Complexities in the genetic structure of Anopheles gambiae populations in west Africa as revealed by microsatellite DNA analysis

Evidence for divergent selection between the molecular forms of Anopheles gambiae: role of predation

BACKGROUND

The molecular forms of Anopheles gambiae are undergoing speciation. They are characterized by a strong assortative mating and they display partial habitat segregation. The M form is mostly found in flooded/irrigated areas whereas the S form dominates in the surrounding areas, but the ecological factors that shape this habitat segregation are not known. Resource competition has been demonstrated between species undergoing divergent selection, but resource competition is not the only factor that can lead to divergence.

RESULTS

In a field experiment using transplantation of first instar larvae, we evaluated the role of larval predators in mediating habitat segregation between the forms. We found a significant difference in the ability of the molecular forms to exploit the different larval sites conditioned on the presence of predators. In absence of predation, the molecular forms outcompeted each other in their respective natural habitats however, the developmental success of the M form was significantly higher than that of the S form in both habitats under predator pressure.

CONCLUSION

Our results provide the first empirical evidence for specific adaptive differences between the molecular forms and stress the role of larval predation as one of the mechanisms contributing to their divergence.

Genetic population structure of Anopheles gambiae in Equatorial Guinea

BACKGROUND

Patterns of genetic structure among mosquito vector populations in islands have received particular attention as these are considered potentially suitable sites for experimental trials on transgenic-based malaria control strategies. In this study, levels of genetic differentiation have been estimated between populations of Anopheles gambiae s.s. from the islands of Bioko and Annobón, and from continental Equatorial Guinea (EG) and Gabon.

METHODS

Genotyping of 11 microsatellite loci located in chromosome 3 was performed in three island samples (two in Bioko and one in Annobón) and three mainland samples (two in EG and one in Gabon). Four samples belonged to the M molecular form and two to the S-form. Microsatellite data was used to estimate genetic diversity parameters, perform demographic equilibrium tests and analyse population differentiation.

RESULTS

High levels of genetic differentiation were found between the more geographically remote island of Annobón and the continent, contrasting with the shallow differentiation between Bioko island, closest to mainland, and continental localities. In Bioko, differentiation between M and S forms was higher than that observed between island and mainland samples of the same molecular form.

CONCLUSION

The observed patterns of population structure seem to be governed by the presence of both physical (the ocean) and biological (the M-S form discontinuity) barriers to gene flow. The significant degree of genetic isolation between M and S forms detected by microsatellite loci located outside the "genomic islands" of speciation identified in A. gambiae s.s. further supports the hypothesis of on-going incipient speciation within this species. The implications of these findings regarding vector control strategies are discussed.

Spatial and temporal genetic structure of Anopheles arabiensis in Southern Zambia over consecutive wet and drought years

No studies have addressed the spatial complexity of Anopheles arabiensis populations in Zambia or the effects of drought on the genetic structure of this species. We genotyped approximately 420 An. arabiensis at 12 microsatellite loci representing 18 collections from the Southern Province of Zambia. Collections spanned three transmission seasons and covered a wet year-drought year-wet year cycle. Anopheles arabiensis within the 2,000 km(2) of the Macha study region were panmictic, with high gene flow between Macha and Namwala, Zambia, which are 80 km apart. There was little evidence for genetic structuring among years, with no significant shifts in allele frequency distributions or observed heterozygosity, and no evidence for a genetic bottleneck despite a drastic reduction in mosquito numbers during the drought year. Anopheles arabiensis in southern Zambia has a large deme size, and the regional genetic structure of this species was little affected by an extended drought period.

Malaria vector control in the third millennium: progress and perspectives of molecular approaches

Remarkable progress has been made towards a deeper understanding of mosquito biology since the completion of the Anopheles gambiae Giles genome project. Combined with the development of efficient transgenic technologies for genetic modification of major vector species and the availability of powerful molecular, genetic and bioinformatics tools, this is allowing the identification of genes involved in mosquito biological functions crucial to malaria transmission, ranging from host-seeking behaviour and innate immunity to insecticide resistance. Moreover, population genetic studies are beginning to elucidate the complex structure of vector populations. Finally, novel methods for malaria control are emerging that are based on the use of genetically modified mosquitoes either to interrupt the journey of the Plasmodium parasite within its insect host or to suppress those mosquito species that function as vectors for parasite transmission.

Evidence for subdivision within the M molecular form of Anopheles gambiae

The principal vector of malaria in sub-Saharan Africa, Anopheles gambiae is subdivided into two molecular forms M and S. Additionally, several chromosomal forms, characterized by the presence of various inversion polymorphisms, have been described. The molecular forms M and S each contain several chromosomal forms, including the Savanna, Mopti and Forest forms. The M and S molecular forms are now considered to be the reproductive units within A. gambiae and it has recently been argued that a low recombination rate in the centromeric region of the X chromosome has facilitated isolation between these forms. The status of the chromosomal forms remains unclear however. Therefore, we studied genetic differentiation between Savanna S, Forest S, Forest M and Mopti M populations using microsatellites. Genetic differentiation between Savanna S and Forest S populations is very low (F(ST) = 0.0053 +/- 0.0049), even across large distances. In comparison, the Mopti M and Forest M populations show a relatively high degree of genetic differentiation (F(ST) = 0.0406 +/- 0.0054) indicating that the M molecular form may not be a single entity, but could be subdivided into at least two distinct chromosomal forms. Previously it was proposed that inversions have played a role in the origin of species within the A. gambiae complex. We argue that a possible subdivision within the M molecular form could be understood through this process, with the acquisition of inversions leading to the expansion of the M molecular form into new habitat, dividing it into two distinct chromosomal forms.

A set of broadly applicable microsatellite markers for analyzing the structure of Culex pipiens (Diptera: Culicidae) populations

Microsatellite markers were isolated and developed from Culex pipiens quinquefasciatus Say (Diptera: Culicidae) sampled in Johannesburg, South Africa, to identify those that are broadly useful for analyzing Cx. pipiens complex populations between continents. Suitable loci should be 1) inherited in a codominant Mendelian manner, 2) polymorphic, 3) selectively neutral, 4) randomly associated, 5) without null alleles, and 6) applicable across broad regions and between diverse biotypes. Loci in Cx. p. quinquefasciatus from Johannesburg ranged from two to 17 alleles per locus and expected heterozygosities (H(e)) were 0.02-0.87. Loci in Cx. p. pipiens L. from Johannesburg had five to 19 alleles per locus and H(e) values ranging from 0.57 to 0.93, whereas those from George, South Africa, had five to 17 alleles per locus and H(e) values ranging from 0.54 to 0.88. Loci in North American mosquitoes were more variable. Cx. p. quinquefasciatus from South Carolina had five to 19 alleles per locus and H(e) values ranging from 0.64 to 0.90, whereas Cx. p. pipiens from Massachusetts had six to 28 alleles per locus and with H(e) values ranging from 0.65 to 0.94. All loci were associated randomly. Overall, four of nine of these new loci satisfied all six criteria for broad utility for analyzing the genetic structure of Cx. pipiens populations.

