References
Alexander, D. H., Novembre, J., Lange, K. (2009). Fast model-based estimation of ancestry in unrelated individuals. Genome Research,;19,1655–64 Allen, J. M., LaFrance, R., Folk, R. A., Johnson, K. P., & Guralnick, R. P. (2018). aTRAM 2.0: An Improved, Flexible Locus Assembler for NGS Data. Evolutionary Bioinformatics, 14, 0–3.https://doi.org/10.1177/1176934318774546Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research, 25, 3389–3402. Aziz, R. K., Bartels, D., Best, A. A., DeJongh, M., Disz, T., Edwards, R. A., Formsma, K., Gerdes, S., Glass, E. M., Kubal, M., Meyer, F., Olsen, G. J., Olson, R., Osterman, A. L., Overbeek, R. A., McNeil, L. K., Paarmann, D., Paczian, T., Parrello, B., Pusch, G. D., Reich, C., Stevens, R., Vassieva, O., Vonstein, V., Wilke, A. & Zagnitko, O. (2008). The RAST Server: rapid annotations using subsystems technology. BMC Genomics, 9, 75. Bankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Dvorkin, M., Kulikov, A. S., Lesin, V. M., Nikolenko, S. I., Pham, S., Prjibelski, A. D., Pyshkin, A. V., Sirotkin, A. V., Vyahhi, N., Tesler, G., Alekseyev & M. A., Pevzner, P. A. (2012). SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing. Journal of Computational Biology, 19, 455–477. Barrett, L. G., Thrall, P. H., Burdon, J. J. & Linde, C. C. (2008). Life history determines genetic structure and evolutionary potential of host–parasite interactions. Trends in Ecology and Evolution, 23, 678–685.https://doi.org/10.1016/j.tree.2008.06.017Bernt, M., Donath, A., Jühling, F., Externbrink, F., Florentz, C., Fritzsch, G., Pütz, J. M., Middendorf, J. & Stadler, P. F. (2013). MITOS: Improved de novo Metazoan Mitochondrial Genome Annotation.Molecular Phylogenetics and Evolution, 69, 313–319. Cameron, S. L., Yoshizawa,K., Mizukoshi, A., Whiting, M. F., & Johnson, K. P. (2011). Mitochondrial genome deletions and minicircles are common in lice (Insecta: Phthiraptera). BMC Genomics, 12, 394.https://doi.org/10.1186/1471-2164-12-394Cerezo, M. L., Kucka, M., Zub, K., Chan, Y. F., & Bryk, J. (2020). Population structure of Apodemus flavicollis and comparison toApodemus sylvaticus in northern Poland based on RAD-seq.BMC Genomics, 21(1), 1–14. Criscione, C., Poulin, R. & Blouin, M. (2005). Molecular ecology of parasites: elucidating ecological and microevolutionary processes.Molecular Ecology, 14, 2247–2257. Čížková, D., Baird, S. J. E., Těšíková, J., Voigt, S., Ľudovít, Ď., Piálek, J., & Goüy de Bellocq, J. (2018). Host subspecific viral strains in European house mice: Murine cytomegalovirus in the Eastern (Mus musculus musculus) and Western house mouse (Mus musculus domesticus). Virology, 521, 92–98.https://doi.org/10.1016/j.virol.2018.05.023Danecek, P., Auton, A., Abecasis, G., Albers, C. A., Banks, E., DePristo, M. A., Handsaker, R. E., Lunter, G., Marth, G. T., Sherry, S. T., McVean, G., Durbin, R. & 1000 Genomes Project Analysis Group (2011). The variant call format and VCFtools. Bioinformatics, 27(15), 2156–2158. https://doi.org/10.1093/bioinformatics/btr330 Darling, A.C.E., Mau, B., Blattner, F.R. & Perna, N.T. (2004). Mauve: Multiple alignment of conserved genomic sequence with rearrangements.Genome Research, 14, 1394–1403. Darriba, D., Taboada, G., Doallo, R. & Posada, D. (2012). jModelTest 2: more models, new heuristics and parallel computing. Nature Methods, 9, 772–772. de Bellocq, J., Wasimuddin, Ribas, A., Bryja, J., Pialek, J. & Baird, S. (2018). Holobiont suture zones: Parasite evidence across the European house mouse hybrid zone. Molecular Ecology, 27, 5214–5227. Dong, W.G., Song, S., Jin, D.