SynGenes: a Python class for standardizing nomenclatures of mitochondrial and chloroplast genes and a web form for enhancing searches for evolutionary analyses

BACKGROUND

The reconstruction of the evolutionary history of organisms has been greatly influenced by the advent of molecular techniques, leading to a significant increase in studies utilizing genomic data from different species. However, the lack of standardization in gene nomenclature poses a challenge in database searches and evolutionary analyses, impacting the accuracy of results obtained.

RESULTS

To address this issue, a Python class for standardizing gene nomenclatures, SynGenes, has been developed. It automatically recognizes and converts different nomenclature variations into a standardized form, facilitating comprehensive and accurate searches. Additionally, SynGenes offers a web form for individual searches using different names associated with the same gene. The SynGenes database contains a total of 545 gene name variations for mitochondrial and 2485 for chloroplasts genes, providing a valuable resource for researchers.

CONCLUSIONS

The SynGenes platform offers a solution for standardizing gene nomenclatures of mitochondrial and chloroplast genes and providing a standardized search solution for specific markers in GenBank. Evaluation of SynGenes effectiveness through research conducted on GenBank and PubMedCentral demonstrated its ability to yield a greater number of outcomes compared to conventional searches, ensuring more comprehensive and accurate results. This tool is crucial for accurate database searches, and consequently, evolutionary analyses, addressing the challenges posed by non-standardized gene nomenclature.

Genomic characterization of a novel Hepatovirus identified in Maranhão state, Brazil

Bats are efficient reservoirs of a number of viruses with zoonotic potential, and are involved directly in the transmission cycle of many zoonoses. In the present study, which is part of a larger project that is documenting the viromes of the bat species found in the Mid-North states of Maranhão and Piauí, we analyzed 16 pooled samples obtained from four species of bat of the genus Artibeus-Artibeus obscurus, Artibeus cinereus, Artibeus lituratus and Artibeus planirostris. We describe and identify a Hepatovirus, denominated Hepatovirus H isolate sotense, which was found in a pool of internal organs (liver and lungs) extracted from a specimen of A. planirostris, a frugivorous bat, collected in the Cerrado biome of Maranhão state. This material was analyzed using new generation sequencing, which produced a contig of 7390 nucleotides and presented a degree of identity with a number of existing Hepatovirus sequences available for bats (amino acid identity of 61.5% with Bat hepatovirus C of Miniopterus cf. manavi, 66.6% with Bat hepatovirus G of Coleura afra, 67.4% with Hepatovirus G2 of Rhinolophus landeri, and 75.3% with Hepatovirus H2 of Rhinolophus landeri). The analysis of the functional domains of this contig confirmed a pattern consistent with the characteristics of the genus Hepatovirus (Picornaviridae). In the phylogenetic tree with several other Hepatovirus species, this genome also grouped in a monophyletic clade with Hepatovirus H (HepV-H1; HepV-H2, and HepV-H3) albeit on an external branch, which suggests that it may be a distinct genotype within this species. This is the first isolate of Hepatovirus H identified in bats from South America, and represents an important discovery, given that most studies of viruses associated with bats in the state of Maranhão have focused on the family Rhabdoviridae.

Comparative cytogenetics of microsatellite distribution in two tetra fishes Astyanax bimaculatus (Linnaeus, 1758) and Psalidodon scabripinnis (Jenyns, 1842)

Background

The main cytogenetic studies of the Characidae family comprise the genera Astyanax and Psalidodon involving the use of repetitive DNA probes. However, for the microsatellite classes, studies are still scarce and the function of these sequences in the genome of these individuals is still not understood. Thus, we aimed to analyze and compare the distribution of microsatellite sequences in the species Astyanax bimaculatus and Psalidodon scabripinnis.

Methods

We collected biopsies from the fins of A. bimaculatus and P. scabripinnis to perform cell culture, followed by chromosome extraction, and mapped the distribution of 14 microsatellites by FISH in both species.

Results and Discussion

The diploid number observed for both species was 2n = 50, with an acrocentric B microchromosome in A. bimaculatus and a metacentric B chromosome in P. scabripinnis. Regarding FISH, 11 probes hybridized in the karyotype of A. bimaculatus mainly in centromeric regions, and 13 probes hybridized in P. scabripinnis, mainly in telomeric regions, in addition to a large accumulation of microsatellite hybridization on its B chromosome.

Conclusion

Comparative FISH mapping of 14 microsatellite motifs revealed different patterns of distribution both in autosomes and supernumerary chromosomes of A. bimaculatus and P. scabripinnis, suggesting independent evolutionary processes in each of these species, representing excellent data on chromosome rearrangements and cytotaxonomy.

Molossusmelini Montani et al. 2021 (Chiroptera, Molossidae) in Brazil: new insights for distribuition, morphology and genetics

Background

The species M.melini has been observed in both the Pampa and Spinal ecoregions of Argentina. Researchers have underscored that distinguishing M.melini from other species within the same genus relies primarily on craniometric and molecular analyses. Morphological measurements alone do not offer a clear differentiation between M.melini and other members of this genus.This study aims to document the presence of M.melini within the Brazilian ecoregion, focusing on its morphological, morphometric and genetic characteristics. By undertaking a comprehensive examination, we seek to contribute valuable insights into the distribution and differentiation of M.melini in this region.

New information

Molossusmelini specimens exhibited a forearm length ranging from 39.9 to 40.08 mm. The average intraspecific divergence was 1.2%, with specimens from the Argentine Pampas clustering in the same clade with a 98% bootstrap support and a posterior probability of: Regarding dorsal colouration, the specimens displayed fur with two bands-a Snow White base colour and apex colours ranging from Olive Brown, Broccoli Brown, Wood Brown to Yellowish-Brown. This marks the first record of M.melini in Brazil, expanding its distribution 1,300 km northeastwards into the Curitiba, Paraná, Atlantic Forest Ecoregion. The findings contribute valuable information on the distribution, morphology, morphometrics and genetics of this species.