Reduced recombination rate and genetic differentiation between the M and S forms of Anopheles gambiae s.s

Genetic differentiation between the largely sympatric molecular forms M and S of Anopheles gambiae appears mostly limited to division 6 and part of division 5 of the X chromosome. This region is adjacent to the centromere and includes the rDNA that was used to define these forms. This localized differentiation between populations that experience gene flow strongly suggests that this region contains genes responsible for reproductive isolation. Regions adjacent to centromeres are known to experience less recombination in several species and it has recently been suggested that low recombination rates can facilitate the accumulation and maintenance of isolation genes in partially isolated populations. Therefore, we measured the recombination rate in division 5D/6 directly and estimate that it is at least 16-fold reduced across this region compared to the remainder of the X chromosome. Additionally, sequence data from four loci from field-collected mosquitoes from several West African countries show very strong differentiation between the molecular forms in division 5D/6, whereas none was observed in two loci elsewhere on the X chromosome. Furthermore, genetic variation was substantially lower in division 5D/6 compared to the two reference loci, and the inferred genealogies of the division 5D/6 genes show patterns consistent with selective sweeps. This suggests that the reduced recombination rate has increased the effect of selection on this region and that our data are consistent with the hypothesis that reduced recombination rates can play a role in the accumulation of isolation genes in the face of gene flow.

Ecological zones rather than molecular forms predict genetic differentiation in the malaria vector Anopheles gambiae s.s. in Ghana

The malaria mosquito Anopheles gambiae s.s. is rapidly becoming a model for studies on the evolution of reproductive isolation. Debate has centered on the taxonomic status of two forms (denoted M and S) within the nominal taxon identified by point mutations in the X-linked rDNA region. Evidence is accumulating that there are significant barriers to gene flow between these forms, but that the barriers are not complete throughout the entire range of their distribution. We sampled populations from across Ghana and southern Burkina Faso, West Africa, from areas where the molecular forms occurred in both sympatry and allopatry. Neither Bayesian clustering methods nor F(ST)-based analysis of microsatellite data found differentiation between the M and S molecular forms, but revealed strong differentiation among different ecological zones, irrespective of M/S status and with no detectable effect of geographical distance. Although no M/S hybrids were found in the samples, admixture analysis detected evidence of contemporary interform gene flow, arguably most pronounced in southern Ghana where forms occur sympatrically. Thus, in the sampled area of West Africa, lack of differentiation between M and S forms likely reflects substantial introgression, and ecological barriers appear to be of greater importance in restricting gene flow.

Reproductive output of female Anopheles gambiae (Diptera: Culicidae): comparison of molecular forms

Knowledge of ecological differences between the molecular forms of Anopheles gambiae Giles (Diptera: Culicidae) might lead to understanding of their unique contribution to disease transmission, to better vector control, and to identification of the forces that have separated them. We compared female fecundity measured as egg batch size in relation to body size between the molecular forms in Mali and contrasted them with their sibling species, Anopheles arabiensis Patton. To determine whether eggs of different egg batches are of similar "quality," we compared the total protein content of first-stage larvae (L1s), collected < 2 h after hatching in deionized water. Egg batch size significantly varied between An. gambiae and An. arabiensis and between the molecular forms of An. gambiae (mean batch size was 186.3, 182.5, and 162.0 eggs in An. arabiensis and the M and the S molecular form of An. gambiae, respectively). After accommodating female body size, however, the difference in batch size was not significant. In the S molecular form, egg protein content was not correlated with egg batch size (r = -0.08, P > 0.7) nor with female body size (r = -0.18, P > 0.4), suggesting that females with more resources invest in more eggs rather than in higher quality eggs. The mean total protein in eggs of the M form (0.407 microg per L1) was 6% higher than that of the S form (0.384 microg per L1), indicating that the M form invests a greater portion of her resources into current (rather than future) reproduction. A greater investment per offspring coupled with larger egg batch size may reflect an adaptation of the M form to low productivity larval sites as independent evidence suggests.

A Bayesian heterogeneous analysis of variance approach to inferring recent selective sweeps

The distribution of microsatellite allele sizes in populations aids in understanding the genetic diversity of species and the evolutionary history of recent selective sweeps. We propose a heterogeneous Bayesian analysis of variance model for inferring loci involved in recent selective sweeps by analyzing the distribution of allele sizes at multiple loci in multiple populations. Our model is shown to be consistent with a multilocus test statistic, ln RV, proposed for identifying microsatellite loci involved in recent selective sweeps. Our methodology differs in that it accepts original allele size data rather than summary statistics and allows the incorporation of prior knowledge about allele frequencies using a hierarchical prior distribution consisting of log normal and gamma probability distributions. Interesting features of the model are its ability to simultaneously analyze allele size data for any number of populations and to cope with the presence of any number of selected loci. The utility of the method is illustrated by application to two sets of microsatellite allele size data for a group of West African Anopheles gambiae populations. The results are consistent with the suppressed-recombination model of speciation, and additional candidate loci on chromosomes 2 (079 and 175) and 3 (088) are discovered that escaped former analysis.

Genetic contribution to variation in larval development time, adult size, and longevity of starved adults of Anopheles gambiae

The variation in mosquito life-history traits such as adult size has been studied with respect to environmental factors, but the genetic contribution to such variation has received almost no consideration. Using a full-sib design of F1s produced by wild caught Anopheles gambiae (M molecular form) females, we estimated broad-sense heritability of larval developmental time, adult size (based on dry weight and wing length), and longevity of starved adults. These traits were correlated (at the phenotypic level) with each other in females and males (|r(p)|>0.5, P<0.001). Longevity of starved adults increased with adult size, and both traits (adult longevity and size) decreased with longer larval development. Genetic correlations were lower (|r(g)|>0.45, P<0.05) but provided consistent evidence against a trade off between adult size and larval development time predicting that a mosquito can develop faster into a smaller adult or be a larger adult by a longer development. Estimates of heritability of the three traits were moderate to high (range: 0.05-0.48) and statistically significant (P<0.05), indicating substantial genetic contribution to the phenotypic variation in these traits. These results suggest that adaptive differences are likely to be found in these traits between A. gambiae populations.

Impact of insecticide-treated bed nets implementation on the genetic structure of Anopheles arabiensis in an area of irrigated rice fields in the Sahelian region of Cameroon

Variation at 12 microsatellite loci was investigated to assess the impact of the implementation of insecticide-treated bed nets (ITNs) on the genetic structure of Anopheles arabiensis in Simatou, a village surrounded by irrigated rice fields in the Sahelian area of Cameroon. The An. arabiensis population of Simatou was sampled twice before ITN implementation, and twice after. Effective population size estimates (N(e)) were similar across each time point, except for the period closely following ITN introduction where a nonsignificant reduction was recorded. Hence, we believe that ITN implementation resulted in a temporary bottleneck, rapidly followed by a demographic expansion. The genetic diversity of the population was not significantly affected since different genetic parameters (allele number, observed and expected heterozygosities) remained stable. Low estimates of genetic differentiation between the populations from Simatou and Lagdo, separated by 300 km, suggested extensive gene flow among populations of An. arabiensis in the Sahelian region of Cameroon. A decrease in the susceptibility to deltamethrin was observed following ITN introduction, but no kdr mutation was detected and a metabolic resistance mechanism is probably involved. The temporary effect of ITNs on the genetic structure of An. arabiensis population suggests that, to optimize the success of any control programme of this species based on ITNs, the control area should be very large and the programme should be implemented for a long period of time.

