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Description of a Puzzling New Long-Legged Pseudopaludicola Miranda-Ribeiro 1926 Species (Anura, Leptodactylidae) from the Araguaia River Floodplain, Brazil
Abstract
Twenty-six species are currently assigned to the genus Pseudopaludicola. One of the most conspicuous lineages within this genus corresponds to the long-legged Pseudopaludicola saltica species group, where the three species, Pseudopaludicola jaredi, Pseudopaludicola murundu, and P. saltica, have tibiotarsal articulation extending beyond the tip of the snout. Here, we describe a fourth species belonging to the P. saltica group based on morphologic, molecular, and acoustic evidence. The new species can be distinguished from the other species assigned to the P. saltica group by a yellowish vocal sac in life (grayish vocal sac in P. jaredi and P. murundu and whitish vocal sac in P. saltica). The new species also emits a unique advertisement call compared to other species of the P. saltica group, resembling the rhythm of a galloping horse. This pattern, however, is remarkably similar to that of the distantly related Pseudopaludicola pocoto, suggesting independent evolution in these two species. The new species is described from a single locality in western Tocantins state, Marianópolis municipality (Brazil), in the Araguaia River floodplain. The new taxon described here is the sixth species of Pseudopaludicola known from the Tocantins.
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The following list includes all recognized species of amphibians, known by vouchers or published information to occur within the political borders of Brazil (as of April 2021). Supra-generic taxonomy follows Frost (2021), as do most generic and species names. Other taxonomic decisions and species exclusions are explained below. All inclusions relative to the previous list (Segalla et al. 2019) are informed in the status column. The known amphibian fauna of Brazil comprises 1188 species, an increase of 95 species compared to the previous list. The vast majority of species are anurans, including 1144 species (two exotic and invasive species) representing 20 families and 107 genera, followed by caecilians, with 39 species in 4 families and
13 genera, and salamanders, with 5 species in a single family and genus.
Registation in Zoobank: urn:lsid:zoobank.org:pub:D19AF1F3-AEF4-40BD-91E-6-43AA8313E2D2
The Molecular Evolutionary Genetics Analysis (MEGA) software has matured to contain a large collection of methods and tools of computational molecular evolution. Here, we describe new additions that make MEGA a more comprehensive tool for building timetrees of species, pathogens, and gene families using rapid relaxed-clock methods. Methods for estimating divergence times and confidence intervals are implemented to use probability densities for calibration constraints for node-dating and sequence sampling dates for tip-dating analyses, which will be supported by new options for tagging sequences with spatiotemporal sampling information, an expanded interactive Node Calibrations Editor, and an extended Tree Explorer to display timetrees. We have now added a Bayesian method for estimating neutral evolutionary probabilities of alleles in a species using multispecies sequence alignments and a machine learning method to test for the autocorrelation of evolutionary rates in phylogenies. The computer memory requirements for the maximum likelihood analysis are reduced significantly through reprogramming, and the graphical user interface (GUI) has been made more responsive and interactive for very big datasets. These enhancements will improve the user experience, quality of results, and the pace of biological discovery. Natively compiled GUI and command-line versions of MEGA11 are available for Microsoft Windows, Linux, and macOS from www.megasoftware.net.
In recent years, the taxonomic knowledge of Pseudopaludicola has increased and it is currently possible to elucidate aspects of the species within this genus such as their geographic distributions. Here we accessed new data on geographic distribution of P. boliviana and three long-legged species of the P. saltica group (P. saltica, P. murundu, and P. jaredi). Based on morphometric, acoustic and genetic data, we accessed the specific status of long-legged specimens from Chapada dos Veadeiros highlands and attributed them to the P. murundu. We also performed a phylogenetic analysis including several populations of the three species. Based on this novel dataset, we discussed the geographical distributions of P. saltica, P. murundu, and P. jaredi, providing new records for them. Pseudopaludicola boliviana is one of the five species of the P. pusilla group and it is thought to be a widely distributed species based on its morphology. Hence, we evaluated the geographic distribution of P. boliviana, using novel acoustic data of specimens from Argentina, Northern Brazil, and Bolivia.
The Neotropical frog genus Pseudopaludicola includes 25 species distributed throughout South America. Herein we review the taxonomic status of P. parnaiba relative to P. canga and the specific identity of the population treated in previous studies as Pseudopaludicola sp. 3 from Barreirinhas in the Brazilian state of Maranhão. The lack of differentiation in advertisement call, morphology, and mitochondrial markers from topotypes and different populations rejects the status of P. parnaiba and Pseudopaludicola sp. 3 from Barreirinhas as distinct species. For these reasons, we suggest to formally consider P. parnaiba as a junior synonym of P. canga. We also found that a population previously reported as P. facureae from central Brazil (Palmeiras de Goiás, Goiás) corresponds to a cryptic species that we describe here as a new species. Lastly, we provide for the first time the phylogenetic positions of P. giarettai, P. llanera and P. pusilla.