Comparative mitochondrial genome brings insights to slight variation in gene proportion and large intergenic spacer and phylogenetic relationship of mudskipper species

Fish mitochondrial genome have been largely studied worldwide for evolutionary and other genetic purposes and the structure and gene organization are commonly conservative. However, several studies have demonstrated that this scenario may present variations in some taxa, showing differentiation on the gene rearrangement. In this study, the complete mitogenome of terrestrial fish Boleophthalmus dussumieri was generated and compared with other species of the Exudercidae fishes. The newly complete mitogenome generated is circular and 16,685 bp of length, and it contained 13 protein-coding genes (PCGs), two ribosomal RNA (rRNAs), 22 transfer RNA genes (tRNAs), and one control region (CR), with high conservative structure, like other Mudskippers. Most of the PCG showed similar codon usage bias. The gene length was found to be different specially for the CR, 12S rRNA gene and ND5 gene in some taxon. All the Boleophthalmus species showed a gene duplication in the CR, except for B. dussumieri, and they presented a long intergenic spacer specially on the tRNA-Pro/ OH Tandem duplication/random loss (TDRL) and dimer-mitogenome and nonrandom loss (DMNL) are suitable to explain the mitogenome rearrangement observed in this study. The phylogenetic analysis well supported the monophyly of all mudskipper species and the analysis positioned the Periophthalmus clade as the most basal of the terrestrial fishes. This finding provides basis and brings insights for gene variation, gene rearrangements and replications showing evidence for variety of mitochondrial structure diversity within mudskippers.

First neurotranscriptome of adults Tambaquis (Colossoma macropomum) with characterization and differential expression between males and females

The Tambaqui is one of the most representative Amazon fish species, being highly exploited in fisheries, aquaculture and as a research model. Nonetheless, data about functional genome are still required to evaluate reproductive and nutrition parameters as well as resistance to pathogens. The of next-generation sequencing has allows assessing the transcriptional processes in non-model species by providing comprehensive gene collections to be used as a database in further genomic applications and increased performance of captive populations. In this study, we relied on RNAseq approach to generate the first transcriptome of the telencephalon from adult males and females of Colossoma macropomum, resulting in a reference dataset for future functional studies. We retrieved 896,238 transcripts, including the identification of 267,785 contigs and 203,790 genes. From this total, 91 transcripts were differentially expressed, being 63 and 28 of them positively regulated for females and males, respectively. The functional annotation resulted in a library of 40 candidate genes for females and 20 for males. The functional enrichment classes comprised reproductive processes (GO:0,048,609; GO:0,003,006; GO:0,044,703; GO:0,032,504; GO:0,019,953) being related to sex differentiation (e.g., SAFB) and immune response (e.g., SLC2A6, AHNAK, NLRC3, NLRP3 and IgC MHC I alpha3), thus indicating that the genes in the neurotranscriptome of Tambaqui participate in sex differentiation and homeostasis of captive specimens. These data are useful to design the selection of genes related to sex determination and animal welfare in raising systems of Tambaqui.

DNA barcoding for the assessment of marine and coastal fish diversity from the Coast of Mozambique

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.

Identification of constrained sequence elements across 239 primate genomes

Noncoding DNA is central to our understanding of human gene regulation and complex diseases1,2, and measuring the evolutionary sequence constraint can establish the functional relevance of putative regulatory elements in the human genome3-9. Identifying the genomic elements that have become constrained specifically in primates has been hampered by the faster evolution of noncoding DNA compared to protein-coding DNA10, the relatively short timescales separating primate species11, and the previously limited availability of whole-genome sequences12. Here we construct a whole-genome alignment of 239 species, representing nearly half of all extant species in the primate order. Using this resource, we identified human regulatory elements that are under selective constraint across primates and other mammals at a 5% false discovery rate. We detected 111,318 DNase I hypersensitivity sites and 267,410 transcription factor binding sites that are constrained specifically in primates but not across other placental mammals and validate their cis-regulatory effects on gene expression. These regulatory elements are enriched for human genetic variants that affect gene expression and complex traits and diseases. Our results highlight the important role of recent evolution in regulatory sequence elements differentiating primates, including humans, from other placental mammals.

Species delimitation by DNA barcoding reveals undescribed diversity in Stelliferinae (Sciaenidae)

Stelliferinae is the third most speciose subfamily of Sciaenidae, with 51 recognized species arranged in five genera. Phylogenies derived from both morphological and molecular data support the monophyly of this subfamily, although there is no general consensus on the intergeneric relationships or the species diversity of this group. We used the barcoding region of the cytochrome oxidase C subunit I (COI) gene to verify the delimitation of Stelliferinae species based on the Automatic Barcode Gap Discovery (ABGD), Generalized Mixed Yule Coalescence (GMYC), and Bayesian Poisson Tree Process (bPTP) methods. In general, the results of these different approaches were congruent, delimiting 30-32 molecular operational taxonomic units (MOTUs), most of which coincided with valid species. Specimens of Stellifer menezesi and Stellifer gomezi were attributed to a single species, which disagrees with the most recent review of this genus. The evidence also indicated that Odontoscion xanthops and Corvula macrops belong to a single MOTU. In contrast, evidence also indicates presence of distinct lineages in both Odontoscion dentex and Bairdiella chrysoura. Such results are compatible with the existence of cryptic species, which is supported by the genetic divergence and haplotype genealogy. Therefore, the results of the present study indicate the existence of undescribed diversity in the Stelliferinae, which reinforces the need for an ample taxonomic review of the fish in this subfamily.

