Filling in a biogeographic gap: the first Trichomycteridae from the Parnaíba River basin (Siluriformes: Trichomycteridae)

Trichomycterid catfishes have long been considered as absent in the Parnaíba River basin, Northeastern Brazil, in what constitutes their most conspicuous gap in geographic distribution. Herein we report on the first occurrence of the family in that basin. The new species is described from the riacho da Volta, right tributary to the upper rio Parnaíba, Piauí State. It is distinguished from its congeners by the combination of two or three pairs of ribs; 36­38 post Weberian vertebrae; a color pattern composed of round, similar-sized, non-coalescent spots; I,5 pectoral-fin rays; the first haemal arch on the 5th or 6th vertebrae; and the first completely fused (to the tip) haemal spine on the 15th vertebra. A putative autapomorphy is the partial (minimally 50% of their length) or total fusion between the anterior arms of the basipterygium. Preliminary evidence suggests that the new species can be related to northern South American forms, a pattern that fits the general Amazonian relationships of the fishes in the Parnaíba River drainage. Although the new species fills in an important qualitative gap in trichomycterid continental distribution, the taxon is apparently rare and extremely restricted in distribution, with the type series being its only record so far. The paucity of trichomycterids in the Parnaíba remains a puzzling biogeographical phenomenon.(AU)

Os bagres tricomicterídeos têm estado surpreendentemente ausentes na bacia do rio Parnaíba, Nordeste do Brasil, no que constitui sua lacuna mais evidente na distribuição. Relatamos a primeira ocorrência da família na bacia. A espécie nova é descrita do riacho da Volta, tributário do lado direito do alto rio Parnaíba em Uruçuí, Piauí. Ela é distinguida de suas congêneres pela combinação de dois ou três pares de costelas; 36­38 vértebras pós weberianas; padrão de coloração composto de manchas arredondas, de tamanhos semelhantes e não coalescentes; I,5 raios nas nadadeiras peitorais; o primeiro arco haemal na 5° ou 6° vértebra, e o primeiro espinho haemal completamente fusionado (até a extremidade) na 15° vértebra. Uma possível autapomorfia é a fusão parcial (mínimo de 50% do seu comprimento) ou total entre os braços anteriores do basiopterígio. Evidências preliminares sugerem que a espécie nova pode estar relacionada com as formas do norte da América do Sul, padrão que se encaixa nas relações amazônicas dos peixes da drenagem do rio Parnaíba. Embora a espécie nova preencha uma importante lacuna na distribuição continental dos tricomicterídeos, o táxon é aparentemente raro e extremamente restrito em distribuição, sendo a série-tipo seu único registro até o momento.(AU)

Population structure and ancestry prediction of Aedes aegypti (Diptera: Culicidae) supports a single African origin of Colombian populations

BACKGROUND A previous phylogeographic study revealed two Aedes aegypti African-related mitochondrial lineages distributed in Colombian's cities with different eco-epidemiologic characteristics with regard to dengue virus (DENV). It has been proposed these lineages might indicate independent invasion sources. OBJECTIVES Assessing to Colombian population structure and to support evidence of its probable source origin. METHODS We analysed a total of 267 individuals from cities of Bello, Riohacha and Villavicencio, which 241 were related to the West and East African mitochondrial lineages (termed here as WAL and EAL, respectively). Eight polymorphic microsatellite loci were analysed aiming population structure. FINDINGS Results indicate substantial gene flow among distant and low-connected cities composing a panmictic population with incipient local differentiation of Ae. aegypti is placed in Colombia. Likewise, genetic evidence indicates no significant differences among individuals related to WAL and EAL is placed. MAIN CONCLUSIONS Minimal genetic differentiation in low-connected Ae. aegypti populations of Colombia, and lack concordance between mitochondrial and nuclear genealogies suggest that Colombian Ae. aegypti shared a common demographic history. Under this scenario, we suggest current Ae. aegypti population structure reflects a single origin instead of contemporary migration, which founding populations have a single source from a mitochondrial polymorphic African ancient.

Evidence on the paleodrainage connectivity during Pleistocene: Phylogeography of a hypoptopomatine endemic to southeastern Brazilian coastal drainages

The coastal basins of southeastern Brazil are influenced by climatic changes that caused sea-level oscillations during the Pleistocene. These marine transgressions and regressions can generate isolation and connection among coastal rivers. In this region, freshwater fishes are excellent models for phylogeographic studies because their distributions may have been affected by geographical and ecological changes resulting from these processes. Therefore, the main objective of this study was to evaluate the effects of Pleistocene sea-level changes on the genetic structure of the loricariid Hisonotus leucofrenatus throughout its area of occurrence. Two genes were sequenced: Cytochrome Oxidase subunit 1 (mitochondrial gene) and rpS7 ribosomal protein gene intron 1 (nuclear gene) from specimens representing 14 river drainages. The genetic data corroborate a divide for freshwater fish by the Serra do Tabuleiro mountain in Santa Catarina State. This divide determines two main genetic groups in H. leucofrenatus: one group to the south and one to the north of this mountain range. The genetic structure observed coincide with the limits of estimated paleodrainage systems for the region, supporting that marine transgressions and regressions during the Pleistocene influenced the biogeographical history of H. leucofrenatus.(AU)

