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The genus Rhinella corresponds to a group of anurans characterized by numerous taxonomic and systemic challenges, leading to their organization into species complexes. Cytogenetic data for this genus thus far are limited to the diploid number and chromosome morphology, which remain highly conserved among the species. In this study, we analyse the karyotypes of three species of the genus Rhinella (Rhinella granulosa, Rhinella margaritifera, and Rhinella marina) using both classical (conventional staining and C-banding) and molecular (FISH-fluorescence in situ hybridization with 18S rDNA, telomeric sequences, and microsatellite probes) cytogenetic approaches. The aim of this study is to provide data that can reveal variations in the distribution of repetitive sequences that can contribute to understanding karyotypic diversification in these species. The results revealed a conserved karyotype across the species, with 2n = 22 and FN = 44, with metacentric and submetacentric chromosomes. C-banding revealed heterochromatic blocks in the pericentromeric region for all species, with a proximal block on the long arms of pairs 3 and 6 in R. marina and on the short arms of pairs 4 and 6 in R. margaritifera. Additionally, 18S rDNA probes hybridized to pair 5 in R. granulosa, to pair 7 in R. marina, and to pair 10 in R. margaritifera. Telomeric sequence probes displayed signals exclusively in the distal region of the chromosomes, while microsatellite DNA probes showed species-specific patterns. These findings indicate that despite a conserved karyotypical macrostructure, chromosomal differences exist among the species due to the accumulation of repetitive sequences. This variation may be attributed to chromosome rearrangements or differential accumulation of these sequences, highlighting the dynamic role of repetitive sequences in the chromosomal evolution of Rhinella species. Ultimately, this study emphasizes the importance of the role of repetitive DNAs in chromosomal rearrangements to elucidate the evolutionary mechanisms leading to independent diversification in the distinct phylogenetic groups of Rhinella. [ABSTRACT FROM AUTHOR]

Background: Ariidae species play a significant role as fishing resources in the Amazon region. However, the family's systematic classification is notably challenging, particularly regarding species delimitation within certain genera. This difficulty arises from pronounced morphological similarities among species, posing obstacles to accurate species recognition. Methods: Following morphological identification, mitochondrial markers (COI and Cytb) were employed to assess the diversity of Ariidae species in the Amazon. Results: Our sampling efforts yielded 12 species, representing 92% of the coastal Amazon region's diversity. Morphological identification findings were largely corroborated by molecular data, particularly for species within the Sciades and Bagre genera. Nonetheless, despite morphological support, Cathorops agassizii and Cathorops spixii displayed minimal genetic divergence (0.010). Similarly, Notarius quadriscutis and Notarius phrygiatus formed a single clade with no genetic divergence, indicating mitochondrial introgression. For the majority of taxa examined, both COI and Cytb demonstrated efficacy as DNA barcodes, with Cytb exhibiting greater polymorphism and resolution. Consequently, the molecular tools utilized proved highly effective for species discrimination and identification. [ABSTRACT FROM AUTHOR]

The ichthyological provinces of Mozambique are understudied hotspots of global fish diversity. In this study, we applied DNA barcoding to identify the composition of the fish fauna from the coast of Mozambique. A total of 143 species belonging to 104 genera, 59 families, and 30 orders were identified. The overall K2P distance of the COI sequences within species ranged from 0.00% to 1.51%, while interspecific distances ranged from 3.64% to 24.49%. Moreover, the study revealed 15 threatened species according to the IUCN Red List of Threatened Species, with elasmobranchs being the most represented group. Additionally, the study also uncovered four new species that were not previously recorded in this geographic area, including Boleophthalmus dussumieri, Maculabatis gerrardi, Hippocampus kelloggi, and Lethrinus miniatus. This study represents the first instance of utilizing molecular references to explore the fish fauna along the Mozambican coast. Our results indicate that DNA barcoding is a dependable technique for the identification and delineation of fish species in the waters of Mozambique. The DNA barcoding library established in this research will be an invaluable asset for advancing the understanding of fish diversity and guiding future conservation initiatives. [ABSTRACT FROM AUTHOR]

The efficiency of the DNA barcoding relies on sequencing fragment of the Cytochrome C Subunit I (COI) gene, which has been claimed as a tool to biodiversity identification from distinct groups. Accordingly, the goal of this study was to identify juvenile fish species along an estuary of Caeté River in the Brazilian Blue Amazon based on. For this purpose, we applied the DNA barcoding and discuss this approach as a tool for discrimination of species in early ontogenetic stages. A 500-bp fragment was obtained from 74 individuals, belonging to 23 species, 20 genera, 13 families and seven orders. About 70% of the 46 haplotypes revealed congruence between morphological and molecular species identification, while 8% of them failed in identification of taxa and 22% demonstrated morphological misidentification. These results proved that COI fragments were effective to diagnose fish species at early life stages, allowing identifying all samples to a species-specific status, except for some taxa whose COI sequences remain unavailable in public databases. Therefore, we recommend the incorporation of DNA barcoding to provide additional support to traditional identification, especially in morphologically controversial groups. In addition, periodic updates and comparative analyses in public COI datasets are encouraged. [ABSTRACT FROM AUTHOR]