Molecular delimitation methods validate morphologically similar species of red snappers (Perciformes: Lutjanidae)

In this study, we tested the taxonomic validation of red snappers species (Southern red snapper Lutjanus purpureus; Silk snapper L. vivanus; Blackfin snapper L. buccanella; and Pacific red snapper L. peru) based on comparative analysis, using four methods for species delimitation. These methods were based on either genetic similarity or phylogenetic trees inferred from two mitochondrial (Cytochrome b and D-loop) and two nuclear (Myostatin and S7 introns) markers. On one hand, the genetic results corroborated the presence of four red snapper species, confirming their taxonomic validation despite their remarkable morphological similarity. On the other hand, few incongruencies in the species delimitation methods were observed according to the phylogenetic reconstruction method (maximum likelihood or Bayesian inference) when using. Based on the phylogenetic results, L. buccanella should represent a more ancient lineage in relation to the clade that encompasses L. purpureus, L. peru and L. vivanus. The single-locus phylogenetic analysis based on Cytb recovered each the red snapper species as a well-supported clade. Overall, this study provided a DNA-based validation of the traditional morphological taxonomy of red snappers.

Sequencing and Analysis of the Mitochondrial Genome of Aedes aegypti (Diptera: Culicidae) from the Brazilian Amazon Region

Aedes aegypti is a mosquito native to the African continent, which is now widespread in the tropical and subtropical regions of the world. In many regions, it represents a major challenge to public health, given its role in the cycle of transmission of important arboviruses, such as Dengue, Zika, and Chikungunya. Considering the epidemiological importance of Ae. aegypti, the present study sequenced the partial mitochondrial genome of a sample collected in the municipality of Balsas, in the Brazilian state of Maranhão, followed by High Throughput Sequencing and phylogenetic analyses. The mitochondrial sequence obtained here was 15,863 bp long, and contained 37 functional subunits (thirteen PCGs, twenty-two tRNAs and two rRNAs) in addition to a partial final portion rich in A+T. The data obtained here contribute to the enrichment of our knowledge of the taxonomy and evolutionary biology of this prominent disease vector. These findings represent an important advancement in the understanding of the characteristics of the populations of northeastern Brazil and provide valuable insights into the taxonomy and evolutionary biology of this prominent disease vector.

Genetic Diversity in Natural Populations of the Near-Threatened Species Lignobrycon myersi (Characiformes, Triportheidae): Implications for Species Conservation

The river basins of Brazil contain a highly diverse ichthyofauna of remarkable endemism, including several threatened species. Accordingly, Lignobrycon myersi is a fish species distributed only in a few rivers from the state of Bahia, northeastern Brazil. Since this species is classified as Near Threatened and is poorly studied, efforts to understand the genetic structure of populations and putative cryptic forms should help define efficient strategies of management and conservation. Herein, the molecular identification and the population genetic diversity of specimens of L. myersi across their range (Almada, Contas, and Cachoeira river basins) were assessed using mitochondrial markers (16S rDNA and D-Loop, respectively). The inferences based on phylogenetics, genetic distance, and species delimitation methods invariably identified all samples as L. myersi. In addition, sequencing of D-loop fragments revealed significant haplotype diversity and a considerable level of population genetic structure. Despite their geographic isolation, these data suggested that populations from Almada and Contas rivers represent a single evolutionary lineage that could be managed as a whole. In contrast, the population from Cachoeira River was highly differentiated from the others and should be managed separately as a unique and endemic unit, particularly focused on the conservation of native habitats.

DNA barcode reveals occurrence of threatened species and hidden diversity on Teleost fish trade in the Coastal Amazon

This study aimed to identify the teleost fish species sold in Bragança, a major fishing hub on the north coast of Brazil. The COI gene analysis was performed for the identification of fish species. The local market uses common names that are not accurate and do not reflect the diversity of the species. 204 sequences were obtained, with 119 haplotypes. 83 species were identified by comparing with public databases and constructing phylogenetic trees, with Carangidae being the most prevalent family. The study also found Haemulon atlanticus, Menticirrhus cuiaranensis and Hoplias misioneira, a newly described species from the Amazon basin, among the samples. Additionally, 73 commercial names were recorded, including 10 categories, and the illegal trade of Epinephelus itajara was detected. The DNA Barcode method proved to be effective for discriminating the species. The study highlights that common and commercial names are vague and underestimate the fish diversity, and that Brazil needs to revise its regulations for commercial and scientific names.

In silico prospecting of the mtDNA of Macrobrachium amazonicum from transcriptome data

BACKGROUND

Macrobrachium amazonicum is a freshwater prawn widely distributed in South America that is undergoing speciation, so the denomination "M. amazonicum complex" is used for it. The mitochondrial cytochrome c oxidase subunit I (COI) gene has been used to elucidate this speciation, but heteroplasmies and pseudogenes have been recorded, making separation difficult. Obtaining genes from cDNA (RNA) rather than genomic DNA is an effective tool to mitigate those two types of occurrences. The aim of this study was to assemble in silico the mitochondrial DNA (mtDNA) of the Amazonian coastal population of M. amazonicum inhabiting the state of Pará.

RESULTS

Sequences were obtained from the prawn's transcriptome using the de novo approach. Six libraries of cDNA from the androgen gland, hepatopancreas, and muscle tissue were used. The mtDNA of M. amazonicum was 14,960 bp in length. It contained 13 protein-coding genes, 21 complete transfer RNAs, and the 12S and 16S subunits of ribosomal RNA. All regions were found on the light strand except tRNAGln, which was on the heavy strand. The control region (D-loop) was not recovered, making for a gap of 793 bp. The cladogram showed the formation of the well-defined Macrobrachium clade, with high support value in the established branches (91-100). The three-dimensional spatial conformation of the mtDNA-encoded proteins showed that most of them were mainly composed of major α-helices that typically shows in those proteins inserted in the membrane (mitochondrial).

CONCLUSIONS

It was possible to assemble a large part of the mitochondrial genome of M. amazonicum in silico using data from other genomes deposited in GenBank and to validate it through the similarities between its COI and 16S genes and those from animals of the same region deposited in GenBank. Depositing the M. amazonicum mtDNA sequences in GenBank may help solve the taxonomic problems recorded for the species, in addition to providing complete sequences of candidate coding genes for use as biomarkers in ecological studies.

