Open Access
Issue
Parasite
Volume 31, 2024
Article Number 13
Number of page(s) 13
DOI https://doi.org/10.1051/parasite/2024013
Published online 06 March 2024
  1. Belkhir K, Borsa P, Chikhi L, Raufaste N, Bonhomme F. 2004. GENETIX 4.05, logiciel sous Windows TM pour la génétique des populations. Montpellier, France: Laboratoire Génome, Populations, Interactions, CNRS UMR 5000, Université de Montpellier II. [Google Scholar]
  2. Benjamini Y, Yekutieli D. 2001. The control of the false discovery rate in multiple testing under dependency. Annals of Statistics, 29, 1165–1188. [CrossRef] [Google Scholar]
  3. Boulangé A, Lejon V, Berthier D, Thévenon S, Gimonneau G, Desquesnes M, Abah S, Agboho P, Chilongo K, Gebre T, Fall AG, Kaba D, Magez S, Masiga D, Matovu E, Moukhtar A, Neves L, Olet PA, Pagabeleguem S, Shereni W, Sorli B, Taioe MO, Tejedor Junco MT, Yagi R, Solano P, Cecchi G. 2022. The COMBAT project: controlling and progressively minimizing the burden of vector-borne animal trypanosomosis in Africa. Open Research Europe, 2, 67. [CrossRef] [PubMed] [Google Scholar]
  4. Bouyer J, Dicko AH, Cecchi G, Ravel S, Guerrini L, Solano P, Vreysen MJB, De Meeûs T, Lancelot R. 2015. Mapping landscape friction to locate isolated tsetse populations candidate for elimination. Proceedings of the National Academy of Sciences of the United States of America, 112, 14575–14580. [CrossRef] [PubMed] [Google Scholar]
  5. Brookfield JFY. 1996. A simple new method for estimating null allele frequency from heterozygote deficiency. Molecular Ecology, 5, 453–455. [CrossRef] [PubMed] [Google Scholar]
  6. Camara O, Biéler S, Bucheton B, Kagbadouno M, Mathu Ndung’u J, Solano P, Camara M. 2021. Accelerating elimination of sleeping sickness from the Guinean littoral through enhanced screening in the post-Ebola context: A retrospective analysis. PLOS Neglected Tropical Diseases, 15, e0009163. [CrossRef] [PubMed] [Google Scholar]
  7. Cavalli-Sforza LL, Edwards AWF. 1967. Phylogenetic analysis: model and estimation procedures. American Journal of Human Genetics, 19, 233–257. [PubMed] [Google Scholar]
  8. Challier A, Laveissière C. 1973. Un nouveau piège pour la capture des glossines (Glossina: Diptera, Muscidae): description et assais sur le terrain. Cahiers de l’ORSTOM, Série Entomologie Médicale et Parasitologie, 11, 251–262. [Google Scholar]
  9. Chapuis MP, Estoup A. 2007. Microsatellite null alleles and estimation of population differentiation. Molecular Biology and Evolution, 24, 621–631. [CrossRef] [PubMed] [Google Scholar]
  10. Coombs JA, Letcher BH, Nislow KH. 2008. CREATE: a software to create input files from diploid genotypic data for 52 genetic software programs. Molecular Ecology Resources, 8, 578–580. [CrossRef] [PubMed] [Google Scholar]
  11. Cornuet JM, Luikart G. 1996. Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics, 144, 2001–2014. [CrossRef] [PubMed] [Google Scholar]
  12. Courtin F, Camara M, Rayaisse JB, Kagbadouno M, Dama E, Camara O, Traore IS, Rouamba J, Peylhard M, Somda MB, Leno M, Lehane MJ, Torr SJ, Solano P, Jamonneau V, Bucheton B. 2015. Reducing human-tsetse contact significantly enhances the efficacy of sleeping sickness active screening campaigns: a promising result in the context of elimination. PLoS Neglected Tropical Diseases, 9, e0003727. [CrossRef] [PubMed] [Google Scholar]
