Section: Ecology
Topic: Ecology, Genetics/Genomics, Population biology

Interplay between historical and current features of the cityscape in shaping the genetic structure of the house mouse (Mus musculus domesticus) in Dakar (Senegal, West Africa)

Stragier, Claire1; Piry, Sylvain2 ; Loiseau, Anne2; Kane, Mamadou1; Sow, Aliou1; Niang, Youssoupha1; Diallo, Mamoudou1; Ndiaye, Arame1; Gauthier, Philippe2; Borderon, Marion3; Granjon, Laurent2; Brouat, Carine2   ; Berthier, Karine4  
1 BIOPASS (IRD-CBGP, CIRAD, ISRA, UCAD), Campus de Bel-Air, BP 1386, CP 18524 Dakar, Senegal
2 CBGP, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
3 Department of Geography and Regional Research, University of Vienna, Austria
4 Pathologie Végétale, INRAE, 84140 Montfavet, France

Corresponding author(s): Brouat, Carine (carine.brouat@ird.fr)

10.24072/pcjournal.85 - Peer Community Journal, Volume 2 (2022), article no. e11.

Get full text PDF Peer reviewed and recommended by PCI
article image

Population genetic approaches may be used to investigate dispersal patterns of species living in highly urbanized environment in order to improve management strategies for biodiversity conservation or pest control. However, in such environment, population genetic structure may reflect both current features of the cityscape and urbanization history. This can be especially relevant when focusing on exotic commensal rodents that have been introduced in numerous primary colonial European settlements. Accounting for spatial and temporal cityscape heterogeneity to determine how past and recent demographic events may interplay to shape current population genetic structure of synanthropic rodents may provide useful insights to manage their populations. In this study, we addressed these issues by focusing on the house mouse, Mus musculus domesticus, in Dakar, Senegal, where the species may have been introduced as soon as Europeans settled in the middle of the nineteenth century. We examined genetic variation at one mitochondrial locus and 15 nuclear microsatellite markers from individuals sampled in 14 sampling sites representing different stages of urbanization history and different socio-economic environments in Dakar. We used various approaches, including model-based genetic clustering and model-free smoothing of pairwise genetic estimates. We further linked observed spatial genetic patterns to historical and current features of Dakar cityscape using random forest and Bayesian conditional autoregressive models. Results are consistent with an introduction of the house mouse at colonial time and the current genetic structure exhibits a gradient-like pattern reflecting the historical process of spatially continuous expansion of the city from the first European settlement. The genetic patterns further suggest that population dynamics of the house mouse is also driven by the spatial heterogeneity of the current cityscape, including socio-economics features, that translate in habitat quality. Our results highlight the potential importance of accounting for past demographic events to understand spatial genetic patterns of nonnative invasive commensal rodents in highly urbanized environment.

Published online:
DOI: 10.24072/pcjournal.85
Type: Research article

Stragier, Claire 1; Piry, Sylvain 2; Loiseau, Anne 2; Kane, Mamadou 1; Sow, Aliou 1; Niang, Youssoupha 1; Diallo, Mamoudou 1; Ndiaye, Arame 1; Gauthier, Philippe 2; Borderon, Marion 3; Granjon, Laurent 2; Brouat, Carine 2; Berthier, Karine 4