The family Carcharhinidae includes the most typical and recognizable sharks, although its internal classification is the subject of extensive debate. In particular, the type genus, Carcharhinus Blainville, 1816, which is also the most speciose, appears to be paraphyletic in relation to a number of morphologically distinct taxa. Isogomphodon oxyrhynchus (Valenciennes, 1839) (the daggernose shark) is a carcharinid, which is endemic to a limited area of the Western Atlantic between Trinidad and Tobago and the Gulf of Maranhão in northern Brazil, one of the smallest ranges of any New World elasmobranch species. In recent decades, I. oxyrhynchus populations have been decimated by anthropogenic impacts, which has led to the classification of the species as critically endangered by the IUCN. However, there is considerable debate on both the validity of the species (I. oxyrhynchus) and the status of Isogomphodon Gill, 1862 as a distinct entity from the genus Carcharhinus. The present study is based on a molecular assessment of the genetic validity of the I. oxyrhynchus that combines mitochondrial and nuclear markers, which were used to identify the biogeographic events responsible for the emergence and dispersal of the species in northern Brazil. The genetic distance analyses and phylogenetic trees confirmed the paraphyly of the genus Carcharhinus, recovering a clade comprising Carcharhinus+I. oxyrhynchus+Prionace glauca (Linnaeus, 1758). Our results indicate not only that the daggernose shark is actually a member of the genus Carcharhinus, but that it is genetically more closely related to Carcharhinus porosus (Ranzani, 1839) than it is to the other Carcharhinus species analyzed. Given this, I. oxyrhynchus and P. glauca are therefore reclassified and recognized as Carcharhinus oxyrhynchus and Carcharhinus glaucus. The daggernose shark, Carcharhinus oxyrhynchus, diverged from C. porosus during the Miocene, when significant geomorphological processes occurred on the northern coast of South America, in particular in relation to the configuration of the Amazon River. It is closely associated with the area of the Amazon plume, and its distinctive morphological features represent autapomorphic ecological adaptations to this unique habitat and do not reflect systematic distinction from Carcharhinus. [ABSTRACT FROM AUTHOR]

Molecular genetic techniques are an effective monitoring tool, but high-quality DNA samples are usually required. In this study, we compared three different protocols of DNA extraction: NaCl (saline); phenol-chloroform and commercial kit (Promega)—from three biological tissues of five individuals of Lutjanus purpureus under two methods of storage. The evaluated items included DNA concentration and purity, processing time and cost, as well as the obtaining of functional sequences. The highest average values of DNA concentration were obtained using the saline procedure and the commercial kit. Pure DNA was only obtained using the saline protocol, evaluated by the ratio of 260/280. The saline and phenol-chloroform protocols were the least expensive methods. The commercial kit costs are counterbalanced by the short time required. The procedure based on phenol-chloroform presented the worst results regarding DNA yield and the time required to perform all steps. The saline and commercial kit protocols showed similar results concerning the amount and quality of extracted DNA. Therefore, the final choice should be based on the available financial resources and the available time for carrying out each procedure of DNA extraction. [ABSTRACT FROM AUTHOR]

Although Astyanax bimaculatus is the most representative species of the genus in the Amazon region, there are no cytogenetic studies of A. bimaculatus species in Amazon region. Thus, we aimed to analyse the chromosome complements of specimens from this area using classic and molecular cytogenetic approaches. The results revealed the existence of a distinct cytotype and this is the first report of the occurrence of a B microchromosome in the species. Overall, these data indicate that the karyotypic evolution of this species is complex, involving the occurrence of chromosomal rearrangements. [ABSTRACT FROM AUTHOR]

Expanding on the foundation of Zeitschrift für Jagdwissenschaft in 1955, the European Journal of Wildlife Research (EJWR) continues to publish original research and reviews on all aspects of wildlife science regardless of the geographic region. Eighteen years after publication of the first issue of EJWR, we briefly reflect on the journal's profile and prospects. Our target audience includes researchers, wildlife biologists, forestry and game management professionals, wildlife veterinarians, and other specialists, but we also aim at providing a resource of relevant information and scientific debate for practitioners and every person interested in wildlife science. With ecosystems being at the highest level of pressure due to land use change and other effects of the global crisis, the journal is in a key position to communicate relevant research to the scientific community around the world. [ABSTRACT FROM AUTHOR]

Boleophthalmus dussumieri is one of the most widely distributed mudskippers and is native to the Persian Gulf in Iran down to the northeast of the Arabian Sea and the coast of India. Nonetheless, the present study is the first to confirm the presence of B. dussumieri in the marine areas of the Mozambique coast. In addition, molecular analysis revealed strong evidence for the existence of two lineages with a high level of nucleotide divergence along the sampled area, revealing a still‐neglected taxonomic condition for this lineage/species. [ABSTRACT FROM AUTHOR]

