Chloroplast DNA variation in European white oaks

Abstract

A consortium of 16 laboratories have studied chloroplast DNA (cpDNA) variation in European white oaks. A common strategy for molecular screening, based on restriction analysis of four PCR-amplified cpDNA fragments, was used to allow comparison among the different laboratories. A total of 2613 oak populations (12,214 individual trees from eight species) were sampled from 37 countries, and analysed with the four fragments. They belong to eight related oak species: Quercus robur, Q. petraea, Q. pubescens, Q. frainetto, Q. faginea, Q. pyrenaica, Q. canariensis and Q. macranthera. During this survey, 45 chloroplast variants were detected and are described together with their phylogenetic relationships, but several of these haplotypes were pooled when there were some risks of confusion across laboratories during the survey, and finally 32 remained that were mapped and used in diversity analyses. A strong phylogeographic structure is apparent from the data, where related haplotypes have broadly similar geographic distributions. In total, six cpDNA lineages are identified, which have distinct geographic distributions, mainly along a longitudinal gradient. Most haplotypes found in northern Europe are also present in the south, whereas the converse is not true, suggesting that the majority of mutations observed were generated prior to postglacial recolonisation, corroborating the conclusions of earlier studies. The description of a new western European lineage constitutes a major finding, compared to earlier phylogenetic treatments. Although the eight oak species studied systematically share cpDNA variants when in sympatry, they partition cpDNA diversity differently, as a consequence of their different ecology and life history attributes. Regional differences in levels of differentiation also exist (either species-specific or general); these seem to be related to the intensity of past and present management of the forests across Europe but also to the level of fragmentation of the range within these regions.

Introduction

Oaks were one of the first plant taxa for which cytoplasmic DNA markers were used to examine geographic variation within and among populations (Kremer et al., 1991, Whittemore and Schaal, 1991, Ferris et al., 1993, Petit et al., 1993a). More recent studies have extended these early results, yielding a detailed picture of chloroplast DNA (cpDNA) variation both range-wide across Europe (Dumolin-Lapègue et al., 1997) and at finer scales within particular regions (Ferris et al., 1995, Ferris et al., 1998, Johnk and Siegismund, 1997, Petit et al., 1997, Dumolin-Lapegue et al., 1998, Dumolin-Lapegue et al., 1999a). The chloroplast genome is known to be maternally inherited in oaks (i.e. transmitted by seeds only; Dumolin et al., 1995) and, as a consequence, displays higher levels of among population variation compared with nuclear markers (Petit et al., 1993b). The absence of paternal leakage has been indirectly inferred by demonstrating the interdependent assorting of mitochondrial and chloroplast genomes (Dumolin-Lapègue et al., 1998). Thus a phylogeny based on the chloroplast (or mitochondrial) genome for oak species is not complicated by recombination, although homoplasy due to convergent or reverse mutations may still arise. Earlier studies have demonstrated that cpDNA variation is geographically structured in oaks and that related haplotypes often have similar distribution (Dumolin-Lapègue et al., 1997). Because of the intrinsic historical information content of these phylogenies, the spatio-temporal dynamics of the maternal lineage can be uncovered by first studying the phylogenetic relationships of cpDNA variants and then mapping their geographic distribution.

Most previous oak phylogeographic studies included several species and demonstrated extensive sharing of cytoplasmic variants amongst species. However, this does not imply that oak species will partition cpDNA diversity in an identical way (Dumolin-Lapègue et al., 1999a). Moreover, the partitioning of cpDNA diversity may also differ according to region; as a consequence, the influence of geography and taxonomy on the partitioning of cpDNA variation should be investigated jointly.

Over the last 4 years, a team of 16 laboratories has cooperated to extend previous studies in order to conduct a detailed European-wide survey of cpDNA variation in oaks (Kremer, 2001). In this paper, the methods used are presented along with a description and phylogenetic analyses of the haplotypes discovered during this survey. This provides a basis for the nine regional papers included in this issue, and for the companion paper dealing with postglacial recolonisation routes (Petit et al., 2002a). Moreover, an analysis of species and regional effects on cpDNA diversity in Europe is presented. Throughout, comparisons are made between measures of diversity that take account of phylogenetic information and those that do not. This allows comparisons to be made between patterns of diversity caused by the mixing of haplotypes belonging to the same cpDNA lineages and those due to the mixture of two or more lineages during recolonisation.