Ruber Clade Research Articles

Insight into the phylogeny and metabolic divergence of Monascus species (M. pilosus, M. ruber, and M. purpureus) at the genome level.

Species of the genus Monascus are economically important and widely used in the production of food colorants and monacolin K. However, they have also been known to produce the mycotoxin citrinin. Currently, taxonomic knowledge of this species at the genome level is insufficient. This study presents genomic similarity analyses through the analysis of the average nucleic acid identity of the genomic sequence and the whole genome alignment. Subsequently, the study constructed a pangenome of Monascus by reannotating all the genomes and identifying a total of 9,539 orthologous gene families. Two phylogenetic trees were constructed based on 4,589 single copy orthologous protein sequences and all the 5,565 orthologous proteins, respectively. In addition, carbohydrate active enzymes, secretome, allergic proteins, as well as secondary metabolite gene clusters were compared among the included 15 Monascus strains. The results clearly revealed a high homology between M. pilosus and M. ruber, and their distant relationship with M. purpureus. Accordingly, all the included 15 Monascus strains should be classified into two distinctly evolutionary clades, namely the M. purpureus clade and the M. pilosus-M. ruber clade. Moreover, gene ontology enrichment showed that the M. pilosus-M. ruber clade had more orthologous genes involved with environmental adaptation than the M. purpureus clade. Compared to Aspergillus oryzae, all the Monascus species had a substantial gene loss of carbohydrate active enzymes. Potential allergenic and fungal virulence factor proteins were also found in the secretome of Monascus. Furthermore, this study identified the pigment synthesis gene clusters present in all included genomes, but with multiple nonessential genes inserted in the gene cluster of M. pilosus and M. ruber compared to M. purpureus. The citrinin gene cluster was found to be intact and highly conserved only among M. purpureus genomes. The monacolin K gene cluster was found only in the genomes of M. pilosus and M. ruber, but the sequence was more conserved in M. ruber. This study provides a paradigm for phylogenetic analysis of the genus Monascus, and it is believed that this report will lead to a better understanding of these food microorganisms in terms of classification, metabolic differentiation, and safety.

On the occurrence of Scinax kennedyi (Pyburn, 1973) (Anura, Hylidae) in the state of Roraima, northern Brazil

Scinax comprises 129 species of treefrogs divided between the S. ruber and the S. catharinae clades. The S. rostratus group belongs to the S. ruber clade, and comprises ten species characterized by having a dark interorbital triangular mark, tubercle on the heel and by vocalizing in a head-down position. Within this group, S. kennedyi and S. rostratus are similar in that they are the only species that do not possess a row of tubercles on the lower jaw. In spite of their morphological similarity, they can be distinguished from each other by male size and advertisement call traits. Scinax kennedyi was described from eastern Colombia, and occurs from central Colombia to western Venezuela, whereas S. rostratus was described from northern Venezuela, and is thought to occur from Panama to eastern Venezuela, and in the Brazilian state of Pará. A recent study reported a population identified as S. rostratus from the state of Roraima, in northern Brazil. However, this population presented substantial differences in male size and advertisement call in comparison to the described for this species, and apparently it best fits the diagnosis of S. kennedyi instead. In view of this, the present study aimed to clarify the identity of this Brazilian population through a reassessment of its specimens and call recordings, together with the examination of data of S. kennedyi from its type locality, and of S. rostratus from northern Venezuela. Acoustic and morphological analyses revealed that specimens from northern Brazil were indeed misidentified as S. rostratus, and hence they were herein reassigned to S. kennedyi. The study therefore demonstrates the occurrence of S. kennedyi in Brazil, extending its distribution ca. 1,120 km east by south from its type locality, and ca. 844 km east-southeast from its easternmost previous record. With this reassessment, a clearer acoustic diagnosis between S. kennedyi and S. rostratus was provided, as well as further data on fine-scale temporal traits of their calls.

A new species of Scinax Wagler (Hylidae: Scinaxini) from the tropical forests of Northeastern Brazil.

We describe a new species of the Scinax ruber clade from Northeastern Brazil that occurs in widely separated geographic areas in the Atlantic Forest of southern Bahia state and the Highland Humid Forest of Serra de Baturité, northeast Ceará state. Scinax tropicalia sp. nov. (holotype coordinates: -14.795694°, -39.172645°) is diagnosed from all 75 currently recognize species of the S. ruber clade by bioacoustical and morphological adult traits, such as duration (0.11-0.31 s) and dominant frequency (1.59-1.85 kHz) of the advertisement call, snout shape rounded, nearly rounded, or semi-circular in dorsal view and rounded to slightly protruding in profile, bilobate vocal sac, absence of pectoral glands and spicule-shaped papillary epidermal projections on nuptial pads, and color pattern on the dorsum of body and hidden surfaces of hindlimbs.