Genomic islands of speciation in Anopheles gambiae

The African malaria mosquito, Anopheles gambiae sensu stricto (A. gambiae), provides a unique opportunity to study the evolution of reproductive isolation because it is divided into two sympatric, partially isolated subtaxa known as M form and S form. With the annotated genome of this species now available, high-throughput techniques can be applied to locate and characterize the genomic regions contributing to reproductive isolation. In order to quantify patterns of differentiation within A. gambiae, we hybridized population samples of genomic DNA from each form to Affymetrix GeneChip microarrays. We found that three regions, together encompassing less than 2.8 Mb, are the only locations where the M and S forms are significantly differentiated. Two of these regions are adjacent to centromeres, on Chromosomes 2L and X, and contain 50 and 12 predicted genes, respectively. Sequenced loci in these regions contain fixed differences between forms and no shared polymorphisms, while no fixed differences were found at nearby control loci. The third region, on Chromosome 2R, contains only five predicted genes; fixed differences in this region were also verified by direct sequencing. These “speciation islands” remain differentiated despite considerable gene flow, and are therefore expected to contain the genes responsible for reproductive isolation. Much effort has recently been applied to locating the genes and genetic changes responsible for reproductive isolation between species. Though much can be inferred about speciation by studying taxa that have diverged for millions of years, studying differentiation between taxa that are in the early stages of isolation will lead to a clearer view of the number and size of regions involved in the genetics of speciation. Despite appreciable levels of gene flow between the M and S forms of A. gambiae, we were able to isolate three small regions of differentiation where genes responsible for ecological and behavioral isolation are likely to be located. We expect reproductive isolation to be due to changes at a small number of loci, as these regions together contain only 67 predicted genes. Concentrating future mapping experiments on these regions should reveal the genes responsible for reproductive isolation between forms.

Using DNA microarrays, the authors identify 3 small regions of the genome that differ between two forms of hybridizing mosquitoes; regions that are likely to contain the genes responsible for reproductive isolation.

On the distribution and genetic differentiation of Anopheles gambiae s.s. molecular forms

This paper summarises published and unpublished data on the spatial and temporal distribution, and on the genetic characterisation of molecular forms M and S of Anopheles gambiae s.s. The two forms are characterised by a high level of gene-flow restriction, by a largely overlapping geographical and temporal distribution, and by a low degree of genetic differentiation. Floating paracentric inversions on chromosome-2 are shown to be shared by the two forms, although with very different frequencies of alternative arrangements, confirming that these inversions are most probably involved in ecotypic adaptation, rather than in the building of reproductive barriers. Further studies and tools are needed to throw light on the genetic and biological differentiation of M and S to improve the knowledge of the real composition of the vector system, of its demography, population genetics and dynamics, also in view of the possible consequences on the transmission of human pathogens in sub-Saharan Africa. Preliminary results and perspectives of the use of transposable element insertion sites as markers of genetic differentiation and tools for population genetic studies are discussed.

Larval development of the molecular forms of Anopheles gambiae (Diptera: Culicidae) in different habitats: a transplantation experiment

We compared the development of the molecular forms of Anopheles gambiae s.s. in different larval habitats. First stage larvae (L1s) of wild-caught females were placed into cages in natural habitats of the M form (rice fields) or the S form (puddles/ quarries). Each cage was covered with cloth, allowing exchange of water, solutes, and small particles, including microorganisms, and was seeded with 100 L1s of a single form (M or S) or by a mixture of 50:50 of M and S forms. Emergence success of both forms in puddles and quarries was three-fold higher than in the rice fields. The emergence rate of the S form was higher than that of the M form in both habitats, but the form x habitat interaction was not significant. In temporary larval sites such as puddles, emergence success of the M form was lower in mixed cages than in single form cages, whereas the reverse was true for the S form, suggesting competition between the forms. The median developmental time was not significantly different between forms. Although these findings demonstrate differences between forms, they do not suggest that their spatial segregation is determined by differences in their exploitation of the physical and chemical conditions in these environments. These results should be regarded with caution because small numbers of first stage larvae could pass through the cloth of the cages.

Gene flow between chromosomal forms of the malaria vector Anopheles funestus in Cameroon, Central Africa, and its relevance in malaria fighting

Knowledge of population structure in a major vector species is fundamental to an understanding of malaria epidemiology and becomes crucial in the context of genetic control strategies that are being developed. Despite its epidemiological importance, the major African malaria vector Anopheles funestus has received far less attention than members of the Anopheles gambiae complex. Previous chromosomal data have shown a high degree of structuring within populations from West Africa and have led to the characterization of two chromosomal forms, "Kiribina" and "Folonzo." In Central Africa, few data were available. We thus undertook assessment of genetic structure of An. funestus populations from Cameroon using chromosomal inversions and microsatellite markers. Microsatellite markers revealed no particular departure from panmixia within each local population and a genetic structure consistent with isolation by distance. However, cytogenetic studies demonstrated high levels of chromosomal heterogeneity, both within and between populations. Distribution of chromosomal inversions was not random and a cline of frequency was observed, according to ecotypic conditions. Strong deficiency of heterokaryotypes was found in certain localities in the transition area, indicating a subdivision of An. funestus in chromosomal forms. An. funestus microsatellite genetic markers located within the breakpoints of inversions are not differentiated in populations, whereas in An. gambiae inversions can affect gene flow at marker loci. These results are relevant to strategies for control of malaria by introduction of transgenes into populations of vectors.

Sex-linked differentiation between incipient species of Anopheles gambiae

Emerging species within the primary malaria vector Anopheles gambiae show different ecological preferences and significant prezygotic reproductive isolation. They are defined by fixed sequence differences in X-linked rDNA, but most previous studies have failed to detect large and significant differentiation between these taxa elsewhere in the genome, except at two other loci on the X chromosome near the rDNA locus. Hypothesizing that this pericentromeric region of the X chromosome may be accumulating differences faster than other regions of the genome, we explored the pattern and extent of differentiation between A. gambiae incipient species and a sibling species, A. arabiensis, from Burkina Faso, West Africa, at 17 microsatellite loci spanning the X chromosome. Interspecific differentiation was large and significant across the entire X chromosome. Among A. gambiae incipient species, we found some of the highest levels of differentiation recorded in a large region including eight independent loci near the centromere of the X chromosome. Outside of this region, no significant differentiation was detected. This pattern suggests that selection is playing a role in the emergence of A. gambiae incipient species. This process, associated with efficient exploitation of anthropogenic modifications to the environment, has public health implications as it fosters the spread of malaria transmission both spatially and temporally.

