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Saarman NP, Son JH, Zhao H, Cosme LV, Kong Y, Li M, Wang S, Weiss BL, Echodu R, Opiro R, Aksoy S, Caccone A. Genomic evidence of sex chromosome aneuploidy and infection-associated genotypes in the tsetse fly Glossina fuscipes, the major vector of African trypanosomiasis in Uganda. Infect Genet Evol 2023; 114:105501. [PMID: 37709241 PMCID: PMC10593118 DOI: 10.1016/j.meegid.2023.105501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 09/07/2023] [Accepted: 09/11/2023] [Indexed: 09/16/2023]
Abstract
The primary vector of the trypanosome parasite causing human and animal African trypanosomiasis in Uganda is the riverine tsetse fly Glossina fuscipes fuscipes (Gff). Our study improved the Gff genome assembly with whole genome 10× Chromium sequencing of a lab reared pupae, identified autosomal versus sex-chromosomal regions of the genome with ddRAD-seq data from 627 field caught Gff, and identified SNPs associated with trypanosome infection with genome-wide association (GWA) analysis in a subset of 351 flies. Results from 10× Chromium sequencing greatly improved Gff genome assembly metrics and assigned a full third of the genome to the sex chromosome. Results from ddRAD-seq suggested possible sex-chromosome aneuploidy in Gff and identified a single autosomal SNP to be highly associated with trypanosome infection. The top associated SNP was ∼1100 bp upstream of the gene lecithin cholesterol acyltransferase (LCAT), an important component of the molecular pathway that initiates trypanosome lysis and protection in mammals. Results suggest that there may be naturally occurring genetic variation in Gff in genomic regions in linkage disequilibrium with LCAT that can protect against trypanosome infection, thereby paving the way for targeted research into novel vector control strategies that can promote parasite resistance in natural populations.
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Affiliation(s)
| | - Jae Hak Son
- Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
| | - Hongyu Zhao
- Yale School of Public Health, New Haven, CT, USA.
| | | | - Yong Kong
- Yale School of Public Health, New Haven, CT, USA.
| | - Mo Li
- Yale School of Public Health, New Haven, CT, USA
| | | | | | | | | | - Serap Aksoy
- Yale School of Public Health, New Haven, CT, USA.
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Son JH, Weiss BL, Schneider DI, Dera KSM, Gstöttenmayer F, Opiro R, Echodu R, Saarman NP, Attardo GM, Onyango M, Abd-Alla AMM, Aksoy S. Infection with endosymbiotic Spiroplasma disrupts tsetse (Glossina fuscipes fuscipes) metabolic and reproductive homeostasis. PLoS Pathog 2021; 17:e1009539. [PMID: 34529715 PMCID: PMC8478229 DOI: 10.1371/journal.ppat.1009539] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 09/28/2021] [Accepted: 09/07/2021] [Indexed: 11/19/2022] Open
Abstract
Tsetse flies (Glossina spp.) house a population-dependent assortment of microorganisms that can include pathogenic African trypanosomes and maternally transmitted endosymbiotic bacteria, the latter of which mediate numerous aspects of their host's metabolic, reproductive, and immune physiologies. One of these endosymbionts, Spiroplasma, was recently discovered to reside within multiple tissues of field captured and laboratory colonized tsetse flies grouped in the Palpalis subgenera. In various arthropods, Spiroplasma induces reproductive abnormalities and pathogen protective phenotypes. In tsetse, Spiroplasma infections also induce a protective phenotype by enhancing the fly's resistance to infection with trypanosomes. However, the potential impact of Spiroplasma on tsetse's viviparous reproductive physiology remains unknown. Herein we employed high-throughput RNA sequencing and laboratory-based functional assays to better characterize the association between Spiroplasma and the metabolic and reproductive physiologies of G. fuscipes fuscipes (Gff), a prominent vector of human disease. Using field-captured Gff, we discovered that Spiroplasma infection induces changes of sex-biased gene expression in reproductive tissues that may be critical for tsetse's reproductive fitness. Using a Gff lab line composed of individuals heterogeneously infected with Spiroplasma, we observed that the bacterium and tsetse host compete for finite nutrients, which negatively impact female fecundity by increasing the length of intrauterine larval development. Additionally, we found that when males are infected with Spiroplasma, the motility of their sperm is compromised following transfer to the female spermatheca. As such, Spiroplasma infections appear to adversely impact male reproductive fitness by decreasing the competitiveness of their sperm. Finally, we determined that the bacterium is maternally transmitted to intrauterine larva at a high frequency, while paternal transmission was also noted in a small number of matings. Taken together, our findings indicate that Spiroplasma exerts a negative impact on tsetse fecundity, an outcome that could be exploited for reducing tsetse population size and thus disease transmission.
