Isolation and characterization of microsatellite DNA markers in the malaria vector Anopheles funestus

Screening of the Anopheles funestus genomic DNA library detected 18 new sequences with dinucleotide tandem repeats. Primers were designed to amplify the loci and 14 out of 18 gave a repeatable and scorable amplification. Deviations from Hardy–Weinberg expectations were tested for each locus in a sample of 30 wild Anopheles funestus females. No heterozygote deficiency was detected for 11 loci of 14, thus revealing the absence of null alleles. The number of alleles per locus ranged from 5 to 15, and observed heterozygosity from 0.13 to 0.85.     

Isolation and characterization of trinucleotide microsatellites in African malaria mosquito Anopheles funestus

We developed microsatellite markers for an important African malaria mosquito Anopheles funestus Giles. The microsatellite‐enriched genomic library was constructed and screened with single‐strand oligonucleotides [(CCT)₁₇, (AAT)₁₇, (CAG)₁₇ and (GA)₂₅] as probes. Among the 47 pairs of polymerase chain reaction primers screened, 31 produced successful and consistent amplification. Although only a few A. funestus individuals from one geographical location were used to screen microsatellite marker polymorphism, 27 markers were found polymorphic and four markers monomorphic. Most polymorphic markers are trinucleotide markers. Isolation of polymorphic microsatellite markers provide useful tools for A. funestus population genetic studies and genome mapping.     

Phylogeny of anopheline (Diptera: Culicidae) species in southern Africa,based on nuclear and mitochondrial genes

A phylogeny of anthropophilic and zoophilic anopheline mosquito species was constructed, using the nuclear internal transcribed spacer 2 (ITS2) and mitochondrial cytochrome oxidase subunit I (COI) genes. The ITS2 alignment, typically difficult due to its noncoding nature and large size variations, was aided by using predicted secondary structure, making this phylogenetically useful gene more amenable to investigation. This phylogeny is unique in explicitly including zoophilic, non‐vector anopheline species in order to illustrate their relationships to malaria vectors. Two new, cryptic species, Anopheles funestus‐like and Anopheles rivulorum‐like, were found to be present in Zambia for the first time. Sequences from the D3 region of the 28S rDNA suggest that the Zambian An. funestus‐like may be a hybrid or geographical variant of An. funestus‐like, previously reported in Malawi. This is the first report of An. rivulorum‐like sympatric with An. rivulorum (Leeson), suggesting that these are separate species rather than geographic variants.     

Analysis of the sporozoite ELISA for estimating infection rates in Mozambican anophelines

Comparisons were undertaken to investigate cost‐effective methods of implementing the enzyme‐linked immunosorbent assay (ELISA) for sporozoite determination in anophelines when large numbers require processing. Comparisons between ELISA plate reader and visual assessments were performed with Anopheles funestus and Anopheles gambiae s.l. (Diptera: Culicidae), as were comparisons between whole‐body mosquito samples, heads and thoraces, and abdomens alone. Rates obtained from pools of five or 10 mosquitoes were compared with those for individual mosquitoes, as were rates obtained using different sampling methods. A total of 41 792 An. funestus and 9431 An. gambiae s.l. collected in light traps, and 22 323 An. funestus and 6860 An. gambiae s.l. from exit collections were analysed. Visual assessments gave results similar to those of machine readings. Sporozoite rates were similar in both species, as were rates by collection method. The use of whole mosquitoes increased estimates of infection rate by 0.6%. Pool size did not affect infection rates of An. gambiae s.l., but rates were higher among individually tested An. funestus than among those tested in pools. For large‐scale surveys, the use of whole mosquitoes in pools of 10 mosquitoes, with correction for overestimation, and the noting of results according to a simple three‐stage visual assessment of positivity is the most cost‐effective approach and is sufficient to obtain reliable data for comparative purposes.     

Isolation and characterization of the first microsatellite loci from the order Psocoptera in the economically important pest insect Liposcelis decolor (Pearman) and cross‐species amplification

A total of 11 microsatellite loci from the invasive insect pest Liposcelis decolor were isolated and characterized of which six loci were polymorphic. A population survey involving a total of 30–192 individuals per locus from five populations revealed a range of four to seven alleles per locus and moderate observed heterozygosities (0.183–0.565), highlighting the utility of these loci in further population genetic studies. Cross‐species amplifications were successful for two to 11 loci in five other Liposcelis species also of international economic importance.     

