References
Alasaad, S., Oleaga, Á., Casais, R., Rossi, L., Min, A. M., Soriguer, R. C., & Gortázar, C. (2011). Temporal stability in the genetic structure of Sarcoptes scabiei under the host-taxon law: empirical evidences from wildlife-derived Sarcoptes mite in Asturias, Spain. Parasites & vectors, 4 (1), 151. doi:10.1186/1756-3305-4-151
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990). Basic local alignment search tool. J Mol Biol, 215 (3), 403-410. doi:10.1016/S0022-2836(05)80360-2
Andriantsoanirina, V., Ariey, F., Izri, A., Bernigaud, C., Fang, F., Charrel, R., Foulet, F., Botterel, F., Guillot, J., Chosidow, O., & Durand, R. (2015). Sarcoptes scabiei mites in humans are distributed into three genetically distinct clades. Clinical Microbiology and Infection, 21 (12), 1107-1114. doi:10.1016/j.cmi.2015.08.002
Andriantsoanirina, V., Ariey, F., Izri, A., Bernigaud, C., Fang, F., Guillot, J., Chosidow, O., & Durand, R. (2015). Wombats acquired scabies from humans and/or dogs from outside Australia. Parasitology research, 114 (6), 2079-2083. doi:10.1007/s00436-015-4422-2
Andriantsoanirina, V., Fang, F., Ariey, F., Izri, A., Foulet, F., Botterel, F., Bernigaud, C., Chosidow, O., Huang, W. Y., Guillot, J., & Durand, R. (2016). Are humans the initial source of canine mange? Parasites & vectors, 9 , 177. doi:10.1186/S13071-016-1456-Y
Arlian, L. G., & Morgan, M. S. (2017). A review of Sarcoptes scabiei : past, present and future.Parasit Vectors, 10 (1), 297. doi:10.1186/s13071-017-2234-1
Arlian, L. G., Runyan, R. A., & Estes, S. A. (1984). Cross infestivity of Sarcoptes scabiei .Journal of the American Academy of Dermatology, 10 (6), 979-986.doi:10.1016/S0190-9622(84)80318-7
Arlian, L. G., Runyan, R. A., & Vyszenski-Moher, D. L. (1988). Water balance and nutrient procurement ofSarcoptes scabiei var. canis (Acari: Sarcoptidae).Journal of medical entomology (1), 64-68. doi:10.1093/jmedent/25.1.64
Ashburner, M. (2000). Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.Nat. Genet., 25 , 25-29. doi:10.1038/75556
Bairoch, A., & Apweiler, R. (2000). The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res, 28 (1), 45-48. doi:10.1093/nar/28.1.45
Bardeleben, C., Moore, R. L., & Wayne, R. K. (2005). Isolation and molecular evolution of the selenocysteine tRNA (Cf TRSP) and RNase P RNA (Cf RPPH1) genes in the dog family, Canidae. Mol Biol Evol, 22 (2), 347-359. doi:10.1093/molbev/msi022
Bhandal, J., Langohr, I. M., Degner, D. A., Yan, X., & Walshaw, R. (2012). Histomorphometric Analysis and Regional Variations of Full Thickness Skin Grafts in Dogs.Veterinary Surgery, 41 (4), 448-454. doi:10.1111/j.1532-950X.2012.00987.x
Birney, E., Clamp, M., & Durbin, R. (2004). GeneWise and Genomewise. Genome Res, 14 (5), 988-995. doi:10.1101/gr.1865504
Bouillon, R., Schuit, F., Antonio, L., & Rastinejad, F. (2020). Vitamin D Binding Protein: A Historic Overview. Frontiers in Endocrinology, 10 , 910. doi:10.3389/fendo.2019.00910
