We present an analysis of supra-familial relationships of monocots based on a combined matrix of nuclear ISS and partial 26S rONA, plastid atpB, matK, ndhF, and rbcL, and mitochondrial atpl DNA sequences. Results are highly congruent with previous analyses and provide higher bootstrap support for nearly all relationships than in previously published analyses. Important changes to the results of previous work are a well-supported position of Petrosaviaceae as sister to all monocots above Acorales and Alismatales and much higher support for the commelinid clade. For the first time, the spine of the monocot tree has some bootstrap support, although support for paraphyly of liliids is still only low to moderate (79-82%). Dioscoreales and Pandanales are sister taxa (moderately supported, 87-92%), and Asparagales are weakly supported (79%) as sister to the commelinids. Analysis of just the four plastid genes reveals that addition of data from the other two genomes contributes to generally better support for most clades, particularly along the spine. A new collection reveals that previous material of Petermannia was misidentified, and now Petermanniaceae should no longer be considered a synonym of Colchicaceae. Arachnitis (Corsiaceae) falls into Liliales, but its exact position is not well supported. Sciaphila (Triuridaceae) falls with Pandanales. Trithuria (Hydatellaceae) falls in Poales near Eriocaulaceae, Mayacaceae, and Xyridaceae, but until a complete set of genes are produced for this taxon, its placement will remain problematic. Within the commelinid clade, Dasypogonaceae are sister to Poales and Arecales sister to the rest of the commelinids, but these relationships are only weakly supported.

Published phylogeny reconstructions of the palm family (Arecaceae) are based on plastid DNA sequences or restriction fragment length polymorphisms (RFLPs), nuclear DNA sequences, morphological characters or a combination thereof, and include between 33 and 90 palm species. The present study represents all previously recognized subfamilies, tribes and subtribes of palms and 161 of the 189 genera. The plastid DNA region mat K was sequenced for 178 palm species and ten commelinid monocot outgroup species, and was combined with new and previously published plastid DNA sequences of trn L-trn F, rps 16 intron and rbcL . The addition of mat K sequences and more taxa resulted in a highly resolved and largely well-supported phylogeny. Most importantly, critical basal nodes are now fully resolved and, in most cases, strongly supported. On the basis of this phylogeny, we have established a new subfamilial classification of the palms, in which five subfamilies are recognized, rather than the six that were included in the previous classification. The circumscriptions of the subfamilies Calamoideae and Nypoideae were corroborated. The phylogeny supported a new circumscription for the subfamily Coryphoideae, including all taxa previously recognized in Coryphoideae with the addition of the tribe Caryoteae, formerly of the subfamily Arecoideae. The phylogenetic analysis also supported a new delimitation for the subfamily Ceroxyloideae that contains the tribes Cyclospatheae and Ceroxyleae, and all genera formerly included in the subfamily Phytelephantoideae, but excludes the tribe Hyophorbeae. Finally, the subfamily Arecoideae was modified to exclude the tribe Caryoteae and to include the tribe Hyophorbeae.

Mapped cpDNA restriction site characters were analyzed cladistically and the resulting phylogenetic hypotheses were used to test monophyly and relationships of the infrageneric classification of Lathyrus (Fabaceae) proposed by Kupicha (1983, Notes from the Royal Botanic Garden Edinburgh 41: 209-244). The validity of previously proposed classification systems and questions presented by these classification schemes were explored. Two cpDNA regions, rpoC (rpoC1, its intron, part of rpoC2, and their intergenic spacer) and IR- (psbA, trnH-GUG, part of ndhF, and their intergenic spacers), were analyzed for 42 Lathyrus and two Vicia species. PCR (polymerase chain reaction) amplified rpoC and IR- products digested with 31 and 27 restriction endonucleases, respectively, resulted in 109 potentially informative characters. The strict consensus tree suggests that several of Kupicha's sections may be combined in order to constitute clades. The widespread section Orobus and the South American section Notolathyrus should be combined. Section Lathyrus, characterized by a twisted style, should either include sections Orobon and Orobastrum or be redefined as three sections, one of which is characterized by a 100 base pair deletion in the IR- region. Finally, a weighted parsimony analysis positions sections Clymenum (excluding L. gloeospermus) and Nissolia, both with phyllodic leaves, as sister sections. The affiliation of Lathyrus gloeospermus (section Clymenum) remains problematic.

Plastid DNA sequences evolve slowly in palms but show that the family is monophyletic and highly divergent relative to other major monocot clades. It is therefore difficult to place the root within the palms because faster evolving, length-variable sequences cannot be aligned with outgroup monocots, and length-conserved regions have been thought to give too few characters to resolve basal nodes. To solve this problem, we combined 94 ingroup and 24 outgroup sequences from the length-conserved rbcL gene with ingroup and alignable outgroup sequences from noncoding rps16 intron and trnL-trnF regions. The separate rps16 intron and trnL-trnF region contained about the same number of variable sites (autapomorphies not included) as rbcL, but gave higher retention indices and more clades with bootstrap support. In general, the strict consensus tree based on combined rbcL, rps16 intron, and trnL-trnF data showed more resolution towards the base of the palm family than previous hypotheses of relationships of the Arecaceae. An important result was the position of subfamily Calamoideae as sister to the rest of the palms, but this received <50% bootstrap support. Another result of systematic significance was the indication that subfamily Phytelephantoideae is related to two tribes from subfamily Ceroxyloideae, Cyclospatheae and Ceroxyleae.

The aim of the present study was to investigate the genetic variation in Danish populations of the endangered European crab apple (Malus sylvestris). Special emphasis was given to hybridization between the wild species and its cultivated relative Malus ×domestica. A total of 178 wild individuals from four Danish populations were studied along with a reference sample of 29 old cultivars. The genetic variation within and among samples was studied at ten microsatellite marker loci. Additionally, a morphological analysis was carried out to identify hybrids and test for correspondence between phenotypic and genotypic indices of hybridization.From application of ordination and a model based cluster analysis to the molecular data, two clusters were identified consisting of wild and cultivated individuals respectively. This indicates that pronounced admixture between the two species is not present. At the population level, a high correspondence was found between geographic isolation from M. ×domestica and genotypic and morphological indices of hybridization. As expected, isolated populations appeared less affected by hybridization than poorly isolated populations. Isolated 'pure' M. sylvestris populations could thus be identified. However, morphological and molecular evidence of hybridization was found to be divergent at the individual level. This is suggestive of some historical introgression into the M. sylvestris gene pool, and indicates that relying exclusively on either morphological or molecular characters as diagnostic markers in studies of hybridization between M. ×domestica and M. sylvestris might lead to fallible results. Combined application of genetic and morphological markers is therefore recommended.3