, , , Genetic Variability: Cryptic Biological Species or Clonal Near-Clades?

English version České info

Micropathogen species definition is extremely difficult, since concepts applied to higher organisms (the biological species concept) are inadequate. In particular, the pathogens here surveyed have given rise to long-lasting controversies about their species status and that of the genotypes that subdivide them. The population genetic approach based on the predominant clonal evolution (PCE) concept proposed by us could bring simple solutions to these controversies, since it permits the description of clearly defined evolutionary entities (clonal multilocus genotypes and near-clades [incompletely isolated clades]) that could be the basis for species description, if the concerned specialists find it justified for applied research. The PCE model also provides a convenient framework for applied studies (molecular epidemiology, vaccine and drug design, clinical research) dealing with these pathogens and others.

Vyšlo v časopise: , , , Genetic Variability: Cryptic Biological Species or Clonal Near-Clades?. PLoS Pathog 10(4): e32767. doi:10.1371/journal.ppat.1003908
Kategorie: Opinion
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.ppat.1003908

Souhrn

Zdroje

1. TibayrencM, KjellbergF, AyalaFJ (1990) A clonal theory of parasitic protozoa: the population structure of Entamoeba, Giardia, Leishmania, Naegleria, Plasmodium, Trichomonas and Trypanosoma, and its medical and taxonomical consequences. Proc Nat Acad Sci U S A 87: 2414–2418.

2. TibayrencM, KjellbergF, ArnaudJ, OuryB, BrenièreSF, et al. (1991) Are eukaryotic microorganisms clonal or sexual? A population genetics vantage. Proc Natl Acad Sci U S A 88: 5129–5133.

3. TibayrencM, AyalaFJ (2012) Reproductive clonality of pathogens: A perspective on pathogenic viruses, bacteria, fungi, and parasitic protozoa. Proc Nat Acad Sci U S A 109: E3305–E3313 doi:10.1073/pnas.1212452109

4. AnderssonJO (2012) Double peaks reveal rare diplomonad sex. Trends Parasitol 28: 46–52.

5. BoversM, HagenF, KuramaeEE, BoekhoutT (2008) Six monophyletic lineages identified within Cryptococcus neoformans and Cryptococcus gattii by multi-locus sequence typing. Fungal Genet Biol 45: 400–421.

6. CooperMA, AdamRD, WorobeyM, SterlingCR (2007) Population Genetics Provides Evidence for Recombination in Giardia. Curr Biol 17: 1984–1988.

7. GateiW, DasP, DuttaP, SenA, CamaV, et al. (2007) Multilocus sequence typing and genetic structure of Cryptosporidium hominis from children in Kolkata, India. Infect Genet Evol 7: 197–205.

8. LinX, HeitmanJ (2006) The Biology of the Cryptococcus neoformans Species Complex. Ann Rev Microbiol 60: 69–105.

9. MorrisonLJ, MallonME, SmithHV, MacLeodA, XiaoL, et al. (2008) The population structure of the Cryptosporidium parvum population in Scotland: A complex picture. Infect Genet Evol 8: 121–129.

10. TibayrencM, AyalaFJ (2013) How clonal are Trypanosoma and Leishmania? Trends Parasitol 29: 264–269.

11. TibayrencM, AyalaFJ (2014) New insights into Clonality and Panmixia in Plasmodium and Toxoplasma. Adv Parasitol 84: 253–268.

12. CaloS, BillmyreBB, HeitmanJ (2013) Generators of Phenotypic Diversity in the Evolution of Pathogenic Microorganisms. PLoS Pathog 9: e1003181 doi:10.1371/journal.ppat.1003181

13. Ortega-PierresG, SmithHV, CaccioSM, ThompsonRC (2009) New tools provide further insights into Giardia and Cryptosporidium biology. Trends Parasitol 25: 410–416.

14. RamírezJD, Tapia-CalleG, GuhlF (2013) Genetic structure of Trypanosoma cruzi in Colombia revealed by a High-throughput Nuclear Multilocus Sequence Typing (nMLST) approach. BMC Genet 14: 96.