As bacias costeiras do sul do Brasil são influenciadas pelas mudanças climáticas que causaram oscilações no nível do mar durante o Pleistoceno. Essas transgressões e regressões marinhas geraram isolamento e conexão entre os rios. Nessa região, as espécies de peixe são excelentes modelos para estudos filogeográficos, pois suas distribuições podem ter sido afetadas por mudanças históricas e ecológicas decorrentes desses processos. Portanto, o objetivo principal deste estudo foi testar os efeitos das alterações do nível do mar durante o Pleistoceno na estrutura genética das populações do loricarídeo Hisonotus leucofrenatus ao longo de sua área de ocorrência. Dois genes foram sequenciados: Citocromo Oxidase subunidade 1 (gene mitocondrial) e o intron 1 da proteína ribossomal rpS7 (gene nuclear) de espécimes representando 14 bacias de drenagens. A estrutura genética observada corrobora uma divisão para peixes de água doce separada pela Serra do Tabuleiro, em Santa Catarina. Essa divisória determina dois grupos principais genéticos em H. leucofrenatus: um grupo ao sul e outro ao norte desse divisor. A estrutura genética também coincide com os limites dos sistemas de paleodrenagens estimados para a região, sustentando que as transgressões e regressões marinhas durante o Pleistoceno influenciaram a história biogeográfica de H. leucofrenatus.(AU)

Phylogeography of Paris poliphylla var. yunnanensis based on chloroplast gene trnL-trnF sequences / 中国中药杂志

Phylogeography is a research hotspot in the field of the genetic diversity and core germplasm construction of endangered rare plants. Paris polyphylla var. yunnanensis is a rare plant species mainly distributed in China. Wild individuals have been overexploited for the last few decades because of increasing demand for such medicines. Therefore, it is great significance to study the phylogeography of P. poliphylla var. yunnanensis based on chloroplast gene trnL-trnF sequences. In this study, chloroplast genes trnL-trnF were used in the phylogeography analysis of 15 wild and 17 cultivated populations of P. polyphylla var. yunnanensis. This study revealed that based on the results of neutrality tests and mismatch analysis, the rapid expansion of wild population has not been detected in P. polyphylla var. yunnanensis. After aligning and sorting the obtained cpDNA sequences, a total of 15 haplotypes were detected in all 32 populations. One haplotype was unique to the wild population, and 5 haplotypes were unique to the cultivated population. It can be seen that the haplotype richness of cultivated population was higher than that of wild population. The wild populations of P. polyphylla var. yunnanensis were divided into two groups according to evolutionary relationship of haplotypes and distribution map of haplotypes. The haplotype of branch Ⅰ was mainly distributed in Guizhou, and the haplotype of branch Ⅱ was located in Yunnan and Huidong, Sichuan. Therefore, it's speculated that Guizhou and the west Yunnan region may be glacial refuge in the evolutionary history of wild populations of P. polyphylla var. yunnanensis, and in order to protect the wild resources more effectively, wild populations of P. polyphylla var. yunnanensis in these two areas should be included in the protection zone.

Phylogeography of the banded butterflyfish, Chaetodon striatus, indicates high connectivity between biogeographic provinces and ecosystems in the western Atlantic

Among the four butterflyfishes of the genus Chaetodon present in the western Atlantic, the banded butterflyfish Chaetodon striatus has the largest distribution range, spanning 44 degrees of latitude (from Massachusetts, USA to Santa Catarina, Brazil). Although the ecology of the banded butterflyfish has been well studied over its entire range, nothing is known about its phylogeography and how biogeographic barriers structure its populations. To assess the level of genetic connectivity among populations from distinct biogeographic provinces and environmental conditions, we collected samples from seven localities: Puerto Rico, in the Caribbean, and Tamandaré, Salvador, Abrolhos, Trindade Island, Arraial do Cabo and Florianópolis, in Brazil. One nuclear (rag 2) and two mitochondrial (control region and cyt b) molecular markers were sequenced. Our findings are consistent with a recent population expansion, around 30-120 thousand years ago, which was found for all populations. Haplotype network analyses point to the Caribbean as a refugium before the population expansion. Results show no geographic pattern of genetic diversity. Indeed, a lack of population structure was found and no isolation was observed across oceanographic barriers, as well as between coral and rocky reef ecosystems. Furthermore, no directionality in the migration pattern was found among populations. Since ecological and environmental characteristics are very diverse across such a vast geographic range, the lack of genetic differentiation suggests that C. striatus evolved ecological plasticity rather than local adaptation in the western Atlantic.(AU)

O peixe-borboleta listrado, Chaetodon striatus, possui a maior distribuição geográfica dentre as quatro espécies de peixes-borboleta do gênero Chaetodon presentes no Oceano Atlântico Ocidental, abrangendo 44° de latitude (entre Massachusetts, EUA até o sul do Brasil). A ecologia alimentar desta espécie é bastante conhecida, considerando a ampla distribuição, porém, pouco se sabe sobre a filogeografia e como as barreiras biogeográficas estruturam as populações. Para acessar a conectividade genética entre as populações de diferentes províncias biogeográficas e diferentes condições ambientais, foram coletadas amostras de sete localidades: Porto Rico, no Caribe, e Tamandaré, Salvador, Abrolhos, Ilha da Trindade, Arraial do Cabo e Florianópolis, no Brasil. Foram sequenciados um gene nuclear (rag 2) e dois genes mitocondriais (região controle e cit B). Para todas as populações, foi identificada uma expansão populacional recente, em torno de 30-120 mil anos atrás. A análise de rede de haplótipos sugere que o Caribe serviu como refúgio antes desta expansão populacional. Os resultados indicam que não há padrão geográfico de diversidade genética. Apesar da existência de barreiras oceanográficas e diferenças na constituição dos recifes (rochosos e coralíneos), não foi encontrada estruturação populacional. Também, não encontramos padrão na direção de migração entre as populações. Os resultados sugerem que C. striatus apresenta plasticidade ecológica, uma vez que não há diferenciação genética entre as populações que habitam ecossistemas tão diferentes ao longo da ampla distribuição no Atlântico Ocidental.(AU)

