Phylogenetically informative markers as diagnostic tools to identify species, hybrids and introgression in Central American and Mexican pines

Genetic markers and phylogenetic analysis were used to characterize the germplasm of a group of Central American and Mexican pines. The morphologically based taxonomy of pines was used as the basis for inference concerning molecular marker divergence. The individual pine accessions for this study were exceptionally well-characterized and broadly distributed individuals. The morphology-based species-level taxonomic distinctions were assumed real. A DNA pooling strategy was used to identify phylogenetically informative RAPD markers. Analyses of the RAPD marker data placed Pinus tecunumanii and P. patula clearly into two different subgroups, supporting the classification of P. tecunumanii as a distinct species rather than a subspecies of P. patula.; Cluster analyses verified overall species relationships resulting from the analysis of RAPD marker differences among pooled DNA samples. These analyses confirmed that Pinus tecunumanii is not a subspecies of P. patula. Population-level analyses of the RAPD data placed P. caribaea in close association with P. tecunumanii groups and P. oocarpa. Analysis of the marker variation of individuals and populations resulted in well-defined groups which were in agreement with the morphologically defined groupings of these species. One exception was the lack of resolution between P. oocarpa and high elevation P. tecunumanii. Also, cluster analyses suggest a clear separation between the two elevation groups of P. tecunumanii, as well as the two geographically defined groups of P. greggii.; The DNA pooling strategy provided a large number of phylogenetically informative markers. Gene frequency data for these markers were obtained from populations and used to devise an efficient means of discriminating among the species groups. Population-level frequency data identified 60 species-diagnostic RAPD markers. Set theory applied to the data identified 20 species-diagnostic markers which distinguish between two subgroups, each consisting of four species groups. Species diagnostic RAPD markers were also identified which best discriminate within each subgroup. Nonparametric discriminant analysis assigned individuals into species groups from a profile of 60 diagnostic markers as well as for a subset of markers chosen to discriminate within and between subgroups. Discriminant functions were constructed to predict species group assignments for individual trees. These analyses resulted in very high average cross validation assignment rates.; Marker variation among and within these pine taxa was analyzed to infer the genetic distinctiveness of species and populations. Phylogenetic analysis of the RAPD marker differences among pooled DNA samples for the 6 pine species revealed genetic divergence which provides a basis for assessing the value of these taxa for conservation. The taxa with the highest conservation value Pinus oocarpa and P. caribaea. Similarly, the within-species phylogenetic analysis of four taxa revealed genetic divergence which provided a basis for assessing the value of populations for conservation. The objective was to explore the amount of diversity conserved when different numbers of provenances are sampled. In all cases, greatest diversity would be maintained by choosing combinations of provenances with greatest phylogenetic distinctiveness within subspecific clades. (Abstract shortened by UMI.)...