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Affiliation(s)
- Jae Hak Son
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Brian L. Weiss
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Daniela I. Schneider
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Kiswend-sida M. Dera
- Insect Pest Control Laboratory, Joint FAO/IAEA Programme of Nuclear Techniques in Food and Agriculture, Vienna, Austria
- Insectarium de Bobo-Dioulasso—Campagne d’Eradication de la mouche Tse´-tse´ et de la Trypanosomiase (IBD-CETT), Bobo-Dioulasso, Burkina Faso
| | - Fabian Gstöttenmayer
- Insect Pest Control Laboratory, Joint FAO/IAEA Programme of Nuclear Techniques in Food and Agriculture, Vienna, Austria
| | - Robert Opiro
- Department of Biology, Faculty of Science, Gulu University, Gulu, Uganda
| | - Richard Echodu
- Department of Biology, Faculty of Science, Gulu University, Gulu, Uganda
| | - Norah P. Saarman
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
| | - Geoffrey M. Attardo
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Maria Onyango
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Adly M. M. Abd-Alla
- Insect Pest Control Laboratory, Joint FAO/IAEA Programme of Nuclear Techniques in Food and Agriculture, Vienna, Austria
| | - Serap Aksoy
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
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Bishop AP, Amatulli G, Hyseni C, Pless E, Bateta R, Okeyo WA, Mireji PO, Okoth S, Malele I, Murilla G, Aksoy S, Caccone A, Saarman NP. A machine learning approach to integrating genetic and ecological data in tsetse flies ( Glossina pallidipes) for spatially explicit vector control planning. Evol Appl 2021; 14:1762-1777. [PMID: 34295362 PMCID: PMC8288027 DOI: 10.1111/eva.13237] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 03/18/2021] [Accepted: 03/22/2021] [Indexed: 11/26/2022] Open
Abstract
Vector control is an effective strategy for reducing vector-borne disease transmission, but requires knowledge of vector habitat use and dispersal patterns. Our goal was to improve this knowledge for the tsetse species Glossina pallidipes, a vector of human and animal African trypanosomiasis, which are diseases that pose serious health and socioeconomic burdens across sub-Saharan Africa. We used random forest regression to (i) build and integrate models of G. pallidipes habitat suitability and genetic connectivity across Kenya and northern Tanzania and (ii) provide novel vector control recommendations. Inputs for the models included field survey records from 349 trap locations, genetic data from 11 microsatellite loci from 659 flies and 29 sampling sites, and remotely sensed environmental data. The suitability and connectivity models explained approximately 80% and 67% of the variance in the occurrence and genetic data and exhibited high accuracy based on cross-validation. The bivariate map showed that suitability and connectivity vary independently across the landscape and was used to inform our vector control recommendations. Post hoc analyses show spatial variation in the correlations between the most important environmental predictors from our models and each response variable (e.g., suitability and connectivity) as well as heterogeneity in expected future climatic change of these predictors. The bivariate map suggests that vector control is most likely to be successful in the Lake Victoria Basin and supports the previous recommendation that G. pallidipes from most of eastern Kenya should be managed as a single unit. We further recommend that future monitoring efforts should focus on tracking potential changes in vector presence and dispersal around the Serengeti and the Lake Victoria Basin based on projected local climatic shifts. The strong performance of the spatial models suggests potential for our integrative methodology to be used to understand future impacts of climate change in this and other vector systems.
