ABSTRACT
Objective To investigate the genetic diversity and genetic differentiation of different geographical isolates of Gohieria fusca.. Methods G. fusca isolates were sampled from Wuhu (WH), Bengbu (BB) and Bozhou cities (BZ) of Anhui Province and Jiaxing City of Zhejiang Province (JX). Mitochondrial cytochrome b (Cytb) and ribosomal internal transcribed spacer (ITS) genes were amplified in WH, BB, BZ and JX isolates of G. fusca using PCR assay. The gene sequences were edited and aligned using the software Chromas 2 and DNASTAR 1.00, and the haplotype, haplotype diversity (Hd) and nucleotide polymorphism (Pi) of each isolate were calculated using the software DnaSP 5.10.00. The genetic differentiation among isolates (Fst) and gene flow value (Nm) were estimated using the software MEGA 10.2, and a phylogenetic tree was built. Tests of neutrality and analysis of molecular variance (AMOVA) were performed using the software Arlequin 3.1 and a haplotype network was built based on the Median-Joining network using the software Network 10.2. Results PCR assay showed that the sizes of the Cytb and ITS genes were 372 bp and 1 301 to 1 320 bp, respectively. All four isolates of G. fusca presented high genetic diversity based on mitochondrial Cytb and ITS genes (Hd = 0.804, Pi = 0.006 91). AMOVA showed genetic differentiation among geographical isolates of G. fusca (Fst = 0.202 40, P < 0.05), and the genetic variation was mainly caused by intra-population variations (79.76%). Gene flow analysis showed a high level of gene flow among G. fusca isolates (Nm > 1). Tests of neutrality based on Cytb gene measured a Tajima’s D value of −1.796 31 (P < 0.05) and a Fu’s FS value of −3.293 98 (P < 0.05) in WH isolate of G. fusca, indicating population expansion in WH isolate of G. fusca. Haplotype network analysis and phylogenetic analysis revealed no remarkable geographical distribution pattern among different geographical isolates of G. fusca. All four isolates of G. fusca presented high genetic diversity (Hd = 0.985, Pi = 0.011 97). AMOVA showed moderate level of genetic differentiation between four isolates (Fst = 0.104 62, P < 0.05). The tests of neutrality based on ITS genes measured a Tajima’s D value of −6.088 20 and a Fu’s FS value of −1.935 99 (both P > 0.05) in the whole isolate of G. fusca, indicating no obviously population expansion. Conclusions The four geographical isolates of G. fusca have high genetic diversity and remarkable genetic differentiation. Since a high level of gene flow is detected among different geographical isolates of G. fusca, no obvious geographical distribution pattern of G. fusca is found.
ABSTRACT
Background and objectives: In America, of the 44 species of Anopheles, nine are main vectors of malaria and, of these, genetic information exists for seven. Hence, this study sought to know the gene flow and diversity of the seven principal vectors of malaria at the Americas level. Methods: For the seven species and the sequences of the mitochondrial cytochrome c oxidase I (COI) gene obtained from the GenBank and Bold System, genetic analyzes of populations and genetic structure were performed and haplotype networks and phylogenetic trees were obtained. Results: For the seven species, 1440 sequences were analyzed and 519 haplotypes were detected. The Hd and ? values were higher within a continental context than by countries. Neutrality tests indicated positive and negative values with most of these being significant (p < 0.05). Phylogenetic analyses for all the species recovered three clades with no geographic pattern among them. Interpretation & conclusion: Studies suggest that native species of Anopheles from the Americas have greater haplotype diversity and low genetic differentiation due to the lack of physical barriers to impede gene flow among these populations. Moreover, all the species are interconnected by roadways. This scenario complicates the epidemiological picture of malaria in the Americas.
ABSTRACT
Pimelodus yuma (formerly Pimelodus blochii) is a freshwater fish, endemic to the Colombian Magdalena-Cauca and Caribbean basins that experiences habitat disturbances resulting from anthropogenic activities. Due to the lack of information about the population genetics of this species, this study developed 14 species-specific microsatellite loci to assess the genetic diversity and population structure of samples from the lower section of the Cauca River. The studied species showed genetic diversity levels higher than the average values reported for Neotropical Siluriformes and significant inbreeding levels as was described for some congeners. Furthermore, P. yuma comprises two coexisting genetic groups that exhibit gene flow along the lower section of the Cauca River. This information constitutes a baseline for future monitoring of the genetic diversity and population structure in an anthropic influenced sector of the Magdalena-Cauca basin.(AU)
Pimelodus yuma (anteriormente Pimelodus blochii) es un pez dulceacuícola endémico de las cuencas colombianas Magdalena-Cauca y Caribe que experimenta alteraciones del hábitat como resultado de actividades antropogénicas. Debido a la falta de información sobre la genética poblacional de esta especie, este estudio desarrolló 14 loci microsatélites especie-específicos para evaluar la diversidad genética y la estructura poblacional de muestras de la sección baja del río Cauca. La especie estudiada mostró niveles de diversidad genética más altos que los valores promedio reportados para Siluriformes neotropicales y niveles de endogamia significativos como se describió para algunos congéneres. Además, P. yuma comprende dos grupos genéticos coexistentes que exhiben flujo de genes a lo largo de la sección baja del río Cauca. Esta información constituye una línea base para futuros monitoreos de la diversidad genética y la estructura poblacional en un sector de influencia antrópica de la cuenca Magdalena-Cauca.(AU)
Subject(s)
