Horacio Schneider

Federal University of Para | UFPA · Program in Genetics and Molecular Biology

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 revi...

Traditionally, Saguinus has been organized into six taxonomic groups: bicolor, inustus, midas, mystax, nigricollis, and oedipus. After recent revisions, taxonomic reclassifications were proposed, including (1) the recognition of Leontocebus as a new genus, and (2) the subdivision of Saguinus into three subgenera. Nonetheless, the contradictory natu...

Night monkeys (Aotus, Cebidae) are a widely distributed genus of Neotropical primates with a poorly understood taxonomy and biogeography. The number of species in the genus varies from one to nine, depending on the author, and there are at least 18 known karyotypes, varying from 2n = 46 to 2n = 58. Historically, night monkeys are divided into two s...

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. leuco...

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 b...

Arapaima is a widely-distributed fish of enormous economic importance in the Amazon region. In the present study, a total of 232 specimens were sampled, 121 from five sites in the Amazon basin and 111 from five sites in the Tocantins-Araguaia basin. The analyses investigated fragments of the Cytochrome b, Control Region, Cytochrome Oxidase I, NADH...

Lutjanus campechanus and Lutjanus purpureus are two commercially important lutjanid fishes (snappers) with non-sympatric distribution throughout Western Atlantic. Even though both taxa have traditionally been regarded as valid species, their taxonomic status remains under debate. In the present study, we used phylogeographic approaches and molecula...

We used molecular tools and a multilocus approach to investigate the phylogeography of Lepidothrix coronata across most of its ample range. We sequenced six DNA fragments to produce phylogenies, molecular dating estimates, analyses of the dynamics of the demographic history of the species and a biogeographic analysis to estimate the events and chan...

Oyster culture activity along the eastern Amazon mangrove coast in Pará state, Brazil, was evaluated using socio-economic data to support its management and future development. Between 2013 and 2014, surveys were carried out in the region's seven oyster culture associations through interviews with the president of each association as well as with 5...

Deltas are dynamic and productive systems of enormous ecological significance, encompassing unique and biologically diverse wetland habitats. Here, we present the first data on the molecular diversity of the fish fauna of the Parnaíba Delta, the largest deltaic formation of the Americas. Partial sequences (626 bp) of the mitochondrial COI gene (Cyt...

Lutjanidae comprises 21 genera and 135 species widespread throughout Atlantic, Indian and Pacific oceans. Nonetheless, the phylogenetic relationships of Lutjaninae remain uncertain. Furthermore, phylogenetic hypotheses for Lutjanus alexandrei, an endemic species from northeastern Brazilian coast, in Lutjanidae are absent so far. Therefore, we carri...

The cephalopod fauna of the southwestern Atlantic is especially poorly-known because sampling is mostly limited to commercial net-fishing operations that are relatively inefficient at obtaining cephalopods associated with complex benthic substrates. Cephalopods have been identified in the diets of many large marine species but, as few hard structur...

The two species of the genus Antilophia, Antilophia bokermanni and Antilophia galeata, are found in environments that are undergoing extensive modification, which may be provoking the loss of their genetic diversity. Nine polymorphic microsatellite loci were characterized and analyzed in each of these species. The distribution of allele frequencies...

The taxonomy of the titi monkeys (Callicebinae) has recently received considerable attention. It is now recognised that this subfamily is composed of three genera with 33 species, seven of them described since 2002. Here, we describe a new species of titi, Plecturocebus, from the municipality of Alta Floresta, Mato Grosso, Brazil. We adopt an integ...

Background The C. macropomum is a characiform fish from the Amazon basin that has been hybridized with other pacu species to produce commercial hybrids, such as the tambacu. However, little is known of the functional genomics of the parental species or these hybrid forms. The transcriptome of C. macropomum and tambacu were sequenced using 454 Roche...

Distribution of the data based on the results obtained in Blast2GO. (TIF)

Top-hit species distribution of the BlastX matches of Colossoma macropomum with the Swiss-Prot protein database. (TIF)

Top-hit species distribution of the BlastX matches of the tambacu with the Swiss-Prot protein database. (TIF)

The functional KEGG classification of the transcripts of the muscle and skin tissue of the tambacu. (TIF)

Alignment of the mitochondrial DNA sequences of the individuals (C. macropomum and tambacu) sequenced in the present study. (XLSX)

The KEGG data for the muscle and skin tissue of Colossoma macropomum. (XLSX)

The Gene Ontology (GO) analysis. Comparative distribution of the GO terms and the numbers of transcripts involved in Biological Processes (BP), Molecular Function (MF), and Cell Components (CC) in the C. macropomum and tambacu. (TIF)

All the DEGs identified in the C. macropomum and tambacu, with their respective RPKM and significance values. (XLSX)

All the genes included in the Heatmap analysis with their respective RPKM and significance values. (CSV)

Distribution of the transcript lengths recorded in the C. macropomum and the tambacu. (TIF)

The functional KEGG classification of the transcripts of the muscle and skin tissue of Colossoma macropomum. (TIF)

All the genes identified in the C. macropomum and tambacu, with their respective RPKM and Log2FC values. (XLSX)

The KEGG data for the muscle and skin tissue of the tambacu. (XLSX)

Background The Arapaima (Arapaima gigas) is one of the world's largest freshwater bony fish, and is found in the rivers of the Amazon basin. This species is a potential aquaculture resource, although reproductive management in captivity is limited in particular due to the lack of external sexual dimorphism. In this study, using the 454 Roche platfo...