Multilevel analyses of genetic differentiation in Anopheles gambiae s.s. reveal patterns of gene flow important for malaria-fighting mosquito projects

Malaria control projects based on the introduction and spread of transgenes into mosquito populations depend on the extent of isolation between those populations. On the basis of the distribution of paracentric inversions, Anopheles gambiae has been subdivided into five subspecific chromosomal forms. Estimating gene flow between and within these forms of An. gambiae presents a number of challenges. We compared patterns of genetic divergence (F(ST)) between sympatric populations of the Bamako and Mopti forms at five sites. We used microsatellite loci within the j inversion on chromosome 2, which is fixed in the Bamako form but absent in the Mopti form, and microsatellites on chromosome 3, a region void of inversions. Estimates of genetic diversity and F(ST)'s suggest genetic exchanges between forms for the third chromosome but little for the j inversion. These results suggest a role for the inversion in speciation. Extensive gene flow within forms among sites resulted in populations clustering according to form despite substantial gene flow between forms. These patterns underscore the low levels of current gene flow between chromosomal forms in this area of sympatry. Introducing refractoriness genes in areas of the genome void of inversions may facilitate their spread within forms but their passage between forms may prove more difficult than previously thought.

Infection patterns of o'nyong nyong virus in the malaria-transmitting mosquito, Anopheles gambiae

Arthropod-borne alphaviruses transmitted by mosquitoes almost exclusively use culicines; however, the alphavirus o'nyong-nyong (ONNV) has the unusual characteristic of being transmitted primarily by anopheline mosquitoes. This unusual attribute makes ONNV a valuable tool in the characterization of mosquito determinants of infection as well as a useful expression system in Anopheles species. We developed a series of recombinant alphaviruses, based upon the genome of ONNV, designed for the expression of heterologous genes. The backbone genome is a full-length infectious cDNA clone of ONNV from which wild-type virus can be rescued. Additional constructs are variants of the primary clone and contain the complete genome plus a duplicated subgenomic promoter element with a multiple cloning site for insertion of heterologous genes. We inserted a green fluorescent protein (GFP) gene downstream of this promoter and used it to characterize infection and dissemination patterns of ONNV within An. gambiae mosquitoes. These experiments allowed us to identify atypical sites of initial infection and dissemination patterns in this mosquito species not frequently observed in comparable culicine infections. The utility of these ONNVs for studies in anopheline mosquitoes includes the potential for identification of vector infection determinants and to serve as tools for antimalaria studies. Viruses that can express a heterologous gene in a vector and rapidly and efficiently infect numerous tissues in An. gambiae mosquitoes will be a valuable asset in parasite-mosquito interaction and interference research.

Revisiting the role of introgression vs shared ancestral polymorphisms as key processes shaping genetic diversity in the recently separated sibling species of the Anopheles gambiae complex

The role of interspecific hybridisation in the evolution of pest species is poorly understood. In mosquito disease vectors this is of particular importance due to the evolution of insecticide resistance and the proposed release of transgenic strains that are refractory to the malaria parasite. In this study, we apply population genetic methods in a novel manner to determine whether mitochondrial DNA sequences have introgressed between the closely related African malaria vectors Anopheles gambiae and A. arabiensis. Our results suggest that speciation was geologically recent and ancestral haplotypes at the ND5 locus are retained in both species. In addition, comparing haplotype frequencies in allopatric and sympatric populations, suggest locale specific unidirectional introgression of mitochondria from A. arabiensis into A. gambiae.

Population structure of the malaria vector Anopheles funestus in Senegal based on microsatellite and cytogenetic data

The study of chromosomal inversions distribution within natural Anopheles funestus populations from West Africa revealed high levels of genetic structuring. In Burkina Faso, this was interpreted as evidence for incipient speciation, and two chromosomal forms were described, namely 'Folonzo' and 'Kiribina'. Assignation of field collected specimens to one chromosomal form depends upon application of an algorithm based on chromosomal inversions. We assessed relevance and applicability of this algorithm on An. funestus populations from Senegal, where both forms occur. Furthermore, we estimated the level of genetic differentiation between populations using microsatellite loci spread over the whole genome. Significant genetic differentiation was revealed between geographical populations of An. funestus, and the pattern observed suggested isolation by distance. Chromosomal heterogeneity was not detected by microsatellite markers. Thus, although incipient speciation could not be ruled out by our data, our results suggest that differential environmental selection pressure acting on inversions should be considered a major factor in shaping their distribution in wild An. funestus populations.

Natural hybridization and the evolution of domesticated, pest and disease organisms

The role of natural hybridization in the evolutionary history of numerous species is well recognized. The impact of introgressive hybridization and hybrid speciation has been documented especially in plant and animal assemblages. However, there remain certain areas of investigation for which natural hybridization and its consequences remain under-studied and under-appreciated. One such area involves the evolution of organisms that positively or negatively affect human populations. In this review, I highlight exemplars of how natural hybridization has contributed to the evolution of (i) domesticated plants and animals; (ii) pests; (iii) human disease vectors; and (iv) human pathogens. I focus on the effects from genetic exchange that may lead to the acquisition of novel phenotypes and thus increase the beneficial or detrimental (to human populations) aspects of the various taxa.

Microsatellite DNA polymorphism and heterozygosity in the malaria vector mosquito Anopheles funestus (Diptera: Culicidae) in east and southern Africa

There has been an increase in malaria cases in southern African countries in recent years due to the presence of populations of Anopheles funestus that are resistant to the pyrethroid class of insecticides. Since A. funestus is one of the major African malaria vectors, knowledge of its genetic structure will benefit control strategies, such as the management of insecticide resistance, by allowing predictions to be made of possible spread of the resistance. This study uses microsatellite DNA markers to analyze samples from five countries in east (Kenya and Uganda), central (Malawi) and southern (South Africa and Mozambique) Africa. There were deviations from Hardy-Weinberg expectations for some loci in all population samples but this was probably due to the presence of null alleles. High levels of genetic diversity were observed (mean alleles per locus = 6.5-10; unbiased H=0.23-0.89). Low differentiation was observed between Kenya and Uganda (average F(ST)=0.002, R(ST)=0.0001) and between Mozambique and South Africa (F(ST)=0.0004, R(ST)=0.02), contrary to high differentiation among the central and southern Africa samples (average F(ST)=0.023, R(ST)=0.027). High differentiation was measured across the region (mean F(ST)=0.04, R(ST)=0.08), east versus Malawi (F(ST)=0.067, R(ST)=0.089) or southern Africa populations (F(ST)=0.068, R(ST)=0.15). A test of isolation by distance along the east-central-south transect gave evidence (R(2)=0.50, P<0.001) that geographic distance limits gene flow in A. funestus.