A neotype for Hyla x-signata Spix, 1824 (Amphibia, Anura, Hylidae)

The uncertain identity of Hyla x-signata Spix, 1824 has been a pervasive problem in the taxonomy of the genus Scinax. A species supposedly distributed from northeastern Brazil northwards to Colombia and Venezuela, described in a few lines without much information and with an accompanying figure, and its type specimen lost during World War II, combined to produce a curious situation. Twenty-one of the 39 species of the S. ruber Clade described in the last 50 years were considered to require a diagnosis from S. x-signatus by their authors. In most cases these had no other alternative than to gather information about this species from indirect sources, frequently pointing out the problems associated with its uncertain identity. In this paper, we review the taxonomic history of Hyla x-signata, designate a neotype, provide a redescription including advertisement call and sequence data, and diagnose it from all other species of the S. ruber Clade.

The tadpole of Scinax camposseabrai (Bokermann) (Amphibia, Anura, Hylidae).

The treefrog Scinax camposseabrai (Bokermann) is endemic to the Brazilian semiarid region and known from the municipalities of Maracás, Igaporã and Curaçá, in the state of Bahia, and from the municipality of Matias Cardoso, northern Minas Gerais state, Brazil (Frost 2019). It was removed from the synonymy of Scinax x-signatus (Spix), recognized as a valid species, and placed in the S. ruber clade (sensu Faivovich et al. 2005) by Caramaschi Cardoso (2006). Taxonomic changes proposed by Duellman et al. (2016) for the genus Scinax were discussed by Lourenço et al. (2016) and Faivovich et al. (2018), and we follow here their suggestion to consider Ololygon and Julianus (erected for the S. uruguayus group) as synonyms of Scinax. This large genus Scinax currently would include 123 species (Frost 2019), many of which have had their larval morphology formerly described. Here, we describe the external morphology of the previously unknown tadpoles of S. camposseabrai.

Comparative analysis based on replication banding reveals the mechanism responsible for the difference in the karyotype constitution of treefrogs Ololygon and Scinax (Arboranae, Hylidae, Scinaxinae).

According to the recent taxonomic and phylogenetic revision of the family Hylidae, species of the former Scinax catharinae (Boulenger, 1888) clade were included in the resurrected genus Ololygon Fitzinger, 1843, while species of the Scinax ruber (Laurenti, 1768) clade were mostly included in the genus Scinax Wagler, 1830, and two were allocated to the newly created genus Julianus Duellman et al., 2016. Although all the species of the former Scinax genus shared a diploid number of 2n = 24 and the same fundamental number of chromosome arms of FN = 48, two karyotypic constitutions were unequivocally recognized, related mainly to the distinct size and morphology of the first two chromosome pairs. Some possible mechanisms for these differences had been suggested, but without any experimental evidence. In this paper, a comparison was carried out based on replication chromosome banding, obtained after DNA incorporation of 5-bromodeoxiuridine in chromosomes of Ololygon and Scinax. The obtained results revealed that the loss of repetitive segments in chromosome pairs 1 and 2 was the mechanism responsible for karyotype difference. The distinct localization of the nucleolus organizer regions in the species of both genera also differentiates the two karyotypic constitutions.

Advertisement call of Scinax camposseabrai (Bokermann, 1968)(Anura: Hylidae), with comments on the call of three species of the Scinax ruber clade.

Scinax camposseabrai was allocated into the Scinax ruber clade by Caramaschi & Cardoso (2006) by overall similarities as snout not pointed, breeding in open areas, and an advertisement calls with multipulsed notes. This assumption about the call was based solely on an onomatopoeia provided by Bokermann (1968). Herein we provide a formal description of the advertisement call of S. camposseabrai and compare it with described calls of other S. ruber clade species. Additionally, we provide descriptions of the advertisement calls of three sympatric species of the S. ruber clade: S. eurydice (Bokermann), S. pachycrus (Miranda-Ribeiro) and S. cf. x-signatus.

A new species of Scinax Wagler (Anura: Hylidae) from Mato Grosso, Brazil.