Bronaugh, R. L., Stewart, R. F., & Congdon, E. R. (1982). Methods for in vitro percutaneous absorption studies. II. Animal models for human skin. Toxicol Appl Pharmacol, 62 (3), 481-488. doi:10.1016/0041-008X(82)90149-1
Burge, C., & Karlin, S. (1997). Prediction of complete gene structures in human genomic DNA. J Mol Biol, 268 (1), 78-94. doi:10.1006/jmbi.1997.0951
Burgess, S. T. G., Bartley, K., Marr, E. J., Wright, H. W., Weaver, R. J., Prickett, J. C., Hughes, M., Haldenby, S., Thi Le, P., Rombauts, S., Van Leeuwen, T., Van de Peer, Y., & Nisbet, A. J. (2018). Draft Genome Assembly of the Sheep Scab Mite, Psoroptes ovis. Genome Announc, 6 (16), 1-14. doi:10.1128/genomeA.00265-18
Burton, J. N., Adey, A., Patwardhan, R. P., Qiu, R., Kitzman, J. O., & Shendure, J. (2013). Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. Nature Biotechnology, 31 (12), 1119-1125. doi:10.1038/nbt.2727
Celniker, S. E., Keelan, D. J., & Lewis, E. B. (1989). The molecular genetics of the bithorax complex of Drosophila: characterization of the products of the Abdominal-B domain.Genes Dev, 3 (9), 1424-1436. doi:10.1101/gad.3.9.1424
Chin, C. S., Alexander, D. H., Marks, P., Klammer, A. A., & Korlach, J. (2013). Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nature Methods, 10 (6), 563-569. doi:10.1038/nmeth.2474
Claudianos, C., Ranson, H., Johnson, R. M., Biswas, S., Schuler, M. A., Berenbaum, M. R., Feyereisen, R., & Oakeshott, J. G. (2006). A deficit of detoxification enzymes: pesticide sensitivity and environmental response in the honeybee. Insect molecular biology, 15 (5), 615-636. doi:10.1111/j.1365-2583.2006.00672.x
Currier, R. W., Walton, S. F., & Currie, B. J. (2011). Scabies in animals and humans: history, evolutionary perspectives, and modern clinical management. Ann N Y Acad Sci, 1230 , E50-60. doi:10.1111/j.1749-6632.2011.06364.x
Darriba, D., Taboada, G. L., Doallo, R., & Posada, D. (2012). jModelTest 2: more models, new heuristics and parallel computing. Nature Methods, 9 (8), 772-772. doi:10.1038/nmeth.2109
De Bie, T., Cristianini, N., Demuth, J. P., & Hahn, M. W. (2006 ). CAFE: a computational tool for the study of gene family evolution. Bioinformatics, 22 (10), 1269-1271. doi:10.1093/bioinformatics/btl097
Dermauw, W., Osborne, E. J., Clark, R. M., Grbic, M., Tirry, L., & Van Leeuwen, T. (2013). A burst of ABC genes in the genome of the polyphagous spider mite Tetranychus urticae.Bmc Genomics, 14 . doi:10.1186/1471-2164-14-317
Edgar, R. C. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic acids research, 32 (5), 1792-1797. doi:10.1093/nar/gkh340
Enayati, A. A., Ranson, H., & Hemingway, J. (2005). Insect glutathione transferases and insecticide resistance. Insect molecular biology, 14 (1), 3-8. doi:10.1111/j.1365-2583.2004.00529.x