1 BIOPASS (IRD-CBGP, CIRAD, ISRA, UCAD), Campus de Bel-Air, BP 1386, CP 18524 Dakar, Senegal
2 CBGP, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
3 Department of Geography and Regional Research, University of Vienna, Austria
4 Pathologie Végétale, INRAE, 84140 Montfavet, France
License: CC-BY 4.0
Copyrights: The authors retain unrestricted copyrights and publishing rights 
@article{10_24072_pcjournal_85,
     author = {Stragier, Claire and Piry, Sylvain and Loiseau, Anne and Kane, Mamadou and Sow, Aliou and Niang, Youssoupha and Diallo, Mamoudou and Ndiaye, Arame and Gauthier, Philippe and Borderon, Marion and Granjon, Laurent and Brouat, Carine and Berthier, Karine},
     title = {Interplay between historical and current features of the cityscape in shaping the genetic structure of the house mouse {(\protect\emph{Mus} musculus domesticus}) in {Dakar} {(Senegal,} {West} {Africa)}},
     journal = {Peer Community Journal},
     eid = {e11},
     publisher = {Peer Community In},
     volume = {2},
     year = {2022},
     doi = {10.24072/pcjournal.85},
     url = {https://peercommunityjournal.org/articles/10.24072/pcjournal.85/}
}
TY  - JOUR
AU  - Stragier, Claire
AU  - Piry, Sylvain
AU  - Loiseau, Anne
AU  - Kane, Mamadou
AU  - Sow, Aliou
AU  - Niang, Youssoupha
AU  - Diallo, Mamoudou
AU  - Ndiaye, Arame
AU  - Gauthier, Philippe
AU  - Borderon, Marion
AU  - Granjon, Laurent
AU  - Brouat, Carine
AU  - Berthier, Karine
TI  - Interplay between historical and current features of the cityscape in shaping the genetic structure of the house mouse (Mus musculus domesticus) in Dakar (Senegal, West Africa)
JO  - Peer Community Journal
PY  - 2022
VL  - 2
PB  - Peer Community In
UR  - https://peercommunityjournal.org/articles/10.24072/pcjournal.85/
DO  - 10.24072/pcjournal.85
ID  - 10_24072_pcjournal_85
ER  - 
%0 Journal Article
%A Stragier, Claire
%A Piry, Sylvain
%A Loiseau, Anne
%A Kane, Mamadou
%A Sow, Aliou
%A Niang, Youssoupha
%A Diallo, Mamoudou
%A Ndiaye, Arame
%A Gauthier, Philippe
%A Borderon, Marion
%A Granjon, Laurent
%A Brouat, Carine
%A Berthier, Karine
%T Interplay between historical and current features of the cityscape in shaping the genetic structure of the house mouse (Mus musculus domesticus) in Dakar (Senegal, West Africa)
%J Peer Community Journal
%D 2022
%V 2
%I Peer Community In
%U https://peercommunityjournal.org/articles/10.24072/pcjournal.85/
%R 10.24072/pcjournal.85
%F 10_24072_pcjournal_85
Stragier, Claire; Piry, Sylvain; Loiseau, Anne; Kane, Mamadou; Sow, Aliou; Niang, Youssoupha; Diallo, Mamoudou; Ndiaye, Arame; Gauthier, Philippe; Borderon, Marion; Granjon, Laurent; Brouat, Carine; Berthier, Karine. Interplay between historical and current features of the cityscape in shaping the genetic structure of the house mouse (Mus musculus domesticus) in Dakar (Senegal, West Africa). Peer Community Journal, Volume 2 (2022), article  no. e11. doi : 10.24072/pcjournal.85. https://peercommunityjournal.org/articles/10.24072/pcjournal.85/

PCI peer reviews and recommendation, and links to data, scripts, code and supplementary information: 10.24072/pci.ecology.100044

Conflict of interest of the recommender and peer reviewers:
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article.

[1] van Adrichem, M. H.; Buijs, J. A.; Goedhart, P. W.; Verboom, J. Factors influencing the density of the brown rat (Rattus norvegicus) in and around houses in Amsterdam, Lutra, Volume 56 (2013) no. 2, pp. 77-91

[2] Angel, A.; Wanless, R. M.; Cooper, J. Review of impacts of the introduced house mouse on islands in the Southern Ocean: are mice equivalent to rats?, Biological Invasions, Volume 11 (2009) no. 7, pp. 1743-1754 | DOI

[3] ANSD Situation économique et sociale du Sénégal en 2013. Agence Nationale de la Statistique et de la Démographie Dakar, p. 48. URL: http://www.ansd.sn/ressources/ses/ chapitres/5-sante-SESN2013.pdf, 2016

[4] Aplin, K. P.; Suzuki, H.; Chinen, A. A.; Chesser, R. T.; ten Have, J.; Donnellan, S. C.; Austin, J.; Frost, A.; Gonzalez, J. P.; Herbreteau, V.; Catzeflis, F.; Soubrier, J.; Fang, Y.-P.; Robins, J.; Matisoo-Smith, E.; Bastos, A. D. S.; Maryanto, I.; Sinaga, M. H.; Denys, C.; Van Den Bussche, R. A.; Conroy, C.; Rowe, K.; Cooper, A. Multiple Geographic Origins of Commensalism and Complex Dispersal History of Black Rats, PLoS ONE, Volume 6 (2011) no. 11 | DOI

[5] Ba, D.; Diaw, A. T.; Leclerc, G.; Mering, C. Analyse de la dynamique spatiale du port de Dakar de 1900 à 2009: enjeux multi-scalaires et aménagements., Cybergeo: European Journal of Geography (2013) | DOI

[6] Benjamini, Y.; Hochberg, Y. Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing, Journal of the Royal Statistical Society: Series B (Methodological), Volume 57 (1995) no. 1, pp. 289-300 | DOI

[7] Berny, P.; Esther, A.; Jacob, J.; Prescott, C. Development of Resistance to Anticoagulant Rodenticides in Rodents, Emerging Topics in Ecotoxicology, Springer International Publishing, Cham, 2018, pp. 259-286 | DOI

[8] Berthier, K.; Charbonnel, N.; Galan, M.; Chaval, Y.; Cosson, J.-F. Migration and recovery of the genetic diversity during the increasing density phase in cyclic vole populations, Molecular Ecology, Volume 15 (2006) no. 9, pp. 2665-2676 | DOI