Herein, we provide the first comprehensive amphibian checklist for the State of Tocantins, North of Brazil, based on field sampling, literature data, and specimens deposited in zoological collections. We performed field surveys from 2012 to 2019 in 12 Tocantins municipalities, totaling 376 days of sampling effort. We analyzed 25 papers from the literature and examined 1311 specimens from collections and collected 750 during field surveys. We recorded 90 amphibian species distributed in 12 anurans and two caecilians families. At least seven undescribed species along the state were recorded. We also present new records for 20 species for the state, nine of them corresponding to Amazonian species, four Cerrado endemic, one Caatinga species, and the widely distributed treefrog Boana crepitans; the others five new records comprise undescribed species. Our data also suggest that the Tocantins amphibian composition is not geographically structured in relation to the biomes, since Amazonian, Caatinga, and Cerrado amphibian lineages have their distribution nearly completely overlapped in the state. We propose that this absence of spatial structuration may be a result of two factors (synergetic or not). First, the events of expansion and retraction of the biomes caused by the Quaternary climatic cycles, which may have mixed the populations of species from different biomes causing the notable pattern of overlapped distribution observed here. Second, the forest environments (e.g. gallery and riparian forests) associated to the Araguaia-Tocantins River basins may have acted as historical dispersal corridors for the Amazonian amphibian lineages into the Cerrado of the Tocantins. Despite the sampling effort of the present study, we stress that gaps of information still remain and further field sampling efforts should be performed along the state. Lastly, taxonomic appraisals involving the species with problematic taxonomic status recorded here should be based on multiples lines of evidences (acoustic, molecular, and morphological data), which will render a more accurate view on the Tocantins amphibian diversity. Such data are extremely necessary under the current high rate of habitat loss across the state, since they can be used to guide public policies of conservation.
The genus of Neotropical frogs Pseudopaludicola Miranda-Ribeiro, 1926 includes 23 species, which occur throughout South America. Herein we describe a new species of Pseudopaludicola from the central region of the state of Minas Gerais (southeastern Brazil). This new species is distinguished by the adult morphology, the advertisement call, and molecular data. It is diagnosed mainly by its small size, terminal phalanges knobbed (lack of any expansion of the digital tips), proportionally short hind limbs, and its advertisement call composed of series of two-pulsed notes, emitted at a high repetition rate. In addition, we report the occurrence of the new species in the southern foothills of the Serra do Cipó National Park, at elevations lower than 800 m above sea level (a.s.l). The sister species of this new taxon is P. mineira Lobo, 1994, which occurs in rupestrian grasslands above 1200 m a.s.l. at the Serra do Cipó National Park and in Serra do Cabral, both in the state of Minas Gerais, Brazil. We also redescribe the advertisement call of P. mineira based on recordings from topotypical males and compare it to calls of related species.
Anurans emit advertisement calls with the purpose of attracting mates and repelling conspecific competitors. The evolution of call traits is expected to be associated with the evolution of anatomical and behavioral traits due to the physics of call emission and transmission. Additionally, since vocalizing might imply a trade‐off with investment in parental care, the evolution of calls is expected to trade‐off with parental care. Here, we investigated the association between body size, calling site, parental care and call properties (call duration, number of notes, peak frequency, frequency bandwidth and call structure) of the advertisement calls of glassfrogs (Centrolenidae)—a family of Neotropical, leaf‐dwelling anurans—using phylogenetic comparative methods. We also explored the tempo and mode of evolution of these traits and compared them with those of three morphological traits associated with body size, locomotion and feeding. We generated and compiled acoustic data for 72 glassfrog species (46% of total species richness), including representatives of all genera. We found that almost all acoustic traits have significant, but generally modest, phylogenetic signal. Peak frequency of calls is significantly associated with body‐size, while call structure is significantly associated with calling site and paternal care. Thus, the evolution of body size and calling site could constrain call evolution. The estimated disparity of acoustic traits was larger than that of morphological traits and the peak in disparity of acoustic traits generally occurred later in the evolution of glassfrogs, indicating a historically recent outset of the acoustic divergence in this clade.
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Pseudopaludicola are small diurnal leiuperid frogs that are recognized by a hemispherical
tubercle on their forearms. Members of this genus are broadly distributed over northern and central South
America with 12 species currently recognized. Pseudopaludicola mirandae was described from six
individuals and discriminated from Pseudopaludicola boliviana based solely on putative differences in
head width. We reexamined the type series of P. mirandae and a large series (including topotypes) of P.
boliviana. We show broadly overlapping ranges in the ratio of head length/width between P. boliviana and
P. mirandae. Also, both taxa share a character state (a tubercle on the heel) that was previously considered
autapomorphic for P. boliviana. Additionally, we document a number of omissions and errors in the original
description of P. mirandae including comparisons with P. boliviana. Our analyses provide evidence
suggesting that P. mirandae is a junior synonym of P. boliviana.
The Neotropical genus Pseudopaludicola includes 21 species, which occur throughout South America. Recent studies suggested that the population of Andaraí, in the state of Bahia, is an undescribed species, related to P. pocoto. Herein we formally describe this new species from lowlands of eastern Brazil. Recognition of this new species is supported by adult morphology, advertisement call, karyotype, and molecular data. It is diagnosed mainly by its small size, terminal phalanges knobbed (lack any expansion of the digital tips), proportionally short hindlimbs, 11 pairs of chromosomes, and advertisement call composed of series of three-pulsed notes, emitted at a high rate. In addition, we report for the first time the presence of P. pocoto in the campo rupestre (rupestrian grasslands) of Chapada Diamantina, a population with a much darker dorsal coloration than the population from the type locality. We also redescribed the advertisement call of P. falcipes based on recordings from topotypic males.