Engelman, D., Kiang, K., Chosidow, O., McCarthy, J., Fuller, C., Lammie, P., Hay, R., Steer, A., & Scabies, m. o. t. I. A. f. t. C. o. (2013). Toward the global control of human scabies: introducing the International Alliance for the Control of Scabies. PLoS Negl Trop Dis, 7 (8), e2167. doi:10.1371/journal.pntd.0002167
Escobar, L. E., Carver, S., Cross, P. C., Rossi, L., Almberg, E. S., Yabsley, M. J., Niedringhaus, K. D., Van Wick, P., Dominguez-Villegas, E., Gakuya, F., Xie, Y., Angelone, S., Gortazar, C., & Astorga, F. (2021). Sarcoptic mange: An emerging panzootic in wildlife. Transboundary and Emerging Diseases . doi:10.1111/tbed.14082
Estes, S. A., Kummel, B., & Arlian, L. (1983). Experimental canine scabies in humans. Journal of the American Academy of Dermatology, 9 (3), 397-401. doi:10.1016/S0190-9622(83)70148-9
Fain, A. (1978). Epidemiological problems of scabies. International Journal of Dermatology, 17 (1), 20-30. doi:10.1111/j.1365-4362.1978.tb06040.x
Fenner, J. N. (2010). Cross-cultural estimation of the human generation interval for use in genetics-based population divergence studies. American Journal of Physical Anthropology, 128 (2), 415-423. doi:10.1002/ajpa.20188
Fernando, D. D., Reynolds, S. L., Hartel, G., Cribier, B., & Fischer, K. (2021). A unique group of scabies mite pseudoproteases promotes cutaneous blood coagulation and delays plasmin-induced fibrinolysis. PLoS Neglected Tropical Diseases, 15 (1), e0008997. doi:10.1371/journal.pntd.0008997
Finn, R. D., Attwood, T. K., Babbitt, P. C., Bateman, A., Bork, P., Bridge, A. J., Chang, H. Y., Dosztányi, Z., El-Gebali, S., Fraser, M., Gough, J., Haft, D., Holliday, G. L., Huang, H., Huang, X., Letunic, I., Lopez, R., Lu, S., Marchler-Bauer, A., Mi, H., Mistry, J., Natale, D. A., Necci, M., Nuka, G., Orengo, C. A., Park, Y., Pesseat, S., Piovesan, D., Potter, S., Rawlings, N. D., Redaschi, N., Richardson, L., Rivoire, C., Sangrador-Vegas, A., Sigrist, C., Sillitoe, I., Smithers, B., Squizzato, S., Sutton, G., Thanki, N., Thomas, P. D., Tosatto, S. C., Wu, C., Xenarios, I., Yeh, L. S., Young, S. Y., & Mitchell, A. L. (2017). InterPro in 2017—beyond protein family and domain annotations. Nucleic acids research (D1), D190-D199. doi:10.1093/nar/gkw1107
Fischer, K., Langendorf, C. G., Irving, J. A., Reynolds, S., Willis, C., Beckham, S., Law, R., Yang, S., Bashtannyk-Puhalovich, T. A., & Mcgowan, S. (2009). Structural Mechanisms of Inactivation in Scabies Mite Serine Protease Paralogues.Journal of molecular biology, 390 (4), 635-645. doi:10.1016/j.jmb.2009.04.082
Fraser, T. A., Charleston, M., Martin, A., Polkinghorne, A., & Carver, S. (2016). The emergence of sarcoptic mange in Australian wildlife: an unresolved debate.Parasites & vectors, 9 (1), 316. doi:10.1186/S13071-016-1578-2
Friedman, R. (1934). The Story of Scabies. Med Life , 381-424.
Friedman, R. (1936). The story of scabies: animal scabies–its relationship to humans. Urol. cutan. Rev, 42 , 513-530.
