Clonal diversity and spatial genetic structure in the long-lived herb, Prairie trillium
Autoři:
Jennifer R. Mandel aff001; C. Kendall Major aff001; Randall J. Bayer aff001; James E. Moore aff003
Působiště autorů:
Department of Biological Sciences, The University of Memphis, Memphis, TN, United States of America
aff001; Center for Biodiversity, The University of Memphis, Memphis, TN, United States of America
aff002; Edward J. Meeman Biological Station, Millington, TN, United States of America
aff003; Department of Biology, Christian Brothers University, Memphis, TN, United States of America
aff004
Vyšlo v časopise:
PLoS ONE 14(10)
Kategorie:
Research Article
doi:
https://doi.org/10.1371/journal.pone.0224123
Souhrn
Combining population genetic studies with demographic surveys in long-lived clonal herbs can yield insight into the population dynamics of clonal plant populations. In this study, we assayed clonal diversity and spatial genetic structure in a population of a long-lived understory herb, Trillium recurvatum, that has been the focus of a demographic study spanning 26 years at the Meeman Biological Station in Memphis, Tennessee, USA. Using a set of five newly developed simple sequence repeat markers first reported here, we assessed 1) the extent of clonal diversity within the Meeman site, 2) the degree to which genetic diversity varies with stage class (juvenile, non-flowering, and flowering adults) at this site, 3) whether there is spatial genetic structure at the Meeman site, and 4) how measures of genetic diversity and inbreeding at the Meeman site compare to two additional nearby populations. Along with these analyses, we calculated and compared traditional population genetic metrics with information theory-based diversity indices. Although clonal propagation was present, the focal population displayed moderate levels of clonal diversity comprising 81 genets from the 174 individuals sampled. In the focal site, we also found that genetic diversity was highest in the flowering stage class when compared to the non-flowering and juvenile classes. We report that genets exhibited spatial genetic structure in the focal site exhibiting values for the Sp statistic of 0.00199 for linear distance and 0.0271 for log distance. Measures of unbiased gene diversity and the inbreeding coefficient were comparable across the sampled populations. Our results provide complementary genetic data to previous demographic studies in T. recurvatum, and these findings provide data for future studies aimed at integrating the degree of clonality, genetic variation, and population dynamics in this species. Our findings suggest that T. recurvatum at the focal Meeman site displays higher levels of sexual reproduction than were previously suggested, and spatial genetic structure estimates were comparable to other plant species with mixed and outcrossing mating strategies.
Klíčová slova:
Genetic polymorphism – Heterozygosity – Inbreeding – Plant genetics – Population genetics – Sexual reproduction – Shannon index – Species diversity
Zdroje
1. Tiffney BH, Niklas KJ. Clonal Growth in land plants: a paleobotanical perspective. In Population biology and the evolution of clonal organisms. Edited by Jackson J.B.C., Buss L.W., and Cook R.E. Yale University Press, New Haven, CT. 1985.
2. Billings WD, Mooney HA. The ecology of arctic and alpine plants. Biol Rev. 1968;43: 481–529. doi: 10.1111/j.1469-185X.1968.tb00968.x
3. Cook RE. Growth and development in clonal plant populations. In: Population Biology of Clonal Organisms. Edited by Jackson J.B.C., Buss L.W. and Cook R.E.. Yale University Press, New Haven, Connecticut, USA pp. 259–296.1985.
4. Klimes L, Klimesova J, Hendricks R, van Groenendal JM. Clonal plant architecture: a comparative analysis of form and function. In The ecology and evolution of clonal plants. Edited by de Kroon H., and van Groenendal JM. Leiden: Backhuys. 1997.
5. Honnay O, Jacquemyn H. A meta-analysis of the relation between mating system, growth form and genotypic diversity in clonal plant species. Evol Ecol. 2008;22: 299–312. doi: 10.1007/s10682-007-9202-8
6. Pluess AR, Stöcklin J. Population genetic diversity of the clonal plant Geum reptans (Rosaceae) in the Swiss Alps. Am J Bot. 2004;91: 2013–2021. doi: 10.3732/ajb.91.12.2013 21652350
7. De Witte LC, J. Longevity of clonal plants: why it matters and how to measure it. Annals Bot. 2010;106: 859–870.
8. Aigner PA. Ecological and genetic effects on demographic processes: pollination, clonality and seed production in Dithyrea maritima. Biol Conserv. 2004;116: 27–34. doi: 10.1016/S0006-3207(03)00170-8
9. Garnder SN, Mangel M. Modeling investments in seeds, clonal offspring, and translocation in a clonal plant. Ecol. 1999;80: 1202–1220. doi: 10.2307/177068
10. Silvertown J. The evolutionary maintenance of sexual reproduction: evidence from the ecological distribution of asexual reproduction in clonal plants. Int J Plant Sci. 2008;169: 157–168. doi: 10.1086/523357
11. Bengtsson BO, Ceplitis A. The balance between sexual and asexual reproduction in plants living in variable environments. J Evol Biol. 2000;13: 415–422. doi: 10.1046/j.1420-9101.2000.00187.x
