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2,445 results for “Genetics: population”
Data from: Population genetic structure and demographic history of Atrina pectinata based on mitochondrial DNA and microsatellite markers
The pen shell, Atrina pectinata, is one of the commercial bivalves in East Asia and thought to be recently affected by anthropogenic pressure (habitat destruction and/or fishing pressure). Information on its population genetic structure is crucial for the conservation of A. pectinata. Considering its long pelagic larval duration and iteroparity with high fecundity, the genetic structure for A. pectinata could be expected to be weak at a fine scale. However, the unusual oceanography in the coasts of China and Korea suggests potential for restricted dispersal of pelagic larvae and geographical differentiation. In addition, environmental changes associated with Pleistocene sea level fluctuations on the East China Sea continental shelf may also have strongly influenced historical population demography and genetic diversity of marine organisms. Here, partial sequences of the mitochondrial Cytochrome c oxidase subunit I (COI) gene and seven microsatellite loci were used to estimate population genetic structure and demographic history of seven samples from Northern China coast and one sample from North Korea coast. Despite high levels of genetic diversity within samples, there was no genetic differentiation among samples from Northern China coast and low but significant genetic differentiation between some of the Chinese samples and the North Korean sample. A late Pleistocene population expansion, probably after the Last Glacial Maximum, was also demonstrated for A. pectinata samples. No recent genetic bottleneck was detected in any of the eight samples. We concluded that both historical recolonization (through population range expansion and demographic expansion in the late Pleistocene) and current gene flow (through larval dispersal) were responsible for the weak level of genetic structure detected in A. pectinata.
Data from: Population genetic structure of the giant cactus Echinopsis terscheckii in northwestern Argentina is shaped by patterns of vegetation cover
Species inhabiting drylands commonly depend on the surrounding vegetation for recruitment under stress, while competition may affect populations in moister environments. Our objective was to analyze how different climates and vegetation affect the fine-scale spatial genetic structure (SGS) of the columnar cactus Echinopsis terscheckii. At four sites we estimated vegetation cover by digitized patches and the normalized difference vegetation index (NDVI). We mapped 30 individuals per population and collected tissue for isozyme electrophoresis using 15 putative loci. Spatial autocorrelation between all possible genotype pairs and the number of genetically homogeneous groups and families were calculated for each population. Greater cover (66%) and average NDVI values were detected in the most humid habitat that consisted of fewer, larger, and more dispersed vegetation patches. All populations were genetically diverse and showed significant SGS. Positive correlations were found between the distance at which maximum autocorrelation and kinship values were reached and vegetation area and patch size. Also higher NDVI values were associated with lower number of patches. Populations exposed to higher precipitation and vegetation cover consisted of sparse individuals that clustered at larger distances whereas vegetation patches in arid climates produced groups of closely related genotypes at small distances. These results support the stress-gradient genetic hypothesis. Under water stress, facilitation promotes establishment underneath patchy vegetation resulting in fine-scale family structure. In moister xerophilous forests competition for resources, i.e. light, results in sparse individuals and thus coarse-scale neighborhoods. This information can guide conservation and/or restoration efforts, such as the spatial scale to be considered in germplasm collection.
Data from: Social and genetic population structure of free-ranging cheetah in Botswana: implications for conservation
Once widely distributed throughout Africa, cheetahs (Acinonyx jubatus) occur today within fragmented populations and are listed as vulnerable by the IUCN. Botswana currently hosts the second largest cheetah population throughout the species' range. This study initiated a molecular genetic survey of wild Botswana cheetah populations. It focused on the relatedness within presumed social groups using 14 microsatellite markers and revealed a higher proportion of unrelated male coalitions than was expected. Based on the unrelated cheetahs only, the estimation of the genetic variation corresponded with results from recent studies on different African populations. The analysis of unrelated individuals indicated limited genetic differentiation between cheetahs from different regions of Botswana. This suggests that the Botswana cheetah population might represent a unique panmictic population as long as sufficient levels of gene flow are maintained within the distribution range. This baseline information will now be incorporated to develop management strategies and set priorities for cheetah conservation in Botswana.