Isolation and characterization of polymorphic microsatellite loci in Acanthoscelides obtectus Say (Coleoptera: Bruchidae)

Six microsatellite loci were isolated from the bruchid Acanthoscelides obtectus Say (Coleoptera: Bruchidae). Each locus was polymorphic, with the number of alleles ranging from 3 to 18. We found high levels of within‐population variation at most loci, with heterozygosities ranging from 0 to 0.75. Cross‐species amplification of these loci was tested in two other species of the genus Acanthoscelides, A. obvelatus Bridwell and A. argillaceus Sharp.     

Isolation and characterization of polymorphic microsatellite loci in Acanthoscelides obvelatus Bridwell (Coleoptera: Bruchidae)

Five microsatellite loci were isolated from the bruchid Acanthoscelides obvelatus Bridwell (Coleoptera: Bruchidae). Each locus was polymorphic, with the number of alleles ranging from two to 15. We found high levels of within‐population variation at most loci, with heterozygosity ranging from 0.182 to 0.900. Cross‐species amplification of these loci was tested in two other species of the genus Acanthoscelides, A. obtectus Say and A. argillaceus Sharp.     

Isolation and characterization of microsatellite loci from a commercial cultivar of Musa acuminata

A genomic library from the commercial diploid cultivar ‘Ouro’ (Musa acuminata), enriched for CT‐ and GT‐repeats, was used to isolate and characterize 23 microsatellite loci. These loci were tested in 10 Musa genotypes, representing various Musa genomic groups with distinct ploidy level. The number of alleles per locus ranged from one to seven, and 20 loci were highly informative. Four loci appeared to amplify B genome‐specific alleles, while three loci seemed to be absent in the B genome. The polymorphism revealed by these loci will be extremely useful for genetic mapping, marker‐assisted selection, germplasm characterization and evolutionary studies in Musa.     

Fifteen microsatellite loci characterized in the golden eagle Aquila chrysaetos (Accipitridae,Aves)

Polymorphic microsatellite loci were identified in order to study golden eagle (Aquila chrysaetos) population fragmentation. Twenty‐six published Aquila and eight published Haliaeetus microsatellite loci were tested for polymorphism in A. chrysaetos. Fifteen loci were polymorphic with between two and six alleles detected per locus. Observed heterozygosity ranged from 0.15 to 0.77 among 177 unrelated individuals from Scotland. There was no evidence for null alleles. Two pairs of loci (Hal‐10 & Aa15 and Hal‐10 & Aa26) displayed linkage disequilibrium.     

Role of species composition in malaria transmission by the Anopheles funestus group (Diptera: Culicidae) in Ghana

Malaria remains a public health problem in Ghana, with Anopheles gambiae and Anopheles funestus as the predominant vectors. While much information exists on the species composition of An. gambiae, very little exists for An. funestus. This study was carried out to determine the species composition of An. funestus Giles populations from three ecological areas in Ghana and investigate their role in malaria transmission. Mosquitoes were collected using human landing and pyrethrum spray methods. A total of 10,254 Anopheles individuals were collected, out of which An. funestus constituted 53.6% (5,496). An. funestus sensu stricto (s.s.) and Anopheles lessoni were identified as the only members of the An. funestus group in all three ecological areas. All 62 sporozoite positive specimens that were identified as An. funestus s.s. were highly anthropophilic with a human blood index in the range of 80–96%, whereas more than 83% of the An. leesoni had fed on either bovine, goat, or sheep. Malaria transmission was higher in the Sahel savannah area than the rest of the ecological zones, with An. funestus s.s. being implicated as a vector of malaria in all ecological zones. Anopheles leesoni occurred in all the ecological areas but played no role in malaria transmission. The study established the importance of An. funestus s.s. in malaria transmission in Ghana.     

Isolation and characterization of Ligustrum micranthum (Oleaceae) microsatellite loci using paired‐end Illumina reads

Twenty‐six microsatellite loci were developed and characterized for Ligustrum micranthum, a species endemic to the Ogasawara Islands, Japan. The genetic structure of this species must be clarified in order to restore the island's ecosystem. A total of 8511 primer pairs were designed from de novo sequencing. Of the 48 primer pairs selected, amplification and polymorphisms were tested using one population each from the Chichijima and Hahajima Islands of the Ogasawara Islands. Twenty‐six microsatellite loci were successfully amplified and the number of alleles for these loci ranged from five to 31 per locus, and the mean expected heterozygosities were 0.858 and 0.849, respectively. No significant deviation from the Hardy–Weinberg equilibrium was observed in either population, and no significant linkage disequilibrium was detected between any locus pair. The microsatellite loci reported in this study can be used in future studies to evaluate the genetic structure and mating system of L. micranthum.     

