Testing the radiation cascade in postglacial radiations of whitefish and their parasites: founder events and host ecology drive parasite evolution
Status PubMed-not-MEDLINE Language English Country Great Britain, England Media electronic-ecollection
Document type Journal Article
PubMed
39328289
PubMed Central
PMC11424076
DOI
10.1093/evlett/qrae025
PII: qrae025
Knihovny.cz E-resources
- Keywords
- Platyhelminthes, RADseq, host repertoire expansion, population genetics, speciation, species flocks,
- Publication type
- Journal Article MeSH
Reciprocal effects of adaptive radiations on the evolution of interspecific interactions, like parasitism, remain barely explored. We test whether the recent radiations of European whitefish (Coregonus spp.) across and within perialpine and subarctic lakes promote its parasite Proteocephalus fallax (Platyhelminthes: Cestoda) to undergo host repertoire expansion via opportunity and ecological fitting, or adaptive radiation by specialization. Using de novo genomic data, we examined P. fallax differentiation across lakes, within lakes across sympatric host species, and the contributions of host genetics versus host habitat use and trophic preferences. Whitefish intralake radiations prompted parasite host repertoire expansion in all lakes, whereas P. fallax differentiation remains incipient among sympatric fish hosts. Whitefish genetic differentiation per se did not explain the genetic differentiation among its parasite populations, ruling out codivergence with the host. Instead, incipient parasite differentiation was driven by whitefish phenotypic radiation in trophic preferences and habitat use in an arena of parasite opportunity and ecological fitting to utilize resources from emerging hosts. Whilst the whitefish radiation provides a substrate for the parasite to differentiate along the same water-depth ecological axis as Coregonus spp., the role of the intermediate hosts in parasite speciation may be overlooked. Parasite multiple-level ecological fitting to both fish and crustacean intermediate hosts resources may be responsible for parasite population substructure in Coregonus spp. We propose parasites' delayed arrival was key to the initial burst of postglacial intralake whitefish diversification, followed by opportunistic tapeworm host repertoire expansion and a delayed nonadaptive radiation cascade of incipient tapeworm differentiation. At the geographical scale, dispersal, founder events, and genetic drift following colonization of spatially heterogeneous landscapes drove strong parasite differentiation. We argue that these microevolutionary processes result in the mirroring of host-parasite phylogenies through phylogenetic tracking at macroevolutionary and geographical scales.
Aquatic Restoration and Fisheries section Federal Office for the Environment Bern Switzerland
Department of Arctic Biology The Arctic University of Norway Tromsø Norway
Department of Genetics and Evolution University of Geneva Geneva Switzerland
Department of Invertebrates Natural History Museum of Geneva Geneva Switzerland
Norwegian College of Fishery Science UiT The Arctic University of Norway Tromsø Norway
See more in PubMed
Abrahamson, W. G., & Blair, C. P. (2008). Sequential radiation through host-race formation: Herbivore diversity leads to diversity in natural enemies. In Tilmon K. (Ed.), Specialization, speciation, and radiation: The evolutionary biology of herbivorous insects (pp. 188–202). University of California Press.
Agosta, S. J. (2023). The Stockholm Paradigm explains the eco-evolutionary dynamics of the biosphere in a changing world, including emerging infectious disease. In Gardner S. L., Brooks D. R., Boeger W. A., & Hoberg E. P. (Eds.), An evolutionary pathway for coping with emerging infectious disease (pp. 29–46). Zea E-Books.
Agosta, S. J., & Brooks, D. R. (2020). The major metaphors of evolution. Springer International Publishing.
Agosta, S. J., Janz, N., & Brooks, D. R. (2010). How specialists can be generalists: Resolving the “parasite paradox” and implications for emerging infectious disease. Zoologia (Curitiba), 27(2), 151–162. 10.1590/s1984-46702010000200001 DOI
Agosta, S. J., & Klemens, J. A. (2008). Ecological fitting by phenotypically flexible genotypes: Implications for species associations, community assembly and evolution. Ecology Letters, 11(11), 1123–1134. 10.1111/j.1461-0248.2008.01237.x PubMed DOI
Alexander, J. M., Atwater, D. Z., Colautti, R. I., & Hargreaves, A. L. (2022). Effects of species interactions on the potential for evolution at species’ range limits. Philosophical Transactions of the Royal Society of London, Series B: Biological Sciences, 377(1848), 20210020. 10.1098/rstb.2021.0020 PubMed DOI PMC
Althoff, D. M., Segraves, K. A., & Johnson, M. T. J. (2014). Testing for coevolutionary diversification: Linking pattern with process. Trends in Ecology & Evolution, 29, 82–89. 10.1016/j.tree.2013.11.003 PubMed DOI
Andrews, S. (2010). FastQC: A quality control tool for high throughput sequence data. Babraham Bioinformatics, Babraham Institute.
