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The Neotropical region hosts 4225 freshwater fish species, ranking first among the world's most diverse regions for freshwater fishes. Our NEOTROPICAL FRESHWATER FISHES data set is the first to produce a large-scale Neotropical freshwater fish inventory, covering the entire Neotropical region from Mexico and the Caribbean in the north to the southern limits in Argentina, Paraguay, Chile, and Uruguay. We compiled 185,787 distribution records, with unique georeferenced coordinates, for the 4225 species, represented by occurrence and abundance data. The number of species for the most numerous orders are as follows: Characiformes (1289), Siluriformes (1384), Cichliformes (354), Cyprinodontiformes (245), and Gymnotiformes (135). The most recorded species was the characid Astyanax fasciatus (4696 records). We registered 116,802 distribution records for native species, compared to 1802 distribution records for nonnative species. The main aim of the NEOTROPICAL FRESHWATER FISHES data set was to make these occurrence and abundance data accessible for international researchers to develop ecological and macroecological studies, from local to regional scales, with focal fish species, families, or orders. We anticipate that the NEOTROPICAL FRESHWATER FISHES data set will be valuable for studies on a wide range of ecological processes, such as trophic cascades, fishery pressure, the effects of habitat loss and fragmentation, and the impacts of species invasion and climate change. There are no copyright restrictions on the data, and please cite this data paper when using the data in publications.

The predicted sequence for thousands of genes revealed by a preliminary low-coverage genome assembly is presented for Brycon orbignyanus, an endangered migratory fish. Neotropical migratory fish stocks have been drastically reduced due to accumulated environmental pressure. Brycon orbignyanus, once one of the main fisheries species in the Platine Basin, is now very rare in nature and relies on spawning programs and a few well preserved or still untouched sites. The use of high-throughput DNA sequencing is still untapped regarding the functional genome information from B. orbignyanus. In order to help bridging this gap, we present a dataset resulting from the first functional annotation from a de novo genome assembly for B. orbignyanus, from short reads (90 bp), obtained by the HiSeq 2000 platform (Illumina). The annotation was performed for scaffolds over 10 kb using the Maker pipeline, with reference sequences taken from the NCBI for the Characiformes order. This annotation resulted in the prediction of 12,734 genes, classified with the aid of PANTHER. The data presented here can facilitate the development of basic research in this threatened species, along with practical biotechnological tools for different areas, such as commercial and environmental fish spawning operations (e.g. hormonal induction, growth) and human health.

Made available in DSpace on 2021-06-25T11:57:39Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-05-01 Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) The Neotropical fish genus Prochilodus includes five species occurring in the main drainages of the eastern Brazilian Shield: P. argenteus, P. costatus, P. lineatus, P. harttii, and P. vimboides. Multi and single locus phylogenies have questioned the monophyly of P. costatus and P. lineatus, and the biogeographic history of these species in the Brazilian Shield has never been explored. We characterized new mitogenomes for these species to reconstruct their evolutionary history, estimated the timing of Prochilodus cladogenesis, and discussed the implications of past geologic events on species diversification. The phylogeny supports the monophyly of both P. costatus and P. lineatus, and indicates a Miocene divergence of P. vimboides, much earlier than subsequent species diversification. The Early Pleistocene split of P. argenteus and P. harttii (similar to 2.1 million years ago-MYA) is hypothesized to be related to recent Quaternary reactivations of the Rio Aracuai Fault that promoted river captures between the eastern tributaries of the Sao Francisco basin and the upper Rio Jequitinhonha in the Serra do Espinhaco mountain range. The time-calibrated phylogeny also indicated a subsequent split of P. costatus and P. lineatus (similar to 1.1 MYA) likely due to Quaternary activities of the Upper Rio Sao Francisco crustal discontinuity and Estrela Fault that catalyzed river captures between the upper Rio Sao Francisco and the Rio Grande of the Parana basin in the Serra da Canastra mountain range. These results provide a temporal context for the diversification of Prochilodus and bring new insights to further study the historical biogeography of other riverine fish groups along the upland basins of the eastern Brazilian Shield. Pontificia Univ Catolica Minas Gerais, Lab Genet Conservacao, Programa Posgrad Biol Vertebrados, Belo Horizonte, MG, Brazil Univ Fed Sao Joao del Rei, Lab Recursos Genet, Programa Posgrad Ecol, Sao Joao Del Rei, Brazil Univ Estadual Paulista, Dept Biol Estrutural & Func, Inst Biociencias, Botucatu, SP, Brazil Univ Fed Sao Joao del Rei, Programa Posgrad Ciencia Comp, Sao Joao Del Rei, Brazil Univ Fed Rio de Janeiro, Inst Bioquim Med Leopoldo Meis, Lab Genom & Biodiversidade, Rio De Janeiro, Brazil Univ Estadual Paulista, Dept Biol Estrutural & Func, Inst Biociencias, Botucatu, SP, Brazil CNPq: 404991/2018-1 FAPESP: 16/11313-8

