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Mol Phylogenet Evol ; 162: 107200, 2021 09.
Artigo em Inglês | MEDLINE | ID: mdl-33984467


New sequencing techniques have allowed us to explore the variation on thousands of genes and elucidate evolutionary relationships of lineages even in complex scenarios, such as when there is rapid diversification. That seems to be the case of species in the genus Anastrepha, which shows great species diversity that has been divided into 21 species groups, several of which show wide geographical distribution. The fraterculus group has several economically important species and it is also an outstanding model for speciation studies, since it includes several lineages that have diverged recently possibly in the presence of interspecific gene flow. Our main goal is to test whether we can infer phylogenetic relationships of recently diverged taxa with gene flow, such as what is expected for the fraterculus group and determine whether certain genes remain informative even in this complex scenario. An analysis of thousands of orthologous genes derived from transcriptome datasets of 10 different lineages across the genus, including some of the economically most important pests, revealed signals of incomplete lineage sorting, vestiges of ancestral introgression between more distant lineages and ongoing gene flow between closely related lineages. Though these patterns affect the phylogenetic signal, the phylogenomic inferences consistently show that the morphologically identified species here investigated are in different evolutionary lineages, with the sole exception involving Brazilian lineages of A. fraterculus, which has been suggested to be a complex assembly of cryptic species. A tree space analysis suggested that genes with greater phylogenetic resolution have evolved under similar selection pressures and are more resilient to intraspecific gene flow, which would make it more likely that these genomic regions may be useful for identifying fraterculus group lineages. Our findings help establish relationships among the most important Anastrepha species groups, as well as bring further data to indicate that the diversification of fraterculus group lineages, and even other lineages in the genus Anastrepha, has been strongly influenced by interspecific gene flow.

Introgressão Genética , Filogenia , Tephritidae/classificação , Tephritidae/genética , Animais , Fluxo Gênico , Genoma de Inseto , Transcriptoma
Rev. peru. biol. (Impr.) ; 27(2): 139-148, abr.-jun 2020. tab, graf
Artigo em Espanhol | LILACS-Express | LILACS | ID: biblio-1144944


Resumen En la Amazonia Peruana los caracoles dulceacuícolas de la familia Ampullariidae son conocidos como churos y originalmente han sido descritas para Perú alrededor de 20 especies. Aunque son muy usadas para alimentación, medicina tradicional y objeto de muchos estudios para su cultivo e industrialización, solamente es mencionada en la literatura la especie Pomacea maculata. Se llevó a cabo la identificación molecular sobre la base del marcador mitocondrial COI, de individuos de churos negros (Pomacea) comercializados en los mercados de Iquitos, así como los usados en platos a la carta en la ciudad de Lima, contrastados con otros individuos de procedencia de su hábitat natural. Se encontró que estos especímenes expendidos corresponden a la especie Pomacea nobilis (Reeve, 1856). El análisis filogenético molecular mostró que P. nobilis es especie hermana de P. guyanensis, en el grupo de P. glauca, distantemente relacionada de P. maculata. Las distancias no corregidas encontradas entre ellas, para el marcador mitocondrial COI, fueron de 11.33% a 13.17%, mientras que con P. maculata fueron de 13.67% a 15.33%. Estos resultados demostraron la eficacia del código de barras de ADN para la identificación y autenticación de la especie, lo que le da un valor agregado para su eventual comercio de exportación.

Abstract In the Peruvian Amazon, freshwater snails of the Ampullariidae family are known as churos, and around 20 species have originally been described for Peru. Although they are widely used for food, traditional medicine and the object of many studies for their cultivation and industrialization, only the species Pomacea maculata is mentioned in the literature. Molecular identification was carried out based on the mitochondrial marker COI of individuals of "churo negro" apple snails (Pomacea) commercialized in the markets of Iquitos, as well as those used in restaurant dishes in the city of Lima, and contrasted with specimens from their natural habitat. It was found that these specimens, correspond to the species Pomacea nobilis (Reeve, 1856). The molecular phylogenetic analysis showed P. nobilis as the sister species of P. guyanensis, in the P. glauca group, distantly related to P. maculata. The uncorrected distances found between them, for the mitochondrial marker COI, were from 11.33% to 13.17%, while with P. maculate were from 13.67% to 15.33%. These results demonstrated the effectiveness of the DNA barcode for the identification and authentication of the species, which gives it added value for its eventual export trade.