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Affiliation(s)
- Anusha P. Bishop
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenCTUSA
- Department of Environmental Science, Policy, & ManagementUniversity of CaliforniaBerkeleyCAUSA
| | | | - Chaz Hyseni
- Department of Ecology and GeneticsUppsala UniversityUppsalaSweden
| | - Evlyn Pless
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenCTUSA
- Department of AnthropologyUniversity of CaliforniaDavisCAUSA
| | - Rosemary Bateta
- Biotechnology Research InstituteKenya Agricultural and Livestock Research OrganizationKikuyu, NairobiKenya
| | - Winnie A. Okeyo
- Biotechnology Research InstituteKenya Agricultural and Livestock Research OrganizationKikuyu, NairobiKenya
- Department of Biomedical Sciences and TechnologySchool of Public Health and Community DevelopmentMaseno UniversityMaseno, KisumuKenya
| | - Paul O. Mireji
- Biotechnology Research InstituteKenya Agricultural and Livestock Research OrganizationKikuyu, NairobiKenya
- Centre for Geographic Medicine Research CoastKenya Medical Research InstituteKilifiKenya
| | - Sylvance Okoth
- Biotechnology Research InstituteKenya Agricultural and Livestock Research OrganizationKikuyu, NairobiKenya
| | - Imna Malele
- Vector and Vector Borne Diseases Research InstituteTanzania Veterinary Laboratory AgencyTangaTanzania
| | - Grace Murilla
- Biotechnology Research InstituteKenya Agricultural and Livestock Research OrganizationKikuyu, NairobiKenya
| | - Serap Aksoy
- Department of Epidemiology of Microbial DiseasesYale School of Public HealthNew HavenCTUSA
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenCTUSA
| | - Norah P. Saarman
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenCTUSA
- Department of BiologyUtah State UniversityLoganUTUSA
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Bateta R, Saarman NP, Okeyo WA, Dion K, Johnson T, Mireji PO, Okoth S, Malele I, Murilla G, Aksoy S, Caccone A. Phylogeography and population structure of the tsetse fly Glossina pallidipes in Kenya and the Serengeti ecosystem. PLoS Negl Trop Dis 2020; 14:e0007855. [PMID: 32092056 PMCID: PMC7058365 DOI: 10.1371/journal.pntd.0007855] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 03/05/2020] [Accepted: 10/17/2019] [Indexed: 02/06/2023] Open
Abstract
Glossina pallidipes is the main vector of animal African trypanosomiasis and a potential vector of human African trypanosomiasis in eastern Africa where it poses a large economic burden and public health threat. Vector control efforts have succeeded in reducing infection rates, but recent resurgence in tsetse fly population density raises concerns that vector control programs require improved strategic planning over larger geographic and temporal scales. Detailed knowledge of population structure and dispersal patterns can provide the required information to improve planning. To this end, we investigated the phylogeography and population structure of G. pallidipes over a large spatial scale in Kenya and northern Tanzania using 11 microsatellite loci genotyped in 600 individuals. Our results indicate distinct genetic clusters east and west of the Great Rift Valley, and less distinct clustering of the northwest separate from the southwest (Serengeti ecosystem). Estimates of genetic differentiation and first-generation migration indicated high genetic connectivity within genetic clusters even across large geographic distances of more than 300 km in the east, but only occasional migration among clusters. Patterns of connectivity suggest isolation by distance across genetic breaks but not within genetic clusters, and imply a major role for river basins in facilitating gene flow in G. pallidipes. Effective population size (Ne) estimates and results from Approximate Bayesian Computation further support that there has been recent G. pallidipes population size fluctuations in the Serengeti ecosystem and the northwest during the last century, but also suggest that the full extent of differences in genetic diversity and population dynamics between the east and the west was established over evolutionary time periods (tentatively on the order of millions of years). Findings provide further support that the Serengeti ecosystem and northwestern Kenya represent independent tsetse populations. Additionally, we present evidence that three previously recognized populations (the Mbeere-Meru, Central Kenya and Coastal "fly belts") act as a single population and should be considered as a single unit in vector control.
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Affiliation(s)
- Rosemary Bateta
- Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, Kikuyu, Nairobi, Kenya
| | - Norah P. Saarman
- Department of Ecology and Evolutionary Biology, Yale University, Connecticut, United States of America
- * E-mail:
| | - Winnie A. Okeyo
- Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, Kikuyu, Nairobi, Kenya
- Department of Biomedical Sciences and Technology, School of Public Health and Community Development, Maseno University, Maseno, Kisumu, Kenya
| | - Kirstin Dion
- Department of Ecology and Evolutionary Biology, Yale University, Connecticut, United States of America
| | - Thomas Johnson
- Department of Ecology and Evolutionary Biology, Yale University, Connecticut, United States of America
| | - Paul O. Mireji
- Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, Kikuyu, Nairobi, Kenya
- Centre for Geographic Medicine Research Coast, Kenya Medical Research Institute, Kilifi, Kenya
| | - Sylvance Okoth
- Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, Kikuyu, Nairobi, Kenya
| | - Imna Malele
- Vector and Vector Borne Diseases Research Institute, Tanzania Veterinary Laboratory Agency, Tanga, Tanzania
| | - Grace Murilla
- Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, Kikuyu, Nairobi, Kenya
| | - Serap Aksoy
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Connecticut, United States of America
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology, Yale University, Connecticut, United States of America
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Saarman NP, Opiro R, Hyseni C, Echodu R, Opiyo EA, Dion K, Johnson T, Aksoy S, Caccone A. The population genomics of multiple tsetse fly (Glossina fuscipes fuscipes) admixture zones in Uganda. Mol Ecol 2019; 28:66-85. [PMID: 30471158 DOI: 10.1111/mec.14957] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 10/26/2018] [Accepted: 11/05/2018] [Indexed: 11/28/2022]
Abstract
Understanding the mechanisms that enforce, maintain or reverse the process of speciation is an important challenge in evolutionary biology. This study investigates the patterns of divergence and discusses the processes that form and maintain divergent lineages of the tsetse fly Glossina fuscipes fuscipes in Uganda. We sampled 251 flies from 18 sites spanning known genetic lineages and the four admixture zones between them. We apply population genomics, hybrid zone and approximate Bayesian computation to the analysis of three types of genetic markers: 55,267 double-digest restriction site-associated DNA (ddRAD) SNPs to assess genome-wide admixture, 16 microsatellites to provide continuity with published data and accurate biogeographic modelling, and a 491-bp fragment of mitochondrial cytochrome oxidase I and II to infer maternal inheritance patterns. Admixture zones correspond with regions impacted by the reorganization of Uganda's river networks that occurred during the formation of the West African Rift system over the last several hundred thousand years. Because tsetse fly population distributions are defined by rivers, admixture zones likely represent both old and new regions of secondary contact. Our results indicate that older hybrid zones contain mostly parental types, while younger zones contain variable hybrid types resulting from multiple generations of interbreeding. These findings suggest that reproductive barriers are nearly complete in the older admixture zones, while nearly absent in the younger admixture zones. Findings are consistent with predictions of hybrid zone theory: Populations in zones of secondary contact transition rapidly from early to late stages of speciation or collapse all together.