Animals , Genetic Variation , Catfishes/genetics , Microsatellite Repeats , Genetics, Population , High-Throughput Nucleotide Sequencing , Fresh WaterABSTRACT
The Neotropical freshwater catfish Pseudopimelodus atricaudus and Pseudopimelodus magnus are two recently discovered species endemic to the Colombian Magdalena-Cauca River basin. In this study, a set of 13 microsatellite loci were developed by using next generation sequence technology to assess the genetic diversity and population structure in P. atricaudus and test for cross-species amplification in P. magnus. Both species exhibited high genetic diversity (P. atricaudus: Na: 9.000 - 9.769 alleles/locus, Ho: 0.760 - 0.804, HE: 0.804 - 0.840; P. magnus: Na: 12.8 - 5.4 alleles/locus, Ho: 0.638 - 0.683, HE: 0.747 - 0.755) compared to the mean levels of genetic diversity reported for Neotropical Siluriformes, and lack of genetic differentiation among sampling sites within the Cauca River (P. atricaudus: F'ST=0.013 - 0.017, P > 0.05, D'est= -0.004 - 0.023, P > 0.05; P. magnus: F'ST= 0.031, P= 0.055; D'est= 0.045, P= 0.058). This work is the first insight on the diversity and the population genetics of species of the family Pseudopimelodidae and provides a framework to further population genetic and conservation analyses needed in this poorly studied family at the microevolutionary level.(AU)
Los bagres neotropicales Pseudopimelodus atricaudus y Pseudopimelodus magnus son dos especies recientemente descubiertas, endémicas de la cuenca Magdalena-Cauca en Colombia. En este estudio, se desarrollaron 13 loci microsatélites usando tecnología de secuenciación de próxima generación para evaluar la diversidad genética y la estructura poblacional de P. atricaudus y evaluar su amplificación cruzada en P. magnus. Ambas especies exhibieron altos valores de diversidad genética (P. atricaudus: Na: 9.000 - 9.769 alelos/locus, HO: 0.760 - 0.804, HE: 0.804 - 0.840; P. magnus: Na: 12.8 - 5.4 alelos/locus, HO: 0.638 - 0.683, HE: 0.747 - 0.755) comparados con los valores promedios de diversidad genética reportados para Siluriformes neotropicales, y ausencia de estructura genética entre los sitios analizados (P. atricaudus: F'ST= 0.013 - 0.017, P > 0.05, D'est= -0.004 - 0.023, P > 0.05; P. magnus: F'ST= 0.031, P= 0.055; D'est= 0.045, P= 0.058). Este trabajo representa la primera aproximación a la diversidad y genética poblacional de especies de la familia Pseudopimelodidae y proporciona un marco de referencia para futuros estudios genético-poblacionales y de conservación, requeridos en esta familia de bagres poco estudiada en el nivel microevolutivo.(AU)
Subject(s)
Animals , Genetic Variation , Catfishes/genetics , Microsatellite Repeats , Genetics, PopulationABSTRACT
The Neotropical catfish genus Pseudoplatystoma comprises eight species of large size, widely distributed in South American basins. The endangered species P. magdaleniatum is endemic to Magdalena basin (Colombia), experiences high fishing pressure and its population genetics is relatively unknown. To study the genetic status and structure of P. magdaleniatum, 25 species-specific polymorphic microsatellite loci were developed using next-generation sequencing and then tested in samples collected in the Magdalena-Cauca basin. Based on 15 of these loci, P. magdaleniatum showed a high number of alleles per locus (9-10), high values of observed (0.762-0.798) and expected (0.770-0.791) heterozygosities, recent reduction of population size and gene flow. These findings constitute a baseline to measure potential changes in genetic diversity and structure of this commercially important species in a basin undergoing high anthropogenic activities.(AU)
El género de bagres neotropicales Pseudoplatystoma comprende ocho especies de gran tamaño, ampliamente distribuidas en las cuencas de Suramérica. La especie en peligro de extinción P. magdaleniatum es endémica de la Cuenca del Magdalena (Colombia), experimenta una alta presión pesquera y su genética poblacional es relativamente desconocida. Para estudiar el estado y estructura genética de P. magdaleniatum, se desarrollaron 25 loci microsatélites polimórficos especie específicos utilizando secuenciación de próxima generación y se evaluaron en muestras recolectadas en la Cuenca del Magdalena-Cauca. Con base en 15 loci, P. magdaleniatum mostró un alto número de alelos por locus (9-10), valores altos de heterocigosidad observada (0.762-0.798) y esperada (0.770-0.791), reducción reciente del tamaño poblacional y flujo génico. Estos hallazgos constituyen una línea de base para medir cambios potenciales en la diversidad y estructura genética de esta especie comercialmente importante en una cuenca sometida a altas actividades antropogénicas.(AU)
Subject(s)
Animals , Genetic Variation , Weights and Measures , Catfishes , Microsatellite Repeats , Endangered SpeciesABSTRACT
ABSCTRACT: Eugenia involucrata DC. is a forest species with high environmental and economic potential. The objective of this study was to quantify the genetic variability and analyzed the genetic structure of three natural fragments located in the central region of the Rio Grande do Sul state, Brazil. We used four microsatellite loci developed for the congener species Eugenia uniflora and using GenAlEx 6.5 software, parameters of genetic variability and its partition among and within fragments were estimated for each locus. We observed high levels of genetic variability (3.67 alleles per locus; HO = 0.815; HE = 0.625; FIS = −0.294), most of which (93%) were distributed within the fragments, suggesting that these individuals came from a single original population. Gene flow between fragments was high (2.35 to 4.56 migrants per generation), resulting in low genetic differentiation indexes (FST values ranging from 0.052 to 0.096). The fragments showed high genetic variability, distributed within the remnants themselves, and low genetic differentiation. Our results have repercussions for planning locally adapted germplasm collections for forest restoration programs, thereby avoiding the implantation of populations with an exogamous depression.
