Systematic review of the frog family Hylidae, with special reference to Hylinae: Phylogenetic analysis and taxonomic revision

Hylidae is a large family of American, Australopapuan, and temperate Eurasian treefrogs of approximately 870 known species, divided among four subfamilies. Although some groups of Hylidae have been addressed phylogenetically, a comprehensive phylogenetic analysis has never been presented. The first goal of this paper is to review the current state of hylid systematics. We focus on the very large subfamily Hylinae (590 species), evaluate the monophyly of named taxa, and examine the evidential basis of the existing taxonomy. The second objective is to perform a phylogenetic analysis using mostly DNA sequence data in order to (1) test the monophyly of the Hylidae; (2) determine its constituent taxa, with special attention to the genera and species groups which form the subfamily Hylinae, and c) propose a new, monophyletic taxonomy consistent with the hypothesized relationships. We present a phylogenetic analysis of hylid frogs based on 276 terminals, including 228 hylids and 48 outgroup taxa. Included are exemplars of all but 1 of the 41 genera of Hylidae (of all four nominal subfamilies) and 39 of the 41 currently recognized species groups of the species-rich genus Hyla. The included taxa allowed us to test the monophyly of 24 of the 35 nonmonotypic genera and 25 species groups of Hyla. The phylogenetic analysis includes approximately 5100 base pairs from four mitochondrial (12S, tRNA valine, 16S, and cytochrome b) and five nuclear genes (rhodopsin, tyrosinase, RAG-1, seventh in absentia, and 28S), and a small data set from foot musculature. Concurring with previous studies, the present analysis indicates that Hemiphractinae are not related to the other three hylid subfamilies. It is therefore removed from the family and tentatively considered a subfamily of the paraphyletic Leptodactylidae. Hylidae is now restricted to Hylinae, Pelodryadinae, and Phyllomedusinae. Our results support a sister-group relationship between Pelodryadinae and Phyllomedusinae, which together form the sister taxon of Hylinae. Agalychnis, Phyllomedusa, Litoria, Hyla, Osteocephalus, Phrynohyas, Ptychohyla, Scinax, Smilisca, and Trachycephalus are not monophyletic. Within Hyla, the H. albomarginata, H. albopunctata, H. arborea, H. boons, H. cinerea, H. eximia, H. geographica, H. granosa, H. microcephala, H. miotympanum, H. tuberculosa, and H. versicolor groups are also demonstrably nonmonophyletic. Hylinae is composed of four major clades. The first of these includes the Andean stream-breeding Hyla, Aplastodiscus, all Gladiator Frogs, and a Tepuian clade. The second clade is composed of the 30-chromosome Hyla, Lysapsus, Pseudis, Scarthyla, Scinax (including the H. uruguaya group), Sphaenorhynchus, and Xenohyla. The third major clade is composed of Nyctimantis, Phrynohyas, Phyllodytes, and all South American/West Indian casque-headed frogs: Aparasphenodon, Argenteohyla, Corythomantis, Osteocephalus, Osteopilus, Tepuihyla, and Trachycephalus. The fourth major clade is composed of most of the Middle American/Holarctic species groups of Hyla and the genera Acris, Anotheca, Duellmanohyla, Plectrohyla, Pseudacris, Ptychohyla, Pternohyla, Smilisca, and Triprion. A new monophyletic taxonomy mirroring these results is presented where Hylinae is divided into four tribes. Of the species currently in Hyla, 297 of the 353 species are placed in 15 genera; of these, 4 are currently recognized, 4 are resurrected names, and 7 are new. Hyla is restricted to H. femoralis and the H. arborea, H. cinerea, H. eximia, and H. versicolor groups, whose contents are redefined. Phrynohyas is placed in the synonymy of Trachycephalus, and Pternohyla is placed in the synonymy of Smilisca. The genus Dendropsophus is resurrected to include all former species of Hyla known or suspected to have 30 chromosomes. Exerodonta is resurrected to include the former Hyla sumichrasti group and some members of the former H. miotympanum group. Hyloscirtus is resurrected for the former Hyla armata, H. bogotensis, and H. larinopygion groups. Hypsiboas is resurrected to include several species groups - many of them redefined here - of Gladiator Frogs. The former Hyla albofrenata and H. albosignata complexes of the H. albomarginata group are included in Aplastodiscus. New generic names are erected for (1) Agalychnis calcarifer and A. craspedopus; (2) Osteocephalus langsdorffii; the (3) Hyla aromatica, (4) H. bromeliacia, (5) H. godmani, (6) H. mixomaculata, (7) H. taeniopus, (8) and H. tuberculosa groups; (9) the clade composed of the H. pictipes and H. pseudopuma groups; and (10) a clade composed of the H. circumdata, H. claresignata, H. martinsi, and H. pseudopseudis groups. Copyright © American Museum of Natural History 2005.