  13. De Meeûs T. 2018. Revisiting FIS, FST, Wahlund effects, and Null alleles. Journal of Heredity, 109, 446–456. [CrossRef] [PubMed] [Google Scholar]
  14. De Meeûs T. 2021. Initiation à la génétique des populations naturelles: applications aux parasites et à leurs vecteurs. 2ème édition revue et augmentée. Marseille: IRD Éditions. [Google Scholar]
  15. De Meeûs T, Chan CT, Ludwig JM, Tsao JI, Patel J, Bhagatwala J, Beati L. 2021. Deceptive combined effects of short allele dominance and stuttering: an example with Ixodes scapularis, the main vector of Lyme disease in the USA. Peer Community Journal, 1, e40. [CrossRef] [Google Scholar]
  16. De Meeûs T, Guégan JF, Teriokhin AT. 2009. MultiTest vol 1.2, a program to binomially combine independent tests and performance comparison with other related methods on proportional data. BMC Bioinformatics, 10, 443. [CrossRef] [PubMed] [Google Scholar]
  17. De Meeûs T, Humair PF, Grunau C, Delaye C, Renaud F. 2004. Non-Mendelian transmission of alleles at microsatellite loci: an example in Ixodes ricinus, the vector of Lyme disease. International Journal for Parasitology, 34, 943–950. [CrossRef] [PubMed] [Google Scholar]
  18. De Meeûs T, McCoy KD, Prugnolle F, Chevillon C, Durand P, Hurtrez-Boussès S, Renaud F. 2007. Population genetics and molecular epidemiology or how to “débusquer la bête”. Infection Genetics and Evolution, 7, 308–332. [CrossRef] [Google Scholar]
  19. De Meeûs T, Noûs C. 2022. A simple procedure to detect, test for the presence of stuttering, and cure stuttered data with spreadsheet programs. Peer Community Journal, 2, e52. [CrossRef] [Google Scholar]
  20. De Meeûs T, Noûs C. 2023. A new and almost perfectly accurate approximation of the eigenvalue effective population size of a dioecious population: comparisons with other estimates and detailed proofs. Peer Community Journal, 3, e51. [CrossRef] [Google Scholar]
  21. De Meeûs T, Ravel S, Solano P, Bouyer J. 2019. Negative density dependent dispersal in tsetse flies: a risk for control campaigns? Trends in Parasitology, 35, 615–621. [CrossRef] [PubMed] [Google Scholar]
  22. Dempster AP, Laird NM, Rubin DB. 1977. Maximum likelihood from incomplete data via the EM algorithm. Journal of the Royal Statistical Society Series B, 39, 1–38. [Google Scholar]
  23. Do C, Waples RS, Peel D, Macbeth GM, Tillett BJ, Ovenden JR. 2014. NeEstimator v2: re-implementation of software for the estimation of contemporary effective population size (Ne) from genetic data. Molecular Ecology Resources, 14, 209–214. [CrossRef] [PubMed] [Google Scholar]
  24. Eperon G, Balasegaram M, Potet J, Mowbray C, Valverde O, Chappuis F. 2014. Treatment options for second-stage gambiense human African trypanosomiasis. Expert Review of Anti-Infective Therapy, 12, 1407–1417. [CrossRef] [PubMed] [Google Scholar]
  25. Fox J. 2005. The R commander: a basic statistics graphical user interface to R. Journal of Statistical Software, 14, 1–42. [Google Scholar]
  26. Fox J. 2007. Extending the R commander by “plug in” packages. R News, 7, 46–52. [Google Scholar]
  27. Franco JR, Cecchi G, Paone M, Diarra A, Grout L, Kadima Ebeja A, Simarro PP, Zhao W, Argaw D. 2022. The elimination of human African trypanosomiasis: Achievements in relation to WHO road map targets for 2020. PLoS Neglected Tropical Diseases, 16, e0010047. [CrossRef] [PubMed] [Google Scholar]
