Population genetics and molecular identification of Crocodylus acutus and C. moreletii (Crocodilia: Crocodylidae) in captive and wildlife populations / Genética de poblaciones e identificación molecular de Crocodylus acutus y C. moreletii (Crocodilia: Crocodylidae) en poblaciones de cautiverio y de vida libre

Abstract Introduction: There is low evidence of genetic diversity and hybridization processes within Crocodylus acutus and C. moreletii populations. Objetive: To evaluate genetic diversity and some phylogenetic relationships in wild and captive populations of C. acutus and C. moreletii using the Barcode of Life Data System (COX1, cytochrome C oxidase subunit 1 gene). Methods: 28 individuals phenotypically like C. acutus located in the state of Guerrero, Oaxaca and Quintana Roo were sampled, as well as animals belonging to C. moreletii located in the states of Tabasco, Campeche, and Quintana Roo. 641 base pairs of nucleotide sequence from COX1 were used to obtain the haplotype and nucleotide diversity per population, and a phylogenetic and network analysis was performed. Results: Evidence of hybridization was found by observing C. moreletti haplotypes in animals phenotypically determined as C. acutus, as well as C. acutus haplotypes in animals classified as C. moreletti. Low haplotypic diversity was observed for C. acutus (0.455 ± 0.123) and for C. moreletii (0.505 ± 0.158). A phylogenetic tree was obtained in which the sequences of C. acutus and C. moreletii were grouped into two well-defined clades. Organisms identified phenotypically as C. acutus but with C. moreletii genes were separated into a different clade within the clade of C. moreletii. Conclusions: There are reproductive individuals with haplotypes different from those of the species. This study provides a small but significant advance in the genetic knowledge of both crocodile species and the use of mitochondrial markers, which in this case, the COX1 gene allowed the detection of hybrid organisms in wild and captive populations. Conservation efforts for both species of crocodiles should prevent the crossing of both threatened species and should require the genetic identification of pure populations, to design effective conservation strategies considering the possibility of natural hybridization in areas of sympatry.

Resumen Introducción: Existe poca evidencia de la diversidad genética y los procesos de hibridación dentro de las poblaciones de Crocodylus acutus y C. moreletii. Objetivo: Evaluar la diversidad genética y algunas relaciones filogenéticas en poblaciones silvestres y cautivas de C. acutus y C. moreletii utilizando el Sistema de Código de Barras de la vida (COX1, subunidad I del gen del citocromo C oxidasa). Métodos: Se muestrearon 28 individuos fenotípicamente similares a C. acutus ubicados en los estados de Guerrero, Oaxaca y Quintana Roo, así como animales pertenecientes a C. moreletii ubicados en los estados de Tabasco, Campeche y Quintana Roo. Se utilizaron 641 pares de bases de la secuencia de nucleótidos de la subunidad I del gen del citocromo C oxidasa para obtener el haplotipo y la diversidad de nucleótidos por población, y se realizó un análisis filogenético y de redes. Resultados: Se encontró evidencia de hibridación al observar haplotipos de C. moreletti en animales determinados fenotípicamente como C. acutus, así como haplotipos de C. acutus en animales clasificados como C. moreletti. Se observó una baja diversidad haplotípica para C. acutus (0.455 ± 0.123) y para C. moreletii (0.505 ± 0.158). Se obtuvo un árbol filogenético en el que las secuencias propias de C. acutus y C. moreletii se agruparon en dos grandes y bien definidos clados. Los organismos identificados fenotípicamente como C. acutus pero con genes de C. moreletii se separaron en un clado diferente dentro del clado de C. moreletii. Conclusiones: Existen individuos reproductores con haplotipos diferentes a los de la especie. Este estudio aporta un pequeño pero significativo avance en el conocimiento genético tanto de las especies de cocodrilos como del uso de marcadores mitocondriales, que, en este caso, el gen COX1 permitió la detección de organismos híbridos en poblaciones silvestres y cautivas. Los esfuerzos de conservación para ambas especies de cocodrilos deben evitar el cruce de ambas especies amenazadas y deben requerir la identificación genética de poblaciones puras, para diseñar estrategias de conservación efectivas considerando la posibilidad de hibridación natural en áreas de simpatría.

