The impact of study design and life history traits on genetic variation of plants determined with AFLPs

Abstract

In this study, we analysed the impact of study design and life history traits on genetic variation of plants determined with amplified fragment length polymorphisms (AFLPs), a technique widely applied in all fields of molecular plant ecology. For the proper interpretation and comparison of genetic variation based upon AFLPs, a meta-analysis based upon a large number of studies of the relationship between study design and plant life history traits on the one hand and of AFLP variation on the other hand is needed but is lacking. To bridge this gap, we extracted data on study design and genetic variation from 115 AFLP studies comprising a total of 152 species. Subsequently, we ascribed the life history traits taxonomic status, life span, frequency, mating system and pollination vector to each of the species. Then, we used linear models to analyse the impact of study design and life history traits on genetic variation. In our data set genetic variation within and among populations depended neither on the number of analysed populations nor the number of analysed individuals per population. However, maximum geographic distance between populations strongly affected genetic variation. Variation within populations decreased while variation among populations increased with maximum geographic distance. Concerning the impact of life history traits, both genetic variation within and among populations depended with increasing strength on the life span, the frequency and the mating system of the species. Following the results of this study, the number of analysed populations or individuals per population is not necessarily a problem when comparing results of different studies, at least when not very low sample sizes are used. However, corresponding study ranges would be highly recommendable, since the maximum geographic distance between populations strongly affects genetic variation.

Appendix

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Ranunculus glacialis	Schönswetter, P., Paun, O., Tribsch, A., Niklfeld, H., 2003a. Out of the Alps: colonization of Northern Europe by East Alpine populations of the Glacier Buttercup Ranunculus glacialis L. (Ranunculaceae). Mol Ecol 12, 3373–3381
Ranunculus glacialis	Schönswetter, P., Tribsch, A., Stehlik, I., Niklfeld, H., 2004c. Glacial history of high alpine Ranunculus glacialis (Ranunculaceae) in the European Alps in a comparative phylogeographical context. Biol J Linn Soc 81, 183–195
Ranunculus pygmaeus	Schönswetter, P., Popp, M., Brochmann, C., 2006b. Rare arctic-alpine plants of the European Alps have different immigration histories: the snow bed species Minuartia biflora and Ranunculus pygmaeus. Mol Ecol 15, 709–720
Rhodiola rosea	Elameen, A., Klemsdal, S.S., Dragland, S., Fjellheim, S., Rognli, O.A., 2008. Genetic diversity in a germplasm collection of roseroot (Rhodiola rosea) in Norway studied by AFLP. Biochem Syst Ecol 36, 706–715
Rhododendron ferrugineum	Escaravage, N., Questiau, S., Pornon, A., Doche, B., Taberlet, P., 1998. Clonal diversity in a Rhododendron ferrugineum L. (Ericaceae) population inferred from AFLP markers. Mol Ecol 7, 975–982
Rubus chamaemorus	Ehrich, D., Alsos, I.G., Brochmann, C., 2008. Where did the northern peatland species survive the dry glacials: cloudberry (Rubus chamaemorus) as an example. J Biogeogr 35, 801–814
Rumex nivalis	Stehlik, I., 2002. Glacial history of the alpine herb Rumex nivalis (Polygonaceae): a comparison of common phylogeographic methods with nested clade analysis. Am J Bot 89, 2007–2016
Salix herbacea	Alsos, I.G., Alm, T., Normand, S., Brochmann, C., 2009. Past and future range shifts and loss of diversity in dwarf willow (Salix herbacea L.) inferred from genetics, fossils and modelling. Glob Ecol Biogeogr 18, 223–239