Genetic differentiation through dispersal and isolation in two freshwater fish species from coastal basins of Northeastern Brazil

The coastal basins in Northeastern Brazil used in this study make up two different ecoregions for freshwater fishes (Amazonas estuary and coastal drainages, and Parnaiba) and two areas of endemism for Characiformes (Maranhão and Parnaíba), and exhibits a diversified yet poorly explored freshwater fish fauna. The population structure and biogeography of two migratory freshwater fish species that are commercially exploited from Maranhão and Parnaíba regions were herein analyzed. Molecular sequence data and statistical analyses were used to estimate haplotypes networks and lineage divergence times and correlated with hydrographic history of drainage and paleodrainages of the region. A total of 171 sequences was produced for both species, Schizodon dissimilis (coI, n = 70) and Prochilodus lacustris (D-loop, n = 101). All analyses identified the presence of three genetically delimited groups of S. dissimilis and six groups of P. lacustris. The lineage time analyses indicate diversification among these species within the past 1 million year. The results indicate the influence of geodispersal in the formation of the ichthyofauna in the studied area through headwater stream capture events and reticulated connections between the mouths of rivers along the coastal plain due to eustatic sea level fluctuations.(AU)

As bacias costeiras do nordeste do Brasil usadas neste estudo compõem duas ecorregiões diferentes para peixes de água doce (Estuário do Amazonas e drenagens costeiras e Parnaíba) e duas áreas de endemismo para Characiformes (Maranhão e Parnaíba), exibindo uma diversificada e ainda pouco explorada fauna de peixes de água doce. A estrutura populacional e biogeografia de duas espécies migradoras de peixes de água doce exploradas comercialmente nas regiões do Maranhão e Parnaíba foram analisadas. Dados de sequências moleculares e análises estatísticas foram utilizados para estimar redes de haplótipos e tempos de divergência entre linhagens, e foram correlacionados com a história hidrográfica das drenagens e paleodrenagens da região. Um total de 171 sequências foram geradas para ambas espécies, Schizodon dissimilis (coI, n = 70) e Prochilodus lacustris (D-loop, n = 101). Todas análises identificaram a presença de três grupos geneticamente delimitados para S. dissimilis e seis grupos para P. lacustris. A análise de tempo de divergência das linhagens indicou uma diversificação entre estas espécies nos últimos 1 Ma. Os resultados indicam influência da geodispersão na formação da ictiofauna do Maranhão, devido eventos de capturas de cabeceira e conexões reticuladas entre as fozes dos rios ao longo da planície costeira devido às flutuações eustáticas do nível do mar.(AU)

Genomic and phylogenetic characterisation of an imported case of SARS-CoV-2 in Amazonas State, Brazil

A new coronavirus [severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)] is currently causing a life-threatening pandemic. In this study, we report the complete genome sequencing and genetic characterisation of a SARS-CoV-2 detected in Manaus, Amazonas, Brazil, and the protocol we designed to generate high-quality SARS-CoV-2 full genome data. The isolate was obtained from an asymptomatic carrier returning from Madrid, Spain. Nucleotide sequence analysis showed a total of nine mutations in comparison with the original human case in Wuhan, China, and support this case as belonging to the recently proposed lineage A.2. Phylogeographic analysis further confirmed the likely European origin of this case. To our knowledge, this is the first SARS-CoV-2 genome obtained from the North Brazilian Region. We believe that the information generated in this study may contribute to the ongoing efforts toward the SARS-CoV-2 emergence.

Análise Epidemiológica e Molecular do vírus Hepatite A em Pacientes Atendidos entre 2013 a 2019 no Ambulatório de Hepatites Virais do Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro / Epidemiological and Molecular Analysis of the Hepatitis A Virus in Patients Attended Between 2013 and 2019 at the Viral Hepatitis Outpatient Clinic of the Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro

Ao longo dos anos vem se observando um declínio do número de casos de infecção pelo vírus da hepatite A (HAV) em crianças, relacionado ao investimento nos programas de vacinação e a melhorias sanitárias. Porém, nota se a mudança desse perfil de infecção, onde indivíduos jovens/adultos vêm sendo mais acometidos. Apesar do vírus ser transmitido principalmente pelo consumo de água e alimentos contaminados, diversos surtos têm ocorrido ao redor do mundo em adultos e sendo relacionados a práticas sexuais. Em nosso país, um aumento no número de casos nos últimos três anos foi observado após um período de declínio de notificações. Assim, este estudo teve como objetivo avaliar os comportamentos de risco e os aspectos moleculares associados à transmissão do HAV em indivíduos atendidos no Ambulatório de Hepatites Virais do Instituto Oswaldo Cruz/FIOCRUZ, Rio de Janeiro, entre os anos de 2017 e 2019. Para tal, foram coletadas amostras de soro e informações socioepidemiológicas de 52 pacientes com anti-HAV IgM reagente, que chegaram ao ambulatório. Posteriormente, essas amostras tiveram o genoma viral extraído e analisado através da técnica de RTPCR. Após detecção, o RNA foi sequenciado e analisado filogeneticamente. Em seguida, foram realizadas análises filogeográficas para obter a rota de dispersão e período de introdução das estirpes virais no país. (AU)

