Ayudando a descifrar el enigma taxonómico, el código de barras de ADN de Megalobulimus spp. (Mollusca, Gastropoda) del departamento de San Martín - Perú

Dentro de la gama de especies de la selva peruana, se encuentran caracoles terrestres de la familia Megalobulimidae (Mollusca, Gastropoda), entre las que destacan Megalobulimus popelairianus, Megalobulimus huascari y Megalobulimus capillaceus, que tienen importancia económica por las propiedades nutricionales de su carne y cosméticas de su baba. Este trabajo tuvo por objetivo principal desarrollar perfiles de ADN de los Megalobulimidae de San Martín, que hagan posible su reconocimiento a nivel específico y estudiar su salud genético poblacional mediante la diversidad genética, todo ello para garantizar su uso sustentable y eventualmente certificar a estas especies en el biocomercio peruano. Se evaluaron 65 muestras biológicas que fueron colectadas en septiembre de 2007 y enero, febrero y marzo de 2008. Se realizó la extracción de ADN con el método del CTAB y cloroformo, alcohol-isoamílico a partir de tejido muscular de pie. Se amplificaron y secuenciaron regiones de los genes rRNA y Citrocromo C oxidasa subunidad I (COI) del genoma mitocondrial con primers internos y universales, respectivamente. Las secuencias de ADN fueron alineadas, caracterizadas, se determinó la calidad de los datos, distancias genéticas, diversidad genética, se realizó la reconstrucción filogenética con NJ, MP, ML e BI y se analizaron los perfiles de ADN. La tasa de éxito de amplificación del COI fue inferior a la del rRNA. Sorprendentemente, las 31 secuencias de ADN de M. capillaceus no mostraron ninguna variante genética. Los ejemplares de difícil identificación entre M. huascari y M. popelairianus (rotulados como Megalobulimus spp.) mostraron bajos valores de divergencia genética (menores al 2%) con M. huascari, además que formaron grupos monofiléticos estadísticamente bien sustentados con el gen COI con todos los métodos utilizados. Las filogenias con el rRNA fueron poco concluyentes y variaron según las metodologías. Los datos combinados de ambos genes arrojaron árboles filogenéticos no resueltos. La carencia de diversidad genética de M. capillaceus, que muy probablemente haya sido producida por la sobreexplotación, pone en riesgo su supervivencia como especie.Among the great variety of species from the Peruvian Amazon forest are the land snails of the family Megalobulimidae (Mollusca, Gastropoda), among them are Megalobulimus popelairianus, Megalobulimus huascari y Megalobulimus capillaceus, that have economic importance for both the nutritional properties of their meat and cosmetic properties of their slime. The main goal of this research was to develop DNA profiles of the Megalobulimidae land snails from San Martin, to allow their recognition at specific level, and to study their population genetic health through the genetic diversity, in order to guarantee their sustainable use and eventually to certify these species in Peruvian biotrade. The biological samples were collected in September of 2007 and January, February and March of 2008. The total DNA extraction was carried out by a CTAB protocol, with chloroform-isoamílic alcohol, from foot muscle tissue of 65 snails. Fragments of the genes rRNA and Cytochrome C oxidase subunit I (COI) of the mitochondrial genome were amplified and sequenced, using internal and universal primers, respectively. DNA sequences were aligned, characterized, determined the data quality, genetic distances, genetic diversity; the phylogenetic reconstruction was performed with NJ, MP, ML and BI; DNA profiles were analyzed. COI amplification rate was lower than the rRNA one. Surprisingly, the 31 DNA sequences of M. capillaceus did not show any genetic variant. Low values of genetic divergence (lower than 2%) between M. huascari and Megalobulimus spp. in both genes were found, besides, they were in a monophyletic group, with robust statistical support for the COI marker. 16S rRNA phylogenies were inconclusive and varied according to the methodologies. The combined data showed unresolved phylograms. M. capillaceus did not show genetic diversity, probably as a result of over hunting, which could threaten its survival as a species.Tesi

Identification of Yarrowia lipolytica (Ascomycota: Hemiascomycetes) as a contaminant in obtaining amplified 28S rRNA gene of mollusks

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, 330 pb para el 16S rRNA, 900 pb para el ITS-2 y 583 pb para el 28S rRNA; un amplificado del último marcador fue de 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 pb for 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

A hierarchical topic modelling approach for tweet clustering

While social media platforms such as Twitter can provide rich and up-to-date information for a wide range of applications, manually digesting such large volumes of data is difficult and costly. Therefore it is important to automatically infer coherent and discriminative topics from tweets. Conventional topic models and document clustering approaches fail to achieve good results due to the noisy and sparse nature of tweets. In this paper, we explore various ways of tackling this challenge and finally propose a two-stage hierarchical topic modelling system that is efficient and effective in alleviating the data sparsity problem. We present an extensive evaluation on two datasets, and report our proposed system achieving the best performance in both document clustering performance and topic coherence

Transcriptome-based phylogenomic analysis reveals evidence of ancient hybridization events in the Mepraia genus (Hemiptera: Reduviidae: Triatominae)

IntroductionThe Mepraia genus is composed of three endemic species in Chile, namely Mepraia spinolai, Mepraia gajardoi, and Mepraia parapatrica, all capable of transmitting the causative agent of Chagas disease. Although species divergence within this genus is supported by morphological, molecular, and geological evidence, it has never been validated by genome-wide data.MethodsIn this sense, a pioneering phylogenomic study was conducted using transcriptome data of the three species, aiming to infer robust phylogenies and evaluate the impact of interspecific gene flow on the evolution of these insects. Our transcriptomes were used to robustly infer the phylogenetic relationships, employing multi-species coalescent and supermatrix approaches, as well as to investigate the occurrence of introgression.Results and discussionThe inferred phylogenies support the monophyly of the three described taxa and infer divergence times, although gene trees display high levels of discordance. Our results indicate widespread introgression among Mepraia lineages. Thus, our results support that Mepraia diversification occurred in a short period resulting in reticulate phylogenies and low genetic diversity. Additionally, we obtained evidence of introgression suggesting that ancient hybridization has had a major role in the evolution of the three Mepraia species

Biodiversidad y endemismo de los caracoles terrestres Megalobulimus y Systrophia en la Amazonia occidental

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. Systrophia did 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.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

Identificación molecular y relaciones evolutivas de Pomacea nobilis, base para la autenticación específica del churo negro de la Amazonia peruana

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.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

Avian haemosporidians in the cattle egret (Bubulcus ibis) from central-western and southern Africa: high diversity and prevalence

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

Genomic Tools in Biological Invasions: Current State and Future Frontiers

Human activities are accelerating rates of biological invasions and climate-driven range expansions globally, yet we understand little of how genomic processes facilitate the invasion process. Although most of the literature has focused on underlying phenotypic correlates of invasiveness, advances in genomic technologies are showing a strong link between genomic variation and invasion success. Here, we consider the ability of genomic tools and technologies to (i) inform mechanistic understanding of biological invasions and (ii) solve real-world issues in predicting and managing biological invasions. For both, we examine the current state of the field and discuss how genomics can be leveraged in the future. In addition, we make recommendations pertinent to broader research issues, such as data sovereignty, metadata standards, collaboration, and science communication best practices that will require concerted efforts from the global invasion genomics community