  28. Frontier S. 1976. Étude de la décroissance des valeurs propres dans une analyse en composantes principales: comparaison avec le modèle du bâton brisé. Journal of Experimental Marine Biology and Ecology, 25, 67–75. [CrossRef] [Google Scholar]
  29. Goudet J. 2003. Fstat (ver. 2.9.4), a program to estimate and test population genetics parameters. Available at http://www.t-de-meeus.fr/Programs/Fstat294.zip, Updated from Goudet (1995). [Google Scholar]
  30. Goudet J. 1995. FSTAT (Version 1.2): A computer program to calculate F-statistics. Journal of Heredity, 86, 485–486. [CrossRef] [Google Scholar]
  31. Goudet J, Raymond M, De Meeûs T, Rousset F. 1996. Testing differentiation in diploid populations. Genetics, 144, 1933–1940. [CrossRef] [PubMed] [Google Scholar]
  32. Hedrick PW. 2005. A standardized genetic differentiation measure. Evolution, 59, 1633–1638. [Google Scholar]
  33. Hijmans RJ, Williams E, Vennes C. 2019. Package “geosphere”: spherical trigonometry. Jou. Vienna, Austria: R Foundation for Statistical Computing. Available at https://CRAN.R-project.org/package=geosphere. [Google Scholar]
  34. Holmes P. 2014. First WHO meeting of stakeholders on elimination of gambiense human african trypanosomiasis. PLoS Neglected Tropical Diseases, 8, e3244. [CrossRef] [PubMed] [Google Scholar]
  35. Jones OR, Wang JL. 2010. COLONY: a program for parentage and sibship inference from multilocus genotype data. Molecular Ecology Resources, 10, 551–555. [CrossRef] [Google Scholar]
  36. Jorde PE, Ryman N. 2007. Unbiased estimator for genetic drift and effective population size. Genetics, 177, 927–935. [CrossRef] [PubMed] [Google Scholar]
  37. Karney CFF. 2013. Algorithms for geodesics. Journal of Geodesy, 87, 43–55. [CrossRef] [Google Scholar]
  38. Mahamat MH, Peka M, Rayaisse JB, Rock KS, Toko MA, Darnas J, Brahim GM, Alkatib AB, Yoni W, Tirados I, Courtin F, Brand SPC, Nersy C, Alfaroukh IO, Torr SJ, Lehane MJ, Solano P. 2017. Adding tsetse control to medical activities contributes to decreasing transmission of sleeping sickness in the Mandoul focus (Chad). PLoS Neglected Tropical Diseases, 11, e0005792. [CrossRef] [PubMed] [Google Scholar]
  39. Manangwa O, De Meeûs T, Grébaut P, Segard A, Byamungu M, Ravel S. 2019. Detecting Wahlund effects together with amplification problems : cryptic species, null alleles and short allele dominance in Glossina pallidipes populations from Tanzania. Molecular Ecology Resources, 19, 757–772. [CrossRef] [PubMed] [Google Scholar]
  40. Meirmans PG. 2006. Using the AMOVA framework to estimate a standardized genetic differentiation measure. Evolution, 60, 2399–2402. [CrossRef] [PubMed] [Google Scholar]
  41. Melachio Tanekou TT, Bouaka Tsakeng CU, Tirados I, Acho A, Bigoga J, Wondji CS, Njiokou F. 2023. Impact of a small-scale tsetse fly control operation with deltamethrin impregnated “Tiny Targets” on tsetse density and trypanosomes’ circulation in the Campo sleeping sickness focus of South Cameroon. PLOS Neglected Tropical Diseases, 17, e0011802. [CrossRef] [PubMed] [Google Scholar]