We present a detailed list of the reptiles and amphibians occurring in two habitat types (tabuleiros and Stational Semidecidual Forest) in the Reserva Biológica Guaribas (REBIO Guaribas), Paraíba State, northeastern Brazil. We sampled species using pitfall traps, transects, and during active searches. We recorded a total of 106 species, including 20 lizards, seven amphisbaenians, 42 snakes, one turtle, two crocodilians, and 34 frogs. Of these, five lizards, six snakes, 14 frogs, seven amphisbaenians, and the turtle were new records for REBIO Guaribas. The frog and snake rarefaction curves reached the asymptote, indicating that we achieved a good estimate of species richness for those taxa. The herpetofauna in REBIO Guaribas is composed of species typical for both forested biomes and open areas. The open areas in REBIO Guaribas occur within an Atlantic Forest matrix and are locally known as tabuleiros, which present typical elements of cerrado savannahs, reinforcing the importance of the open areas in species composition and maintenance of regional fauna. We outline the importance of long-term inventories, such as in REBIO Guaribas, especially due to the higher number of rare species found, which provides essential information for species and habitat management.
We describe a new anuran species of the genus Pseudopaludicola that inhabits sandy areas in resting as associated to the Atlantic Forest biome in the state of Espírito Santo, Brazil. The new species is characterized by: SVL 11.7-14.6 mm in males, 14.0-16.7 mm in females; body slender; fingertips knobbed, with a central groove; hindlimbs short; abdominal fold complete; arytenoid cartilages wide; prepollex with base and two segments; prehallux with base and one segment; frontoparietal fontanelle partially exposed; advertisement call with one note composed of two isolated pulses per call; call dominant frequency ranging 4,380-4,884 Hz; diploid chromosome number 22; and Ag-NORs on 8q subterminal. In addition, its 16S rDNA sequence shows high genetic distances when compared to sequences of related species, which provides strong evidence that the new species is an independent lineage.
A recently published phylogeny corroborated the monophyly of the genus Pseudopaludicola and recognized a clade that included two species that share the same chromosome number: P. ameghini and P. ternetzi. However, historically these two sister species have undergone many taxonomic changes and so far they do not have a clear taxonomic diagnosis in relation one another. In this study we carry out a male specimen analysis and an acoustic comparison between both. We recorded and analyzed 44 adult males of P. ternetzi: 18 males from Ituiutaba (MG), eight from Minaçu (GO), and 18 from Pontal do Araguaia (MT). We also analyzed 11 adult males of P. ameghini: five from Chapada dos Guimarães (MT; type locality), two from Santo Antonio do Laverger (MT), and four from Cáceres (MT). A sample of 610 notes was analyzed using Raven Pro 1.5. For the multivariate, multidimensional analysis/plots and statistical tests, we used three R packages: randomForest, rfPermute and coin, respectively. Pseudopaludicola ternetzi can be easily distinguished from P. ameghini by its higher pulse and note rates (both traits with non-overlapping values). We also found significant differences (p < 0.01) between them in other temporal traits such as note duration, internote interval, pulses per note, pulse duration and interpulse interval. The two species could not be distinguished in peak of dominant frequency (p = 0.6). In addition, we recognize that both species have a similar external morphology and high intraspecific variation on dorsal color patterns, which may have led to misleading identifications based on their external morphology. Moreover, both species can also be differentiated from the remaining 19 Pseudopaludicola species by their acoustic traits.
Vocalizations of anuran amphibians have received much attention in studies of behavioral ecology and physiology, but also provide informative characters for identifying and delimiting species. We here review the terminology and variation of frog calls from a perspective of integrative taxonomy, and provide hands-on protocols for recording, analyzing, comparing, interpreting and describing these sounds. Our focus is on advertisement calls, which serve as premating isolation mechanisms and, therefore, convey important taxonomic information. We provide recommendations for terminology of frog vocalizations, with call, note and pulse being the fundamental subunits to be used in descriptions and comparisons. However, due to the complexity and diversity of these signals, an unequivocal application of the terms call and note can be challenging. We therefore provide two coherent concepts that either follow a note-centered approach (defining uninterrupted units of sound as notes, and their entirety as call) or a call-centered approach (defining uninterrupted units as call whenever they are separated by long silent intervals) in terminology. Based on surveys of literature, we show that numerous call traits can be highly variable within and between individuals of one species. Despite idiosyncrasies of species and higher taxa, the duration of calls or notes, pulse rate within notes, and number of pulses per note appear to be more static within individuals and somewhat less affected by temperature. Therefore, these variables might often be preferable as taxonomic characters over call rate or note rate, which are heavily influenced by various factors. Dominant frequency is also comparatively static and only weakly affected by temperature, but depends strongly on body size. As with other taxonomic characters, strong call divergence is typically indicative of species-level differences, whereas call similarities of two populations are no evidence for them being conspecific. Taxonomic conclusions can especially be drawn when the general advertisement call structure of two candidate species is radically different and qualitative call differences are thus observed. On the other hand, quantitative differences in call traits might substantially vary within and among conspecific populations, and require careful evaluation and analysis. We provide guidelines for the taxonomic interpretation of advertisement call differences in sympatric and allopatric situations, and emphasize the need for an integrative use of multiple datasets (bioacoustics, morphology, genetics), particularly for allopatric scenarios. We show that small-sized frogs often emit calls with frequency components in the ultrasound spectrum, although it is unlikely that these high frequencies are of biological relevance for the majority of them, and we illustrate that detection of upper harmonics depends also on recording distance because higher frequencies are attenuated more strongly. Bioacoustics remains a prime approach in integrative taxonomy of anurans if uncertainty due to possible intraspecific variation and technical artifacts is adequately considered and acknowledged.