[9] Berthier, K.; Galan, M.; Foltete, J. C.; Charbonnel, N.; Cosson, J. F. Genetic structure of the cyclic fossorial water vole (Arvicola terrestris): landscape and demographic influences, Molecular Ecology, Volume 14 (2005) no. 9, pp. 2861-2871 | DOI

[10] Berthier, K.; Garba, M.; Leblois, R.; Navascués, M.; Tatard, C.; Gauthier, P.; Gagaré, S.; Piry, S.; Brouat, C.; Dalecky, A.; Loiseau, A.; Dobigny, G. Black rat invasion of inland Sahel: insights from interviews and population genetics in south-western Niger, Biological Journal of the Linnean Society, Volume 119 (2016) no. 4, pp. 748-765 | DOI

[11] Besag, J.; York, J.; Mollié, A. Bayesian image restoration, with two applications in spatial statistics, Annals of the Institute of Statistical Mathematics, Volume 43 (1991) no. 1, pp. 1-20 | DOI

[12] Blangiardo, M.; Cameletti, M. Spatial and Spatio-temporal Bayesian Models with R-INLA, John Wiley & Sons, Ltd, Chichester, UK, 2015, 320 pages | DOI

[13] Bloom, D. E.; Canning, D.; Fink, G. Urbanization and the Wealth of Nations, Science, Volume 319 (2008) no. 5864, pp. 772-775 | DOI

[14] Bonhomme, F.; Searle, J. B.; Pialek, J. House mouse phylogeography, Evolution of the House Mouse, Cambridge University Press, Cambridge, 2012, pp. 278-296 | DOI

[15] Bonhomme, F.; Orth, A.; Cucchi, T.; Rajabi-Maham, H.; Catalan, J.; Boursot, P.; Auffray, J.-C.; Britton-Davidian, J. Genetic differentiation of the house mouse around the Mediterranean basin: matrilineal footprints of early and late colonization, Proceedings of the Royal Society B: Biological Sciences, Volume 278 (2010) no. 1708, pp. 1034-1043 | DOI

[16] Bonwitt, J.; Sáez, A. M.; Lamin, J.; Ansumana, R.; Dawson, M.; Buanie, J.; Lamin, J.; Sondufu, D.; Borchert, M.; Sahr, F.; Fichet-Calvet, E.; Brown, H. At Home with Mastomys and Rattus: Human–Rodent Interactions and Potential for Primary Transmission of Lassa Virus in Domestic Spaces, The American Journal of Tropical Medicine and Hygiene, Volume 96 (2017) no. 4, pp. 935-943 | DOI

[17] Borderon M; Oliveau S; Machault V; Vignolles C; Lacaux JP; NDonky A Qualifier les espaces urbains à Dakar, Sénégal. Résultats préliminaires de l'approche croisée entre télédétection et données censitaires spatialisées, Cybergeo: European Journal of Geography (2014) | DOI

[18] Breiman, L. Random forests, Machine Learning, Volume 45 (2001) no. 1, pp. 5-32 | DOI

[19] Byers, K. A.; Lee, M. J.; Patrick, D. M.; Himsworth, C. G. Rats About Town: A Systematic Review of Rat Movement in Urban Ecosystems, Frontiers in Ecology and Evolution, Volume 7 (2019) | DOI

[20] Castiglia, R.; Annesi, F.; Capanna, E. Geographical pattern of genetic variation in the Robertsonian system of Mus musculus domesticus in central Italy, Biological Journal of the Linnean Society, Volume 84 (2005) no. 3, pp. 395-405 | DOI

[21] Chapuis, M.-P.; Lecoq, M.; Michalakis, Y.; Loiseau, A.; Sword, G. A.; Piry, S.; Estoup, A. Do outbreaks affect genetic population structure? A worldwide survey inLocusta migratoria, a pest plagued by microsatellite null alleles, Molecular Ecology, Volume 17 (2008) no. 16, pp. 3640-3653 | DOI

[22] Chapuis, M.-P.; Estoup, A. Microsatellite Null Alleles and Estimation of Population Differentiation, Molecular Biology and Evolution, Volume 24 (2006) no. 3, pp. 621-631 | DOI

[23] Chen, M.; Zhang, H.; Liu, W.; Zhang, W. The Global Pattern of Urbanization and Economic Growth: Evidence from the Last Three Decades, PLoS ONE, Volume 9 (2014) no. 8, pp. 1-15 | DOI

[24] Clegg, S. M.; Degnan, S. M.; Kikkawa, J.; Moritz, C.; Estoup, A.; Owens, I. P. F. Genetic consequences of sequential founder events by an island-colonizing bird, Proceedings of the National Academy of Sciences, Volume 99 (2002) no. 12, pp. 8127-8132 | DOI

[25] Cohen, B. Urbanization in developing countries: Current trends, future projections, and key challenges for sustainability, Technology in Society, Volume 28 (2006) no. 1-2, pp. 63-80 | DOI

