The genetic relationship between R. microplus and R. decoloratus ticks in South Africa and their population structure

Agapow, 2001, Indices of multilocus linkage disequilibrium, Mol. Ecol. Notes, 1, 101, 10.1046/j.1471-8278.2000.00014.x Ali, 2016, A revision of two distinct species of Rhipicephalus: R. microplus and R. australis, Ciencia Rural, Santa Maria, 46, 1240, 10.1590/0103-8478cr20151416 Anisimova, 2003, Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites, Genetics, 164, 1229, 10.1093/genetics/164.3.1229 Arenas, 2013, The importance and application of the ancestral recombination graph, Front. Genet., 4 Barker, 1998, Distinguishing species and populations of Rhipicephaline ticks with ITS 2 ribosomal RNA, J. Parasitol., 84, 887, 10.2307/3284614 Baron, 2015, SNP analysis infers that recombination is involved in the evolution of amitraz resistance in Rhipicephalus microplus, PLoS One, 10, 1, 10.1371/journal.pone.0131341 Beati, 2001, Analysis of the systematic relationships among ticks of the genera Rhipicephalus and Boophilus (Acari: Ixodidae) based on mitochondrial 12S Ribosomal DNA gene sequences and morphological charachters, J. Parasitol., 87, 32, 10.1645/0022-3395(2001)087[0032:AOTSRA]2.0.CO;2 Black, 1994, Phylogeny of hard- and soft-tick taxa (Acari: Ixodida) based on mitochondrial 16S rDNA sequences, PNAS, 91, 10034, 10.1073/pnas.91.21.10034 Burger, 2014, Phylogenetic analysis of mitochondrial genome sequences indicates that the cattle tick, Rhipicephalus (Boophilus) microplus, contains a cryptic species, Mol. Phylogenet. Evol., 76, 241, 10.1016/j.ympev.2014.03.017 Busch, 2014, Widespread movement of invasive cattle fever ticks (Rhipicephalus microplus) in southern Texas leads to shared local infestations on cattle and deer, Parasites Vectors, 7, 1 Chao, 2011, Species identification of Ixodes granulatus (Acari: Ixodidae) based on internal transcribed spacer 2 (ITS2) sequences, Exp. Appl. Acarol., 54, 51, 10.1007/s10493-010-9419-z Chigagure, 2000, Microsatellite loci of the cattle tick Boophilus microplus (Acari: Ixodidae), Exp. Appl. Acarol., 24, 951, 10.1023/A:1010732024895 Cutullè, 2009, Population structure of Australian isolates of the cattle tick Rhipicephalus (Boophilus) microplus, Vet. Parasitol., 161, 283, 10.1016/j.vetpar.2009.01.005 Dabert, 2010, Molecular phylogeny of acariform mites (Acari, Arachnida): strong conflict between phylogenetic signal and long-branch attraction artifacts, Mol. Phylogenet. Evol., 56, 222, 10.1016/j.ympev.2009.12.020 de la Fuente, 2003, Advances in the identification and characterization of protective antigens for recombinant vaccines against tick infestations, Expert Rev. Vaccines, 2, 583, 10.1586/14760584.2.4.583 De Matos, 2009, The comparative prevalence of five ixodid tick species infesting cattle and goats in Maputo Province, Mozambique, Onderstepoort J. Vet. Res., 76, 201, 10.4102/ojvr.v76i2.45 De meeûs, 2010, Swift sympatric adaptation of a species of cattle tick to a new deer host in New Caledonia, Infect., Genet. Evol., 10, 976, 10.1016/j.meegid.2010.06.005 Delaye, 1997, Population genetic structure of Ixodes ricinus in Switzerland from allozymic data: no evidence of divergence between nearby sites, Int. J. Parasitol., 27, 769, 10.1016/S0020-7519(97)00040-4 Dinnis, 2014, Multilocus sequence typing using mitochondrial genes (mtMLST) reveals geographic population structure of Ixodes ricinus ticks, Ticks Tick-borne Dis., 5, 152, 10.1016/j.ttbdis.2013.10.001 Earl, 2012, STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method, Conserv. Genet. Resour., 4, 359, 10.1007/s12686-011-9548-7 Ellegren, 2004, Microsatellites: Simple sequences with complex evolution, Nat. Rev. Genet., 5, 435, 10.1038/nrg1348 Estrada-Pena, 