A broad panel of tens of thousands of microsatellite loci is unveiled for an endangered piracema (i.e. migratory) South American fish, Brycon orbignyanus. Once one of the main fisheries resources in the Platine Basin, it is now almost extinct in nature and focus of intense aquaculture activity. A total of 178.2 million paired-end reads (90 bases long) were obtained through the use of sequencing-by-synthesis (from a primary genomic library of 500 bp DNA fragments) and is made available through NCBI's Sequence Read Archive, SRA accession SRX3350440. Short reads were assembled de novo and screening for perfect microsatellite motifs revealed more than 81 thousands unique microsatellite loci, for which primer pairs were proposed. A total of 29 polymorphic microsatellite markers were already previously validated for this panel. A partial genomic assembly is hereby presented and these genomic resources are publicly made available. These data will foster the rapid development of hundreds of new DNA markers for genetic diversity studies, conservation initiatives and management practices for this important and depleted species. The availability of such preliminary genomic data will also be of use in the areas of bioinformatics, ecology, genetics and evolution.

The objective of this work was to evaluate 41 microsatellite markers for heterologous amplifications in piracanjuba (Brycon orbignyanus). Some markers were tested for the first time. Loci were optimized for PCR conditions and applied to a sample of 49 individuals. Thirty-one loci resulted in PCR product formation, whereas ten loci yielded intelligible polymorphic patterns in the evaluated sample and can be used for amplifications in this species. From the evaluated markers, four loci (BoM1, BoM13, Bh6, and Bh16) are valid to be applied in the study of piracanjuba.

A broad panel of tens of thousands of microsatellite loci is unveiled for an endangered piracema (i.e. migratory) South American fish, Brycon orbignyanus. Once one of the main fisheries resources in the Platine Basin, it is now almost extinct in nature and focus of intense aquaculture activity. A total of 178.2 million paired-end reads (90 bases long) were obtained through the use of sequencing-by-synthesis (from a primary genomic library of 500 bp DNA fragments) and is made available through NCBI’s Sequence Read Archive, SRA accession SRX3350440. Short reads were assembled de novo and screening for perfect microsatellite motifs revealed more than 81 thousands unique microsatellite loci, for which primer pairs were proposed. A total of 29 polymorphic microsatellite markers were already previously validated for this panel. A partial genomic assembly is hereby presented and these genomic resources are publicly made available. These data will foster the rapid development of hundreds of new DNA markers for genetic diversity studies, conservation initiatives and management practices for this important and depleted species. The availability of such preliminary genomic data will also be of use in the areas of bioinformatics, ecology, genetics and evolution.

