Population genetics of Anopheles arabiensis, the primary malaria vector in the Republic of Sudan

Background Anopheles arabiensis is a member of Anopheles gambiae complex and the main malaria vector in Sudan. There is insufficient population genetics data available on An. arabiensis for an understanding of vector population structure and genetics, which are important for the malaria vector control programmes in this country. The objective of this investigation is to study the population structure, gene flow and isolation by distance among An. arabiensis populations for developing control strategies. Methods Mosquitoes were collected from six sites located in three different states in Sudan, Khartoum, Kassala and Sennar, using pyrethrum spray catch of indoor resting mosquitoes. Anopheline mosquitoes were identified morphologically and based on species specific nucleotide sequences in the ribosomal DNA intergenic spacers (IGS). Seven published An. gambiae microsatellite loci primers were used to amplify the DNA of An. arabiensis samples. Results PCR confirmed that An. arabiensis was the main malaria vector found in the six localities. Of the seven microsatellite loci utilized, six were found to be highly polymorphic across populations, with high allelic richness and heterozygosity with the remaining one being monomorphic. Deviation from Hardy–Weinberg expectations were found in 21 out of 42 tests in the six populations due to heterozygote deficiency. Bayesian clustering analysis revealed two gene pools, grouping samples into two population clusters; one includes four and the other includes two populations. The clusters were not grouped according to the three states but were instead an admixture. The genetic distances between pairs of populations ranged from 0.06 to 0.24. Significant FST was observed between all pairwise analyses of An. arabiensis populations. The Kassala state population indicated high genetic differentiation (FST ranged from 0.17 to 0.24) from other populations, including one which is also located in the same state. High gene flow (Nm = 1.6–8.2) was detected among populations within respective clusters but limited between clusters particularly with respect to Kassala state. There was evidence of a bottleneck event in one of the populations (Al Haj Yousif site). No isolation by distance pattern was detected among populations. Conclusions This study revealed low levels of population differentiation with high gene flow among the An. arabiensis populations investigated in Sudan, with the exception of Kassala state.

Phylogeny, Connectivity and Dispersal Patterns of the Giant Kelp Macrocystis (Phaeophyceae)

<p>Macrocystis represents the most widely distributed kelp genus, providing structure and energy for one of the most productive ecosystems on earth. Despite its ecological and economical importance, many aspects of its taxonomy, distribution and dispersal still remain unknown. Using different molecular markers I studied the taxonomy, phylogeography and dispersal patterns of Macrocystis. The analysis involves samples from different populations throughout the world. Using the DNA barcoding method I, confirmed previous suggestions that the genus must be considered as monospecific, M. pyrifera being the only species. The effects of historical and contemporary events on the haplotype distribution were determined by analyzing samples from the southeastern Pacific (SEP) using the atp8-S mitochondrial marker. The last glacial maximum as well as oceanographic anomalies (El Niño phenomena) may be important factors driving the genetic pattern along the SEP. The genetic structure in southern Chile was also analyzed in more detail, especially in the Chilean Fjords. Samples from attached and floating kelp individuals revealed that dispersal via kelp rafts is possible. Finally, a global analysis using COI sequences showed shared haplotypes along vast distances in the Northern and Southern hemispheres, recent dispersal and high gene flow can explain such genetic homogeneity. Additionally, microsatellite analysis confirmed that gene flow along the Southern Ocean is occurring over ecological time scales, where rafting of detached reproductive kelps seems to be facilitated by the Antarctic Circumpolar Current connecting populations in the Southern Hemisphere. This study has provided valuable genetic evidence to understand factors shaping the genetic structure of this important ecologically and economically species. It also contributes important knowledge for conservation and management strategies, especially in places where M. pyrifera has been harvested. In summary, the results of this study confirm previous suggestions of high gene flow among M. pyrifera populations at different scales. It also provides evidence suggesting that kelp rafts act as an important dispersal mechanism in this species, thus giving important information to understand the factors shaping the evolution of the largest seaweed on earth.</p>

Phylogeny, Connectivity and Dispersal Patterns of the Giant Kelp Macrocystis (Phaeophyceae)

<p>Macrocystis represents the most widely distributed kelp genus, providing structure and energy for one of the most productive ecosystems on earth. Despite its ecological and economical importance, many aspects of its taxonomy, distribution and dispersal still remain unknown. Using different molecular markers I studied the taxonomy, phylogeography and dispersal patterns of Macrocystis. The analysis involves samples from different populations throughout the world. Using the DNA barcoding method I, confirmed previous suggestions that the genus must be considered as monospecific, M. pyrifera being the only species. The effects of historical and contemporary events on the haplotype distribution were determined by analyzing samples from the southeastern Pacific (SEP) using the atp8-S mitochondrial marker. The last glacial maximum as well as oceanographic anomalies (El Niño phenomena) may be important factors driving the genetic pattern along the SEP. The genetic structure in southern Chile was also analyzed in more detail, especially in the Chilean Fjords. Samples from attached and floating kelp individuals revealed that dispersal via kelp rafts is possible. Finally, a global analysis using COI sequences showed shared haplotypes along vast distances in the Northern and Southern hemispheres, recent dispersal and high gene flow can explain such genetic homogeneity. Additionally, microsatellite analysis confirmed that gene flow along the Southern Ocean is occurring over ecological time scales, where rafting of detached reproductive kelps seems to be facilitated by the Antarctic Circumpolar Current connecting populations in the Southern Hemisphere. This study has provided valuable genetic evidence to understand factors shaping the genetic structure of this important ecologically and economically species. It also contributes important knowledge for conservation and management strategies, especially in places where M. pyrifera has been harvested. In summary, the results of this study confirm previous suggestions of high gene flow among M. pyrifera populations at different scales. It also provides evidence suggesting that kelp rafts act as an important dispersal mechanism in this species, thus giving important information to understand the factors shaping the evolution of the largest seaweed on earth.</p>

