American Journal of Botany 89 12 2007 2016 2002 GLACIAL HISTORY OF THE ALPINE HERB RUMEX NIVALIS POLYGONACEAE A COMPARISON OF COMMON PHYLOGEOGRAPHIC METHODS WITH NESTED CLADE ANALYSIS1 IVANA STEHLIK2 Institute of Systematic Botany University of Zurich Zollikerstrasse 107 CH 8008 Zurich Switzerland The glacial history of the alpine herb Rumex nivalis was investigated using amplified fragment length polymorphisms AFLPs and restriction fragment length polymorphisms with polymerase chain reaction PCR RFLPs of cpDNA Both traditional statistical methods widely applied in phylogeographic research and nested clade analysis were used The AFLPs indicated little geographic structure probably due to the wind pollinated reproductive system of the dioecious R nivalis Because cpDNA haplotypes exhibited distinct distributional patterns correlation between AFLPs and PCR RFLPs was low The results of common statistical methods and of nested clade analysis were largely congruent Both supported in situ survival of one group of common haplotypes in the Central Alps For another group of common haplotypes classical phylogeographic analyses gave strong evidence for survival in peripheral refugia at the northern alpine border whereas this conclusion was not as clearly supported in the nested clade analysis Nested clade analysis provided several detailed insights on past and ongoing populational demographic processes Thus it is a valuable tool in the phylogeographical analysis of haplotype data but it should preferably be combined with other statistical analyses In situations with low genetic variation in cpDNA classical phylogeographic analytical tools on nuclear DNA will still be the methods of choice Key words AFLP glacial survival methodological comparison migration nested clade analysis nunataks PCR RFLPs of cpDNA Pleistocene glaciation Nested clade analysis was developed to reconstruct the evolutionary history of populations by combining a cladogram of the genetic relationships among haplotypes within these populations and their geographic distribution Templeton Boerwinkle and Sing 1987 Population structure thereby can be separated from population history if it is rigorously and objectively assessed Templeton Routman and Phillips 1995 Templeton 1998 Thereby nested clade analysis can discriminate between phylogeographic associations due to recurrent but restricted gene flow vs historical events operating at the population level such as past fragmentatian colonization or range expansion Templeton 1998 Haplotypes are first linked in a cladogram that portrays the evolutionary steps connecting them to one another The accuracy of the following analysis depends on the absence of recombination in case of nuclear genomes and the reliability of the estimated cladogram topology Templeton and Sing 1993 A program for nested clade analysis of the geographic distribution of haplotypes has recently become available GEODIS 2 0 Posada Crandall and Templeton 2000 program available at http bioag byu edu zoology crandallplab geodis htm This has stimulated phylogeographic investigations of mitochondrial DNA in animals mtDNA e g Creer et al 2001 Mardulyn 2001 Seddon et al 2001 Turgeon and Bernatchez 2001 and of ribosomal DNA in fungi James et al 2001 whereas studies of cpDNA Manuscript received 12 March 2002 revision accepted 27 June 2002 The author thanks Rolf Holderegger for his help in the field and Konrad Bachmann Elena Conti Rolf Holderegger Peter Linder and Jakob Schneller for fruitful discussions and comments on the manuscript I would like to express my gratitude to Alan Templeton for his help to nest the haplotypes of Rumex nivalis This research was supported by the Swiss National Science Foundation SNF grant number 31 55390 98 to J J Schneller and grants from the Swiss Alpine Club SAC and the Georges and Antoine Claraz Schenkung both to I Stehlik 2 E mail ivana systbot unizh ch 1 in plants using nested clade analysis are still scarce e g Maskas and Cruzan 2000 Currently much research is aimed to elucidate specific phylogeographic processes that have shaped the genetic pattern of alpine plants of the European Alps and of the Arctic Nordal and Jonsell 1998 Widmer and Baltisberger 1999 Gugerli and Holderegger 2001 Hagen Giese and Brochmann 2001 Stehlik Schneller and Bachmann 2001 2002 Stehlik Tribsch and Scho nswetter 2001 Zhang Comes and Kadereit 2001 Holderegger Stehlik and Abbott 2002 A broad array of traditional statistical approaches to analyze molecular genetic data has been used in these studies Among the more frequently applied are cluster analyses or ordination methods neighbor joining UPGMA unweighted pair group method using arithmetic averages correspondence analysis Mantel tests of the relationships of different classifications of individuals to geographic subunits e g in populations in regions AMOVA analysis of molecular variance census of rare alleles in specific geographic subunits within a taxon or methods to detect isolation by distance Nested clade analysis seems to be very promising in that it unifies many characteristics of these traditional methods and at the same time appears to be more powerful in disentangling older from more recent population level processes Posada Crandall and Templeton 2000 Many phylogeographic investigations will probably use nested clade analysis in the near future It is therefore of interest to apply nested clade analysis and more traditional methods to the same data and to see whether they will come to equivalent or complementary phylogeographic conclusions Therefore I subjected molecular genetic data on populations of the European endemic Rumex nivalis Hegetschw Polygonaceae to both an array of classical statistics as used e g in Stehlik Schneller and Bachmann 2001 2002 and to nested clade analysis In phylogeographic investigations of the European alpine plants Eritrichium nanum Boraginaceae and Erinus alpinus 2007 2008 AMERICAN JOURNAL OF BOTANY Vol 89 Fig 1 The 23 populations sampled of Rumex nivalis in the Alps and the species total distribution according to Meusel Ja ger and Weinert 1965 inset Twenty two populations were sampled in the western part of the species distribution and one population from the eastern distribution limit was included for comparison Rumex nivalis also occurs in Montenegro Wagenitz 1981 The letters indicate the haplotypes found in four plants from each population in the PCR RFLP of cpDNA Haplotypes were ordered alphabetically according to
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