Araujo, S. B. L., Braga, M. P., Brooks, D. R., Agosta, S. J., Hoberg, E. P., Von Hartenthal, F. W., & Boeger, W. A. (2015). Understanding host-switching by ecological fitting. [Article]. PLoS One, 10(10), e0139225. 10.1371/journal.pone.0139225 PubMed DOI PMC
Barker, S. C. (1994). Phylogeny and classification, origins, and evolution of host associations of lice. International Journal for Parasitology, 24(8), 1285–1291. 10.1016/0020-7519(94)90195-3 PubMed DOI
Bernatchez, L. (2004). Ecological theory of adaptive radiation: An empirical assessment from coregonine fishes (Salmoniformes). In Hendry A. P. & Stearns S. C. (Eds.), Evolution illuminated: Salmon and their relatives (pp. 175–207). Oxford Academic.
Beveridge, I., Chilton, N. B., & Spratt, D. M. (2002). The occurrence of species flocks in the nematode genus Cloacina (Strongyloidea: Cloacininae), parasitic in the stomachs of kangaroos and wallabies. Australian Journal of Zoology, 50(6), 597–620. 10.1071/zo02038 DOI
Bhat, S., Amundsen, P. -A., Knudsen, R., Gjelland, K., Fevolden, S.-E., Bernatchez, L., & Præbel, K. (2014). Speciation reversal in European whitefish (Coregonus lavaretus (L.)) caused by competitor invasion. PLoS One, 9(3), e91208. 10.1371/journal.pone.0091208 PubMed DOI PMC
Blasco-Costa, I., Hayward, A., Poulin, R., & Balbuena, J. A. (2021). Next-generation cophylogeny: Unravelling eco-evolutionary processes. Trends in Ecology & Evolution, 36(10), 907–918. 10.1016/j.tree.2021.06.006 PubMed DOI
Blasco-Costa, I., & Poulin, R. (2013). Host traits explain the genetic structure of parasites: A meta-analysis. Parasitology, 140(10), 1316–1322. 10.1017/S0031182013000784 PubMed DOI
Blasco-Costa, I., & Poulin, R. (2017). Parasite life-cycle studies: A plea to resurrect an old parasitological tradition. Journal of Helminthology, 91(6), 647–656. 10.1017/S0022149X16000924 PubMed DOI
Brabec, J., Rochat, E. C., Knudsen, R., Scholz, T., & Blasco-Costa, I. (2023). Mining various genomic resources to resolve old alpha-taxonomy questions: A test of the species hypothesis of the Proteocephalus longicollis species complex (Cestoda: Platyhelminthes) from salmonid fishes. International Journal for Parasitology, 53(4), 197–205. 10.1016/j.ijpara.2022.12.005 PubMed DOI
Braga, M. P., Araujo, S. B. L., Agosta, S., Brooks, D., Hoberg, E., Nylin, S., Janz, N., & Boeger, W. A. (2018). Host use dynamics in a heterogeneous fitness landscape generates oscillations in host range and diversification. Evolution, 72(9), 1773–1783. 10.1111/evo.13557 PubMed DOI
Brodersen, J., Post, D. M., & Seehausen, O. (2018). Upward adaptive radiation cascades: Predator diversification induced by prey diversification. Trends in Ecology & Evolution, 33(1), 59–70. 10.1016/j.tree.2017.09.016 PubMed DOI
Brooks, D. R., Hoberg, E. P., & Boeger, W. A. (2019). The Stockholm Paradigm. University of Chicago Press.
Brooks, D. R., & McLennan, D. A. (2012). The nature of diversity: An evolutionary voyage of discovery. University of Chicago Press.
Chubb, J. C. (1982). Seasonal occurrence of helminths in freshwater fishes. Part IV. Adult Cestoda, Nematoda and Acanthocephala. Advances in Parasitology, 20, 1–292. 10.1016/s0065-308x(08)60539-4 PubMed DOI
Clayton, D. H., Bush, S. E., & Johnson, K. P. (2015). Coevolution of life on hosts: Integrating ecology and history. University of Chicago Press.