Spatial and temporal variation in kinship among Anopheles gambiae (Diptera: Culicidae) mosquitoes

Genetic relatedness (kinship) among Anopheles gambiae Giles female mosquitoes was assessed using microsatellite loci in five locations across Africa and in nine samples taken between 1994 and 1999 in western Kenya. We assessed variation among samples in kinship as well as the effect of distance on kinship. Relatedness within populations was low, and differences among samples taken at various times from one locale and from different locales were minimal. Mosquitoes collected from the same compound were slightly more closely related than those collected from different compounds. Our results suggest that newly emerged female siblings move relatively short distances into a few nearby compounds for blood feeding, but that they lay eggs in a more distant location. Kinship decreased nonlinearly with increasing distance. The strongest relationship between kinship and distance was observed for mosquitoes collected 0-3 km apart (-0.014/km, P < 0.001). The effect of distance decreased with increasing distance between mosquitoes; at 7 km or more, the kinship/distance slope approached zero and the intercept became negative, suggesting that beyond this range kinship does not decline with distance. This distance may thus represent the upper limit of the diameter of the basic reproductive unit. Nevertheless, the effect of distance on kinship is weak, reflecting extensive dispersal. Because females mate within days after emergence from larval habitats, where the likelihood of mating with a sibling is presumably highest, we propose a slight inbreeding effect.

Population substructures in the soil invertebrate Orchesella cincta, as revealed by microsatellite and TE-AFLP markers

Microsatellite and three enzyme-amplified fragment length polymorphism (TE-AFLP) DNA markers were used to describe the population genetic structure in the soil dwelling collembolan Orchesella cincta (L.). Two forests were sampled according to a three-level nested hierarchical design, with fixed distances among samples within a parcel and among parcels within a forest. The largest component of variation was found at the smallest scale, within parcels (77-97%), while the smallest component of variation was found between forests. The two different methods to study population structure indicated a similar allocation of variance. Population genetic substructuring was revealed between samples on a scale of 50 m; the degree of substructuring however, varied between parcels and forests. One forest showed a high degree of structure as revealed by microsatellites, while another showed a low degree of structure. A significant deviation from random-mating (average FIS = 0.23) over the two forests was detected. Two of 18 samples showed a difference in population genetic structure between males and females. We discuss the fact that the population genetic structure of O. cincta is significantly affected by long-range dispersal, even though it is a small and wingless insect. This interpretation is supported by observations on tree-climbing behaviour in this species that may facilitate air dispersal. As a consequence, the assumption that migration a priori may be neglected in demographic analysis of O. cincta is incorrect.

Issues in public health entomology

Public health entomology focuses on the population biology of vector-borne infections, seeking to understand how such pathogens perpetuate over time and attempting to devise methods for reducing the burden that they impose on human health. As public health entomology passes its centennial, a series of pervasive research themes and spirited debates characterize the discipline, many reflecting a tension between field and laboratory research. In particular, institutional support for population-based research and training programs has fallen behind that for those using modern lab-based approaches. Discussion of modes of intervention against vector-borne infections (such as deployment of genetically modified vectors, the role of DDT in malaria control, host-targeted acaricides for Lyme disease risk reduction, and truck-mounted aerosol spraying against West Nile virus transmission) illustrates the discipline's need for strengthening population-based research programs. Even with the advent of molecular methods for describing population structure, the basis for anophelism without malaria (or its eastern North American counterpart, ixodism without borreliosis) remains elusive. Such methods have not yet been extensively used to examine the phylogeography and geographical origins of zoonoses such as Lyme disease. Basic ecological questions remain poorly explored: What regulates vector populations? How may mixtures of pathogens be maintained by a single vector? What factors might limit the invasion of Asian mosquitoes into North American sites? Putative effects of "global warming" remain speculative given our relative inability to answer such questions. Finally, policy and administrative issues such as the "no-nits" dictum in American schools, the Roll Back Malaria program, and legal liability for risk due to vector-borne infections serve to demonstrate further the nature of the crossroads that the discipline of public health entomology faces at the start of the 21st Century.

KDR mutation, a genetic marker to assess events of introgression between the molecular M and S forms of Anopheles gambiae (Diptera: Culicidae) in the tropical savannah area of West Africa

A sodium channel 'kdr'-type mutation was identified in the M form of Anopheles gambiae from Burkina Faso in the tropical savannah area belt. The molecular M form of An. gambiae is found at high frequencies in the flooded rice cultivation area of Kou Valley, where the insecticide selection pressure is limited. The spread of the mutation in the M population is an ongoing process, as it increased from a frequency of 0.006 in 1999 to 0.02 in 2000. The S molecular form occurs in sympatry in our study village, with the M form at a relatively low frequency. The common 'kdr' mutation was previously detected in this area in the S form, and has probably invaded the M population through genetic introgression. This impacts on the question of actual levels of gene flow between the two molecular forms in tropical savannah areas. A hybrid M/S individual was identified during the course of this study, which was homozygous for the 'kdr' mutation. Pyrethroid resistant An. gambiae were caught in October and November, which is the time of year that the molecular S form migrates into this area as rain-fed breeding sites in the cotton fields dry out.

Genetic markers for study of the anopheline vectors of human malaria

Human malaria is truly a disease of global proportions and is one of the most broadly distributed vector-borne infections. Anopheline mosquitoes are the exclusive vectors of human malaria. A handful of species predominate as the most notorious malaria vectors, but the species and forms involved in the transmission of human malaria world-wide are incredibly diverse. Many of the anophelines that vector malaria exist as members of species complexes that often contain vector and non-vector species. Additionally, single anopheline species often exhibit significant heterogeneity across the species' range. This phenotypic and genotypic plasticity exacerbates the difficulties in identification of vector populations and implementation of effective surveillance and control strategies. Polytene chromosome investigations were among the first to provide researchers with tangible genetic markers that could be used to differentiate between what are now recognised as species and chromosomal forms of anopheline mosquitoes. The advent of the polymerase chain reaction gave access to the molecular genetics of genomes and the techniques that followed have facilitated investigation of the genetics of individual specimens or population size samples. The variety and number of genetic markers available for the study of malaria vectors has literally exploded in the last 10 years. Markers have expanded from the 'traditional tools' to include a vast array of molecular markers. Contemporary markers range from what are now referred to as 'classical genetic markers' to methods used to detect and identify single nucleotide polymorphisms and finally to highly polymorphic markers. One of the greatest advantages of this wide variety of genetic markers is that researchers may choose to utilise any combination of markers or techniques to address multifaceted questions relating to malaria transmission. These molecular markers have proven useful in a wide variety of applications including molecular taxonomy, evolutionary systematics, population genetics, genetic mapping, and investigation of defined phenotypes.