RESUMO: Eugenia involucrata DC. é uma espécie florestal com elevado potencial ambiental e econômico. O presente trabalho teve por objetivo quantificar a variabilidade e analisar a estruturação genética em três fragmentos naturais localizados na região central do estado do Rio Grande do Sul, Brasil. Com o emprego de quatro locos microssatélites desenvolvidos para a espécie congênere Eugenia uniflora e usando-se o software GenAlEx 6.5, foram estimados parâmetros de variabilidade genética, para cada loco, e sua partição entre e dentro dos fragmentos. Foram observados altos índices de variabilidade genética (3,67 alelos por loco; HO = 0,815; HE = 0,625; FIS = -0,294), com a maior proporção (93%) distribuída dentro dos fragmentos, sugerindo que os indivíduos estudados são provenientes de uma única população original. O fluxo gênico foi elevado entre os fragmentos, variando de 2,35 a 4,56 migrantes por geração, resultando em baixo índice de diferenciação genética (FST), entre 0,052 a 0,096. Os fragmentos estudados apresentam elevada variabilidade genética, a maior parte distribuída dentro dos próprios remanescentes, e baixa diferenciação genética. Os resultados observados têm repercussões no planejamento de coleta de germoplasma com adaptação local para programas de restauração florestal, assim evitando a implantação de populações com depressão exogâmica.
ABSTRACT
Rosewood, Aniba rosaeodora is an endangered species in Amazon forests and its natural stands have been heavily depleted due to over-exploitation for the cosmetic industry. This study aimed to investigate the genetic diversity and population structure of 90 rosewood accessions from eight localities in the Peruvian Amazon through 11 Inter Simple Sequence Repeats (ISSR) primers. The ISSR primers produced a sum of 378 bands, of which 375 (99.2%) were polymorphic, with an average polymorphism information content (PIC) value of 0.774. The mean effective number of alleles (Ne), Shannon informative index (I), gene diversity (He) and total gene diversity (Ht) were 1.485, 0.294, 0.453 and 0.252, respectively. Analysis of molecular variance (AMOVA) showed the presence of maximum variability within populations (88%). The Structure algorithm, neighbor joining and principal coordinate analysis (PCoA) grouped the 90 rosewood accessions into three main populations (A, B and C). Diversity indices at the inter-population level revealed a greater genetic diversity in population A, due to higher gene flow. The neighbor-joining analysis grouped populations A and B, while population C was found to be divergent at the inter population level. We concluded that population A reflects higher genetic diversity and should be prioritized for future management and conservation plans. (AU)
Subject(s)
Genetic Variation , Endangered Species , Gene FlowABSTRACT
Abstract Background: Romosinuano cattle breed in Mexico has endured isolation and it is necessary to characterize it in order to facilitate sustainable genetic management. Objective: To assess the evolution of the structure and genetic diversity of the Romosinuano breed in Mexico, through pedigree analysis. Methods: Pedigree data was obtained from Asociación Mexicana de Criadores de Ganado Romosinuano y Lechero Tropical (AMCROLET). The ENDOG program (4.8 version) was used to analyze two datasets, one that includes upgrading from F1 animals (UP) and the other with only straight-bred cattle (SP). For both datasets, three reference populations were defined: 1998-2003 (RP1), 2004-2009 (RP2), and 2010-2017 (RP3). The pedigree included 3,432 animals in UP and 1,518 in SP. Demographic parameters were: Generation interval (GI), equivalent number of generations (EG), pedigree completeness index (PCI), and gene flow among herds. Genetic parameters were: Inbreeding (F) and average relatedness (AR) coefficients, effective population size (Nec), effective number of founders and ancestors, and number of founder genome equivalents. Results: The GI varied from 6.10 to 6.54 for UP, and from 6.47 to 7.16 yr for SP. The EG of the UP and SP improved >63% from RP1 to RP3. The PCI increased over time. No nucleus or isolated herds were found. For RP3, F and AR reached 2.08 and 5.12% in the UP, and 2.55 and 5.94% in the SP. For RP3, Nec was 57 in the UP and 45 in the SP. Genetic diversity losses were attributed mainly (>66%) to genetic drift, except for RP3 in the SP (44%). Conclusions: A reduction of the genetic diversity has been occurring after the Romosinuano breed association was established in Mexico, and this is mainly due to random loss of genes.
Resumen Antecedentes: La raza bovina Romosinuano ha estado prácticamente aislada en México y requiere ser caracterizada para un manejo genético sostenible. Objetivo: Evaluar la evolución de la estructura y diversidad genética de la raza Romosinuano en México, mediante el análisis del pedigrí. Métodos: Los datos genealógicos provinieron de la Asociación Mexicana de Criadores de Ganado Romosinuano y Lechero Tropical (AMCROLET). Los análisis se realizaron con el programa ENDOG (versión 4.8) para dos bases de datos, una que incluyó animales en cruzamiento absorbente (UP) a partir de F1 y la otra con sólo animales puros (SP). Para ambas bases de datos se definieron tres poblaciones de referencia: 1998-2003 (RP1), 2004- 2009 (RP2), y 2010-2017 (RP3). El pedigrí incluyó 3.432 animales en la UP y 1.518 en la SP. Los parámetros demográficos fueron: intervalo generacional (GI), número de generaciones equivalentes (EG), índice de completitud del pedigrí (PCI), y flujo de genes entre hatos. Los parámetros genéticos fueron: coeficientes de consanguinidad (F) y de relación genética aditiva (AR), tamaño efectivo de la población (Nec), número efectivo de fundadores y ancestros, y número equivalente de genomas fundadores. Resultados: El GI varió de 6,10 a 6,54 para la UP, y de 6,47 a 7,16 años para la SP. El EG de la UP y la SP mejoró >63%, de RP1 a RP3. El PCI aumentó a través de los años, pero más para la SP que para la UP. No se encontraron hatos núcleo o aislados. Para RP3, F y AR alcanzaron 2,08 y 5,12% en la UP, y 2,55 y 5,94% en la SP. Para RP3, Nec fue 57 en la UP y 45 en la SP. Más de 66% de las pérdidas en diversidad genética se debieron a deriva genética, excepto para RP3 en la UP (44%). Conclusiones: una reducción de la diversidad genética ha estado ocurriendo después de que se formó la asociación de criadores de ganado Romosinuano en México, y es debida principalmente a pérdidas aleatorias de genes.