PLoS One ; 14(2): e0212425, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30794584


We described the geographic distribution of 82 haemosporidian lineages (Plasmodium, Haemoproteus, and Leucocytozoon) in the cattle egret sampled in five countries in central-western and southern Africa. Seventy-three lineages have not previously been reported. We determined the prevalence of three haemosporidians in the samples. We investigated the influence of the internal environment of the host and environmental variables on the Plasmodium diversity and whether environmental variables may explain spatial variations in the prevalence of Plasmodium. We screened DNA from 509 blood samples from nestlings in 15 African colonies for infection by sequencing the cytochrome b gene of parasites. The molecular phylogenetic analysis was performed using Bayesian methods and including sequences from the MalAvi and GeneBank databases. We found 62 new Plasmodium lineages in a clade with MYCAME02, which is a lineage described in waterbirds and recently identified in birds of prey as Plasmodium paranucleophilum. Two Haemoproteus lineages identified in cattle egret formed a distinct group with Haemoproteus catharti and MYCAMH1 (Haemoproteus spp.). Seven Leucocytozoon lineages found in the cattle egret clustered with Leucocytozoon californicus. We found different Plasmodium diversities among the colonies sampled, demonstrating that the internal environment of the host is not the primary determinant of diversity. A linear mixed-effects multivariate model showed that precipitation was positively associated with Plasmodium diversity when controlling for the effects of temperature, colony composition (mixed and non-mixed species) and country. Moreover, a generalized mixed model showed that temperature was positively associated with the prevalence of Plasmodium when controlling for precipitation, elevation and country. We conclude that the cattle egret is a good model for future haemosporidian studies, as we found a significant number of new lineages in this host, which occupies regions with different climate characteristics where environmental variables exert an influence on the diversity and prevalence of Plasmodium.

Doenças das Aves/epidemiologia , Aves/parasitologia , Haemosporida/genética , Haemosporida/isolamento & purificação , Infecções Protozoárias em Animais/epidemiologia , África/epidemiologia , Animais , Doenças das Aves/parasitologia , DNA de Protozoário/genética , DNA de Protozoário/isolamento & purificação , Variação Genética , Haemosporida/patogenicidade , Interações Hospedeiro-Parasita , Malária/epidemiologia , Malária/parasitologia , Malária/veterinária , Filogenia , Filogeografia , Plasmodium/genética , Plasmodium/isolamento & purificação , Plasmodium/patogenicidade , Prevalência , Infecções Protozoárias em Animais/parasitologia
Genome Biol Evol ; 10(1): 380-395, 2018 01 01.
Artigo em Inglês | MEDLINE | ID: mdl-29346618


Several studies have demonstrated that genes differentially expressed between sexes (sex-biased genes) tend to evolve faster than unbiased genes, particularly in males. The reason for this accelerated evolution is not clear, but several explanations have involved adaptive and nonadaptive mechanisms. Furthermore, the differences of sex-biased expression patterns of closely related species are also little explored out of Drosophila. To address the evolutionary processes involved with sex-biased expression in species with incipient differentiation, we analyzed male and female transcriptomes of Anastrepha fraterculus and Anastrepha obliqua, a pair of species that have diverged recently, likely in the presence of gene flow. Using these data, we inferred differentiation indexes and evolutionary rates and tested for signals of selection in thousands of genes expressed in head and reproductive transcriptomes from both species. Our results indicate that sex-biased and reproductive-biased genes evolve faster than unbiased genes in both species, which is due to both adaptive pressure and relaxed constraints. Furthermore, among male-biased genes evolving under positive selection, we identified some related to sexual functions such as courtship behavior and fertility. These findings suggest that sex-biased genes may have played important roles in the establishment of reproductive isolation between these species, due to a combination of selection and drift, and unveil a plethora of genetic markers useful for more studies in these species and their differentiation.

Evolução Molecular , Genes de Insetos , Tephritidae/genética , Animais , Feminino , Fluxo Gênico , Masculino , Isolamento Reprodutivo , Seleção Genética , Caracteres Sexuais , Tephritidae/fisiologia , Transcriptoma
Sci Rep ; 7(1): 2194, 2017 05 19.
Artigo em Inglês | MEDLINE | ID: mdl-28526847


We studied two species of closely related South American fruit flies, Anastrepha fraterculus and Anastrepha obliqua which, despite being able to interbreed, still show some ecological and reproductive differences. Because part of these differences, such as host and mate preferences, may be related to olfactory perception, we focused our investigation on the differential expression of Odorant-binding protein (OBP) gene family, which participate in initial steps of the olfactory signal transduction cascade. We investigated patterns of expression of eight OBP genes by qPCR in male and female head tissues of both species. The expression patterns of these OBPs suggest that some OBP genes are more likely involved with the location of food resources, while others seem to be associated with mate and pheromone perception. Furthermore, the expression patterns obtained at different reproductive stages indicate that OBP expression levels changed significantly after mating in males and females of both species. All eight OBP genes analyzed here showed significant levels of differential expression between A. fraterculus and A. obliqua, suggesting that they may hold important roles in their olfactory perception differences, and consequently, may potentially be involved in their differentiation.