Cytogenetic analysis of three sympatric Gymnotus species (Teleostei: Gymnotidae) from the Fundo Stream, MG, Brazil

Three sympatric species of Gymnotus from the Fundo stream, a small tributary of the Sapucai river, Minas Gerais State, Brazil, were studied in relation to their karyology. Gymnotus sylvius presented 2n=40 chromosomes (36 m/sm+4 st/a), Gymnotus sp. presented 2n=50 (26 m/sm+ 24 st/a) and Gymnotus paraguensis had 2n=54 (50 m/sm+4 st/a). C-banding demonstrated positively stained heterochromatic blocks in the centromeric position of few chromosomes on G. sylvius and in the centromeric region of all chromosomes on G. paraguensis samples. The nucleolus organizer region (NOR) was located on the short arm of one st chromosome pair in G. sylvius and Gymnotus sp., and in the interstitial position on the short arm of the pair number one and below the centromere on a third chromosome on G. paraguensis. The cytogenetic data obtained indicate that Gymnotus sp. represent a new Gymnotus specie with a karyotypic constitution never observed on others species from this genus. Some aspects related to the chromosome diversification of these Gymnotus are discussed. © 2007 The Japan Mendel Society.

Cytogenetic and random amplified polymorphic DNA analysis of Leptodactylus species from rural and urban environments (Anura, Amphibia)

Cytogenetic and random amplified polymorphic DNA analyses carried out in the species Leptodactylus podicipinus, L. ocellatus, L. labyrinthicus, and L. fuscus from rural and urban habitats of the northwest region of São Paulo State, Brazil, showed that the karyotypes (2n = 22), constitutive heterochromatin distribution and nucleolus organizer region (NOR) location did not differ between the populations from the two environments. The in situ hybridization with an rDNA probe confirmed the location of the NORs on chromosome 8 revealing an in tandem duplication of that region in one of the chromosomes of L. fuscus. DAPI showed that part of the C-band-positive heterochromatin is rich in AT, including that in the proximity the NORs in L. podicipinus and L. ocellatus. The molecular analyses showed that the two populations (urban and rural) of L. podicipinus and L. fuscus are similar from a genetic point of view. The urban and rural populations of species L. ocellatus and L. labyrinthicus showed differences in genetic structures, probably due to urbanization which interferes with the dispersion of those frogs. The marked differences observed between the two populations of L. ocellatus can be representing the cryptic condition of the species. Unweighted pair-group method of analysis and genetic distance analysis detected the genetic proximity between L. ocellatus and L. fuscus. The results indicate that there was no reduction in the genetic diversity in the populations from the urban environment; however, the survival of these frogs would not be guaranteed in the case of an increase in human impact especially for populations of L. labyrinthicus and L. ocellatus. ©FUNPEC-RP.