[26] Combs, M.; Byers, K. A.; Ghersi, B. M.; Blum, M. J.; Caccone, A.; Costa, F.; Himsworth, C. G.; Richardson, J. L.; Munshi-South, J. Urban rat races: spatial population genomics of brown rats (Rattus norvegicus) compared across multiple cities, Proceedings of the Royal Society B: Biological Sciences, Volume 285 (2018) no. 1880 | DOI

[27] Combs, M.; Puckett, E. E.; Richardson, J.; Mims, D.; Munshi‐South, J. Spatial population genomics of the brown rat (Rattus norvegicus) in New York City, Molecular Ecology, Volume 27 (2018) no. 1, pp. 83-98 | DOI

[28] Comps, B.; Gömöry, D.; Letouzey, J.; Thiébaut, B.; Petit, R. J. Diverging Trends Between Heterozygosity and Allelic Richness During Postglacial Colonization in the European Beech, Genetics, Volume 157 (2001) no. 1, pp. 389-397 | DOI

[29] Cucchi, T.; Auffray, J.-C.; Vigne, J.-D.; Pialek, J. On the origin of the house mouse synanthropy and dispersal in the Near East and Europe, Evolution of the House Mouse, Cambridge University Press, Cambridge, 2012, pp. 65-93 | DOI

[30] Dalecky, A.; Bâ, K.; Piry, S.; Lippens, C.; Diagne, C. A.; Kane, M.; Sow, A.; Diallo, M.; Niang, Y.; Konečný, A.; Sarr, N.; Artige, E.; Charbonnel, N.; Granjon, L.; Duplantier, J.-M.; Brouat, C. Range expansion of the invasive house mouse Mus musculus domesticus in Senegal, West Africa: a synthesis of trapping data over three decades, 1983-2014, Mammal Review, Volume 45 (2015) no. 3, pp. 176-190 | DOI

[31] Diallo, A.; Ndam, N. T.; Moussiliou, A.; Dos Santos, S.; Ndonky, A.; Borderon, M.; Oliveau, S.; Lalou, R.; Le Hesran, J.-Y. Asymptomatic Carriage of Plasmodium in Urban Dakar: The Risk of Malaria Should Not Be Underestimated, PLoS ONE, Volume 7 (2012) no. 2 | DOI

[32] Dobson, F. S. Chapter 14. Gene Dynamics and Social Behavior In: Rodent Societies: An Ecological and Evolutionary Perspective, edited by Jerry O. Wolff and Paul W. Sherman, University of Chicago Press, Chicago (2008), pp. 163-172 | DOI

[33] Dray, S.; Saïd, S.; Débias, F. Spatial ordination of vegetation data using a generalization of Wartenberg's multivariate spatial correlation, Journal of Vegetation Science, Volume 19 (2008) no. 1, pp. 45-56 | DOI

[34] Dray, S.; Saïd, S.; Débias, F. Spatial ordination of vegetation data using a generalization of Wartenberg's multivariate spatial correlation, Journal of Vegetation Science, Volume 19 (2008) no. 1, pp. 45-56 | DOI

[35] Evanno, G.; Regnaut, S.; Goudet, J. Detecting the number of clusters of individuals using the software structure: a simulation study, Molecular Ecology, Volume 14 (2005) no. 8, pp. 2611-2620 | DOI

[36] Falush, D.; Stephens, M.; Pritchard, J. K. Inference of Population Structure Using Multilocus Genotype Data: Linked Loci and Correlated Allele Frequencies, Genetics, Volume 164 (2003) no. 4, pp. 1567-1587 | DOI

[37] Feng, A. Y. T.; Himsworth, C. G. The secret life of the city rat: a review of the ecology of urban Norway and black rats (Rattus norvegicus and Rattus rattus), Urban Ecosystems, Volume 17 (2014) no. 1, pp. 149-162 | DOI

[38] Foll, M.; Gaggiotti, O. Identifying the Environmental Factors That Determine the Genetic Structure of Populations, Genetics, Volume 174 (2006) no. 2, pp. 875-891 | DOI

[39] Förster, D. W.; Gündüz, İ.; Nunes, A. C.; Gabriel, S.; Ramalhinho, M. G.; Mathias, M. L.; Britton-Davidian, J.; Searle, J. B. Molecular insights into the colonization and chromosomal diversification of Madeiran house mice, Molecular Ecology, Volume 18 (2009) no. 21, pp. 4477-4494 | DOI

[40] Gabriel, S. I.; Stevens, M. I.; Mathias, M. d. L.; Searle, J. B. Of Mice and ‘Convicts’: Origin of the Australian House Mouse, Mus musculus, PLoS ONE, Volume 6 (2011) no. 12 | DOI