15. TibayrencM, AyalaFJ (2013) Unisexual reproduction is a particular case of clonality. Comment on: Feretzaki F, Heitman J. (2013) Unisexual Reproduction Drives Evolution of Eukaryotic Microbial Pathogens. PLoS Pathog 9: e1003674 doi:10.1371/journal.ppat.1003674

16. BirkyCWJr (2009) Giardia Sex? Yes, but how and how much? Trends Parasitol 26: 70–74.

17. HeitmanJ (2006) Sexual reproduction and the evolution of microbial pathogens. Curr Biol 16: R711–R725.

18. NiM, FeretzakiM, LiW, Floyd-AveretteA, MieczkowskiP, et al. (2013) Unisexual and Heterosexual Meiotic Reproduction Generate Aneuploidy and Phenotypic Diversity De Novo in the Yeast Cryptococcus neoformans. PLoS Biol 11: e1001653 doi:10.1371/journal.pbio.1001653

19. XuJ (2006) Fundamentals of Fungal Molecular Population Genetic Analyses. Curr Issues Mol Biol 8: 75–80.

20. LehtonenJ, SchmidtDJ, HeubelK, KokkoH (2013) Evolutionary and ecological implications of sexual parasitism. Trends Ecol Evol 28: 297–306.

21. FeretzakiF, HeitmanJ (2013) Unisexual Reproduction Drives Evolution of Eukaryotic Microbial Pathogens. PLoS Pathog 9: e1003674 doi:10.1371/journal.ppat.1003674

22. RougeronV, De MeeûsT, Kako OuragaS, HideM, BañulsAL (2010) “Everything You Always Wanted to Know about Sex (but Were Afraid to Ask)” in Leishmania after Two Decades of Laboratory and Field Analyses. PLoS Pathog 6: e1001004 doi:10.1371/journal.ppat.1001004

23. MessengerLA, LlewellynMS, BhattacharyyaT, FranzénO, LewisMD, et al. (2012) Multiple Mitochondrial Introgression Events and Heteroplasmy in Trypanosoma cruzi Revealed by Maxicircle MLST and Next Generation Sequencing. PLoS Negl Trop Dis 6: e1584 doi:10.1371/journal.pntd.0001584

24. CacciòSM, RyanU (2008) Molecular epidemiology of giardiasis. Molec Biochem Parasitol 160: 75–80.

25. EstevesF, GasparJ, TavaresA, MoserI, AntunesF, et al. (2010) Population structure of Pneumocystis jirovecii isolated from immunodeficiency virus-positive patients. Infect Genet Evol 10: 192–199.

26. KhayhanK, HagenF, PanW, SimwamiS, FisherMC, et al. (2013) Geographically Structured Populations of Cryptococcus neoformans Variety grubii in Asia Correlate with HIV Status and Show a Clonal Population Structure. PLoS ONE 8: e72222 doi:10.1371/journal.pone.0072222

27. Maynard SmithJ, SmithNH, O'RourkeM, SprattBG (1993) How clonal are bacteria? Proc Natl Acad Sci U S A 90: 4384–4388.

28. SchurkoAM, NeimanM, LogsdonJMJr (2008) Signs of sex: what we know and how we know it. Trends Ecol Evol 2: 208–217.

29. Avise JC (2004) Molecular markers, Natural History and Evolution. 2nd ed. New York, London: Chapman & Hall.

30. NgamskulrungrojP, GilgadoF, FaganelloJ, LitvintsevaAP, LealAL, et al. (2009) Genetic Diversity of the Cryptococcus Species Complex Suggests that Cryptococcus gattii Deserves to Have Varieties. PLoS ONE 4: e5862 doi:10.1371/journal.pone.0005862

31. VoelzK, MaH, PhadkeS, ByrnesEJ, ZhuP, et al. (2013) Transmission of Hypervirulence Traits via Sexual Reproduction within and between Lineages of the Human Fungal Pathogen Cryptococcus gattii. PLoS Genet 9: e1003771 doi:10.1371/journal.pgen.1003771

32. CampbellLT, CurrieBJ, KrockenbergerM, MalikR, MeyerW, et al. (2005) Clonality and Recombination in Genetically Differentiated Subgroups of Cryptococcus gattii. Eukaryotic Cell 4: 1403–1409.