Cytogenetic analysis in the spermatogenesis of Triatoma melanosoma (Reduviidae; Heteroptera)

Triatomines are of great concern in public health because they are vectors of Chagas' disease. This study presents an analysis of the species Triatoma melanosoma. The cytogenetic characteristics of triatomines include holocentric chromosomes, post-reductional meiosis in the sex chromosomes and nucleolar fragmentation in the meiotic cycle. The methodology utilized consisted of the techniques of lacto-acetic orcein staining and silver ion impregnation. The organs analyzed were adult testicles. The results enabled to classify the chromosomes by number and size, being three large, eight medium and one small heterochromosome. The three largest chromosomes and the heterochromosomes showed heteropyknotic chromatin in meiosis. The heterochromosomes in 8.05% of the cells in metaphase I behaved as pseudobivalents, contrasting with 91.95% of the cells with individualized sex chromosomes, confirming the achiasmatic nature of these chromosomes. However, the pseudobivalents occurred prominently in metaphase II (78.38%), this fact probably is related to the post-reductional nature of the sex chromosomes. The nucleolus in T. melanosoma persisted until the diplotene phase after which it began to fragment. Nucleolar corpuscles were observed in metaphases I and II and during anaphases I and II, these characteristics being related to the phenomenon of nucleolar persistence. In the initial spermatids, peripheral silver ion impregnation occurred, which could be analogous to the pre-nucleolar corpuscles observed after fragmentation. Thus, this study extends our knowledge of the characteristics of triatomines, in particular, heteropyknotic degree, kinetic activity, formation of sex chromosome achiasmatic pseudobivalency, confirmation of the fragmentation phenomenon, and post-meiotic nucleolar reactivation. ©FUNPEC-RP.

Subtelomeric region of chromosome 2 in patients with autism spectrum disorders

Autism spectrum disorders are severe psychiatric diseases commonly identified in the population. They are diagnosed during childhood and the etiology has been much debated due to their variations and complexity. Onset is early and characterized as communication and social interaction disorders and as repetitive and stereotyped behavior. Austistic disorders may occur together with various genetic and chromosomal diseases. Several chromosomal regions and genes are implicated in the predisposition for these diseases, in particular those with products expressed in the central nervous system. There are reports of autistic and mentally handicapped patients with submicroscopic subtelomeric alterations at the distal end of the long arm of chromosome 2. Additionally, there is evidence that alterations at 2q37 cause brain malformations that result in the autistic phenotype. These alterations are very small and not identified by routine cytogenetics to which patients are normally submitted, which may result in an underestimation of the diagnosis. This study aimed at evaluating the 2q37 region in patients with autistic disorders. Twenty patients were studied utilizing the fluorescence in situ hybridization technique with a specific probe for 2q37. All of them were also studied by the GTC banding technique to identify possible chromosomal diseases. No alterations were observed in the 2q37 region of the individuals studied, and no patient presented chromosomal diseases. This result may be due to the small sample size analyzed. The introduction of routine analysis of the 2q37 region for patients with autistic disorders depends on further studies. ©FUNPEC-RP.

Cytogenetic analysis in Thoracocharax stellatus (Kner, 1858) (Characiformes, Gasteropelecidae) from Paraguay river basin, Mato Grosso, Brazil

Thoracocharax stellatus (Characiformes, Gasteropelecidae) is a small Neotropical species of fish, widely distributed in several rivers of South America. Evidence for karyotype heteromorphysm in populations from different geographical regions has been reported for this species. In this way, populations of T. stellatus from the Paraguay River basin were cytogenetically characterized and the results were compared with other studies performed in the same species but from different basins. The results showed a diploid number of 2n = 54 for T. stellatus, with chromosomes arranged in 6 metacentric (m), 6 submetacentric (sm), 2 subtelocentric (st) and 40 acrocentric (a), for both sexes, with a simple Nucleolus Organiser Region (NOR) system reported by the techniques of silver nitrate impregnation and fluorescent in situ hybridisation (FISH) using 18S rDNA sequences as probe. The distribution of constitutive heterochromatin, observed by the C-band technique and Chromomycin A3 staining showed great similarity among the analyzed populations and consists mainly of discrete blocks in the pericentromeric and telomeric regions of most chromosomes. The presence of female heterogamety was alsoobserved indicating a ZZ/ZW system with W chromosome almost totally heterochromatic. The results also show cytogenetic diversity of the group and are useful to understand the mechanisms of karyotype evolution of the family. © Edson Lourenço da Silva et al.