Expressão Gênica , Receptores Odorantes/genética , Tephritidae/genética , Animais , Feminino , Perfilação da Expressão Gênica , Regulação da Expressão Gênica , Masculino , Receptores Odorantes/metabolismo , Especificidade da Espécie , Tephritidae/metabolismo , Transcriptoma
PLoS One ; 12(4): e0174997, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-28406967


Chagas disease is one of the main parasitic diseases found in Latin America and it is estimated that between six and seven million people are infected worldwide. Its etiologic agent, the protozoan Trypanosoma cruzi, is transmitted by triatomines, some of which from the genus Rhodnius. Twenty species are currently recognized in this genus, including some closely related species with low levels of morphological differentiation, such as Rhodnius montenegrensis and Rhodnius robustus. In order to investigate genetic differences between these two species, we generated large-scale RNA-sequencing data (consisting of four RNA-seq libraries) from the heads and salivary glands of males of R. montenegrensis and R. robustus. Transcriptome assemblies produced for each species resulted in 64,952 contigs for R. montenegrensis and 70,894 contigs for R. robustus, with N50 of approximately 2,100 for both species. SNP calling based on the more complete R. robustus assembly revealed 3,055 fixed interspecific differences and 216 transcripts with high levels of divergence which contained only fixed differences between the two species. A gene ontology enrichment analysis revealed that these highly differentiated transcripts were enriched for eight GO terms related to AP-2 adaptor complex, as well as other interesting genes that could be involved in their differentiation. The results show that R. montenegrensis and R. robustus have a substantial quantity of fixed interspecific polymorphisms, which suggests a high degree of genetic divergence between the two species and likely corroborates the species status of R. montenegrensis.

Ontologia Genética , Hemípteros , Proteínas de Insetos , Transcriptoma/fisiologia , Animais , Feminino , Hemípteros/classificação , Hemípteros/genética , Hemípteros/metabolismo , Proteínas de Insetos/biossíntese , Proteínas de Insetos/genética , Masculino , Especificidade da Espécie
PLoS One ; 11(10): e0164441, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-27723778


The South America encompasses the highest levels of biodiversity found anywhere in the world and its rich biota is distributed among many different biogeographical regions. However, many regions of South America are still poorly studied, including its xeric environments, such as the threatened Caatinga and Cerrado phytogeographical domains. In particular, the effects of Quaternary climatic events on the demography of endemic species from xeric habitats are poorly understood. The present study uses an integrative approach to reconstruct the evolutionary history of Partamona rustica, an endemic stingless bee from dry forest diagonal in Brazil, in a spatial-temporal framework. In this sense, we sequenced four mitochondrial genes and genotyped eight microsatellite loci. Our results identified two population groups: one to the west and the other to the east of the São Francisco River Valley (SFRV). These groups split in the late Pleistocene, and the Approximate Bayesian Computation approach and phylogenetic reconstruction indicated that P. rustica originated in the west of the SFRV, subsequently colonising eastern region. Our tests of migration detected reduced gene flow between these groups. Finally, our results also indicated that the inferences both from the genetic data analyses and from the spatial distribution modelling are compatible with historical demographic stability.

Abelhas/fisiologia , Repetições de Microssatélites , Modelos Biológicos , Animais , Brasil , Florestas , Filogeografia
G3 (Bethesda) ; 6(10): 3283-3295, 2016 10 13.
Artigo em Inglês | MEDLINE | ID: mdl-27558666