Crotti, M., Bean, C. W., Gowans, A. R. D., Winfield, I. J., Butowska, M., Wanzenböck, J., Bondarencko, G., Praebel, K., Adams, C. E., & Elmer, K. R. (2021). Complex and divergent histories gave rise to genome-wide divergence patterns amongst European whitefish (Coregonus lavaretus). Journal of Evolutionary Biology, 34(12), 1954–1969. 10.1111/jeb.13948 PubMed DOI PMC
Curtis, L. A. (2003). Tenure of individual larval trematode infections in an estuarine gastropod. Journal of the Marine Biological Association of the United Kingdom, 83(5), 1047–1051. 10.1017/s0025315403008257h DOI
Danecek, 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. 10.1093/bioinformatics/btr330 PubMed DOI PMC
de Vienne, D., Refrégier, G., López‐Villavicencio, M., Tellier, A., Hood, M., & Giraud, T. (2013). Cospeciation vs host‐shift speciation: Methods for testing, evidence from natural associations and relation to coevolution. New Phytologist, 198, 347–385. 10.1111/nph.12150 PubMed DOI
De-Kayne, R., Selz, O. M., Marques, D. A., Frei, D., Seehausen, O., & Feulner, P. G. D. (2022). Genomic architecture of adaptive radiation and hybridization in Alpine whitefish. Nature Communications, 13(1), 4479. 10.1038/s41467-022-32181-8 PubMed DOI PMC
Desdevises, Y., Morand, S., Jousson, O., & Legendre, P. (2002). Coevolution between Lamellodiscus (Monogenea: Diplectanidae) and Sparidae (Teleostei): The study of a complex host-parasite system. Evolution, 56(12), 2459–2471. 10.1111/j.0014-3820.2002.tb00171.x PubMed DOI
Do, C., Waples, R. S., Peel, D., Macbeth, G. M., Tillett, B. J., & Ovenden, J. R. (2014). NeEstimator v2: Re-implementation of software for the estimation of contemporary effective population size (Ne) from genetic data. Molecular Ecology Resources, 14(1), 209–214. 10.1111/1755-0998.12157 PubMed DOI
Drábková, M., Jachníková, N., Tyml, T., Sehadová, H., Ditrich, O., Myšková, E., Hypša, V., & Štefka, J. (2019). Population co-divergence in common cuttlefish (Sepia officinalis) and its dicyemid parasite in the Mediterranean Sea. Scientific Reports, 9(1), 14300. 10.1038/s41598-019-50555-9 PubMed DOI PMC
Dray, S., Bauman, D., Blanchet, G., Borcard, D., Clappe, S., Guénard, G., Jombart, T., Larocque, G., Legendre, P., Madi, N. & Wagner, H. H. (2023). adespatial: Multivariate multiscale spatial analysis. R package version 0.3-20. https://CRAN.R-project.org/package=adespatial
Earl, D. A., & vonHoldt, B. M. (2012). STRUCTURE HARVESTER: A website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources, 4(2), 359–361. 10.1007/s12686-011-9548-7 DOI
Eaton, D. A. R., & Overcast, I. (2020). ipyrad: Interactive assembly and analysis of RADseq datasets. Bioinformatics, 36(8), 2592–2594. 10.1093/bioinformatics/btz966 PubMed DOI
Evanno, G., Regnaut, S., & Goudet, J. (2005). Detecting the number of clusters of individuals using the software structure: A simulation study. Molecular Ecology, 14(8), 2611–2620. 10.1111/j.1365-294X.2005.02553.x PubMed DOI
Feder, J. L., & Forbes, A. A. (2010). Sequential speciation and the diversity of parasitic insects. Ecological Entomology, 35(s1), 67–76. 10.1111/j.1365-2311.2009.01144.x DOI
Galbreath, K. E., & Hoberg, E. P. (2012). Return to Beringia: Parasites reveal cryptic biogeographic history of North American pikas. Proceedings Biological Sciences, 279(1727), 371–378. 10.1098/rspb.2011.0482 PubMed DOI PMC
Galbreath, K. E., & Hoberg, E. P. (2015). Host responses to cycles of climate change shape parasite diversity across North America’s Intermountain West. Folia Zoologica, 64(3), 218–232. 10.25225/fozo.v64.i3.a4.2015 DOI
