No abstract

The role of polyploidy, particularly allopolyploidy, in plant diversification is a subject of debate. Whole-genome duplications precede the origins of many major clades (e.g., angiosperms, Brassicaceae, Poaceae), suggesting that polyploidy drives diversification. However, theoretical arguments and empirical studies suggest that polyploid lineages may actually have lower speciation rates and higher extinction rates than diploid lineages. We focus here on the grass tribe Andropogoneae, an economically and ecologically important group of C 4 species with a high frequency of polyploids. A phylogeny was constructed for ca. 10% of the species of the clade, based on sequences of four concatenated low-copy nuclear loci. Genetic allopolyploidy was documented using the characteristic pattern of double-labeled gene trees. At least 32% of the species sampled are the result of genetic allopolyploidy and result from 28 distinct tetraploidy events plus an additional six hexaploidy events. This number is a minimum, and the actual frequency could be considerably higher. The parental genomes of most Andropogoneae polyploids diverged in the Late Miocene coincident with the expansion of the major C 4 grasslands that dominate the earth today. The well-documented whole-genome duplication in Zea mays ssp. mays occurred after the divergence of Zea and Sorghum. We find no evidence that polyploidization is followed by an increase in net diversification rate; nonetheless, allopolyploidy itself is a major mode of speciation. P olyploidy (whole-genome duplication) is often linked with the acquisition of new traits and subsequent species diversification, particularly in plants (1, 2). Ancient polyploidy correlates with major land-plant radiations (3) and the origins of orders, large families, and major clades (4-7) although, in many cases, sharp changes in diversification rates are delayed for millions of years after the polyploidization event (1). This phylogenetic pattern has led to the hypothesis that polyploidy causes or promotes diversification. Good mechanistic reasons support such a hypothesis. Studies of naturally occurring and synthetic polyploids find changes in gene expression, gene loss, release of transposons, and changes in morphology and physiology immediately after polyploidy (4,(8)(9)(10)(11)(12)). This pattern is particularly true for allopolyploids, which originate from a cross between genetically distinct parents often representing different species; in such cases, the biological changes seen after polyploidization may not reflect the effects of genome doubling per se, but rather the effect of hybridization between distantly related progenitors (4).Despite the appeal of the hypothesis that polyploidy causes diversification, there is evidence to the contrary. As noted by Stebbins (13), "polyploidy has been important in the diversification of species and genera within families, but not in the origin of the families and orders themselves," implying that polyploidy is only a minor force in diversification (see also ref. 14). ...

Maize (Zea mays or corn), both a major food source and an important cytogenetic model, evolved from a tetraploid that arose about 4.8 million years ago (Mya). As a result, maize has extensive duplicated regions within its genome. We have sequenced the two copies of one such region, generating 7.8 Mb of sequence spanning 17.4 cM of the short arm of chromosome 1 and 6.6 Mb (25.6 cM) from the long arm of chromosome 9. Rice, which did not undergo a similar whole genome duplication event, has only one orthologous region (4.9 Mb) on the short arm of chromosome 3, and can be used as reference for the maize homoeologous regions. Alignment of the three regions allowed identification of syntenic blocks, and indicated that the maize regions have undergone differential contraction in genic and intergenic regions and expansion by the insertion of retrotransposable elements. Approximately 9% of the predicted genes in each duplicated region are completely missing in the rice genome, and almost 20% have moved to other genomic locations. Predicted genes within these regions tend to be larger in maize than in rice, primarily because of the presence of predicted genes in maize with larger introns. Interestingly, the general gene methylation patterns in the maize homoeologous regions do not appear to have changed with contraction or expansion of their chromosomes. In addition, no differences in methylation of single genes and tandemly repeated gene copies have been detected. These results, therefore, provide new insights into the diploidization of polyploid species.