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). ...

SETARIA VIRIDIS is a diploid species and has contributed to several polyploid derivatives. The most morphologically similar of the polyploids is S. faberi, which differs in spikelet features, phylogenetics, genome size, and ecological response to drought. Researchers using field-collected S. viridis as a model organism will benefit from the clear delimitation provided in this study.

Setaria viridis (L.) P. Beauv. and its domesticated form, S. italica (L.) P. Beauv., have been developed over the past few years as model systems for C 4 photosynthesis and for the analysis of bioenergy traits. S. viridis is native to Eurasia, but is now a ubiquitous weed. An analysis of the population structure of a set of 232 S. viridis lines, mostly from North America but also comprising some accessions from around the world, using 11 SSR markers, showed that S. viridis populations in the US largely separate by latitude and/or climatic zone. S. viridis populations from the Northern US and Canada (north of 44°N) group with accessions from Western Europe, while populations in the Mid and Southern US predominantly group with accessions from Turkey and Iran. We hypothesize that S. viridis in the US was most likely introduced from Europe, and that introductions were competitive only in regions that had climatic conditions that were similar to those in the regions of origins. This hypothesis is supported by the fact that Canadian S. viridis lines were fast cycling and undersized when grown in the Mid-Western and Southern US compared to their morphology in their native environment. A comparison of the population structure obtained with 11 SSR markers and *40,000 single nucleotide polymorphisms (SNPs) in a common set of S. viridis germplasm showed that both methods essentially yielded the same groupings, although admixture was identified at a higher frequency in the SNP analysis. Small numbers of SSR markers can thus 123Genet Resour Crop Evol (2017) 64:367-378 DOI 10.1007 be used effectively to discern the population structure in this inbreeding species.