The family Syngnathidae contains 52 seahorse species, which inhabit a range of habitats including coral reefs, seagrass beds and coastal estuaries. The seahorse Hippocampus kelloggi is among the most widely distributed species, occurring from Indo-West Pacific to East Africa. This species was included in the IUCN Red List in 2017 and is classified as vulnerable according to A2cd criteria. In this study, three specimens collected from the central coast of Mozambique were investigated and based on morphology and mitochondrial subunit of cytochrome oxidase I (COI) were identified as H. kelloggi. These results confirmed for the first time the extensive range of occurrence of H. kelloggi on the central coast of Mozambique. [ABSTRACT FROM AUTHOR]

Intelligent Personal Assistants (IPAs), such as Amazon's Alexa, are now widely used for an ample variety of tasks, ranging from personal management to education. These tools have shown considerable promise for student-educator interactions, especially at a distance, a potential that has come to the forefront during the ongoing COVID-19 pandemic. Even so, this potential is still underexploited, even in the current scenario. Alexa's apps are known as skills, which include all the different commands that Alexa is capable of executing. It is important to note, however, that the use of such technology is work-intensive and can be relatively complex. Given this, to facilitate the development of new skills in Alexa, we have developed an online tool that permits the creation of questions and answers, as well as honing the interaction between Alexa and the user. We have named this tool ForAlexa, which has two types of forms, Question-And-Answer (Q&A) and Random-Quote. Both these forms allow the user to build intents (an activity that is invoked by a spoken request from the user), but with slightly different functions. The Q&A form is used to compile answers that Alexa will offer in response to an utterance (question), while the Random-Quote extends the interaction between Alexa and the user, based on the questions asked in the first form. ForAlexa also has a help assistant, as well as a manual, which explains all the steps necessary for the design of an intent. This tool allows educators to develop apps quickly and easily for their classes and this type of app could be an alternative to be used for students with special needs, such as the visually-impaired. [ABSTRACT FROM AUTHOR]

While there is little doubt that the species is the lowest independent evolutionary unit, understanding the many different species concepts is a difficult task, even for university students. In the present study, we propose a didactic sequence that involves fieldwork, laboratory analyses, experimental cultures, and computational work in an integrated strategy for the comprehension of the phenetic, ecological, biological, and phylogenetic species concepts. This activity is based on the observation of the morphological, ecological, biological, and phylogenetic characteristics of samples of two copepod crustaceans, Acartia tonsa Dana, 1849 and Acartia lilljeborgi Giesbrecht, 1889 (Copepoda, Calanoida). These species were the focus of a simple practical that contributes to the effective comprehension of the four species concepts mentioned above, using straightforward methods that can be standardized easily in the laboratory and classroom. The practical activities developed for the didactic sequence presented here not only made the classes more interesting and motivational, but also contributed to the more effective assimilation of the content, as well as the more effective consolidation of the knowledge presented in the class. It is important to note that these activities can be developed at different educational levels (i.e., undergraduate and graduate students), and can be applied to other types of organism (e.g., amphibians, insects or other copepods), as long as their characteristics are adequate for the systematic exploration of the four species concepts included here. [ABSTRACT FROM AUTHOR]

The Atlantic goliath grouper, Epinephelus itajara (Lichtenstein, 1822), is considered a critically endangered species. Since 2002, fishing, storage, transport, and marketing of E. itajara has been prohibited in Brazil. However, there are records of fishing of E. itajara in the Brazilian state of Pará. This study recorded the illegal sale of E. itajara fillets in the municipality of Bragança, as well as fraud resulting from the substitution of one species for another. Through two distinct molecular procedures, 22 fillet samples sold as Atlantic goliath grouper were investigated. In total, 21 (95.5%) samples were confirmed as belonging to E. itajara and one was not. This demonstrates the weakness in the inspection process, which must be urgently adjusted, and it also revealed the need for a consistent, permanent, and effective program to raise awareness in the community of the damage caused by the illegal purchase and the need to preserve E. itajara. [ABSTRACT FROM AUTHOR]

ABSTRACT Aim Location Taxon Methods Results Main Conclusions The Amazon rainforest is one of the most biodiverse regions on earth, but our understanding of the processes that have shaped its patterns of diversity remains incomplete. One hypothesis for Amazonian speciation is the river‐refuge hypothesis, which suggests that retraction of forests away from the periphery of Amazonia, where rivers are narrow, facilitated divergence of populations separated by wide rivers. Later re‐expansion of forests would have allowed secondary contact between these populations, and co‐occurring hybrid zones may reveal the location where expanding forests first reconnected. Here, we test whether a widespread Amazonian songbird species shows evidence of population contact zones in the eastern headwaters of the Tapajós river, hypothesised to be an area of secondary contact under the river‐refuge hypothesis.Amazon and Atlantic forests of South America.Ceratopipra rubrocapilla (Pipridae, Passeriformes).We sampled 147 C. rubrocapilla (Red‐headed Manakin) across its vast range, with 70 samples sequenced using reduced‐representation genomic sequencing and 139 sequenced at the mitochondrial gene cytochrome b. We use population genetic and phylogenetic analyses to investigate patterns of gene flow and population structure across the range, with a particular focus on samples from the headwaters of the Tapajós River to evaluate the potential role of the river‐refuge hypothesis.We observe shallow population structure and evidence for widespread gene flow across the range of C. rubrocapilla. Patterns in the Tapajós headwaters match predictions of the river‐refuge hypothesis, with eastern headwater samples most similar to samples farther west on the opposite bank of the Tapajós River.The close co‐occurrence between population contact zones within C. rubrocapilla and other previously studied hybrid zones reinforces the hypothesis that the eastern Tapajós headwaters is where rainforest populations reconnected in the past, following predictions of the river‐refuge hypothesis of Amazonian speciation. [ABSTRACT FROM AUTHOR]