Genetic differentiation in the African malaria vector, Anopheles gambiae s.s., and the problem of taxonomic status

Of the seven recognized species of the Anopheles gambiae complex, A. gambiae s.s. is the most widespread and most important vector of malaria. It is becoming clear that, in parts of West Africa, this nominal species is not a single panmictic unit. We found that the internal transcribed spacer (ITS) of the X-linked rDNA has two distinct sequences with three fixed nucleotide differences; we detected no heterozygotes at these three sites, even in areas of sympatry of the two ITS types. The intergenic spacer (IGS) of this region also displays two distinct sequences that are in almost complete linkage disequilibrium with the distinct ITS alleles. We have designated these two types as S/type I and M/type II. These rDNA types correspond at least partly to the previously recognized chromosomal forms. Here we expand the geographic range of sampling to 251 individuals from 38 populations. Outside of West Africa, a single rDNA type, S/type I, corresponds to the Savanna chromosomal form. In West Africa, both types are often found in a single local sample. To understand if these findings might be due to unusual behavior of the rDNA region, we sequenced the same region for 46 A. arabiensis, a sympatric sibling species. No such distinct discontinuity was observed for this species. Autosomal inversions in one chromosome arm (2R), an insecticide resistance gene on 2L, and this single X-linked region indicate at least two genetically differentiated subpopulations of A. gambiae. Yet, rather extensive studies of other regions of the genome have failed to reveal genetic discontinuity. Evidently, incomplete genetic isolation exists within this single nominal species.

Molecular systematics of Anopheles: from subgenera to subpopulations

The century-old discovery of the role of Anopheles in human malaria transmission precipitated intense study of this genus at the alpha taxonomy level, but until recently little attention was focused on the systematics of this group. The application of molecular approaches to systematic problems ranging from subgeneric relationships to relationships at and below the species level is helping to address questions such as anopheline phylogenetics and biogeography, the nature of species boundaries, and the forces that have structured genetic variation within species. Current knowledge in these areas is reviewed, with an emphasis on the Anopheles gambiae model. The recent publication of the genome of this anopheline mosquito will have a profound impact on inquiries at all taxonomic levels, supplying better tools for estimating phylogeny and population structure in the short term, and ultimately allowing the identification of genes and/or regulatory networks underlying ecological differentiation, speciation, and vectorial capacity.

Identification and characterization of microsatellite markers in the Chagas disease vector Triatoma dimidiata

Triatoma dimidiata, one of the major vectors of Chagas disease in Central America, is found in both domestic and peri-domestic habitats. Questions concerning population boundaries, infestation rates, insecticide resistance, and geographic dispersal of triatomine bugs persist and may be resolved using genetic markers such as microsatellites. Microsatellites are short tandem repeats found dispersed throughout a genome and can be useful for genotypic identification. We developed a plasmid library from the genomic DNA isolated from a single T. dimidiata adult collected in Guatemala. Ten thousand clones were screened using a probe consisting of nine microsatellite oligonucleotides. Eight loci appear polymorphic among populations found in Guatemala, Honduras, and Mexico, and thus are potentially useful for population genetic applications.

Microsatellite markers for population genetic studies in Aedes aegypti (Diptera: Culicidae) from Côte d'Ivoire: evidence for a microgeographic genetic differentiation of mosquitoes from Bouaké

In West Africa, Aedes aegypti (Diptera: Culicidae) (Linnaeus, C., 1762. Zweyter Theil, enhalt Beschreibungen veschiedener wichtiger Naturalien. In: Hasselquist, F. (Ed.), Reise nach Palastina in den Jahren von 1749 bis 1752, Rostock, Germany, pp. 267-606) represents the principal vector of yellow fever. This study reports the use of microsatellite markers to characterise various A. aegypti populations from Côte d'Ivoire according to a north-south transect, and to perform a temporal genetic survey of the mosquitoes. Three microsatellite loci were used to analyse individuals from four different places: Kabolo, Bouaké, and two different districts of Abidjan. We found that the four populations are genetically distinct except the two Abidjan populations. In the Bouaké population, the coexistence of two cryptic species, not morphologically distinguishable, seems to account for the extensive heterozygote deficiency observed. Comparison of mosquitoes from Bouaké 1 year apart indicated that a dramatic change occurred in the structuring of this population over time. Taken together these results indicate that microsatellite markers could be useful for identifying various populations of A. aegypti on a microgeographic scale and to assess for temporal variation within mosquito populations.

Evidence for genetic differentiation between the molecular forms M and S within the Forest chromosomal form of Anopheles gambiae in an area of sympatry

We studied genetic variation at ten microsatellite DNA loci in Anopheles gambiae populations from the Forest chromosomal form collected in four villages in Cameroon (Central Africa). Both recently described M and S molecular forms occur in sympatry in this area. Geographic differentiation within form was low (Fst < 0.017) despite geographical distance between collection sites ranging from 35 to 350 km. However, higher (Fst > 0.035) and statistically significant levels of genetic differentiation were observed between forms, being the highest between sympatric M and S populations collected within the same village. Results were consistent across all loci spread throughout the genome, therefore reflecting a genome-wide pattern. Considering previous findings of strong assortative mating within forms and general lack of hybrids in areas of sympatry, we propose that there is now sufficient direct and indirect evidence to consider both M and S molecular forms of An. gambiae as distinct species that have probably speciated recently.

A comparative genomic analysis of two distant diptera, the fruit fly, Drosophila melanogaster, and the malaria mosquito, Anopheles gambiae

Genome evolution entails changes in the DNA sequence of genes and intergenic regions, changes in gene numbers, and also changes in gene order along the chromosomes. Genes are reshuffled by chromosomal rearrangements such as deletions/insertions, inversions, translocations, and transpositions. Here we report a comparative study of genome organization in the main African malaria vector, Anopheles gambiae, relative to the recently determined sequence of the Drosophila melanogaster genome. The ancestral lines of these two dipteran insects are thought to have separated approximately 250 Myr, a long period that makes this genome comparison especially interesting. Sequence comparisons have identified 113 pairs of putative orthologs of the two species. Chromosomal mapping of orthologous genes reveals that each polytene chromosome arm has a homolog in the other species. Between 41% and 73% of the known orthologous genes remain linked in the respective homologous chromosomal arms, with the remainder translocated to various nonhomologous arms. Within homologous arms, gene order is extensively reshuffled, but a limited degree of conserved local synteny (microsynteny) can be recognized.

Spatial and habitat distribution of Anopheles gambiae and Anopheles arabiensis (Diptera: Culicidae) in Banambani village, Mali

We studied the larval distribution and composition of Anopheles arabiensis Patton, An. gambiae s.s. Giles, and its forms, among local habitats; and their association with the adults between these habitats in Banambani village, Mali during the mid-rainy seasons of 1997-1999. For species and form identification we used polymerase chain reaction (PCR) and PCR-restriction fragment-length polymorphism (RFLP). Differences among species in the distribution of larvae were observed in 1998, but not in 1997 or 1999, although they were on the borderline of statistical significance. Differences among the M and S molecular forms were statistically significant in 1999 when rainfall was high, but not in the two prior, drier sampling periods. Combining all information into the Fisher multiple comparisons test, there were statistically significant differences between species and molecular forms during the 3-yr study period. Hybrid larvae between the M and S forms were observed (0.57%), the first such observation to our knowledge. In spite of differences among larval distribution, no differences of adult species composition were observed among habitats. Factors that influence the distributions of An. gambiae larval populations are discussed.