Com a análise dos dados dos prontuários, observou-se que 78,9% (41/52) pacientes eram do sexo masculino, nas faixas etárias 20 a 29 anos (n=24/52) e de 30 a 39 anos (n=20/52) com media 32,1 anos, sendo 63,5% (n=33) dele(a)s homens/mulheres que fazem sexo com homens/mulheres (HSH/MSM), e 89,9% eram residentes na região norte da cidade do Rio de Janeiro. Observou-se uma baixa frequência de exposição a fatores hídricos, alimentares e parenterais na população estudada, sendo 42,3%, 42,3%, 34,7%, respectivamente. Já algumas práticas sexuais apresentaram elevada frequência, destacando o sexo oral (75%) e sexo anal (65,3%). Através das análises filogenéticas, foi identificado um único subgenótipo IA da população estudada. Quatro clados deste subgenótipo foram formados, dos quais, três agruparamse as sequências dos estirpes virais provenientes de surtos Europeus/Asiáticos, e um clado, formado por estirpes virais previamente circulantes no Brasil. Através da filogeografia, foi possível inferir o ano e país de introdução, além da data de origem das estirpes virais no Brasil. A estirpe VRD_521_2016 foi possivelmente introduzida entre 2016-2017 pela Espanha com provável origem em 2013, a RIVM-HAV16-090 europeia/asiática e V16-25801, possivelmente introduzida pela Alemanha, entre 20142015 e 2015-2016 respectivamente, com provável origem em 2000 e 2011. Nossos achados reforçam a necessidade de ampliação do acesso à vacina contra o HAV a grupos adultos de risco e do monitoramento da entrada de novos patógenos no Brasil. Além disso, medidas educativas são úteis para impedir a disseminação do HAV em populações-chave como os HSH. (AU)

Phylogenetics applied to the human immunodeficiency virus type 1 (HIV-1): from the cross-species transmissions to the contact network inferences

Phylogenetic analyses were crucial to elucidate the origin and spread of the pandemic human immunodeficiency virus type 1 (HIV-1) group M virus, both during the pre-epidemic period of cryptic dissemination in human populations as well as during the epidemic phase of spread. The use of phylogenetics and phylodynamics approaches has provided important insights to track the founder events that resulted in the spread of HIV-1 strains across vast geographic areas, specific countries and within geographically restricted communities. In the recent years, the use of phylogenetic analysis combined with the huge availability of HIV sequences has become an increasingly important approach to reconstruct HIV transmission networks and understand transmission dynamics in concentrated and generalised epidemics. Significant efforts to obtain viral sequences from newly HIV-infected individuals could certainly contribute to detect rapidly expanding HIV-1 lineages, identify key populations at high-risk and understand what public health interventions should be prioritised in different scenarios.

Development of a small panel of SNPs to infer ancestry in Chileans that distinguishes Aymara and Mapuche components

BACKGROUND: Current South American populations trace their origins mainly to three continental ancestries, i.e. European, Amerindian and African. Individual variation in relative proportions of each of these ancestries may be confounded with socio-economic factors due to population stratification. Therefore, ancestry is a potential confounder variable that should be considered in epidemiologic studies and in public health plans. However, there are few studies that have assessed the ancestry of the current admixed Chilean population. This is partly due to the high cost of genome-scale technologies commonly used to estimate ancestry. In this study we have designed a small panel of SNPs to accurately assess ancestry in the largest sampling to date of the Chilean mestizo population (n = 3349) from eight cities. Our panel is also able to distinguish between the two main Amerindian components of Chileans: Aymara from the north and Mapuche from the south. RESULTS: A panel of 150 ancestry-informative markers (AIMs) of SNP type was selected to maximize ancestry informativeness and genome coverage. Of these, 147 were successfully genotyped by KASPar assays in 2843 samples, with an average missing rate of 0.012, and a 0.95 concordance with microarray data. The ancestries estimated with the panel of AIMs had relative high correlations (0.88 for European, 0.91 for Amerindian, 0.70 for Aymara, and 0.68 for Mapuche components) with those obtained with AXIOM LAT1 array. The country's average ancestry was 0.53 ± 0.14 European, 0.04 ± 0.04 African, and 0.42 ± 0.14 Amerindian, disaggregated into 0.18 ± 0.15 Aymara and 0.25 ± 0.13 Mapuche. However, Mapuche ancestry was highest in the south (40.03%) and Aymara in the north (35.61%) as expected from the historical location of these ethnic groups. We make our results available through an online app and demonstrate how it can be used to adjust for ancestry when testing association between incidence of a disease and nongenetic risk factors. CONCLUSIONS: We have conducted the most extensive sampling, across many different cities, of current Chilean population. Ancestry varied significantly by latitude and human development. The panel of AIMs is available to the community for estimating ancestry at low cost in Chileans and other populations with similar ancestry.

Phylogeography of msp4 genotypes of Anaplasma marginale in beef cattle from the Brazilian Pantanal / Filogeografia de genótipos msp4 de Anaplasma marginale em gado de corte no Pantanal brasileiro

Abstract The msp4 gene of A. marginale is unicodon, stable and mostly homogeneous, being considered as a useful marker for phylogeographic characterization of this bacterium. The objective of this work was to analyze the phylogeography of A. marginale based on the msp4 gene in beef cattle from the Brazilian Pantanal, compared to those found in other regions worldwide. The blood samples investigated were collected from 400 animals (200 cows and 200 calves) reared in five extensive breeding farms in this region. The results indicated that of the evaluated samples, 56.75% (227/400) were positive for A. marginale based on the msp1β gene by quantitatitve PCR (qPCR), while 8.37% (19/227) were positive for the msp4 gene in the conventional PCR. In the Network distance analysis, 14 sequences from the Brazilian Pantanal were grouped into a single group with those from Thailand, India, Spain, Colombia, Parana (Brazil), Mexico, Portugal, Argentina, China, Venezuela, Australia, Italy and Minas Gerais (Brazil). Among 68 sequences from Brazil and the world, 15 genotypes were present while genotype number one (#1) was the most distributed worldwide. Both Splitstree and network analyses showed that the A. marginale msp4 sequences detected in beef cattle from the Brazilian Pantanal showed low polymorphism, with the formation of one genogroup phylogenetically related to those found in ruminants from South and Central America, Europe, and Asia.