Data from: High genetic diversity and low population structure in Porter's sunflower (Helianthus porteri)
Granite outcrops in the southeastern United States are rare and isolated habitats that support edaphically controlled communities dominated by herbaceous plants. They harbor rare and endemic species that are expected to have low genetic variability and high population structure due to small populations sizes and their disjunct habitat. We test this expectation for an annual outcrop endemic, Helianthus porteri (Porter's sunflower). Contrary to expectation, H. porteri has relatively high genetic diversity (He = 0.681) and relatively low genetic structure among the native populations (FST = 0.077) when compared to five other Helianthus species (N = 288; 18 EST-SSR markers). These findings suggest greater gene flow than expected. The potential for gene flow is supported by the analysis of transplant populations established with propagules from a common source in 1959. One population established close to a native popualtion (1.5 km) at the edge of the natural range is genetically similar to and shares rare alleles with the adjancent native population and is distinct from the central source population. In contrast, a transplant population established north of the native range has remained similar to the source population. The relatively high genetic diversity and low population structure of this species, combined with the long term success of transplanted populations, bodes well for its persistence as long as the habitat persists.
Data from: Genetic sex assignment in wild populations using GBS data: a statistical threshold approach
Establishing the sex of individuals in wild systems can be challenging and often requires genetic testing. Genotyping-by-sequencing (GBS) and other reduced representation DNA sequencing (RRS) protocols (e.g., RADseq, ddRAD) have enabled the analysis of genetic data on an unprecedented scale. Here, we present a novel approach for the discovery and statistical validation of sex-specific loci in GBS datasets. We used GBS to genotype 166 New Zealand fur seals (NZFS, Arctocephalus forsteri) of known sex. We retained monomorphic loci as potential sex-specific markers in the locus discovery phase. We then used (i) a sex-specific locus threshold (SSLT) to identify significantly male-specific loci within our dataset and (ii) a significant sex-assignment threshold (SSAT) to confidently assign sex in silico the presence or absence of significantly male-specific loci to individuals in our dataset treated as unknowns (98.9% accuracy for females; 95.8% for males, estimated via cross-validation). Furthermore, we assigned sex to 86 individuals of true unknown sex using our SSAT, and assessed the effect of SSLT adjustments on these assignments. From 90 verified sex-specific loci, we developed a panel of three sex-specific PCR primers that we used to ascertain sex independently of our GBS data, which we show amplify reliably in at least three other pinniped species. Using monomorphic loci normally discarded from large SNP datasets is an effective way to identify robust sex-linked markers for non-model species. Our novel pipeline can be used to identify and statistically validate monomorphic and polymorphic sex-specific markers across a range of species and RRS datasets.
Data from: Trapped within the city: Integrating demography, time since isolation and population-specific traits to assess the genetic effects of urbanization
Urbanization is a severe form of habitat fragmentation that can cause many species to be locally extirpated and many others to become trapped and isolated within an urban matrix. The role of drift in reducing genetic diversity and increasing genetic differentiation is well recognized in urban populations. However, explicit incorporation and analysis of the demographic and temporal factors promoting drift in urban environments are poorly studied. Here, we genotyped 15 microsatellites in 320 fire salamanders from the historical city of Oviedo (Est. 8th century) to assess the effects of time since isolation, demographic history (historical effective population size; Ne) and patch size on genetic diversity, population structure and contemporary Ne. Our results indicate that urban populations of fire salamanders are highly differentiated, most likely due to the recent Ne declines, as calculated in coalescence analyses, concomitant with the urban development of Oviedo. However, urbanization only caused a small loss of genetic diversity. Regression modelling showed that patch size was positively associated with contemporary Ne, while we found only moderate support for the effects of demographic history when excluding populations with unresolved history. This highlights the interplay between different factors in determining current genetic diversity and structure. Overall, the results of our study on urban populations of fire salamanders provide some of the very first insights into the mechanisms affecting changes in genetic diversity and population differentiation via drift in urban environments, a crucial subject in a world where increasing urbanization is forecasted.