Karyotype analysis of seven species of the tribe lophiohylini (Hylinae, Hylidae, Anura), with conventional and molecular cytogenetic techniques

Few species of the tribe Lophiohylini have been karyotyped so far, and earlier analyses were performed mainly with standard staining. Based on the analysis of seven species with use of routine banding and molecular cytogenetic techniques, the karyotypes were compared and the cytogenetic data were evaluated in the light of the current phylogenies. A karyotype with 2n = 24 and NOR in the chromosome 10 detected by Ag-impregnation and FISH with an rDNA probe was shared by Aparasphenodon bokermanni Miranda-Ribeiro, 1920, Itapotihyla langsdorffii (Duméril and Bibron, 1841), Trachycephalus sp., T. mesophaeus (Hensel, 1867), and T. typhonius (Linnaeus, 1758). Phyllodytes edelmoi Peixoto, Caramaschi et Freire, 2003 and P. luteolus (Wied-Neuwied, 1824) had reduced the diploid number from 2n = 24 to 2n = 22 with one of the small-sized pairs clearly missing, and NOR in the large chromosome 2, but the karyotypes were distinct regarding the morphology of chromosome pairs 4 and 6. Based on the cytogenetic and phylogenetic data, it was presumed that the chromosome evolution occurred from an ancestral type with 2n = 24, in which a small chromosome had been translocated to one or more unidentified chromosomes. Whichever hypothesis is more probable, other rearrangements should have occurred later, to explain the karyotype differences between the two species of Phyllodytes Wagler, 1830. The majority of the species presented a small amount of centromeric C-banded heterochromatin and these regions were GC-rich. The FISH technique using a telomeric probe identified the chromosome ends and possibly (TTAGGG)n-like sequences in the repetitive DNA out of the telomeres in I. langsdorffii and P. edelmoi. The data herein obtained represent an important contribution for characterizing the karyotype variability within the tribe Lophiohylini scarcely analysed so far. © Simone Lilian Gruber et al.

Interclonal Variations in the Molecular Karyotype of Trypanosoma cruzi: Chromosome Rearrangements in a Single Cell-Derived Clone of the G Strain

Trypanosoma cruzi comprises a pool of populations which are genetically diverse in terms of DNA content, growth and infectivity. Inter- and intra-strain karyotype heterogeneities have been reported, suggesting that chromosomal rearrangements occurred during the evolution of this parasite. Clone D11 is a single-cell-derived clone of the T. cruzi G strain selected by the minimal dilution method and by infecting Vero cells with metacyclic trypomastigotes. Here we report that the karyotype of clone D11 differs from that of the G strain in both number and size of chromosomal bands. Large chromosomal rearrangement was observed in the chromosomes carrying the tubulin loci. However, most of the chromosome length polymorphisms were of small amplitude, and the absence of one band in clone D11 in relation to its reference position in the G strain could be correlated to the presence of a novel band migrating above or below this position. Despite the presence of chromosomal polymorphism, large syntenic groups were conserved between the isolates. The appearance of new chromosomal bands in clone D11 could be explained by chromosome fusion followed by a chromosome break or interchromosomal exchange of large DNA segments. Our results also suggest that telomeric regions are involved in this process. The variant represented by clone D11 could have been induced by the stress of the cloning procedure or could, as has been suggested for Leishmania infantum, have emerged from a multiclonal, mosaic parasite population submitted to frequent DNA amplification/deletion events, leading to a 'mosaic' structure with different individuals having differently sized versions of the same chromosomes. If this is the case, the variant represented by clone D11 would be better adapted to survive the stress induced by cloning, which includes intracellular development in the mammalian cell. Karyotype polymorphism could be part of the T. cruzi arsenal for responding to environmental pressure. © 2013 Lima et al.

Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution

Background: Centromeres are essential for chromosome segregation, yet their DNA sequences evolve rapidly. In most animals and plants that have been studied, centromeres contain megabase-scale arrays of tandem repeats. Despite their importance, very little is known about the degree to which centromere tandem repeats share common properties between different species across different phyla. We used bioinformatic methods to identify high-copy tandem repeats from 282 species using publicly available genomic sequence and our own data.Results: Our methods are compatible with all current sequencing technologies. Long Pacific Biosciences sequence reads allowed us to find tandem repeat monomers up to 1,419 bp. We assumed that the most abundant tandem repeat is the centromere DNA, which was true for most species whose centromeres have been previously characterized, suggesting this is a general property of genomes. High-copy centromere tandem repeats were found in almost all animal and plant genomes, but repeat monomers were highly variable in sequence composition and length. Furthermore, phylogenetic analysis of sequence homology showed little evidence of sequence conservation beyond approximately 50 million years of divergence. We find that despite an overall lack of sequence conservation, centromere tandem repeats from diverse species showed similar modes of evolution.Conclusions: While centromere position in most eukaryotes is epigenetically determined, our results indicate that tandem repeats are highly prevalent at centromeres of both animal and plant genomes. This suggests a functional role for such repeats, perhaps in promoting concerted evolution of centromere DNA across chromosomes.

A genetic linkage study in Brazil identifies a new locus for persistent developmental stuttering on chromosome 10

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Molecular analysis of community-acquired methicillin-resistant Staphylococcus aureus isolated from skin and soft tissue infections, Botucatu Medical School, Brazil

Community acquired methicillin Staphylococcus aureus (CA-MRSA) was first reported in 1981, infecting people without risk factors. These strains harbor the Staphylococcal Cassette Chromosome mec (SCCmec) type IV, which contains the mecA gene codifying for methicillin resistance. CA-MRSA strains usually carry PVL (Panton-Valentine Leukocidin), a virulence factor responsible for tissue invasion, causing systemic infections and leading to serious complications. The aims of this work were to detect the mecA gene, SCCmec characterization and to detect the PVL gene of the S. aureus strains isolated from patients diagnosed with skin and soft tissue infections attending the Dermatology Service, of the Botucatu Medical School, Brazil. Among 127 collected samples, 66 (51.9%) were S. aureus and, from these, 7 (10.6%) harbored mecA gene, 3 (42%) with cassette type IV, and none of these samples carried the PVL gene, but it was detected in 10 (15.1%) samples of S. aureus methicillin sensitive (MSSA). Our study suggests the S. aureus strains that harbor PVL gene and MRSA are present in the community as important pathogens.

Sex chromosome composition revealed in Characidium fishes (Characiformes: Crenuchidae) by molecular cytogenetic methods

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Possible interspecific origin of the B chromosome of Hypsiboas albopunctatus (Spix, 1824) (Anura, Hylidae), revealed by microdissection, chromosome painting, and reverse hybridisation

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

A step to the gigantic genome of the desert locust: chromosome sizes and repeated DNAs

The desert locust (Schistocerca gregaria) has been used as material for numerous cytogenetic studies. Its genome size is estimated to be 8.55 Gb of DNA comprised in 11 autosomes and the X chromosome. Its X0/XX sex chromosome determinism therefore results in females having 24 chromosomes whereas males have 23. Surprisingly, little is known about the DNA content of this locust's huge chromosomes. Here, we use the Feulgen Image Analysis Densitometry and C-banding techniques to respectively estimate the DNA quantity and heterochromatin content of each chromosome. We also identify three satellite DNAs using both restriction endonucleases and next-generation sequencing. We then use fluorescent in situ hybridization to determine the chromosomal location of these satellite DNAs as well as that of six tandem repeat DNA gene families. The combination of the results obtained in this work allows distinguishing between the different chromosomes not only by size, but also by the kind of repetitive DNAs that they contain. The recent publication of the draft genome of the migratory locust (Locusta migratoria), the largest animal genome hitherto sequenced, invites for sequencing even larger genomes. S. gregaria is a pest that causes high economic losses. It is thus among the primary candidates for genome sequencing. But this species genome is about 50 % larger than that of L. migratoria, and although next-generation sequencing currently allows sequencing large genomes, sequencing it would mean a greater challenge. The chromosome sizes and markers provided here should not only help planning the sequencing project and guide the assembly but would also facilitate assigning assembled linkage groups to actual chromosomes.