Genetic differentiation of the malaria vector Anopheles gambiae across Nigeria suggests that selection limits gene flow

Gene flow was investigated in Anopheles gambiae from eight localities that span the ecological zones of Nigeria (arid savanna zones in the north gradually turn into humid forest zones in the south). Genetic differentiation was measured over 10 microsatellite loci and, to determine any effects of selection, five loci were located within chromosome inversions and the other five were outside inversions. Over all loci, the largest estimates of differentiation were in comparisons between localities in the savanna vs. forest zones (range FST 0.024-0.087, Nm 2.6-10.1; RST 0.014-0.100, Nm 2.2-16.4). However, three loci located within inversions on chromosome II, whose frequencies varied clinically from north to south, were responsible for virtually all of the differentiation. When the three loci were removed, genetic distances across the remaining seven loci were markedly reduced even between localities in the forest and savanna zones (range FST 0.001-0.019, Nm 12.7-226.1) or no longer significant (P > 0.05) in the case of RST. Although tests of isolation by distance gave seemingly equivocal results, geographical distance does not appear to limit gene flow. These observations suggest that gene flow is extensive across the country but that selection on genes located within some inversions on chromosome II counters the homogenizing effects of gene flow.

Population genetic structure of the malaria mosquito Anopheles arabiensis across Nigeria suggests range expansion

Ten microsatellite loci, four located within and six outside chromosome inversions, were employed to study the genetic structure of Anopheles arabiensis across the ecological zones of Nigeria (arid savannah in the north gradually turns into humid forest in the south). Regardless of location within or outside inversions, genetic variability at all loci was characterized by a reduction in both the number of alleles per locus and heterozygosity from savannah to forest. Across all loci, all but one allele in the forest also occurred in the savannah, whereas at least 78 alleles in the savannah were missing in the forest. Genetic differentiation increased with geographical distance; consequently, genetic distances between zones exceeded those within zones. The largest genetic distances were between localities at the extremes of the transect (range F(ST) = 0.196-0.258 and R(ST) = 0.183-0.468) and were as large as those between A. arabiensis and Anopheles gambiae s.s. Gene flow across the country was very low, so that Nm between the extremes of the transect was < 1. These data suggest that A. arabiensis has extended its range from the savannah into the forest during which it experienced a reduction in effective population size due to sequential founder effects. Gene flow post range expansion appears too restricted by geographical distance to homogenize the gene pool of A. arabiensis across Nigeria.

When genetic distance matters: measuring genetic differentiation at microsatellite loci in whole-genome scans of recent and incipient mosquito species

Genetic distance measurements are an important tool to differentiate field populations of disease vectors such as the mosquito vectors of malaria. Here, we have measured the genetic differentiation between Anopheles arabiensis and Anopheles gambiae, as well as between proposed emerging species of the latter taxon, in whole genome scans by using 23-25 microsatellite loci. In doing so, we have reviewed and evaluated the advantages and disadvantages of standard parameters of genetic distance, F(ST), R(ST), (delta mu)(2), and D. Further, we have introduced new parameters, D' and D(K), which have well defined statistical significance tests and complement the standard parameters to advantage. D' is a modification of D, whereas D(K) is a measure of covariance based on Pearson's correlation coefficient. We find that A. gambiae and A. arabiensis are closely related at most autosomal loci but appear to be distantly related on the basis of X-linked chromosomal loci within the chromosomal Xag inversion. The M and S molecular forms of A. gambiae are practically indistinguishable but differ significantly at two microsatellite loci from the proximal region of the X, outside the Xag inversion. At one of these loci, both M and S molecular forms differ significantly from A. arabiensis, but remarkably, at the other locus, A. arabiensis is indistinguishable from the M molecular form of A. gambiae. These data support the recent proposal of genetically differentiated M and S molecular forms of A. gambiae.

Linear and spatial organization of polytene chromosomes of the African malaria mosquito Anopheles funestus

Anopheles funestus Giles is one of the major malaria vectors in Africa, but little is known about its genetics. Lack of a cytogenetic map characterized by regions has hindered the progress of genetic research with this important species. This study developed a cytogenetic map of An. funestus using ovarian nurse cell polytene chromosomes. We demonstrate an important application with the cytogenetic map for characterizing various chromosomal inversions for specimens collected from coastal Kenya. The linear and spatial organization of An. funestus polytene chromosomes was compared with the best-studied malaria mosquito, An. gambiae Giles. Comparisons of chromosome morphology between the two species have revealed that the most extensive chromosomal rearrangement occurs in pericentromeric heterochromatin of autosomes. Differences in pericentromeric heterochromatin types correlate with nuclear organization differences between An. funestus and An. gambiae. Attachments of chromosomes to the nuclear envelope strongly depend on the presence of diffusive beta-heterochromatin. Thus, An. funestus and An. gambiae exhibit species-specific characteristics in chromosome-linear and -spatial organizations.

Evidence for recent population expansion in the evolutionary history of the malaria vectors Anopheles arabiensis and Anopheles gambiae

Gene flow in malaria vectors is usually estimated based on differentiation indices (e.g., F(ST)) in order to predict the contemporary spread of genes such as those conferring resistance to insecticides. This approach is reliant on a number of assumptions, the most crucial, and the one most likely to be violated in these species, being mutation-migration-drift equilibrium. Tests of this assumption for the African malaria vectors Anopheles gambiae and Anopheles arabiensis are the focus of this study. We analyzed variation at 18 microsatellite loci and the ND5 region of the mitochondrial genome in two populations of each species. Equilibrium was rejected by six of eight tests for the A. gambiae population from western Kenya and by three tests in eastern Kenya. In western Kenya, all departures from equilibrium were consistent with a recent population expansion, but in eastern Kenya, there were traces of a recent expansion and a bottleneck. Equilibrium was also rejected by two of the eight tests for both A. arabiensis populations; the departure from equilibrium was consistent with an expansion. These multiple-locus tests detected a genomewide effect and therefore a demographic event rather than a locus-specific effect, as would be caused by selection. Disequilibrium due to a recent expansion in these species implies that rates of gene flow, as inferred from differentiation indices, are overestimates as they include a historical component. We argue that the same effect applies to the majority of pest species due to the correlation of their demography with that of humans.

DNA analysis of transferred sperm reveals significant levels of gene flow between molecular forms of Anopheles gambiae

Anopheles gambiae populations in west Africa are complex, being composed of multiple, sympatric subpopulations. Recent studies have failed to reveal significant genetic differences among subpopulations, stimulating a debate regarding the levels of gene flow among them. The observed homogeneity may be the consequence of substantial contemporary gene flow or it may be that reproductive isolation is complete, but too recent for the accumulation of significant levels of genic divergence. Here, we report the results of a study estimating contemporary levels of gene flow between An. gambiae subpopulations by analysing females and transferred sperm removed from their reproductive systems. A total of 251 female and associated sperm extracts was analysed from a single site in Mali. Two molecular forms of An. gambiae, the M- and S-forms, occurred in sympatry at this site. Overall, we found very strong positive assortative mating within forms, however, we did observe significant hybridization between forms. In the M subpopulation 2/195 females (1.03%) contained sperm from S-form males and in 55 S-form females we found one female containing M-form sperm (1.82%). We also identified a mated M xS hybrid adult female. From mating frequencies, we estimate the Nem between the M- and S-form at 16.8, and from the adult hybrid frequency at 5.6. These values are consistent with our earlier estimate, based on FST for 21 microsatellite loci in which Nem = 5.8. We conclude that the general lack of genetic divergence between the M and S subpopulations of An. gambiae can be explained entirely by contemporary gene flow.