First Record of Molecular Confirmation, Phylogeny and Haplotype Diversity of Haemonchus contortus from Gaddi (breed) Goats of North India

Abstract: In the present study, molecular identification and genotypic characterization of H. contortus was carried out targeting 28S-18S rRNA intergenic spacer. Faecal samples of Gaddi goats were collected and subjected to qualitative screening. The samples exhibiting the presence of strongyle type eggs were introduced to faecal culturing. The larvae retrieved were molecularly confirmed as of H. contortus species and the phylogenetics was performed. For the estimation of evolutionary divergence in between the present study isolates with the GenBank archived sequences, maximum composite likelihood model was employed. Nucleotide and haplotype diversity indices and Fu's Fs were also estimated. Approximately 260 bp size amplicons retrieved were confirmatory for the presence of H. contortus species. Phylogenetic analysis also accentuated that present parasite isolates were of H. contortus only. The nucleotide diversity (π) obtained was 0.06696, whereas, haplotype diversity was 0.92549 [95% CI: 0.77778-1.0000]. In between the isolates, Fu's Fs statistic value was positive (1.566), evidencing a deficiency of alleles, which would have happened due to recent population bottleneck. The recovered representative sequences were deposited in GenBank under the accession numbers LC600315-LC600317.To the best of our knowledge, the present study is the first report of phylogeny and haplotype diversity of H. contortus isolated from Gaddi goats of North India. The present study would also serve the basis for future detailed molecular epidemiological studies using discriminative markers for the assessment of genetic diversity in different populations of H. contortus in different hosts of the study area.

CO1-Based DNA barcoding for assessing diversity of Pteropus giganteus from the state of Azad Jammu Kashmir, Pakistan / Código de barras de DNA à base de CO1 para avaliar a diversidade de Pteropus giganteus do estado de Azad Jammu e Caxemira, Paquistão

Abstract The flying fox (Pteropus giganteus) also familiar with the name of the greater Indian fruit Bat belongs to the order Chiroptera and family Pteropodidae. Current research emphasis on the DNA barcoding of P. giganteus in Azad Jammu Kashmir. Bat sequences were amplified and PCR products were sequenced and examined by bioinformatics software. Congeneric and conspecific, nucleotide composition and K2P nucleotide deviation, haplotype diversity and the number of haplotypes were estimated. The analysis showed that all of the five studied samples of P. giganteus had low G contents (G 19.8%) than C (27.8%), A (25.1%) and T (27.3%) contents. The calculated haplotype diversity was 0.60% and the mean intraspecific K2P distance was 0.001% having a high number of transitional substitutions. The study suggested that P. giganteus (R=0.00) do not deviate from the neutral evolution. It was determined from the conclusion that this mtDNA gene is a better marker for identification of Bat species than nuclear genes due to its distinctive characteristics and may serve as a landmark for the identification of interconnected species at the molecular level and in the determination of population genetics.

Resumo A raposa-voadora (Pteropus giganteus), também conhecida como morcego indiano, pertence à ordem dos Chiroptera e à família Pteropodidae. A presente pesquisa dá ênfase ao código de barras de DNA de P. giganteus em Azad Jammu e Caxemira. Sequências genéticas dos morcegos foram amplificadas, e os produtos de PCR foram sequenciados e examinados por software de bioinformática. De espécies congenérica e coespecífica, foram estimados composição nucleotídica e desvio de nucleotídeos K2P, diversidade de haplótipos e número de haplótipos. A análise mostrou que todas as cinco amostras estudadas de P. giganteus apresentaram baixos teores de G (19,8%) em comparação com C (27,8%), A (25,1%) e T (27,3%). A diversidade de haplótipos calculada foi de 0,60%, e a distância média intraespecífica de K2P foi de 0,001%, com um elevado número de substituições transicionais. O estudo sugeriu que P. giganteus (R = 0,00) não se desviou da evolução neutra. É possível concluir que o gene mtDNA é um marcador favorável para identificação de espécies de morcegos do que genes nucleares por causa de suas características distintivas e pode servir como um marco para a identificação de espécies interconectadas em nível molecular e para a determinação genética de populações.

CO1-Based DNA barcoding for assessing diversity of Pteropus giganteus from the state of Azad Jammu Kashmir, Pakistan

Abstract The flying fox (Pteropus giganteus) also familiar with the name of the greater Indian fruit Bat belongs to the order Chiroptera and family Pteropodidae. Current research emphasis on the DNA barcoding of P. giganteus in Azad Jammu Kashmir. Bat sequences were amplified and PCR products were sequenced and examined by bioinformatics software. Congeneric and conspecific, nucleotide composition and K2P nucleotide deviation, haplotype diversity and the number of haplotypes were estimated. The analysis showed that all of the five studied samples of P. giganteus had low G contents (G 19.8%) than C (27.8%), A (25.1%) and T (27.3%) contents. The calculated haplotype diversity was 0.60% and the mean intraspecific K2P distance was 0.001% having a high number of transitional substitutions. The study suggested that P. giganteus (R=0.00) do not deviate from the neutral evolution. It was determined from the conclusion that this mtDNA gene is a better marker for identification of Bat species than nuclear genes due to its distinctive characteristics and may serve as a landmark for the identification of interconnected species at the molecular level and in the determination of population genetics.