We describe a new species, Pseudopaludicola canga, from the Serra dos Carajás highlands in Brazilian Amazonian forest. The new species is a member of the Pseudopaludicola pusilla group and is characterized mainly by its large size. The described species may represent another endemic species of the Serra dos Carajás.
Two new species of Pseudopaludicola from midwestern Brazil are described. One of them, distributed in Bolivian and Brazilian areas within the Upper Paraguay and Upper Guaporé river basins, is characterized by the presence of a conspicuous conical tubercle on each heel, by T-shaped terminal phalanges, and so belongs to the formally recognized Pseudopaludicola pusilla group. The advertisement call is composed of a series of 14-720 notes with concatenated pulses-each lasting for 5-25 ms-and mean dominant frequency of 5071 ± 242 Hz. The second species, restricted to the southeastern-most region of the Brazilian state of Mato Grosso, is characterized mainly by a 2n = 18 karyotype, an advertisement call composed of series of 12-287 notes with concatenated pulses and mean dominant frequency of 4167.7 ± 287.5 Hz. A detailed description of the karyotype of this latter species is also provided.
A recently published phylogeny corroborated the monophyly of the genus Pseudopaludicola and revealed several potential undescribed taxa. In this first integrative taxonomic study within the genus Pseudopaludicola, we describe the sister clade to the remaining long-legged species (Pseudopaludicola saltica + Pseudopaludicola murundu), the third recognized species of the monophyletic P. saltica clade, as a new species from northeastern Brazil. The new species is included in the P. saltica species group based on morphological (the presence of long hind limbs) and molecular evidence (mitochondrial genes). It is diagnosed by single, dark, subgular vocal sac with dark longitudinal folds in males, the presence of eleven pairs of chromosomes, and by an advertisement call composed of notes with up to seven non-concatenated pulses separated by regular interpulse intervals. We also describe the karyotype and tadpoles of the new species and compare them with the other long-legged species. Our populations are supported as an undescribed and independently evolving species within the P. saltica clade based on the generalized mixed Yule-coalescent (GMYC) species delimitation method. Although almost morphologically cryptic to P. saltica and P. murundu, this new species is distinguishable by means of acoustical and genetic traits.
We describe the chromosome morphology, C-bands, NORs position, and DAPI/CMA3 staining of five species of Pseudopaludicola (P. boliviana, P. canga, P. falcipes, P. mystacalis, and P. ternetzi) from several populations from Argentina, Brazil, Paraguay, and Uruguay. In addition, the telomeric sequence locations of P. mystacalis and P. canga are evaluated using FISH. We re-analyse the progressive reduction of chromosome numbers recently proposed for the genus by optimisation of character basic chromosome numbers (x) and fundamental chromosome numbers (FN) on current phylogenetic hypotheses. Our evidence supports a progressive reduction of chromosome numbers in Pseudopaludicola, and multiple origins of the karyotype 2n = 20. Additionally, we discuss the interpretation of the current Pseudopaludicola phylogenetic hypothesis and a series of inconsistencies in the chromosome literature for the genus.
Standardization and repeatability is at the heart of all scientific research, yet very little literature exists to standardize morphometric measurements within vertebrate groups. This is particularly true for amphibians. Our study attempts to rectify this lack of methodological standardization for the measurement of morphological characters in anurans through an extensive literature survey of 136 species descriptions representing 45 currently recognized families of frogs. The survey revealed 42 morphological measurements represented in five percent or more of the literature reviewed. All measurements are listed by most commonly used name, acronym, and most precise definition, and we provide statistics summarizing the variation in measurement use and description from the surveyed literature. Of these 42 measurements, a subset of 16 were found in the top 75% of all surveyed descriptions and identified as a focal set of recommended measurements in an effort to standardize the morphometric measurements that describe anuran species diversity. Illustrations of these 16 measurements are provided as a visual reference for standardizing their measurement.
Las relaciones filogenéticas entre las especies del género Pseudopaludicola son analizadas en base a caracteres externos y osteológicos. Se estudiaron once especies de Physalaemus las que fueron empleadas como grupo externo en análisis donde se trataron ambos géneros en conjunto. Se hicieron corridas enraizando alternativamente en las distintas especies de Physalaemus y sumando además a Leplodactylus en la matriz verificándose la monofilia del género Pseudopaludicola. Como resultado de este análisis se obtuvieron tres topologias de relaciones entre las especies del género, siendo el consenso estricto: (ternelsi mineira (sallica falcipes)(myslacalis (pusilla (boliviana (ceralophyes /lanera))). En este trabajo se apoya la monofilia del grupo pusilla proponiéndose una hipótesis distinta de relaciones entre sus integrantes a la propuesta por Lynch (1989). Phylogenetics relationships between ftogs of the leptodactylid genus Pseudopaludicola are analyzed using both osteological and external characters. Some species of Physalaemus (eleven) are included in the analysis with Pseudopaludicola. Rooting with Leptodactylus or with any species of Physalaemus the monophyly ofthe genus is maintained. Three different trees for Pseudopaludicola were obtained, their strict consensus is: (temetzi mineira (saltica falcipes) (mystacalis (pusilla (boliviana (ceratophyes /lanera))). According to Lynch (1989) the pusilla group is monophyletic, but the internal arrangement among its species is different in this analysis.