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Affiliation(s)
- Norah P Saarman
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut
| | - Robert Opiro
- Department of Biology, Faculty of Science, Gulu University, Uganda
| | - Chaz Hyseni
- Department of Biology, University of Mississippi, Oxford, Mississippi
| | - Richard Echodu
- Department of Biology, Faculty of Science, Gulu University, Uganda
| | | | - Kirstin Dion
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut
| | - Thomas Johnson
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut
| | - Serap Aksoy
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut
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Grove S, Saarman NP, Gilbert GS, Faircloth B, Haubensak KA, Parker IM. Ectomycorrhizas and tree seedling establishment are strongly influenced by forest edge proximity but not soil inoculum. Ecol Appl 2019; 29:e01867. [PMID: 30710404 DOI: 10.1002/eap.1867] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 12/22/2018] [Accepted: 01/07/2019] [Indexed: 06/09/2023]
Abstract
Reforestation is challenging when timber harvested areas have been degraded, invaded by nonnative species, or are of marginal suitability to begin with. Conifers form mutualistic partnerships with ectomycorrhizal fungi (EMF) to obtain greater access to soil resources, and these partnerships may be especially important in degraded areas. However, timber harvest can impact mycorrhizal fungi by removing or compacting topsoil, removing host plants, and warming and drying the soil. We used a field experiment to evaluate the role of EMF in Douglas-fir reforestation in clearcuts invaded by Cytisus scoparius (Scotch broom) where traditional reforestation approaches have repeatedly failed. We tested how planting distance from intact Douglas-fir forest edges influenced reforestation success and whether inoculation with forest soils can be used to restore EMF relationships. We used an Illumina DNA sequencing approach to measure the abundance, richness and composition of ectomycorrhizal fungi on Douglas-fir roots, and assessed differences in Douglas-fir seedling survival and growth near to and far from forest edges with and without forest soil inoculum. Planting Douglas-fir seedlings near forest edges increased seedling survival, growth, and EMF root colonization. Edge proximity had no effect on EMF richness but did change fungal community composition. Inoculations with forest soil did not increase EMF abundance or richness or change community composition, nor did it improve seedling establishment. With Illumina sequencing, we identified two to three times greater species richness than described in previous edge effects studies. Of the 95 EMF species we identified, 40% of the species occurred on less than 5% of the seedlings. The ability to detect fungi at low abundance may explain why we did not detect differences in EMF richness with distance to hosts as previous studies. Our findings suggest that forest edges are suitable for reforestation, even when the interiors of deforested areas are not. We advocate for timber harvest designs that maximize edge habitat where ectomycorrhizal fungi contribute to tree establishment. However, this study does not support the use of inoculation with forest soil as a simple method to enhance EMF and seedling survival.
