BACKGROUND: Laelaps agilis C.L. Koch, 1836 is one the most abundant and widespread parasitic mite species in the Western Palearctic. It is a permanent ectoparasite associated with the Apodemus genus, which transmits Hepatozoon species via the host's blood. Phylogenetic relationships, genealogy and host specificity of the mite are uncertain in the Western Palearctic. Here, we investigated the population genetic structure of 132 individual mites across Europe from their Apodemus and Clethrionomys hosts. Phylogenetic relationships and genetic variation of the populations were analyzed using cytochrome c oxidase subunit I (COI) gene sequences. RESULTS: We recovered three main mtDNA lineages within L. agilis in the Western Palearctic, which differentiated between 1.02 and 1.79 million years ago during the Pleistocene period: (i) Lineage A, including structured populations from Western Europe and the Czech Republic, (ii) Lineage B, which included only a few individuals from Greece and the Czech Republic; and (iii) Lineage C, which comprised admixed populations from Western and Eastern Europe. Contrary to their population genetic differentiation, the lineages did not show signs of specificity to different hosts. Finally, we confirmed that the sympatric congener L. clethrionomydis is represented by a separated monophyletic lineage. CONCLUSION: Differences in the depth of population structure between L. agilis Lineages A and C, corroborated by the neutrality tests and demographic history analyses, suggested a stable population size in the structured Lineage A and a rapid range expansion for the geographically admixed Lineage C. We hypothesized that the two lineages were associated with hosts experiencing different glaciation histories. The lack of host specificity in L. agilis lineages was in contrast to the co-occurring highly host-specific lineages of Polyplax serrata lice, sharing Apodemus hosts. The incongruence was attributed to the differences in mobility between the parasites, allowing mites to switch hosts more often.

Faculty of Science University of South Bohemia Branišovska 1760 370 05 České Budějovice Czech Republic

Institute of Parasitology and Institute of Zoology Slovak Academy of Sciences Hlinkova 3 040 01 Košice Slovakia

Institute of Parasitology Biology Centre CAS Branišovská 31 370 05 České Budějovice Czech Republic

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Templeton AR. Species and Speciation. In: Howard DJ, Berlocher SH, editors. Endless forms: species and speciation. New York: Oxford University Press; 1998. p. 32-43.

Taylor SA, Larson EL. Insights from genomes into the evolutionary importance and prevalence of hybridization in nature. Nat Ecol Evol. 2019;3:170–177. doi: 10.1038/s41559-018-0777-y. PubMed DOI

Cole R, Viney M. Correction to: The population genetics of parasitic nematodes of wild animals. Parasit Vectors. 2019;12:1. doi: 10.1186/s13071-018-3137-5. PubMed DOI PMC

Huyse T, Poulin R, Théron A, Theron A. Speciation in parasites: a population genetics approach. Trends Parasitol. 2005;21:469–475. doi: 10.1016/j.pt.2005.08.009. PubMed DOI

Bueter C, Weckstein J, Johnson KP, Bates JM, Gordon CE. Comparative phylogenetic histories of two louse genera found on Catharus thrushes and other birds. J Parasitol. 2009;95:295–307. doi: 10.1645/GE-1642.1. PubMed DOI

Louhi K-R, Karvonen A, Rellstab C, Jokela J. Is the population genetic structure of complex life cycle parasites determined by the geographic range of the most motile host? Infect Genet Evol. 2010;10:1271–1277. doi: 10.1016/j.meegid.2010.08.013. PubMed DOI

Bouzid W, Štefka J, Hypša V, Lek S, Scholz T, Legal L, et al. Geography and host specificity: Two forces behind the genetic structure of the freshwater fish parasite Ligula intestinalis (Cestoda: Diphyllobothriidae) Int J Parasitol. 2008;38:1465–1479. doi: 10.1016/j.ijpara.2008.03.008. PubMed DOI

Du Toit N, Matthee S, Matthee CA. The sympatric occurrence of two genetically divergent lineages of sucking louse, Polyplax arvicanthis (Phthiraptera: Anoplura), on the four-striped mouse genus, Rhabdomys (Rodentia: Muridae) Parasitology. 2013;140:604. doi: 10.1017/S003118201200217X. PubMed DOI