Herein, we conduct a comparative study based mainly on the acoustic variation of calls of four Pseudopaludicola species that share a trilled advertisement call pattern, as well as revisit their diagnoses, and update their distribution. Acoustic variation was helpful for species delimitation: two temporal traits distinguished P. facureae from P. hyleaustralis, and both species from P. canga and P. parnaiba, whereas the latter two species could not be distinguished from each other. Therefore, additional evidence is required to establish the taxonomic status of P. parnaiba in relation to P. canga, since neither morphology, body size, color patterns, or bioacoustics supported the separation between these species. This frog genus has a conservative morphology and a great variety of calling patterns. Therefore, the association between specimens and calling patterns is crucial for more reliable species identifications and understanding its distributional patterns and implications for conservation.
In this paper, we provide an updated diagnosis for Pseudopaludicola giarettai based on the morphometric and acoustic variation observed with the assessment of new populations, plus an expansion of its distribution range. Our results support that all acoustic variation observed might be attributed to intraspecific variation. The variation in body size and dorsal stripe patterns observed for Pseudopaludicola giarettai reinforces that the distinctive whistling ad‑ vertisement call pattern is the most reliable evidence line to diagnose it from its congeners, whereas morphological (robust body, glandular dorsum) and morphometric (body size) features vary considerably within and among populations so that they should no longer be employed as diagnostic features of Pseudopaludicola giarettai.
Due to minute size, overall morphological similarities, scarcity of diagnostic characters after preservation, and usual sympatric or even syntopic occurrence of two or more species of Pseudopaludicola, the taxonomy of the genus is not yet a matter of consensus. Three species in the genus Pseudopaludicola Miranda-Ribeiro, 1926 were described by Cope in 1887, based on material obtained at Chapada dos Guimarães, mid-western state of Mato Grosso, Brazil. One of these species, Pseudopaludicola ameghini, was subsequently synonymized to P. mystacalis. In this paper we present morphological and bioacoustic evidences supporting a full specific status for the three sympatric species of Pseudopaludicola described from Chapada dos Guimarães, including Pseudopaludicola ameghini Cope, 1887.
The main objectives of this paper were to update the distribution range of Pseudopaludicola boliviana in Argentina, to determine its diet composition and the feeding patterns, to analyze some reproductive variables as mature ova count and diameter in relation to female snoutvent length, to describe the advertisement call for Argentinean populations, and to identify and to localize its helminth parasites. Eleven prey types were identified; dipterans were more important both in number (23.53%) and in volume (41.30%); other important preys were collembolans, arachnids and coleopterans. The trophic niche width was 7.15 and the standardized trophic niche value was 0.61. Ovarian complement (number of mature ova for female) ranged from 50 to 319 (mean 175.3 ± 86.12), while ovum diameter ranged from 0.2 to 0.4 mm (mean 0.27 ± 0.062). The nuptial call is composed by five notes. The dominant frequency ranged from 3.488 to 5.927 kHz; emphasized frequency fluctuated between 4.942 and 5.224 kHz. A total of 10 helminth species (larvae and adults) were found in 54 (96%) infected frogs. Helminths were represented by Trematoda (7 species), Cestoda (1), Nematoda (1), and Acanthocephala (1).
We review Seewave, new software for analysing and synthesizing sounds. Seewave is free and works on a wide variety of operating systems as an extension of the R operating environment. Its current 67 functions allow the user to achieve time, amplitude and frequency analyses, to estimate quantitative differences between sounds, and to generate new sounds for playback experiments. Thanks to its implementation in the R environment, Seewave is fully modular. All functions can be combined for complex data acquisition and graphical output, they can be part of important scripts for batch processing and they can be modified ad libitum. New functions can also be written, making Seewave a truly open-source tool.
A new species of Pseudopaludicola is described from the Cerrado of southeastern Brazil. The new taxon is diagnosed from the P. pusilla species group by the absence of either T-shaped terminal phalanges or toe tips expanded, and promptly distinguished from all (13) recognized taxa currently assigned to Pseudopaludicola by possessing isolated (instead of reg-ular call series), long (117–187 ms) and non-pulsed advertisement calls.
A new species of Pseudopaludicola is described from human-altered areas originally covered by Semideciduous Forest in northwestern state of São Paulo, southeastern Brazil. Morphologically, the new species differs from four species belonging to the P. pusilla group by the absence of either T-shaped terminal phalanges or toe tips expanded, and from all other congeners except P. canga and P. facureae by possessing an areolate vocal sac, with dark reticulation. The higher duration (300-700 ms) of each single, pulsed note (9-36 nonconcatenated pulses) that compose the call in the new species distinguishes it from all other 14 species of Pseudopaludicola with calls already described (10-290 ms). Absence of harmonics also differ the advertisement call of the new species from the call of its sister species P. facureae, even though these two species presented unexpected low genetic distances. Although we could not identify any single morphological character distinguishing the new species from P. facureae, a PCA and DFA performed using 12 morphometric variables evidenced significant size differences between these two species.