Distribution of contigs length obtained by pyrosequencing in the platform 454 Roche. (TIF)

Gene ontology (GO) at the second level of GO terms obtained for skin and liver transcripts of A. gigas. (TIF)

Full list of gene with acession number, mappead reads counts, RPKM, Foldchange, and log2 Fold Change, obtained for the liver and skin libraries of A.gigas. (CSV)

Up-regulated genes between male and female liver of A. gigas. (CSV)

Up-regulated genes between male and female skin of A. gigas. (CSV)

List of the genes used to generate the heatmap, with their respective RPKMs. (CSV)

List of the genes cited in the present manuscript. (CSV)

Gene ontology (GO) at the second level of GO terms obtained for all transcripts of the male, all transcripts of the female and the complete transcriptome of A. gigas. (TIF)

Capuchin monkeys are currently represented by four species of Cebus and eight of Sapajus. This group is taxonomically complex and several questions still need to be clarified. In the current study, using mtDNA markers and a larger sample representation than in previous studies, we seek to understand the phylogenetic relationships among the capuchin...

The melanocortin-1 receptor gene is the most widely-used marker for the investigation of the genetic determination of melanic plumage patterns. Studies of a number of wild bird species have shown an association between non-synonymous mutations of the MC1R gene and the presence of melanic variants. The genus Antilophia (Pipridae) includes only two m...

Titi monkeys, subfamily Callicebinae, are a diverse, species-rich group of Neotropical primates with an extensive range across South America. Their distribution in space and time makes them an interesting primate model for addressing questions of Neotropical historical biogeography. Our aim was to reconstruct the biogeographic history of Callicebin...

LINE-1 (L1) retrotransposons constitute the dominant category of transposons in mammalian genomes. L1 elements are active in the vast majority of mammals, and only a few cases of L1 extinction have been documented. The only possible case of extinction in primates was suggested for South American spider monkeys. However, these previous studies were...

We evaluated the relationship between Celeus undatus and Celeus grammicus, with the objective of clarifying their evolutionary history. We analysed fragments of the mitochondrial and nuclear genes of 57 specimens. For comparative purposes, we inspected the plumage patterns of 77 skins. Our findings highlight the absence of reciprocal monophyly betw...

Lepidothrix is the most diverse genus of the family Pipridae, with eight recognized species. Although the genus' monophyly has been supported by both molecular and morphological characters, phylogenetic relationships and species limits within Lepidothrix remain uncertain. In the present study, we combined molecular sequences of mitochondrial (ND2 a...

The Caribbean Red Snapper (Pargo) Lutjanus purpureus is the most economically important snapper in Brazil, which is sold, among other forms, as frozen fillets. During the process of transformation into fillets there is the removal of the distinctive morphological traits, being able to favor the substitution by less valued species. In addition, ther...

The loss of variability in farmed populations and the risks of interactions with wild populations support the need for the genetic monitoring of species farmed throughout the world. In Brazil, the tambaqui is the most widely farmed native fish species. Despite this, there are no data on the pedigree of the farmed stocks, and the potential for inter...

Este livro tem por objetivo apresentar ao usuário, iniciante em análise filogenética e filogenômica, as metodologias e os programas mais modernos e mais utilizados na literatura científica da área de uma forma simples e objetiva, assim como algumas noções de bioinformática. Para aqueles que pretendem se aprofundar nesta área e em áreas conexas rela...

Phylogenies based on morphological and molecular data confirm the monophyly of the subfamily Stelliferinae; however, there is no consensus on the intergeneric and interspecific relationships in the group. Previous studies suggested the non-monophyly of Ophioscion and Stellifer, and possible cryptic species in Ophioscion punctatissimus. Therefore, w...

Here, we report trading of endangered shark species in a world hotspot for elasmobranch conservation in Brazil. Data on shark fisheries are scarce in Brazil, although the northern and northeastern regions have the highest indices of shark bycatch. Harvest is made primarily with processed carcasses lacking head and fins, which hampers reliable speci...

Methods used in `BioGeoBEARS’ with the four areas from Lima et al. (2017).

DS2 time consensus tree with the estimates of ancestral areas of the capuchin monkeys considering the four areas proposed by Lima et al. (2017).

