Almost three decades ago Alec Jeffreys published his seminal Nature papers on the use of minisatellite probes for DNA fingerprinting of humans (Jeffreys and colleagues Nature 1985, 314:67–73 and Nature 1985, 316:76–79). The new technology was soon adopted for many other organisms including plants, and when Hilde Nybom, Kurt Weising and Alec Jeffreys first met at the very First International Conference on DNA Fingerprinting in Berne, Switzerland, in 1990, everybody was enthusiastic about the novel method that allowed us for the first time to discriminate between humans, animals, plants and fungi on the individual level using DNA markers. A newsletter coined “Fingerprint News” was launched, T-shirts were sold, and the proceedings of the Berne conference filled a first book on “DNA fingerprinting: approaches and applications”. Four more conferences were about to follow, one on each continent, and Alec Jeffreys of course was invited to all of them. Since these early days, methodologies have undergone a rapid evolution and diversification. A multitude of techniques have been developed, optimized, and eventually abandoned when novel and more efficient and/or more reliable methods appeared. Despite some overlap between the lifetimes of the different technologies, three phases can be defined that coincide with major technological advances. Whereas the first phase of DNA fingerprinting (“the past”) was dominated by restriction fragment analysis in conjunction with Southern blot hybridization, the advent of the PCR in the late 1980s gave way to the development of PCR-based single- or multi-locus profiling techniques in the second phase. Given that many routine applications of plant DNA fingerprinting still rely on PCR-based markers, we here refer to these methods as “DNA fingerprinting in the present”, and include numerous examples in the present review. The beginning of the third phase actually dates back to 2005, when several novel, highly parallel DNA sequencing strategies were developed that increased the throughput over current Sanger sequencing technology 1000-fold and more. High-speed DNA sequencing was soon also exploited for DNA fingerprinting in plants, either in terms of facilitated marker development, or directly in the sense of “genotyping-by-sequencing”. Whereas these novel approaches are applied at an ever increasing rate also in non-model species, they are still far from routine, and we therefore treat them here as “DNA fingerprinting in the future”.

A reconstruction of the phylogeny of Bromeliaceae based on sequence data from three noncoding chloroplast DNA markers (trnL intron, trnT–trnL, and trnT–trnF intergenic spacer [IGS]) is presented, including 26 genera and 33 species. Relationships of Bromelioideae and phylogeny within this subfamily were analyzed in more detail on the basis of two of these markers (trnL intron and trnL–trnF IGS) using a set of 37 genera/74 species of Bromeliaceae, including 28 genera/60 species of Bromelioideae. Sister group relationships of Bromelioideae were not resolved with sufficient reliability, but the most likely candidates are the genera Fosterella and Puya. The basal phylogeny of Bromelioideae also was not resolved. Greigia, Ochagavia/Fascicularia/Fernseea, Deinacanthon, Bromelia, and a ‘‘core group’’ of the remaining Bromelioideae formed a basal polytomy. Within Bromelioideae, the AFLP technique was applied to assess relationships among selected groups of genera. In the Ochagavia/Fascicularia group (5 species and subspecies/16 accessions), AFLP data fully confirmed the systematic relationships based on morphological and anatomical characters. Investigation of 30 Aechmea species (33 accessions), including all subgenera and one species each from the related genera Ursulaea, Portea, Chevaliera, and Streptocalyx produced no resolution for several of the species. Clades that received good bootstrap support generally did not correspond with the delimitation of subgenera of Aechmea. Additionally, leaf blade anatomy of these species was investigated. The results corresponded partly with those of the AFLP analysis. Generic rank for Ursulaea and Portea was not supported.