Resumo O gene msp4 de A. marginale é unicodon, estável e pouco heterogêneo, sendo considerado como um marcador útil para caracterização filogeográfica desta bactéria. Este trabalho teve como objetivo analisar a filogeografia de A. marginale com base no gene msp4 em bovinos de corte do Pantanal Brasileiro, comparativamente a outra regiões do mundo. Alíquotas de sangue foram colhidas de 400 bovinos (200 vacas e 200 bezerros) em cinco propriedades de cria e recria extensiva. Como resultado, 56,75% (227/400) mostraram-se positivas para A. marginale pela qPCR para o gene msp1β e destas, 8,37% (19/227) amostras foram positivas na PCR convencional para o gene msp4. Na análise de distância Network, 14 sequências do Pantanal brasileiro foram agrupadas em um único grupo com as da Thailândia, Índia, Espanha, Colômbia, Paraná (Brasil), México, Portugal, Argentina, China, Venezuela, Austrália, Italia e Minas Gerais (Brasil). Dentre 68 sequências do Brasil e do mundo, constatou-se a presença de 15 genótipos, sendo o genótipo número um (#1) o mais distribuído. As sequências msp4 de A. marginale detectadas em bovinos de corte no Pantanal brasileiro apresentaram baixo polimorfismo com formação de dois genogrupos filogeneticamente relacionados àqueles encontrados em ruminantes de países das América do Sul e Central, Europa e Ásia.

Phylogeographic distribution of asperisporium caricae isolates in brazilian southeastern and northeastern coastal regions / Distribuição filogeográfica de isolados de Asperisporium caricae no litoral do sudeste e nordeste brasileiro

Papaya (Carica papaya L.) is one of the main tropical fruits consumed in Brazil. The country is also one of the main papaya exporters, but one of the factors hindering its production lies on foliar diseases such as papaya black spot, which is caused by fungus Asperisporium caricae. This pathogen is widely distributed in the main producing regions of the Brazilian coastal area. Phylogeographic studies contribute to the knowledge about the genetic diversity and geographical distribution of genealogical lineages (haplotypes) and help better understanding the reproductive and evolutionary processes of closely related species or of a single species. Such information is useful in studies about phytopathogenic fungi because it enables identifying the most prevalent genealogical lineages in a given location, as well as inferring dispersal routes and providing information on the origin and frequency of exotic material introduction events. Results in this type of study can significantly help developing new disease control strategies. Literature still lacks studies on the Papaya x A. caricae pathosystem. Based on the phylogenetic and phylogeographic analysis applied to nucleotide sequences of the Internal transcribed spacer (ITS) gene, we herein address the genealogical and dispersal events recorded for this pathogen in order to better understand its evolution in, and adaptation to, Brazilian orchards. Three haplotypes were identified among the A. caricae isolates; their distribution was mostly related to the geographic distance between sample collection regions rather than to any reproductive or evolutionary processes presented by the species. The low variability among the herein studied isolates may result from the physiological specialization (survival exclusively associated with the host plant) and from the regional transport of contaminated fruits (with lesions and spores), besides the low contribution of reproductive events, which corroborate the lack of knowledge about the sexual stages of A. caricae.

O mamoeiro (Carica papaya L.), é uma das principais frutas tropicais consumidas no Brasil. O país é um dos principais exportadores de mamão e um dos gargalos da produção mundial está diretamente ligado à ocorrência de doenças foliares, podendo-se destacar a pinta-preta do mamoeiro, causada pelo fungo Asperisporium caricae. O patógeno está amplamente distribuído nas principais regiões produtoras, as quais englobam grande parte do litoral Brasileiro. Estudos filogeográficos contribuem não só para oconhecimento da diversidade genética e da distribuição geográfica das linhagens genealógicas (haplótipos), como também contribuem para o conhecimento dos processos reprodutivos e evolutivos de uma espécie ou de espécies estreitamente relacionadas. No estudo de fungos fitopatogênicos, tais informações são úteis para identificar linhagens genealógicas mais prevalentes em um determinado local, inferir as rotas de dispersão e fornecer informações sobre a origem e frequência dos eventos de introdução de material exótico. Este tipo de estudo produz resultados que podem colaborar significativamente na elaboração de novas estratégias de controle da doença. Não existe, até o presente momento, este tipo de estudo para o patossistema Mamoeiro x A. caricae. Neste trabalho, por meio da análise filogenética e filogeográfica, a partir de sequências nucleotídicas do gene Internal transcribed spacer (ITS), discutimos os eventos genealógicos e de dispersão deste patógeno com o intuito de compreender melhor sua evolução e adaptação nos pomares brasileiros. Dentre os isolados de A. caricae foram identificados 3 haplótipos, sendo sua distribuição relacionada mais ao distanciamento geográfico das regiões das coletas das amostras do que a eventuais processos reprodutivos ou evolutivos da espécie. Acredita-se que a baixa variabilidade dentre os isolados estudados seja explicada pela especialização fisiológica (sobrevivência exclusivamente associada à planta hospedeira) e ao transporte regional de frutos contaminados (com lesões e esporos), sendo baixa a contribuição de eventos reprodutivos, o que corrobora o desconhecimento de fase sexual de A. caricae.