Resumo Antecedentes: A raça bovina Romosinuano tem estado praticamente isolada no México e precisa ser caracterizada para um manejo genético sustentável. Objetivo: Avaliar a evolução da estrutura e diversidade genética da raça Romosinuano no México, através da análise de pedigree. Métodos: Os dados genealógicos vieram da Asociación Mexicana de Criadores de Ganado Romosinuano y Lechero Tropical (AMCROLET). As análises foram feitas com o programa ENDOG (versão 4.8) para duas bases de dados, uma que incluiu animais em cruzamento absorvente (UP) a partir da F1 e a outra base de dados somente com animais puros (SP). Para ambas bases de dados foram definidas três populações de referência: 1998-2003 (RP1), 2004-2009 (RP2) e 2010-2017 (RP3). O pedigree incluiu 3.432 animais na UP e 1.518 na SP. Os parâmetros demográficos foram: intervalo entre gerações (GI), número de gerações equivalentes (EG), índice de completude do pedigree (PCI), e fluxo de genes entre rebanhos. Os parâmetros genéticos foram: coeficiente de consanguinidade (F) e da relação genética aditiva (AR), tamanho efetivo da população (Nec), número efetivo de fundadores e ancestrais, e número equivalente de genomas fundadores. Resultados: O GI variou de 6,10 a 6,54 para a UP, e de 6,47 a 7,16 anos para a SP. EG da UP e a SP melhorou >63%, de RP1 a RP3. O PCI aumentou ao longo dos anos, mas mais para a SP do que para o UP. Não se encontraram rebanhos núcleo ou isolados. Para RP3, F e AR alcançaram 2,08 e 5,12% na UP, e 2,55 e 5,94% na SP. Para RP3, Nec foi 57 na UP e 45 na SP. Mais de 66% das perdas em diversidade genética foram ocasionadas pela deriva genética, exceto para RP3 no UP (44%). Conclusões: Depois que a associação da raça Romosinuano foi estabelecida no México, tem ocorrido uma redução da diversidade genética, principalmente devido a perdas aleatórias de genes.
ABSTRACT
Isolation-with-migration (IM) models have become popular for explaining population divergence in the presence of migrations. Bayesian methods are commonly used to estimate IM models, but they are limited to small data analysis or simple model inference. Recently three methods, IMa3, MIST, and AIM, resolved these limitations. Here, we describe the major problems addressed by these three software and compare differences among their inference methods, despite their use of the same standard likelihood function.
Subject(s)
Bayes Theorem , Gene Flow , Likelihood Functions , Phylogeny , Statistics as TopicABSTRACT
Pollen and seed dispersal patterns greatly influence the spatial distribution of plant genetic diversity. Microsatellite-based parentage analysis provides accurate estimates of contemporary gene dispersal. Although most tropical trees have been shown to exhibit widespread pollen dispersal, few studies have estimated contemporary gene dispersal after seedling establishment. Bertholletia excelsa (Lecythidaceae) is pollinated by large-bodied bees, while previous seed-tracking experiments suggest their seeds are mainly dispersed across very short distances by scatter-hoarding rodents, who primarily act as seed predators. Here we used parentage analysis to provide contemporary estimates of pollen and seed dispersal in B. excelsa recruits. We examined six 25-ha plots located in two natural stands in the Acre River valley, in the southwestern Brazilian Amazon. We used 11 microsatellite markers to estimate genetic diversity and fixation index parameters in adults, seedlings and saplings. Genetic diversity was moderate and did not differ across size classes or sampling locations. We assigned pollen and seed parents for < 20% of the recruits, indicating that most events of realized gene flow occurred beyond our 25-ha plots. Only 10 parentage assignments were confirmed with 80% confidence. Pollen distance ranged from 33 to 372 m and seed dispersal from 58 to 655 m. Actual seed-dispersal distances were far greater than the estimates obtained in previous seed-tracking experiments. Thus, studies encompassing larger sampling areas are necessary to determine a more representative spatial scale of B. excelsas pollen and seed dispersal capacity in natural stands.