2003, Climate change decreases habitat suitability for some tick species (Acari: Ixodidae) in South Africa, Onderstepoort J. Vet. Res., 70, 79 Estrada-Peña, 2006, The known distribution and ecological preferences of the tick subgenus Boophilus (Acari: Ixodidae) in Africa and Latin America, Exp. Appl. Acarol., 38, 219, 10.1007/s10493-006-0003-5 Evanno, 2005, Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study, Mol. Ecol., 14, 2611, 10.1111/j.1365-294X.2005.02553.x Faircloth, 2008, MSATCOMMANDER: detection of microsatellite repeat arrays and automated, locus-specific primer design, Mol. Ecol. Resour., 8, 92, 10.1111/j.1471-8286.2007.01884.x Falush, 2003, Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies, Genetics, 164, 1567, 10.1093/genetics/164.4.1567 Guichoux, 2011, Current trends in microsatellite genotyping, Mol. Ecol. Resour., 11, 591, 10.1111/j.1755-0998.2011.03014.x Hall, 1999, BioEdit: Biological sequence alignment editor for Win95/98/NT/2K/XP, Nucl. Acids Symp. Ser., 41, 95 Hlinka, 2002, Evolution of the secondary structure of the rRNA internal transcribed spacer 2 (ITS2) in hard ticks (Ixodidae, Arthropoda), Heredity, 88, 275, 10.1038/sj.hdy.6800040 Holleley, 2009, Multiplex Manager 1.0: a crossplatform computer program that plans and optimizes multiplex PCR, Biotechniques, 46, 511, 10.2144/000113156 Hulce, 2011, GeneMarker® genotyping software: tools to increase the statistical power of DNA fragment analysis, J. Biomed. Tech., 22, S35 Jombart, 2008, Adegenet: a R package for the multivariate analysis of genetic markers, Bioinformatics, 24, 1403, 10.1093/bioinformatics/btn129 Jombart, 2010, Discriminate analysis of principal components: a new method for the analysis of genetically structured populations, BMC Genet., 11, 94, 10.1186/1471-2156-11-94 Kanduma, 2015, Multi-locus genotyping reveals absence of genetic structure in field populations of the brown ear tick (Rhipicephalus appendiculatus) in Kenya, Ticks Tick-borne Dis., 7, 26, 10.1016/j.ttbdis.2015.08.001 Katoh, 2013, MAFFT multiple sequence alignment software version 7: improvements in performance and usability, Mol. Biol. Evol., 30, 772, 10.1093/molbev/mst010 Kawazoe, 2008, Redundant species, cryptic host-associated divergence, and secondary shift in Sennertia mites (Acari: Chaetodactylidae) associated with four large carpenter bees (Hymenoptera: Apidae: Xylocopa) in the Japanese island arc, Mol. Phylogenet. Evol., 49, 503, 10.1016/j.ympev.2008.07.024 Koffi, 2006, Characterization of polymorphic microsatellite loci within a young Boophilus microplus metapopulation, Mol. Ecol. Notes, 6, 502, 10.1111/j.1471-8286.2006.01295.x Latrofa, 2013, Comparative analyses of mitochondrial and nuclear genetic markers for the molecular identification of Rhipicephalus spp., Infect., Genet. Evol., 20, 422, 10.1016/j.meegid.2013.09.027 Leite, 2016, Arthropod evolution and development: recent insights from chelicerates and myriapods, Curr. Opin. Genet. Dev., 39, 93, 10.1016/j.gde.2016.06.002 2009 Lempereur, 2010, Development and validation of a PCR–RFLP test to identify African Rhipicephalus (Boophilus) ticks, Acta Trop., 114, 55, 10.1016/j.actatropica.2010.01.004 Low, 2015, Molecular characterisation of the tick Rhipicephalus microplus in Malaysia: new insights into the cryptic diversity and distinct genetic assemblages throughout the world, Parasites Vectors, 8, 1, 10.1186/s13071-015-0956-5 Lyngsø, 2005, 239 Madder, M., Horak, I.G. Tick Photodatabase. Tick Species. Belgium and Pretoria: Institute of Tropical Medicine Antwerpen-Belgium and the University of Pretoria; 2010. p. Rhipicephalus, Amblyomma, Hyalomma. Murrell, 2000, Phylogenetic analysis of the Rhipicephalinae ticks indicate that the genus Rhipicephalus is