From the "Out of Africa Theory" Study to the Application of "DNA Biogeographic Ancestry Inference" in Criminal Investigation / 法医学杂志

Genetic markers, such as single nucleotide polymorphism （SNP）, insertion/deletion （InDel）, were discovered and widely used with the development of whole genome sequencing and bioinformatics technology. The origin and genetic structure of the modern population had been gradually revealed from the perspective of genetics. The study on biogeographic ancestry inference in the field of forensic genetics emerged and developed rapidly, providing clues and scientific basis for the determination of investigation direction and for the narrow of the scope of investigation in the process of case investigation. This paper briefly reviews the research progress, inference methods and development trends of DNA ancestry inference technology.

A new species of Characidium (Characiformes: Crenuchidae) from coastal basins in the Atlantic Rainforest of eastern Brazil, with phylogenetic and phylogeographic insights into the Characidium alipioi species group

A new species of Characidium from southeastern Brazil is described based on morphological and molecular evidence from specimens collected between the rio Jucuruçu and rio Doce basins. The new species belongs to a group of species within Characidium with an unscaled area in the isthmus and is distinguished from these species, except C. alipioi, C. fasciatum, C. hasemani, and C. kamakan, by the greater distance (greater than 10% SL) and presence of 5-7 scales between the anus and the anal fin, and presence of 14 series of scales around the caudal peduncle. The species is distinguished from C. alipioi by having 4 series of scales above the lateral line (vs. 5 series) and greater distance between the anus and the anal fin; from C. fasciatum and C. kamakan, by the smaller body depth at the dorsal-fin origin, at the anal-fin origin, and at the caudal peduncle; from C. hasemani, by the short distances between the tip of the snout and the pelvic fin, the tip of the snout and the anal fin, and the tip of the snout and the tip of anal fin. The new species forms a presumably monophyletic group with C. alipioi and C. kamakan.(AU)

Uma nova espécie de Characidium do sudeste do Brasil é descrita com base em evidências morfológicas e moleculares provenientes de exemplares coletados entre as bacias dos rios Jucuruçu e Doce. A nova espécie pertence a um grupo de espécies de Characidium com área desprovida de escamas no ístmo e difere dessas espécies, exceto C. alipioi, C. fasciatum, C. hasemani e C. kamakan, pela grande distância (maior que 10% do comprimento padrão, CP) e presença de 5-7 escamas entre o ânus e a nadadeira anal, e pela presença de 14 séries de escamas em torno do pedúnculo caudal. A espécie difere de C. alipioi pela presença de 4 séries de escamas acima da linha lateral (vs. 5 séries) e maior distância entre o ânus e a nadadeira anal; de C. fasciatum e C. kamakan, pela menor altura do corpo na origem da nadadeira dorsal, na origem da nadadeira anal, e no pedúnculo caudal; de C. hasemani, pela menor distância entre a ponta do focinho e a nadadeira pélvica, a ponta do focinho e a nadadeira anal, e a ponta do focinho e a ponta da nadadeira anal. A nova espécie forma um grupo presumidamente monofilético com C. alipioi e C. kamakan.(AU)

Combination of surveillance tools reveals that Yellow Fever virus can remain in the same Atlantic Forest area at least for three transmission seasons

BACKGROUND In Brazil, the Yellow Fever virus (YFV) is endemic in the Amazon, from where it eventually expands into epidemic waves. Coastal south-eastern (SE) Brazil, which has been a YFV-free region for eight decades, has reported a severe sylvatic outbreak since 2016. The virus spread from the north toward the south of the Rio de Janeiro (RJ) state, causing 307 human cases with 105 deaths during the 2016-2017 and 2017-2018 transmission seasons. It is unclear, however, whether the YFV would persist in the coastal Atlantic Forest of RJ during subsequent transmission seasons. OBJECTIVES To conduct a real-time surveillance and assess the potential persistence of YFV in the coastal Atlantic Forest of RJ during the 2018-2019 transmission season. METHODS We combined epizootic surveillance with fast diagnostic and molecular, phylogenetic, and evolutionary analyses. FINDINGS Using this integrative strategy, we detected the first evidence of YFV re-emergence in the third transmission season (2018-2019) in a dying howler monkey from the central region of the RJ state. The YFV detected in 2019 has the molecular signature associated with the current SE YFV outbreak and exhibited a close phylogenetic relationship with the YFV lineage that circulated in the same Atlantic Forest fragment during the past seasons. This lineage circulated along the coastal side of the Serra do Mar mountain chain, and its evolution seems to be mainly driven by genetic drift. The potential bridge vector Aedes albopictus was found probing on the recently dead howler monkey in the forest edge, very close to urban areas. MAIN CONCLUSIONS Collectively, our data revealed that YFV transmission persisted at the same Atlantic Forest area for at least three consecutive transmission seasons without the need of new introductions. Our real-time surveillance strategy permitted health authorities to take preventive actions within 48 h after the detection of the sick non-human primate. The local virus persistence and the proximity of the epizootic forest to urban areas reinforces the concern with regards to the risk of re-urbanisation and seasonal re-emergence of YFV, stressing the need for continuous effective surveillance and high vaccination coverage in the SE region, particularly in RJ, an important tourist location.

Lutzomyia longipalpis (Diptera: Psychodidae) Argentina-Bolivia border: new report and genetic diversity

American visceral leishmaniasis (AVL) has two main scenarios of transmission as follows: scattered cases in rural areas and urban outbreaks. Urban AVL is in active dispersion from the northeastern border of Argentina-Paraguay-Brazil to the South. The presence of Lutzomyia longipalpis was initially reported in urban environments in the northwestern border of the country. The presence of Lu. longipalpis, environmental variables associated with its distribution, and its genetic diversity were assessed in Salvador Mazza, Argentina, on the border with Bolivia. The genetic analysis showed high haplotype diversity, low nucleotide diversity, and low nucleotide polymorphism index. We discuss the hypothesis of an expanding urban population with introgressive hybridisation of older haplogroups found in their path in natural forest or rural environments, acquiring a new adaptability to urban environments, and the possibility of changes in vector capacity.