12. Ellstrand NC, Roose ML. Patterns of genotypic diversity in clonal plant species. Am J Bot. 1987;74: 123–131.
13. Widén B, Cronberg N, Widén M. Genotypic diversity, molecular markers and spatial distribution of genets in clonal plants, a literature survey. Folia Geobotanica. 1994;29: 245–263. doi: 10.1007/BF02803799
14. Vekemans X, Hardy OJ. New insights from fine-scale spatial genetic structure analyses in plant populations. Mol Ecol. 2014;13: 921–935.
15. Harada Y, Iwasa Y. Analyses of Spatial Patterns and Population Processes of Clonal Plants. Res Popul Ecol. 1996;38: 153–164.
16. Sawyer NW. Reproductive ecology of Trillium recurvatum (Trilliaceae) in Wisconsin. Am Mid Nat. 2010;163: 146–160. doi: 10.1674/0003-0031-163.1.146
17. Moore JE, Franklin SB, Weins G, Collins BS. Long-term demography of Trillium recurvatum (Beck) on loess bluffs in western TN. AoB PLANTS. 2012; doi: 10.1093/aobpla/pls015
18. Knight TM. The effects of herbivory and pollen limitation on a declining population of Trillium grandiflorum. Ecol Appl. 2004;14: 915–928.
19. Leege LM, Thompson JS, Parris DJ. The responses of rare common trilliums (Trillium reliquum, T. cuneatum, and T. maculatum) to deer herbivory and invasive honeysuckle removal. Castanea. 2010;75: 433–443. doi: 10.2179/09-048.1
20. Wagenius S, Londsdorf E, Neuhauser C. Patch aging and the S-allee effect: breeding system effects on the demographic response of plants to habitat fragmentation. Am Nat. 2007;169: 383–397. doi: 10.1086/511313 17230399
21. O’Connor RP. Special Plant Abstract for Trillium recurvatum (prairie trillium). Lansing, MI: Michigan Natural Features Inventory. 2007.
22. Kalisz S, Hanzawa FM, Tonsor SJ, Thiede DA, Voigt S. Ant-mediated seed dispersal alters pattern of relatedness in a population of Trillium grandiflorum. Ecol. 1999;80: 2620–2634.
23. Case FW, Case RB. Trilliums. Timber Press, Portland, OR. 1997.
24. McCarthy KP. An analysis of gully development in Meeman-Shelby Forest State Park, Tennessee. MSc thesis, Department of Geography, The University of Memphis, Memphis, TN. 1990.
25. Hamilton MB, Pincus EL, Di-Fiore A, Fleischer RC. Universal linker and ligation procedures for construction of genomic DNA libraries enriched for microsatellites. Biotechniques. 1999;27:500–507. doi: 10.2144/99273st03 10489609
26. Pellicer J, Kelly LJ, Leitch IJ, Zomlefer WB, Fay MF. A universe of dwarfs and giants: genome size and chromosome evolution in the monocot family Melanthiaceae. New Phytologist. 2014;201:1484–1497. doi: 10.1111/nph.12617 24299166
27. Faircloth B.C., 2008. MSATCOMMANDER: Detection of microsatellite repeat arrays and automated, locus‐specific primer design. Molecular ecology resources, 8(1), pp.92–94. doi: 10.1111/j.1471-8286.2007.01884.x 21585724
28. Schuelke M. An economic method for the fluorescent labeling of PCR fragments. Nat Biotechnol. 2000;18:233–234. doi: 10.1038/72708 10657137
29. Van Oosterhout C, Hutchinson WF, Wills DP, Shipley P. MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes. 2004;4: 535–538.
30. Mandel JR. Clonal diversity, spatial dynamics, and small genetic population size in the rare sunflower, Helianthus verticillatus. Conserv Genet. 2010;11: 2055–2059. doi: 10.1007/s10592-010-0062-3
31. Bentley KE, Mauricio R. High degree of clonal reproduction and lack of large-scale geographic patterning mark the introduced range of the invasive vine, kudzu (Pueraria montana var. lobate), in North America. Am J Bot. 2016;103: 1499–1507. doi: 10.3732/ajb.1500434 27555435
32. Meirmans PG, Van Tienderen PH. GENOTYPE and GENODIVE: two programs for the analysis of genetic diversity of asexual organisms. Mol Ecol Resources. 2004;4: 792–794. doi: 10.1111/j.1471-8286.2004.00770.x
33. Peakall E, Smouse PR. GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research. Bioinformatics. 2012;28: 1367–4803.