Characterization of polymorphic microsatellite loci for the invasive monk parakeet (Myiopsitta monachus)

Microsatellite loci were characterized for the monk parakeet (Myiopsitta monachus) from a GT_n‐enriched genomic library. Twelve of 14 microsatellite loci were polymorphic, averaging 6.7 alleles per locus across the 20 individuals genotyped. Mean expected heterozygosity was 0.72, with locus‐specific values ranging from 0.53 to 0.90. An equally high multilocus probability of identity (2.48 × 10^?12) was revealed for this set of loci. In addition, all 12 loci were demonstrated to cross‐amplify to varying extents within three additional parrot genera suggesting their potential utility for population‐level studies in a broad range of Neotropical psittacines.     

Isolation of 39 polymorphic microsatellite loci and the development of a fluorescently labelled marker set for the Eurasian badger (Meles meles) (Carnivora: Mustelidae)

We have isolated 78 microsatellite loci from the Eurasian badger (Meles meles). Of the 52 loci characterized, 39 were found to be polymorphic. A fluorescently labelled primer set was developed to enable individual‐specific 17‐locus genotypes to be obtained efficiently.     

Isolation and characterization of polymorphic microsatellite markers in Amorphophallus paeoniifolius (Dennst.) Nicolson,Araceae

Amorphophallus paeoniifolius is an herbaceous perennial tuber crop distributed widely in many Asian countries. We isolated 19 polymorphic loci from A. paeoniifolius using a dual‐suppression‐PCR technique. These loci provide microsatellite markers with high polymorphism ranging from three to 24 alleles per locus. The observed and expected heterozygosities ranged from 0.521 to 0.854 and from 0.766 to 0.930, respectively. This high allelic diversity indicates that our markers are suitable for a population study in A. paeoniifolius.     

Isolation and characterization of microsatellite markers for Viola mirabilis (Violaceae) using a next‐generation sequencing platform

We isolated and characterized microsatellite loci in Viola mirabilis (Violaceae), an endangered species from South Korea. Twenty‐three polymorphic microsatellite loci were developed and tested in Korean, Chinese and Japanese populations. The number of alleles per locus varied from two to eight. The observed and expected heterozygosities within the three populations were 0.000–0.625 and 0.469–0.695, respectively. A total of six loci in the Korean population, one locus in the Chinese population and seven loci in the Japanese population deviated from Hardy–Weinberg equilibrium. We expect that these newly developed microsatellite markers will contribute to understanding the phylogeography and population genetics of V. mirabilis, which will aid in developing conservation strategies for this species.     

Behavioural and insecticidal effects of organophosphate‐, carbamate‐ and pyrethroid‐treated mosquito nets against African malaria vectors

Three insecticides – the pyrethroid deltamethrin, the carbamate carbosulfan and the organophosphate chlorpyrifos‐methyl – were tested on mosquito nets in experimental huts to determine their potential for introduction as malaria control measures. Their behavioural effects and efficacy were examined in Anopheles gambiae Giles s.s. (Diptera: Culicidae) and Anopheles funestus Giles s.s. in Muheza, Tanzania, and in Anopheles arabiensis Patton and Culex quinquefasciatus Say in Moshi, Tanzania. A standardized dosage of 25 mg/m² plus high dosages of carbosulfan (50 mg/m², 100 mg/m² and 200 mg/m²) and chlorpyrifos‐methyl (100 mg/m²) were used to compare the three types of insecticide. At 25 mg/m², the rank order of the insecticides for insecticide‐induced mortality in wild An. gambiae and An. funestus was, respectively, carbosulfan (88%, 86%) > deltamethrin (79%, 78%) > chlorpyrifos‐methyl (35%, 53%). The rank order of the insecticides for blood‐feeding inhibition (reduction in the number of blood‐fed mosquitoes compared with control) in wild An. gambiae and An. funestus was deltamethrin > chlorpyrifos‐methyl > carbosulfan. Carbosulfan was particularly toxic to endophilic anophelines at 200 mg/m², killing 100% of An. gambiae and 98% of An. funestus that entered the huts. It was less effective against the more exophilic An. arabiensis (67% mortality) and carbamate‐resistant Cx quinquefasciatus (36% mortality). Carbosulfan deterred anophelines from entering huts, but did not deter carbamate‐resistant Cx quinquefasciatus. Deltamethrin reduced the proportion of insects engaged in blood‐feeding, probably as a consequence of contact irritancy, whereas carbosulfan seemed to provide personal protection through deterred entry or perhaps a spatial repellent action. Any deployment of carbosulfan as an individual treatment on nets should be carried out on a large scale to reduce the risk of diverting mosquitoes to unprotected individuals. Chlorpyrifos‐methyl was inferior to deltamethrin in terms of mortality and blood‐feeding inhibition and would be better deployed on a net in combination with a pyrethroid to control insecticide‐resistant mosquitoes.     

