Description of haplotypes

A description of 39 haplotypes found during the survey is provided as a table (including color codes to be used for the maps), as well as a tree displaying the relationships between haplotypes.

The haplotypes have been detected on the basis of the information provided by four PCR fragments, each digested by one restriction enzyme: DT-TaqI, AS-HinfI, CD-TaqI, and TF (either HinfI or TaqI). 25 of these haplotypes have been described before (22 in Dumolin-Lapègue et al. 1997 (excluding haplotype 23 = Q. cerris), and 3 more in Dumolin-Lapègue et al. 1998). 14 haplotypes are described for the first time, along with the patterns corresponding to three other European oak species non included in the survey (Q. cerris [=haplotype 23], Q. suber, Q. ilex). Four restriction-diagrams obtained in small acrylamide gels are provided for the 42 types (DT-TaqI, AS-HinfI, CD-TaqI, and TF-HinfI). Other haplotypes that have been discovered during the course of the project are not described here for one or more of the following reasons: (i) they occurred in only one locality,

Some participants did not analysed all fragments systematically, but only those that had been shown to discriminate among the haplotypes discovered in preliminary screening within a given region. In addition, the resolution was not always as good as in the gels used to prepare the restriction-diagrams presented here. Furthermore, two alternative restriction enzymes had been used in the analysis of fragment TF (HinfI and TaqI). As a consequence, some haplotypes shown in the diagrams are likely to be mistaken one for the other by some participants; in such a case, they were given subscripts (e.g., haplotypes 5a, 5b, and 5c) solely to indicate this. All haplotypes are included in the phylogenetic tree, but distribution maps will be presented only for the ‘merged’ haplotypes (i.e., a single map will be presented for haplotype 5 (=haplotypes 5a + 5b +5 c), rather than three separate maps, for instance; this is reflected in the colour codes which is the s

In most cases, these 33 haplotypes should have been detected by all participants if they had been present among their samples: at least one fragment (or combination of fragments) of these haplotypes allows their clear identification. Nevertheless, due to the number of laboratories involved in the present study and the difficulty to standardise all methods, a bias in favour of the most frequent haplotypes is possible, especially when these haplotypes occur away from their main distribution.

Some fragments not considered systematically or characterised by many levels difficult to differentiate during a systematic and large-scale study are also illustrated; although they were not used to identify the 33 ‘main’ haplotypes, they provide additional characters useful to identify the relationships of the haplotypes with each other. For instance, fragment AS6 (which is highly polymorphic and may harbour cpSSRs) was not scored by most groups but is represented here to provide a complete description of the haplotypes and to improve the characterisation of the haplotypes for establishing the phylogenetic tree.

R. Petit, 19.11.1999