33. AndersonTJ, HauboldB, WilliamsJT, Estrada-FrancoJG, RichardsonL, et al. (2000) Microsatellite markers reveal a spectrum of population structures in the malaria parasite Plasmodium falciparum. Mol Biol Evol 17: 1467–1482.

34. AgrawalAF (2006) Evolution of Sex: Why Do Organisms Shuffle Their Genotypes? Curr Biol 16: R696–R704.

35. BirkyCW (2005) Sex: is Giardia doing it in the dark? Curr Biol 15: R56–R58.

36. MonisPT, CaccioSM, ThompsonRCA (2009) Variation in Giardia: towards a taxonomic revision of the genus. Trends Parasitol 25: 93–100.

37. TakumiK, SwartA, MankT, Lasek-NesselquistE, LebbadM, et al. (2012) Population-based analyses of Giardia duodenalis is consistent with the clonal assemblage structure. Parasit Vectors 5: 168.

38. CampbellLT, CarterDE (2006) Looking for sex in the fungal pathogens Cryptococcus neoformans and Cryptococcus gattii. FEMS Yeast Res 6: 588–598.

39. CarricondeF, GilgadoF, ArthurI, EllisD, MalikR, et al. (2011) Clonality and α-a Recombination in the Australian Cryptococcus gattii VGII Population - An Emerging Outbreak in Australia. PLoS ONE 6: e16936 doi:10.1371/journal.pone.0016936

40. ChowdharyA, HiremathSS, SunS, KowshikT, RandhawaHS, et al. (2011) Genetic differentiation, recombination and clonal expansion in environmental populations of Cryptococcus gattii in India. Environm Microbiol 13: 1875–1888.

41. LiW, AveretteAF, Desnos-OllivierM, NiM, DromerF, et al. (2012) Genetic Diversity and Genomic Plasticity of Cryptococcus neoformans AD Hybrid Strains. G3 (Bethesda) 2: 83–97.

42. ChaturvediV, ChaturvediS (2011) Cryptococcus gattii: a resurgent fungal pathogen. Trends Microbiol 19: 564–571.

43. FraserJA, GilesSS, WeninkEC, Geunes-BoyerSG, WrightJR, et al. (2005) Same-sex mating and the origin of the Vancouver Island Cryptococcus gattii outbreak. Nature 437: 1360–1364.

44. LitvintsevaAP, MitchellTG (2012) Population Genetic Analyses Reveal the African Origin and Strain Variation of Cryptococcus neoformans var. grubii. PLoS Pathog 8: e1002495 doi:10.1371/journal.ppat.1002495

45. MatosO, EstevesF (2010) Pneumocystis jirovecii multilocus gene sequencing: findings and implications. Future Microbiol 5: 1257–1267.

46. CacciòSM, SprongH (2010) Giardia duodenalis: Genetic recombination and its implications for taxonomy and molecular epidemiology. Exp Parasitol 124: 107–112.

47. FengY, XiaoL (2011) Zoonotic Potential and Molecular Epidemiology of Giardia Species and Giardiasis. Clin Microbiol Rev 24: 110 doi:10.1128/CMR.00033-10

48. RyanA, CacciòSM (2013) Zoonotic potential of Giardia. Int J Parasitol 43: 943–956.

49. MazarsE, GuyotK, DurandI, Dei-CasE, BoucherS, et al. (1997) Isoenzyme Diversity in Pneumocystis carinii from Rats, Mice, and Rabbits. J Infect Dis 175: 655–660.

50. Aliouat-DenisCM, ChabéM, DemancheC, AliouatEM, ViscogliosiE, et al. (2008) Pneumocystis species, co-evolution and pathogenic power. Infect Genet Evol 8: 708–726.