The Serra Spanish mackerel, Scomberomorus brasiliensis, is one of the most important fishery resources in the western tropical Atlantic, including northern and eastern Brazil. Despite its economic importance, few genetic markers have been sequenced in this species, and little is known of its population genetics. The present study evaluated the genetic variability of 110 individuals, representing three distinct Brazilian populations (Macapá, Fortaleza and Paranaguá), based on a segment of the mitochondrial Control Region. The sequences revealed high levels of genetic diversity, and suggested marked connectivity among the studied populations. A variable repeat was also found in the 3’ portion of the studied Control Region fragment, which may prove useful as a marker in future genetic population studies of S. brasiliensis. [ABSTRACT FROM AUTHOR]

The Atlantic goliath grouper, Epinephelus itajara (Lichtenstein, 1822), is considered a critically endangered species. In Brazil, the harvesting, transportation, and sale of E. itajara or it's by products have been prohibited, but illegal harvesting still occurs. This study developed a simple, sensitive and accurate procedure for the safe identification of E. itajara by polymerase chain reaction (PCR). A specific primer (16S-RYOP4) was designed, synthesized and grouped with universal primers. The efficiency of specific amplification of the new set of primers was proven using samples of E. itajara, four species of epinephelids and five other species of fish marketed in northern Brazil. This procedure can be used to inspect products sold in stores, supermarkets and fairs, especially in places of reduced scientific, technological and economic development, where there is a record of illegal fishing and selling of E. itajara. [ABSTRACT FROM AUTHOR]

Abstract Background The classical perspective that interspecific hybridization in animals is rare has been changing due to a growing list of empirical examples showing the occurrence of gene flow between closely related species. Using sequence data from cyt b mitochondrial gene and three intron nuclear genes (RPL9, c-myc, and RPL3) we investigated patterns of nucleotide polymorphism and divergence between two closely related toad species R. marina and R. schneideri. By comparing levels of differentiation at nuclear and mtDNA levels we were able to describe patterns of introgression and infer the history of hybridization between these species. Results All nuclear loci are essentially concordant in revealing two well differentiated groups of haplotypes, corresponding to the morphologically-defined species R. marina and R. schneideri. Mitochondrial DNA analysis also revealed two well-differentiated groups of haplotypes but, in stark contrast with the nuclear genealogies, all R. schneideri sequences are clustered with sequences of R. marina from the right Amazon bank (RAB), while R. marina sequences from the left Amazon bank (LAB) are monophyletic. An Isolation-with-Migration (IM) analysis using nuclear data showed that R. marina and R. schneideri diverged at ≈ 1.69 Myr (early Pleistocene), while R. marina populations from LAB and RAB diverged at ≈ 0.33 Myr (middle Pleistocene). This time of divergence is not consistent with the split between LAB and RAB populations obtained with mtDNA data (≈ 1.59 Myr), which is notably similar to the estimate obtained with nuclear genes between R. marina and R. schneideri. Coalescent simulations of mtDNA phylogeny under the speciation history inferred from nuclear genes rejected the hypothesis of incomplete lineage sorting to explain the conflicting signal between mtDNA and nuclear-based phylogenies. Conclusions The cytonuclear discordance seems to reflect the occurrence of interspecific hybridization between these two closely related toad species. Overall, our results suggest a phenomenon of extensive mtDNA unidirectional introgression from the previously occurring R. schneideri into the invading R. marina. We hypothesize that climatic-induced range shifts during the Pleistocene/Holocene may have played an important role in the observed patterns of introgression.