paraphyletic, Mol. Phylogenet. Evol., 16, 1, 10.1006/mpev.2000.0762 Murrell, 2001, Recurrent gains and losses of large (84–109 bp) repeats in the rDNA internal transcribed spacer 2 (ITS2) of rhipicephaline ticks, Insect Mol. Biol., 10, 587, 10.1046/j.0962-1075.2001.00298.x Navajas, 2000, The application of molecular markers in the study of diversity in acarology: a review, Exp. Appl. Acarol., 24, 751, 10.1023/A:1006497906793 Navajas, 2010, DNA-based methods for eriophyoid mite studies: review, critical aspects, prospects and challenges, Exp. Appl. Acarol., 51, 257, 10.1007/s10493-009-9301-z Nyangiwe, 2011, Ticks on pastures and on two breeds of cattle in the Eastern Cape province, South Africa, Onderstepoort J. Vet. Res., 78, 1, 10.4102/ojvr.v78i1.320 Oberem, 2006, 209 Oberholster, 2013 Peakall, 2012, GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research – an update, Bioinformatics, 28, 2537, 10.1093/bioinformatics/bts460 Poland, 2007, Heterogeneity in vaccine immune response: the role of immunogenetics and the emerging field of vaccinomics, Clin. Pharmacol. Ther., 82, 653, 10.1038/sj.clpt.6100415 Price, 2005, SNAP: workbench management tool for evolutionary population genetic analysis, Bioinformatics, 21, 402, 10.1093/bioinformatics/bti003 Pritchard, 2000, Inference of population structure using multilocus genotype data, Genetics, 155, 945, 10.1093/genetics/155.2.945 Regier, 2010, Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences, Nature, 463, 1079, 10.1038/nature08742 Rodriguez-Vivas, 2011, Evolution of acaricide resistance: Phenotypic and genotypic changes in field populations of Rhipicephalus (Boophilus) microplus in response to pyrethroid selection pressure, Int. J. Parasitol., 41, 895, 10.1016/j.ijpara.2011.03.012 Roy, 2009, Delimiting species boudaries within Dermanyssus Duges, 1834 (Acari: Dermanyssidae) using a total evidence approach, Mol. Phylogenet. Evol., 50, 446, 10.1016/j.ympev.2008.11.012 Schäffer, 2010, Phylogenetic analysis of European Scutovertex mites (Acari: Oribatida, Scutoverticidae) reveals paraphyly and cryptic diversity: a molecular genetic and morphological appraoch, Mol. Phylogenet. Evol., 55, 677, 10.1016/j.ympev.2009.11.025 Schierup, 2000, Consequences of recombination on traditional phylogenetic analysis, Genetics, 156, 879, 10.1093/genetics/156.2.879 Song, 2011, Phylogenetic and phylogeographic relationships in Ixodes holocyclus and Ixodes cornuatus (Acari: Ixodidae) inferred from COX1 and ITS2 sequences, Int. J. Parasitol., 41, 871, 10.1016/j.ijpara.2011.03.008 Tamura, 1993, Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees, Mol. Biol. Evol., 10, 512 Tamura, 2011, MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods, Mol. Biol. Evol., 10, 2731, 10.1093/molbev/msr121 Terkawi, 2011, Serological survey of Babesia bovis and Babesia bigemina in cattle in South Africa, Vet. Parasitol., 182, 337, 10.1016/j.vetpar.2011.05.047 Thiel, 2003, Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.), Theory Appl. Genet., 106, 411, 10.1007/s00122-002-1031-0 Tonetti, 2009, Ticks and tick-borne pathogens from wildlife in the Free State Province, South Africa, J. Wildl. Dis., 45, 437, 10.7589/0090-3558-45.2.437 Tønnensen, 2002 Tønnensen, 2004, Displacement of Boophilus decoloratus by Boophilus microplus in the Soutpansberg region, Limpopo Province, South Africa, Exp. Appl. Acarol., 32, 199, 10.1023/B:APPA.0000021789.44411.b5 Walker, A.R., Bouattour, A., Camicas, J.L., Estrada-Peña, A., Horak, I.G., Latif, A.A., et al. Ticks of domestic animals in Africa: a guide to identification of species. Edinburgh: Bioscience Reports; 2003, pp. 149–167. Yang, 2012, Molecular phylogenetics: principles and practice, Nat. Rev. Genet., 13, 303, 10.1038/nrg3186