[41] García-Rodríguez, O.; Andreou, D.; Herman, J. S.; Mitsainas, G. P.; Searle, J. B.; Bonhomme, F.; Hadjisterkotis, E.; Schutkowski, H.; Stafford, R.; Stewart, J. R.; Hardouin, E. A. Cyprus as an ancient hub for house mice and humans, Journal of Biogeography, Volume 45 (2018) no. 12, pp. 2619-2630 | DOI

[42] Gardner-Santana, L. C.; Norris, D. E.; Fornadel, C. M.; Hinson, E. R.; Klein, S. L.; Glass, G. E. Commensal ecology, urban landscapes, and their influence on the genetic characteristics of city-dwelling Norway rats (Rattus norvegicus), Molecular Ecology, Volume 18 (2009) no. 13, pp. 2766-2778 | DOI

[43] Goudet, J. FSTAT: a program to estimate and test gene diversities and fixation indices (Version 2.9.3). URL: https://www2.unil.ch/popgen/softwares/fstat.htm., 2001

[44] Greenbaum, G.; Templeton, A. R.; Zarmi, Y.; Bar-David, S. Allelic Richness following Population Founding Events – A Stochastic Modeling Framework Incorporating Gene Flow and Genetic Drift, PLoS ONE, Volume 9 (2014) no. 12 | DOI

[45] UN-Habitat Sénégal: Profil Urbain de Dakar. Tech. rep. Programme des Nations Unies pour les Etablissements Humains, p. 36. https://mirror.unhabitat.org/pmss/getElectronicVersion.asp?nr=2757&alt=1, 2008

[46] Hall, T. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. In: Nucleic acids symposium series, Volume 41 (1999), pp. 95-98

[47] Haniza, M. Z.; Adams, S.; Jones, E. P.; MacNicoll, A.; Mallon, E. B.; Smith, R. H.; Lambert, M. S. Large-scale structure of brown rat (Rattus norvegicus) populations in England: effects on rodenticide resistance, PeerJ, Volume 3 (2015) | DOI

[48] Hardy, O. J.; Vekemans, X. spagedi: a versatile computer program to analyse spatial genetic structure at the individual or population levels, Molecular Ecology Notes, Volume 2 (2002) no. 4, pp. 618-620 | DOI

[49] Harris, D. Constructing Dakar: Cultural theory and colonial power relations in French African urban development. PhD thesis. Arts & Social Sciences: Department of History. URL: http://summit.sfu.ca/item/11899. (2011)

[50] Harris, S. E.; Xue, A. T.; Alvarado-Serrano, D.; Boehm, J. T.; Joseph, T.; Hickerson, M. J.; Munshi-South, J. Urbanization shapes the demographic history of a native rodent (the white-footed mouse, Peromyscus leucopus ) in New York City, Biology Letters, Volume 12 (2016) no. 4 | DOI

[51] Held, L.; Schrödle, B.; Rue, H. Posterior and Cross-validatory Predictive Checks: A Comparison of MCMC and INLA, Statistical Modelling and Regression Structures, Physica-Verlag HD, Heidelberg, 2010, pp. 91-110 | DOI

[52] Hothorn, T. Survival ensembles, Biostatistics, Volume 7 (2005) no. 3, pp. 355-373 | DOI

[53] Ihle, S.; Ravaoarimanana, I.; Thomas, M.; Tautz, D. An Analysis of Signatures of Selective Sweeps in Natural Populations of the House Mouse, Molecular Biology and Evolution, Volume 23 (2006) no. 4, pp. 790-797 | DOI

[54] Jakobsson, M.; Rosenberg, N. A. CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure, Bioinformatics, Volume 23 (2007) no. 14, pp. 1801-1806 | DOI

[55] Jassat, W.; Naicker, N.; Naidoo, S.; Mathee, A. Rodent control in urban communities in Johannesburg, South Africa: from research to action, International Journal of Environmental Health Research, Volume 23 (2013) no. 6, pp. 474-483 | DOI

[56] Johnson, M. T. J.; Munshi-South, J. Evolution of life in urban environments, Science, Volume 358 (2017) no. 6363 | DOI

[57] Jones, E. P.; Eager, H. M.; Gabriel, S. I.; Jóhannesdóttir, F.; Searle, J. B. Genetic tracking of mice and other bioproxies to infer human history, Trends in Genetics, Volume 29 (2013) no. 5, pp. 298-308 | DOI

[58] Jones, E. P.; Jóhannesdóttir, F.; Gündüz, İ.; Richards, M. B.; Searle, J. B. The expansion of the house mouse into north‐western Europe, Journal of Zoology, Volume 283 (2011) no. 4, pp. 257-268 | DOI

[59] Jones, E.; Skirnisson, K.; McGovern, T.; Gilbert, M.; Willerslev, E.; Searle, J. Fellow travellers: a concordance of colonization patterns between mice and men in the North Atlantic region, BMC Evolutionary Biology, Volume 12 (2012) no. 1 | DOI

