Although molecular methods are a major advance over phenological or root connectivity studies in the identification of clonal plants, there is still a level of ambiguity associated with two types of error: misidentification of genetically similar seedlings as clones and misidentification of dissimilar fingerprints from clones as genetically distinct individuals. We have addressed the second of these error types by determining the level of variation for AFLP fingerprints in Salix exigua, and then by developing a threshold value of Jaccard's similarity index for assigning individuals to clones or to siblings. Variation in AFLP banding patterns among clones was partitioned into three potential sources; clones, stems within-clones and foliage within-stems. Most of the variation was attributable to clones and then to stems within-clones. To provide an objective means of identifying clones, we developed a method for establishing a threshold similarity index to assign individuals to the same clone. Our method yielded a Jaccard similarity threshold of 0.983 that resulted in a potential pairwise error rate of 8.1% putative clone assigned to siblings and 1.5% sibling assigned to clones. The method was tested on independent clonal and sibling individuals resulting in the same threshold value and similar error rates. We applied our method to assign individuals to clones in a population of S. exigua along the Cosumnes River, California. A total of 11 clones were identified, with one clone including 43% of the individuals sampled. Our results show that this approach can be useful in the accurate identification of clones.

Two issues that have captured the attention of tropical plant evolutionary biologists in recent years

The four western North American red oak species (Quercus wislizeni, Q. parvula, Q. agrifolia, and Q. kelloggii) are known to produce hybrid products in all interspecific combinations. However, it is unknown whether hybrids are transitory resulting from interspecific gene flow or whether they are maintained through extrinsic selection. Here, we examine cryptic hybrid structure in Q. wislizeni through a broad region including contact and isolation from three other western North American red oaks using amplified fragment length polymorphism molecular markers. All four species were simultaneously detected in the genetic background of individuals morphologically assigned to Q. wislizeni, although the contribution of Q. kelloggii was minor. In some cases, introgression was detected well outside the region of sympatry with one of the parental species. Molecular structure at the individual level indicated this was due to long-distance pollen dispersal and not to local extinction of parental species. Species admixture proportions were correlated with climatic variables and greater proportions of Q. agrifolia and Q. parvula were present in the genetic background of Q. wislizeni in sites with cooler and more humid summers, corresponding with habitat preferences of the parental species. Partial Mantel tests indicated that climate was more important than distance from pollen source in this association. Despite high levels of introgression, species integrity was maintained in some populations in close proximity to the other species, providing further support to environmental selection in determining population genetic structure. Thus, the contribution of species mixtures to population genetic structure varies across the landscape according to availability of pollen, but more importantly to varying environmental selection pressures that produce a complex pattern of hybrid and pure gene pools.

Clonality in plants is widespread and includes species that span temporally and spatially heterogeneous environments. Yet, theory predicts that clonally reproducing plants evolve at slower rates, risk accumulating more mutations than sexuals, and potentially lack the benefits of DNA repair mechanisms afforded by meiosis. Does the apparent success of clonal plants contradict the severe costs of clonal reproduction suggested by theory? We examine how epigenetics may confer ecological advantages to clonal plants that could outweigh these evolutionary costs. Relying to various degrees on vegetative reproduction, the capacity to conserve or reverse gene regulation changes over cell divisions has clear potential for optimization of plasticity and acclimation in response to environmental variation encountered. Clonal plants may be one of the best examples of organisms taking advantage of epigenetic acclimation as an alternative to the slower mechanisms of adaptation through natural selection. If epigenetic processes are important in matching organismal response to the environment, this may prove to be a mechanism that will buffer plants against the challenges of current and future rapid environmental changes.Theory predicts that clonally reproducing plants evolve at slower rates, risk accumulating more mutations than sexuals, and potentially lack the benefits of DNA repair mechanisms afforded by meiosis mutational meltdown, Lynch et al. 1993; Muller's ratchet, Muller 1964). This suggests they are successful for evolutionarily short periods of time and under stable environments (Silvertown 2008). Yet, clonality in plants is widespread and includes species that span heterogeneous environments, are long-lived and face a range of environmental changes during their lifetime, and have survived major climatic changes such as those of the Pleistocene. Today, clonal plants make up perhaps 40 % of our planet's flora (Tiffney and Niklas 1985) dominate grasslands, deserts, wetlands, and tundras as major primary producers, comprise some of our most important crops, including almost all bioenergy crops, and feature many of the most invasive plants. Some of earth's largest, tallest, oldest, most extensive, and rarest plants are clonal. Being extremely modular organisms, clonal plants, whether large integrated clones, or fragmented into Communicated by C. Holzapfel.

European black pine (Pinus nigra Arn.) is a widely distributed Mediterranean conifer. To test the hypothesis that fragmented populations in western Europe survived in situ during the last glacial rather than having been re-colonized in the postglacial period, genetic variation was assessed using a suite of 10 chloroplast DNA microsatellites. Among 311 individuals analysed, 235 haplotypes were detected revealing high levels of chloroplast haplotype diversity in most populations. Bayesian analysis using a model of linked loci, with no prior assumption of population structure, assigned individuals to 10 clusters that corresponded well with the six predefined sampling regions, while an analysis carried out at the population level and assuming unlinked loci, recovered the original six sampling regions. This regional structure was supported by a biogeographical analysis that detected five barriers, with the two most significant separating Alps from Corsica and southern Italy, and southern Spain from the Pyrenees. No signals of demographic expansion were detected, and comparisons of R(ST) with pR(ST) suggested that a stepwise mutational model was important in regional differentiation, but not in population-within-region differentiation. These tests support long-term persistence of the species within the six regions. The temporal depth estimate, assuming a high mutation rate in coalescent modelling, placed the deepest split between the Alps and the other regions at about 150 000 years ago, and the most recent split of Pyrenees from southern France at about 30 000 years ago. Taken together, the data suggest that chloroplast DNA is structured in black pine and disjunct populations in western Europe are likely to have been present during the Last Glacial Maximum.