Os padrões de dispersão de pólen e sementes influenciam a distribuição espacial da diversidade genética. Muitas espécies arbóreas tropicais apresentam ampla dispersão de pólen, mas poucos estudos avaliaram fluxo gênico a partir de plântulas. Bertholletia excelsa (Lecythidaceae) é polinizada por abelhas e as sementes são dispersas por roedores do tipo scatter-hoarders (que estocam recursos em diferentes pontos de sua área de vida), que atuam primariamente como predadores de sementes. Experimentos de remoção de sementes tem mostrado que a dispersão de sementes por esses roedores é espacialmente limitada. Nosso objetivo foi obter estimativas de dispersão de pólen e sementes em B. excelsa a partir da análise de parentesco de regenerantes. Nós estudamos seis parcelas de 25 ha, em duas áreas de floresta nativa no vale do Rio Acre, no sudoeste da Amazônia brasileira. Parâmetros de diversidade genética e índice de fixação foram estimados em adultos, varetas e plântulas com 11 marcadores microssatélites. A diversidade genética foi moderada e não diferiu entre classes de tamanho ou entre localidades. A paternidade foi determinada em menos de 20% dos regenerantes, indicando que a maioria dos eventos de fluxo gênico ocorreu em distâncias maiores que as encontradas nas parcelas de 25 ha. As distâncias de pólen variaram de 33 a 372 m e as de dispersão de sementes variaram de 58 a 655 m. As distâncias de dispersão obtidas neste estudo excedem em muito as estimativas obtidas em experimentos de remoção de sementes. Estudos envolvendo áreas maiores são necessários para que possamos aprofundar nosso conhecimento sobre capacidade de dispersão de pólen e sementes em populações naturais de B. excelsa.
Subject(s)
Bertholletia/genetics , Plant Dispersal/genetics , Seed Dispersal/genetics , Pollen/genetics , Gene Flow , Polymerase Chain Reaction , Genetic VariationABSTRACT
Introducción. A pesar de los recientes reportes de infección con Plasmodium spp. en poblaciones relacionadas con los linajes noroeste y sureste, Anopheles triannulatus no está incriminado como vector de la transmisión de malaria en Colombia. La diversidad genética puede delimitar la información sobre el flujo génico y la diferenciación poblacional entre localidades con malaria. Objetivo. Estimar la diversidad genética de An. triannulatus en cinco municipios con alta y baja incidencia de malaria en el departamento de Córdoba. Materiales y métodos. La recolección entomológica se hizo entre agosto y noviembre de 2016 en los municipios de Tierralta, Puerto Libertador, Montelíbano, Sahagún y Planeta Rica. Como marcador genético, se utilizó la región de código de barras de ADN del gen mitocondrial COI. El análisis genético incluyó la estimación de los parámetros de diversidad haplotípica, estructura genética y flujo génico, la prueba D de neutralidad de Tajima, la red de haplotipos y las relaciones filogenéticas. Resultados. Se obtuvieron 148 secuencias parciales de 655 nucleótidos del gen COI, de los cuales se derivaron 44 haplotipos. Los haplotipos H2 y H21 fueron los más frecuentes en las poblaciones. Los valores de la prueba D de Tajima fueron negativos y no significativos (p>0,10). Los estimadores de estructura genética (FST=0,01427) y de flujo génico (Nm=17,27) evidenciaron que no hubo diferenciación genética en las poblaciones muestreadas debido al importante intercambio de migrantes. Mediante las inferencias filogenéticas y la red de haplotipos, se identificó una sola especie sin diferenciación geográfica o de linajes en el rango geográfico estudiado. Conclusión. La diversidad genética calculada para An. triannulatus en este contexto, indicó que las poblaciones están en un intercambio constante.
Introduction: Anopheles triannulatus is not incriminated as a vector of malaria transmission in Colombia despite recent reports of infection with Plasmodium spp. in populations related to the northwestern and southeastern lineages. Genetic diversity can delimit information about gene flow and population differentiation in localities with malaria. Objective: To estimate the genetic diversity of An. triannulatus in five municipalities with high and low incidence of malaria in the department of Córdoba. Materials and methods: The entomological collections were done between August and November, 2016, in Tierralta, Puerto Libertador, Montelíbano, Sahagún, and Planeta Rica. We used the COI barcoding fragment as molecular marker. The genetic analysis included the estimation of genetic parameters such as the diversity haplotype, the genetic structure, the gene flow, the Tajima's D test, the haplotype network, and the phylogenetic relationship. Results: We obtained 148 sequences with a length of 655 nucleotides of the COI gene, from which we derived 44 haplotypes. The H2 and H21 haplotypes were the most frequent in the populations. The values of the Tajima's D test were negative and not significant (p>0.10). The genetic structure index (FST=0.01427) and the gene flow (Nm=17.27) evidenced no differentiation between sampled populations due to the high exchange of migrants. Using phylogenetic inferences and the haplotype network, we identified one single species without geographic differentiation or lineages in the geographic range studied. Conclusions: The genetic diversity calculated for An. triannulatus in this context indicated stable populations in constant exchange.
Subject(s)
Anopheles/genetics , Genetic Variation , Haplotypes , Colombia , Gene FlowABSTRACT
Abstract The Southern Brazilian Highlands are composed by a mosaic of Mixed Ombrophilous Forest (MOF) and grassland formations, an interesting landscape for the study of population structure. We analyzed the genetic diversity within and among populations of the MOF-endemic bromeliad Vriesea reitzii by genotyping seven nuclear microsatellite loci in 187 individuals from six populations. We characterized levels of genetic diversity and assessed the genetic structure among populations. Vriesea reitzii populations showed high levels of genetic variation (number of alleles 28 - 43, allelic richness 3.589 - 5.531) and moderate levels of genetic differentiation (FST = 0.123, RST = 0.096). The high levels of genetic diversity may be explained by species life-history traits, such as habit and mating system. The moderate structure may be a product of the combination of ancient and contemporary gene flow, resulting from the expansion of the forest in the Holocene, and/or due to facilitated dispersal mediated by the MOF's mosaic landscape. The genetic results indicated no imminent threat to this bromeliad. However, the species is highly associated with the MOF, putting landscape conservation at the center of conservation efforts for the species' maintenance.