[60] Kajdacsi, B.; Costa, F.; Hyseni, C.; Porter, F.; Brown, J.; Rodrigues, G.; Farias, H.; Reis, M. G.; Childs, J. E.; Ko, A. I.; Caccone, A. Urban population genetics of slum-dwelling rats (Rattus norvegicus) in Salvador, Brazil, Molecular Ecology, Volume 22 (2013) no. 20, pp. 5056-5070 | DOI

[61] King, C. M. How genetics, history and geography limit potential explanations of invasions by house mice Mus musculus in New Zealand, Biological Invasions, Volume 18 (2016) no. 6, pp. 1533-1550 | DOI

[62] Lambert, M.; Vial, F.; Pietravalle, S.; Cowan, D. Results of a 15-year systematic survey of commensal rodents in English dwellings, Scientific Reports, Volume 7 (2017) no. 1 | DOI

[63] Lippens, C.; Estoup, A.; Hima, M. K.; Loiseau, A.; Tatard, C.; Dalecky, A.; Bâ, K.; Kane, M.; Diallo, M.; Sow, A.; Niang, Y.; Piry, S.; Berthier, K.; Leblois, R.; Duplantier, J.-M.; Brouat, C. Genetic structure and invasion history of the house mouse (Mus musculus domesticus) in Senegal, West Africa: a legacy of colonial and contemporary times, Heredity, Volume 119 (2017) no. 2, pp. 64-75 | DOI

[64] Loiselle, B. A.; Sork, V. L.; Nason, J.; Graham, C. Spatial genetic structure of a tropical understory shrub, PSYCHOTRIA OFFICINALIS (RuBIACEAE), American Journal of Botany, Volume 82 (1995) no. 11, pp. 1420-1425 | DOI

[65] Lourenço, A.; Álvarez, D.; Wang, I. J.; Velo-Antón, G. Trapped within the city: integrating demography, time since isolation and population-specific traits to assess the genetic effects of urbanization, Molecular Ecology, Volume 26 (2017) no. 6, pp. 1498-1514 | DOI

[66] Lucaccioni, H.; Granjon, L.; Dalecky, A.; Fossati, O.; Le Fur, J.; Duplantier, J.-M.; Handschumacher, P. From Human Geography to Biological Invasions: The Black Rat Distribution in the Changing Southeastern of Senegal, PLOS ONE, Volume 11 (2016) no. 9 | DOI

[67] M'Bokolo, E. Peste et société urbaine à Dakar : l'épidémie de 1914., Cahiers d’études africaines, Volume 22 (1982) no. 85, pp. 13-46 | DOI

[68] MacKay, J. W.; Alexander, A.; Hauber, M. E.; Murphy, E. C.; Clout, M. N. Does genetic variation among invasive house mice in New Zealand affect eradication success?, New Zealand Journal of Ecology. https://www.jstor.org/ stable/24060753. (2013), pp. 18-25

[69] Makundi, R. H.; Massawe, A. W. Ecologically based rodent management in Africa: potential and challenges, Wildlife Research, Volume 38 (2011) no. 7, pp. 588-595 | DOI

[70] Marston, C. G.; Danson, F. M.; Armitage, R. P.; Giraudoux, P.; Pleydell, D. R.; Wang, Q.; Qui, J.; Craig, P. S. A random forest approach for predicting the presence of Echinococcus multilocularis intermediate host Ochotona spp. presence in relation to landscape characteristics in western China, Applied Geography, Volume 55 (2014), pp. 176-183 | DOI

[71] Martins, T. G.; Simpson, D.; Lindgren, F.; Rue, H. Bayesian computing with INLA: New features, Computational Statistics & Data Analysis, Volume 67 (2013), pp. 68-83 | DOI

[72] Masi, E.; Pino, F. A.; Santos, M. d. G. S.; Genehr, L.; Albuquerque, J. O. M.; Bancher, A. M.; Alves, J. C. M. Socioeconomic and environmental risk factors for urban rodent infestation in Sao Paulo, Brazil, Journal of Pest Science, Volume 83 (2010) no. 3, pp. 231-241 | DOI

[73] McKinney, M. L. Urbanization as a major cause of biotic homogenization, Biological Conservation, Volume 127 (2006) no. 3, pp. 247-260 | DOI

[74] Meerburg, B. G.; Singleton, G. R.; Kijlstra, A. Rodent-borne diseases and their risks for public health, Critical Reviews in Microbiology, Volume 35 (2009) no. 3, pp. 221-270 | DOI

[75] Munshi‐South, J.; Zolnik, C. P.; Harris, S. E. Population genomics of the Anthropocene: urbanization is negatively associated with genome‐wide variation in white‐footed mouse populations, Evolutionary Applications, Volume 9 (2016) no. 4, pp. 546-564 | DOI

