from all species of the B. ephippium species group based on morphological characters (especially osteology and head shape), advertisement call and divergence in partial mitochondrial DNA gene sequences (16S). The new species is genetically similar to B. margaritatus and morphologically similar to B. ephippium. It can be differentiated from B. ephippium by the presence of dark faded spots on skull and post-cranial plates, presence of black connective tissue connective tissue scattered over dorsal musculature, parotic plate morphology, smaller snout-vent length (adult SVL: males 13.46-15.92 mm; females 16.04-17.69 mm) and 3% genetic distance. We also present natural history data and discuss the robustness of the integrative approach, geographic distribution, genetic data, behaviour, fluorescence in ontogeny, and conservation status.

The Diversity and Evolution of Sex Chromosomes in Frogs

Frogs are ideal organisms for studying sex chromosome evolution because of their diversity in sex chromosome differentiation and sex-determination systems. We review 222 anuran frogs, spanning ~220 Myr of divergence, with characterized sex chromosomes, and discuss their evolution, phylogenetic distribution and transitions between homomorphic and heteromorphic states, as well as between sex-determination systems. Most (~75%) anurans have homomorphic sex chromosomes, with XY systems being three times more common than ZW systems. Most remaining anurans (~25%) have heteromorphic sex chromosomes, with XY and ZW systems almost equally represented. There are Y-autosome fusions in 11 species, and no W-/Z-/X-autosome fusions are known. The phylogeny represents at least 19 transitions between sex-determination systems and at least 16 cases of independent evolution of heteromorphic sex chromosomes from homomorphy, the likely ancestral state. Five lineages mostly have heteromorphic sex chromosomes, which might have evolved due to demographic and sexual selection attributes of those lineages. Males do not recombine over most of their genome, regardless of which is the heterogametic sex. Nevertheless, telomere-restricted recombination between ZW chromosomes has evolved at least once. More comparative genomic studies are needed to understand the evolutionary trajectories of sex chromosomes among frog lineages, especially in the ZW systems.

Frank Beach Award Winner: Lessons from poison frogs on ecological drivers of behavioral diversification

Variation in natural behavior is tightly linked to the ecological resources with which they co-evolved. This review discusses poison frog behavior and neuroendocrinology to illustrate how ecological factors drive diversification of behavior and its underlying neural mechanisms. Poison frogs show tremendous diversity in reproductive strategies that are tightly linked to water resources in their environment. Different species utilize particular pool sizes to rear their offspring, which has selected for sex differences in parental behavior among poison frog species. Tadpole behavior reflects the behavioral diversity of adults, where tadpoles can display social group living or violent aggression and begging behavior, which are all associated with pool size and occupancy. Using this behavioral diversity among poison frog species, we have identified core brain regions, like the hippocampus and preoptic area, as being involved in regulating different aspects of amphibian parental behavior. In contrast to core brain regions, the neuromodulators governing these behaviors seem to be more labile across species. This work exemplifies how comparative studies are a prime experimental system to study how evolution tunes neural circuits that give rise to the diversity of behaviors we observe in the natural world. Finally, this review ends on a more important form of diversity - that of our scientific community - and how community outreach, decolonization of field based science, and inclusion of groups historically excluded from conducting research are needed for the scientific enterprise to transform into something truly beneficial for all members of our society.

Fifty years after: A taxonomic revision of the amphibian species from the Ecuadorian biodiversity hotspot Abra de Zamora, with description of two new Pristimantis species

Abra de Zamora is an important biodiversity hotspot in southern Ecuador. Between 1938 and 2010, eleven species of frogs were described from here: Lynchius flavomaculatus, Gastrotheca psychrophila, Pristimantis balionotus, P. colodactylus, P. cryptomelas, P. percultus, P. versicolor, P. vidua, Telmatobius cirrhacelis, P. andinognomus, and Atelopus podocarpus. Unfortunately, many of these species were not re-encountered after their original description, and for the majority DNA samples were not available, making their phylogenetic position unknown. In this study, we assess the current state of the amphibians from Abra de Zamora, by: i. redescribing the species which were first reported from the area, by contributing genetic delimitation (for L. flavomaculatus, P. balionotus, P. colodactylus, P. percultus, and P. vidua), release call (L. flavomaculatus) and advertisement call descriptions (for P. balionotus, P. vidua and P. versicolor); ii. presenting an updated amphibian species list of Abra de Zamora, with the description of two additional Pristimantis species; iii. updating the distribution of these species, including data collected in similar montane habitats from surrounding areas; and iv. amending recommendations regarding their conservation status.