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Affiliation(s)
- Sara Grove
- Ecology and Evolutionary Biology, University of California, Santa Cruz, California, 95064, USA
- Biological Sciences and Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, 86011, USA
| | - Norah P Saarman
- Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, 06511, USA
| | - Gregory S Gilbert
- Environmental Studies, University of California, Santa Cruz, California, 95064, USA
| | - Brant Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana, 70803, USA
| | - Karen A Haubensak
- Biological Sciences and Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, 86011, USA
| | - Ingrid M Parker
- Ecology and Evolutionary Biology, University of California, Santa Cruz, California, 95064, USA
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Okeyo WA, Saarman NP, Bateta R, Dion K, Mengual M, Mireji PO, Ouma C, Okoth S, Murilla G, Aksoy S, Caccone A. Genetic Differentiation of Glossina pallidipes Tsetse Flies in Southern Kenya. Am J Trop Med Hyg 2018; 99:945-953. [PMID: 30105964 PMCID: PMC6159567 DOI: 10.4269/ajtmh.18-0154] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 06/15/2018] [Indexed: 11/07/2022] Open
Abstract
The tsetse fly Glossina pallidipes, the major vector of the parasite that causes animal African trypanosomiasis in Kenya, has been subject to intense control measures with only limited success. The G. pallidipes population dynamics and dispersal patterns that underlie limited success in vector control campaigns remain unresolved, and knowledge on genetic connectivity can provide insights, and thereby improve control and monitoring efforts. We therefore investigated the population structure and estimated migration and demographic parameters in G. pallidipes using genotypic data from 11 microsatellite loci scored in 250 tsetse flies collected from eight localities in Kenya. Clustering analysis identified two genetically distinct eastern and western clusters (mean between-cluster F ST = 0.202) separated by the Great Rift Valley. We also found evidence of admixture and migration between the eastern and western clusters, isolation by distance, and a widespread signal of inbreeding. We detected differences in population dynamics and dispersal patterns between the western and eastern clusters. These included lower genetic diversity (allelic richness; 7.48 versus 10.99), higher relatedness (percent related individuals; 21.4% versus 9.1%), and greater genetic differentiation (mean within-cluster F ST; 0.183 versus 0.018) in the western than the eastern cluster. Findings are consistent with the presence of smaller, less well-connected populations in Western relative to eastern Kenya. These data suggest that recent anthropogenic influences such as land use changes and vector control programs have influenced population dynamics in G. pallidipes in Kenya, and that vector control efforts should include some region-specific strategies to effectively control this disease vector.
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Affiliation(s)
- Winnie A. Okeyo
- Department of Biomedical Sciences and Technology, School of Public Health and Community Development, Maseno University, Kisumu, Kenya
- Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, Nairobi, Kenya
- Yale School of Public Health, Yale University, New Haven, Connecticut
| | - Norah P. Saarman
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, Connecticut
| | - Rosemary Bateta
- Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, Nairobi, Kenya
| | - Kirstin Dion
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, Connecticut
| | - Michael Mengual
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, Connecticut
| | - Paul O. Mireji
- Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, Nairobi, Kenya
- Yale School of Public Health, Yale University, New Haven, Connecticut
- Center for Geographic Medicine Research Coast, Kenya Medical Research Institute, Kilifi, Kenya
| | - Collins Ouma
- Department of Biomedical Sciences and Technology, School of Public Health and Community Development, Maseno University, Kisumu, Kenya
| | - Sylvance Okoth
- Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, Nairobi, Kenya
| | - Grace Murilla
- Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, Nairobi, Kenya
- Yale School of Public Health, Yale University, New Haven, Connecticut
| | - Serap Aksoy
- Yale School of Public Health, Yale University, New Haven, Connecticut
| | - Adalgisa Caccone
- Yale School of Public Health, Yale University, New Haven, Connecticut
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, Connecticut
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Saarman NP, Kober KM, Simison WB, Pogson GH. Sequence-Based Analysis of Thermal Adaptation and Protein Energy Landscapes in an Invasive Blue Mussel (Mytilus galloprovincialis). Genome Biol Evol 2018; 9:2739-2751. [PMID: 28985307 PMCID: PMC5647807 DOI: 10.1093/gbe/evx190] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/13/2017] [Indexed: 12/12/2022] Open
Abstract
Adaptive responses to thermal stress in poikilotherms plays an important role in determining competitive ability and species distributions. Amino acid substitutions that affect protein stability and modify the thermal optima of orthologous proteins may be particularly important in this context. Here, we examine a set of 2,770 protein-coding genes to determine if proteins in a highly invasive heat tolerant blue mussel (Mytilus galloprovincialis) contain signals of adaptive increases in protein stability relative to orthologs in a more cold tolerant M. trossulus. Such thermal adaptations might help to explain, mechanistically, the success with which the invasive marine mussel M. galloprovincialis has displaced native species in contact zones in the eastern (California) and western (Japan) Pacific. We tested for stabilizing amino acid substitutions in warm tolerant M. galloprovincialis relative to cold tolerant M. trossulus with a generalized linear model that compares in silico estimates of recent changes in protein stability among closely related congeners. Fixed substitutions in M. galloprovincialis were 3,180.0 calories per mol per substitution more stabilizing at genes with both elevated dN/dS ratios and transcriptional responses to heat stress, and 705.8 calories per mol per substitution more stabilizing across all 2,770 loci investigated. Amino acid substitutions concentrated in a small number of genes were more stabilizing in M. galloprovincialis compared with cold tolerant M. trossulus. We also tested for, but did not find, enrichment of a priori GO terms in genes with elevated dN/dS ratios in M. galloprovincialis. This might indicate that selection for thermodynamic stability is generic across all lineages, and suggests that the high change in estimated protein stability that we observed in M. galloprovincialis is driven by selection for extra stabilizing substitutions, rather than by higher incidence of selection in a greater number of genes in this lineage. Nonetheless, our finding of more stabilizing amino acid changes in the warm adapted lineage is important because it suggests that adaption for thermal stability has contributed to M. galloprovincialis’ superior tolerance to heat stress, and that pairing tests for positive selection and tests for transcriptional response to heat stress can identify candidates of protein stability adaptation.