Genetic diversity analysis in the Brazilian Amazon reveals a new evolutionary lineage and new karyotype for the genus Mesomys (Rodentia, Echimyidae, Eumysopinae)

Morphological, molecular and chromosomal studies in the genera Lonchothrix and Mesomys have contributed to a better understanding of taxonomic design, phylogenetic relationships and karyotypic patterns. Recent molecular investigations have shown a yet undescribed diversity, suggesting that these taxa are even more diverse than previously assumed. Furthermore, some authors have questioned the limits of geographic distribution in the Amazon region for the species M. hispidus and M. stimulax. In this sense, the current study sought to understand the karyotypic evolution and geographic limits of the genus Mesomys, based on classical (G- and C-banding) and molecular cytogenetic analysis (FISH using rDNA 18S and telomeric probes) and through the sequencing of mitochondrial genes Cytochrome b (Cytb) and Cytochrome Oxidase-Subunit I (CO using phylogeny, species delimitation and time of divergence, from samples of different locations in the Brazilian Amazon. The species M. stimulax and Mesomys sp. presented 2n = 60/FN = 110, while M. hispidus presented 2n = 60/FN = 112, hitherto unpublished. Molecular dating showed that Mesomys diversification occurred during the Plio-Pleistocene period, with M. occultus diverging at around 5.1 Ma, followed by Mesomys sp. (4.1 Ma) and, more recently, the separation between M. hispidus and M. stimulax (3.5 Ma). The ABGD and ASAP species delimiters support the formation of 7 and 8 potential species of the genus Mesomys, respectively. Furthermore, in both analyzes Mesomys sp. was recovered as a valid species. Our multidisciplinary approach involving karyotypic, molecular and biogeographic analysis is the first performed in Mesomys, with the description of a new karyotype for M. hispidus, a new independent lineage for the genus and new distribution data for M. hispidus and M. stimulax.

Molecular characterization of juvenile fish from the Amazon estuary using DNA barcoding approach

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.

Genetic connectivity and population expansion inferred from multilocus analysis in Lutjanus alexandrei (Lutjanidae-Perciformes), an endemic snapper from Northeastern Brazilian coast

Previous studies about the genetic diversity, connectivity and demographic history in Lutjanidae fishes have reported a common pattern of genetic homogeneity and expansion in populations from Western South Atlantic. In the present work, we inferred the population structure, the levels of genetic diversity and the demographic history of the Brazilian snapper Lutjanus alexandrei, a recently described and endemic species from Northeastern coast of Brazil. Five different fragments, including mitochondrial DNA (Control Region, Cyt b and ND4) and nuclear DNA (Myostatin and S7) regions were analyzed in 120 specimens of L. alexandrei from four localities in Northeastern Brazil, representing the first study of population genetics in this species. High levels of genetic diversity were observed following a panmictic pattern, probably related to the larval dispersal by the current tides along the Brazilian coast. In addition, both demographic history and neutrality tests indicated that L. alexandrei has undergone population expansion during Pleistocene. In this sense, the sea level variation from this period could have increased the available resources and suitable habitats for the Brazilian snapper.

Molecular Evidence Supports Five Lineages within Chiropotes (Pitheciidae, Platyrrhini)

Pitheciines have unique dental specializations among New World monkeys that allow them to feed on fruits with hard pericarps, thus playing a major role as seed predators. The three extant pitheciine genera, Pithecia, Cacajao and Chiropotes, are all endemic to the Amazon region. Because of the uncertainties about interspecific relationships, we reviewed the systematics and taxonomy of the genus Chiropotes. The phylogenetic analyses were performed based on Maximum Likelihood and Bayesian Inference, while species delimitation analyses were carried out using multispecies coalescent methods. In addition, we estimated genetic distances, divergence time and the probable ancestral distribution of this genus. Our results support five species of Chiropotes that emerged during the Plio-Pleistocene. Biogeographic estimates suggest that the ancestor of the current Chiropotes species occupied the endemism areas from Rondônia and Tapajós. Later, subsequent radiation and founder effects associated with the formation of the Amazonian basins probably determined the speciation events within Chiropotes.

Genetic Differentiation of Aedes aegypti (Diptera: Culicidae) in Areas with High Rates of Infestation in Mid-North Region of Brazil

Aedes aegypti is the principal vector of the arboviruses-yellow fever, dengue virus, chikungunya, and zika virus. Given the epidemiological importance of this mosquito, its capacity to adapt to different habitats, and its resistance to many types of control measures, systematic research into the genetic variability of the populations of this mosquito is one of the most important steps toward a better understanding of its population structure and vector competence. In this context, the present study verified the presence of distinct genetic lineages of Ae. aegypti in areas with high infestation rates, based on the analysis of microsatellite markers. The samples were collected in nine municipalities with high building infestation rates in the Mid-North region of Brazil. Six microsatellite loci were genotyped in the 138 samples, producing a total of 32 alleles, varying from one to nine alleles per locus in each of the different populations. The AMOVA revealed greater within-population genetic differentiation with high fixation rates. The general analysis of population structure, based on a Bayesian approach, revealed K = 2, with two Ae. aegypti lineages that were highly differentiated genetically. These data on the connectivity of the populations and the genetic isolation of the lineages provide important insights for the development of innovative strategies for the control of the populations of this important disease vector.