Gakuya, F., Rossi, L., Ombui, J., Maingi, N., Muchemi, G., Ogara, W., Soriguer, R. C., & Alasaad, S. (2011). The curse of the prey: Sarcoptes mite molecular analysis reveals potential prey-to-predator parasitic infestation in wild animals from Masai Mara, Kenya. Parasites & vectors, 4 , 193. doi:10.1186/1756-3305-4-193
Grabherr, M. G., Haas, B. J., Yassour, M., Levin, J. Z., Thompson, D. A., & Amit, I. (2011). Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol, 29 . doi:10.1038/nbt.1883
Gu, X. B., Liu, G. H., Song, H. Q., Liu, T. Y., Yang, G. Y., & Zhu, X. Q. (2014). The complete mitochondrial genome of the scab mite Psoroptes cuniculi (Arthropoda: Arachnida) provides insights into Acari phylogeny. Parasit Vectors, 7 , 340. doi:10.1186/1756-3305-7-340
Guigo, R., Knudsen, S., Drake, N., & Smith, T. (1992). Prediction of gene structure. J Mol Biol, 226 (1), 141-157. doi:10.1016/0022-2836(92)90130-C
Haas, B. J., Delcher, A. L., Mount, S. M., Wortman, J. R., Smith, J., Hannick, L. I., Rama, M., Ronning, C. M., Rusch, D. B., & Town, C. D. (2003). Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies.Nucleic acids research (19), 5654-5666. doi:10.1093/nar/gkg770
Haas, B. J., Salzberg, S. L., Zhu, W., Pertea, M., Allen, J. E., Orvis, J., White, O., Buell, C. R., & Wortman, J. R. (2008). Automated eukaryotic gene structure annotation using EVidenceModeler and the program to assemble spliced alignments.Genome biology, 9 (1). doi:10.1186/Gb-2008-9-1-R7
Halliday, R., OConnor, B., & Baker, A. (2000). ”Global Diversity of Mites”. In Peter H. Raven; Tania Williams (eds.).Nature and human society: the quest for a sustainable world: proceedings of the 1997 Forum on Biodiversity. National Academies (192–212).
Hammond, S. A., Tsonis, C., Sellins, K., Rushlow, K., Scharton-Kersten, T., Colditz, I., & Glenn, G. M. (2000). Transcutaneous immunization of domestic animals: opportunities and challenges. Advanced Drug Delivery Reviews, 43 (1), 45-55. doi:10.1016/S0169-409X(00)00076-4
Hay, R. J., Johns, N. E., Williams, H. C., Bolliger, I. W., Dellavalle, R. P., Margolis, D. J., Marks, R., Naldi, L., Weinstock, M. A., & Wulf, S. K. (2014). The global burden of skin disease in 2010: an analysis of the prevalence and impact of skin conditions. Journal of Investigative Dermatology, 134 (6), 1527-1534. doi:10.1038/jid.2013.446
Heukelbach, J., & Feldmeier, H. (2006). Scabies. Lancet, 367 (9524), 1767-1774. doi:10.1016/S0140-6736(06)68772-2
Hoy, M. A., Waterhouse, R. M., Wu, K., Estep, A. S., Ioannidis, P., Palmer, W. J., Pomerantz, A. F., Simão, F. A., Thomas, J., & Jiggins, F. M. (2016). Genome sequencing of the phytoseiid predatory mite Metaseiulus occidentalis reveals completely atomized Hox genes and superdynamic intron evolution. Genome Biology and Evolution, 8 (6), 1762-1775. doi:10.1093/gbe/evw048
Hu, X. S., Yeh, F. C., Hu, Y., Deng, L. T., Ennos, R. A., & Chen, X. Y. (2017). High mutation rates explain low population genetic divergence at copy-number-variable loci in Homo sapiens. Scientific Reports, 7 , 1-13. doi:10.1038/Srep43178