Data from: Northern range expansion of European populations of the wasp spider Argiope bruennichi is associated with global warming correlated genetic admixture and specific temperature adaptations
Poleward range expansions are observed for an increasing number of species, which may be an effect of global warming during the past decades. However, it is still not clear in how far these expansions reflect simple geographical shifts of species ranges, or whether new genetic adaptations play a role as well. Here, we analyse the expansion of the wasp spider Argiope bruennichi into Northern Europe during the last century. We have used a range-wide sampling of contemporary populations and historical specimens from museums to trace the phylogeography and genetic changes associated with the range shift. Based on the analysis of mitochondrial, microsatellite and SNP markers, we observe a higher level of genetic diversity in the expanding populations, apparently due to admixture of formerly isolated lineages. Using reciprocal transplant experiments for testing overwintering tolerance, as well as temperature preference and tolerance tests in the laboratory, we find that the invading spiders have possibly shifted their temperature niche. This may be a key adaptation for survival in Northern latitudes. The museum samples allow a reconstruction of the invasion's genetic history. A first, small-scale range shift started around 1930, in parallel with the onset of global warming. A more massive invasion of Northern Europe associated with genetic admixture and morphological changes occurred in later decades. We suggest that the latter range expansion into far Northern latitudes may be a consequence of the admixture that provided the genetic material for adaptations to new environmental regimes. Hence, global warming could have facilitated the initial admixture of populations and this resulted in genetic lineages with new habitat preferences.
Data from: Population differentiation determined from putative neutral and divergent adaptive genetic markers in Eulachon (Thaleichthys pacificus, Osmeridae), an anadromous Pacific smelt.
Twelve eulachon (Thaleichthys pacificus, Osmeridae) populations ranging from Cook Inlet, Alaska and along the west coast of North America to the Columbia River were examined by restriction-site-associated DNA (RAD) sequencing to elucidate patterns of neutral and adaptive variation in this high geneflow species. A total of 4104 single-nucleotide polymorphisms (SNPs) were discovered across the genome, with 193 putatively adaptive SNPs as determined by FST outlier tests. Estimates of population structure in eulachon with the putatively adaptive SNPs were similar, but provided greater resolution of stocks compared with a putatively neutral panel of 3911 SNPs or previous estimates with 14 microsatellites. A cline of increasing measures of genetic diversity from south to north was found in the adaptive panel, but not in the neutral markers (SNPs or microsatellites). This may indicate divergent selective pressures in differing freshwater and marine environments between regional eulachon populations and that these adaptive diversity patterns not seen with neutral markers could be a consideration when determining genetic boundaries for conservation purposes. Estimates of effective population size (Ne) were similar with the neutral SNP panel and microsatellites and may be utilized to monitor population status for eulachon where census sizes are difficult to obtain. Greater differentiation with the panel of putatively adaptive SNPs provided higher individual assignment accuracy compared to the neutral panel or microsatellites for stock identification purposes. This study presents the first SNPs that have been developed for eulachon, and analyses with these markers highlighted the importance of integrating genome-wide neutral and adaptive genetic variation for the applications of conservation and management.