Development of rapid and cost-effective multiplex PCR assays to differentiate catfish of the genus Brachyplatystoma (Pimelodidae-Siluriformes) sold in Brazil

The catfishes Brachyplatystoma filamentosum (Kumakuma), Brachyplatystoma vaillantii (Laulao catfish), and Brachyplatystoma rousseauxii (gilded catfish) are important fishery resources in Brazil, where they are sold both fresh and in the form of fillets or steaks. These species have morphological similarities, thus, they can be easily misidentified or substituted, especially after processed. Therefore, accurate, sensitive, and reliable methods are needed for the identification of these species to avoid commercial fraud. In the present study, we develop two multiplex PCR assays for the identification of the three catfish species. Each multiplex protocol combined three species-specific forward primers and a universal reverse primer to produce banding patterns able to discriminate the target species unequivocally. The length of the cytochrome C oxidase subunit I (COI) fragments was approximately 254 bp for B. rousseauxii, 405 bp for B. vaillantii, and 466 bp for B. filamentosum, while the control region (CR) assay produced fragments of approximately 290 bp for B. filamentosum, 451 bp for B. vaillantii, and 580 bp for B. rousseauxii. The protocols were sensitive enough to detect the target species at a DNA concentration of 1 ng/µL, with the exception of the CR of B. vaillantii, in which the fragment was only detectable at 10 ng/µL. Therefore, the multiplex assays developed in the present study were sensitive, accurate, efficient, rapid, and cost-effective for the unequivocal identification of the target species of Brachyplatystoma. They can be utilized by fish processing industries to certify their products, or by government agencies to authenticate products and prevent fraudulent commercial substitutions.

A global catalog of whole-genome diversity from 233 primate species

The rich diversity of morphology and behavior displayed across primate species provides an informative context in which to study the impact of genomic diversity on fundamental biological processes. Analysis of that diversity provides insight into long-standing questions in evolutionary and conservation biology and is urgent given severe threats these species are facing. Here, we present high-coverage whole-genome data from 233 primate species representing 86% of genera and all 16 families. This dataset was used, together with fossil calibration, to create a nuclear DNA phylogeny and to reassess evolutionary divergence times among primate clades. We found within-species genetic diversity across families and geographic regions to be associated with climate and sociality, but not with extinction risk. Furthermore, mutation rates differ across species, potentially influenced by effective population sizes. Lastly, we identified extensive recurrence of missense mutations previously thought to be human specific. This study will open a wide range of research avenues for future primate genomic research.

The landscape of tolerated genetic variation in humans and primates

Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole-genome sequencing data for 809 individuals from 233 primate species and identified 4.3 million common protein-altering variants with orthologs in humans. We show that these variants can be inferred to have nondeleterious effects in humans based on their presence at high allele frequencies in other primate populations. We use this resource to classify 6% of all possible human protein-altering variants as likely benign and impute the pathogenicity of the remaining 94% of variants with deep learning, achieving state-of-the-art accuracy for diagnosing pathogenic variants in patients with genetic diseases.

The landscape of tolerated genetic variation in humans and primates

Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole genome sequencing data for 809 individuals from 233 primate species, and identified 4.3 million common protein-altering variants with orthologs in human. We show that these variants can be inferred to have non-deleterious effects in human based on their presence at high allele frequencies in other primate populations. We use this resource to classify 6% of all possible human protein-altering variants as likely benign and impute the pathogenicity of the remaining 94% of variants with deep learning, achieving state-of-the-art accuracy for diagnosing pathogenic variants in patients with genetic diseases.

One Sentence Summary

Deep learning classifier trained on 4.3 million common primate missense variants predicts variant pathogenicity in humans.

Quality analysis of genomic DNA and authentication of fisheries products based on distinct methods of DNA extraction

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.

First record of mudskipper Boleophthalmus dussumieri (Gobiidae: Oxudercinae) on the coast of Mozambique and evidence of two putative lineages along its known distribution range

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.

Phylogenetic relationships and the origin of New World soles (Teleostei: Pleuronectiformes: Achiridae): The role of estuarine habitats

Even though the monophyletic status of Achiridae has been supported by morphological and molecular data, the interrelationships within the representatives of this family are poorly resolved. In the present study, we carried out the most complete molecular phylogenetic analysis of this group, encompassing all genera and employing both nuclear (Rhodopsin, Recombination activator [Rag 1], Mixed - lineage Leukemia [MLL] and Early Growth Response Protein 3 [EGR3]) and mitochondrial (Cytochrome C Oxidase Subunit I [COI], Cytochrome B [CytB], ATPase 6.8, 16S and 12S RNAr) genes. All topologies based on Maximum Likelihood, Bayesian inferences and Bayesian Inference of the Multispecies Coalescent confirmed the monophyletism of Achiridae, in spite of some incongruences in relation to Achirus mucuri, A. lineatus, Apionichthys finis and Trinectes microphthalmus. In fact, Achirus and Trinectes proved to be non-monophyletic genera while Hypoclinemus mentalis was closely related to A. achirus, suggesting this species should be reevaluated. We provided evidence that Achiridae has first arisen in estuaries (about 23.5 million years ago) and some lineages have evolved independently to either marine or freshwater habitats. Furthermore, we propose a diversification scenario of New World soles involving at least two events of marine incursions during Miocene and Pliocene - Pleistocene associated with natural geographic barriers (Victoria-Trindade chain), the width and exposure of continental shelf and headwater capture along the Amazon basin. Finally, the evolutionary dependence of Achirid soles on estuaries, characterized as highly dynamic environments, has probably driven the recent divergence of many species of Achiridae.

Phylogenetic relationships of sleeper gobies (Eleotridae: Gobiiformes: Gobioidei), with comments on the position of the miniature genus Microphilypnus

Microphilypnus and Leptophilypnion are miniaturized genera within the family Eleotridae. The evolutionary relationships among these taxa are still poorly understood, and molecular analyses are restricted to mitochondrial genes, which have not been conclusive. We compiled both mitochondrial and nuclear genes to study the phylogenetic position of Microphilypnus and the evolutionary history and relationships of eleotrids. We propose that Microphilypnus and Leptophilypnus (a non-miniature genus) are not sister groups as suggested by previous studies, but rather separate lineages that arose in the early Eocene, with Leptophilypnus recovered as a sister group to the other analyzed eleotrids. In fact, Microphilypnus is currently associated with the Neotropical clade Guavina/Dormitator/Gobiomorus. We also identified a well-supported clade that indicated Gobiomorus and Hemieleotris as paraphyletic groups, besides a close relationship among Calumia godeffroyi, Bunaka gyrinoides, Eleotris and Erotelis species. This is the first comprehensive report about the evolutionary relationships in members of the family Eleotridae, including multiloci and multispecies approaches. Therefore, we provided new insights about the phylogenetic position of some taxa absent in previous studies, such as the miniature genus Microphilypnus and a recently described species of Eleotris from South America.