Bokermmanohyla saxicola is endemic to the Espinhaco Mountain Range (southeastern Brazil), and broadly distributed in montane meadows of the Serra do Cipo. Four microsatellite regions were located through genomic library screening for this frog, two of which were chosen for population structure analyses given their high variability levels (10–11 alleles assayed in 75 tadpoles from five different streams). Overall Fst was 0.056, and the studied demes fitted isolation by distance model expectations, but the increase of Fst values was unrelated to increases in geographic distance, as it would be expected in drift-gene flow equilibrium conditions. Microsatellite markers revealed lack of pairwise genetic differentiation in spatially close demes and also in some distant ones, a pattern that may be caused by the combination of limited migration ability and past event effects contingent upon suitable habitat conditions for frog movement.

The venom of Loxosceles intermedia was investigated for the presence of insecticidal toxins active against Spodoptera frugiperda (Lepdoptera: Noctuidade), an insect that has caused great reductions in corn production in Brazil. A combination of gel filtration (Sephadex G-100) and ion-exchange chromatography (Carboxymethyl Cellulose, CM 52) resulted in four major fractions that were submitted to biological assay. Fraction 4 was further purified by a reverse phase HPLC (C18 Column) resulting in peptides active against Spodoptera frugiperda. Three new potential insecticidal toxins named LiTx x 1, LiTx x 2 and LiTx x 3 were identified. The partial amino terminal sequences of these peptides were obtained and used to clone the corresponding cDNAs with the help of degenerate oligonucleotides. The amino acid sequence deduced from the cDNA of LiTx x 1, LiTx x 2 and LiTx x 3 revealed mature proteins of approximately 7.4, 7.9 and 5.6 kDa.

The first complete mitochondrial genome for the Anostomidae fish family has been announced. Piracema fishes are the potamodromous migratory species from South America, which undergo lengthy and dramatic yearly reproductive upstream runs. The piracema species Leporinus piavussu has recently been described after a long misidentification history. Its mitogenome, assembled using NGS data and Sanger sequencing, consists in a 16,682 bp circular molecule (GenBank accession number KM886569). The exact sequence and position of 37 mitochondrial genes and the control region is established. A possible case of heteroplasmy was found with NGS and corroborated by Sanger sequencing. These results will positively contribute to the debate about this group’s taxonomy, evolution and conservation.

The cursor complex is a group within the Akodon genus of South American rodents, formed by Akodon cursor and A. montensis. Correct distinction between these two species is of great importance since they can harbor different Hantavirus strains. These species are only distinguishable by means of karyotypic or internal anatomic features, requiring dissection; recently, some other genetic methods have become available. We developed RAPD markers capable of distinguishing between A. cursor and A. montensis. Samples included 42 individuals of A. cursor from four localities and 16 individuals of A. montensis from two localities. Fifty-five bands, 41 of which were polymorphic, were analyzed. A principal component analysis showed that this set of markers could successfully distinguish between the two species, mainly based on three RAPD bands. The number of bands in each population was compared within a 95% confidence interval as a measure of intraspecific variability. The A. cursor populations were found to have marked genetic structure across the study area (AMOVA; F(ST )= 0.21), which in part might be because of the relatively limited dispersal capabilities of this species. Species-specific bands, with potential for species identification, were identified.