Trypanosoma janseni n. sp. (Trypanosomatida: Trypanosomatidae) isolated from Didelphis aurita (Mammalia: Didelphidae) in the Atlantic Rainforest of Rio de Janeiro, Brazil: integrative taxonomy and phylogeography within the Trypanosoma cruzi clade

BACKGROUND Didelphis spp. are a South American marsupial species that are among the most ancient hosts for the Trypanosoma spp. OBJECTIVES We characterise a new species (Trypanosoma janseni n. sp.) isolated from the spleen and liver tissues of Didelphis aurita in the Atlantic Rainforest of Rio de Janeiro, Brazil. METHODS The parasites were isolated and a growth curve was performed in NNN and Schneider's media containing 10% foetal bovine serum. Parasite morphology was evaluated via light microscopy on Giemsa-stained culture smears, as well as scanning and transmission electron microscopy. Molecular taxonomy was based on a partial region (737-bp) of the small subunit (18S) ribosomal RNA gene and 708 bp of the nuclear marker, glycosomal glyceraldehyde-3-phosphate dehydrogenase (gGAPDH) genes. Maximum likelihood and Bayesian inference methods were used to perform a species coalescent analysis and to generate individual and concatenated gene trees. Divergence times among species that belong to the T. cruzi clade were also inferred. FINDINGS In vitro growth curves demonstrated a very short log phase, achieving a maximum growth rate at day 3 followed by a sharp decline. Only epimastigote forms were observed under light and scanning microscopy. Transmission electron microscopy analysis showed structures typical to Trypanosoma spp., except one structure that presented as single-membraned, usually grouped in stacks of three or four. Phylogeography analyses confirmed the distinct species status of T. janseni n. sp. within the T. cruzi clade. Trypanosoma janseni n. sp. clusters with T. wauwau in a well-supported clade, which is exclusive and monophyletic. The separation of the South American T. wauwau + T. janseni coincides with the separation of the Southern Super Continent. CONCLUSIONS This clade is a sister group of the trypanosomes found in Australian marsupials and its discovery sheds light on the initial diversification process based on what we currently know about the T. cruzi clade.

A history of the biogeography of Amazonian fishes

The history of knowledge about Amazonian biogeography is as rich as its fish community, and a fascinating theme of study in itself. Several current paradigms and controversies about Amazonian fish biogeography are rooted in principles dating from the second half of the 18th to the first half of the 19th centuries. The present work establishes a relationship between current biogeographical ideas and their old predecessors, on the basis of a chronologically-oriented historical continuity analysis. The advent of evolutionary theory has not contributed significantly to a transformation of the knowledge on the biogeography of Amazonian fishes. On the other hand, the two main schools of biogeographical thought (dispersalist and vicariant) had major implications on how Amazonian fish distribution is interpreted. The process was gradual and many hypotheses have combined elements from each of the two schools. Chronologically, practically the entire tradition of Amazonian biogeography takes place within the evolutionary paradigm, although its founder Louis Agassiz was himself an anti-evolutionist. The birth of Amazonian biogeography is Agassiz´s travel in Amazon. That document makes it clear that the author did not consider dispersal as a valid explanation for the biogeographical patterns he found. Later, Carl Eigenmann helps to spread the dispersalist tradition as a model for biogeographical explanations in fish distributions, a phase which lasted until the late 20th century. A major shift occurs with the contributions of Marylin Weitzman, Stanley Weitzman and Richard Vari, who associated the temporal framework of phylogenetic hypotheses with distribution patterns, underscoring the predictive power of vicariant biogeography. The present-day paradigm begins with the work of John Lundberg and attempts to incorporate geomorphological and phylogenetic information into integrative biogeographical hypotheses. Some emblematic problems have delayed proposition of general hypotheses on the phylogenetic biogeography of South American fishes, such as the poor state of knowledge of their species-level systematics; an incomplete distributional record for most species and sparse or non-existent data on the phylogenetic history of most supraspecific taxa. Such drawbacks are now being corrected at a fast pace. Recent advances on geographical distribution and an increasing number of phylogenetic hypotheses will allow unprecedented large-scale biogeographic analyses, including those based on event models and Bayesian inference. Thus, the biogeography of South American fishes, especially Amazonian ones, should soon experiment a new age of progress. The success of that new phase will depend on its ability to recognize and segregate multiple overlapping temporal layers of hydrological changes, and to develop analytical tools that can deal with temporal mixing.(AU)