Bothma JC, Matthee S, Matthee CA. Comparative phylogeography between parasitic sucking lice and their host the Namaqua rock mouse, Micaelamys namaquensis (Rodentia: Muridae) Zool J Linn Soc. 2021;192:1017–1028. doi: 10.1093/zoolinnean/zlaa122. DOI

Krasnov BR, Mouillot D, Khokhlova IS, Shenbrot GI, Poulin R. Compositional and phylogenetic dissimilarity of host communities drives dissimilarity of ectoparasite assemblages: geographical variation and scale-dependence. Parasitology. 2012;139:338–347. doi: 10.1017/S0031182011002058. PubMed DOI

Bordes F, Blumstein DT, Morand S. Rodent sociality and parasite diversity. Biol Lett. 2007;3:692–694. doi: 10.1098/rsbl.2007.0393. PubMed DOI PMC

Whiteman NK, Parker PG. Effects of host sociality on ectoparasite population biology. J Parasitol. 2004;90:939–947. doi: 10.1645/GE-310R. PubMed DOI

Fernandes FR, da Silva AS, Cruz LD. Transmission networks and ectoparasite mite burdens in Oecomys paricola (Rodentia: Cricetidae) Parasitology. 2021;148:443–450. doi: 10.1017/S0031182020002231. PubMed DOI PMC

Martinů J, Hypša V, Štefka J. Host specificity driving genetic structure and diversity in ectoparasite populations: Coevolutionary patterns in Apodemus mice and their lice. Ecol Evol. 2018;8:10008–22. doi: 10.1002/ece3.4424. PubMed DOI PMC

Bittencourt EB, Rocha CFD. Host-ectoparasite specificity in a small mammal community in an area of Atlantic Rain Forest (Ilha Grande, State of Rio de Janeiro) Southeastern Brazil Mem Inst Oswaldo Cruz. 2003;98:793–798. doi: 10.1590/S0074-02762003000600015. PubMed DOI

Benitez-Ibalo AP, Aguiar LD, Benedetto IMD Di, Mangold AJ, Milano F, Debárbora VN. Ectoparasites associated with rodents (Rodentia) and marsupials (Didelphimorphia) from northeastern Argentina: new host and locality records. Rev Mex Biodivers. 2020;91. 10.22201/ib.20078706e.2020.91.3161.

Štefka J, Hypša V. Host specificity and genealogy of the louse Polyplax serrata on field mice, Apodemus species: a case of parasite duplication or colonisation? Int J Parasitol. 2008;38:731–741. doi: 10.1016/j.ijpara.2007.09.011. PubMed DOI

Martinů J, Štefka J, Poosakkannu A, Hypša V. “Parasite turnover zone” at secondary contact: A new pattern in host–parasite population genetics. Mol Ecol. 2020;29:4653–64. doi: 10.1111/mec.15653. PubMed DOI

Engelbrecht A, Matthee S, Du Toit N, Matthee CA. Limited dispersal in an ectoparasitic mite, Laelaps giganteus, contributes to significant phylogeographic congruence with the rodent host. Rhabdomys Mol Ecol. 2016;25:1006–1021. doi: 10.1111/mec.13523. PubMed DOI

Matthee CA, Engelbrecht A, Matthee S. Comparative phylogeography of parasitic Laelaps mites contribute new insights into the specialist-generalist variation hypothesis (SGVH) BMC Evol Biol. 2018;18:131. doi: 10.1186/s12862-018-1245-7. PubMed DOI PMC

Engelbrecht A, Matthee CA, Ueckermann EA, Matthee S. Evidence of cryptic speciation in mesostigmatid mites from South Africa. Parasitology. 2014;141:1322. doi: 10.1017/S0031182014000584. PubMed DOI

Mašán P, Fenďa P. A Review of the Laelapid Mites Associated with Terrestrial Mammals in Slovakia, with a Key to the European Species:(Acari: Mesostigmata: Dermanyssoidea) Slovak Academy of Sciences: Institute of Zoology; 2010.