Species distributed across vast continental areas and across major biomes provide unique model systems for studies of biotic diversification, yet also constitute daunting financial, logistic and political challenges for data collection across such regions. The tree frog Dendropsophus minutus (Anura: Hylidae) is a nominal species, continentally distributed in South America, that may represent a complex of multiple species, each with a more limited distribution. To understand the spatial pattern of molecular diversity throughout the range of this species complex, we obtained DNA sequence data from two mitochondrial genes, cytochrome oxidase I (COI) and the 16S rhibosomal gene (16S) for 407 samples of D. minutus and closely related species distributed across eleven countries, effectively comprising the entire range of the group. We performed phylogenetic and spatially explicit phylogeographic analyses to assess the genetic structure of lineages and infer ancestral areas. We found 43 statistically supported, deep mitochondrial lineages, several of which may represent currently unrecognized distinct species. One major clade, containing 25 divergent lineages, includes samples from the type locality of D. minutus. We defined that clade as the D. minutus complex. The remaining lineages together with the D. minutus complex constitute the D. minutus species group. Historical analyses support an Amazonian origin for the D. minutus species group with a subsequent dispersal to eastern Brazil where the D. minutus complex originated. According to our dataset, a total of eight mtDNA lineages have ranges .100,000 km2. One of them occupies an area of almost one million km2 encompassing multiple biomes. Our results, at a spatial scale and resolution unprecedented for a Neotropical vertebrate, confirm that widespread amphibian species occur in lowland South America, yet at the same time a large proportion of cryptic diversity still remains to be discovered.
A new species of Pseudopaludicola is described from the state of Mato Grosso, western Brazil. The new species inhabits the transition zone between Brazilian Cerrado and Amazon rainforest in northern Mato Grosso, and is characterized by its medium size (snout-vent length 12–17 mm), lack of T-shaped terminal phalanges, toe tips not expanded laterally, presence of two antebrachial tubercles, and smooth upper eyelids. The advertisement call of the new species consists of a series composed of 11–74 non-pulsed notes. Mean dominant frequency is 3938 Hz. Each note presents a slight ascendant frequency modulation in its first half, and another ascendant modulation in its last half. We also present new data on the distribution and conservation status of Pseudopaludicola canga.
Here, we present a molecular phylogenetic analysis of the Neotropical genus Pseudopaludicola focusing on species relationships including 11 of the 17 known species of Pseudopaludicola; several samples of Pseudopaludicola are not assigned to any species; and 34 terminal species as an outgroup. The study was based on the analysis of approximately 2.3 kb of the sequence of the mitochondrial 12S rRNA, tRNAval and 16S rRNA genes through maximum parsimony and Bayesian phylogenetic reconstruction approaches. Our results showed that Pseudopaludicola is a well‐supported monophyletic group organized into four major clades and confirmed that the assemblage of species that lack T‐shaped terminal phalanges is paraphyletic with respect to the P. pusilla Group. Chromosomal data mapped on the cladogram showed a direct correlation among the four clades and observed chromosome numbers (2n = 22, 20, 18 and 16) with a progressive reduction in the chromosome number. Overall, our findings suggest that some taxonomic changes are necessary and reinforce the need for a revision of the genus Pseudopaludicola.
For most frogs, advertisement calls are essential for reproductive success, conveying information on species identity, male quality, sexual state and location. While the evolutionary divergence of call characters has been examined in a number of species, the relative impacts of genetic drift or natural and sexual selection remain unclear. Insights into the evolutionary trajectory of vocal signals can be gained by examining how advertisement calls vary in a phylogenetic context. Evolution by genetic drift would be supported if more closely related species express more similar songs. Conversely, a poor correlation between evolutionary history and song expression would suggest evolution shaped by natural or sexual selection. Here, we measure seven song characters in 20 described and two undescribed species of African clawed frogs (genera Xenopus and Silurana) and four populations of X. laevis. We identify three call types - click, burst and trill - that can be distinguished by click number, call rate and intensity modulation. A fourth type is biphasic, consisting of two of the above. Call types vary in complexity from the simplest, a click, to the most complex, a biphasic call. Maximum parsimony analysis of variation in call type suggests that the ancestral type was of intermediate complexity. Each call type evolved independently more than once and call type is typically not shared by closely related species. These results indicate that call type is homoplasious and has low phylogenetic signal. We conclude that the evolution of call type is not due to genetic drift, but is under selective pressure.
We surveyed the herpetofauna from the Complex of Planalto da Ibiapaba (CPI), CE, Brazil, during twoyears, using five sampling methods and information available in the literature. The amphibians are represented by 38 species distributed into nine families. The reptiles found summed 84 species, distributed into 25 families. Most amphibians collected exhibited wide occurrence along CPI, where we recorded 24 species (63.2%), which occurred at least in 60% of the sampled environments. Reptiles showed a different pattern, since 52 species (62.6%) had a restricted distribution (up to two environments). Sixteen species out of 25 considered as rare in CPI are restricted to relict moist forests. We also applied a rarity-vulnerability index to determine the most susceptible species. Pristimantis sp., Adelophryne baturitensis Hoogmoed, Borges, and Cascon, 1994, Pseudopaludicola sp. (aff. saltica), Scinax fuscomarginatus (A. Lutz, 1925), and Odontophrynus carvalhoi Savage & Cei, 1965 were the most vulnerable amphibians in CPI. Reptiles showed a more diverse range in the scale of rarity with 40species considered vulnerable. Among the vulnerable reptiles Leposoma baturitensis Rodrigues & Borges, 1997, Bothrops sp. (gr. atrox), Atractus ronnie Passos, Fernandes & Borges-Nojosa, 2007, Apostolepis sp. (gr. pimy), and Mesoclemmys perplexa Bour & Zaher, 2005 were the rarest species found in the whole complex of Ibiapaba mountain range. Results indicate that about 70% of the species found in Ceará are present in this complex. Also, CPI is the area of the Caatinga biome with the highest species richness, including rare and threatened species.