Determining levels of cryptic diversity within the endemic frog genera, Indirana and Walkerana, of the Western Ghats, India

A large number of species in the tropics are awaiting discovery, many due to their cryptic morphology ie. lack of discernable morphological difference. We explored the presence of cryptic lineages within the frog genera, Indirana and Walkerana, which are endemic to the Western Ghats of Peninsular India. By reconstructing a phylogeny using 5 genes and robust geographic sampling, we delimited 19 lineages along a population—species continuum, using multiple criteria including haplotype clusters, genetic distance, morphological distinctness, and geographical separation. Of these 19 lineages, 14 belonged to the genus Indirana and 5 to the genus Walkerana. Divergence dating analyses revealed that the clade comprising Indirana and Walkerana began diversifying around 71 mya and the most recent common ancestor of Indirana and Walkerana split around 43 mya. We tested for the presence of cryptic lineages by examining the relationship between genetic and morphological divergence among related pairs within a pool of 15 lineages. The pairs showed strong morphological conservatism across varying levels of genetic divergence. Our results highlight the prevalence of morphologically cryptic lineages in these ancient endemic clades of the Western Ghats. This emphasizes the significance of other axes, such as geography, in species delimitation. With increasing threats to amphibian habitats, it is imperative that cryptic lineages are identified so that appropriate conservation measures can be implemented.

Multiple origins of green coloration in frogs mediated by a novel biliverdin-binding serpin

Many vertebrates have distinctive blue-green bones and other tissues due to unusually high biliverdin concentrations-a phenomenon called chlorosis. Despite its prevalence, the biochemical basis, biology, and evolution of chlorosis are poorly understood. In this study, we show that the occurrence of high biliverdin in anurans (frogs and toads) has evolved multiple times during their evolutionary history, and relies on the same mechanism-the presence of a class of serpin family proteins that bind biliverdin. Using a diverse combination of techniques, we purified these serpins from several species of nonmodel treefrogs and developed a pipeline that allowed us to assemble their complete amino acid and nucleotide sequences. The described proteins, hereafter named biliverdin-binding serpins (BBS), have absorption spectra that mimic those of phytochromes and bacteriophytochromes. Our models showed that physiological concentration of BBSs fine-tune the color of the animals, providing the physiological basis for crypsis in green foliage even under near-infrared light. Additionally, we found that these BBSs are most similar to human glycoprotein alpha-1-antitrypsin, but with a remarkable functional diversification. Our results present molecular and functional evidence of recurrent evolution of chlorosis, describe a biliverdin-binding protein in vertebrates, and introduce a function for a member of the serpin superfamily, the largest and most ubiquitous group of protease inhibitors.

Rapid adaptation to invasive predators overwhelms natural gradients of intraspecific variation

Invasive predators can exert strong selection on native populations. If selection is strong enough, populations could lose the phenotypic variation caused by adaptation to heterogeneous environments. We compare frog tadpoles prior to and 14 years following invasion by crayfish. Prior to the invasion, populations differed in their intrinsic developmental rate, with tadpoles from cold areas reaching metamorphosis sooner than those from warm areas. Following the invasion, tadpoles from invaded populations develop faster than those from non-invaded populations. This ontogenetic shift overwhelmed the intraspecific variation between populations in a few generations, to the point where invaded populations develop at a similar rate regardless of climate. Rapid development can have costs, as fast-developing froglets have a smaller body size and poorer jumping performance, but compensatory growth counteracts some costs of development acceleration. Strong selection by invasive species can disrupt local adaptations by dampening intraspecific phenotypic variation, with complex consequences on lifetime fitness.

Yellow sea mediated segregation between North East Asian Dryophytes species

While comparatively few amphibian species have been described on the North East Asian mainland in the last decades, several species have been the subject of taxonomical debates in relation to the Yellow sea. Here, we sampled Dryophytes sp. treefrogs from the Republic of Korea, the Democratic People's Republic of Korea and the People's Republic of China to clarify the status of this clade around the Yellow sea and determine the impact of sea level change on treefrogs' phylogenetic relationships. Based on genetics, call properties, adult morphology, tadpole morphology and niche modelling, we determined the segregated status species of D. suweonensis and D. immaculatus. We then proceeded to describe a new treefrog species, D. flaviventris sp. nov., from the central lowlands of the Republic of Korea. The new species is geographically segregated from D. suweonensis by the Chilgap mountain range and known to occur only in the area of Buyeo, Nonsan and Iksan in the Republic of Korea. While the Yellow sea is the principal element to the current isolation of the three clades, the paleorivers of the Yellow sea basin are likely to have been the major factor for the divergences within this clade. We recommend conducting rapid conservation assessments as these species are present on very narrow and declining ranges.