Hughes, C. L., & Kaufman, T. C. (2002). Hox genes and the evolution of the arthropod body plan.Evol Dev, 4 (6), 459-499. doi:10.1046/j.1525-142X.2002.02034.x
Jones, P., Binns, D., Chang, H., Fraser, M., Li, W., McAnulla, C., McWilliam, H., Maslen, J., Mitchell, A., Nuka, G., Pesseat, S., Quinn, A., Sangrador-Vegas, A., Scheremetjew, M., Yong, S., Lopez, R., & Hunter, S. (2014). InterProScan 5: genome-scale protein function classification. Bioinformatics, 30 (9), 1236-1240. doi:10.1093/bioinformatics/btu031
Jordi, Casanova, and, Ernesto, Sánchez-Herrero, Ginés, & Morata. (1986). Identification and characterization of a parasegment specific regulatory element of the abdominal-B gene of drosophila. Cell, 47 (4), 627-636. doi:10.1016/0092-8674(86)90627-6
Jurka, J., Kapitonov, V. V., Pavlicek, A., Klonowski, P., Kohany, O., & Walichiewicz, J. (2005). Repbase Update, a database of eukaryotic repetitive elements.Cytogenet Genome Res, 110 (1-4), 462-467. doi:10.1159/000084979
Kanehisa, & Goto. (2000). KEGG: kyoto encyclopedia of genes and genomes. Nucleic acids research, 28 (1), 27-30. doi:10.1093/nar/28.1.27
Karch, F., Bender, W., & Weiffenbach, B. (1990). abdA expression in Drosophila embryos.Genes & Development, 4 (9), 1573-1587. doi:10.1101/gad.4.9.1573
Karimkhani, C., Dellavalle, R. P., Coffeng, L. E., Flohr, C., & Naghavi, M. (2017). Global skin disease morbidity and mortality an update from the global burden of disease study 2013. JAMA Dermatology, 153 (5), 406-412. doi:10.1001/jamadermatol.2016.5538
Katoh, K., & Standley, D. (2014). MAFFT: iterative refinement and additional methods. . Methods Mol Biol, 1079 131-146 doi:10.1007/978-1-62703-646-7_8
Kent, W. J. (2002). BLAT–the BLAST-like alignment tool. Genome Res, 12 (4), 656-664. doi:10.1101/gr.229202
Kingsford, C. (2011). A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics, 27 (6), 764-770. doi:10.1093/bioinformatics/btr011
Koren, S., Walenz, B. P., Berlin, K., Miller, J. R., Bergman, N. H., & Phillippy, A. M. (2017). Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Research, 27 (5), 722-736. doi:10.1101/gr.215087.116
Korf, I. (2004). Gene finding in novel genomes. BMC Bioinformatics, 5 , 59. doi:10.1186/1471-2105-5-59
Korhonen, P. K., Gasser, R. B., Ma, G. X., Wang, T., Stroehlein, A. J., Young, N. D., Ang, C. S., Fernando, D. D., Lu, H. C., Taylor, S., Reynolds, S. L., Mofiz, E., Najaraj, S. H., Gowda, H., Madugundu, A., Renuse, S., Holt, D., Pandey, A., Papenfuss, A. T., & Fischer, K. (2020). High-quality nuclear genome forSarcoptes scabiei -A critical resource for a neglected parasite.PLoS Neglected Tropical Diseases, 14 (10). doi:10.1371/journal.pntd.0008720
Kraabl, M., Gundersen, V., Fangel, K., & Olstad, K. (2015). The taxonomy, life cycle and pathology of Sarcoptes scabiei and Notoedres cati (Acarina, Sarcoptidae): A review in a Fennoscandian wildlife perspective. Fauna Norvegica, 35 , 21-33. doi:10.5324/fn.v35i0.1652
Krantz, G. (2009).Introduction. In: Krantz GW, Walter DE, eds. In A Manual of Acarology (pp. 1-2).