Several fruit flies species of the Anastrepha fraterculus group are of great economic importance for the damage they cause to a variety of fleshy fruits. Some species in this group have diverged recently, with evidence of introgression, showing similar morphological attributes that render their identification difficult, reinforcing the relevance of identifying new molecular markers that may differentiate species. We investigated genes expressed in head tissues from two closely related species: A. obliqua and A. fraterculus, aiming to identify fixed single nucleotide polymorphisms (SNPs) and highly differentiated transcripts, which, considering that these species still experience some level of gene flow, could indicate potential candidate genes involved in their differentiation process. We generated multiple libraries from head tissues of these two species, at different reproductive stages, for both sexes. Our analyses indicate that the de novo transcriptome assemblies are fairly complete. We also produced a hybrid assembly to map each species' reads, and identified 67,470 SNPs in A. fraterculus, 39,252 in A. obliqua, and 6386 that were common to both species. We identified 164 highly differentiated unigenes that had a mean interspecific index ([Formula: see text]) of at least 0.94. We selected unigenes that had Ka/Ks higher than 0.5, or had at least three or more highly differentiated SNPs as potential candidate genes for species differentiation. Among these candidates, we identified proteases, regulators of redox homeostasis, and an odorant-binding protein (Obp99c), among other genes. The head transcriptomes described here enabled the identification of thousands of genes hitherto unavailable for these species, and generated a set of candidate genes that are potentially important to genetically identify species and understand the speciation process in the presence of gene flow of A. obliqua and A. fraterculus.

Fluxo Gênico , Genes de Insetos , Variação Genética , Tephritidae/genética , Transcriptoma , Alelos , Animais , Biologia Computacional/métodos , Evolução Molecular , Perfilação da Expressão Gênica , Sequenciamento de Nucleotídeos em Larga Escala , Anotação de Sequência Molecular , Especificidade de Órgãos/genética , Polimorfismo de Nucleotídeo Único , Seleção Genética , Especificidade da Espécie
J Parasitol ; 99(3): 522-7, 2013 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-23259406


This study documents the prevalences and lineages of hemoparasites in wood stork nestlings from 3 regions of the American continent: southeastern United States (n = 90), northern Brazil (n = 74), and central-western Brazil (n = 125). Identification was based on PCR amplification of a mitochondrial small subunit ribosomal RNA gene. A fragment of the hemoparasite cytochrome B gene in infected individuals was utilized for Bayesian phylogenetic analysis. Four wood stork nestlings were infected by Haemoproteus, 1 from northern Brazil and 3 from the United States, and all shared the same haplotype. Morphological analysis confirmed the infection of the U.S. birds by Haemoproteus. Infection by Plasmodium was found in wood stork nestlings from northern (6) and central-western Brazil (14). Five Plasmodium lineages (MYCAMP1-2, and MYCAMP4-6) were found in the Brazilian central-western region and 3 Plasmodium lineages (MYCAMP2-3, and MYCAMP7) were found in the northern region. The most prevalent haplotype (MYCAMP2) differs from the others by 1 mutation, and the less prevalent haplotypes are derived from MYCAMP2. We did not find Plasmodium or Haemoproteus in nestlings younger than 15 and 30 days old, respectively. This is the first documentation of Plasmodium and Haemoproteus infection in wood storks in Brazilian breeding populations. Potential connectivity among wood stork populations was indirectly supported by the presence of identical Haemoproteus lineages in U.S. and northern Brazilian populations, and by the presence of identical Plasmodium haplotypes in the northern and central-western Brazilian populations.

Doenças das Aves/parasitologia , Haemosporida/isolamento & purificação , Malária Aviária/parasitologia , Infecções Protozoárias em Animais/parasitologia , Animais , Teorema de Bayes , Doenças das Aves/sangue , Doenças das Aves/epidemiologia , Aves , Brasil/epidemiologia , DNA de Protozoário/sangue , DNA de Protozoário/isolamento & purificação , Florida/epidemiologia , Georgia/epidemiologia , Haemosporida/classificação , Haemosporida/genética , Malária Aviária/sangue , Malária Aviária/epidemiologia , Plasmodium/classificação , Plasmodium/genética , Plasmodium/isolamento & purificação , Reação em Cadeia da Polimerase/veterinária , Prevalência , Infecções Protozoárias em Animais/sangue , Infecções Protozoárias em Animais/epidemiologia , Áreas Alagadas
Rev. peru. biol. (Impr.) ; 19(1): 59-74, abr. 2012. ilus, tab
Artigo em Espanhol | LIPECS | ID: biblio-1111445