Sanguisorba officinalis	Musche, M., Settele, J., Durka, W., 2008. Genetic population structure and reproductive fitness in the plant Sanguisorba officinalis in populations supporting colonies of an endangered Maculinea butterfly. Int J Plant Sci 169, 253–262
Saponaria bellidifolia	Csergö, A.-M., Schönswetter, P., Gyöngyvér, M., Deák, T., Boşcaiu, N., Höhn, M., 2009. Genetic structure of peripheral, island-like populations: a case study of Saponaria bellidifolia Sm. (Caryophyllaceae) from the Southeastern Carpathians. Plant Syst Evol 278, 33–41
Saponaria pumila	Tribsch, A., Schönswetter, P., Stuessy, T.F., 2002. Saponaria pumila (Caryophyllaceae) and the ice age in the European Alps. Am J Bot 89, 2024–2033
Saxifraga aizoides	Raffl, C., Schönswetter, P., Erschbamer, B., 2006. ‘Sax-sess’—genetics of primary succession in a pioneer species on two parallel glacier forelands. Mol Ecol 15, 2433–2440
Saxifraga bryoides	Unpublished Diploma Thesis (Hoiß, B., 2007. Leben im Gletschervorfeld—populationsbiologische und -genetische Untersuchungen am Moos-Steinbrech (Saxifraga bryoides). University of Regensburg)
Saxifraga caespitosa	Chwedorzewska, K.J., Wojtun, B., Bednarek, P., 2005. Genetic and morphological variation of Saxifraga caespitosa L. from Spitsbergen (Svalbard): a preliminary study. Polar Biol 28, 802–804
Saxifraga callosa	Grassi, F., Labra, M., Minuto, L., Casazza, G., Sala, F., 2006. Natural hybridization in Saxifraga callosa Sm. Plant Biol 8, 243–252
Saxifraga cernua	Kapralov, M.V., Gabrielsen, T.M., Sarapultsev, I.E., Brochmann, C., 2006. Genetic enrichment of the arctic clonal Saxifraga cernua at its southern periphery via the alpine sexual Saxifraga sibirica. Mol Ecol 15, 3401–3411
Saxifraga stellaris	Unpublished Diploma Thesis (Fraunhofer, C., 2006. Molekular- und populationsökologische Analyse von Saxifraga stallaris L. entlang eines Fließgewässersystems in den Zentralalpen (Stubaital, Tirol, Österreich). University of Regensburg)
Saxifraga tridactylites	Reisch, C., 2007. Genetic structure of Saxifraga tridactylites (Saxifragaceae) from natural and man-made habitats. Conserv Genet 8, 893–902
Schoenus ferrugineus	Scotti, I., Mariani, A., Verona, V., Candolini, A., Cenci, C.A., Olivieri, A.M., 2002. AFLP markers and cytotaxonomic analysis reveal hybridisation in the genus Schoenus (Cyperaceae) Genome 45, 222–228
Schoenus nigricans
Senecio vulgaris	Haldimann, P., Steinger, T., Müller-Schärer, H., 2003. Low genetic differentiation among seasonal cohorts in Senecio vulgaris as revealed by amplified fragment length polymorphism analysis. Mol Ecol 12, 2541–2551
Senecio vulgaris	Steinger, T., Haldimann, P., Leiss, K.A., Müller-Schärer, H., 2002. Does natural selection promote population divergence? A comparative analysis of population structure using amplified fragment length polymorphism markers and quantitative traits. Mol Ecol 11, 2583–2590
Sherardia arvensis	Listl, D., Reisch, C., 2013. Genetics of indigenous and archeophytic populations—how fragmentation and land use affect populations of the arable weed Sherardia arvensis L. Folia Geobotanica, under review
Silene dioica	Karrenberg, S., Favre, A., 2008. Genetic and ecological differentiation in the hybridizing campions Silene dioica and S. latifolia. Evolution 62, 763–773
Silene latifolia
Silene rupestris	Kropf, M., Comes, H.P., Kadereit, J.W., 2006. Long-distance dispersal vs vicariance: the origin and genetic diversity of alpine plants in the Spanish Sierra Nevada. New Phytol 172, 169–184
Silene tatarica	Tero, N., Aspi, J., Siikamäki, P., Jäkäläniemi, A., Tuomi, J., 2003. Genetic structure and gene flow in a metapopulation of an endangered plant species, Silene tatarica. Mol Ecol 12, 2073–2085