Data from: Population genetic analysis of white sturgeon (Acipenser transmontanus) in the Fraser River
White sturgeon (Acipenser transmontanus) in the Fraser River are listed as imperiled (the second highest possible rating) by the British Columbia Conservation Data Centre. A difficulty in trying to protect this species in the Fraser River and elsewhere is the lack of knowledge regarding their population biology. Variation in the mitochondrial DNA control region and at four microsatellite loci was examined in order to characterize white sturgeon samples from throughout the Fraser River mainstem and from a major tributary, the Nechako River. Samples from the adjacent Columbia River were analyzed for comparison. In contrast to previous work, present data indicate that white sturgeon population structure in this region reflects post-glacial dispersal more than it does recent anthropogenic effects. The data divided the Fraser into four biogeographic regions: (i) the lower Fraser, below Hell's Gate; (ii) the middle Fraser, between Hell's Gate and river km 553; (iii) the upper Fraser, above the Nechako confluence; and (iv) the Nechako River. These four groups are concordant with those suggested by tag and recapture and catch per unit effort data, and are separated by what have been identified as barriers to white sturgeon migration. Based on concordance between these different types of data, it is argued that the four groups identified here merit evolutionarily significant unit (ESU) status.
Data from: Linking genetic diversity and temporal fluctuations in population abundance of the introduced feral cat (Felis silvestris catus) on the Kerguelen Archipelago.
Linking temporal variations of genetic diversity, including allelic richness and heterozygosity, and spatio-temporal fluctuations in population abundance has emerged as an important tool for understanding demographic and evolutionary processes in natural populations. This so-called 'genetic monitoring' was conducted across 12 consecutive years (1996-2007) at three sites for the feral cat, introduced onto the Kerguelen Archipelago fifty years ago. Temporal changes in allelic richness and heterozygosity at 18 microsatellite DNA loci were compared to temporal changes in the adult population abundance index, obtained by typical demographic monitoring. No association was found at the island spatial scale but we observed an association between genetic diversity and adult population indices from year to year within each study site. More particularly, the magnitude of successive increases or decreases in the adult population abundance index appeared to be the major factor linking the trajectories of genetic diversity and adult population abundance indices. Natal dispersal and/or local recruitment, both facilitated by high juvenile survival when the adult population size is small, are proposed as the major demographic processes contributing to such an observed pattern. Finally, we suggested avoiding the use of the harmonic mean as an estimator of long-term population size to study the relationships between demographic fluctuations and heterozygosity in populations characterized by strong multi-annual density fluctuations.
Data from: Phylogeny and biogeography of the American live oaks (Quercus subsection Virentes): a genomic and population genetics approach
The nature and timing of evolution of niche differentiation among closely related species remains an important question in ecology and evolution. The American live oak clade, Virentes, which spans the unglaciated temperate and tropical regions of North America and Mesoamerica, provides an instructive system in which to examine speciation and niche evolution. We generated a fossil-calibrated phylogeny of Virentes using RADseq data to estimate divergence times and used nuclear microsatellites, chloroplast sequences and an intron region of nitrate reductase (NIA-i3) to examine genetic diversity within species, rates of gene flow among species and ancestral population size of disjunct sister species. Transitions in functional and morphological traits associated with ecological and climatic niche axes were examined across the phylogeny. We found the Virentes to be monophyletic with three subclades, including a southwest clade, a southeastern US clade and a Central American/Cuban clade. Despite high leaf morphological variation within species and transpecific chloroplast haplotypes, RADseq and nuclear SSR data showed genetic coherence of species. We estimated a crown date for Virentes of 11 Ma and implicated the formation of the Sea of Cortés in a speciation event ~5 Ma. Tree height at maturity, associated with fire tolerance, differs among the sympatric species, while freezing tolerance appears to have diverged repeatedly across the tropical–temperate divide. Sympatric species thus show evidence of ecological niche differentiation but share climatic niches, while allopatric and parapatric species conserve ecological niches, but diverge in climatic niches. The mode of speciation and/or degree of co-occurrence may thus influence which niche axis plants diverge along.