A new species of Pseudopaludicola is described from the Cerrado of southeastern Brazil. Pseudopaludicola facureae sp. nov. is diagnosed from the P. pusilla species group by the absence of either T-shaped terminal phalanges or toe tips expanded, and distinguished from almost all recognized taxa currently assigned to Pseudopaludicola (except P. canga, P. giarettai, and P. hyleaustralis) by possessing a non-pulsed advertisement call. However, the advertisement call of the new species consists of the emission of well-defined call series, whereas the advertisement call of P. giarettai is long (117-187 ms) and with an isolated emission pattern; respecting to P. canga, the new species emits very long notes series (up to 53 notes/advertisement call), compared to the short call series of P. canga (up to 9 notes/advertisement call); considering P. hyleaustralis, the new species has a shorter note duration (15-35 ms), higher note rate per minute (480-1860), and higher dominant frequency (4076-5108).
We describe a new species of Pseudopaludicola endemic to the Caatinga ecoregion of northeastern Brazil. The new species is characterized morphologically by small size, lack of T-shape terminal phalanges, smooth upper eyelids, presence of abdominal and vocal sac folds, light cream-colored vocal sac, and short hind limbs with tibia–tarsal articulation reaching the eye. The tadpole has a globular body shape, low tail fins, and a ventral oral disc bordered by a single row of marginal papillae with a wide anterior gap and two ventrolateral gaps; oral formula: 2(2)/2(1). The advertisement call consists of a well-defined sequence of notes comprising three nonconcatenated pulses, each with long interpulse intervals (111 6 21 ms) and average note duration of 238 6 31 ms. The mean dominant frequency is 5636 6 300 Hz, and increases from the first to the last pulse in each note. The advertisement call easily distinguishes the new species from all other congeners for which calls are known.
Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community.
I present some of the most notable new features and extensions of RAxML, such as, a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX, and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date, 50 page user manual covering all new RAxML options is available.
The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML.
Alexandros.Stamatakis@h-its.org.
Pseudopaludicola canga was described by Giaretta & Kokubum (2003) based on 74 individuals previously assigned to P. mystacalis by Lobo (1995). In the diagnosis of P. canga, the original authors assigned the presence of terminal T-shaped phalanges as a character state for this taxon. However, the osteology of P. cangais not described and the presence of toe tips not expanded laterally is a characteristic share with all members of Pseudopaludicola unassigned to any group. In this work is describe for first time the osteology of P. canga, re-examining the external morphology providing a new diagnosis and establishing the taxonomic position of P. canga in the framework of phylogenetic hypothesis proposed by Lobo
(1995). Additionally, is compared the toe tip digit IV, between P. falcipes and all the species included in the P. pusilla group and updated the type locality of P. canga. The osteology reveals that P. canga has the toe tips not T-shaped as mentioned by the original authors and this characteristic has important consequences for the diagnosis of the species. Additionally, the erroneous inclusion of P. canga in the P. pusilla group is confirmed by the phylogenetic analysis.
The CIPRES Science Gateway (CSG) provides researchers and educators with browser-based access to community codes for inference of phylogenetic relationships from DNA and protein sequence data. The CSG allows users to deploy jobs on the high-performance computers of the TeraGrid without requiring detailed knowledge of their complexities. Use of the CSG has grown rapidly; through March 2011 it had more than 2,200 users and enabled more than 180 peer-reviewed publications. The rapid growth in resource consumption was accommodated by deploying codes on Trestles, a new TeraGrid computer. Tools and policies were developed to insure efficient and effective resource use. This paper describes progress in managing the growth of this public cyberinfrastructure resource and reviews the domain science that it has enabled.
Based on field observations and pitfall sampling, we determined the species richness, relative abundance, and reproductive habitat of terrestrial frogs in three municipalities in the Triângulo Mineiro region, south Cerrado biome, in southeastern Brazil. We found thirty-two species of terrestrial frogs, belonging to the families Brachycephalidae, Bufonidae, Cycloramphidae, Dendrobatidae, Leiuperidae, Leptodactylidae and Microhylidae. Most of the species were found in open areas and reproduced in human-generated environments, such as artificial lakes (10 species) and ponds (14 species). Dominance was high, with Physalaemus cuvieri Fitzinger, 1826 (Leiuperidae) representing 48% of sampled frogs. A larger number of individuals was captured in the wet season, when most of the species were reproducing. Compared to other areas of Cerrado biome, the Triângulo Mineiro sites presented a larger number of species, which may be attributed to the larger sampled area and greater sampling effort, lower altitude and presence of human generated habitats. The richness of terrestrial frogs was also larger than that in some forested localities in southeastern Brazil, indicating that the number of species cannot be explained only by precipitation and type of vegetation cover. The greater abundance of individuals during the wet season may be related to a greater movement of adults to breeding sites and to juvenile recruitment/dispersion. The heterogeneity of environments in the Cerrado biome, including its several isolated highlands, contributes to its high (local and regional) diversity of frogs.