Kumar, S., Stecher, G., & Tamura, K. (2016). MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Molecular biology and evolution, 33 (7), 1870-1874. doi:10.1093/molbev/msw054
Li, H. (2011). A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data.Bioinformatics, 27 (21), 2987-2993. doi:10.1093/bioinformatics/btr509
Li, H., & Durbin, R. (2009). Fast and accurate short read alignment with Burrows-Wheeler transform.Bioinformatics, 25 (14), 1754-1760. doi:10.1093/bioinformatics/btp324
Li, H., & Durbin, R. (2011). Inference of human population history from individual whole-genome sequences. Nature, 475 (7355), 493-496. doi:10.1038/nature10231
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 (16), 2078-2079. doi:10.1093/bioinformatics/btp352
Li, L., Stoeckert, C. J. J., & Roos, D. S. (2003). OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes. Genome Research, 13 (9), 2178-2189. doi:10.1101/gr.1224503
Li, X., Schuler, M. A., & Berenbaum, M. R. (2007). Molecular mechanisms of metabolic resistance to synthetic and natural xenobiotics. Annual Review of Entomology, 52 (1), 231-253. doi:10.1146/annurev.ento.51.110104.151104
Majoros, W. H., Pertea, M., & Salzberg, S. L. (2004). TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders. Bioinformatics, 20 (16), 2878-2879. doi:10.1093/bioinformatics/bth315
Matsuyama, R., Yabusaki, T., Kuninaga, N., Morimoto, T., Okano, T., Suzuki, M., & Asano, M. (2015). Coexistence of two different genotypes of Sarcoptes scabiei derived from companion dogs and wild raccoon dogs in Gifu, Japan: The genetic evidence for transmission between domestic and wild canids.Veterinary parasitology, 212 (3), 356-360. doi:10.1016/j.vetpar.2015.06.023
Mofiz, E., Holt, D. C., Seemann, T., Currie, B. J., Fischer, K., & Papenfuss, A. T. (2016). Genomic resources and draft assemblies of the human and porcine varieties of scabies mites, Sarcoptes scabiei var. hominis and var. suis.Gigascience, 5 (1), 23. doi:10.1186/s13742-016-0129-2
Mulder, N. J., Apweiler, R., Attwood, T. K., Bairoch, A., Bateman, A., Binns, D., Bork, P., Buillard, V., Cerutti, L., Copley, R., Courcelle, E., Das, U., Daugherty, L., Dibley, M., Finn, R., Fleischmann, W., Gough, J., Haft, D., Hulo, N., Hunter, S., Kahn, D., Kanapin, A., Kejariwal, A., Labarga, A., Langendijk-Genevaux, P. S., Lonsdale, D., Lopez, R., Letunic, I., Madera, M., Maslen, J., McAnulla, C., McDowall, J., Mistry, J., Mitchell, A., Nikolskaya, A. N., Orchard, S., Orengo, C., Petryszak, R., Selengut, J. D., Sigrist, C. J., Thomas, P. D., Valentin, F., Wilson, D., Wu, C. H., & Yeats, C. (2007). New developments in the InterPro database. Nucleic Acids Res, 35 (Database issue), D224-228. doi:10.1093/nar/gkl841
Nasvall, J., Sun, L., Roth, J. R., & Andersson, D. I. (2012). Real-Time Evolution of New Genes by Innovation, Amplification, and Divergence. Science, 338 (6105), 384-387. doi:10.1126/science.1226521
Neste, D. V., & Lachapelle, J. M. (1981). Host-parasite relationships in hyperkeratotic (Norwegian) scabies: pathological and immunological findings. British Journal of Dermatology, 105 (6). doi:10.1111/j.1365-2133.1981.tb00977.x
Nicoli, S., Padula, C., Aversa, V., Vietti, B., Wertz, P. W., Millet, A., Falson, F., Govoni, P., & Santi, P. (2008). Characterization of rabbit ear skin as a skin model for in vitro transdermal permeation experiments: histology, lipid composition and permeability. Skin Pharmacology & Physiology, 21 (4), 218-226. doi:10.1159/000135638