Elopiformes is one of the most ancient orders of Teleostei fishes and includes the Megalopidae and Elopidae families. Although relevant to scientific research, cytogenetic and molecular data are lacking for both families. Here, we compared Elopiformes species from the perspective of genetic divergence and cytogenetics to elucidate the chromosomal diversification and evolutionary processes of Elopiformes. The cytogenetic results showed that Megalops atlanticus and Elops smithi are 2n = 50, with differences in their chromosomal formulas. The distributions of heterochromatin and repetitive DNA sequences revealed many characteristics shared between Elopiformes and other basal lineages of Teleostei fishes. In addition, the results suggested that different chromosomal rearrangements have occurred in the analysed Elopiformes species. The species tree indicated that Megalopidae and Elopidae were monophyletic groups, but the genetic divergence was higher for Megalops species than for Elops species. The small divergence and sympatric distribution of Elops species may not prevent hybridization. However, the karyotype differentiation may be an effective post-zygotic mechanism preventing continuous hybridization, and it could be the key factor in this speciation process. In conclusion, this is the first report of Elopiformes species that integrates molecular and cytogenetic data. Our results emphasize the importance of cytogenetic data for further defining Elopidae species. • Cytogenetic and molecular data revealed karyotype divergence in Elopiformes. • Cytogenetic patterns of Elopiformes are similar to other ancient fishes lineages. • Chromosome rearrangements are observed between Elopiformes species. • Possibly speciation by chromosomal rearrangements was observed for Elopids. [ABSTRACT FROM AUTHOR]

The study of natural hybrid zones can illuminate aspects of lineage divergence and speciation in morphologically cryptic taxa. We studied a hybrid zone between two highly divergent but morphologically similar lineages (south‐western and south‐eastern) of the Iberian endemic Bosca's newt (Lissotriton boscai) in SW Iberia with a multilocus dataset (microsatellites, nuclear and mitochondrial genes). STRUCTURE and NEWHYBRIDS analyses retrieved few admixed individuals, which classified as backcrosses involving parental individuals of the south‐western lineage. Our results show asymmetric introgression of mtDNA beyond the contact from this lineage into the south‐eastern lineage. Analysis of nongeographic introgression patterns revealed asymmetries in the direction of introgression, but except for mtDNA, we did not find evidence for nonconcordant introgression patterns across nuclear loci. Analysis of a 150‐km transect across the hybrid zone showed broadly coincident cline widths (ca. 3.2–27.9 km), and concordant cline centres across all markers, except for mtDNA that is displaced ca. 60 km northward. Results from ecological niche modelling show that the hybrid zone is in a climatically homogenous area with suitable habitat for the species, suggesting that contact between the two lineages is unlikely to occur further south as their distributions are currently separated by an extensive area of unfavourable habitat. Taken together, our findings suggest the genetic structure of this hybrid zone results from the interplay of historical (biogeographic) and population‐level processes. The narrowness and coincidence of genetic clines can be explained by weak selection against hybrids and reflect a degree of reproductive isolation that is consistent with cryptic speciation. [ABSTRACT FROM AUTHOR]

Chicken have a considerable impact in South American rural household economy as a source of animal protein (eggs and meat) and a major role in cultural traditions (e.g., cockfighting, religious ceremonies, folklore). A large number of phenotypes and its heterogeneity are due to the multitude of environments (from arid to tropical rain forest and high altitude) and agricultural systems (highly industrialized to subsistence agriculture). This heterogeneity also represents the successive introduction of domestic chicken into this continent, which some consider predating Columbus' arrival to South America. In this study, we have used next-generation restriction site-associated DNA sequencing to scan for genome-wide variation across 145 South American chickens representing local populations from six countries of South America (Colombia, Brazil, Ecuador, Peru, Bolivia, and Chile). After quality control, the genotypes of 122,801 single nucleotide polymorphisms (SNPs) were used to assess the genomic diversity and interpopulation genetic relationship between those populations and their potential sources. The estimated population genetic diversity displayed that the gamefowl has the least diverse population (θπ = 0.86; θS = 0.70). This population is also the most divergent (F ST = 0.11) among the South American populations. The allele-sharing analysis and the admixture analysis revealed that the current diversity displayed by these populations resulted from multiple admixture events with a strong influence of the modern commercial egg-layer chicken (ranging between 44% and 79%). It also revealed an unknown genetic component that is mostly present in the Easter Island population that is also present in local chicken populations from the South American Pacific fringe. [ABSTRACT FROM AUTHOR]

The mimetic juveniles of a number of carangid fish species resemble plant parts floating near the water surface, such as leaves, seeds and other plant debris. The present study is the first to verify the morphological similarities and ecomorphological relationships between three carangids (Oligoplites saurus, Oligoplites palometa and Trachinotus falcatus) and their associated plant models. Behavioral observations were conducted in the estuary of Curuçá River, in northeastern Pará (Brazil) between August 2015 and July 2016. Individual fishes and associated floating objects (models) were sampled for comparative analysis using both geometric and morphometric approaches. While the mimetic fish and their models retain their own distinct, intrinsic morphological features, a high degree of morphological similarity was found between each fish species and its model. The morphometric analyses revealed a general tendency of isometric development in all three fish species, probably related to their pelagic habitats, during all ontogenetic stages. [ABSTRACT FROM AUTHOR]