A new species of the Scinax ruber Clade is described from Municipality of Barra do Garças, State of Mato Grosso, Brazil. It is diagnosed by its size (SVL 29.4-35.4 mm in males); dorsum with a background that varies from light and dark gray to dark brown, with round and irregular dark blotches; hidden surfaces of thigh and shank light or dark brown, with lighter, large and irregular blotches (yellow in life); and nuptial pad that covers the medial margin of Metacarpal I, and obscures the posterior portion and the outer margin of the inner metacarpal tubercle. It is most similar with Scinax rupestris, from which it differs by having larger adult males; less developed nuptial pad; and hidden surfaces of thigh and light or dark brown, with lighter, large and irregular blotches (yellow in life). The new species occurs near the headwaters of permanent or temporary streams, where males call from vegetation or rocks at the margins of small streams.

The complex vocalization of Scinax cardosoi (Anura: Hylidae), with comments on advertisement calls in the S. ruber Clade

A vocalização complexa de Scinax cardosoi (Anura: Hylidae), com comentários sobre cantos de anúncio no Clado de S. ruber. A vocalização complexa de Scinax cardosoi de uma população do estado de Minas Gerais no sudeste brasileiro é descrita e comparada com os dados acústicos disponíveis para outras espécies do Clado de S. ruber. Três tipos diferentes de cantos pulsados e agudos foram identificados, denominados cantos “curto,” “longo” e “trinado”. Cantos curtos (16–66 ms) lembram chios e consistem em sinais pulsados (8–28 pulsos/canto) com modulações de amplitude regulares ao longo de sua duração e pico de amplitude aproximadamente na metade de sua duração. Cantos longos (268–518 ms) lembram risadinhas e têm menor amplitude quando comparados a cantos curtos; tipicamente, consistem em séries de notas pulsadas (1–6 notas/canto). Cantos trinados lembram zunidos de insetos e apresentam a menor amplitude dentre os três tipos de cantos; consistem em séries muito longas (1,1–3,0 s) de notas pulsadas (9–25 notas/canto). Dados acústicos são taxonomicamente informativos no Clado de S. ruber, fornecendo evidências fenotípicas à diagnose de S. cardosoi além das características propostas em sua descrição original. O repertório vocal de S. cardosoi assemelha-se mais aos repertórios vocais complexos (vários tipos de cantos emitidos em combinações variadas) de espécies do Clado de S. catharinae do que ao de algumas espécies do Clado de S. ruber, os quais tendem a ter uma estrutura do canto mais simples (um tipo único de nota multipulsionada).

Scinax cruentommus (Anura: Hylidae) in the upper Rio Negro drainage, Amazonas state, Brazil, with the redescription of its advertisement call

Scinax cruentommus (Anura: Hylidae) na bacia do alto Rio Negro, Amazonas, Brasil, com a redescrição do seu canto de anúncio. Nós apresentamos o primeiro registro de Scinax cruentommus no alto Rio Negro, Amazonas, Brasil. Nós também redescrevemos o seu canto de anúncio e fazemos comparações acústicas com os dados disponíveis para outras espécies do Clado de Scinax ruber da bacia amazônica. Com a obtenção de novos dados para S. cruentommus, os parâmetros acústicos suplementaram a sua diagnose congenérica em relação às outras espécies amazônicas do Clado de S. ruber além das características propostas em sua descrição original.

A New Species of the Scinax ruber Clade (Anura, Hylidae) from the Espinhaço Range, Northeastern Brazil

Abstract: A new species belonging to the Scinax ruber clade, morphologically similar to S. cabralensis and S. rupestris, is described from the Municipality of Miguel Calmon, State of Bahia, northeastern Brazil. This locality belongs to the northern portion of the Espinhaco Range known as Chapada Diamantina, a semiarid region in central Bahia State. The new species can be distinguished from all congeners of the S. ruber clade by a combination of adult (size, morphology, color pattern, and advertisement call) as well as larval (external morphology, and oral cavity) characteristics. The description of this frog adds another species, and the first of the S. ruber clade, to those that are endemic to Chapada Diamantina.

Fossil and genetic evidence for the polyphyletic nature of the planktonic foraminifera "Globigerinoides", and description of the new genus Trilobatus.