Norton, R. A., Bonamo, P. M., Grierson, J. D., & Shear, W. A. (1988). Oribatid mite fossils from a terrestrial Devonian deposit near Gilboa, New York. Journal of Paleontology, 62 (2), 259-269. doi:10.1017/S0022336000029905
Orion, E., Marcos, B., Davidovici, B., & Wolf, R. (2006). Itch and scratch: scabies and pediculosis.Clinics in Dermatology, 24 (3), 168-175. doi:10.1016/j.clindermatol.2005.11.001
Pace, R. M., Grbic, M., & Nagy, L. M. (2016). Composition and genomic organization of arthropod Hox clusters. Evodevo, 7 , 11. doi:10.1186/s13227-016-0048-4
Parra, G., Bradnam, K., & Korf, I. (2007). CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics, 23 (9), 1061-1067. doi:10.1093/bioinformatics/btm071
Pence, D. B., & Ueckermann, E. (2002). Sarcoptic mange in wildlife. Revue scientifique et technique (International Office of Epizootics), 21 (2), 385-398. doi:10.20506/rst.21.2.1335
Petrunkevitch, & Alexander. (1952). An Introduction to Acarology. American Journal of Public Health & the Nations Health, 42 (8), 1010-1010. doi:10.2136/sssaj1952.03615995001600030028x
Pick, L. (2016). Hox genes, evo-devo, and the case of the ftz gene. Chromosoma, 125 (3), 535-551. doi:10.1007/s00412-015-0553-6
Price, A. L., Jones, N. C., & Pevzner, P. A. (2005). De novo identification of repeat families in large genomes. Bioinformatics, 21 Suppl 1 , i351-358. doi:10.1093/bioinformatics/bti1018
Rasero, R., Rossi, L., Soglia, D., Maione, S., & Alasaad, S. (2010). Host taxon-derived Sarcoptes mite in European wild animals revealed by microsatellite markers.Biological Conservation, 143 (5), 1269-1277. doi:10.1016/j.biocon.2010.03.001
Rider, S. D., Jr., Morgan, M. S., & Arlian, L. G. (2015). Draft genome of the scabies mite. Parasit Vectors, 8 , 585. doi:10.1186/s13071-015-1198-2
Roach, M. J., Schmidt, S. A., & Borneman, A. R. (2018). Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies. BMC Bioinformatics, 19 (1), 1-10. doi:10.1186/S12859-018-2485-7
Romani, L., Steer, A. C., Whitfeld, M. J., & Kaldor, J. M. (2015). Prevalence of scabies and impetigo worldwide: a systematic review. Lancet Infectious Diseases, 15 (8), 960-967. doi:10.1016/S1473-3099(15)00132-2
Savolainen, P., Zhang, Y. P., Luo, J., Lundeberg, J., & Leitner, T. (2002). Genetic evidence for an East Asian origin of domestic dogs. Science, 298 (5598), 1610-1613. doi:10.1126/science.1073906
Simao, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V., & Zdobnov, E. M. (2015). BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics, 31 (19), 3210-3212. doi:10.1093/bioinformatics/btv351
Skoglund, P., Ersmark, E., Palkopoulou, E., & Dalen, L. (2015). Ancient Wolf Genome Reveals an Early Divergence of Domestic Dog Ancestors and Admixture into High-Latitude Breeds. Current Biology, 25 (11), 1515-1519. doi:10.1016/j.cub.2015.04.019
Stamatakis, A. (2006). RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics, 22 (21), 2688-2690. doi:10.1093/bioinformatics/btl446
Stanke, M., & Morgenstern, B. (2005). AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints. Nucleic Acids Res, 33 (Web Server issue), W465-467. doi:10.1093/nar/gki458
Sudhir, K., Glen, S., Michael, S., & Blair, H. S. (2017). TimeTree: A Resource for Timelines, Timetrees, and Divergence Times. Molecular Biology & Evolution (7), 1812-1819. doi:10.1093/molbev/msx116
Trapnell, C., Pachter, L., & Salzberg, S. L. (2009). TopHat: discovering splice junctions with RNA-Seq. Bioinformatics, 25 (9), 1105-1111. doi:10.1093/bioinformatics/btp120