Vinarski MV, Korallo-Vinarskaya NP. An annotated catalogue of the gamasid mites associated with small mammals in Asiatic Russia. The family Laelapidae s. str.(Acari: Mesostigmata: Gamasina) Zootaxa. 2016;4111:223–45. doi: 10.11646/zootaxa.4111.3.2. PubMed DOI

Martins-Hatano F, Gettinger D, Bergallo HG. Ecology and host specificity of laelapine mites (Acari: Laelapidae) of small mammals in an Atlantic Forest area of Brazil. J Parasitol. 2002;88:36–40. doi: 10.1645/0022-3395(2002. PubMed DOI

Radovsky FJ. The evolution of parasitism and the distribution of some dermanyssoid mites (Mesostigmata) on vertebrate hosts. In: Mites. Springer;1994:186–217. 10.1007/978-1-4615-2389-5_8.

Radovsky FJ. Evolution of mammalian mesostigmate mites. 1985.

Poláčiková Z. Ecology of mites (Acarina) on small mammals (Eulipotyphla, Rodentia) in Podunajská nížina plain. Biologia (Bratisl) 2013;68:162–9. doi: 10.2478/s11756-012-0133-7. DOI

Mašán P, Stanko M. Mesostigmatic mites (Acari) and fleas (Siphonaptera) associated with nests of mound-building mouse, Mus spicilegus Petényi, 1882 (Mammalia, Rodentia) Acta Parasitol. 2005;50:228–234.

Miťková K, Berthová L, Kalúz S, Kazimírová M, Burdová L, Kocianová E. First detections of Rickettsia helvetica and R. monacensis in ectoparasitic mites (Laelapidae and Trombiculidae) infesting rodents in south-western Slovakia. Parasitol Res. 2015;114:2465–72. doi: 10.1007/s00436-015-4443-x. PubMed DOI

Karg W. Die freilebenden Gamasina (Gamasides) Raubmilben Die Tierwelt Deutschlands. 1971;59:1–475.

Netušil J, Žákovská A, Vostal K, Norek A, Stanko M. The occurrence of Borrelia burgdorferi sensu lato in certain ectoparasites (Mesostigmata, Siphonaptera) of Apodemus flavicollis and Myodes glareolus in chosen localities in the Czech Republic. Acta Parasitol. 2013;58:337–41. doi: 10.2478/s11686-013-0147-5. PubMed DOI

Frank C. The importance of Laelaps agilis CL Koch 1836 (Mesostigmata: Parasitiformae) as a vector of Hepatozoon sylvatici Coles 1914 (Sporozoa: Haemogregarinidae)(author’s transl) Z Parasitenkd. 1977;53:307–310. doi: 10.1007/BF00389948. PubMed DOI

Špitalská E, Kraljik J, Miklisová D, Boldišová E, Sparagano OAE, Stanko M. Circulation of Rickettsia species and rickettsial endosymbionts among small mammals and their ectoparasites in Eastern Slovakia. Parasitol Res. 2020;119:2047–2057. doi: 10.1007/s00436-020-06701-8. PubMed DOI

Radzijevskaja J, Kaminskienė E, Lipatova I, Mardosaitė-Busaitienė D, Balčiauskas L, Stanko M, et al. Prevalence and diversity of Rickettsia species in ectoparasites collected from small rodents in Lithuania. Parasit Vectors. 2018;11:1–10. doi: 10.1186/s13071-018-2947-9. PubMed DOI PMC

Dowling APG, Oconnor BM. Phylogeny of dermanyssoidea (Acari: Parasitiformes) suggests multiple origins of parasitism. Acarologia. 2010;50:113–129. doi: 10.1051/acarologia/20101957. DOI

Du Toit N, van Vuuren Jansen B, Matthee S, Matthee CA. Biome specificity of distinct genetic lineages within the four-striped mouse Rhabdomys pumilio (Rodentia: Muridae) from southern Africa with implications for taxonomy. Mol Phylogenet Evol. 2012;65:75–86. doi: 10.1016/j.ympev.2012.05.036. PubMed DOI

Lecompte E, Aplin K, Denys C, Catzeflis F, Chades M, Chevret P. Phylogeny and biogeography of African Murinae based on mitochondrial and nuclear gene sequences, with a new tribal classification of the subfamily. BMC Evol Biol. 2008;8:1–21. doi: 10.1186/1471-2148-8-199. PubMed DOI PMC