Background: Cane toads (Rhinella marina) are an iconic invasive species introduced to 4 continents and well utilized for studies of rapid evolution in introduced environments. Despite the long introduction history of this species, its profound ecological impacts, and its utility for demonstrating evolutionary principles, genetic information is sparse. Here we produce a de novo transcriptome spanning multiple tissues and life stages to enable investigation of the genetic basis of previously identified rapid phenotypic change over the introduced range. Findings: Using approximately 1.9 billion reads from developing tadpoles and 6 adult tissue-specific cDNA libraries, as well as a transcriptome assembly pipeline encompassing 100 separate de novo assemblies, we constructed 62 202 transcripts, of which we functionally annotated ~50%. Our transcriptome assembly exhibits 90% full-length completeness of the Benchmarking Universal Single-Copy Orthologs data set. Robust assembly metrics and comparisons with several available anuran transcriptomes and genomes indicate that our cane toad assembly is one of the most complete anuran genomic resources available. Conclusions: This comprehensive anuran transcriptome will provide a valuable resource for investigation of genes under selection during invasion in cane toads, but will also greatly expand our general knowledge of anuran genomes, which are underrepresented in the literature. The data set is publically available in NCBI and GigaDB to serve as a resource for other researchers. [ABSTRACT FROM AUTHOR]

Introgression following hybridization is increasingly accepted as a widespread evolutionary phenomenon in animal species. Previous studies have suggested an extensive unidirectional introgression between two common Neotropical toads (Rhinella marina and R. schneideri). Here, we sought to investigate the extent of hybridization between these species and the evolutionary consequences of this process. For this, we used a comprehensive suite of molecular markers (one mtDNA, three scnDNA, and seven microsatellites) and an expanded sample. Our multilocus approach revealed a complex pattern of hybridization, involving an undocumented cryptic evolutionary lineage (RAB2). This new lineage is likely to have had a long, independent, and evolutionary history, as revealed by the split time from both R. marina and R. schneideri that was inferred to have occurred in the Late Miocene/Early Pliocene (~6 Myr, 95% CI; 3.79-8.32). Interestingly, RAB2 occurs in sympatry/syntopy with some populations of R. marina from RAB, where cases of introgression were apparent at both the mtDNA and nuclear levels. Unexpectedly, however, no evidence of ongoing gene flow between R. marina and R. schneideri was detected, suggesting that the extensive cytonuclear discordance found in R. schneideri probably reflects an ancient introgression following hybridization with R. marina. Overall, this study showed that potentially overlooked cryptic lineages might contribute to biased inferences in the patterns of introgressive hybridization. These findings highlight the pitfalls of inferring evolutionary processes in groups of morphologically cryptic species. [ABSTRACT FROM AUTHOR]

This study tested the effectiveness of COI barcodes for the discrimination of anuran species from the Amazon basin and other Neotropical regions. Barcodes were determined for a total of 59 species, with a further 58 species being included from GenBank. In most cases, distinguishing species using the barcodes was straightforward. Each species had a distinct COI barcode or codes, with intraspecific distances ranging from 0% to 9.9%. However, relatively high intraspecific divergence (11.4-19.4%) was observed in some species, such as Ranitomeya ventrimaculata, Craugastor fitzingeri, Hypsiboas leptolineatus, Scinax fuscomarginatus and Leptodactylus knudseni, which may reflect errors of identification or the presence of a species complex. Intraspecific distances recorded in species for which samples were obtained from GenBank (Engystomops pustulosus, Atelopus varius, Craugastor podiciferus, and Dendropsophus labialis) were greater than those between many pairs of species. Interspecific distances ranged between 11-39%. Overall, the clear differences observed between most intra- and inter-specific distances indicate that the COI barcode is an effective tool for the identification of Neotropical species in most of the cases analyzed in the present study. [ABSTRACT FROM AUTHOR]

This study presents evidence of concerted evolution in the mitochondrial control region of the frogPseudopaludicola canga. Four repeat units of 88 bp (as well as a fifth, incomplete unit) were observed in the 5′ domain, with the duplicated segments of the same specimen being more related to one another than to the equivalent regions in other specimens, as a result of concerted evolution. We highlight that drawing conclusions from phylogeographical analysis using the control region containing VNTRs must be interpreted with caution, because it violated a basic assumption of phylogeny, since the regions cannot be treated as independent characters. [ABSTRACT FROM AUTHOR]

Fishes of the genus Eleotris present highly conserved morphology, which may make their recognition difficult. Here, two cryptic Eleotris lineages from five locations along the coast of Brazil were identified using the COI gene and two nuclear fragments. High bootstrap and posteriori values supported those lineages, and the genetic distance of COI varied from 6% between the two lineages to 14.1% from other western Atlantic Eleotris species, such as E. pisonis , E. amblyopsis and E. perniger. The reciprocal monophyly for both types of markers, the divergences between those lineages and the other Eleotris species from the Brazilian coast may, in fact, represent two new cryptic species. The cryptic lineages and currently recognized species were collected in distinct environments, reinforcing the need for further sampling to understand the real distribution of each taxon. [ABSTRACT FROM AUTHOR]