ForAlexa, an online tool for the rapid development of artificial intelligence skills for the teaching of evolutionary biology using Amazon's Alexa

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.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1186/s12052-022-00169-z.

The complete mitogenome of Paralonchurus dumerilii (Perciformes: Sciaenidae)

We herein describe the complete mitochondrial genome of Paralonchurus dumerilii (Sciaenidae) and infer its phylogenetic position within the family. The genome is 16,498 bp long and featured by 13 protein-coding genes (PCGs), two rRNAs, 22 tRNAs, and a control region (D-loop). Our phylogenetic analysis suggests a basal position of P. dumerilii as the sister group of the other species of Sciaenidae analyzed.

205 newly assembled mitogenomes provide mixed evidence for rivers as drivers of speciation for Amazonian primates

Mitochondrial DNA remains a cornerstone for molecular ecology, especially for study species from which high‐quality tissue samples cannot be easily obtained. Methods using mitochondrial markers are usually reliant on reference databases, but these are often incomplete. Furthermore, available mitochondrial genomes often lack crucial metadata, such as sampling location, limiting their utility for many analyses. Here, we assembled 205 new mitochondrial genomes for platyrrhine primates, most from the Amazon and with known sampling locations. We present a dated mitogenomic phylogeny based on these samples along with additional published platyrrhine mitogenomes, and use this to assess support for the long‐standing riverine barrier hypothesis (RBH), which proposes that river formation was a major driver of speciation in Amazonian primates. Along the Amazon, Negro, and Madeira rivers, we found mixed support for the RBH. While we identified divergences that coincide with a river barrier, only some occur synchronously and also overlap with the proposed dates of river formation. The most compelling evidence is for the Amazon river potentially driving speciation within bearded saki monkeys (Chiropotes spp.) and within the smallest extant platyrrhines, the marmosets and tamarins. However, we also found that even large rivers do not appear to be barriers for some primates, including howler monkeys (Alouatta spp.), uakaris (Cacajao spp.), sakis (Pithecia spp.), and robust capuchins (Sapajus spp.). Our results support a more nuanced, clade‐specific effect of riverine barriers and suggest that other evolutionary mechanisms, besides the RBH and allopatric speciation, may have played an important role in the diversification of platyrrhines.

Molecular data reveal multiple lineages of Scinax nebulosus (Spix, 1824) (Anura: Hylidae) with Plio-Pleistocene diversification in different Brazilian regions

To understand the organism's history, we can start assessing the complexity of the biome where they occur. In this study, we used a region of the mitochondrial genome, the rRNA 16S, to evaluate the genetic differentiation in Scinax nebulosus along with its geographical range highlighting important Brazilian biomes as Restinga, Cerrado, Amazon, and Atlantic Forest. Geographically structured genetic divergence was observed within the species S. nebulosus. The values of the fixation index (Фst) and the pairwise Fst index were high and significant regarding this structuring. Besides, the haplotype network corroborates these results with the haplotypes arrangement found by separating the S. nebulosus populations in two major groups: North and Northeast. The lineage delimitation analyses indicate the occurrence of several lineages with divergence mainly between the samples from the Northeast group. Thus, we can suggest that S. nebulosus may present itself as a group of cryptic species due to the genetic characteristics found. The existence of a mosaic of heterogeneous habitats may explain the genetic divergence found, which justifies the existence of cryptic species in this group. However, this hypothesis needs more detail in molecular studies, including large sample sizes and other population and demographic analyses.

DNA barcode reveals candidate species of Scinax and Ololygon (Anura: Hylidae) in Atlantic Forest

Molecular species delimitation methods are efficient tools to identify species, including the discovery of new taxa and cryptic organisms, thus being useful to biodiversity studies. In the present work, 16S mitochondrial sequences and cytochrome oxidase I (COI) were used to evaluate the richness of species in the genus Scinax and Ololygon from a biodiversity hotspot in Atlantic Forest. A total of 109 specimens formally belonging to eight species of Scinax and three species of Ololygon were collected in 13 localities along the state of Bahia (northeastern Brazil) and one site in Espírito Santo (southeastern Brazil). Of the Scinax species collected in this study, three were morphologically differentiated from other described species and identified as putative new species (Scinax sp.1, Scinax sp.2 and Scinax sp.3). The species delimitations were inferred using three different methods: ABGD, PTP and mPTP which allowed recognizing 11 Scinax species and five Ololygon species. Scinax sp. 1, Scinax sp. 2 and Scinax sp. 3, have been confirmed as new putative species and Ololygon argyreornata possibly contains cryptic species. We suggest additional studies, including morphological and bioacoustic data to validate these new putative species.

Prospection of putative genes for digestive enzymes based on functional genome of the hepatopancreas of Amazon river prawn

Over recent years, Macrobrachium amazonicum has become a popular species for shrimp farming due to their fast growth, high survival rates, and marketability. Several studies have focused on the development of new technology for the culture of this species, but many aspects of their nutrition and physiology remain unknown. Thus, the goal of the present study was to obtain transcripts of putative genes encoding digestive enzymes, based on a library of the cDNA from the hepatopancreas of M. amazonicum, sequenced in the Ion TorrentTM platform. We identified fragments of nine genes related to digestive enzymes, acting over proteins, carbohydrates and lipids. Endo and exoproteases were also recorded in the hepatopancreas, indicating adaptation to the digestion of protein-rich foods. Nonetheless, the enzymes involved in the carbohydrate metabolism formed the largest functional group in M. amazonicum, including enzymes related to the digestion of starch, chitin, and cellulose. These findings indicate that the species has a genetic apparatus of a well-adapted omnivorous animal. This information may provide important insights for the selection of ingredients for the formulation of a more appropriate diet to the enzymatic repertoire of M. amazonicum.

