Genetic structure in both mtDNA and microsatellites confirmed the presence of two distinct lineages of G. f. fuscipes
in Uganda 
. This genetic differentiation, if associated with differences in physiology, behavior, and/or symbiont composition affecting vector competence 
, could have important implications for the epidemiology of trypanosomiasis, as well as vector control. However, the deep structure of G. f. fuscipes
in Uganda appears to reflect an ancient event that divided northern and southern lineages, and in light of evidence for modern gene flow, is likely to be impermanent.
The isolation of northern and southern lineages, which appear to have diverged on the order of several hundreds of thousands of years before present, may have been facilitated by habitat fragmentation during extreme drought cycles in East Africa that ended only 70,000 years ago 
. Following the Last Glacial Maximum approximately 20,000 years ago 
, a period when Lake Victoria may have been totally dry 
, increasingly moist conditions would have favored the expansion of the riverine species G. f. fuscipes
from dry period refugia. Given the perfect latitudinal partitioning of mitochondrial groups, the two divergent lineages likely expanded into their present distribution via distinct pathways. These paths may have split to the north and south of the Blue and Rwenzori mountain ranges, both of which form a barrier to direct colonization from the west. As evidenced by the distribution of mtDNA haplotypes, these two groups currently meet along a zone of contact extending from Bunghazi (BN) in eastern Uganda to Masindi (MS) in western Uganda. This zone of contact falls to the south of Lake Kyoga, which was formerly proposed as a barrier to gene flow between northern and southern flies 
. Given the absence of obvious alternative geographical barriers to gene flow and the fairly narrow zone of contact, we speculate that northern and southern flies have come into contact only recently.
At present, evidence for admixture between the northern and southern flies is not uniform along the zone of contact. In Bunghazi (BN), we did not detect any deviation from HWE and almost all flies exhibited a mix of southern and northern ancestry, irrespective of their maternal lineage. In this portion of the contact zone, therefore, no barriers to mating are evident between northern and southern lineages. Given the hybrid dysgenesis observed among cryptic taxa within G. palpalis palpalis 
, this observation warrants experimental confirmation. Elsewhere in the contact zone, flies exhibited genetic signatures consistent with the introgression of a northern mtDNA haplotype into a nuclear background that allied almost exclusively with either southeastern (JN) or western (MS) flies. This scenario is consistent with rare female-biased dispersal into the contact zone from the north and chance amplification of that northern haplotype by drift in a small effective female population. Wolbachia
-induced mating incompatibility could also have played a role in driving the northern lineage to relatively high frequency, a possibility currently being investigated. In Junda (JN) and Masindi (MS), the homogeneous nuclear background did not support admixture of northern and southern flies. However, just north of the contact zone, flies captured along the Nile River at Murchison Falls (MF) and along Lake Kyoga at Bugondo (BG) exhibited strong signals of mixed ancestry, confirming our observation in Bunghazi that gene flow between northern and southern lineages is possible and ongoing.
Given the evidence of admixture highlighted above, the genetic differentiation between northern and southern lineages may simply represent a signature of historical allopatric fragmentation that has little bearing on the current movement of genes. However, Bayesian assignment probabilities (), which provide an estimate of an individual's recent ancestry, suggested that the directionality of gene flow is constrained, both across the zone of contact and on a wider scale. Importantly, individuals to the south of the zone of contact in southeastern Uganda (blue) exhibited negligible recent shared ancestry with either flies just to the north, or even with flies from western Uganda, some of which possessed identical mtDNA lineages. This is indicative of little modern gene flow from the north or west into the southeast and lends support for PATTEC's choice of the Lake Victoria region as a suitably isolated target for tsetse intervention 
. In contrast, individuals in the north and west tended to exhibit traces of ancestry from populations lying to the south or southeast, suggestive of a north or northwestern bias to gene flow. We hypothesize that this bias in direction may be linked to passive dispersal of pupae via seasonally flooded river systems, such as the Nile, Semliki and Achwa, all of which follow a north or northwesterly course in Uganda. In support of this mechanism, experimental tests have shown that pupae of both G. tachinoides
and G. submorsitans
, can survive for periods of at least 24 hours while submerged in water or saturated soil 
. Water-borne dispersal, unlike the bidirectional volant dispersal of adult tsetse through habitat adjacent to rivers and lakes, may constrain the direction of movement, but may also allow G. f. fuscipes
to disperse in the absence of contiguous tracts of favorable habitat. This warrants consideration when devising vector control strategies.