Data from: Habitat discontinuities separate genetically divergent populations of a rocky shore marine fish
Habitat fragmentation has been suggested to be responsible for major genetic differentiations in a range of marine organisms. In this study, we combined genetic data and environmental information to unravel the relative role of geography and habitat heterogeneity on patterns of genetic population structure of corkwing wrasse (Symphodus melops), a rocky shore species at the northern limit of its distribution range in Scandinavia. Our results revealed a major genetic break separating populations inhabiting the western and southern coasts of Norway. This genetic break coincides with the longest stretch of sand in the whole study area, suggesting habitat fragmentation as a major driver of genetic differentiation of this obligate rocky shore benthic fish in Scandinavia. The complex fjords systems extending along the western coast of Norway appeared responsible for further regional genetic structuring. Our findings indicate that habitat discontinuities may lead to significant genetic fragmentation over short geographical distances, even for marine species with a pelagic larval phase, as for this rocky shore fish.
Data from: Temporal variation in genetic diversity and effective population size of Mediterranean and subalpine Arabidopsis thaliana populations
Currently there exists a limited knowledge on the extent of temporal variation in population genetic parameters of natural populations. Here we study the extent of temporal variation in population genetics by genotyping 151 genome-wide SNP markers polymorphic in 466 individuals collected from nine populations of the annual plant Arabidopsis thaliana during four years. Populations are located along an altitudinal climatic gradient from Mediterranean to subalpine environments in NE Spain, which has been shown to influence key demographic attributes and life-cycle adaptations. Genetically, A. thaliana populations were more variable across space than over time. Common multilocus genotypes were detected several years in the same population, whereas low-frequency multilocus genotypes appeared only one year. High-elevation populations were genetically poorer and more variable over time than low-elevation populations, which might be caused by a higher overall demographic instability at higher altitudes. Estimated effective population sizes were very low but also showed a significant decreasing trend with increasing altitude, suggesting a deeper impact of genetic drift at high-elevation populations. In comparison with single-year samplings, repeated genotyping over time captured substantially higher amount of genetic variation contained in A. thaliana populations. Furthermore, repeated genotyping of populations provided novel information on the genetic properties of A. thaliana populations and allowed hypothesizing on their underlying mechanisms. Therefore, including temporal genotyping programs into traditional population genetic studies can significantly increase our understanding of the dynamics of natural populations.
Data from: Population genetic structure of the western cherry fruit fly Rhagoletis indifferens (Diptera: Tephritidae) in British Columbia, Canada
1. Population connectivity and movement are key ecological parameters influencing the impact of pests, and are important considerations in control strategies. For many insects, these parameters are difficult to assess directly, although they may be assessed indirectly using population genetic data. 2. We used microsatellite markers to examine population genetic structure of the western cherry fruit fly, the main pest of cherry crops in western North America, in British Columbia, Canada, and make inferences about connectivity and potential for movement among populations. 3. Comparing populations from four geographical regions (separated by up to approximately 400 km), we found significant genetic differentiation both among and within regions. Using populations as the units of analysis, we observed significant isolation by distance (IBD) at larger spatial scales but not below approximately 20 km. By contrast, using individual flies as the units of analysis, we found significant IBD at scales as small as < 100 m. We saw no evidence of genetic differentiation among populations sampled from different species/varieties of plants. 4. Our results suggest that the movement of individual flies is limited, although high levels of gene flow are maintained at scales of up to 20 km, possibly through combined effects of stepping-stone gene flow and large population sizes.
Data from: Structure and genetic variability of golden mussel (Limnoperna fortunei) populations from Brazilian reservoirs
The golden mussel, Limnoperna fortunei a highly invasive species in Brazil, has generated productive, economical, and biological impacts. To evaluate genetic structure and variability of L. fortunei populations present in fish farms in the reservoirs of Canoas I (CANFF), Rosana (ROSFF), and Capivara (CAPFF) (Paranapanema river, Paraná, Brazil), eight microsatellite loci were amplified. Five of those eight loci resulted in 38 alleles. The observed heterozygosity (Ho) was lower than the expected heterozygosity (He) in all populations, with a deviation from the Hardy-Weinberg equilibrium (HWE). The average value for the inbreeding coefficient (Fis) was positive and significative for all populations. There was higher genetic variability within populations than among them. The fixation index (Fst) showed a small genetic variability among these populations. The occurrence of gene flow was identified in all populations, along with the lack of a recent bottleneck effect. The clustering analysis yielded K = 2, with genetic similarity between the three populations. The results demonstrate low genetic structure and suggest a founding population with greater genetic variability (ROSFF). Our data point to the possible dispersal of L. fortunei aided by anthropic factors in the upstream direction. It was concluded that the three populations presented a unique genetic pool for Paranapanema river, with occurrence of gene flow.