51. PlutzerJ, OngerthJ, KaranisP (2010) Giardia taxonomy, phylogeny and epidemiology: Facts and open questions. Int J Hyg Environm Health 213: 321–333.

52. WielingaCM, ThompsonRCA (2007) Comparative evaluation of Giardia duodenalis sequence data. Parasitol 134: 1795–1821.

53. WidmerG, SullivanS (2012) Genomics and population biology of Cryptosporidium species. Parasite Immunol 34: 61–71.

54. De WaeleV, Van den BroeckF, HuyseT, McGrathG, HigginsI, et al. (2013) Panmictic Structure of the Cryptosporidium parvum Population in Irish Calves: Influence of Prevalence and Host Movement. Appl Environ Microbiol 79: 2534–2541.

55. HergesGR, WidmerG, ClarkME, KhanE, GiddingsCW, et al. (2012) Evidence that Cryptosporidium parvum Populations Are Panmictic and Unstructured in the Upper Midwest of the United States. Appl Environ Microbiol 78: 8096–8101.

56. SuC, KhanA, ZhouP, MajumdaraD, AjzenbergD, et al. (2012) Globally diverse Toxoplasmagondii isolates comprise six major clades originating from a small number of distinct ancestral lineages. Proc Nat Acad Sci U S A 109: 5844–5849.

57. XuJ (2006) Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances. Molec Ecol 15: 1713–1731.

58. ZingalesB, MilesMA, CampbellD, TibayrencM, MacedoAM, et al. (2012) The revised Trypanosoma cruzi subspecific nomenclature: rationale, epidemiological relevance and research applications. Infect Genet Evol 12: 240–253.

59. TanrıverdiS, GrinbergA, ChalmersRM, HunterPR, PetrovicZ, et al. (2008) Inferences about the Global Population Structures of Cryptosporidium parvum and Cryptosporidium hominis. Appl Env Microbiol 74: 7227–7234.

60. FengY, YangW, Ryan U ZhangL, KvácM, et al. (2011) Development of a Multilocus Sequence Tool for Typing Cryptosporidium muris and Cryptosporidium andersoni. J Clin Microbiol 49: 34–41.

61. WangR, JianF, ZhangL, NingC, LiuA, et al. (2012) Multilocus Sequence Subtyping and Genetic Structure of Cryptosporidium muris and Cryptosporidium andersoni. PLoS ONE 7: e43782 doi:10.1371/journal.pone.0043782

62. NgouanesavanhT, GuyotK, CertadG, Le FichouxY, ChartierC, et al. (2006) Cryptosporidium Population Genetics: Evidence of Clonality in Isolates from France and Haiti. J Euk Microbiol 53: S33–S36.

63. XiaoL (2010) Molecular epidemiology of cryptosporidiosis: An update. Exp Parasitol 124: 80–89.

64. WidmerG, LeeY (2010) Comparison of Single- and Multilocus Genetic Diversity in the Protozoan Parasites Cryptosporidium parvum and C. hominis. Appl Environm Microbiol 76: 6639–6644.

65. TibayrencM (1993) Entameba, Giardia and Toxoplasma: clones or cryptic species? Parasitol Today 9: 102–105.

66. Dobzhansky T (1937) Genetics and the origin of species. New York: Columbia University Press.

67. Cracraft J (1983) Species concept and speciation analysis. In: Johnson RF, editor. Current ornithology. New York: Plenum Press. pp. 159–187

68. FayerR (2010) Taxonomy and species delimitation in Cryptosporidium. Exp Parasitol 124: 90–97.

69. Lasek-NesselquistE, WelchDM, ThompstonRCA, SteuartRF, SoginML (2009) Genetic Exchange Within and Between Assemblages of Giardia duodenalis. J Euk Microbiol 56: 504–518.

70. XuF, Jerlström-HultqvistJ, AnderssonJO (2012) Genome-Wide Analyses of Recombination Suggest That Giardia intestinalis Assemblages Represent Different Species. Mol Biol Evol 29: 2895–2898.