The genetic architecture of tristyly and its breakdown to self‐fertilization

The floral polymorphism tristyly involves three style morphs with a reciprocal arrangement of stigma and anther heights governed by two diallelic loci (S and M). Tristyly functions to promote cross‐pollination, but modifications to stamen position commonly cause transitions to selfing. Here, we integrate whole‐genome sequencing and genetic mapping to investigate the genetic architecture of the M locus and the genetic basis of independent transitions to selfing in tristylous Eichhornia paniculata. We crossed independently derived semi‐homostylous selfing variants of the long‐ and mid‐styled morph fixed for alternate alleles at the M locus (ssmm and ssMM, respectively), and backcrossed the F₁ to the parental ssmm genotype. We phenotyped and genotyped 462 backcross progeny using 1450 genotyping‐by‐sequencing (GBS) markers and performed composite interval mapping to identify quantitative trait loci (QTL) governing style‐length and anther‐height variation. A QTL associated with the primary style‐morph differences (style length and anther height) mapped to linkage group 5 and spanned ~13–27.5 Mbp of assembled sequence. Bulk segregant analysis identified 334 genes containing SNPs potentially linked to the M locus. The stamen modifications characterizing each selfing variant were governed by loci on different linkage groups. Our results provide an important step towards identifying the M locus and demonstrate that transitions to selfing have originated by independent sets of mating‐system modifier genes unlinked to the M locus, a pattern inconsistent with a recombinational origin of selfing variants at a putative supergene.     

Isolation and characterization of microsatellite loci from mangrove red snapper Lutjanus argentimaculatus

Lutjanus argentimaculatus, also called mangrove red snapper, is a commercially important fish in East Asia. A proper understanding of population structure is primarily linked with the management of genetic resources in exploiting marine fisheries. Herein, seven microsatellite loci, which showed high polymorphism (observed heterozygosity per locus ranging from 0.3571 to 0.7857 and expected heterozygosity per locus ranging from 0.6236 to 0.8821), were isolated and characterized from L. argentimaculatus. Cross‐species amplifications also indicate that primers designed for these loci may be useful for further studies about other closely phylogenetic species of the family Lutjanidae.     

Microsatellite loci for behavioural studies of Eclectus parrot (Eclectus roratus: Aves)

Ten polymorphic microsatellite loci were isolated from the cooperatively breeding and sexually dichromatic Eclectus parrot (Eclectus roratus). Nine loci were in Hardy–Weinberg equilibrium and unlinked. One locus, Ero1, was presumed to be sex‐linked since females, the heterogametic sex, were all homozygous, whereas 72% of males were heterozygous. A DNA database search revealed that Ero8 is probably an independent isolation of the microsatellite locus AgGT83 of the parrot Amozona guildingii. With high heterozygosity (0.41–0.89) and number of alleles (two to 13), these loci should prove useful for investigating the mating system of these unusual Australasian parrots.     

Isolation and characterization of 20 polymorphic microsatellite loci for Scaptodrosophila hibisci

Scaptodrosophila hibisci is an endemic Australian Drosophilidae that breeds in the flowers of native Hibiscus . Here we report the isolation and amplification of 20 polymorphic microsatellite loci . We cloned these microsatellites because loci developed for Drosophila melanogaster failed to amplify in S. hibisci . Null alleles were detected at six loci, and five were X‐linked. Two of the primer pairs amplified an unlinked ‘bonus’ locus. One locus containing juxtaposed microsatellite loci was suitable for designing an additional set of primers. Mean number of alleles per locus was 10, mean H _O and H _E per locus were 0.532 and 0.636, respectively.