Chromosome evolution in Lophyohylini (Amphibia, Anura, Hylinae)

The hyline tribe Lophyohylini includes 87 species of treefrogs, of which cytogenetics aspects have been studied in less than 20% of them. In order to evaluate the evolution of some of its chromosome characters (NOR position, C-bands, and DAPI/CMA₃ bands), we studied the karyotypes of 21 lophyohylines, 16 of them for the first time, and analyzed them in a phylogenetic context. Most species showed similar karyotypes regarding chromosome number (2n = 24) and morphology (FN = 48), excepting Phyllodytes edelmoi and Osteocephalus buckleyi with 2n = 22 (FN = 44) and 2n = 28 (FN = 50), respectively. The NOR location was variable among species and provided valuable phylogenetic information. This marker was located in pair 11 in all species of Trachycephalus, Itapotihyla langsdorffii, and Nyctimantis arapapa, representing the plesiomorphic condition of Lophyohylini. Besides, other apomorphic states were recovered for the clades comprising N. rugiceps and N. siemersi (NOR in pair 5), and Dryaderces pearsoni, Osteocephalus, and Osteopilus (NOR in pair 9). Phyllodytes presented variation for NORs position; they were in pair 2 in P. edelmoi, pair 7 in P. melanomystax, and pair 8 in P. gyrinaethes and P. praeceptor. Polymorphisms in size, number, and activity of this marker were observed for N. siemersi, Osteocephalus fuscifacies, and some species of Trachycephalus. Remarkably, in N. siemersi NORs were detected on a single chromosome in the two specimens studied by this technique, raising the question of how this complex polymorphism is maintained. Interstitial telomeric sequences were found in P. edelmoi, P. melanomystax, and Osteocephalus buckleyi, and their presence seems to be not related to the chromosome reorganization events. Finally, some species showed spontaneous rearrangements, possibly as a consequence of an uncommon phenomenon in anuran cytogenetics: the presence of fragile sites or secondary constrictions not associated with NORs. We propose that this rare feature would have played an important role in the evolution of this group of frogs. From the evidence obtained in this and previous studies, we conclude that Lophyohylini presents a complex chromosome evolution.

Polyploidy breaks speciation barriers in Australian burrowing frogs Neobatrachus

Polyploidy has played an important role in evolution across the tree of life but it is still unclear how polyploid lineages may persist after their initial formation. While both common and well-studied in plants, polyploidy is rare in animals and generally less understood. The Australian burrowing frog genus Neobatrachus is comprised of six diploid and three polyploid species and offers a powerful animal polyploid model system. We generated exome-capture sequence data from 87 individuals representing all nine species of Neobatrachus to investigate species-level relationships, the origin and inheritance mode of polyploid species, and the population genomic effects of polyploidy on genus-wide demography. We describe rapid speciation of diploid Neobatrachus species and show that the three independently originated polyploid species have tetrasomic or mixed inheritance. We document higher genetic diversity in tetraploids, resulting from widespread gene flow between the tetraploids, asymmetric inter-ploidy gene flow directed from sympatric diploids to tetraploids, and isolation of diploid species from each other. We also constructed models of ecologically suitable areas for each species to investigate the impact of climate on differing ploidy levels. These models suggest substantial change in suitable areas compared to past climate, which correspond to population genomic estimates of demographic histories. We propose that Neobatrachus diploids may be suffering the early genomic impacts of climate-induced habitat loss, while tetraploids appear to be avoiding this fate, possibly due to widespread gene flow. Finally, we demonstrate that Neobatrachus is an attractive model to study the effects of ploidy on the evolution of adaptation in animals.