Data from: Genetically distinct populations of northern shrimp, Pandalus borealis, in the North Atlantic: adaptation to different temperatures as an isolation factor
The large-scale population genetic structure of northern shrimp, Pandalus borealis, was investigated over the species' range in the North Atlantic, identifying multiple genetically distinct groups. Genetic divergence among sample localities varied among 10 microsatellite loci (range: FST = −0.0002 to 0.0475) with a highly significant average (FST = 0.0149; P < 0.0001). In contrast, little or no genetic differences were observed among temporal replicates from the same localities (FST = 0.0004; P = 0.33). Spatial genetic patterns were compared to geographic distances, patterns of larval drift obtained through oceanographic modelling, and temperature differences, within a multiple linear regression framework. The best-fit model included all three factors and explained approximately 29% of all spatial genetic divergence. However, geographic distance and larval drift alone had only minor effects (2.5–4.7%) on large-scale genetic differentiation patterns, whereas bottom temperature differences explained most (26%). Larval drift was found to promote genetic homogeneity in parts of the study area with strong currents, but appeared ineffective across large temperature gradients. These findings highlight the breakdown of gene flow in a species with a long pelagic larval phase (up to 3 months) and indicate a role for local adaptation to temperature conditions in promoting evolutionary diversification and speciation in the marine environment.
Data from: Genetic rescue increases fitness and aids rapid recovery of an endangered marsupial population
Genetic rescue has now been attempted in several threatened species, but the contribution of genetics per se to any increase in population health can be hard to identify. Rescue is expected to be particularly useful when individuals are introduced into small isolated populations with low levels of genetic variation. Here we consider such a situation by documenting genetic rescue in the mountain pygmy possum, Burramys parvus. Rapid population recovery occurred in the target population after the introduction of a small number of males from a large genetically diverged population. Initial hybrid fitness was more than two-fold higher than non-hybrids; hybrid animals had a larger body size, and female hybrids produced more pouch young and lived longer. Genetic rescue likely contributed to the largest population size ever being recorded at this site. These data point to genetic rescue as being a potentially useful option for the recovery of small threatened populations.
Data from: Genetic connectivity and diversity in inselberg populations of Acacia woodmaniorum, a rare endemic of the Yilgarn Craton banded iron formations
Historically rare plant species with disjunct population distributions and small population sizes might be expected to show significant genetic structure and low levels of genetic diversity due to the effects of inbreeding and genetic drift. Across the globe terrestrial inselbergs are habitat for rich, often rare and endemic flora and are valuable systems for investigating evolutionary processes that shape patterns of genetic structure and levels of genetic diversity at the landscape scale. We assessed genetic structure and levels of genetic diversity across the range of the historically rare inselberg endemic Acacia woodmaniorum. Phylogeographic and genetic structure indicates that connectivity is not sufficient to produce a panmictic population across the limited geographic range of the species. However, historical levels of gene flow are sufficient to maintain a high degree of adaptive connectivity across the landscape. Genetic diversity indicates gene flow is sufficient to largely counteract any negative genetic effects of inbreeding and random genetic drift in even the most disjunct or smallest populations. Phylogeographic and genetic structure, a signal of isolation by distance, and a lack of evidence of recent genetic bottlenecks suggest long term stability of contemporary population distributions and population sizes. There is some evidence that genetic connectivity among disjunct outcrops may be facilitated by the occasional long distance dispersal of Acacia polyads carried by insect pollinators moved by prevailing winds.