Whatever the dominant mode of dispersal, analyses of isolation by distance using microsatellites reflected an equilibrium between gene flow and drift in both northern and southern regions. In northern Uganda, the slope of the regression of genetic distance on geographic distance was shallow relative to that observed in southern Uganda, suggesting that the homogenizing influence of gene flow is relatively stronger in the north versus the south. The relatively low genetic divergences observed over large geographic distances may have also been influenced by a recent history of sequential founder events occurring from west to east across northern Uganda, a process that is supported by the significant decline in allelic diversity with longitude across the north. Both scenarios emphasize the vagility of G. f. fuscipes, albeit at different time scales. In southern Uganda, the slope of the regression of genetic distance on geographic distance was steeper, and at large geographic distances, was driven by the major genetic discontinuity between flies on either side of the gulf in G. f. fuscipes' predicted range (between Kabunkanga (KB) and Nkumba (NA); ). Although mtDNA signatures reflect a historical connection between western and southeastern populations, currently, there appears to be little gene flow and these populations warrant separate consideration. In western Uganda, IBD was not apparent, perhaps owing to the low sample size, or perhaps owing to the fact that nearest-neighbor geographical distances did not capture actual dispersal distances between sites (e.g., measured along riverine corridors). In southeastern Uganda, on the other hand, the signal of IBD was relatively strong, suggesting that ongoing exchange of genetic material is moderating the random allelic variation that would otherwise accumulate in isolated populations undergoing genetic drift alone. The exception was the population from Ndere Island (ND), which was more differentiated than expected based on the pattern of IBD observed in neighboring populations, perhaps due to its isolation from the mainland or its small effective population size. The latter may be the critical factor since Buvuma Island (BV) did not exhibit the same discontinuity. For Buvuma Island, the open water separating the island from the mainland appeared to be no more of a barrier to dispersal than the habitat separating neighboring mainland populations.
The signal of gene flow obtained from IBD analysis is consistent with estimates of dispersal rates for riverine tsetse, which are on the order of tens of kilometers per year 
. Reflecting this dispersal capacity, at the smallest scale of analysis, individual populations of G. f. fuscipes
in Uganda appeared to be genetically homogeneous over the 1–5 km2
trapping area that formed our fundamental sampling unit. Although we detected significant deviations from HWE for two loci in a handful of these populations, we did not observe consistent trends in FIS
that would provide evidence for any finer scale substructuring of tsetse populations, such as that observed in G. palpalis
, a related species of riverine tsetse 
. Extending beyond the immediate trapping locality, we observed significant but relatively small differentiation (FST
<~0.1) between most populations separated by less than 100 km. This level of differentiation is similar to the differentiation observed among populations of G. palpalis
at similar scales in Burkina Faso and Equatorial Guinea 
. Several of these studies have focused on the isolation implied by this differentiation, but with rare exception 
, absolute values of genetic isolation have yet to be reconciled with actual dispersal rates or the outcomes of vector control. Future efforts should focus on calibrating the consequences of genetic differentiation, perhaps by measuring the rate of reinfestation following eradication of the many tsetse populations for which genetic isolation indices now exist.
Previous observation of significant FST
values among populations of G. f. fuscipes
in Uganda prompted the conclusion that genetic drift is a much stronger force than gene flow and that perhaps dispersal tendencies have been overestimated 
. In this study, high FST
values and little evidence for IBD in mtDNA provided some support for this conclusion, at least among females; however, for microsatellite data, IBD analyses were in accord with higher levels of current gene flow. Even if our microsatellite-based estimates of FST
are deemed to be high, modeling has shown that high FST
may persist in the face of high gene flow if environmental heterogeneity contributes to a large variance in the size of individual populations 
. Our estimates of Ne
for G. f. fuscipes
in Uganda, though subject to large confidence intervals, were variable across populations, indicating that this condition may be met. Interestingly though, with the exception of Okame (OK), a site that has experienced continuous trapping of tsetse over the last several years, we did not find strong evidence for bottlenecks in the majority of populations considered. Our power to detect bottlenecks was likely low, since the transient signal of reduced allelic diversity that is indicative of a bottleneck, is unlikely to persist across multiple demographic cycles in populations with historically low Ne 
. At several sites to which we made repeat visits, we observed large changes in trapping rates over the course of a year (unpubl. data), which were presumably linked to changes in water availability and habitat composition. Therefore, it remains possible that severe dry season demographic contractions and attendant high levels of genetic drift could be muting stronger signals of gene flow 
. Strategies for control of G. f. fuscipes
in Uganda should account for the movement of tsetse consistent with this gene flow.
In conclusion, implied levels of gene flow among populations of G. f. fuscipes in Uganda appear to be consistent with high dispersal capacity, though confirmation of this will require the coordination of genetic studies with mark-recapture experiments. Interestingly, open water did not appear to present an unusual barrier to gene flow and we speculate that rivers may serve as a conduit for passive dispersal. Contrary to hypotheses invoking modern geographical barriers, the largest scale genetic structure apparent in Ugandan populations of G. f. fuscipes appears to have arisen from an ancient event that divided northern and southern lineages. Evidence for admixture between these lineages suggests that this structure may be impermanent but future studies should explore the viability of hybrid flies, particularly in light of the northerly-biased gene flow evident across the zone of contact.