[76] Nei, M. Molecular Evolutionary Genetics, Columbia University Press, 1987 | DOI

[77] Nei, M.; Maruyama, T.; Chakraborty, R. The Bottleneck Effect and Genetic Variability in Populations, Evolution, Volume 29 (1975) no. 1, pp. 1-10 | DOI

[78] Parreira, B. R.; Chikhi, L. On some genetic consequences of social structure, mating systems, dispersal, and sampling, Proceedings of the National Academy of Sciences, Volume 112 (2015) no. 26 | DOI

[79] Parsons, M. H.; Banks, P. B.; Deutsch, M. A.; Corrigan, R. F.; Munshi-South, J. Trends in urban rat ecology: a framework to define the prevailing knowledge gaps and incentives for academia, pest management professionals (PMPs) and public health agencies to participate, Journal of Urban Ecology, Volume 3 (2017) no. 1 | DOI

[80] Pélissier P Atlas du Sénégal, Jeune Afrique, Paris, 1983, 72 pages

[81] Piry, S.; Chapuis, M.; Gauffre, B.; Papaïx, J.; Cruaud, A.; Berthier, K. Mapping Averaged Pairwise Information (MAPI): a new exploratory tool to uncover spatial structure, Methods in Ecology and Evolution, Volume 7 (2016) no. 12, pp. 1463-1475 | DOI

[82] Pocock, M. J. O.; Hauffe, H. C.; Searle, J. B. Dispersal in house mice, Biological Journal of the Linnean Society, Volume 84 (2005) no. 3, pp. 565-583 | DOI

[83] Pritchard, J. K.; Stephens, M.; Donnelly, P. Inference of Population Structure Using Multilocus Genotype Data, Genetics, Volume 155 (2000) no. 2, pp. 945-959 | DOI

[84] Puckett, E. E.; Park, J.; Combs, M.; Blum, M. J.; Bryant, J. E.; Caccone, A.; Costa, F.; Deinum, E. E.; Esther, A.; Himsworth, C. G.; Keightley, P. D.; Ko, A.; Lundkvist, Å.; McElhinney, L. M.; Morand, S.; Robins, J.; Russell, J.; Strand, T. M.; Suarez, O.; Yon, L.; Munshi-South, J. Global population divergence and admixture of the brown rat (Rattus norvegicus), Proceedings of the Royal Society B: Biological Sciences, Volume 283 (2016) no. 1841 | DOI

[85] R Core Team R: A language and environment for statistical computing. URL: https://www.R-project.org/., 2019

[86] Rajabi-Maham, H.; Orth, A.; Bonhomme, F. Phylogeography and postglacial expansion of Mus musculus domesticus inferred from mitochondrial DNA coalescent, from Iran to Europe, Molecular Ecology, Volume 17 (2008) no. 2, pp. 627-641 | DOI

[87] Richardson, J. L.; Brady, S. P.; Wang, I. J.; Spear, S. F. Navigating the pitfalls and promise of landscape genetics, Molecular Ecology, Volume 25 (2016) no. 4, pp. 849-863 | DOI

[88] Richardson, J. L.; Burak, M. K.; Hernandez, C.; Shirvell, J. M.; Mariani, C.; Carvalho-Pereira, T. S. A.; Pertile, A. C.; Panti-May, J. A.; Pedra, G. G.; Serrano, S.; Taylor, J.; Carvalho, M.; Rodrigues, G.; Costa, F.; Childs, J. E.; Ko, A. I.; Caccone, A. Using fine-scale spatial genetics of Norway rats to improve control efforts and reduce leptospirosis risk in urban slum environments, Evolutionary Applications, Volume 10 (2017) no. 4, pp. 323-337 | DOI

[89] Rosenberg, N. A. DISTRUCT: a program for the graphical display of population structure, Molecular Ecology Notes, Volume 4 (2004) no. 1, pp. 137-138 | DOI

[90] Rouhana S ; Ranarifidy D ; Sinet A ; Chomentowski V; Avner P; Godin L Revue de l’urbanisation: villes émergentes pour un Sénégal émergent. Tech. rep. Washington, D.C.: World Bank Group, pp. 126., 2015

[91] Rousset, F. genepop’007: a complete re-implementation of the genepop software for Windows and Linux, Molecular Ecology Resources, Volume 8 (2008) no. 1, pp. 103-106 | DOI

[92] Rousset, F. Genetic Differentiation and Estimation of Gene Flow from F-Statistics Under Isolation by Distance, Genetics, Volume 145 (1997) no. 4, pp. 1219-1228 | DOI

[93] Rozas, J.; Ferrer-Mata, A.; Sánchez-DelBarrio, J. C.; Guirao-Rico, S.; Librado, P.; Ramos-Onsins, S. E.; Sánchez-Gracia, A. DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets, Molecular Biology and Evolution, Volume 34 (2017) no. 12, pp. 3299-3302 | DOI