ABSTRACT
Resumen El objetivo de este trabajo fue evaluar la diversidad genética de las poblaciones de palomas domésticas (Columba livia) por medio del uso de genes que codifican la coloración y diseño del plumaje, en Ciénaga de Oro (Córdoba, Colombia). Se realizaron muestreos aleatorios en cinco colonias de Ciénaga de Oro, en el periodo comprendido entre junio y agosto de 2015. Mediante excursiones urbanas, observación directa y registros fotográficos, se estudiaron 325 palomas. Se utilizaron los marcadores autosómicos que codifican la coloración y diseño del plumaje: Grizzle (G), Spread (S), Checker (C) y el locus ligado al sexo Ash-Red (B). Los parámetros genéticos -frecuencia alélica, diversidad genética, equilibrio Hardy-Weinberg y estructura poblacional- fueron calculados con el programa PopGene 1.31. La estructura genética y la distancia genética se evaluaron mediante el programa FSTAT v. 2.9.3.2. La elaboración del dendrograma se realizó con el programa MEGA 5.2. El marcador de mayor frecuencia alélica fue Spread, mientras que el marcador Ash-Red presentó los valores más bajos. Se obtuvo escasa diferenciación genética entre las poblaciones y un elevado flujo génico. Se observó un exceso de heterocigotos; a esto se le suma la ausencia de equilibrio Hardy-Weinberg. Se evidenció posible selección natural para el marcador Spread.
Abstract This study aimed to evaluate the genetic diversity of domestic pigeon populations (Columba livia), using genes that are responsible for encoding plumage color and design, in Ciénaga de Oro (Córdoba, Colombia). Random samplings were performed in 5 colonies of Ciénaga de Oro from June to August 2015. By means of urban excursions, direct observation and photographic records, 325 pigeons were studied. Autosomal markers encoding plumage color and design were used: Grizzle (G), Spread (S), Checker (C), and the sex-linked Ash-Red locus (B). Genetic parameters-allele frequency, genetic diversity, Hardy-Weinberg equilibrium, and population structure-were calculated using the PopGene 1.31 program. Genetic structure and genetic distance were evaluated using the FSTAT v. 2.9.3.2 program. A dendrogram was elaborated using the MEGA 5.2 program. The marker with the highest allele frequency was Spread, while the Ash-Red marker showed the lowest values. Little genetic differentiation between populations and high gene flow were obtained. An excess of heterozygotes was observed, in addition to the absence of Hardy-Weinberg equilibrium. A possible natural selection for the Spread marker was evidenced.
Resumo O objetivo deste trabalho foi avaliar a diversidade genética das populações de pombos domésticos (Columba livia) por meio do uso de genes que codificam a coloração e desenho da plumagem, em Ciénaga de Oro (Córdoba, Colômbia). Se realizaram amostragens aleatórias em 5 colônias de Ciénaga de Oro, no periodo compreendido entre junho e agosto de 2015. Mediante excursões urbanas, observação direta e registros fotográficos, se estudaram 325 pombos. Se utilizaram os marcadores autossômicos que codificam a coloração e desenho da plumagem: Grizzle (G), Spread (S), Checker (C) e o locus ligado ao sexo Ash-Red (B). Os parâmetros genéticos - frequência alélica, diversidade gené tica, equilíbrio Hardy-Weinberg e estrutura populacional - foram calculados com o programa PopGene 1.31. A estrutura genética e a distância genética foram avaliadas mediante o programa FSTAT v. 2.9.3.2. A elaboração do dendrograma se realizou com o programa MEGA 5.2. O marcador de maior frequência alélica foi Spread, em quanto que o marcador Ash-Red apresentou os valores mais baixos. Obteve-se escassa diferenciação genética entre as populações e um elevado fluxo génico. Pôde-se observar um excesso de heterozigotos; a isto soma-se a ausência de equilíbrio Hardy-Weinberg. Constatou-se possível seleção natural para o marcador Spread.
ABSTRACT
The chub mackerel, Scomber japonicus supports an important fishery in the Southeast Pacific, however, its population genetics is currently unknown. In the present study, we examined the genetic structure, the gene flow and the historical demography of this species in the Northern Humboldt Current System. Samples were collected during summer of years 2013-2014 from three fishing points (Paita, Ventanilla and Ilo), covering 12 degrees of latitude along the coast of Peru. A 532 bp segment of the mitochondrial control region was sequenced in 72 individuals, which allowed us to detect a total of 29 polymorphic sites, 35 haplotypes, moderate-to-high levels of haplotype diversity (0.793 - 0.969) and very low levels of nucleotide diversity (0.004 - 0.008). Gene flow analysis showed high levels of connectivity among populations in the sampling areas. Analysis of molecular variance (ФST = 0.00868, P = 0.1837), population pairwise ФST comparisons and genetic differentiation tests confirmed the lack of genetic structuring among the three localities. These analyses suggest that sampling sites analyzed can be considered as a single gene pool. Migratory behavior, the high dispersal potential of early stages and the lack of oceanographic barriers may explain its genetic homogeneity along the Peruvian sea. Historical demography was also examined. Neutrality tests, mismatch distribution and Bayesian skyline plot suggested a population expansion scenario that took place during the Late Pleistocene. This study provides novel information on population genetics of the chub mackerel in the Southeast Pacific.