Microsatellite loci are not abundant in all arthropod genomes: analyses in the hard tick, Ixodes scapularis and the yellow fever mosquito, Aedes aegypti

Plasmid libraries enriched for microsatellites were generated in the tick, Ixodes scapularis and in the mosquito Aedes aegypti. Libraries were enriched for genomic DNA containing (AC)n, (AG)n, (ATG)n, (CAG)n, (TAG)n, (AAT)n, (CTGY)n or (GATA)n motifs. Clones containing each motif were sequenced in both species for PCR primer design. In I. scapularis, most primers amplified a single locus and alleles varied in the number of microsatellite repeats and segregated as codominant markers. In contrast (AC)n, (TAG)n and (GATA)n microsatellite loci extracted from Ae. aegypti appeared to be members of multigene families. A primer pair designed to amplify a particular TAG locus instead amplified many independently segregating loci, some of which did not contain TAG microsatellites. Alleles at the TAG loci segregated as dominant markers and there was limited evidence for length variation among alleles. These results suggest that microsatellite loci are not universally abundant in arthropod genomes nor do alleles always segregate as codominant markers.

Microsatellite DNA polymorphism and heterozygosity among field and laboratory populations of Anopheles gambiae ss (Diptera: Culicidae)

We compared microsatellite polymorphism at nine loci located on chromosome 3 among two colonies and a field population of Anopheles gambiae sensu stricto Giles mosquitoes. Numbers of microsatellite alleles observed at each locus and mean heterozygosities were drastically reduced among laboratory colonies. Genetic analysis of the field population used in this study revealed an unprecedented frequency of rare alleles (<0.05). In contrast, colony samples revealed large numbers of alleles with frequencies >0.50. Partitioning of field data to assess the impact of rare alleles, null alleles, and sample size on estimates of mean heterozygosity revealed the plasticity of this measurement and suggests that heterozygosity may be reliably estimated from relatively small collections using microsatellites.

Gene flow among populations of the malaria vector, Anopheles gambiae, in Mali, West Africa

The population structure of the Anopheles gambiae complex is unusual, with several sibling species often occupying a single area and, in one of these species, An. gambiae sensu stricto, as many as three "chromosomal forms" occurring together. The chromosomal forms are thought to be intermediate between populations and species, distinguishable by patterns of chromosome gene arrangements. The extent of reproductive isolation among these forms has been debated. To better characterize this structure we measured effective population size, N(e), and migration rates, m, or their product by both direct and indirect means. Gene flow among villages within each chromosomal form was found to be large (N(e)m > 40), was intermediate between chromosomal forms (N(e)m approximately 3-30), and was low between species (N(e)m approximately 0.17-1.3). A recently developed means for distinguishing among certain of the forms using PCR indicated rates of gene flow consistent with those observed using the other genetic markers.

Patterns of DNA sequence variation in chromosomally recognized taxa of Anopheles gambiae: evidence from rDNA and single-copy loci

Patterns of DNA sequence variation in the ribosomal DNA (rDNA) second internal transcribed spacer (ITS2) and five unlinked single-copy nuclear loci were examined for evidence of reproductive isolation among four chromosomally recognized taxa of Anopheles gambiae from West Africa: Savanna, Bamako, Mopti and Forest, as well as sibling species An. arabiensis and An. merus. Included among the single-copy loci were three sequence-tagged random amplified polymorphic DNA (RAPD) loci, two of which (R15 and R37) had been reported as discriminating between Mopti and other chromosomal forms. Each of the five single-copy sequences were highly polymorphic in most samples. However, the R15 and R37 loci had no diagnostic value, and therefore are not recommended as tools in recognition of field-collected An. gambiae chromosomal forms. Although pairwise comparisons between species generally revealed significant levels of differentiation at all five loci, variation was not partitioned by chromosomal form within An. gambiae at any single-copy locus examined. The few exceptions to these trends appear related to a location either inside or nearby chromosomal inversions. At the tryptophan oxygenase locus inside inversion 2Rb, variation was structured only by inversion orientation and not by taxonomic designation even between An. gambiae and An. arabiensis, providing the first molecular evidence that the 2Rb inversion was transferred between species by introgressive hybridization. By contrast, the rDNA showed fixed differences between species and a difference diagnostic for Mopti, consistent with effective, if not complete, reproductive isolation. The apparent disagreement between the data from this locus and multiple single-copy loci within An. gambiae may be explained by the much lower effective population size of rDNA, owing to concerted evolution, which confers increased sensitivity at much shorter divergence times. Taken together with the accompanying reports by della Torre et al. (2001), Favia et al. (2001) and Gentile et al. (2001), our data suggest that neutral molecular markers may not have the sensitivity required to detect isolation between these recently established taxa.

Attempts to molecularly distinguish cryptic taxa in Anopheles gambiae s.s

Analyses of inversions in polytene chromosomes indicate that, in West Africa, Anopheles gambiae (sensu stricto) may be a complex of more than a single taxonomic unit, and these units have been called chromosomal forms. In order to determine whether this genetic discontinuity extends to the rest of the genome, as would be expected if reproductive isolation exists, we have sequenced several regions of both the nuclear and mitochondrial genomes. With one exception, we were unable to identify any nucleotide sites that differentiate the chromosomal forms. The exception was the internal transcribed spacer (ITS) of the ribosomal DNA (rDNA). Three sites in this region distinguish Mopti chromosomal form from Savanna and Bamako in Mali and Burkina Faso. However, outside these two countries, the association between chromosomal form and rDNA type does not always hold. Together with the variants in the rDNA intergenic spacer (IGS) described in the accompanying papers (della Torre et al., 2001; Favia et al., 2001), we can recognize two major types of rDNA, Type I and Type II (corresponding to molecular forms S and M in della Torre et al., 2001). Type I is widespread in West Africa and is the only type found outside of West Africa (i.e. Tanzania and Madagascar). Type II is confined to West Africa. We were unable to detect any heterozygosity for the ITS types even in five collections containing both types. A sample from the island of São Tomé could not be classified into either Type I or Type II as the rDNA had characteristics of both. In general, our results confirm that An. gambiae is not a single pan-mictic unit, but exactly how to define any new taxa remains problematic. Finally, we have found minor variants of the major rDNA types fixed in local populations; contrary to most previous studies, this suggests restricted gene flow among populations of this species.