The number of described species of Pseudopaludicola has increased at unprecedented rates over the past two decades. This increase was mainly driven by the sampling effort in regions historically neglected and the use of evidence from bioacoustic, genetic, and morphological datasets combined. Here, we describe a new species of Pseudopaludicola from a transitional zone between Amazonia and Cerrado in western Tocantins State as revealed through morphological, molecular, and bioacoustic analysis. Pseudopaludicola javae sp. nov. is distinguished from its congeners by its small size; knobbed terminal phalanges; smooth upper eyelids and heel; relatively short hind limbs; smooth, whitish, and subgular inflated vocal sac with few melanophores around the jaw; and advertisement call composed of an irregular series of multipulsed notes with 10–17 nonconcatenated pulses separated by intervals of 3–55 ms, emitted at a rate of 27–51 pulses/sec. The new species occurs in four Tocantins municipalities, all in the Araguaia–Tocantins interfluve. We also provide the first records of Pseudopaludicola jazmynmcdonaldae outside the type locality (Caseara Municipality, Tocantins State), extending its distribution nearly 245 km southward from Caseara. Pseudopaludicola javae sp. nov. is the second species of Pseudopaludicola described recently from western Tocantins.
A large proportion of the biodiversity of Amazonia, one of the most diverse rainforest areas in the world, is yet to be formally described. One such case is the Neotropical frog genus Adenomera. We here evaluate the species richness and historical biogeography of the Adenomera heyeri clade by integrating molecular phylogenetic and species delimitation analyses with morphological and acoustic data. Our results uncovered ten new candidate species with interfluve-associated distributions across Amazonia. In this study, six of these are formally named and described. The new species partly correspond to previously identified candidate lineages ‘sp. F’ and ‘sp. G’ and also to previously unreported lineages. Because of their rarity and unequal sampling effort of the A. heyeri clade across Amazonia, conservation assessments for the six newly described species are still premature. Regarding the biogeography of the A. heyeri clade, our data support a northern Amazonian origin with two independent dispersals into the South American Dry Diagonal. Although riverine barriers have a relevant role as environmental filters by isolating lineages in interfluves, dispersal rather than vicariance must have played a central role in the diversification of this frog clade.
We describe here a new species of Pseudopaludicola (P. murundu sp. nov.) that is found in the central portion of the state of São Paulo, Brazil. This new species is related to P. saltica, from which it distinguishes by the presence of a single, dark, and subgular vocal sac with dark longitudinal folds in males, immaculate to light brown nuptial pads in males that cover the external part of the finger I, from the wrist to the second phalanx, and 11 pairs of chromosomes without heteromorphic sex chromosomes. From all other species of the genus it distinguishes by presenting very long hindlimbs, with tibio-tarsal articulation reaching beyond the end of the snout, and absence of T-shaped terminal phalanges. Tadpoles, advertisement call, and the karyotype are described as well.
We describe here a new species of Pseudopaludicola (P. murundu sp. nov.) that is found in the central portion of the state of São Paulo, Brazil. This new species is related to P. saltica, from which it distinguishes by the presence of a single, dark, and subgular vocal sac with dark longitudinal folds in males, immaculate to light brown nuptial pads in males that cover the external part of the finger I, from the wrist to the second phalanx, and 11 pairs of chromosomes without heteromorphic sex chromosomes. From all other species of the genus it distinguishes by presenting very long hindlimbs, with tibio-tarsal articulation reaching beyond the end of the snout, and absence of T-shaped terminal phalanges. Tadpoles, advertisement call, and the karyotype are described as well.
The monophyletic genus Pseudopaludicola (synapomorphy: hypertrophied antebrachial tubercle) occurs widely in northern South America where it is represented by the monophyletic Pseudopaludicola pusilla group (synapomorphy: T-shaped terminal phalanges on toes). The P. pusilla group consists of four species: P. boliviana Parker, distributed in an Amazonian arc from Surinam to Colombia to Bolivia and Paraguay; P. ceratophyes Rivero and Serna, known only from Leticia, Colombia; P. pusilla (Ruthven), distributed in northern Colombia (and south into the valley of the Rio Magdalena) and northwestern Venezuela (trans-Andean); and a new species, described from the Ilanos of northeastern Colombia and adjacent Venezuela.
New primers (N 24) for the amplification and se-quencing of the complete or near complete 12S ribo-somal DNA, about 1000 bp of the control region, 390 bp of cytochrome oxidase I, and the near complete cyto-chrome b are described. The 12S ribosomal DNA primers successfully amplify DNA in tetrapods; other primers successfully amplify DNA in bufonoids and other anurans. An overview of published literature and sequence data banks identified 170 mitochondrial and 96 nuclear DNA primers that have been used or are highly likely to be useful in amphibians. Primer sequences, their locations within genes, and sequence location and identity in Xenopus and human and/or mouse are presented for each primer. The utility of each primer was estimated by identifying the smallest, yet most inclusive, taxonomic category within which each primer has been successful. Primers from all published sources are mapped together. We hope that these new primers, as well as the list of primers that have been useful in amphibians, will encourage further systematic and population genetic studies of amphibians.