La caballa, Scomber japonicus soporta una pesquería importante en el Pacífico Sudeste, sin embargo, su genética de poblaciones se desconoce actualmente. En el presente estudio se examinó la estructura genética, el flujo génico y la demografía histórica de esta especie en la parte norte del Sistema de la Corriente de Humboldt. Las muestras fueron colectadas en los veranos del 2013 y 2014 en tres puntos de desembarco de pesca (Paita, Ventanilla e Ilo) cubriendo 12 grados de latitud frente a la costa peruana. Se secuenció un segmento de 532 pb de la región control mitocondrial en 72 individuos, el cual permitió detectar un total de 29 sitios polimórficos, 35 haplotipos, niveles moderados altos de diversidad haplotípica (0.793 - 0.969) y muy bajos niveles de diversidad nucleotídica (0.004 - 0.008). El análisis de flujo génico mostró altos niveles de conectividad entre las poblaciones en las áreas de muestreo. El análisis de varianza molecular (ФST = 0.00868, P = 0.1837), las comparaciones ФST a pares de poblaciones y las pruebas de diferenciación genética confirmaron la carencia de estructuración genética entre las tres localidades. Estos análisis sugieren que los sitios de muestreo analizados pueden ser considerados como un solo grupo genético. El comportamiento migratorio, el alto potencial de dispersión de los estadios tempranos de desarrollo y la ausencia de barreras oceanográficas pueden explicar su homogeneidad genética a lo largo del mar peruano. También se examinó la demografía histórica. Las pruebas de neutralidad, la distribución mismatch y el Bayesian Skyline Plot sugirieron un escenario de expansión poblacional que tuvo lugar durante el Pleistoceno Superior. Este estudio provee información nueva con respecto a la genética de poblaciones de la caballa en el Pacífico Sudeste.
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Abstract Colossoma macropomum is the second largest scaled fish of the Amazon. It is economically important for commercial fisheries and for aquaculture, but few studies have examined the diversity and genetic structure of natural populations of this species. The aim of this study was to investigate the levels of genetic variability and connectivity that exist between three natural populations of C. macropomum from the Amazon basin. In total, 247 samples were collected from the municipalities of Tefé, Manaus, and Santarém. The populations were genotyped using a panel of 12 multiplex microsatellite markers. The genetic diversity found in these populations was high and similar to other populations described in the literature. These populations showed a pattern of high gene flow associated with the lack of a genetic structure pattern, indicating that the number of migrants per generation and recent migration rates are high. The values of the FST, RST, and exact test of differentiation were not significant for pairwise comparisons between populations. The Bayesian population clustering analysis indicated a single population. Thus, the data provide evidence for high genetic diversity and high gene flow among C. macropomum populations in the investigated region of the Amazon basin. This information is important for programs aiming at the conservation of natural populations.
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ABSTRACT Aedes (Stegomyia) aegypti is the vector responsible for the transmission of the viruses that cause zika, yellow and chikungunya fevers, the four dengue fever serotypes (DENV - 1, 2, 3, 4), and hemorrhagic dengue fever in tropical and subtropical regions around the world. The present study investigated the genetic differentiation of the 15 populations of this vector in the Brazilian state of Maranhão, based on the mitochondrial ND4 marker. A total of 177 sequences were obtained for Aedes aegypti, with a fragment of 337 bps, 15 haplotypes, 15 polymorphics sites, haplotype diversity of h = 0.6938, and nucleotide diversity of π = 0.01486. The neutrality tests (D and Fs) were not significant. The AMOVA revealed that most of the variation (58.47%) was found within populations, with FST = 0.41533 (p < 0.05). Possible isolation by distance was tested and a significant correlation coefficient (r = 0.3486; p = 0.0040) was found using the Mantel test. The phylogenetic relationships among the 15 haplotypes indicated the existence of two distinct clades. This finding, together with the population parameters, was consistent with a pattern of genetic structuring that underpinned the genetic differentiation of the study populations in Maranhão, and was characterized by the presence of distinct lineages of Aedes aegypti.
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Objective To verify phylogeography and genetic structure of Acanthamoeba populations among the Iranian clinical isolates and natural/artificial environments distributed in various regions of the country. Methods We searched electronic databases including Medline, PubMed, Science Direct, Scopus and Google Scholar from 2005 to 2016. To explore the genetic variability of Acanthamoeba sp, 205 sequences were retrieved from keratitis patients, immunosuppressed cases and environmental sources as of various geographies of Iran. Results T4 genotype was the predominant strain in Iran, and the rare genotypes belonged to T2, T3, T5 (Acanthamoeba lenticulata), T6, T9, T11, T13 and T15 (Acanthamoeba jacobsi). A total of 47 unique haplotypes of T4 were identified. A parsimonious network of the sequence haplotypes demonstrated star-like feature containing haplogroups IR6 (34.1%) and IR7 (31.2%) as the most common haplotypes. In accordance with the analysis of molecular variance, the high value of haplotype diversity (0.612–0.848) of Acanthamoeba T4 represented genetic variability within populations. Neutrality indices of the 18S ribosomal RNA demonstrated negative values in all populations which represented a considerable divergence from neutrality. The majority of genetic diversity belonged to the infected contact lens and dust samples in immunodeficiency and ophthalmology wards, which indicated potential routes for exposure to a pathogenic Acanthamoeba sp. in at-risk individuals. A pairwise fixation index (F
ABSTRACT
OBJECTIVE@#To verify phylogeography and genetic structure of Acanthamoeba populations among the Iranian clinical isolates and natural/artificial environments distributed in various regions of the country.@*METHODS@#We searched electronic databases including Medline, PubMed, Science Direct, Scopus and Google Scholar from 2005 to 2016. To explore the genetic variability of Acanthamoeba sp, 205 sequences were retrieved from keratitis patients, immunosuppressed cases and environmental sources as of various geographies of Iran.@*RESULTS@#T4 genotype was the predominant strain in Iran, and the rare genotypes belonged to T2, T3, T5 (Acanthamoeba lenticulata), T6, T9, T11, T13 and T15 (Acanthamoeba jacobsi). A total of 47 unique haplotypes of T4 were identified. A parsimonious network of the sequence haplotypes demonstrated star-like feature containing haplogroups IR6 (34.1%) and IR7 (31.2%) as the most common haplotypes. In accordance with the analysis of molecular variance, the high value of haplotype diversity (0.612-0.848) of Acanthamoeba T4 represented genetic variability within populations. Neutrality indices of the 18S ribosomal RNA demonstrated negative values in all populations which represented a considerable divergence from neutrality. The majority of genetic diversity belonged to the infected contact lens and dust samples in immunodeficiency and ophthalmology wards, which indicated potential routes for exposure to a pathogenic Acanthamoeba sp. in at-risk individuals. A pairwise fixation index (F) was from low to high values (0.02433-0.41892). The statistically F points out that T4 is genetically differentiated between north-west, north-south and central-south metapopulations, but not differentiated between west-central, west-south, central-south, and north-central isolates.@*CONCLUSIONS@#An occurrence of IR6 and IR7 displays that possibly a gene flow of Acanthamoeba T4 occurred after the founder effect or bottleneck experience through ecological changes or host mobility. This is the first systematic review and meta-analysis providing new approaches into gene migration and transmission patterns of Acanthamoeba sp, and targeting at the high-risk individuals/sources among the various regions of Iran.