-C., Guo, X.-G., & Shao, R. (2014). Fragmented mitochondrial genomes of the rat lice, Polyplax asiatica and Polyplax spinulosa: intra-genus variation in fragmentation pattern and a possible link between the extent of fragmentation and the length of life cycle. BMC Genomics, 15, 44.https://doi.org/10.1186/1471-2164-15-44du Toit, N., van Vuuren, B., Matthee, S. & Matthee, C. (2013). Biogeography and host-related factors trump parasite life history: limited congruence among the genetic structures of specific ectoparasitic lice and their rodent hosts. Molecular Ecology, 22, 5185–5204. Gómez-Díaz, E., González-Solís, J., Peinado, J. A. & Page, R. D. M (2007). Lack of host-dependent genetic structure in ectoparasites ofCalonectris shearwaters. Molecular Ecology, 16, 5204–5215. Guindon S., Dufayard J.F., Lefort V., Anisimova M., Hordijk W. & Gascuel O. (2010). New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0. Systematic Biology, 59, 307–21. Guindon, S. & Gascuel, O. (2003). A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.Systematic Biology, 52, 696–704. Hafner, D., Hafner, M., Spradling, T., Light, J. & Demastes, J. (2019). Temporal and spatial dynamics of competitive parapatry in chewing lice.Ecology and Evolution, 9, 7410–7424. Harper, S., Spradling, T., Demastes, J. & Calhoun, C. (2015). Host behaviour drives parasite genetics at multiple geographic scales: population genetics of the chewing louse, Thomomydoecus minor.Molecular Ecology, 24, 4129–4144. Hill, G.E. (2019). Mitonuclear Ecology. Oxford Series in Ecology and Evolution. 302 pp. Jarne, P. & Theron, A. (2001). Genetic structure in natural populations of flukes and snails: a practical approach and review. Parasitology, 123, 27–40. Johnson, K. P., Allen, J. M., Olds, B. P., Mugisha, L., Reed, D. L., Paige, K. N., & Pittendrigh, B. R. (2014). Rates of genomic divergence in humans, chimpanzees and their lice. Proceedings of Royal Society B, 281, 20132174. doi.org/10.1098/rspb.2013.2174 Jones, P. H. & Britten, H. B. (2010). The absence of concordant population genetic structurein the black-tailed prairie dog and the flea, Oropsylla hirsuta, with implications for the spread ofYersinia pestis. Molecular Ecology, 19, 2038–2049. Kolmogorov, M., Yuan, J., Lin, Y., & Pevzner, P. A. (2019). Assembly of long, error-prone reads using repeat graphs. Nature biotechnology, 37, 540. Kopelman, N. M., Mayzel, J., Jakobsson, M., Rosenberg, N. A, Mayrose, I. (2015). CLUMPAK: a program for identifying clustering modes and packaging population structure inferences across K. Molecular Ecology Resources, 15, 1179–1191.https://doi:10.1111/1755-0998.12387Langmead, B., Salzberg, S. (2012). Fast gapped-read alignment with Bowtie 2.Nature Methods, 9, 357–359. Lee, T. H., Guo, H., Wang, X., Kim, C., & Paterson, A. H. (2014). SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data.BMC Genomics, 15. Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G. & Durbin, R. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25, 2078–2079. Louhi, K. J., Karvonen, A., Rellstab, Ch. & Jokela, J. (2010). Is the population genetic structure of complex life cycle parasites determined by the geographic range of the most motile host?Infection, Genetics and Evolution, 10, 1271–1277. Martinů, J., Hypša, V. & Štefka, J. (2018). Host specificity driving genetic structure and diversity in ectoparasite populations: Coevolutionary patterns in Apodemus mice and their lice.Ecology and Evolution, 8, 10008–10022. Maze-Guilmo, E., Blanchet, S., McCoy, K. & Loot, G. (2016). Host dispersal as the driver of parasite genetic structure: a paradigm lost?Ecology Letters, 19, 336-347. McCoy, K. D., Chapuis, E., Tirard, C., Boulinier, T., Michalakis, Y., Le Bohec, C., Le Maho, Y. & Gauthier-Clerc M. (2005). Recurrent evolution of host-specialized races in a globally distributed parasite.Proceedings of the Royal Society B -Biological Sciences, 272, 2389–2395. Nieberding, C., Morand, S., Libois, R. & Michaux, J. (2004). A parasite reveals cryptic phylogeographic history of its host. Proceedings of the Royal Society B-Biological Sciences, 271, 2559–2568. Page, R. D. M. (2003). Tangled Trees: phylogeny, cospeciation and coevolution. (Roderic D.M Page, Ed.). Chicago: University of Chicago Press,. Page, R. D. M., Lee. P. L. M., Becher, S. A., Griffiths, R. & Clayton, D. H. (1998). A Different Tempo of Mitochondrial DNA Evolution in Birds and Their Parasitic Lice.Molecular Phylogenetics and Evolution, 9, 276–293. Říhová, J., Nováková, E., Husník, F. & Hypša, V. (2017). LegionellaBecoming a Mutualist: Adaptive Processes Shaping the Genome of Symbiont in the Louse Polyplax serrata. Genome Biology and Evolution, 9, 2946–2957. Song, F., Li, H., Liu, G. H., Wang, W., James, P., Colwell, D. D. & Shao, R. (2019). Mitochondrial genome fragmentation unites the parasitic lice of Eutherian mammals. Systematic Biology, 68, 430–440.https://doi.org/10.1093/sysbio/syy062Štefka, J., Hoeck, P. E. a, Keller, L. F., & Smith, V. S. (2011). A hitchhikers guide to the Galápagos: co-phylogeography of Galápagos mockingbirds and their parasites. BMC Evolutionary Biology, 11, 284. Sweet, A. D., & Johnson, K. P. (2018). The role of parasite dispersal in shaping a host-parasite system at multiple evolutionary scales.Molecular Ecology, 2724, 5104–5119.https://doi.org/10.1111/mec.14937Theodosopoulos, A. N., Hund, A. K., & Taylor, S. A. (2019). Parasites and Host Species Barriers in Animal Hybrid Zones. Trends in Ecology and Evolution, 34, 19–30.https://doi.org/10.1016/j.tree.2018.09.011Van der Auwera, G. A., Carneiro, M. O., Hartl, C., Poplin, R., Del Angel, G., Levy‐Moonshine, A., Jordan, T., Shakir, K., Roazen, D., Thibault, J., Banks, E., Garimella, K. V., Altshuler, D., Gabriel, S. & DePristo, M. A. (2013). From FastQ data to high confidence variant calls: the genome analysis toolkit best practices pipeline. Current Protocols in Bioinformatics, 43, 11.10.1–33. Waterhouse, R. M., Seppey, M., Simão, F. A., Manni, M., Ioannidis, P., Klioutchnikov, G. & Zdobnov, E. M. (2017). BUSCO applications from quality assessments to gene prediction and phylogenomics.Molecular Biology and Evolution, 35, 543–548. Whiteman, N. K., Kimball, R. T. & Parker, P.G. (2007). Co-phylogeography and comparative population genetics of the threatened Galápagos hawk and three ectoparasite species: ecology shapes population histories within parasite communities. Molecular Ecology, 16, 4759–4773. Wolff, J. N., Ladoukakis, E. D., Enríquez, J. A., & Dowling, D. K. (2014). Mitonuclear interactions: Evolutionary consequences over multiple biological scales. Philosophical Transactions of the Royal Society B: Biological Sciences, 369, 20130443.