Trapnell, C., Williams, B. A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M. J., Salzberg, S. L., Wold, B. J., & Pachter, L. (2010). Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnology, 28 (5), 511-U174. doi:10.1038/nbt.1621
Van Neste, D. (1984). Intraepidermal localization of scabies mites overlooked? Journal of the American Academy of Dermatology, 10 (4), 676-676. doi:10.1016/S0190-9622(84)80287-X
Vilella, A. J., Severin, J., Ureta-Vidal, A., Heng, L., Durbin, R., & Birney, E. (2009). EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. Genome Research, 19 (2), 327-335. doi:10.1101/gr.073585.107
Waldron, R., McGowan, J., Gordon, N., McCarthy, C., Mitchell, E. B., Doyle, S., & Fitzpatrick, D. A. (2017). Draft Genome Sequence of Dermatophagoides pteronyssinus, the European House Dust Mite. Genome Announc, 5 (32), e00789-00717. doi:10.1128/genomeA.00789-17
Walker, B. J., Abeel, T., Shea, T., Priest, M., Abouelliel, A., Sakthikumar, S., Cuomo, C. A., Zeng, Q. D., Wortman, J., Young, S. K., & Earl, A. M. (2014). Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement. PLoS One, 9 (11), 1-14. doi:10.1371/journal.pone.0112963
Walton, S., Choy, J., Bonson, A., Valle, A., McBroom, J., Taplin, D., Arlian, L., Mathews, J., Currie, B., & Kemp, D. (1999). Genetically distinct dog-derived and human-derivedSarcoptes scabiei in scabies-endemic communities in northern Australia. The American journal of tropical medicine and hygiene, 61 (4), 542-547. doi:10.1016/j.metabol.2007.06.007
Walton, S., Dougall, A., Pizzutto, S., Holt, D., Taplin, D., Arlian, L., Morgan, M., Currie, B., & Kemp, D. (2004). Genetic epidemiology of Sarcoptes scabiei (Acari: Sarcoptidae) in northern Australia. International journal for parasitology, 34 (7), 839-849. doi:10.1016/j.ijpara.2004.04.002
Wang, G. D., Zhai, W., Yang, H. C., Wang, L., Zhong, L., Liu, Y. H., Fan, R. X., Yin, T. T., Zhu, C. L., Poyarkov, A. D., Irwin, D. M., Hytonen, M. K., Lohi, H., Wu, C. I., Savolainen, P., & Zhang, Y. P. (2016). Out of southern East Asia: the natural history of domestic dogs across the world. Cell Res, 26 (1), 21-33. doi:10.1038/cr.2015.147
Wang, G. D., Zhai, W. W., Yang, H. C., Fan, R. X., Cao, X., Zhong, L., Wang, L., Liu, F., Wu, H., Cheng, L. G., Poyarkov, A. D., Poyarkov, N. A., Tang, S. S., Zhao, W. M., Gao, Y., Lv, X. M., Irwin, D. M., Savolainen, P., Wu, C. I., & Zhang, Y. P. (2013). The genomics of selection in dogs and the parallel evolution between dogs and humans. Nature communications, 4 . doi:ARTN 186010.1038/ncomms2814
Wayne, R. K., Geffen, E., Girman, D. J., Koepfli, K. P., Lau, L. M., & Marshall, C. R. (1997). Molecular systematics of the Canidae. Syst Biol, 46 (4), 622-653. doi:10.1093/sysbio/46.4.622
WHO. (2017). Neglected tropical diseases. In (Vol. 2017, pp. accessed July 9, 2017). Geneva: World Health Organization.
Wolfes, A. C., & Dean, C. (2020). The diversity of synaptotagmin isoforms. Current Opinion in Neurobiology, 63 , 198-209. doi:10.1016/j.conb.2020.04.006
Xu, Z., & Wang, H. (2007). LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Res, 35 (Web Server issue), W265-268. doi:10.1093/nar/gkm286
Yang, Z. (2007). PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol., 24 , 1586-1591. doi:10.1093/molbev/msm088
Yu, X. J., Zheng, H. K., Wang, J., Wang, W., & Su, B. (2006). Detecting lineage-specific adaptive evolution of brain-expressed genes in human using rhesus macaque as outgroup. Genomics, 88 (6), 745-751. doi:10.1016/j.ygeno.2006.05.008