[94] Salem, G. Grand Dakar, un quartier charnière du Cap Vert: densification du bâti et organisation sociale. ORSTOM, p 120. URL: https://horizon.documentation.ird.fr/ exl-doc/pleins_textes/divers14-11/43361.pdf, 1981

[95] Santos, N. d. J.; Sousa, E.; Reis, M. G.; Ko, A. I.; Costa, F. Rat infestation associated with environmental deficiencies in an urban slum community with high risk of leptospirosis transmission, Cadernos de Saúde Pública, Volume 33 (2017) no. 2 | DOI

[96] Sikes, R. S.; Gannon, W. L. Guidelines of the American Society of Mammalogists for the use of wild mammals in research, Journal of Mammalogy, Volume 92 (2011) no. 1, pp. 235-253 | DOI

[97] Singleton, G. R.; Hinds, L. A.; Krebs, C. J.; Spratt, D. M. Rats, mice and people: rodent biology and management, ACIAR Monograph Vol. 96. Australian Centre for International Agricultural Research (ACIAR), Canberra, Australia, p. 114. URL: http:// www.suaire.sua.ac.tz/handle/123456789/1097, 2003

[98] Singleton, G.; Hinds, L.; Leirs, H.; Zhang, Z. Ecologically-based Rodent Management , Vol. 59. ACIAR Monograph. Canberra: Australian Centre for International Agricultural Research (ACIAR), p. 494. URL: http://hdl.handle.net/102.100.100/211210? index=1., 1999

[99] Singleton, G. R.; Jacob, J.; Krebs, C. J.; Monadjem, A. A meeting of mice and men: rodent impacts on food security, human diseases and wildlife conservation; ecosystem benefits; fascinating biological models, Wildlife Research, Volume 42 (2015) no. 2, pp. 83-85 | DOI

[100] Sinou, A. Comptoirs et villes coloniales du Sénégal: Saint-Louis, Gorée, Dakar. Khartala-ORSTOM, p. 364. URL: https://horizon.documentation.ird.fr/exl-doc/pleins_ textes/pleins_textes_7/b_fdi_03_05/37474.pdf, 1993

[101] Solano, E.; Franchini, P.; Colangelo, P.; Capanna, E.; Castiglia, R. Multiple origins of the western European house mouse in the Aeolian Archipelago: clues from mtDNA and chromosomes, Biological Invasions, Volume 15 (2013) no. 4, pp. 729-739 | DOI

[102] Storey, J. D. A direct approach to false discovery rates, Journal of the Royal Statistical Society: Series B (Statistical Methodology), Volume 64 (2002) no. 3, pp. 479-498 | DOI

[103] Storz, J. F.; Baze, M.; Waite, J. L.; Hoffmann, F. G.; Opazo, J. C.; Hayes, J. P. Complex Signatures of Selection and Gene Conversion in the Duplicated Globin Genes of House Mice, Genetics, Volume 177 (2007) no. 1, pp. 481-500 | DOI

[104] Strobl, C.; Boulesteix, A.-L.; Kneib, T.; Augustin, T.; Zeileis, A. Conditional variable importance for random forests, BMC Bioinformatics, Volume 9 (2008) no. 1 | DOI

[105] Strobl, C.; Hothorn, T.; Zeileis, A. Party on!, The R Journal, Volume 1 (2009) no. 2, pp. 14-17 | DOI

[106] Suzuki, H.; Nunome, M.; Kinoshita, G.; Aplin, K. P.; Vogel, P.; Kryukov, A. P.; Jin, M.-L.; Han, S.-H.; Maryanto, I.; Tsuchiya, K.; Ikeda, H.; Shiroishi, T.; Yonekawa, H.; Moriwaki, K. Evolutionary and dispersal history of Eurasian house mice Mus musculus clarified by more extensive geographic sampling of mitochondrial DNA, Heredity, Volume 111 (2013) no. 5, pp. 375-390 | DOI

[107] Team QD QGIS Geographic Information System. URL: http://qgis.osgeo.org, 2018

[108] Temminck, C. J. Esquisses zoologiques sur la côte de Guiné ... 1ère partie, les mammifères., E.J. Brill,, Leiden, 1853 | DOI

[109] Vernière, M. Pikine, « ville nouvelle » de Dakar. Un cas de pseudo-urbanisation, L'Espace géographique, Volume 2 (1973) no. 2, pp. 107-126 | DOI

[110] Weir, B. S.; Cockerham, C. C. Estimating F-Statistics for the Analysis of Population Structure, Evolution, Volume 38 (1984) no. 6, pp. 1358-1370 | DOI

[111] Wright, M. N.; Ziegler, A. ranger: A Fast Implementation of Random Forests for High Dimensional Data in C++ and R, Journal of Statistical Software, Volume 77 (2017) no. 1, pp. 1-17 | DOI

Cited by Sources:

block.super