Michael F. Fay

Phylogeny of the eudicots : a nearly complete familial analysis based on rbcL gene sequences

A phylogenetic analysis of 589 plastid rbcL gene sequences representing nearly all eudicot families (a total of 308 families; seven photosynthetic and four parasitic families are missing) was performed, and bootstrap re-sampling was used to assess support for clades. Based on these data, the ordinal classification of eudicots is revised following the previous classification of angiosperms by the Angiosperm Phylogeny Group (APG). Putative additional orders are discussed (e.g. Dilleniales, Escalloniales, Vitales), and several additional families are assigned to orders for future updates of the APG classification. The use of rbcL alone in such a large matrix was found to be practical in discovering and providing bootstrap support for most orders. Combination of these data with other matrices for the rest of the angiosperms should provide the framework for a complete phylogeny to be used in macro-evolutionary studies.

Cross‐species transfer of nuclear microsatellite markers: potential and limitations

Molecular ecologists increasingly require ‘universal’ genetic markers that can easily be transferred between species. The distribution of cross‐species transferability of nuclear microsatellite loci is highly uneven across taxa, being greater in animals and highly variable in flowering plants. The potential for successful cross‐species transfer appears highest in species with long generation times, mixed or outcrossing breeding systems, and where genome size in the target species is small compared to the source. We discuss the implications of these findings and close with an outlook on potential alternative sources of cross‐species transferable markers.

Conservation of rare and endangered plants using in vitro methods

SummaryMany botanic gardens now have tissue culture laboratories for the micropropagation of plants that are difficult to propagate by conventional horticultural techniques. In many cases the work centers on rare and endangered species. Examples of the use of different techniques including micropropagation, in vitro seed germination, dual culture with symbiotic fungi, and regeneration from callus are discussed with reference to their application to plant germplasm conservation.

Rapid and recent origin of species richness in the Cape flora of South Africa

The Cape flora of South Africa grows in a continental area with many diverse and endemic species. We need to understand the evolutionary origins and ages of such ‘hotspots’ to conserve them effectively. In volcanic islands the timing of diversification can be precisely measured with potassium–argon dating. In contrast, the history of these continental species is based upon an incomplete fossil record and relatively imprecise isotopic palaeotemperature signatures. Here we use molecular phylogenetics and precise dating of two island species within the same clade as the continental taxa to show recent speciation in a species-rich genus characteristic of the Cape flora. The results indicate that diversification began approximately 7–8 Myr ago, coincident with extensive aridification caused by changes in ocean currents. The recent origin of endemic species diversity in the Cape flora shows that large continental bursts of speciation can occur rapidly over timescales comparable to those previously associated with oceanic island radiations.

Simultaneous parsimony jackknife analysis of 2538 rbcL DNA sequences reveals support for major clades of green plants, land plants, seed plants and flowering plants

The ever-larger data matrices resulting from continuing improvements in DNA sequencing techniques require faster and more efficient methods of phylogenetic analysis. Here we explore a promising new method, parsimony jackknifing, by analyzing a matrix comprising 2538 sequences of the chloroplast generbcL. The sequences included cover a broad taxonomic range, from cyanobacteria to flowering plants. Several parsimony jackknife analyses were performed, both with and without branch-swapping and multiple random addition sequences: 1) including all positions; 2) including only first and second codon positions; 3) including only third positions; and 4) using only transversions. The best resolution was obtained using all positions. Removal of third positions or transitions led to massive loss of resolution, although using only transversions somewhat improved basal resolution. While branch-swapping improved both resolution and the support found for several groups, most of the groups could be recovered by faster simple analyses. Designed to eliminate groups poorly supported by the data, parsimony jackknifing recognizes 1400 groups on the basis of allrbcL positions. These include major taxa such as green plants, land plants, flowering plants, monocots and eudicots. We include appendices of supported angiosperm families, as well as larger groups.

When in doubt, put it in Flacourtiaceae: a molecular phylogenetic analysis based on plastid rbcL DNA sequences

Summary. Circumscription of Flacourtiaceae was investigated with a phylogenetic analysis of plastid rbcL DNA sequences, and the family was found to be composed of two clades that are more closely related to other families in Malpighiales than to each other. In one of these, that containing the type genus Flacourtia, Salicaceae are embedded, whereas the other clade includes the members of the peculiar and poorly known South African Achariaceae. The latter family name is conserved against all listed synonyms. Thus we propose the recognition of two families: i) Salicaceae sensu lato, including tribes Banareae, Bembicieae, Scolopieae, Samydeae (syn. Casearieae), Homalieae, Flacourtieae, Prockieae and Saliceae, as well as Abatieae (by some authors of Passifloraceae) and Scyphostegieae (Scyphostegia of the monogeneric Scyphostegiaceae); and ii) Achariaceae sensu lato, including tribes Pangieae, Lindackerieae, Erythrospermeae and Acharieae (Acharia, Ceratiosicyos and Guthriea of Achariaceae). Several genera considered by many previous authors to be members of Flacourtiaceae are excluded from Malpighiales: Berberidopsis and Aphloia fall near the base of the higher eudicots. Several tribes require different names from those used in previous systems, and we include an appendix indicating a tentative revised tribal taxonomy for both Salicaceae and Achariaceae sensu lato.