Climate Change in Fisheries and Aquaculture: Analysis of the Impact Caused by Idai and Kenneth Cyclones in Mozambique

Fisheries and Aquaculture are among the most popular activities in coastal regions of the world. In addition, both correspond to high-risk activities within a climate change context as they are vulnerable to environmental changes that threaten the socio-economic sustainability of the fishing communities that depend on fish for food security and income generation. In 2019, the central part of Mozambique was hit by two unprecedented cyclones: Idai and Kenneth that killed over 600 people and left nearly 2.2 million people in need of urgent assistance. The aim of the present study was to investigate the impacts these cyclones had on fisheries and aquaculture in the provinces of Sofala and Zambézia in Mozambique. The study further seeks to propose strategies that could be adopted by the communities to minimize the risks in the future. For the construction of the database, both secondary and primary data collection approaches were used to characterize the cyclone events. Secondary data was collected through sector reports and previously published articles, while primary data was collected through interviews with fishers, sector employees, and aquaculture producers in the affected provinces. The results revealed that these natural events had both a direct and indirect impact on fishing, as they affected more than 1,440 fishermen that lost 590 vessels, 1,800 fishing gear, and 67 boat engines in Sofala province. In Zambézia province, aquaculture producers lost 169 fish ponds, two cages, and 606,000 lost fry, while in Sofala province, 58 fish tanks, 204 cages, and 257,500 fish fry were lost. Overall, our study reveals the vulnerability of fisheries and aquaculture to extreme events particularly the cyclones in Mozambique. Lack of knowledge regarding climate change, advanced preventive measures, and poor adaptive capacity makes the sectors more vulnerable to disasters. Therefore, it is recommended to improve awareness programs, introduce measures and policies that promote resilience and optimum adaptive efficiency.

An integrative analysis uncovers a new, pseudo-cryptic species of Amazonian marmoset (Primates: Callitrichidae: Mico) from the arc of deforestation

Amazonia has the richest primate fauna in the world. Nonetheless, the diversity and distribution of Amazonian primates remain little known and the scarcity of baseline data challenges their conservation. These challenges are especially acute in the Amazonian arc of deforestation, the 2500 km long southern edge of the Amazonian biome that is rapidly being deforested and converted to agricultural and pastoral landscapes. Amazonian marmosets of the genus Mico are little known endemics of this region and therefore a priority for research and conservation efforts. However, even nascent conservation efforts are hampered by taxonomic uncertainties in this group, such as the existence of a potentially new species from the Juruena-Teles Pires interfluve hidden within the M. emiliae epithet. Here we test if these marmosets belong to a distinct species using new morphological, phylogenomic, and geographic distribution data analysed within an integrative taxonomic framework. We discovered a new, pseudo-cryptic Mico species hidden within the epithet M. emiliae, here described and named after Horacio Schneider, the pioneer of molecular phylogenetics of Neotropical primates. We also clarify the distribution, evolutionary and morphological relationships of four other Mico species, bridging Linnean, Wallacean, and Darwinian shortfalls in the conservation of primates in the Amazonian arc of deforestation.

High genetic diversity detected in the mitochondrial Control Region of the Serra Spanish Mackerel, Scomberomorus brasiliensis (Collette, Russo & Zavala, 1978) along the Brazilian coast

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.

Re-visiting the occurrence of mislabeling in frozen "pescada-branca" (Cynoscion leiarchus and Plagioscion squamosissimus - Sciaenidae) sold in Brazil using DNA barcoding and octaplex PCR assay

In Brazil, Cynoscion leiarchus and Plagioscion squamosissimus are the species allowed to be labeled as "pescada-branca". These species have high economic value, especially when sold in the form of fillets. Therefore, when morphological traits are removed, fish are highly prone to be substituted, which has been reported for species of the family Sciaenidae sold in Brazil, including "pescada-branca". We have sequenced 618 bp of the COI of 143 samples to re-evaluate the occurrence of substitutions in frozen "pescada-branca" marketed in Brazil. We observed more than 73% of mislabeling, with only 26.57% being P. squamosissimus, and none, C. leiarchus. In general, the substitutes were closely related Sciaenidae, but cheaper species, which indicates commercial fraud. Based on these results we used 1.2 kb of COI to develop an octaplex PCR assay that unequivocally identified the target species and six substitute species through the banding pattern. Specific reverse primers combined with a universal forward primer were used in the protocol and identified the species C. leiarchus (~290 bp), N. microps (~340 bp), M. ancylodon (~470 bp), C. acoupa (~540 bp), C. microlepidotus (~850 bp), P. auratus (~950 bp), C. virescens (~1050 bp), and P. squamosissimus (~1140 bp). The DNA barcoding and the multiplex PCR were accurate and specific to authenticate processed products labeled as "pescada-branca". The multiplex assay constitutes a cost-effective alternative for the authentication of these products and other sciaenids. Additionally, we suggest that the multiplex assay can be adopted by both companies and regulatory agencies to prevent commercial fraud in the marketing of processed fishery products in Brazil and other countries where these products are commercialized.

Mitochondrial heteroplasmy and pseudogenes in the freshwater prawn, Macrobrachium amazonicum (Heller, 1862): DNA barcoding and phylogeographic implications

The mitochondrial cytochrome oxidase c subunit 1 (COI) gene has been widely used in phylogenetic studies of crustaceans and analyses in population genetics. As COI studies have become more popular, there has been an increase in the number of reports of the presence of nuclear insertions of mitochondrial DNA (Numts) and mitochondrial heteroplasmy. Here, we provide evidence of both types of event in the COI sequences of Macrobrachium amazonicum, an economically important freshwater prawn, which is widespread in South America. Heteroplasmy and Numts were confirmed by different methods of DNA extraction (genomic, mitochondrial, and nuclear-enriched DNA), cloning, and sequencing, and were observed in 11 of the 14 populations sampled, primarily in the Amazon region. We discuss how the occurrence of these events affects the interpretation of the genetic relationships among the M. amazonicum populations, and we recommend caution when using COI for genetic inferences in prawns of the genus Macrobrachium, and in particular that any analysis should include nuclear markers.