The Amazonian coast has several unique geological characteristics resulting from the interaction between drainage pattern of the Amazon River and the Atlantic Ocean. It is one of the most extensive and sedimentologically dynamic regions of the world, with a large number of continental islands mostly formed less than 10,000 years ago. The natural distribution of the cane toad (Rhinella marina), one of the world’s most successful invasive species, in this complex Amazonian system provides an intriguing model for the investigation of the effects of isolation or the combined effects of isolation and habitat dynamic changes on patterns of genetic variability and population differentiation. We used nine fast-evolving microsatellite loci to contrast patterns of genetic variability in six coastal (three mainlands and three islands) populations of the cane toad near the mouth of the Amazon River. Results from Bayesian multilocus clustering approach and Discriminant Analyses of Principal Component were congruent in showing that each island population was genetically differentiated from the mainland populations. All FST values obtained from all pairwise comparisons were significant, ranging from 0.048 to 0.186. Estimates of both recent and historical gene flow were not significantly different from zero across all population pairs, except the two mainland populations inhabiting continuous habitats. Patterns of population differentiation, with a high level of population substructure and absence/restricted gene flow, suggested that island populations of R. marina are likely isolated since the Holocene sea-level rise. However, considering the similar levels of genetic variability found in both island and mainland populations, it is reliable to assume that they were also isolated for longer periods. Given the genetic uniqueness of each cane toad population, together with the high natural vulnerability of the coastal regions and intense human pressures, we suggest that these populations should be treated as discrete units for conservation management purposes. [ABSTRACT FROM AUTHOR]

Mimesis is a relatively widespread phenomenon among reef fish, but the ontogenetic processes relevant for mimetic associations in fish are still poorly understood. In the present study, the allometric growth of two allopatric leaf-mimetic species of ephippid fishes, Chaetodipterus faber from the Atlantic and Platax orbicularis from the Indo-Pacific, was analyzed using ten morphological variables. The development of fins was considered owing to the importance of these structures for mimetic behaviors during early life stages. Despite the anatomical and behavioral similarities in both juvenile and adult stages, C. faber and P. orbicularis showed distinct patterns of growth. The overall shape of C. faber transforms from a rounded-shape in mimetic juveniles to a lengthened profile in adults, while in P. orbicularis, juveniles present an oblong profile including dorsal and anal fins, with relative fin size diminishing while the overall profile grows rounder in adults. Although the two species are closely-related, the present results suggest that growth patterns in C. faber and P. orbicularis are different, and are probably independent events in ephippids that have resulted from similar selective processes. [ABSTRACT FROM AUTHOR]

Historical events, such as changes in sea level during the Pleistocene glacial cycles, had a strong impact on coastal habitats, limiting connectivity and promoting the genetic divergence of various species. In this study, we evaluated the influence of climate oscillations and the possibility of estuary function as a barrier to gene flow among populations of the four-eyed fish, Anableps anableps. This species is fully estuarine-resident, has internal fertilization, is viviparous and does not migrate across long distances. These features make the four-eyed fish an excellent model for the study of evolutionary processes related to genetic differentiation of species and populations in estuaries. The evolutionary history of A. anableps was inferred from phylogeographic and population analyses using sequences of the mitochondrial DNA Control Region of 13 populations distributed in the Amazon and Northeast Coast of Brazil from Calcoene (Amapa) to Parnaiba (Piaui). The 83 retrieved haplotypes show a pattern of four distinct mitochondrial lineages, with up to 3.4% nucleotide divergence among them. The evolutionary reconstruction suggests that these lineages diverged recently in the late Pleistocene/early Holocene after the Atlantic Ocean reaching current levels. Analysis of variability, neutrality and the genetic expansion pattern revealed that the lineages have distinct characteristics, which were shaped by the different geomorphological features of coastal regions combined with sea level oscillations over a very long period of time. Only few neighboring populations show a discreet gene flow. This study may also be helpful for designing new experiments to better understand the geomorphological evolutionary history of the estuaries of the Amazon and the Northeast Coast of Brazil using estuarine-resident species as a model. [ABSTRACT FROM AUTHOR]

Schneider, H., Bernardi, J. A. R., da Cunha, D. B., Tagliaro, C. H., Vallinoto, M., Ferrari, S. F. & Sampaio, I. (2011). A molecular analysis of the evolutionary relationships in the Callitrichinae, with emphasis on the position of the dwarf marmoset. - Zoologica Scripta, 41, 1-10. The phylogenetic relationships among the Neotropical primates of the subfamily Callitrichinae (marmosets and tamarins) are controversial, especially with regard to the proposal of a new marmoset genus, Callibella, based on the analysis of sequences of a single mitochondrial gene. In this study, we combine the fast-evolving mitochondrial Control Region with four nuclear regions containing Alu elements in an attempt to provide a more conclusive assessment of the phylogenetic relationships among the marmosets ( Callithrix, Cebuella and Mico), with special attention to the validity of Callibella. A large, representative sample of specimens was obtained, which include all the recognized genera and principal morphological and geographic groupings. The results of the analysis indicate unequivocally the existence of three independent lineages, corresponding to the Atlantic Forest ( Callithrix), Amazonian ( Mico) and pygmy marmoset ( Cebuella) groups. The evidence also confirms the monophyletic relationship of the dwarf marmoset ( Callibella) with the Amazonian marmosets ( Mico), which indicates conclusively that this taxon is a member of the genus Mico, upholding the original description of the species as Mico humilis. [ABSTRACT FROM AUTHOR]

