The polyploid Hawaiian silversword alliance (Asteraceae), a spectacular example of adaptive radiation in plants, was shown previously to have descended from North American tarweeds of the Madia/Raillardiopsis group, a primarily diploid assemblage. The origin of the polyploid condition in the silversword alliance was not resolved in earlier biosystematic, cytogenetic, and molecular studies, apart from the determination that polyploidy in modern species of Madia/Raillardiopsis arose independent of that of the Hawaiian group. We determined that two floral homeotic genes, ASAP3/TM6 and ASAP1, are found in duplicate copies within members of the Hawaiian silversword alliance and appear to have arisen as a result of interspecific hybridization between two North American tarweed species. Our molecular phylogenetic analyses of the ASAP3/TM6 loci suggest that the interspecific hybridization event in the ancestry of the Hawaiian silversword alliance involved members of lineages that include Raillardiopsis muirii (and perhaps Madia nutans) and Raillardiopsis scabrida. The ASAP1 analysis also indicates that the two species of Raillardiopsis are among the closest North American relatives of the Hawaiian silversword alliance. Previous biosystematic evidence demonstrates the potential for allopolyploid formation between members of the two North American tarweed lineages; a vigorous hybrid between R. muirii and R. scabrida has been produced that formed viable, mostly tetraporate (diploid) pollen, in keeping with observed meiotic failure. Various genetic consequences of allopolyploidy may help to explain the phenomenal evolutionary diversification of the silversword alliance.

The disparity between rates of morphological and molecular evolution remains a key paradox in evolutionary genetics. A proposed resolution to this paradox has been the conjecture that morphological evolution proceeds via diversification in regulatory loci, and that phenotypic evolution may correlate better with regulatory gene divergence. This conjecture can be tested by examining rates of regulatory gene evolution in species that display rapid morphological diversification within adaptive radiations. We have isolated homologues to the Arabidopsis APETALA3 (ASAP3͞TM6) and APETALA1 (ASAP1) floral regulatory genes and the CHLOROPHYLL A͞B BINDING PROTEIN9 (ASCAB9) photosynthetic structural gene from species in the Hawaiian silversword alliance, a premier example of plant adaptive radiation. We have compared rates of regulatory and structural gene evolution in the Hawaiian species to those in related species of North American tarweeds. Molecular evolutionary analyses indicate significant increases in nonsynonymous relative to synonymous nucleotide substitution rates in the ASAP3͞TM6 and ASAP1 regulatory genes in the rapidly evolving Hawaiian species. By contrast, no general increase is evident in neutral mutation rates for these loci in the Hawaiian species. An increase in nonsynonymous relative to synonymous nucleotide substitution rate is also evident in the ASCAB9 structural gene in the Hawaiian species, but not to the extent displayed in the regulatory loci. The significantly accelerated rates of regulatory gene evolution in the Hawaiian species may reflect the influence of allopolyploidy or of selection and adaptive divergence. The analyses suggest that accelerated rates of regulatory gene evolution may accompany rapid morphological diversification in adaptive radiations.floral regulatory loci ͉ MADS-box ͉ CAB9 ͉ Hawaiian silversword alliance R ates of morphological evolution are generally not correlated with rates of molecular evolution. This paradoxical observation was highlighted early by Wilson and coworkers (1-3), and subsequent molecular studies in species groups that have undergone recent adaptive radiations, such as African rift lake cichlids (4), columbines (5), and the Hawaiian silversword alliance (6), have documented marked incongruities in rates of morphological and molecular evolution. A proposed resolution to this paradox has been the conjecture that evolutionary changes in regulatory genes, rather than large-scale diversification in structural genes, may be responsible for interspecific variation in organismal morphologies (1)(2)(3)(7)(8)(9). This conjecture is reinforced by molecular developmental studies that indicate that dramatic shifts in organismal structure may arise from mutations at key regulatory loci (7-9). One test of this conjecture is to examine whether there is a significant acceleration in rates of regulatory gene evolution in species that display rapid morphological diversification within adaptive radiations.The Hawaiian silversword alliance (Asteraceae: Heliantheae-Madiinae) is...

It has been estimated that about 30% of the genes in the human genome are regulated by microRNAs (miRNAs). These are short RNA sequences that can down-regulate the levels of mRNAs or proteins in animals and plants. Genes regulated by miRNAs are called targets. Typically, methods for target prediction are based solely on sequence data and on the structure information. In this paper we propose a Bayesian graphical modeling approach that infers the miRNA regulatory network by integrating expression levels of miRNAs with their potential mRNA targets and, via the prior probability model, with their sequence/structure information. We use a directed graphical model with a particular structure adapted to our data based on biological considerations. We then achieve network inference using stochastic search methods for variable selection that allow us to explore the huge model space via MCMC. A time-dependent coefficients model is also implemented. We consider experimental data from a study on a very well-known developmental toxicant causing neural tube defects, hyperthermia. Some of the pairs of target gene and miRNA we identify seem very plausible and warrant future investigation. Our proposed method is general and can be easily applied to other types of network inference by integrating multiple data sources.

The vast landscape of environmental chemicals has motivated the need for alternative methods to traditional whole-animal bioassays in toxicity testing. Embryonic stem (ES) cells provide an in vitro model of embryonic development and an alternative method for assessing developmental toxicity. Here, we evaluated 309 environmental chemicals, mostly food-use pesticides, from the ToxCast™ chemical library using a mouse ES cell platform. ES cells were cultured in the absence of pluripotency factors to promote spontaneous differentiation and in the presence of DMSO-solubilized chemicals at different concentrations to test the effects of exposure on differentiation and cytotoxicity. Cardiomyocyte differentiation (α,β myosin heavy chain; MYH6/MYH7) and cytotoxicity (DRAQ5™/Sapphire700™) were measured by In-Cell Western™ analysis. Half-maximal activity concentration (AC50) values for differentiation and cytotoxicity endpoints were determined, with 18% of the chemical library showing significant activity on either endpoint. Mining these effects against the ToxCast Phase I assays (∼500) revealed significant associations for a subset of chemicals (26) that perturbed transcription-based activities and impaired ES cell differentiation. Increased transcriptional activity of several critical developmental genes including BMPR2, PAX6 and OCT1 were strongly associated with decreased ES cell differentiation. Multiple genes involved in reactive oxygen species signaling pathways (NRF2, ABCG2, GSTA2, HIF1A) were strongly associated with decreased ES cell differentiation as well. A multivariate model built from these data revealed alterations in ABCG2 transporter was a strong predictor of impaired ES cell differentiation. Taken together, these results provide an initial characterization of metabolic and regulatory pathways by which some environmental chemicals may act to disrupt ES cell growth and differentiation.