Galbreath, K. E., Makarikov, A. A., Bell, K. C., Greiman, S. E., Allen, J. M., Haas, G. M. S., Li, C., Cook, J. A., & Hoberg, E. P. (2023). Late Cenozoic history and the role of Beringia in assembling a Holarctic cestode species complex. Molecular Phylogenetics and Evolution, 183, 107775. 10.1016/j.ympev.2023.107775 PubMed DOI
Gillespie, R. G., Bennett, G. M., De Meester, L., Feder, J. L., Fleischer, R. C., Harmon, L. J., Hendry, A. P., Knope, M. L., Mallet, J., Martin, C., Parent, C. E., Patton, A. H., Pfennig, K. S., Rubinoff, D., Schluter, D., Seehausen, O., Shaw, K. L., Stacy, E., Stervander, M., … Wogan, G. O. U. (2020). Comparing adaptive radiations across space, time, and taxa. The Journal of Heredity, 111(1), 1–20. 10.1093/jhered/esz064 PubMed DOI PMC
Gobbin, T. P., Tiemersma, R., Leone, G., Seehausen, O., & Maan, M. E. (2021). Patterns of ectoparasite infection in wild-caught and laboratory-bred cichlid fish, and their hybrids, implicate extrinsic rather than intrinsic causes of species differences in infection. Hydrobiologia, 848(16), 3817–3831. 10.1007/s10750-020-04423-7 PubMed DOI PMC
Goudet, J. (2005). hierfstat, a package for r to compute and test hierarchical F-statistics. Molecular Ecology Notes, 5, 184–186. 10.1111/j.1471-8286.2004.00828.x DOI
Haas, G. M. S., Hoberg, E. P., Cook, J. A., Henttonen, H., Makarikov, A. A., Gallagher, S. R., Dokuchaev, N. E., & Galbreath, K. E. (2020). Taxon pulse dynamics, episodic dispersal and host colonization across Beringia drive diversification of a Holarctic tapeworm assemblage. Journal of Biogeography, 47(11), 2457–2471. 10.1111/jbi.13949 DOI
Hafner, M. S., Sudman, P. D., Villablanca, F. X., Spradling, T. A., Demastes, J. W., & Nadler, S. A. (1994). Disparate rates of molecular evolution in cospeciating hosts and parasites. Science, 265(5175), 1087–1090. 10.1126/science.8066445 PubMed DOI
Hanzelová, V., & Scholz, T. (1999). Species of Proteocephalus Weinland, 1858 (Cestoda: Proteocephalidae), parasites of coregonid and salmonid fishes from North America: Taxonomic reappraisal. The Journal of Parasitology, 85(1), 94–101. 10.2307/3285708 PubMed DOI
Ho, S. Y., Lanfear, R., Bromham, L., Phillips, M. J., Soubrier, J., Rodrigo, A. G., & Cooper, A. (2011). Time-dependent rates of molecular evolution. Molecular Ecology, 20(15), 3087–3101. 10.1111/j.1365-294X.2011.05178.x PubMed DOI
Hoberg, E. P., & Brooks, D. R. (2008). A macroevolutionary mosaic: Episodic host-switching, geographical colonization and diversification in complex host–parasite systems. Journal of Biogeography, 35(9), 1533–1550. 10.1111/j.1365-2699.2008.01951.x DOI
Hudson, A. G., Vonlanthen, P., Müller, R., Seehausen, O., Jankun, M., & Brzuzan, P. (2007). Review: The geography of speciation and adaptive radiation in coregonines. Advances in Limnology, 60, 111–146.
Hudson, A. G., Vonlanthen, P., & Seehausen, O. (2011). Rapid parallel adaptive radiations from a single hybridogenic ancestral population. Proceedings Biological Sciences, 278(1702), 58–66. 10.1098/rspb.2010.0925 PubMed DOI PMC
Huyse, T., Poulin, R., & Theron, A. (2005). Speciation in parasites: A population genetics approach. Trends in Parasitology, 21(10), 469–475. 10.1016/j.pt.2005.08.009 PubMed DOI
Huyse, T., & Volckaert, F. A. M. (2005). Comparing host and parasite phylogenies: Gyrodactylus flatworms jumping from goby to goby. Systematic Biology, 54(5), 710–718. 10.1080/10635150500221036 PubMed DOI
Ingram, T., Hudson, A. G., Vonlanthen, P., & Seehausen, O. (2012). Does water depth or diet divergence predict progress towards ecological speciation in whitefish radiations? Evolutionary Ecology Research, 14, 487–502.