Planktonic foraminifera are one of the most abundant and diverse protists in the oceans. Their utility as paleo proxies requires rigorous taxonomy and comparison with living and genetically related counterparts. We merge genetic and fossil evidence of “Globigerinoides”, characterized by supplementary apertures on spiral side, in a new approach to trace their “total evidence phylogeny” since their first appearance in the latest Paleogene. Combined fossil and molecular genetic data indicate that this genus, as traditionally understood, is polyphyletic. Both datasets indicate the existence of two distinct lineages that evolved independently. One group includes “Globigerinoides” trilobus and its descendants, the extant “Globigerinoides” sacculifer, Orbulina universa and Sphaeroidinella dehiscens. The second group includes the Globigerinoides ruber clade with the extant G. conglobatus and G. elongatus and ancestors. In molecular phylogenies, the trilobus group is not the sister taxon of the ruber group. The ruber group clusters consistently together with the modern Globoturborotalita rubescens as a sister taxon. The re-analysis of the fossil record indicates that the first “Globigerinoides” in the late Oligocene are ancestral to the trilobus group, whereas the ruber group first appeared at the base of the Miocene with representatives distinct from the trilobus group. Therefore, polyphyly of the genus "Globigerinoides" as currently defined can only be avoided either by broadening the genus concept to include G. rubescens and a large number of fossil species without supplementary apertures, or if the trilobus group is assigned to a separate genus. Since the former is not feasible due to the lack of a clear diagnosis for such a broad genus, we erect a new genus Trilobatus for the trilobus group (type species Globigerina triloba Reuss) and amend Globoturborotalita and Globigerinoides to clarify morphology and wall textures of these genera. In the new concept, Trilobatus n. gen. is paraphyletic and gave rise to the Praeorbulina / Orbulina and Sphaeroidinellopsis / Sphaeroidinella lineages.

Cytogenetic analysis of Scinaxauratus and Scinaxeurydice (Anura, Hylidae) with emphasis on cytotaxonomy.

Scinax Wagler, 1830 is a species-rich genus of amphibians with relatively few detailed chromosomal reports. In this work, cytogenetic analyses of Scinax auratus (Wied-Neuwied, 1821) and Scinax eurydice (Bokermann, 1968) were carried out based on conventional (Giemsa staining, Ag-NOR and C-banding) and cytomolecular (base-specific fluorochrome staining and fluorescence in situ hybridization – FISH of ribosomal probes) techniques. Both species shared the same karyotype, location of active nucleolar organizer regions on pair 11 and GC-rich heterochromatin, as reported for most species in Scinax ruber clade. Interpopulation chromosomal variation was observed in Scinax eurydice, indicating the occurrence of cryptic species. The mapping of 18S ribosomal genes by FISH is reported for the first time in both species.

A new species of Rock-Dwelling Scinax Wagler (Anura: Hylidae) from Chapada dos Veadeiros, Central Brazil.

A new species of the Scinax ruber clade is described from Chapada dos Veadeiros region, Central Brazil. The new species is diagnosed by having SVL 21.9-27.7 mm in males and 26.7-31.7 mm in females; snout acuminate in dorsal view and rounded in profile; medium-sized tympanum; vocal sac single, median, subgular, that does not reach the pectoral region; iris iridescent yellow, with some thin, darker reticulations; tadpoles with ventral oral disc; P-3 regular and unmodified as a labial arm; absence of keratinized and colored plates on the sides of the lower jaw-sheath; presence of a keratinized and colored spur on each side behind the lower jaw-sheath; dorsolateral eyes, ventrally invisible; and advertisement call composed of 8-14 notes each with 4-18 pulses, and duration of 290-420 ms. The new species uses temporary creeks in rock meadows above 1.000 m a.s.l. and males calls from rock outcrops. The dorsal color pattern enables this species to camouflage in this kind of surfaces.

Taxonomic Revision of the Scinax alter Species Complex (Anura: Hylidae)

Scinax alter, a taxon belonging to the S. ruber clade, has been previously suggested to represent a species complex. We analyzed variation among populations of Scinax alter using advertisement calls, dorsal color pattern, and external morphology. We identified three diagnosable groups distributed throughout the Atlantic Forest of eastern Brazil, which differ mainly in the advertisement call, dorsal drawing pattern, snout–vent length, and presence of tubercles on tarsus. Scinax alter was restricted to populations from south of Bahia State to Rio de Janeiro State, and two new species were related to the southern populations: Scinax imbegue, from Parque das Nascentes, Municipality of Blumenau (27°03′S, 49°05′W, 412 m a.s.l.), Santa Catarina State, Brazil, and Scinax tymbamirim, from Córrego Grande (27°35′S, 48°31′W, at sea level), Municipality of Florianópolis, Santa Catarina State, Brazil.