Barrier to gene flow between two ecologically divergent Populus species, P. alba (white poplar) and P. tremula (European aspen): the role of ecology and life history in gene introgression

The renewed interest in the use of hybrid zones for studying speciation calls for the identification and study of hybrid zones across a wide range of organisms, especially in long‐lived taxa for which it is often difficult to generate interpopulation variation through controlled crosses. Here, we report on the extent and direction of introgression between two members of the ‘model tree’ genus Populus: Populus alba (white poplar) and Populus tremula (European aspen), across a large zone of sympatry located in the Danube valley. We genotyped 93 hybrid morphotypes and samples from four parental reference populations from within and outside the zone of sympatry for a genome‐wide set of 20 nuclear microsatellites and eight plastid DNA restriction site polymorphisms. Our results indicate that introgression occurs preferentially from P. tremula to P. alba via P. tremula pollen. This unidirectional pattern is facilitated by high levels of pollen vs. seed dispersal in P. tremula (pollen/seed flow = 23.9) and by great ecological opportunity in the lowland floodplain forest in proximity to P. alba seed parents, which maintains gene flow in the direction of P. alba despite smaller effective population sizes (Ne) in this species (P. alba Nec. 500–550; P. tremula Nec. 550–700). Our results indicate that hybrid zones will be valuable tools for studying the genetic architecture of the barrier to gene flow between these two ecologically divergent Populus species.

Molecular systematics of Iridaceae : evidence from four plastid DNA regions

Iridaceae are one of the largest families of Lilianae and probably also among the best studied of monocotyledons. To further evaluate generic, tribal, and subfamilial relationships we have produced four plastid DNA data sets for 57 genera of Iridaceae plus outgroups: rps4, rbcL (both protein-coding genes), the trnL intron, and the trnL-F intergenic spacer. All four matrices produce similar although not identical trees, and we thus analyzed them in a combined analysis, which produced a highly resolved and well-supported topology, in spite of the fact that the partition homogeneity test indicated strong incongruence. In each of the individual trees, some genera or groups of genera are misplaced relative to morphological cladistic studies, but the combined analysis produced a pattern much more similar to these previous ideas of relationships. In the combined tree, all subfamilies were resolved as monophyletic, except Nivenioideae that formed a grade in which Ixioideae were embedded. Achlorophyllous Geosiris (sometimes referred to Geosiridaceae or Burmanniaceae) fell within the nivenioid grade. Most of the tribes were monophyletic, and Isophysis (Tasmanian) was sister to the rest of the family; Diplarrhena (Australian) fell in a well-supported position as sister to Irideae/Sisyrinchieae/Tigridieae/Mariceae (i.e., Iridoideae); Bobartia of Sisyrinchieae is supported as a member of Irideae. The paraphyly of Nivenioideae is suspicious due to extremely high levels of sequence divergence, and when they were constrained to be monophyletic the resulting trees were only slightly less parsimonious (<1.0%). However, this subfamily also lacks clear morphological synapomorphies and is highly heterogeneous, so it is difficult to develop a strong case on nonmolecular grounds for their monophyly.

Taxonomic Affinities of Medusagyne oppositifolia (Medusagynaceae)

Medusagyne oppositifolia Baker is the sole member of Medusagynaceae Engl. & Gilg and its phylogenetic position has been unclear. Analysis of rbcL sequence data indicates a close and strongly supported relationship to Ochnaceae and Quiinaceae, but does not resolve the relationships between these taxa. Together the three families form a monophyletic group with a somewhat more distant relationship to other linalean groups including Malpighiaceae, Linaceae and phyllanthoid Euphorbiaceae.

Amplified fragment length polymorphisms (AFLP) reveal details of polyploid evolution in Dactylorhiza (Orchidaceae)

The utility of the PCR-based AFLP technique (polymerase chain reaction; amplified fragment length polymorphisms) was explored in elucidating details of polyploid evolution in the Eurasian orchid genus Dactylorhiza. We emphasized Swedish taxa but also included some material from the British Isles and elsewhere in Europe. Three different sets of primers, amplifying different subsets of restriction fragments, independently revealed similar patterns for relationships among the Dactylorhiza samples investigated. The AFLP data support the general picture of polyploid evolution in Dactylorhiza, i.e., that allotetraploid derivatives have arisen repeatedly as a result of hybridization beween the two parental groups D. incarnata s.l. (sensu lato; diploid marsh orchids) and the D. maculata group (spotted orchids). Within the incarnata s.l. group, morphologically defined varieties were interdigitated. The D. maculata group consisted of two distinct subgroups, one containing autotetraploid D. maculata subsp. maculata and the other containing diploid D. maculata subsp. fuchsii. Allotetraploids showed a high degree of additivity for the putative parental genomes, and relationships among them were partly correlated to morphologically based entities, but also to geographic distribution. Thus, allotetraploid taxa from the British Isles clustered together, rather than with morphologically similar plants from other areas.