Deoxyribozymes: useful DNA catalysts in vitro and in vivo.

Deoxyribozymes (DNA enzymes; DNAzymes) are catalytic DNA sequences. Using the technique of in vitro selection, individual deoxyribozymes have been identified that catalyze RNA cleavage, RNA ligation, and a growing range of other chemical reactions. DNA enzymes have been used in vitro for applications such as biochemical RNA manipulation and analytical assays for metal ions, small organic compounds, oligonucleotides, and proteins. Deoxyribozymes have also been utilized as in vivo therapeutic agents to destroy specific mRNA targets. Although many conceptual and practical challenges remain to be addressed, deoxyribozymes have substantial promise to contribute meaningfully for applications both in vitro and in vivo.

Evolutionary divergence of LFY function in the mustards Arabidopsis thaliana and Leavenworthia crassa.

LEAFY (LFY), a transcription factor involved in the regulation of flower development in Arabidopsis thaliana, has been identified as a candidate gene in the diversification of plant architecture in Brassicaceae. Previous research with Leavenworthia crassa, which produces solitary flowers in the axils of rosette leaves, has shown that the L. crassa LFY ortholog, LcrLFY, rescues most aspects of flower development in A. thaliana but showed two novel traits: flowers produced additional petals and inflorescences produced terminal flowers. In this paper, we explore the molecular mechanisms responsible for these novel phenotypes. We used microarray hybridizations to identify 32 genes differentially expressed between a transgenic LcrLFY line and a control transgenic LFY line. Of particular interest, TERMINAL FLOWER 1 (TFL1) transcripts were found at elevated levels in LcrLFY lines. To distinguish regulatory versus functional changes within the LcrLFY locus, reciprocal chimeric transgenes between LcrLFY and LFY were constructed. These lines implicate divergence of LcrLFY cis-regulation as the primary cause of both novel transgenic phenotypes but implicate divergence of LcrLFY protein function as the primary cause of elevated TFL1 levels. Taken together these results show that LcrLFY has diverged from A. thaliana in both the cis-regulatory and protein-coding regions and imply that molecular coevolution of LcrLFY and the L. crassa TFL1 ortholog, LcrTFL1, contributed to the evolution of rosette flowering.

Phylogenetic overdispersion in Floridian oak communities.

Closely related species that occur together in communities and experience similar environmental conditions are likely to share phenotypic traits because of the process of environmental filtering. At the same time, species that are too similar are unlikely to co-occur because of competitive exclusion. In an effort to explain the coexistence of 17 oak species within forest communities in North Central Florida, we examined correlations between the phylogenetic relatedness of oak species, their degree of co-occurrence within communities and niche overlap across environmental gradients, and their similarity in ecophysiological and life-history traits. We show that the oaks are phylogenetically overdispersed because co-occurring species are more distantly related than expected by chance, and oaks within the same clade show less niche overlap than expected. Hence, communities are more likely to include members of both the red oak and the white + live oak clades than only members of one clade. This pattern of phylogenetic overdispersion arises because traits important for habitat specialization show evolutionary convergence. We hypothesize further that certain conserved traits permit coexistence of distantly related congeners. These results provide an explanation for how oak diversity is maintained at the community level in North Central Florida.

LEAFY and the evolution of rosette flowering in violet cress (Jonopsidium acaule, Brassicaceae).

Arabidopsis and most other Brassicaceae produce an elongated inflorescence of mainly ebracteate flowers. However, the early-flowering species violet cress (Jonopsidium acaule) and a handful of other species produce flowers singly in the axils of rosette leaves. In Arabidopsis the gene LEAFY (LFY) is implicated in both the determination of flower meristem identity and in the suppression of leaves (bracts) that would otherwise subtend the flowers. In this study we examined the role of LFY homologs in the evolution of rosette flowering in violet cress. We cloned two LFY homologs, vcLFY1 and vcLFY2, from violet cress. Their exon sequences show ∼90% nucleotide similarity with Arabidopsis LFY and 99% similarity to each other. We used in situ hybridization to study vcLFY expression in violet cress. The patterns were very similar to LFY in Arabidopsis except for stronger expression in the shoot apical meristem outside of the region of flower meristem initiation. It is possible that the relatively diffuse expression of vcLFY contributes to the lack of bract suppression in violet cress. Additionally, the earliest flowers produced by violet cress express vcLFY, suggesting that accelerated flowering in violet cress could also result from changes in the regulation of vcLFY.

Phylogeny of the core Malvales: evidence from ndhF sequence data.