Calls of five species of the Scinax ruber (Anura: Hylidae) clade from Brazil with comments on their taxonomy

Calls of five species of the Scinax ruber (Anura: Hylidae) clade from Brazil with comments on their taxonomy

Calls of five species of the Scinax ruber (Anura: Hylidae) clade from Brazil with comments on their taxonomy

As currently defined, tree frogs of the genus Scinax comprises the most species-rich genus within Hylinae. Although in the last decades there have been an increasing number of taxonomic studies on Scinax, populations of several species still deserve further studies to assess their taxonomic status. The purpose of this paper is to contribute to the taxonomy and zoogeography of some species of Scinax from Brazil assigned to the Scinax ruber clade through the description/redescription of their advertisement calls. The advertisement call of S. duartei from topotypic specimens and the call of S. acuminatus are described here for the first time. The call of S. duartei is in disagreement with descriptions from the literature what suggests that an unnamed species is hidden under this specific name. Redescriptions of the calls of S. crospedospilus, S. eurydice, and S. hayii are also provided and compared with previous studies. In order to better assess the taxonomic status of species with advertisement calls that present more than one emphasized frequency, as in some species of the Scinax ruber clade, we recommend special attention in the descriptions of the spectral components of these calls.

A New Miniature Treefrog of the Scinax ruber Clade from the Cerrado of Central Brazil (Anura: Hylidae)

Abstract We describe a new species of treefrog of the Scinax ruber clade related to Scinax fuscomarginatus from southwest of the state of Goias in central Brazil. The new species is characterized by its small size (snout–vent length of males, 15.9–18.6 mm; females, 18.1–18.7 mm), very slender body, a snout that is strongly acute in lateral view and subelliptical in dorsal view, two lateral broad blackish stripes from the posterior corner of the eye to inguinal region, reduced toe webbing, and advertisement calls that are a single pulsed note with a pulse period of 2–13 ms and a dominant frequency of 2.51–5.95 kHz. Vocalizations of the new species and S. fuscomarginatus, Scinax parkeri, Scinax squalirostris, and Scinax wandae are provided and discussed.

Karyotypic Data on 28 Species of Scinax (Amphibia: Anura: Hylidae): Diversity and Informative Variation

The hylid frog genus Scinax is the most species-rich within Hylinae, with more than 100 recognized species grouped in the S. catharinae and S. ruber clades. The karyotypes of 14 species of the S. catharinae clade and 14 of the S. ruber clade were analyzed, several of them for the first time. All studied species presented 2n = 2x = 24 biarmed chromosomes (FN = 48) and no identifiable sex chromosomes. There are two alternate states associated with the size and morphology of pair 1, corresponding to the S. catharinae clade and to the S. ruber clade. The morphology of pairs 2 and 6 also differentiate the species of both major clades. Species of the S. ruber clade in general have Ag-NORs in pair 11, as is commonly observed among hylines with 2n = 24. The Ag-NORs' position in the long arms of pair 11 is interstitial in S. fuscomarginatus, S. fuscovarius, S. nasicus, S. similis, S. squalirostris, and S. uruguayus, and terminal in S. acuminatus, S. curicica, S. duartei, S. granulatus, S. hayii, and S. perereca. The single exception among species of the S. ruber clade is S. alter, which has terminal Ag-NORs at the long arms of pair 3. Most species of the S. catharinae clade have Ag-NORs in pair 6, representing a putative synapomorphy of this clade, while the Ag-NORs in pair 11 that occur in S. canastrensis are most parsimoniously interpreted as a reversion. C-banding is predominantly centromeric, but in the S. catharinae clade there is a greater amount of heterochromatin than in the S. ruber clade. This study corroborates the occurrence of informative variation, some already considered in a previous cladistic analysis, and reports new characters, outlining the significance of cytogenetic data for the systematics of Scinax.

The Advertisement Call ofScinax similis(Cochran, 1952) (Amphibia, Anura)

ABSTRACT. The advertisement call is responsible for attracting females and helps the calling male to keep the acoustic territory by warning other males of its position. This call is species-specific and, because of this, it is frequently used in studies of taxonomy and phylogeny. In this study, we describe the advertisement call of Scinax similis recorded in Mage, State of Rio de Janeiro, Brazil, and compare it with the call presented by Haddad et al. in audio form. The advertisement call of Scinax similis is short and composed of one multipulsed note with two bands of frequency of similar intensity. The dominant frequency was found in the second band. The difference in the advertisement call of S. similis from the Municipality of Mage and the call presented by Haddad et al. can be interpreted as variation between populations and/or social context consequences. Between Brazilian species of the Scinax ruber clade, the call of S. similis is similar to that of S. auratus and S. juncae.