  42. Ndung’u JM, Boulangé A, Picado A, Mugenyi A, Mortensen A, Hope A, Mollo BG, Bucheton B, Wamboga C, Waiswa C, Kaba D, Matovu E, Courtin F, Garrod G, Gimonneau G, Bingham GV, Hassane HM, Tirados I, Saldanha I, Kabore J, Rayaisse JB, Bart JM, Lingley J, Esterhuizen J, Longbottom J, Pulford J, Kouakou L, Sanogo L, Cunningham L, Camara M, Koffi M, Stanton M, Lehane M, Kagbadouno MS, Camara O, Bessell P, Mallaye P, Solano P, Selby R, Dunkley S, Torr S, Biéler S, Lejon V, Jamonneau V, Yoni W, Katz Z. 2020. Trypa-NO! contributes to the elimination of gambiense human African trypanosomiasis by combining tsetse control with “screen, diagnose and treat” using innovative tools and strategies. PLoS Neglected Tropical Diseases, 14, e0008738. [CrossRef] [PubMed] [Google Scholar]
  43. Nei M, Chesser RK. 1983. Estimation of fixation indices and gene diversities. Annals of Human Genetics, 47, 253–259. [CrossRef] [PubMed] [Google Scholar]
  44. Nei M, Tajima F. 1981. Genetic drift and estimation of effective population size. Genetics, 98, 625–640. [CrossRef] [PubMed] [Google Scholar]
  45. Nomura T. 2008. Estimation of effective number of breeders from molecular coancestry of single cohort sample. Evolutionary Applications, 1, 462–474. [CrossRef] [PubMed] [Google Scholar]
  46. Peel D, Waples RS, Macbeth GM, Do C, Ovenden JR. 2013. Accounting for missing data in the estimation of contemporary genetic effective population size (Ne). Molecular Ecology Resources, 13, 243–253. [CrossRef] [PubMed] [Google Scholar]
  47. Piry S, Luikart G, Cornuet JM. 1999. BOTTLENECK: A computer program for detecting recent reductions in the effective population size using allele frequency data. Journal of Heredity, 90, 502–503. [CrossRef] [Google Scholar]
  48. Pollak E. 1983. A new method for estimating the effective population size from allele frequency changes. Genetics, 104, 531–548. [CrossRef] [PubMed] [Google Scholar]
  49. Ravel S, De Meeûs T, Dujardin JP, Zeze DG, Gooding RH, Dusfour I, Sane B, Cuny G, Solano P. 2007. The tsetse fly Glossina palpalis palpalis is composed of several genetically differentiated small populations in the sleeping sickness focus of Bonon, Côte d’Ivoire. Infection, Genetics and Evolution, 7, 116–125. [CrossRef] [PubMed] [Google Scholar]
  50. Ravel S, Mahamat MH, Ségard A, Argiles-Herrero R, Bouyer J, Rayaisse J-B, Solano P, Mollo BG, Pèka M, Darnas J, Belem AMG, Yoni W, Noûs C, De Meeûs T. 2023. Population genetics of Glossina fuscipes fuscipes from southern Chad. Peer Community Journal, 3, e31. [CrossRef] [Google Scholar]
  51. Ravel S, Sere M, Manangwa O, Kagbadouno M, Mahamat MH, Shereni W, Okeyo WA, Argiles-Herrero R, De Meeûs T. 2020. Developing and quality testing of microsatellite loci for four species of Glossina. Infection, Genetics and Evolution, 85, 104515. [CrossRef] [PubMed] [Google Scholar]
  52. Rayaisse JB, Esterhuizen J, Tirados I, Kaba D, Salou E, Diarrassouba A, Vale GA, Lehane MJ, Torr SJ, Solano P. 2011. Towards an optimal design of target for tsetse control: comparisons of novel targets for the control of Palpalis group tsetse in West Africa. PLoS Neglected Tropical Diseases, 5, e1332. [CrossRef] [PubMed] [Google Scholar]
  53. R-Core-Team. 2022. R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing. Available at https://www.R-project.org. [Google Scholar]
  54. Rousset F. 1997. Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics, 145, 1219–1228. [CrossRef] [PubMed] [Google Scholar]
  55. Séré M, Thévenon S, Belem AMG, De Meeûs T. 2017. Comparison of different genetic distances to test isolation by distance between populations. Heredity, 119, 55–63. [CrossRef] [PubMed] [Google Scholar]