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Affiliation(s)
- Norah P Saarman
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz.,Department of Ecology and Evolutionary Biology, Yale University
| | - Kord M Kober
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz.,Department of Physiological Nursing, University of California, San Francisco.,Institute for Computational Health Sciences, University of California, San Francisco
| | - W Brian Simison
- Center for Comparative Genomics, California Academy of Sciences, San Francisco, California
| | - Grant H Pogson
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz
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9
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Okeyo WA, Saarman NP, Mengual M, Dion K, Bateta R, Mireji PO, Okoth S, Ouma JO, Ouma C, Ochieng J, Murilla G, Aksoy S, Caccone A. Temporal genetic differentiation in Glossina pallidipes tsetse fly populations in Kenya. Parasit Vectors 2017; 10:471. [PMID: 29017572 PMCID: PMC5635580 DOI: 10.1186/s13071-017-2415-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 10/01/2017] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Glossina pallidipes is a major vector of both Human and Animal African Trypanosomiasis (HAT and AAT) in Kenya. The disease imposes economic burden on endemic regions in Kenya, including south-western Kenya, which has undergone intense but unsuccessful tsetse fly control measures. We genotyped 387 G. pallidipes flies at 13 microsatellite markers to evaluate levels of temporal genetic variation in two regions that have been subjected to intensive eradication campaigns from the 1960s to the 1980s. One of the regions, Nguruman Escarpment, has been subject to habitat alteration due to human activities, while the other, Ruma National Park, has not. In addition, Nguruman Escarpment is impacted by the movement of grazing animals into the area from neighboring regions during the drought season. We collected our samples from three geographically close sampling sites for each of the two regions. Samples were collected between the years 2003 and 2015, spanning ~96 tsetse fly generations. RESULTS We established that allelic richness averaged 3.49 and 3.63, and temporal Ne estimates averaged 594 in Nguruman Escarpment and 1120 in Ruma National Park. This suggests that genetic diversity is similar to what was found in previous studies of G. pallidipes in Uganda and Kenya, implying that we could not detect a reduction in genetic diversity following the extensive control efforts during the 1960s to the 1980s. However, we did find differences in temporal patterns of genetic variation between the two regions, indicated by clustering analysis, pairwise FST, and Fisher's exact tests for changes in allele and genotype frequencies. In Nguruman Escarpment, findings indicated differentiation among samples collected in different years, and evidence of local genetic bottlenecks in two locations previous to 2003, and between 2009 and 2015. In contrast, there was no consistent evidence of differentiation among samples collected in different years, and no evidence of local genetic bottlenecks in Ruma National Park. CONCLUSION Our findings suggest that, despite extensive control measures especially between the 1960s and the 1980s, tsetse flies in these regions persist with levels of genetic diversity similar to that found in populations that did not experience extensive control measures. Our findings also indicate temporal genetic differentiation in Nguruman Escarpment detected at a scale of > 80 generations, and no similar temporal differentiation in Ruma National Park. The different level of temporal differentiation between the two regions indicates that genetic drift is stronger in Nugruman Escarpment, for as-yet unknown reasons, which may include differences in land management. This suggests land management may have an impact on G. pallidipes population genetics, and reinforces the importance of long term monitoring of vector populations in estimates of parameters needed to model and plan effective species-specific control measures.