34. Campbell LG, Lee D, Shukla K, Waite TA, Bartsch D. An ecological approach to measuring the evolutionary consequences of gene flow from crops to wild or weedy relatives. Appl Plant Sci. 2016;4: 1500114. doi: 10.3732/apps.1500114
35. Mandel JR, Ramsey AJ, Iorizzo M, Simon PW. Patterns of gene flow between crop and wild carrot, Daucus carota (Apiaceae) in the United States. PLoS ONE. 2016; e0161971. doi: 10.1371/journal.pone.0161971 27603516
36. Sherwin WB, Chao A, Jost L, Smouse PE. Information Theory Broadens the Spectrum of Molecular Ecology and Evolution. Trends Ecol Evol. 2017;32: 948–63. doi: 10.1016/j.tree.2017.09.012 29126564
37. Nei M. Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics. 1978;89: 583–590. 17248844
38. Kamvar ZN, Tabima JF, Grünwald NJ. Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction. 2014; PeerJ 2:e281. doi: 10.7717/peerj.281 24688859
39. R Core Team. R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing. 2016;Version 3.3.2.
40. Mantel N. The detection of disease clustering and a generalized regression approach. Cancer Res. 1967;27: 209–220. 6018555
41. Hardy OJ, Vekemans X. SPAGeDI: A versatile computer program to analyse spatial 6 genetic structure at the individual or population levels. Mol Ecol Notes. 2002; 2: 618–620.
42. Halkett F, Simon JC, Balloux F. Tackling the population genetics of clonal and partially clonal organisms. Tren Ecol & Evol. 2005;20: 194–201.
43. Gaudeul M, Delahaye T, Muller S. AFLP markers show low levels of clonal propagation and high genotypic diversity in the rare, southernmost populations of Linnaea borealis L.(Caprifoliaceae) in the Western Alps. Genetica. 2019;147: 79–90. doi: 10.1007/s10709-019-00054-6 30767171
44. Gonzales E, Hamrick JL, Smouse PE. Comparison of clonal diversity in mountain and Piedmont populations of Trillium cuneatum (Melanthiaceae‐Trilliaceae), a forest understory species. Am J Bot. 2008;95: 1254–1261. doi: 10.3732/ajb.2007159 21632330
45. Gonzales E, Hamrick JL. Distribution of genetic diversity among disjunct populations of the rare forest understory herb, Trillium reliquum. Heredity. 2005;95: 306. doi: 10.1038/sj.hdy.6800719 16094302
46. Walker AN, Foré SA, Collins BS. Fine-scale structure patterning of Trillium maculatum (Liliaceae) population. Botany. 2009; 87: 223–230. doi: 10.1139/Bo8-135
47. Abreu AG, Grombone-Guaratini MT, Moreira T. Genetic diversity and age class structure of seedings and saplings after a mast flowering of bamboo in the Brazilian Atlantic Forest. Int J Plant Sci. 2014;175: 319–327. doi: 10.1086/674448
48. Gargiulo R, Ilves A, Kaart T, Fay MF, Kull T. High genetic diversity in a threatened clonal species, Cypripedium calceolus (Orchidaceae), enables long-term stability of the species in different biogeographical regions in Estonia. Bot J Linn Soc. 2018;186: 560–571.
49. Jacquemyn H, Brys R, Honnay O, Hermy M, ROLDÁN‐RUIZ I. Local forest environment largely affects below‐ground growth, clonal diversity and fine‐scale spatial genetic structure in the temperate deciduous forest herb Paris quadrifolia. Mol Ecol. 2005;14: 4479–4488. doi: 10.1111/j.1365-294X.2005.02741.x 16313608
50. Arnaud‐Haond S, Duarte CM, Alberto F, Serrao EA. Standardizing methods to address clonality in population studies. Mol Ecol. 2007;16: 5115–5139. doi: 10.1111/j.1365-294X.2007.03535.x 17944846
Článek vyšel v časopise
PLOS One
2019 Číslo 10
- S diagnostikou Parkinsonovy nemoci může nově pomoci AI nástroj pro hodnocení mrkacího reflexu
- Je libo čepici místo mozkového implantátu?
- Pomůže v budoucnu s triáží na pohotovostech umělá inteligence?
- AI může chirurgům poskytnout cenná data i zpětnou vazbu v reálném čase
- Nová metoda odlišení nádorové tkáně může zpřesnit resekci glioblastomů
Nejčtenější v tomto čísle
- Correction: Low dose naltrexone: Effects on medication in rheumatoid and seropositive arthritis. A nationwide register-based controlled quasi-experimental before-after study
- Combining CDK4/6 inhibitors ribociclib and palbociclib with cytotoxic agents does not enhance cytotoxicity
- Experimentally validated simulation of coronary stents considering different dogboning ratios and asymmetric stent positioning
- Risk factors associated with IgA vasculitis with nephritis (Henoch–Schönlein purpura nephritis) progressing to unfavorable outcomes: A meta-analysis
Zvyšte si kvalifikaci online z pohodlí domova
Všechny kurzy