This study presents a molecular phylogeny of the Saguinus genus, based on the analysis of the DNA sequences of five nuclear loci with Alu insertions in 10 species. The concatenated alignment produced a polytomic arrangement with four main groups, although only two clades-the Amazonian ( S. midas, S. niger, and S. bicolor) and the Colombian ( S. leucopus and S. oedipus) tamarins-were statistically significant. The emergence of the midas- bicolor clade was estimated at about 5 million years ago (mya), and that of the Colombian clade, at 4.6 mya. The phylogenetic relationships among the mustached tamarins ( S. mystax, S. imperator, and S. labiatus) remained unresolved, as did the internal arrangement of the midas group. The lack of a clear consensus on the phylogeny of this group may be related to rapid bursts of evolutionary change within the context of a highly dynamic environment, which may be difficult to resolve using the available quantitative approaches. On the other hand, the discrepancies between mtDNA and nDNA in resolving phylogenies strongly indicate the role of reticulated evolution in the evolutionary history of this group. We hope that the advance of whole genome sequencing technology and increasing information on nuclear markers and SNPs, coupled with a better understanding of the geological phenomena that took place in western Amazonia over the past 20 million years, will shed further light on the phylogenetic history of these New World primates. Am J Phys Anthropol, 2011. © 2011 Wiley-Liss, Inc. [ABSTRACT FROM AUTHOR]

The mullets of the family Mugilidae, and in particular the species of the genus Mugil, are characterized by highly conserved morphological features, which hinder taxonomic classi￠cation considerably. Given this, the present study aimed to evaluate the efficiency of the 5S rDNA gene ^ a rapid and low cost genotyping marker ^ for the discrimination of Mugil species.Variations in the banding pattern permitted the reliable di!erentiation of four species ^ Mugil curema, Mugil incilis, Mugil sp. and Mugil hospes ^ although those of three others (Mugil liza, Mugil platanus and Mugil cephalus) were identical. This suggests that these three forms have diverged very recently, on a time scale that has limitedchanges in the length of the fragments of the 5S rDNA gene. The results of the study con￠rm the e⁄ciency of this marker as a diagnostic tool for the identi￠cation of Mugil species, and its usefulness for population management and pisciculture, an important economic activity involving this group. [ABSTRACT FROM AUTHOR]

We report new primers for the amplification and sequencing of 11 nuclear markers in squamate reptiles and anuran amphibians (five in squamates, six in anurans). Ten out of the 11 loci are introns (three of which are linked) that were amplified using an exon-primed, intron-crossing (EPIC) PCR strategy, whereas an eleventh locus spans part of a protein-coding gene. Squamate and anuran primers were initially developed for Lacerta schreiberi (Squamata: Lacertidae) and Pelodytes spp. (Anura: Pelodytidae), respectively. Cross-species amplification of the squamate markers was evaluated in four genera representing two additional families, whereas for anurans three genera corresponding to three additional families were tested. Three out of the five loci were successfully sequenced in all squamate taxa tested. Cross-amplification of the six anuran markers had lower, but still significant, success. We predict these markers will be of great utility for both population genetics and phylogenetic studies. [ABSTRACT FROM AUTHOR]

Vallinoto, M., Sequeira, F., Sodré, D., Bernardi, J. A. R., Sampaio, I. & Schneider, H. (2009). Phylogeny and biogeography of the Rhinella marina species complex (Amphibia, Bufonidae) revisited: implications for Neotropical diversification hypotheses. — Zoologica Scripta, 39, 128–140. A number of distinct hypotheses have been proposed to account for the origin of the considerable biological diversity found in the Neotropics, which is still a matter of intense debate. Here, we conducted a phylogenetic analysis of the Rhinella marina complex, a group of species widely distributed in Central and South America, combining published data with new sequences of three mtDNA genes (12S, 16S and cyt b) in order to clarify the evolutionary relationships and biogeographical history of the group. We included eight of the ten currently recognized R. marina group species and several outgroups. Maximum parsimony, maximum likelihood, and Bayesian inference analyses produced similar topologies, with two well-supported main clades, each characterized by a deep subdivision. One of these major clades includes the samples of R. marina from Central America and Ecuador (west of the Andes), whereas the other comprises the remaining species of the group and samples of R. marina from the Amazon basin and other areas east of the Andes. A Bayesian coalescent-based method (BEAST) dated the divergence between the two major clades, and between the Central American and Ecuadorian clades to the Miocene, matching the timing of other Central-South American faunal divergences. Taken together, the results highlight the importance of Tertiary events such as the Pebas/marine incursions into the Amazon basin and Andean uplift for the diversification and historical biogeography of R. marina, making such taxa paraphyletic, and provide new perspectives on the debate on its species status. [ABSTRACT FROM AUTHOR]