Sisymbrium austriacum	Jacquemyn, H., Honnay, O., Van Looy, K., Breyne, P., 2006. Spatiotemporal structure of genetic variation of a spreading plant metapopulation on dynamic riverbanks along the Meuse river. Heredity 96, 471–478
Sparganium emersum	Pollux, B.J.A., Jong, M.D.E., Steegh, A., Verbruggen, E., van Groenendael, J.M., Ouborg, N.J., 2007. Reproductive strategy, clonal structure and genetic diversity in populations of the aquatic macrophyte Sparganium emersum in river systems Mol Ecol 16, 313–325
Suaeda maritima	Prinz, K., Weising, K., Hensen, I., 2009. Genetic structure of coastal and inland populations of the annual halophyte Suaeda maritima (L.) DUMORT. in Central Europe, inferred from amplified fragment length polymorphism markers. Plant Biol 11, 812–820
Succisa pratensis	Smulders, M.J.M., van der Schoot, J., Geerts, R.H.E.M., Antonisse-de Jong, A.G., Korevaar, H., Van der Wurff, A.W.G., Vosman, B., 2000. Genetic diversity and the reintroduction of meadow species. Plant Biol 2, 447–454
Taraxacum officinale	van der Hulst, R.G.M., Mes, T.H.M., den Nijs, H.C.M., Bachmann, K., 2000. Amplified fragment length polymorphism (AFLP) markers reveal that population structure of triploid dandelions (Taraxacum officinale) exhibits both clonality and recombination. Mol Ecol 9, 1–8
Teesdalia nudicaulis	Unpublished Diploma Thesis (Traore, Z., 2006. Die genetische Diversität und Fitness der seltenen und gefährdeten Pflanzenart Teesdalia nudicaulis im Binnendünengebiet bei Siegenburg. University of Regensburg)
Trifolium pallescens	Raffl, C., Holderegger, R., Parson, W., Erschbamer, B., 2008. Patterns in genetic diversity of Trifolium pallescens populations do not reflect chronosequence on alpine glacier forelands. Heredity 100, 526–532
Trifolium repens	van Treuren, R., Bas, N., Goossens, P.J., Jansen, J., van Soest, L.J.M., 2005. Genetic diversity in perennial ryegrass and white clover among old dutch grasslands as compared to cultivars and nature reserves. Mol Ecol 14, 39–52
Trollius europaeus	Despres, L., Loriot, S., Gaudeul, M., 2002. Geographic pattern of genetic variation in the European globeflower Trollius europaeus L. (Ranunculaceae) inferred from amplified fragment length polymorphism markers. Mol Ecol 11, 2337–2347
Vaccinium uliginosum	Eidesen, P.B., Alsos, I.G., Popp, M., Stensrud, Ø., Suda, J., Brochmann, C., 2007a. Nuclear vs. plastid data: complex Pleistocene history of a circumpolar key species. Mol Ecol 16, 3902–3925
Veronica alpina	Albach, D.C., Schönswetter, P., Tribsch, A., 2006. Comparative phylogeography of the Veronica alpina complex in Europe and North America. Mol Ecol 15, 3269–3286
Veronica bellidioides
Veronica arvensis	Unpublished Diploma Thesis (Ferstl, B., 2008. Populationsökologie und –genetik häufiger und seltener Arten—ein Vergleich von Veronica arvensis und V. praecox. University of Regensburg)
Veronica praecox
Vicia pisiformis	Jonsson, M., Bertilsson, M., Ehrlén, J., Lönn, M., 2008. Genetic divergence of climatically marginal populations of Vicia pisiformis on the Scandinavian Peninsula. Hereditas 145, 1–8
Viola elatior	Eckstein, R.L., O’Neill, R.A., Danihelka, J., Otte, A., Köhler, W., 2006. Genetic structure among and within peripheral and central populations of three endangered floodplain violets. Mol Ecol 15, 2367–2379
Viola pumila
Viola stagnina
Viola suavis	Mereda Jr., P., Hodálová, I., Mártonfi, P., Kučera, J., Lihová, J., 2008. Intraspecific Variation in Viola suavis in Europe: Parallel Evolution of White-flowered Morphotypes. Ann Bot 102, 443–462
Viscum album	Stanton, S., Honnay, O., Jacquemyn, H., Roldán-Ruiz, I., 2009. A comparison of the population genetic structure of parasitic Viscum album from two landscapes differing in degree of fragmentation. Plant Syst Evol 281, 161–169