List of species with their respective samples, codes, ID.

Characteristics of the datasets.

Comparison among the estimated models in `BioGeoBEARS’ considering the four areas.

The integration of approaches that allow the incorporation of stochasticity of gene histories with phylogenetic methods resulted in new approaches for the old issue of species delimitation. Nevertheless, coalescent methods seem problematic for taxa with large effective population size and shallow temporal diversification (like marine fishes). Here,...

The pygmy marmoset, Cebuella pygmaea, the smallest of the New World monkeys, has one of the largest geographical distributions of the Amazonian primates. Two forms have been recognized: Cebuella pygmaea pygmaea (Spix, 1823), and C. p. niveiventrisLönnberg, 1940. In this study, we investigated if the separation of pygmy marmosets into these two clad...

Black pepper (Piper nigrum L.) is the most traded spice worldwide and therefore has great economic value. One of the major limitations of its production is yield losses in fields due to root rot, a disease caused by Fusarium solani f. sp. piperis. This soil-borne pathogen disseminates rapidly in tropical countries. Biotechnological breeding is ofte...

Population genetic structure, genetic diversity and molecular demography of lane snapper Lutjanus synagris were assessed using mitochondrial DNA (control region, cytochrome b and NADH Dehydrogenase, subunit 4) and two nuclear introns (intron 2 of the S7 ribosomal protein gene - S7-2, and intron 6 of the L3 ribosomal protein gene - RPL3). Here, we c...

The western portion of the Atlantic Ocean exhibits different hydrographic, geomorphological and climatic characteristics which may interfere with the genetic structure of fish species inhabiting coastal waters. Studies of mitochondrial DNA indicate that species with a broad geographic distribution tend to exhibit some degree of genetic structure. M...

To determine a hypothetical scenario that accounts for the diversifi cation of the two species of the genus Antilophia , we conducted multilocus molecular comparisons and species distribution modeling for the two taxa, which have distinct male plumage coloration patterns and allopatric geographic distributions, despite the high degree of genetic si...

In the present study, a novel set of eight EPIC primers were developed for Lutjanus purpureus and assayed in five other marine teleosts including three lutjanids, one scianid and one anablepid. Most of the genomic regions used in this study presented genetic diversity indexes equal or greater than the intragenic regions commonly used in population...

Maciel, A. O., Sampaio, M. I. C., Hoogmoed, M. S., Schneider, H. (2017). Phylogenetic relationships of the largest lungless tetrapod (Gymnophiona, Atretochoana) and the evolution of lunglessness in caecilians. — Zoologica Scripta, 00, 1–9. Atretochoana eiselti is the largest extant lungless tetrapod. This species is one of the fully aquatic caecili...

The mangrove killifish Kryptolebias hermaphroditus is reported to the southeast and northeast regions of Brazil. Recently, a specimen of K. hermaphroditus was collected in a shallow running seawater stream at Ajuruteua beach, Pará state, northern Brazil. This new record is ca. 1,350 km from the nearest previously known occurrence in Rio Grande do N...

In the present study, we investigated the possible existence of new lineages of peripatids through comparisons between known Neotropical species and specimens obtained from two locations in Pará, a state in eastern Brazilian Amazonia using a molecular approach based on sequences of the mtDNA genes COI, 16Sr RNA, and 18S RNA. The analyses included a...

Fraud involving fish products is regularly reported and investigated using genetic methods. However, no such approach has been applied to snappers, despite the commercial relevance of these fish. This study proposes an authentication protocol with multiplex PCR for three species of snappers (Lutjanus purpureus, L. synagris, and Ocyurus chrysurus)....

The Araripe Manakin (Antilophia bokermanni) is a “Critically endangered” bird species endemic to northeastern Brazil. The habitat of the species has suffered intense fragmentation and degradation in recent years, resulting in a decline in population numbers. The present study evaluated the genetic diversity and structure of this population through...

Colossoma macropomum is a resistant species native of Amazonas and Orinoco river basins. It is regarded as the second largest finfish of Solimões and Amazon rivers, representing a major fishery resource in Amazonas and an important species in tropical aquaculture. MicroRNAs are non-coding endogenous riboregulators of nearly 22 nucleotides that play...

Species with wide geographic distributions can consist of different lineages or even different species. The present study evaluated the molecular diversity of the family Eleotridae analyzing sequences of the COI gene from species collected in different locations in the Neotropical as well as sequences from BOLD and GenBank. The analysis revealed th...

- Specimen information.

- Maximum-likelihood tree for three genes (COI, 16S, 18S).

Aedes (Stegomyia) aegypti is the vector responsible for the transmission of the viruses that cause zika, yellow and chikungunya fevers, the four dengue fever serotypes (DENV – 1, 2, 3, 4), and hemorrhagic dengue fever in tropical and subtropical regions around the world. The present study investigated the genetic differentiation of the 15 populatio...