The monophyly of the group comprising the core malvalean families, Bombacaceae, Malvaceae, Sterculiaceae, and Tiliaceae, was recently confirmed by molecular studies, but the internal structure of this clade is poorly understood. In this study, we examined sequences of the chloroplast ndhF gene (aligned length 2226 bp) from 70 exemplars representing 35 of the 39 putative tribes of core Malvales. The monophyly of one traditional family, the Malvaceae, was supported in the trees resulting from these data, but the other three families, as traditionally circumscribed, are nonmonophyletic. In addition, the following relationships were well supported: (1) a clade, /Malvatheca, consisting of traditional Malvaceae and Bombacaceae (except some members of tribe Durioneae), plus Fremontodendron and Chiranthodendron, which are usually treated as Sterculiaceae; (2) a clade, /Malvadendrina, supported by a unique 21-bp (base pair) deletion and consisting of /Malvatheca, plus five additional subclades, including representatives of Sterculiaceae and Tiliaceae, and Durionieae; (3) a clade, /Byttneriina, with genera traditionally assigned to several tribes of Tiliaceae, plus exemplars of tribes Byttnerieae, Hermannieae, and Lasiopetaleae of Sterculiaceae. The most striking departures from traditional classifications are the following: Durio and relatives appear to be more closely related to Helicteres and Reevesia (Sterculiaceae) than to Bombacaceae; several genera traditionally considered as Bombacaceae (Camptostemon, Matisia, Phragmotheca, and Quararibea) or Sterculiaceae (Chiranthodendron and Fremontodendron) appear as sister lineages to the traditional Malvaceae; the traditional tribe Helictereae (Sterculiaceae) is polyphyletic; and Sterculiaceae and Tiliaceae, as traditionally circumscribed, represent polyphyletic groups that cannot sensibly be maintained with their traditional limits for purposes of classification. We discuss morphological characters and conclude that there has been extensive homoplasy in characters previously used to delineate major taxonomic groups in core Malvales. The topologies here also suggest that /Malvatheca do not have as a synapormophy monothecate anthers, as has been previously supposed but, instead, may be united by dithecate, transversely septate (polysporangiate) anthers, as found in basal members of both /Bombacoideae and /Malvoideae. Thus, "monothecate" anthers may have been derived at least twice, independently, within the /Bombacoideae (core Bombacaceae) and /Malvoideae (traditional Malvaceae).

Plant development: Genetic clues to petal evolution.

A recent study of the expression of floral organ identity genes in buttercups, poppies and their relatives has shed light on the evolutionary origin of petals.

The evolution of plant development.

There has been much recent interest in the evolution of plant development and especially in trying to understand the developmental genetic basis of morphological evolution. Significant progress has been made in understanding the evolution of floral organization and the mechanisms that might underlie the evolution of compound leaves and inflorescence morphology. These advances are reinforcing the idea that phenotypic evolution can proceed via changes at few loci of large effect and that promoter evolution may be an important and frequent mechanism.

Biogeography and floral evolution of baobabs (Adansonia, Bombacaceae) as inferred from multiple data sets.

The phylogeny of baobab trees was analyzed using four data sets: chloroplast DNA restriction sites, sequences of the chloroplast rpl16 intron, sequences of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA, and morphology. We sampled each of the eight species of Adansonia plus three outgroup taxa from tribe Adansonieae. These data were analyzed singly and in combination using parsimony. ITS and morphology provided the greatest resolution and were largely concordant. The two chloroplast data sets showed concordance with one another but showed significant conflict with ITS and morphology. A possible explanation for the conflict is genealogical discordance within the Malagasy Longitubae, perhaps due to introgression events. A maximum-likelihood analysis of branching times shows that the dispersal between Africa and Australia occurred well after the fragmentation of Gondwana and therefore involved overwater dispersal. The phylogeny does not permit unambiguous reconstruction of floral evolution but suggests the plausible hypothesis that hawkmoth pollination was ancestral in Adansonia and that there were two parallel switches to pollination by mammals in the genus.

Individuality and the existence of species through time.

The individuality of species provides the basis for linking practical taxonomy with evolutionary and ecological theory. An individual is here defined as a collection of parts (lower-level entities) that are mutually connected. Different types of species individual exist, based on different types of connection between organisms. An interbreeding species is a group of organisms connected by the potential to share common descendants, whereas a genealogical species is integrated by the sharing of common ancestors. Such species definitions serve to set the limits of species at a moment of time and these slices connect through time to form time-extended lineages. This perspective on the nature of individuality has implications that conflict with traditional views of species and lineages: (1) Several types of connections among organisms may serve to individuate species in parallel (species pluralism); (2) each kind of species corresponds to a distinct kind of lineage; (3) although lineage branching is the most obvious criterion to break lineages into diachronic species, it cannot be justified simply by reference to species individuality; (4) species (like other individuals) have fuzzy boundaries; (5) if we wish to retain a species rank, we should focus on either the most- or least-inclusive individual in a nested series; (6) not all organisms will be in any species; and (7) named species taxa are best interpreted as hypotheses of real species. Although species individuality requires significant changes to systematic practice and challenges some preconceptions we may have about the ontology of species, it provides the only sound basis for asserting that species exist independently of human perception.