López-Antoñanzas R, Renaud S, Peláez-Campomanes P, Azar D, Kachacha G, Knoll F. First levantine fossil murines shed new light on the earliest intercontinental dispersal of mice. Sci Rep. 2019;9:1–16. doi: 10.1038/s41598-019-47894-y. PubMed DOI PMC

Serizawa K, Suzuki H, Tsuchiya K. A Phylogenetic View on Species Radiation in Apodemus Inferred from Variation of Nuclear and Mitochondrial Genes. Biochem Genet. 2000;38:27–40. doi: 10.1023/A:1001828203201. PubMed DOI

Suárez EM, Mein P. Revision of the genera Parapodemus, Apodemus, Rhagamys and Rhagapodemus (Rodentia, Mammalia) Geobios. 1998;31:87–97. doi: 10.1016/s0016-6995(98)80099-5. DOI

Ambros M. Poznámby k výskytu a rozs˘ irenie roztoc˘ a Lakcaps clethrionomydis Lange, 1955 (Acari: Dermanyssidae) na Slovensku. Biol. 1990;45:791–800.

Du Toit N, van Vuuren BJ, Matthee S, Matthee CA. Biogeography and host-related factors trump parasite life history: limited congruence among the genetic structures of specific ectoparasitic lice and their rodent hosts. Mol Ecol. 2013;22:5185–5204. doi: 10.1111/mec.12459. PubMed DOI

Walker M, Head MJ, Lowe J, Berkelhammer M, BjÖrck S, Cheng H, et al. Subdividing the Holocene Series/Epoch: formalization of stages/ages and subseries/subepochs, and designation of GSSPs and auxiliary stratotypes. J Quat Sci. 2019;34:173–186. doi: 10.1002/jqs.3097. DOI

Slatkin M. Gene flow in natural populations. Annu Rev Ecol Syst. 1985;16:393–430. doi: 10.1146/annurev.es.16.110185.002141. DOI

Rogers AR, Harpending H. Population growth makes waves in the distribution of pairwise genetic differences. Mol Biol Evol. 1992;9:552–569. doi: 10.1093/oxfordjournals.molbev.a040727. PubMed DOI

Nieberding CM, Olivieri I. Parasites: proxies for host genealogy and ecology? Trends Ecol Evol. 2007;22:156–65. doi: 10.1016/j.tree.2006.11.012. PubMed DOI

Li S, Jovelin R, Yoshiga T, Tanaka R, Cutter AD. Specialist versus generalist life histories and nucleotide diversity in Caenorhabditis nematodes. Proc R Soc B Biol Sci. 2014;281(1777):20132858. doi: 10.1098/rspb.2013.2858. PubMed DOI PMC

Berkman LK, Nielsen CK, Roy CL, Heist EJ. Comparative Genetic Structure of Sympatric Leporids in Southern Illinois. J Mammal. 2015;96:552–563. doi: 10.1093/jmammal/gyv060. DOI

Janecka JE, Tewes ME, Davis IA, Haines AM, Caso A, Blankenship TL, et al. Genetic differences in the response to landscape fragmentation by a habitat generalist, the bobcat, and a habitat specialist, the ocelot. Conserv Genet. 2016;17:1093–1108. doi: 10.1007/s10592-016-0846-1. DOI

Avise JC. Phylogeography: the history and formation of species. Cambridge: Harvard University Press; 2000.

Hewitt G. The genetic legacy of the Quaternary ice ages. Nature. 2000;405:907–913. doi: 10.1038/35016000. PubMed DOI

Nieberding C, Libois R, Douady CJ, Morand S, Michaux JR. Phylogeography of a nematode (Heligmosomoides polygyrus) in the western Palearctic region: persistence of northern cryptic populations during ice ages? Mol Ecol. 2005;14:765–79. doi: 10.1111/j.1365-294X.2005.02440.x. PubMed DOI

Royer A, Montuire S, Legendre S, Discamps E, Jeannet M, Lécuyer C. Investigating the influence of climate changes on rodent communities at a regional-scale (MIS 1–3, Southwestern France) PLoS ONE. 2016;11:1–25. doi: 10.1371/journal.pone.0145600. PubMed DOI PMC