Identification of the taxonomic status of Scinax nebulosus and Scinax constrictus (Scinaxinae, Anura) based on molecular markers

The validation of many anuran species is based on a strictly descriptive, morphological analysis of a small number of specimens with a limited geographic distribution. The Scinax Wagler, 1830 genus is a controversial group with many doubtful taxa and taxonomic uncertainties, due a high number of cryptic species. One example is the pair of species Scinax constrictus and Scinax nebulosus, which share a similar morphology. Scinax constrictus is restricted to the Brazilian Cerrado savanna, while S. nebulosus is widely distributed throughout northern South America. Despite the validation of many anuran species, discriminations based only on morphological traits is quite difficult due to the high conservative morphology of some groups. In this context, the present study uses mitochondrial and nuclear genes to provide a more consistent diagnosis and test the validity of S. constrictus as a distinct species from S. nebulosus, as well as evaluate the position of these taxa within the Scinax genus. The topologies obtained herein uphold the monophyletic status of Scinax based on all molecular markers assessed in this study, in all analytical approaches, with high levels of statistical support.

Revisiting the phylogeny of the genus Lolliguncula Steenstrup 1881 improves understanding of their biogeography and proves the validity of Lolliguncula argus Brakoniecki & Roper, 1985

The biogeography of American loliginid squids has been improved in recent years, but certain key taxa have been missing. Given that the most accurate phylogenies and estimates of divergence times of common ancestors depend heavily on good taxonomic coverage we have reanalyzed the genus Lolliguncula in light of new samples that increase the geographic and taxonomic coverage. New sequences were produced using standard methods to update an existing dataset for COI, 16S and Rhodopsin markers. Data was analyzed using various species delimitation methods, rigorous phylogenetic analyses and estimates of divergence times between clades. Within Lolliguncula we recover five monophyletic lineages that relate to the known species L. argus, L. diomedeae, L. panamensis, L. brevis North Atlantic and L. brevis South Atlantic. Except when using low divergence thresholds in ABGD, species delimitation methods only identify four of these lineages as distinct species, grouping L. argus and L. diomedeae as a single species. However, considering the reciprocal monophyly, recent divergence time estimate and morphological diagnoses we refrain from synonymizing L. argus within L. diomedeae, considering them very recently diverged species. The biogeography of the American loliginids is discussed, wherein basal cladogenesis in both Lolliguncula and Doryteuthis occur between the Atlantic and Pacific about 45 mya, with subsequent speciation around 20 mya associated with seafloor changes during the formation of the Caribbean. The recent speciation between L. argus and L. diomedeae is associated to oceanic environmental changes associated with glaciation, deep sea cooling and tropical upwelling.

Molecular phylogenetic inference of the howler monkey radiation (Primates: Alouatta)

Howler monkeys (Alouatta), comprising between nine and 14 species and ranging from southern Mexico to northern Argentina, are the most widely distributed platyrrhines. Previous phylogenetic studies of howlers have used chromosomal and morphological characters and a limited number of molecular markers; however, branching patterns conflict between studies or remain unresolved. We performed a new phylogenetic analysis of Alouatta using both concatenated and coalescent-based species tree approaches based on 14 unlinked non-coding intergenic nuclear regions. Our taxon sampling included five of the seven South American species (Alouatta caraya, Alouatta belzebul, Alouatta guariba, Alouatta seniculus, Alouatta sara) and the two recognized species from Mesoamerica (Alouatta pigra, Alouatta palliata). Similarly to previous studies, our phylogenies supported a Mesoamerican clade and a South American clade. For the South American howlers, both methods recovered the Atlantic Forest endemic A. guariba as sister to all remaining South American species, albeit with moderate support. Moreover, we found no support for the previously proposed sister relationship between A. guariba and A. belzebul. For the first time, a clade composed of A. sara and A. caraya was identified. The relationships among the other South American howlers, however, were not fully supported. Our estimates for divergence times within Alouatta are generally older compared to estimates in earlier studies. However, they conform to recent studies proposing a Miocene age for the Isthmus of Panama and for the uplift of the northern Andes. Our results also point to an early genetic isolation of A. guariba in the Atlantic Forest, in agreement with the hypothesis of biotic exchange across South American rain forests in the Miocene. Collectively, these findings contribute to a better understanding of the diversification processes among howler monkey species; however, they also suggest that further comprehension of the evolutionary history of the Alouatta radiation will rely on broadened taxonomic, geographic, and genomic sampling.

Phylogenetic relationships in the genus Cheracebus (Callicebinae, Pitheciidae)

Cheracebus is a new genus of New World primate of the family Pitheciidae, subfamily Callicebinae. Until recently, Cheracebus was classified as the torquatus species group of the genus Callicebus. The genus Cheracebus has six species: C. lucifer, C. lugens, C. regulus, C. medemi, C. torquatus, and C. purinus, which are all endemic to the Amazon biome. Before the present study, there had been no conclusive interpretation of the phylogenetic relationships among most of the Cheracebus species. The present study tests the monophyly of the genus and investigates the relationships among the different Cheracebus species, based on DNA sequencing of 16 mitochondrial and nuclear markers. The phylogenetic analyses were based on Maximum Likelihood, Bayesian Inference, and multispecies coalescent approaches. The divergence times and genetic distances between the Cheracebus taxa were also estimated. The analyses confirmed the monophyly of the genus and a well-supported topology, with the following arrangement: ((C. torquatus, C. lugens), (C. lucifer (C. purinus, C. regulus))). A well-differentiated clade was also identified within part of the geographic range of C. lugens, which warrants further investigation to confirm its taxonomic status.