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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 (

Phylogenetic relationships of Asphodelaceae were investigated by parsimony analysis of 57 monocotrbcL nucleotide sequences, including 17 genera that have at some time been assigned to the family. All genera of Asphodelaceae except for three (Hemiphylacus, Paradisea and Simethis) form a strongly supported monophyletic group with Hemerocallidaceae and Xanthorrhoeaceae as their immediate sister taxa. In a second analysis, we added 34 plastid trnL-F sequences (an intron and a spacer between two transfer RNA genes) for the Asphodelaceae clade and nearest outgroup families (Doryanthaceae, Hemerocallidaceae, Iridaceae, Ixioliriaceae, Tecophilaeaceae and Xanthorrhoeaceae) in an attempt to improve resolution and levels of internal support. The results from the separate analyses produced highly similar although not identical results. No strongly supported incongruent groups occurred, and we combined both sequence regions in one analysis, which demonstrated improved results. Strong support exists for a monophyletic subfamily Alooideae, but this leaves a paraphyletic subfamily Asphodeloideae because Bulbine/Jodrellia alone are strongly supported as the sister group of Alooideae. Characters that have been used to separate Alooideae as a distinct group (either as here a subfamily or as a separate family by other authors), such as secondary growth and bimodal karyotypes, are found in at least some members of Asphodeloideae, particularly in Bulbine and Jodrellia for the karyotypes, making Alooideae less easily recognized.

Infections with the malaria parasite Plasmodium falciparum result in more than 1 million deaths each year worldwide. Deciphering the evolutionary history and genetic variation of P. falciparum is critical for understanding the evolution of drug resistance, identifying potential vaccine candidates and appreciating the effect of parasite variation on prevalence and severity of malaria in humans. Most studies of natural variation in P. falciparum have been either in depth over small genomic regions (up to the size of a small chromosome) or genome wide but only at low resolution. In an effort to complement these studies with genome-wide data, we undertook shotgun sequencing of a Ghanaian clinical isolate (with fivefold coverage), the IT laboratory isolate (with onefold coverage) and the chimpanzee parasite P. reichenowi (with twofold coverage). We compared these sequences with the fully sequenced P. falciparum 3D7 isolate genome. We describe the most salient features of P. falciparum polymorphism and adaptive evolution with relation to gene function, transcript and protein expression and cellular localization. This analysis uncovers the primary evolutionary changes that have occurred since the P. falciparum-P. reichenowi speciation and changes that are occurring within P. falciparum.

Nat. Genet. 39, 120–125 (2007); published online 10 December 2006; corrected after print 8 February 2007 In the original version of this paper, the authors failed to acknowledge that sequencing of the P. falciparum IT laboratory isolate was funded by a European Union 6th Framework Program grant to the BioMalPar Consortium (contract number LSHP-LT-2004-503578).

Phylogenetic relationships of Limoniastrum and other genera of subfamily Staticoideae (Plumbaginaceae) were studied using parsimony analysis of the plastid gene rbc L, the intron of trn L and the intergene spacer of trnL - trn F. Our analysis showed that Limoniastrum was polyphyletic. Limoniastrum ifniense , in both rbc L and combined data analyses, is sister to Armeria and Psylliostachys , whereas in the trn L-F (intron and spacer combined) analysis it is sister to a clade composed of Acantholimon , Dictyolimon and the remaining species of Limoniastrum. In all analyses, the five remaining species of Limoniastrum (excluding Limoniastrum ifniense ) formed a clade with two groups of species L. monopetalum+L. guyonianum and those sometimes considered as the segregate genus Bubania ( L. feei, L. weygandiorum and L. rechingeri ). Levels of sequence divergence among these three groups of Limoniastrum were greater than for other well supported genera in the family and, in combination with morphological differences and paucity of synapomorphies, led us to conclude that separate generic status for each of the three clades is warranted.