Filipi K, Marková S, Searle JB, Kotlík P. Mitogenomic phylogenetics of the bank vole Clethrionomys glareolus, a model system for studying end-glacial colonization of Europe. Mol Phylogenet Evol. 2015;82 PA:245–57. doi: 10.1016/j.ympev.2014.10.016. PubMed DOI

Michaux JR, Libois R, Filippucci MG. So close and so different: Comparative phylogeography of two small mammal species, the Yellow-necked fieldmouse (Apodemus flavicollis) and the Woodmouse (Apodemus sylvaticus) in the Western Palearctic region. Heredity (Edinb) 2005;94:52–63. doi: 10.1038/sj.hdy.6800561. PubMed DOI

Herman JS, Jóhannesdóttir F, Jones EP, Mcdevitt AD, Michaux JR, White TA, et al. Post-glacial colonization of Europe by the wood mouse, Apodemus sylvaticus: Evidence of a northern refugium and dispersal with humans. Biol J Linn Soc. 2017;120:313–332. doi: 10.1111/bij.12882. DOI

Kotlík P, Deffontaine V, Mascheretti S, Zima J, Michaux JR, Searle JB. A northern glacial refugium for bank voles (Clethrionomys glareolus) Proc Natl Acad Sci. 2006;103:14860–14864. doi: 10.1073/pnas.0603237103. PubMed DOI PMC

Schlinkert H, Ludwig M, Batáry P, Holzschuh A, Kovács-Hostyánszki A, Tscharntke T, et al. Forest specialist and generalist small mammals in forest edges and hedges. Wildlife Biol. 2016;22:86–94. doi: 10.2981/wlb.00176. DOI

Renaud S, Michaux J, Schmidt DN, Aguilar JP, Mein P, Auffray JC. Morphological evolution, ecological diversification and climate change in rodents. Proc R Soc B Biol Sci. 2005;272:609–617. doi: 10.1098/rspb.2004.2992. PubMed DOI PMC

Hafner MS, Sudman PD, Villablanca FX, Spradling TA, Demastes JW, Nadler SA. Disparate rates of molecular evolution in cospeciating hosts and parasites. Sci. 1994;265:1087–90. doi: 10.1126/science.8066445. PubMed DOI

Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol Mar Biol Biotechnol. 1994;3:294–299. doi: 10.1071/ZO9660275. PubMed DOI

Mácová A, Hoblíková A, Hypša V, Stanko M, Martinů J, Kvičerová J. Mysteries of host switching: Diversification and host specificity in rodent-coccidia associations. Mol Phylogenet Evol. 2018;127:179–89. 10.1016/j.ympev.2018.05.009. PubMed

Bellinvia E. A phylogenetic study of the genus Apodemus by sequencing the mitochondrial DNA control region. J Zool Syst Evol Res. 2004;42:289–297. doi: 10.1111/j.1439-0469.2004.00270.x. DOI

Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 2011;28:2731–2739. doi: 10.1093/molbev/msr121. PubMed DOI PMC

Xia X, Xie Z. DAMBE: software package for data analysis in molecular biology and evolution. J Hered. 2001;92:371–373. doi: 10.1093/jhered/92.4.371. PubMed DOI

Xia X, Xie Z, Salemi M, Chen L, Wang Y. An index of substitution saturation and its application. Mol Phylogenet Evol. 2003;26:1–7. doi: 10.1016/S1055-7903(02)00326-3. PubMed DOI

Librado P, Rozas J. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics. 2009;25:1451–1452. doi: 10.1093/bioinformatics/btp187. PubMed DOI

Lanfear R, Frandsen PB, Wright AM, Senfeld T, Calcott B. Partitionfinder 2: New methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses. Mol Biol Evol. 2017;34:772–773. doi: 10.1093/molbev/msw260. PubMed DOI

Lanfear R, Calcott B, Ho SYW, Guindon S. PartitionFinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. Mol Biol Evol. 2012;29:1695–701. 10.1093/molbev/mss020. PubMed

Ronquist F, Huelsenbeck JP. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics. 2003;19:1572–1574. doi: 10.1093/bioinformatics/btg180. PubMed DOI

