The contribution of gene expression modulation to phenotypic evolution is of major importance to an understanding of the origin of divergent or convergent phenotypes during and following polyploid speciation. Here we analysed genome-wide gene expression in two subspecies of the allotetraploid species, Senecio mohavensis A. Gray, and its diploid parents S. flavus (Decne.) Sch. Bip. and S. glaucus L.. The tetraploid is morphologically much more similar to S. flavus, leading to earlier confusion

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... er its taxonomic status. By means of an analysis of transcriptomes of all three species, we show that gene expression divergence between the parent species is relatively low (ca. 14% of loci), whereas there is significant unequal expression between ca. 20-25% of the parental homoeologues (gene copies) in the tetraploid. The majority of the expression bias in the tetraploid is in favour of S. flavus homoeologues (ca. 65% of the differentially expressed loci), and overall expression of this parental species sub-genome is higher than that of the S. glaucus sub-genome. To determine whether absence of expression of a particular S. glaucus homoeologue in the allotetraploid could be due to loss of DNA, we carried out a PCR-based assay and confirmed that in three out of 10 loci the S. glaucus homoeologue appeared absent. Our results suggest that biased gene expression is one cause of the allotetraploid S. mohavensis being more similar in morphology to one of its parent, S. flavus, and that such bias could result, in part, from loss of S. glaucus homoeologues at some loci in the allotetraploid. A c c e p t e d M a n u s c r i p t 2003). However, the link between gene expression variation and phenotypic evolution in polyploids is not well known. To this end, we chose to investigate gene expression variation in an allopolyploid and its diploid progenitor species where the allopolyploid is much more similar in morphology to one of its parental species. The allotetraploid, Senecio mohavensis A. Gray (Asteraceae) (2n=40), A c c e p t e d M a n u s c r i p t comprises a subspecies restricted to the Mojave Desert area in North America, ssp. mohavensis, and a North African subspecies, ssp. breviflorus (Kadereit) M. Coleman (Coleman, Forbes and Abbott, 2001; Coleman, et al., 2003; Liston, Rieseberg and Elias, 1989) . Its allopolyploid status was established from molecular work (see below) with S. flavus (Dechne.) Sch. Bip. (2n=20) and S. glaucus L. ssp. coronopifolius (Maire) Alexander (2n=20) designated as its diploid parents. Both parent species occur in North Africa and are absent from North America (Kadereit, et al., 2006) , and are estimated to have diverged ca. 10 million years (MY) ago with the allopolyploid forming very recently, most likely within the last 1 MY (Coleman, et al., 2003) . The presence of S. mohavensis in North America is attributed to long distance dispersal from North Africa (Coleman et al., 2003) . Senecio mohavensis was initially thought to be a subspecies of S. flavus (i.e. S. flavus (Decne.) Schultz Bip. ssp. breviflorus Kadereit [Kadereit, 1984]) until it was established to be tetraploid (Coleman, et al., 2001) . This previous designation was primarily due to the morphological similarity between S. mohavensis ssp. breviflorus and S. flavus which both occur in North Africa. Senecio flavus, however, has non-radiate capitula, whereas S. mohavensis is typically radiate. Molecular analysis further revealed that S. mohavensis resembled S. glaucus with regard to both its plastid DNA and ITS sequences (Coleman, et al., 2003; Comes and Abbott, 2001) , but exhibited the additive genotype of its two parent species for sequences of two nuclear loci, PgiC and Scyc2 (Chapman, 2004) and for a range of randomly amplified nuclear markers (Comes and Abbott, 2001; Kadereit, et al., 2006) . By sequencing pooled transcriptomes of the four taxa we were able to investigate the gross divergence in expression between the parental homoeologues in S. mohavensis as well as identify the number of homoeologues in the tetraploid that are differentially expressed, and the direction of expression bias for these homoeologues. Several homoeologues showed differential expression, prompting a follow-up PCR-based assay to determine if the parental DNA had been lost, or was present but transcriptionally silenced. Materials and Methods Morphological analysis Achenes (i.e. single seeded fruits) of the four taxa were collected from the wild in the following countries: S. glaucus -Morocco, Tunisia and Israel; S. flavus -Morocco, Spain (the Canary Islands), and Egypt; S. mohavensis ssp. mohavensis -USA (Arizona, California and Nevada); and S. mohavensis ssp. breviflorus -Egypt, Israel and Saudi Arabia. Achenes were germinated on filter paper in a