Janz, N., & Nylin, S. (2008). The oscillation hypothesis of host-plant range and speciation. In Berkeley T. K. J. (Ed.), Specialization, speciation, and radiation: The evolutionary biology of herbivorous insects (pp. 203–215). University of California Press.
Johnson, P. T., Wood, C. L., Joseph, M. B., Preston, D. L., Haas, S. E., & Springer, Y. P. (2016). Habitat heterogeneity drives the host-diversity-begets-parasite-diversity relationship: Evidence from experimental and field studies. Ecology Letters, 19(7), 752–761. 10.1111/ele.12609 PubMed DOI PMC
Jombart, T., & Ahmed, I. (2011). adegenet 1.3-1: New tools for the analysis of genome-wide SNP data. Bioinformatics, 27(21), 3070–3071. 10.1093/bioinformatics/btr521 PubMed DOI PMC
Kamiya, T., O’Dwyer, K., Nakagawa, S., & Poulin, R. (2014). What determines species richness of parasitic organisms? A meta-analysis across animal, plant and fungal hosts. Biological Reviews of the Cambridge Philosophical Society, 89(1), 123–134. 10.1111/brv.12046 PubMed DOI
Karvonen, A., Lundsgaard-Hansen, B., Jokela, J., & Seehausen, O. (2013). Differentiation in parasitism among ecotypes of whitefish segregating along depth gradients. Oikos, 122, 122–128. 10.1111/j.1600-0706.2012.20555.x DOI
Karvonen, A., & Seehausen, O. (2012). The role of parasitism in adaptive radiations—when might parasites promote and when might they constrain ecological speciation? International Journal of Ecology, 2012, 1–20. 10.1155/2012/280169 DOI
Kmentová, N., Koblmüller, S., Van Steenberge, M., Artois, T., Muterezi Bukinga, F., Mulimbwa N’sibula, T., Muzumani Risasi, D., Masilya Mulungula, P., Gelnar, M., & Vanhove, M. P. M. (2020). Failure to diverge in African Great Lakes: The case of Dolicirroplectanum lacustre gen. nov. comb. nov. (Monogenea, Diplectanidae) infecting latid hosts. Journal of Great Lakes Research, 46(5), 1113–1130. 10.1016/j.jglr.2019.09.022 DOI
Kolmogorov, M., Yuan, J., Lin, Y., & Pevzner, P. A. (2019). Assembly of long, error-prone reads using repeat graphs. Nature Biotechnology, 37(5), 540–546. 10.1038/s41587-019-0072-8 PubMed DOI
Larose, C., & Schwander, T. (2016). Nematode endoparasites do not codiversify with their stick insect hosts. Ecology and Evolution, 6(15), 5446–5458. 10.1002/ece3.2264 PubMed DOI PMC
Lawton, J. H. (1983). Plant architecture and the diversity of phytophagous Insects. Annual Review of Entomology, 28(1), 23–39. 10.1146/annurev.en.28.010183.000323 DOI
Li, H., & Durbin, R. (2009). Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics, 25(14), 1754–1760. 10.1093/bioinformatics/btp324 PubMed DOI PMC
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., & Durbin, R.; 1000 Genome Project Data Processing Subgroup. (2009). The sequence alignment/map format and SAM tools. Bioinformatics, 25(16), 2078–2079. 10.1093/bioinformatics/btp352 PubMed DOI PMC
Louhi, K. R., Karvonen, A., Rellstab, C., & 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(8), 1271–1277. 10.1016/j.meegid.2010.08.013 PubMed DOI
Lucek, K., Keller, I., Nolte, A. W., & Seehausen, O. (2018). Distinct colonization waves underlie the diversification of the freshwater sculpin (Cottus gobio) in the Central European Alpine region. Journal of Evolutionary Biology, 31(9), 1254–1267. 10.1111/jeb.13339 PubMed DOI