Data from: Combined analyses of kinship and FST suggest potential drivers of chaotic genetic patchiness in high gene flow populations
We combine kinship estimates with traditional F-statistics to explain contemporary drivers of population genetic differentiation despite high gene flow. We investigate range-wide population genetic structure of the California spiny (or red rock) lobster (Panulirus interruptus) and find slight, but significant global population differentiation in mtDNA (ΦST = 0.006, P = 0.001; Dest_Chao = 0.025) and seven nuclear microsatellites (FST = 0.004, P < 0.001; Dest_Chao = 0.03), despite the species' 240- to 330-day pelagic larval duration. Significant population structure does not correlate with distance between sampling locations, and pairwise FST between adjacent sites often exceeds that among geographically distant locations. This result would typically be interpreted as unexplainable, chaotic genetic patchiness. However, kinship levels differ significantly among sites (pseudo-F16,988 = 1.39, P = 0.001), and ten of 17 sample sites have significantly greater numbers of kin than expected by chance (P < 0.05). Moreover, a higher proportion of kin within sites strongly correlates with greater genetic differentiation among sites (Dest_Chao, R2 = 0.66, P < 0.005). Sites with elevated mean kinship were geographically proximate to regions of high upwelling intensity (R2 = 0.41, P = 0.0009). These results indicate that P. interruptus does not maintain a single homogenous population, despite extreme dispersal potential. Instead, these lobsters appear to either have substantial localized recruitment or maintain planktonic larval cohesiveness whereby siblings more likely settle together than disperse across sites. More broadly, our results contribute to a growing number of studies showing that low FST and high family structure across populations can coexist, illuminating the foundations of cryptic genetic patterns and the nature of marine dispersal.
Data from: Genetic diversity and population structure of the tsetse fly Glossina fuscipes fuscipes (Diptera: Glossinidae) in Northern Uganda: implications for vector control
Uganda is the only country where the chronic and acute forms of human African Trypanosomiasis (HAT) or sleeping sickness both occur and are separated by < 100 km in areas north of Lake Kyoga. In Uganda, Glossina fuscipes fuscipes is the main vector of the Trypanosoma parasites responsible for these diseases as well for the animal African Trypanosomiasis (AAT), or Nagana. We used highly polymorphic microsatellite loci and a mitochondrial DNA (mtDNA) marker to provide fine scale spatial resolution of genetic structure of G. f. fuscipes from 42 sampling sites from the northern region of Uganda where a merger of the two disease belts is feared. Based on microsatellite analyses, we found that G. f. fuscipes in northern Uganda are structured into three distinct genetic clusters with varying degrees of interconnectivity among them. Based on genetic assignment and spatial location, we grouped the sampling sites into four genetic units corresponding to northwestern Uganda in the Albert Nile drainage, northeastern Uganda in the Lake Kyoga drainage, western Uganda in the Victoria Nile drainage, and a transition zone between the two northern genetic clusters characterized by high level of genetic admixture. An analysis using HYBRIDLAB supported a hybrid swarm model as most consistent with tsetse genotypes in these admixed samples. Results of mtDNA analyses revealed the presence of 30 haplotypes representing three main haplogroups, whose location broadly overlaps with the microsatellite defined clusters. Migration analyses based on microsatellites point to moderate migration among the northern units located in the Albert Nile, Achwa River, Okole River, and Lake Kyoga drainages, but not between the northern units and the Victoria Nile drainage in the west. Effective population size estimates were variable with low to moderate sizes in most populations and with evidence of recent population bottlenecks, especially in the northeast unit of the Lake Kyoga drainage. Our microsatellite and mtDNA based analyses indicate that G. f. fuscipes movement along the Achwa and Okole rivers may facilitate northwest expansion of the Rhodesiense disease belt in Uganda. We identified tsetse migration corridors and recommend a rolling carpet approach from south of Lake Kyoga northward to minimize disease dispersal and prevent vector re-colonization. Additionally, our findings highlight the need for continuing tsetse monitoring efforts during and after control.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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OpenNeuro
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