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Plasmodium falciparum malaria parasite had developed resistance to almost all the currently used antimalarial drugs. The purpose of the study was to come across the genetic distances in P. falciparum dhps gene sequences circulating in Assam. A partial fragment of P. falciparum dhps gene containing major single nucleotide polymorphisms associated with sulphadoxine resistance were amplified and sequenced. Thereafter specific bioinformatics tools like BioEdit v7.0.9, ClustalW in Mega 5, DnaSP version v.5.10.01 etc were used for the analysis. A total of 100 P. falciparum positive cases in different malaria endemic areas of Assam were included for the study. Based upon the mutation analysis, a total of seven different P. falciparum dhps genotypes were observed with five variable sites. Maximum five haplotypes were found in the P. falciparum isolates from Jorhat district of Assam. Four polymorphic sites were observed in the P. falciparum dhps gene sequences in Karbi Anglong, NC Hills, Chirang and Jorhat whereas the isolates from other study areas had three polymorphic sites. A statistically significant positive value of Tajima’s D were observed among the P. falciparum field isolates in Assam indicating that there is an excess of intermediate frequency alleles and can result from population bottlenecks, structure and/or balancing selection. Extensive gene flow took place among the P. falciparum population of Jorhat with Sivasagar, Chirang with Sivasagar and Chirang with Karbi Anglong. However, large genetic differentiation was observed among the P. falciparum isolates of NC Hills with Lakhimpur, Tinsukia, Dibrugarh and Golaghat and also the parasite population of Karbi Anglong with Lakhimpur and Tinsukia signifying little gene flow among the population. This finding has shown that mutant Pfdhps gene associated with sulphadoxine resistance is circulating in Assam. It is believed that, the parasite population may have undergone high level of breeding.
ABSTRACT
La palma de aceite Elaeis guineesis Jacq. posee gran importancia debido al aceite que se extrae de sus frutos, del cual se obtienen derivados refinados de gran valor comercial como el biodiesel, entre otros. Esta investigación buscó determinar la estructura y diversidad genética de 311 muestras de palma de aceite proveniente de la República de Camerún mediante 10 marcadores microsatélite. Los resultados mostraron valores promedio para el número medio de alelos por locus de Na=8.433 y un número efectivo de alelos por locus de Ne=4.756; las diferencias entre estos valores permiten inferir que los 106 alelos encontrados para estas poblaciones son considerados alelos raros. Adicionalmente, el valor de diversidad genética fue alto (valor medio de He= 0.781) respecto a reportes de varios autores. La varianza molecular obtenida evidenció que el mayor porcentaje (80 %) se encuentra dentro de los individuos. Los análisis mostraron que no se definió ningún tipo de estructura poblacional, lo que permitió inferir un alto flujo genético entre las zonas geográficas, esto corroborado por los altos valores de diversidad genética obtenidos. Los 311 genotipos evaluados fueron definidos como una población natural heterogénea heterocigota, apta para favorecer el aumento de la base genética de las poblaciones cultivadas de palma de aceite.
Oil palm Elaeis guineesis Jacq. is of great importance because of the oil extracted from its fruits, whose refined derivatives are commercially valuable as biodiesel, among others uses. This study sought to determine the structure and genetic diversity of 311 oil palm samples from the Republic of Cameroon with 10 microsatellite markers. The results showed values for the average number of alleles per locus of Na= 8.433 and effective number of alleles per locus of Ne= 4.756; from the differences between these values, it can be inferred that the 106 alleles found for these populations could be considered rare alleles. Additionally the value of genetic diversity was high (mean value of He= 0.781) compared to reports of several authors. The obtained molecular variance showed that the highest percentage (80 %) was found within the individuals. The analysis did not show any defined population structure, which allowed us to infer a high gene flow among the geographic zones, corroborated it by the high genetic diversity values obtained. The 311 genotypes were defined as a heterogeneous heterozygous natural population suitable to increase the genetic base of oil palm cultivated populations.