Lundsgaard-Hansen, B., Matthews, B., Thierry, A., & Seehausen, O. (2017). The legacy of ecosystem effects caused by adaptive radiation. Copeia, 105, 550–557. 10.1643/ce-16-514 DOI
Lutzoni, F., Nowak, M. D., Alfaro, M. E., Reeb, V., Miadlikowska, J., Krug, M., Arnold, A. E., Lewis, L. A., Swofford, D. L., Hibbett, D., Hilu, K., James, T. Y., Quandt, D., & Magallón, S. (2018). Contemporaneous radiations of fungi and plants linked to symbiosis. Nature Communications, 9(1), 5451. 10.1038/s41467-018-07849-9 PubMed DOI PMC
Malcicka, M., Agosta, S. J., & Harvey, J. A. (2015). Multi level ecological fitting: Indirect life cycles are not a barrier to host switching and invasion. Global Change Biology, 21(9), 3210–3218. 10.1111/gcb.12928 PubMed DOI
Mastretta-Yanes, A., Arrigo, N., Alvarez, N., Jorgensen, T. H., Piñero, D., & Emerson, B. C. (2015). Restriction site-associated DNA sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference. Molecular Ecology Resources, 15(1), 28–41. 10.1111/1755-0998.12291 PubMed DOI
Mazé-Guilmo, E., Blanchet, S., McCoy, K. D., & Loot, G. (2016). Host dispersal as the driver of parasite genetic structure: A paradigm lost? Ecology Letters, 19(3), 336–347. 10.1111/ele.12564 PubMed DOI
Mendlová, M., Desdevises, Y., Civáňová, K., Pariselle, A., & Šimková, A. (2012). Monogeneans of West African cichlid fish: Evolution and cophylogenetic Interactions. PLoS One, 7(5), e37268. 10.1371/journal.pone.0037268 PubMed DOI PMC
Moore, J. (1987). Asexual reproduction and environmental predictability in cestodes (Cyclophyllidea: Taeniidae). Evolution, 35(4), 723–741. 10.2307/2408243 PubMed DOI
Nazarizadeh, M., Nováková, M., Loot, G., Gabagambi, N. P., Fatemizadeh, F., Osano, O., Presswell, B., Poulin, R., Vitál, Z., Scholz, T., Halajian, A., Trucchi, E., Kočová, P., & Štefka, J. (2023). Historical dispersal and host-switching formed the evolutionary history of a globally distributed multi-host parasite – The Ligula intestinalis species complex. Molecular Phylogenetics and Evolution, 180, 107677. 10.1016/j.ympev.2022.107677 PubMed DOI
Nieberding, C., Libois, R., Douady, C. J., Morand, S., & Michaux, J. R. (2005). Phylogeography of a nematode (Heligmosomoides polygyrus) in the western Palearctic region: Persistence of northern cryptic populations during ice ages? Molecular Ecology, 14(3), 765–779. 10.1111/j.1365-294X.2005.02440.x PubMed DOI
Nylin, S., Agosta, S., Bensch, S., Boeger, W. A., Braga, M. P., Brooks, D. R., Forister, M. L., Hambäck, P. A., Hoberg, E. P., Nyman, T., Schäpers, A., Stigall, A. L., Wheat, C. W., Österling, M., & Janz, N. (2018). Embracing colonizations: A new paradigm for species association dynamics. Trends in Ecology & Evolution, 33(1), 4–14. 10.1016/j.tree.2017.10.005 PubMed DOI
Oksanen, J., Simpson, G., Blanchet, F., Kindt, R., Legendre, P., Minchin, P., O’Hara, R., Solymos, P., Stevens, M., Szoecs, E., Wagner, H., Barbour, M., Bedward, M., Bolker, B., Borcard, D., Carvalho, G., Chirico, M, De Caceres, M., Durand, S., Evangelista, H., FitzJohn, R., Friendly, M., Furneaux, B., Hannigan, G., Hill, M., Lahti, L., McGlinn, D., Ouellette, M., Ribeiro Cunha, E., Smith, T., Stier, A., Ter Braak, C. & Weedon, J. (2020). vegan: Community ecology package. R package version 2.5-7.