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Affiliation(s)
- Winnie A. Okeyo
- Yale School of Public Health, Yale University, New Haven, CT USA
- Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, Nairobi, Kikuyu Kenya
- Department of Biomedical Science and Technology, School of Public Health and Community Development, Maseno University, Kisumu, Maseno Kenya
| | - Norah P. Saarman
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT USA
| | - Michael Mengual
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT USA
| | - Kirstin Dion
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT USA
| | - Rosemary Bateta
- Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, Nairobi, Kikuyu Kenya
| | - Paul O. Mireji
- Yale School of Public Health, Yale University, New Haven, CT USA
- Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, Nairobi, Kikuyu Kenya
- Centre for Geographic Medicine Research Coast, Kenya Medical Research Institute, Kilifi, Kenya
| | - Sylvance Okoth
- Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, Nairobi, Kikuyu Kenya
| | - Johnson O. Ouma
- Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, Nairobi, Kikuyu Kenya
- Africa Technical Research Center, Vector Health International, Arusha, Tanzania
| | - Collins Ouma
- Department of Biomedical Science and Technology, School of Public Health and Community Development, Maseno University, Kisumu, Maseno Kenya
| | - Joel Ochieng
- Centre for Biotechnology and Bioinformatics, University of Nairobi, Nairobi, Kenya
| | - Grace Murilla
- Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, Nairobi, Kikuyu Kenya
| | - Serap Aksoy
- Yale School of Public Health, Yale University, New Haven, CT USA
| | - Adalgisa Caccone
- Yale School of Public Health, Yale University, New Haven, CT USA
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT USA
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10
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Saarman NP, Gloria-Soria A, Anderson EC, Evans BR, Pless E, Cosme LV, Gonzalez-Acosta C, Kamgang B, Wesson DM, Powell JR. Effective population sizes of a major vector of human diseases, Aedes aegypti. Evol Appl 2017; 10:1031-1039. [PMID: 29151858 PMCID: PMC5680635 DOI: 10.1111/eva.12508] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 06/09/2017] [Indexed: 01/13/2023] Open
Abstract
The effective population size (Ne) is a fundamental parameter in population genetics that determines the relative strength of selection and random genetic drift, the effect of migration, levels of inbreeding, and linkage disequilibrium. In many cases where it has been estimated in animals, Ne is on the order of 10%–20% of the census size. In this study, we use 12 microsatellite markers and 14,888 single nucleotide polymorphisms (SNPs) to empirically estimate Ne in Aedes aegypti, the major vector of yellow fever, dengue, chikungunya, and Zika viruses. We used the method of temporal sampling to estimate Ne on a global dataset made up of 46 samples of Ae. aegypti that included multiple time points from 17 widely distributed geographic localities. Our Ne estimates for Ae. aegypti fell within a broad range (~25–3,000) and averaged between 400 and 600 across all localities and time points sampled. Adult census size (Nc) estimates for this species range between one and five thousand, so the Ne/Nc ratio is about the same as for most animals. These Ne values are lower than estimates available for other insects and have important implications for the design of genetic control strategies to reduce the impact of this species of mosquito on human health.
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Affiliation(s)
| | | | - Eric C Anderson
- Fisheries Ecology Division Southwest Fisheries Science Center National Marine Fisheries Service and University of California Santa Cruz CA USA
| | | | | | | | | | - Basile Kamgang
- LSTM/OCEAC Research Unit Organisation de Coordination pour la lutte contre les Endémies en Afrique Centrale Yaoundé Cameroon
| | - Dawn M Wesson
- Department of Tropical Medicine Tulane University New Orleans LA USA
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11
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Kamidi CM, Saarman NP, Dion K, Mireji PO, Ouma C, Murilla G, Aksoy S, Schnaufer A, Caccone A. Multiple evolutionary origins of Trypanosoma evansi in Kenya. PLoS Negl Trop Dis 2017; 11:e0005895. [PMID: 28880965 PMCID: PMC5605091 DOI: 10.1371/journal.pntd.0005895] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 09/19/2017] [Accepted: 08/22/2017] [Indexed: 11/19/2022] Open
Abstract
Trypanosoma evansi is the parasite causing surra, a form of trypanosomiasis in camels and other livestock, and a serious economic burden in Kenya and many other parts of the world. Trypanosoma evansi transmission can be sustained mechanically by tabanid and Stomoxys biting flies, whereas the closely related African trypanosomes T. brucei brucei and T. b. rhodesiense require cyclical development in tsetse flies (genus Glossina) for transmission. In this study, we investigated the evolutionary origins of T. evansi. We used 15 polymorphic microsatellites to quantify levels and patterns of genetic diversity among 41 T. evansi isolates and 66 isolates of T. b. brucei (n = 51) and T. b. rhodesiense (n = 15), including many from Kenya, a region where T. evansi may have evolved from T. brucei. We found that T. evansi strains belong to at least two distinct T. brucei genetic units and contain genetic diversity that is similar to that in T. brucei strains. Results indicated that the 41 T. evansi isolates originated from multiple T. brucei strains from different genetic backgrounds, implying independent origins of T. evansi from T. brucei strains. This surprising finding further suggested that the acquisition of the ability of T. evansi to be transmitted mechanically, and thus the ability to escape the obligate link with the African tsetse fly vector, has occurred repeatedly. These findings, if confirmed, have epidemiological implications, as T. brucei strains from different genetic backgrounds can become either causative agents of a dangerous, cosmopolitan livestock disease or of a lethal human disease, like for T. b. rhodesiense.