A história do conhecimento da biogeografia amazônica é tão rica quanto sua comunidade de peixes e um tema fascinante de estudo em si. Vários paradigmas e controvérsias atuais sobre a biogeografia de peixes amazônicos estão enraizados em princípios que datam da segunda metade do século 18 até a primeira metade do século 19. O presente trabalho estabelece uma relação entre as idéias biogeográficas atuais e seus antecessores antigos a partir de uma análise histórica cronologicamente orientada. O advento da teoria evolutiva não contribuiu significativamente para a transformação do conhecimento sobre a biogeografia dos peixes amazônicos. Por outro lado, as duas principais escolas de pensamento biogeográfico (dispersalista e vicariante) tiveram grandes implicações sobre a interpretação da distribuição de peixes amazônicos. O processo foi gradual e muitas hipóteses combinaram elementos de cada uma das duas tradições. Cronologicamente, praticamente toda a história da biogeografia amazônica ocorre dentro do paradigma evolutivo, embora seu fundador Louis Agassiz fosse ele próprio um anti-evolucionista. O nascimento da biogeografia amazônica é o relatório de viagem de Agassiz na Amazônia. Esse documento deixa claro que o autor não considerou o dispersalismo como uma explicação válida para os padrões biogeográficos que encontrou. Mais tarde, Carl Eigenmann ajuda a disseminar a tradição dispersalista como modelo para explicações biogeográficas na distribuição de peixes, uma fase que perdurou até o final do século 20. Uma grande mudança ocorre com as contribuições de Marylin Weitzman, Stanley Weitzman e Richard Vari, que associaram a dimensão temporal de hipóteses filogenéticas com padrões de distribuição, revelando o poder preditivo da biogeografia vicariante. O paradigma atual começa com o trabalho de John Lundberg e busca incorporar informações geomorfológicas e filogenéticas em hipóteses biogeográficas integrativas. Alguns problemas emblemáticos atrasaram a proposição de hipóteses gerais sobre a biogeografia vicariante de peixes da América do Sul, como o mau estado de conhecimento de sua sistemática em nível de espécie; o registro de distribuição geográfica incompleto para a maioria das espécies e dados escassos ou inexistentes sobre a história filogenética da maioria dos táxons supraespecíficos. Essas desvantagens agora estão sendo corrigidas em um ritmo acelerado. Avanços recentes na distribuição geográfica e um número crescente de hipóteses filogenéticas permitirão inéditas análises biogeográficas de grande escala, inclusive aquelas baseadas em modelos de eventos e inferência bayesiana. Assim, a biogeografia dos peixes sul-americanos, especialmente os amazônicos, deve experimentar em breve uma nova era de progresso. O sucesso dessa nova fase dependerá de sua capacidade de reconhecer e segregar múltiplas camadas temporais sobrepostas de mudanças hidrológicas e desenvolver ferramentas analíticas que possam lidar com a mistura temporal.(AU)

A review of the systematic biology of fossil and living bony-tongue fishes, Osteoglossomorpha (Actinopterygii: Teleostei)

The bony-tongue fishes, Osteoglossomorpha, have been the focus of a great deal of morphological, systematic, and evolutionary study, due in part to their basal position among extant teleostean fishes. This group includes the mooneyes (Hiodontidae), knifefishes (Notopteridae), the abu (Gymnarchidae), elephantfishes (Mormyridae), arawanas and pirarucu (Osteoglossidae), and the African butterfly fish (Pantodontidae). This morphologically heterogeneous group also has a long and diverse fossil record, including taxa from all continents and both freshwater and marine deposits. The phylogenetic relationships among most extant osteoglossomorph families are widely agreed upon. However, there is still much to discover about the systematic biology of these fishes, particularly with regard to the phylogenetic affinities of several fossil taxa, within Mormyridae, and the position of Pantodon. In this paper we review the state of knowledge for osteoglossomorph fishes. We first provide an overview of the diversity of Osteoglossomorpha, and then discuss studies of the phylogeny of Osteoglossomorpha from both morphological and molecular perspectives, as well as biogeographic analyses of the group. Finally, we offer our perspectives on future needs for research on the systematic biology of Osteoglossomorpha.(AU)

Os peixes da Superordem Osteoglossomorpha têm sido foco de inúmeros estudos sobre a morfologia, sistemática e evolução, particularmente devido à sua posição basal dentre os peixes teleósteos. Fazem parte deste grupo os "mooneyes" (Hiodontidae), "knifefishes" (Notopteridae), o "abu" (Gymnarchidae), peixes-elefante (Mormyridae), aruanãs e pirarucu (Osteoglossidae), e o peixe-borboleta africano (Pantodontidae). Esse grupo de morfologia heterogênea possui um longo e diverso registro fóssil, incluindo táxons de todos os continentes, oriundos tanto de depósitos de água doce quanto marinhos. As relações filogenéticas dentre a maioria das famílias de osteoglossomorfos é amplamente aceita. Entretanto, há muito a ser descoberto sobre a sistemática biológica desses peixes, particularmente com relação às afinidades filogenéticas de inúmeros fósseis, relações dentro de Mormyridae, e a posição filogenética de Pantodon. Neste manuscrito nós revisamos o atual estado de conhecimento dos peixes osteoglossomorfos. Nós primeiramente provemos uma abordagem geral da diversidade de Osteoglossomorpha, e então discutimos os estudos filogenéticos sobre Osteoglossomorpha sob a perspectiva morfológica e molecular, assim como uma análise biogeográfica do grupo. Finalmente, oferecemos nossas perspectivas sobre os futuros passos para pesquisa sobre a sistemática biológica de Osteoglossomorpha.(AU)

Advances in Cryptococcus genomics: insights into the evolution of pathogenesis

Cryptococcus species are the causative agents of cryptococcal meningitis, a significant source of mortality in immunocompromised individuals. Initial work on the molecular epidemiology of this fungal pathogen utilized genotyping approaches to describe the genetic diversity and biogeography of two species, Cryptococcus neoformans and Cryptococcus gattii. Whole genome sequencing of representatives of both species resulted in reference assemblies enabling a wide array of downstream studies and genomic resources. With the increasing availability of whole genome sequencing, both species have now had hundreds of individual isolates sequenced, providing fine-scale insight into the evolution and diversification of Cryptococcus and allowing for the first genome-wide association studies to identify genetic variants associated with human virulence. Sequencing has also begun to examine the microevolution of isolates during prolonged infection and to identify variants specific to outbreak lineages, highlighting the potential role of hyper-mutation in evolving within short time scales. We can anticipate that further advances in sequencing technology and sequencing microbial genomes at scale, including metagenomics approaches, will continue to refine our view of how the evolution of Cryptococcus drives its success as a pathogen.