Østbye, K., Amundsen, P. A., Bernatchez, L., Klemetsen, A., Knudsen, R., Kristoffersen, R., Naesje, T. F., & Hindar, K. (2006). Parallel evolution of ecomorphological traits in the European whitefish Coregonus lavaretus (L.) species complex during postglacial times. Molecular Ecology, 15(13), 3983–4001. 10.1111/j.1365-294X.2006.03062.x PubMed DOI
Østbye, K., Bernatchez, L., Naesje, T., Himberg, K. J., & Hindar, K. (2005). Evolutionary history of the European whitefish Coregonus lavaretus (L.) species complex as inferred from mtDNA phylogeography and gill‐raker numbers. Molecular Ecology, 14, 4371–4387. 10.1111/j.1365-294X.2005.02737.x PubMed DOI
Park, E., Jorge, F., & Poulin, R. (2020). Shared geographic histories and dispersal contribute to congruent phylogenies between amphipods and their microsporidian parasites at regional and global scales. Molecular Ecology, 29(17), 3330–3345. 10.1111/mec.15562 PubMed DOI
Paterson, A. M., & Poulin, R. (1999). Have chondracanthid copepods co-speciated with their teleost hosts? Systematic Parasitology, 44(2), 79–85. 10.1023/a:1006255822947 PubMed DOI
Paterson, S., Vogwill, T., Buckling, A., Benmayor, R., Spiers, A. J., Thomson, N. R., Quail, M., Smith, F., Walker, D., Libberton, B., Fenton, A., Hall, N., & Brockhurst, M. A. (2010). Antagonistic coevolution accelerates molecular evolution. Nature, 464(7286), 275–278. 10.1038/nature08798 PubMed DOI PMC
Perrot-Minnot, M. -J., Špakulová, M., Wattier, R., Kotlík, P., Düşen, S., & Aydoğdu, A., et al.. (2018). Contrasting phylogeography of two Western Palaearctic fish parasites despite similar life cycles. Journal of Biogeography, 45, 101–115. 10.1111/jbi.13118 DOI
Peakall, R., & Smouse, P. E. (2012). GenAlEx 6.5: genetic analysis in excel. Population genetic software for teaching and research—an update. Bioinformatics, 28(19), 2537–2539. 10.1093/bioinformatics/bts460 PubMed DOI PMC
Peterson, B. K., Weber, J. N., Kay, E. H., Fisher, H. S., & Hoekstra, H. E. (2012). Double digest RADseq: An inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS One, 7(5), e37135. 10.1371/journal.pone.0037135 PubMed DOI PMC
Phillips, B. L., Kelehear, C., Pizzatto, L., Brown, G. P., Barton, D., & Shine, R. (2010). Parasites and pathogens lag behind their host during periods of host range advance. Ecology, 91(3), 872–881. 10.1890/09-0530.1 PubMed DOI
Poulin, R. (2011). Evolutionary ecology of parasites. Princeton University Press.
Poulin, R., & Morand, S. (2004). Parasite biodiversity. Smithsonian Institution Press.
Praebel, K., Knudsen, R., Siwertsson, A., Karhunen, M., Kahilainen, K. K., Ovaskainen, O., Østbye, K., Peruzzi, S., Fevolden, S.-E. & Amundsen, P.-A. (2013). Ecological speciation in postglacial European whitefish: Rapid adaptive radiations into the littoral, pelagic, and profundal lake habitats. Ecology and Evolution, 3, 4970–4986. 10.1002/ece3.867 PubMed DOI PMC
Prugnolle, F., Théron, A., Pointier, J. P., Jabbour-Zahab, R., Jarne, P., Durand, P., & de Meeûs, T. (2005). Dispersal in a parasitic worm and its two hosts: Consequence for local adaptation. Evolution, 59(2), 296–303. 10.1111/j.0014-3820.2005.tb00990.x PubMed DOI
Rahmouni, C., Vanhove, M. P. M., Koblmüller, S., & Šimková, A. (2022). Molecular phylogeny and speciation patterns in host-specific monogeneans (Cichlidogyrus, Dactylogyridae) parasitizing cichlid fishes (Cichliformes, Cichlidae) in Lake Tanganyika. International Journal for Parasitology, 52(6), 359–375. 10.1016/j.ijpara.2021.12.004 PubMed DOI
Ricklefs, R. E., Outlaw, D. C., Svensson-Coelho, M., Medeiros, M. C. I., Ellis, V. A., & Latta, S. (2014). Species formation by host shifting in avian malaria parasites. Proceedings of the National Academy of Sciences, 111(41), 14816–14821. 10.1073/pnas.1416356111 PubMed DOI PMC
Rougeux, C., Gagnaire, P. A., & Bernatchez, L. (2019). Model‐based demographic inference of introgression history in European whitefish species pairs’. Journal of Evolutionary Biology, 32(8), 806–817. 10.1111/jeb.13482 PubMed DOI
Sánchez-Hernández, J., Finstad, A. G., Arnekleiv, J. V., Kjærstad, G., & Amundsen, P. -A. (2021). Beyond ecological opportunity: Prey diversity rather than abundance shapes predator niche variation. Freshwater Biology, 66, 44–61. 10.1111/fwb.13606 DOI
Schluter, D. (2000). The ecology of adaptive radiation. Oxford University Press.