Progesterone: An enigmatic ligand for the mineralocorticoid receptor

The progesterone receptor (PR) mediates progesterone regulation of female reproductive physiology, as well as gene transcription in non-reproductive tissues, such as brain, bone, lung and vasculature, in both women and men. An unusual property of progesterone is its high affinity for the mineralocorticoid receptor (MR), which regulates electrolyte transport in the kidney in humans and other terrestrial vertebrates. In humans, rats, alligators and frogs, progesterone antagonizes activation of the MR by aldosterone, the physiological mineralocorticoid in terrestrial vertebrates. In contrast, in elephant shark, ray-finned fishes and chickens, progesterone activates the MR. Interestingly, cartilaginous fishes and ray-finned fishes do not synthesize aldosterone, raising the question of which steroid(s) activate the MR in cartilaginous fishes and ray-finned fishes. The simpler synthesis of progesterone, compared to cortisol and other corticosteroids, makes progesterone a candidate physiological activator of the MR in elephant sharks and ray-finned fishes. Elephant shark and ray-finned fish MRs are expressed in diverse tissues, including heart, brain and lung, as well as, ovary and testis, two reproductive tissues that are targets for progesterone, which together suggests a multi-faceted physiological role for progesterone activation of the MR in elephant shark and ray-finned fish. The functional consequences of progesterone as an antagonist of some terrestrial vertebrate MRs and as an agonist of fish and chicken MRs are not fully understood. The physiological activities of progesterone through binding to vertebrate MRs merits further investigation.

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.

One step beyond a broad molecular phylogenetic analysis: Species delimitation of Adenomera marmorata Steindachner, 1867 (Anura: Leptodactylidae)

Taxonomists always have had intense discussions about how species should be delimited and recently many studies have used integrative approaches by combining molecular, morphological, and bioacoustic data. Although these studies are paramount for understanding species diversity, few of them actually formalize species delimitations to the final step of nomenclatural acts. Historically, the Neotropical frog genus Adenomera has been considered as a difficult taxonomic group because it comprises many morphologically similar species exhibiting high levels of intraspecific polymorphism. A recent work using molecular data shed light on the phylogenetic relationships within the genus and identified several lineages that may correspond to undescribed species but did not delimit species boundaries. In the Atlantic Forest, a clade formed by A. marmorata and two putative species (Adenomera sp. J and Adenomera sp. K) were identified. In this paper, we combine morphological, acoustic, and molecular data in order to evaluate species limits within this Atlantic Forest Adenomera clade. We provide a redescription of A. marmorata and restrict its type locality to the Tijuca Massif, in the Municipality of Rio de Janeiro, Brazil. Our results do not support A. marmorata and the two candidate species as diagnosable distinct species. Therefore A. marmorata corresponds to a species with pronounced morphological and acoustic variation in the genus and a complex phylogeographic structure.

Diversity of Antimicrobial Peptides in Three Partially Sympatric Frog Species in Northeast Asia and Implications for Evolution

Antimicrobial peptides (AMPs) are evolutionarily ancient molecules that play an essential role in innate immunity across taxa from invertebrates to vertebrates. The evolution system of AMP system has not been well explained in the literature. In this study, we cloned and sequenced AMP transcriptomes of three frog species, namely Rana dybowskii, Rana amurensis, and Pelophylax nigromaculatus, which are partially sympatric in northeast Asia, but show different habitat preferences. We found that each species contained 7 to 14 families of AMPs and the diversity was higher in species with a large geographic range and greater habitat variation. All AMPs are phylogenetically related but not associated with the speciation process. Most AMP genes were under negative selection. We propose that the diversification and addition of novel functions and improvement of antimicrobial efficiency are facilitated by the expansion of family members and numbers. We also documented significant negative correlation of net charges and numbers of amino acid residues between the propiece and mature peptide segments. This supports the Net Charge Balance Hypothesis. We propose the Cut Point Sliding Hypothesis as a novel diversification mechanism to explain the correlation in lengths of the two segments.

Genomewide analysis of microsatellite markers based on sequenced database in two anuran species

Eukaryotic and prokaryotic cell genomes exhibit multiple microsatellites. In this study, we characterized microsatellites in genomes and genes of Nanorana parkeri and Xenopus laevis. This characterization was used for gene ontology (GO) analysis of coding sequences (CDS). Compared to the genome of N. parkeri, the genome of X. laevis is larger and contains more number of microsatellites, but the diversity of both species are similar. Trinucleotide repeats in the genome of N. parkeri and dinucleotide and tetranucleotide repeats inthe genome of X. laevis were the most diverse. In both the species, diversity of microsatellites was highest in intergenic regions, followed by intron and exon regions, and lowest in coding regions. Microsatellites in CDS are thus subject to higher selective pressure. Many microsatellites are concentrated upstream and downstream of genes in both species, suggesting suppression of repeats in the middle of protein-CDS. Repeats are enriched in regions near gene termini purely due to the biophysical constraints of protein structure. In GO analysis, two and five unique GO terms, only found in N. parkeri and X. laevis, respectively, indicate advantageous mutations during species evolution. Biological process, cellular component and molecular function ontology reflected in the GO analysis predicted that the microsatellites located in CDS can alter protein function and may provide a molecular basis for species adaptation to new and changing environments.