Rambaut A, Drummond AJ, Xie D, Baele G, Suchard MA. Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Syst Biol. 2018;67:901–4. doi: 10.1093/sysbio/syy032. PubMed DOI PMC

Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods. 2017;14:587–589. doi: 10.1038/nmeth.4285. PubMed DOI PMC

Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, von Haeseler A, et al. IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era. Mol Biol Evol. 2020;37:1530–1534. doi: 10.1093/molbev/msaa015. PubMed DOI PMC

Hoang DT, Chernomor O, von Haeseler A, Minh BQ, Vinh LS. UFBoot2: Improving the Ultrafast Bootstrap Approximation. Mol Biol Evol. 2018;35:518–522. doi: 10.1093/molbev/msx281. PubMed DOI PMC

Drummond AJ, Suchard MA, Xie D, Rambaut A. Bayesian Phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol. 2012;29:1969–73. doi: 10.1093/molbev/mss075. PubMed DOI PMC

Hirschmann W. fossil mite of the genus Dendrolaelaps (Acarina, Mesostigmata, Digamasellidae) found in amber from Chiapas. Mexico. 1971;1971(63):69–70.

Dunlop JA, Walter DE, Kontschán J. A putative fossil sejid mite (Parasitiformes: Mesostigmata) in baltic amber re-identified as an anystine (acariformes: Prostigmata) Acarologia. 2018;58:665–72. doi: 10.24349/acarologia/20184263. DOI

Fraser TA, Shao R, Fountain-Jones NM, Charleston M, Martin A, Whiteley P, et al. Mitochondrial genome sequencing reveals potential origins of the scabies mite Sarcoptes scabiei infesting two iconic Australian marsupials. BMC Evol Biol. 2017;17:1–9. doi: 10.1186/s12862-017-1086-9. PubMed DOI PMC

Palopoli MF, Fergus DJ, Minot S, Pei DT, Simison WB, Fernandez-Silva I, et al. Global divergence of the human follicle mite Demodex folliculorum: persistent associations between host ancestry and mite lineages. Proc Natl Acad Sci. 2015;112:15958–63. 10.1073/pnas.1512609112. PubMed PMC

Duchêne S, Lanfear R, Ho SYW. The impact of calibration and clock-model choice on molecular estimates of divergence times. Mol Phylogenet Evol. 2014;78:277–289. doi: 10.1016/j.ympev.2014.05.032. PubMed DOI

Heath TA, Moore BR. Bayesian inference of species divergence times. In: Chen MH, Kuo L, Lewis PO, editors. Bayesian phylogenetics: methods, algorithms, and applications. Florida: CRC Press; 2014. p. 277-318.

Leigh JW, Bryant D. POPART: Full-feature software for haplotype network construction. Methods Ecol Evol. 2015;6:1110–1116. doi: 10.1111/2041-210X.12410. DOI

Corander J, Marttinen P, Sirén J, Tang J. BAPS: Bayesian analysis of population structure. Man ver. 2005:1–27. http://www.helsinki.fi/bsg/software/BAPS/macSnow/BAPS6manual.pdf.

Excoffier L, Lischer HEL. Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour. 2010;10:564–7. doi: 10.1111/j.1755-0998.2010.02847.x. PubMed DOI

Bouckaert R, Heled J, Kühnert D, Vaughan T, Wu C-H, Xie D, et al. BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Comput Biol. 2014;10:e1003537. doi: 10.1371/journal.pcbi.1003537. PubMed DOI PMC

Ho SYW, Shapiro B. Skyline-plot methods for estimating demographic history from nucleotide sequences. Mol Ecol Resour. 2011;11:423–434. doi: 10.1111/j.1755-0998.2011.02988.x. PubMed DOI

Heled J. Extended Bayesian Skyline Plot tutorial. Analysis. 2008; Figure 1:16.

RStudio Team. RStudio: Integrated Development for R. RStudio, PBC, Boston, MA. http://www.rstudio.com/.

Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 1989;123:585–595. doi: 10.1093/genetics/123.3.585. PubMed DOI PMC

Fu YX. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics. 1997;147:915–925. doi: 10.1093/genetics/147.2.915. PubMed DOI PMC