En este trabajo realizamos un estudio biogeográfico de dos géneros de caracoles terrestres amazónicos, Megalobulimus (Strophocheilidae) y Systrophia (Scolodontidae). Se utilizaron individuos colectados en diversas localidades de la Amazonia peruana así como información bibliográfica. Se utilizaron los marcadores moleculares 5.8S-ITS2-28S rRNA y 16S rRNA para reconstruir filogenias y obtener hipótesis sobre las relaciones evolutivas entre los géneros amazónicos y otras especies de distribución global. La filogenia nuclear permitió determinar la posición evolutiva de ambos géneros y la filogenia mitocondrial permitió la diferenciación de las especies a nivel intragenérico. Megalobulimus formó parte del clado no-achatinoideo en la filogenia de los gastrópodos Stylommatophora, como lo esperado, pero no pudo ser demostrada su cercanía a la familia Acavidae, mientras que Systrophia quedó fuera de los dos clados establecidos, formando uno basal dentro de los Stylommatophora. El gen mitocondrial 16S rRNA permitió diferenciar a las especies de Megalobulimus, actuando como código de barras de ADN de estos caracoles comestibles. El análisis de distribución geográfica reveló varios endemismos para la Amazonia peruana para especies de ambos géneros, resaltando las unidades biogeográficas de Chanchamayo e Inambari.

In this work we performed a biogeographic study of two genera of Amazonian land snails, Megalobulimus (Strophocheilidae) and Systrophia (Scolodontidae). We used samples from different regions of the Peruvian Amazon, as well as bibliographic information. We analyzed both nuclear (5.8S-ITS2-28S rRNA) and mitochondrial (16S rRNA) genes to reconstruct phylogenies and obtain hypotheses concerning the evolutionary relationships among Amazonian genera and other species with global distribution. The nuclear phylogeny allowed us to determine the evolutionary position of both genera, and the mitochondrial phylogeny permitted the differentiation of species at the intrageneric level. We found that Megalobulimus clustered with the non-achatinoid clade within Stylommatophora, as expected, but its relationship to family Acavidae could not be demonstrated. Systrophiadid not cluster with any of the two established clades, but formed a basal one within Stylommatophora. The mitochondrial gene 16S rRNA allowed us to differentiate Megalobulimus species, and performed well for DNA barcoding of these edible snails. Biogeographical analysis revealed several endemic species in the Peruvian Amazon within both genera, highlighting the Chanchamayo and Inambari biogeographic units.

Animais , Biodiversidade , Código de Barras de DNA Taxonômico , Ecossistema Amazônico , Filogenia , Gastrópodes , Gastrópodes/classificação
Rev. peru. biol. (Impr.) ; 17(1): 59-64, abr. 2010. ilus, tab
Artigo em Espanhol | LIPECS | ID: biblio-1111319


En el presente trabajo se identifica una secuencia de DNA no esperada proveniente de los amplificados del gen 28S rRNA de moluscos terrestres. Las extracciones de DNA se realizaron del tejido del pie de caracoles terrestres por el método del CTAB modificado. Las PCRs fueron llevadas a cabo con primers universales para el gen COI e iniciadores diseñados para moluscos, para el marcador 16S rRNA, 28S rRNA y la región ITS-2. Los tamaños aproximados de las bandas de los amplificados de moluscos fueron de 706 pb para el COI, 330pb para el 16S rRNA, 900 pb para el ITS-2 y 583 pb para el 28S rRNA; un amplificado del último marcador fuede una longitud inesperada, ~340 pb. Las secuencias de DNA fueron comparadas con la base de datos del GenBank mediante el programa BLASTn y la muestra con la banda de tamaño inesperado resultó en un 100% de identidad y cobertura del 99% con el gen 26S rRNA de la levadura Yarrowia lipolytica. El análisis filogenético con Neighbour-Joining y los valores de divergencia confirmaron la identificación, proporcionando resultados que apoyan la ubicación taxonómica de la especie dentro del clado de los Hemiascomycetes.

In this paper we identify an unexpected DNA sequence from the amplicons of 28S rRNA gene of terrestrial mollusks. DNA extractions were performed from foot tissues of land snails using a modified CTAB protocol. PCRs were carried out with universal primers for COI gene and oligonucleotides designed for molluscs, for the markers 16S rRNA, 28S rRNA, and ITS-2. Amplified lengths were 706 pb for COI, 330 pb for 16S rRNA, 900 pbfor ITS-2, and 583 pb for 28S rRNA. One amplicon of the last marker was of an unexpected length, ~340 pb. DNA sequences were compared in the GenBank database through the BLASTn program and the sample, with the unexpected length, resulted in 100% identity and 99% query coverage with 26S rRNA gene of the yeast Yarrowia lipolytica. Phylogenetic analysis with Neighbour-Joining and the divergence values confirmed the identification, providing results that support the taxonomic placement of the species within the Hemiascomycetes clade.

DNA , RNA , Ascomicetos , Caramujos , Gastrópodes , Yarrowia