  56. She JX, Autem M, Kotulas G, Pasteur N, Bonhomme F. 1987. Multivariate analysis of genetic exchanges between Solea aegyptiaca and Solea senegalensis (Teleosts, Soleidae). Biological Journal of the Linnean Society, 32, 357–371. [CrossRef] [Google Scholar]
  57. Solano P, Ravel S, De Meeûs T. 2010. How can tsetse population genetics contribute to African trypanosomiasis control? Trends in Parasitology, 26, 255–263. [CrossRef] [PubMed] [Google Scholar]
  58. Teriokhin AT, De Meeûs T, Guegan JF. 2007. On the power of some binomial modifications of the Bonferroni multiple test. Zhurnal Obshchei Biologii, 68, 332–340. [PubMed] [Google Scholar]
  59. Van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P. 2004. MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Molecular Ecology Notes, 4, 535–538. [Google Scholar]
  60. Vitalis R. 2002. Estim 1.2-2: a computer program to infer population parameters from one- and two-locus gene identity probabilities, updated from Vitalis and Couvet (2001). Molecular Ecology Notes, 1, 354–356. [CrossRef] [Google Scholar]
  61. Vitalis R, Couvet D. 2001. Estimation of effective population size and migration rate from one- and two-locus identity measures. Genetics, 157, 911–925. [CrossRef] [PubMed] [Google Scholar]
  62. Vitalis R, Couvet D. 2001. ESTIM 1.0: a computer program to infer population parameters from one- and two-locus gene identity probabilities. Molecular Ecology Notes, 1, 354–356. [CrossRef] [Google Scholar]
  63. Wang J. 2015. Does GST underestimate genetic differentiation from marker data? Molecular Ecology, 24, 3546–3558. [CrossRef] [PubMed] [Google Scholar]
  64. Wang JL. 2009. A new method for estimating effective population sizes from a single sample of multilocus genotypes. Molecular Ecology, 18, 2148–2164. [CrossRef] [PubMed] [Google Scholar]
  65. Wang JL, Whitlock MC. 2003. Estimating effective population size and migration rates from genetic samples over space and time. Genetics, 163, 429–446. [CrossRef] [PubMed] [Google Scholar]
  66. Waples RS. 2006. A bias correction for estimates of effective population size based on linkage disequilibrium at unlinked gene loci. Conservation Genetics, 7, 167–184. [CrossRef] [Google Scholar]
  67. Watts PC, Rousset F, Saccheri IJ, Leblois R, Kemp SJ, Thompson DJ. 2007. Compatible genetic and ecological estimates of dispersal rates in insect (Coenagrion mercuriale: Odonata: Zygoptera) populations: analysis of “neighbourhood size” using a more precise estimator. Molecular Ecology, 16, 737–751. [CrossRef] [PubMed] [Google Scholar]
  68. Weir BS, Cockerham CC. 1984. Estimating F-statistics for the analysis of population structure. Evolution, 38, 1358–1370. [Google Scholar]
  69. Wright S. 1965. The interpretation of population structure by F-statistics with special regard to system of mating. Evolution, 19, 395–420. [CrossRef] [Google Scholar]

Current usage metrics show cumulative count of Article Views (full-text article views including HTML views, PDF and ePub downloads, according to the available data) and Abstracts Views on Vision4Press platform.

Data correspond to usage on the plateform after 2015. The current usage metrics is available 48-96 hours after online publication and is updated daily on week days.

Initial download of the metrics may take a while.