Foram estudados aspectos genético-populacionais de duas espécies da família Didelphidae e testada a adequação da metodologia de DNA Barcode para fins de identificação. O estudo molecular de 40 gambás da espécie Didelphis albiventris que habitam um fragmento urbano da Mata Atlântica brasileira foi realizado a partir da análise de seqüências de 653 pb da subunidade I do gene da citocromo oxidase c. Foram observados três haplótipos proximamente ligados, baixa diversidade nucleotídica e diversidade haplotípica de 59,1%. A simpatria entre D. albiventris e D. aurita foi molecularmente confirmada para a capital do estado de Minas Gerais (BHMR) e também para a região de Piracema, distantes 94 Km, através da utilização da metodologia de DNA barcode, demonstrando que a técnica é apropriada para efetivamente discriminar essas espécies de gambás. Expandindo os trabalhos populacionais com D. albiventris, utilizamos o mesmo fragmento da COI para realizar aanálise de 93 amostras biológicas provenientes de sete localidades brasileiras, com distâncias lineares que variam entre 58 e cerca de 1800 km, com a finalidade de analisar o efeito da distância geográfica sobre a variabilidade e sobre a diferenciação genética. A rede haplotípica resultante exibe nove haplótipos distribuídos em dois grupos genéticos totalmente compatíveis com as duas distantes áreas geográficas estudadas, o estado de Minas Gerais, localizado no sudeste brasileiro, e o estado do Rio Grande do Sul, no extremo sul do país; dentro de cada grupo, observamos baixa diversidade nucleotídica e diversidade haplotípica elevada, sugerindo que suas populações são compostas por haplótipos proximamente relacionados. Índices de moderados a altos de diferenciação genética (FST) e sinal filogeográfico muito fraco caracterizam as comparações entre os demes dentro do estado de Minas Gerais, e estão correlacionados com a presença de haplótipos exclusivos (privativos). Em maior escala geográfica, as comparações entre Minas Gerais e Rio Grande do Sul produziram valores de FST altos e padrão filogeográfico forte. Como as taxas de dispersão são reconhecidamente maiores nos machos de Didelphis, estes provavelmente contribuem mais para o fluxo gênico, e trabalhando com um marcador genético de herança materna, não podemos argumentar sobre a diversidade de D. albiventris de modo completo. Nossos resultados informam sobre a história mutacional das linhagens genealógicas maternas. O cenário observado é inesperado e sugere fortemente que o fluxo de genes mitocondriais não foi suficiente para manter a coesão populacional. Como esperado, Marmosops incanus mostra resultados completamente diferentes dos exibidos por D. albiventris. M. incanus demonstra significativa preferência de habitat, tendo sido apontado como espécie indicadora, por exibir elevada sensibilidade à fragmentação (Rocha et al., 2011), exibe também características ecológicas, como baixa mobilidade e semelparidade (Lorini et al. 1994; Loretto & Vieira, 2008), que podem comprometer aconexão entre populações de diferentes demes. Estudamos um fragmento de 509 pb do gene da COI, de indivíduos coletados em 17 localidades brasileiras e observamos a influência da distância geográfica na diferenciação genética entre as populações. As distâncias genéticas entre os haplótipos de diferentes demes e o grande número de formas privativas produziram uma rede, caracterizada pelo grande número de passos entre alguns dos haplótipos estudados. Valores de FST elevados, indicando forte estruturação genética, altos valores para o percentual de variação observado entre filogrupos e elevada correlação entre as distâncias genéticas e as geográficas caracterizam as análises interpopulacionais; a rede haplotípica e as árvores filogeográficas demonstram claramente a compatibilidade quase absoluta entre oshaplogrupos moleculares e o agrupamento geográfico. O padrão observado de distribuição geográfica das linhagens genealógicas é caracterizado pelo sinal filogeográfico forte; nossos resultados, especialmente os elevados valores de divergência entre os demes, sugerem que, mais do que o efeito da fragmentação de habitats, a história de vida de M. incanus é a chave central para explicá-los. A estrutura genética forte e a grande variação entre filogrupos estão relacionadas a processos antigos que influenciaram a distribuição geográfica das linhagens, refletindo eventos de fragmentação que antecedem a destruição do habitat natural governada pela ocupação humana. Características ecológicas de M. incanus, como baixa mobilidade e alta sensibilidade à fragmentação do habitat, são desfavoráveis ao fluxo gênico, concorrendo para a manutenção dos altos níveis de diferenciação genética. We studied population genetics aspects of two species of the family Didelphidae and the suitability of the DNA barcode methodology to effectively identify them. A molecular study of a 653 bp sequence of cytochrome c oxidase, subunit I from 40 Didelphis albiventris froman urban fragment of the Brazilian Atlantic Forest, showed three closely connected haplotypes, low nucleotide