Scholz, T. (1999). Life cycles of species of Proteocephalus, parasites of fishes in the Palearctic Region: A review. Journal of Helminthology, 73(1), 1–19. 10.1017/S0022149X99000013 PubMed DOI
Scholz, T., & Hanzelová, V. (1998). Tapeworms of the genus Proteocephalus Weinland, 1858 (Cestoda: Proteocephalidae), parasites of fishes in Europe. (Vol. 2/98). Academia.
Selz, O. M., Dönz, C. J., Vonlanthen, P., & Seehausen, O. (2020). A taxonomic revision of the whitefish of lakes Brienz and Thun, Switzerland, with descriptions of four new species (Teleostei, Coregonidae). ZooKeys, 989, 79–162. 10.3897/zookeys.989.32822 PubMed DOI PMC
Simão, 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. 10.1093/bioinformatics/btv351 PubMed DOI
Siwertsson, A., Knudsen, R., Praebel, K., Adams, C. E., Newton, J., & Amundsen, P. -A. (2013). Discrete foraging niches promote ecological, phenotypic, and genetic divergence in sympatric whitefish (Coregonus lavaretus). Evolutionary Ecology, 27, 547–564. 10.1007/s10682-012-9607-x DOI
R Core Team. (2021). R: A language and environment for statistical computing.
Thompson, J. N. (2005). The geographic mosaic of coevolution. The University of Chicago Press.
Van 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, 11.10.11–11.10.33. 10.1002/0471250953.bi1110s43 PubMed DOI PMC
Van der Auwera, G. A. & O’Connor, B. D. (2020). Genomics in the cloud: using docker, GATK, and WDL in Terra. O’Reilly Media.
Vanhove, M. P. M., Pariselle, A., Van Steenberge, M., Raeymaekers, J. A. M., Hablützel, P. I., Gillardin, C., Hellemans, B., Breman, F. C., Koblmüller, S., Sturmbauer, C., Snoeks, J., Volckaert, F. A. M., & Huyse, T. (2015). Hidden biodiversity in an ancient lake: Phylogenetic congruence between Lake Tanganyika tropheine cichlids and their monogenean flatworm parasites. Scientific Reports, 5(1), 13669. 10.1038/srep13669 PubMed DOI PMC
Vonlanthen, P., Bittner, D., Hudson, A. G., Young, K. A., Mueller, R., Lundsgaard-Hansen, B., Roy, D., Di Piazza, S., Largiader, C. R., & Seehausen, O. (2012). Eutrophication causes speciation reversal in whitefish adaptive radiations. Nature, 482, 357–362. 10.1038/nature10824 PubMed DOI
Walsh, M. R., DeLong, J. P., Hanley, T. C., & Post, D. M. (2012). A cascade of evolutionary change alters consumer-resource dynamics and ecosystem function. Proceedings Biological Sciences, 279(1741), 3184–3192. 10.1098/rspb.2012.0496 PubMed DOI PMC
Waples, R. S., & Do, C. (2010). Linkage disequilibrium estimates of contemporary N e using highly variable genetic markers: A largely untapped resource for applied conservation and evolution. Evolutionary Applications, 3(3), 244–262. 10.1111/j.1752-4571.2009.00104.x PubMed DOI PMC
Warren, R. L., Coombe, L., Mohamadi, H., Zhang, J., Jaquish, B., Isabel, N., Jones, S. J. M., Bousquet, J., Bohlmann, J., & Birol, I. (2019). ntEdit: Scalable genome sequence polishing. Bioinformatics, 35(21), 4430–4432. 10.1093/bioinformatics/btz400 PubMed DOI PMC
Weir, B. S., & Cockerham, C. C. (1984). Estimating F-statistics for the analysis of population structure. Evolution, 38(6), 1358–1370. 10.1111/j.1558-5646.1984.tb05657.x. https://www.jstor.org/stable/2408641 PubMed DOI