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Affiliation(s)
- Christine M. Kamidi
- Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, Kikuyu, Kenya
- Department of Biomedical Sciences and Technology, School of Public Health and Community Development, Maseno University, Maseno, Kenya
- Yale School of Public Health, Department of Epidemiology of Microbial Diseases, New Haven, CT, United States of America
| | - Norah P. Saarman
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, United States of America
| | - Kirstin Dion
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, United States of America
| | - Paul O. Mireji
- Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, Kikuyu, Kenya
- Yale School of Public Health, Department of Epidemiology of Microbial Diseases, New Haven, CT, United States of America
- Centre for Geographic Medicine Research Coast, Kenya Medical Research Institute, Kilifi, Kenya
| | - Collins Ouma
- Department of Biomedical Sciences and Technology, School of Public Health and Community Development, Maseno University, Maseno, Kenya
| | - Grace Murilla
- Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, Kikuyu, Kenya
| | - Serap Aksoy
- Yale School of Public Health, Department of Epidemiology of Microbial Diseases, New Haven, CT, United States of America
| | - Achim Schnaufer
- Centre for Immunity, Infection & Evolution, and Institute of Immunology & Infection Research, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Adalgisa Caccone
- Yale School of Public Health, Department of Epidemiology of Microbial Diseases, New Haven, CT, United States of America
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, United States of America
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12
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Opiro R, Saarman NP, Echodu R, Opiyo EA, Dion K, Halyard A, Aksoy S, Caccone A. Evidence of temporal stability in allelic and mitochondrial haplotype diversity in populations of Glossina fuscipes fuscipes (Diptera: Glossinidae) in northern Uganda. Parasit Vectors 2016; 9:258. [PMID: 27141947 PMCID: PMC4855780 DOI: 10.1186/s13071-016-1522-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 04/20/2016] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Glossina fuscipes fuscipes is a tsetse species of high economic importance in Uganda where it is responsible for transmitting animal African trypanosomiasis (AAT) and both the chronic and acute forms of human African trypanosomiasis (HAT). We used genotype data from 17 microsatellites and a mitochondrial DNA marker to assess temporal changes in gene frequency for samples collected between the periods ranging from 2008 to 2014 in nine localities spanning regions known to harbor the two forms of HAT in northern Uganda. RESULTS Our findings suggest that the majority of the studied populations in both HAT foci are genetically stable across the time span sampled. Pairwise estimates of differentiation using standardized FST and Jost's DEST between time points sampled for each site were generally low and ranged between 0.0019 and 0.1312 for both sets of indices. We observed the highest values of FST and DEST between time points sampled from Kitgum (KT), Karuma (KR), Moyo (MY) and Pader (PD), and the possible reasons for this are discussed. Effective population size (Ne) estimates using Waple's temporal method ranged from 103 (95% CI: 73-138) in Kitgum to 962 (95% CI: 669-1309) in Oculoi (OC). Additionally, evidence of a bottleneck event was detected in only one population at one time point sampled; Aminakwach (AM-27) from December 2014 (P < 0.03889). CONCLUSION Findings suggest general temporal stability of tsetse vectors in foci of both forms of HAT in northern Uganda. Genetic stability and the moderate effective population sizes imply that a re-emergence of vectors from local residual populations missed by control efforts is an important risk. This underscores the need for more sensitive sampling and monitoring to detect residual populations following control activities.
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Affiliation(s)
- Robert Opiro
- Department of Biology, Faculty of Science, Gulu University, Gulu, Uganda.
| | - Norah P Saarman
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Richard Echodu
- Department of Biology, Faculty of Science, Gulu University, Gulu, Uganda
| | - Elizabeth A Opiyo
- Department of Biology, Faculty of Science, Gulu University, Gulu, Uganda
| | - Kirstin Dion
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Alexis Halyard
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Serap Aksoy
- Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
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13
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Saarman NP, Pogson GH. Introgression between invasive and native blue mussels (genusMytilus) in the central California hybrid zone. Mol Ecol 2015; 24:4723-38. [DOI: 10.1111/mec.13340] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 07/28/2015] [Accepted: 07/29/2015] [Indexed: 01/05/2023]
Affiliation(s)
- Norah P. Saarman
- Department of Ecology and Evolutionary Biology; Yale University; PO Box 208106 New Haven CT 06520-8106 USA
| | - Grant H. Pogson
- Department of Ecology and Evolutionary Biology; UC Santa Cruz; Santa Cruz CA 95064 USA
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