Microsatellite markers from Peronospora tabacina, the cause of blue mold of tobacco, reveal species origin, population structure, and high gene flow

Peronospora tabacina is an obligate parasite that causes blue mold of tobacco. The pathogen reproduces primarily asexually by sporangia, and sexual oospores are a rarely observed form of propagation. A collection of 122 isolates of P. tabacina was genotyped using nine microsatellites to assess the population structure of individuals from subpopulations collected from Central, Southern, and Eastern Europe, the Middle East, Central and North America, and Australia. Genetic variation among the six subpopulations accounted for about 8% of total variation with moderate levels of genetic differentiation, high gene flow among these subpopulations, and a positive correlation between geographic and genetic distance (r = 0.225; P<0.001). Evidence of linkage disequilibrium (P<0.001) showed that populations contained partially clonal subpopulations, except subpopulations from Australia and Mediterranean Europe. High genetic variation and population structure among samples could be explained by continuous gene flow across continents via infected transplant exchange and/or long-distance dispersal of sporangia via wind currents. This study analyzed the most numerous P. tabacina collection to date and allowed conclusions on the migration, mutation, and evolutionary history of this obligate biotrophic oomycete. The evidence pointed to the species origin in Australia and identified intra- and inter-continental migration patterns of this important pathogen.

Gender-based Genetic Variability of Ailanthus excelsa Roxb, Populations Using, RAPD, ISSR and SCoT Markers

Ailanthus excelsa Roxb. is an economically important and multipurpose dioecious tree species of India, mainly used for fodder and timber. Gender-based genetic diversity of five populations of two sites (Jodhpur, Rajasthan and Deesa, Gujarat) of A. excelsa was assessed. A total of 42 RAPD, 20 ISSR and 23 SCoT primers were screened for DNA amplification of 232 individuals. Out of which only 25 primers (13 RAPD, 6 ISSR and 6 SCoT) were found polymorphic. The SCoT markers were showed the highest value for PIC, MI, Rp value, Nei’s gene diversity and Shannon’s index, as compared with the other two markers. Female individuals in all five populations had slightly higher genetic diversity as compared with male individuals. A high level of genetic diversity (55%) was detected within the populations of male and female individuals. High gene flow (6.70) and low genetic differentiation (0.069) values were found between Jodhpur and Deesa sites. Principal component analysis for all populations were accounted for 48.7% of the genetic variation. The Mantel test showed significant correlation (R = 0.178, P = .01) between genetic and geographic distances. The present study showed that SCoT markers were best for genetic diversity assessment in A. excelsa over RAPD and ISSR markers. High gene flow and low genetic differentiation in A. excelsa indicates its poor population fragmentation despite long geographic distances.

Population Genetic of Anopheles Arabiensis Patton(Diptera: Culicidae) the Malaria Vector in the Republic of Sudan.

Background Anopheles arabiensis is a member of An. gambiae complex and a main malaria vector in Sudan. There is no sufficient An. arabiensis population genetic data available an understanding of vector population structure and genetics are important to the malaria vector control programs. The objective of this investigation is to study the population structure, gene flow and isolation by distance among An. arabiensis for developing control strategies Methods Mosquitoes were collected from six sites in Sudan using pyrethrum spray catch of indoor resting mosquitoes. Anopheline mosquitos were identified morphologically and based on species specific nucleotide sequences in the ribosomal DNA intergenic spacers (IGS). Seven microsatellite loci published An. gambiae primers were used to amplify the DNA of An. arabiensis samples. Results PCR confirmed that An. arabiensis was the main malaria vector found in the six localities. Of the seven microsatellite loci utilized, six were found to be highly polymorphic across populations, with high allelic richness and heterozygosity with the remaining one being monomorphic. Deviation from Hardy-Weinberg expectations were found in 21 out of 42 tests in the six populations due to heterozygotes deficiency. Bayesian clustering analysis revealed two gene pools, grouping samples into two population clusters; one includes four and the other includes two populations. The genetic distances between pairs of populations ranged from 0.06 to 0.24. Significant F ST was observed between all An. arabiensis populations . Kr population indicated high genetic differentiation (F ST ranged from 0.17 to 0.24). High gene flow (Nm= 1.6–8.2) was detected between clusters. There was evidence of a bottleneck event in the Hj population. No isolation by distance pattern was detected among populations. Conclusions This study revealed low levels of population differentiation with high gene flow among six An. arabiensis populations in Sudan.

High gene flow maintains genetic diversity following selection for high EPSPS copy number in the weed kochia (Amaranthaceae)

Kochia, a major weed species, has evolved resistance to four herbicide modes of action. Herbicide resistance appears to spread quickly, which could result in diminished standing genetic variation, reducing the ability of populations to adapt further. Here we used double digest restriction enzyme associated sequencing to determine the level of gene flow among kochia populations and whether selection for glyphosate resistance reduces genetic variation. Canadian Prairie populations show little to no genetic differentiation (FST = 0.01) and no correlation between genetic and geographic distance (r2 = − 0.02 p = 0.56), indicating high gene flow and no population structure. There is some evidence that kochia populations are genetically depauperate compared to other weed species, but genetic diversity did not differ between glyphosate susceptible and resistant populations or individuals. The inbreeding coefficients suggest there are 23% fewer heterozygotes in these populations than expected with random mating, and no variation was found within the chloroplast. These results indicate that any alleles for herbicide resistance can be expected to spread quickly through kochia populations, but there is little evidence this spread will reduce the species’ genetic variation or limit the species’ ability to respond to further selection pressure.