Resumo A raposa-voadora (Pteropus giganteus), também conhecida como morcego indiano, pertence à ordem dos Chiroptera e à família Pteropodidae. A presente pesquisa dá ênfase ao código de barras de DNA de P. giganteus em Azad Jammu e Caxemira. Sequências genéticas dos morcegos foram amplificadas, e os produtos de PCR foram sequenciados e examinados por software de bioinformática. De espécies congenérica e coespecífica, foram estimados composição nucleotídica e desvio de nucleotídeos K2P, diversidade de haplótipos e número de haplótipos. A análise mostrou que todas as cinco amostras estudadas de P. giganteus apresentaram baixos teores de G (19,8%) em comparação com C (27,8%), A (25,1%) e T (27,3%). A diversidade de haplótipos calculada foi de 0,60%, e a distância média intraespecífica de K2P foi de 0,001%, com um elevado número de substituições transicionais. O estudo sugeriu que P. giganteus (R = 0,00) não se desviou da evolução neutra. É possível concluir que o gene mtDNA é um marcador favorável para identificação de espécies de morcegos do que genes nucleares por causa de suas características distintivas e pode servir como um marco para a identificação de espécies interconectadas em nível molecular e para a determinação genética de populações.

Population genetic structure of malaria vector Anopheles stephensi using mitochondrial Cytochrome oxidase II gene in Indian populations.

The genetic differentiation in A. stephensi based on haplotype diversity using Restriction Fragment Length Polymorphism and by sequencing of CO II gene across different localities in India has been analyzed. The presence of only one DraI restriction site in CO II gene conferred to haplotype B indicating that the gene is very much conserved and the gene flow is not affected even by a major geographical distance barrier. The sequencing and analysisof various population parameters revealed seven haplotypes in all populations. The West Bengal population was found to be more genetically diverse than others. The geographic distance between populations was found to be contributing to the genetic differentiation. The sign of demographic expansion were found in three of the five populations. The local geographic barriers were found to be ineffective in prevention of gene flow.

Polimorfismos de 17 marcadores STR del cromosoma-Y en una muestra poblacional del altiplano cundiboyacense / Polymorphism of 17 Y-chromosome STR markers in a sample from the cundiboyacense plateau

Introducción: La tipificación molecular de ADN de cromosoma-Y es una herramienta de reconocida importancia en el proceso de identificación de individuos de género masculino en diversos casos forenses. Actualmente es una herramienta de apoyo para los laboratorios de genética estatales en la identificación de víctimas del conflicto armado en Colombia, dentro de los procesos enmarcados en la Ley de Justicia y Paz. En este estudiose determina el haplotipo del cromosoma-Y que será comparado con parientes por línea paaterna de género masculino, con el fin de realizar el análisis estadístico de estos marcadores, aportar a una base de datos colombiana y comparar con parientes de la línea masculina. Objetivo: Realizar una caracterización de haplotipos mediante análisis de marcadores moleculares, STR del cromosoma-Y en una muestra de población del altiplano cundiboyacense colombiano. Discusión: Los valores de diversidad haplotípica, poder de discriminación y probabilidad de coincidencia al azar corroboran la utilidad del análisis de STR-Y en casos de filiación por línea paterna y son coherentes con los valores observados en el inicio del desarrollo de bases de datos de haplotipos.Conclusión: Los datos del análisis de los 17 marcadores STR-Y, recogidos en el presente estudio, aportan haplotipos de población del altiplano cundiboyacense, la cual es una de las concentraciones de población más significativas en Colombia. Estos resultados corresponden a una recopilación de datos informativos que permiten mejorar una base de datos en la que se genere la estimación real de frecuencias haplotípicas de STR-Y para su aplicación en la práctica forense y estudios de poblaciones humanas.

Introduction: The application of Y-Chromosome molecular DNA typing is a tool of recognized importance in the process of identification of male individuals in various forensic cases, and currently it is now a support tool for genetic laboratories seeking to identify victims of the armed conflict in Colombia within the legal process of ®Justice and Peace¼. In this report, the Y-chromosome haplotype is determined and statistical analyses are performed to improve databases of Colombian Y-chromosome for comparison with relatives of the male line. Objective: Characterization of haplotypes through analysis of Y-chromosome STR molecular markers in a sample of Colombian Cundiboyacense highland population. Discussion: The values of haplotype diversity, discrimination power, and probability of random coincidence showed the usefulness of Y-STR analysis in cases of patrilineal descent and are consistent with values observed in the early development of haplotype databases. Conclusion: The data analysis of the 17-Y STR markers obtained in this study provide haplotypes for the Cundiboyacense highlands, one of the most significant concentrations of population in Colombia, and serves as an informative database for forensic practice and genetic studies for human populations.