diversity and a haplotype diversity of 59.1%. We confirmed the sympatry between D. albiventris and D. aurita for the BHMR region, located on the capital of Minas Gerais state, and also for the 94 Km distant Piracema region, using DNA barcode methodology, which demonstrates the suitability of these techniques to effectively discriminate between these opossum species. Expanding the population surveys of D. albiventris, we used the COI fragment to 93 biological samples from seven Brazilian localities with linear distances ranging between 58 and about 1800 km, to study the effect of geographicdistances on variability and genetic differentiation. The haplotype network exhibits nine haplotypes distributed in two genetic clusters completely compatible with the two distant geographic areas of Minas Gerais, Southeastern Brazil, and Rio Grande do Sul, South Brazil. Within each cluster we observed low nucleotide diversity and high haplotype diversity,suggesting that their populations are composed of closely related haplotypes. Moderate to high FST differentiation values were observed and a very weak phylogeographic signal characterized interdemes comparisons within Minas Gerais, which were correlated with thepresence of closely and exclusive haplotypes. In a larger geographic scale, comparisons between Minas Gerais and Rio Grande do Sul produced a high FST values and a strong phylogeographic pattern. As Didelphis dispersion rates are recognized to be greater in males,they probably contribute more for gene flow. Working with a maternal inherited genetic marker, we can not argument about complete D. albiventris diversity. Our results informed only on the mutational history that corresponds to maternal lineages genealogical information.The observed scenario was unexpected and strongly suggests that mtDNA gene flow was not enough to maintain population cohesion. As expected, Marmosops incanus showed completely different results. M. incanus shows significant habitat preference and has been pointed out as an indicator species, being sensitive to habitat fragmentation (Rocha et al., 2011). It also exhibits ecological characteristics like low mobility and semelparity (Lorini et al. 1994; Loretto & Vieira, 2008), which can compromise interdemes connection. We studied a 509 bp fragment of COI obtained from specimens collected in 17 Brazilian localities andobserved the influence of geographic distance in genetic differentiation among populations. The genetic distances between demes haplotypes and the great number of forms produced a network with a large number of steps between some studied haplotypes. Large FST, indicating strong genetic structure, great values for phylogroups variation and elevated correlation between genetic and geographical distances characterized interpopulational analyses. Haplotype network and phylogeographic trees clearly showed molecular haplogroups mostly compatible with geographic clustering. The observed pattern of geographic distribution ofgenealogic lineages showed strong phylogeographic signal; our findings, specially the great divergence values between demes, suggest that, more than one effect of habitats fragmentation, M. incanus life history is central to explain the observed results. The strong genetic structure and the great variation among phylogroups are related to ancient processes that influenced lineages geographic distribution reflecting fragmentation events that predate human driven habitat destruction. M. incanus ecological characteristics, like low mobility and high sensibility to habitat fragmentation, are not suitable to gene flow, allowing the maintenance of high levels of genetic differentiation.

A diversidade genética presente em uma população do roedor silvestre Thrichomys apereoides do norte de Minas foi analisada através do marcador mitocondrial da região controle, D loop. Os indivíduos são provenientes de três pontos de coleta distintos. Foram encontrados dezenove haplótipos os quais encontram se distribuídos nos três pontos onde as coletas foram realizadas. A população apresentou alta diversidade haplotípica e baixa diversidade nucleotídica como já observado em alguns estudos de outras famílias de roedores. As análises dos testes de neutralidade apontaram para uma população que está em recente expansão demográfica, o que não pode ser observado através das diferenças par a par nas freqüências dos nucleotídeos. The genetic diversity presented in a population of wild rodent Thrichomys apereoides from the northern of Minas was analyzed through the mitochondrial marker of control region, D loop. The individuals came from three different collection points. There were found nineteen haplotypes which were distributed in three points, where the colletions were made. The population showed high haplotype diversity and low nucleotide diversity as observed in some studies of other rodents families. Tests analyzes of neutrality pointed to a population which is in recent demographic expansion, which cannot be observed through the pairwise differences in the frequencies of nucleotides.