APOMIXIS, POLYPLOIDY, AND SPECIATION IN
            <i>DICHANTHIUM</i>

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). ...

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“…The complex phylogenetic structure of the BCD clade confirms and extends data collected over 40 y ago by de Wet and Harlan (42) (Fig. 2B).…”

Section: Discussionsupporting

confidence: 86%

Allopolyploidy, diversification, and the Miocene grassland expansion

Estep

McKain

Díaz

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

202

284

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“…Coelorachis and Chionachne are sister to the Zea/Tripsacum clade, which seems reasonable given that Coelorachis has been proposed to be an intermediate between the monoecious Andropogoneae and other members of the tribe (Reeves and Mangelsdorf 1935). The monophyly of the Australian species S. matarakense and S. australiense and the close relationship between Bothriochloa and Capillipedium have also been reported elsewhere (de Wet and Harlan 1969;Sun et al 1994;Spangler et al 1999).…”

Section: Structural Domains Of Tb1mentioning

confidence: 72%

Molecular Evolution of the teosinte branched Gene Among Maize and Related Grasses

Lukens¹,

Doebley²

2001

Molecular Biology and Evolution

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Several authors have proposed that changes in a small number of regulatory genes may be sufficient for the evolution of novel morphologies. Recent analyses have indicated that teosinte branched1 (tb1), a putative bHLH transcription factor, played such a role during the morphological evolution of maize from its wild ancestor, teosinte. To address whether or not tb1 played a similar role during the evolution of the Andropogoneae, the tribe to which maize belongs, and to examine the rate and pattern of tb1 evolution within this tribe, we analyzed tb1-like sequences from 23 members of the Andropogoneae and five other grasses. Our analysis revealed that the TB1 protein evolves slowly within three conserved domains but rapidly outside these domains. The nonconserved regions of the gene are characterized by both a high nonsynonymous substitution rate and frequent indels. The ratio of nonsynonymous substitutions per nonsynonymous site (d N ) to synonymous substitutions per synonymous site (d S ) was not significantly greater than 1.0, providing no evidence for positive selection. However, the d N /d S ratio varied significantly among lineages and was high compared with those of other plant nuclear genes. Variation in the d N /d S ratio among the Andropogoneae could be explained by unequal levels of purifying selection among lineages. Consistent with this interpretation, the rate of nonsynonymous substitution differed along several lineages, while the synonymous substitution rate did not differ significantly. Finally, using tb1, we examined phylogenetic relationships within the Andropogoneae. The phylogeny suggests that the tribe underwent a rapid radiation during its early history and that the monoecious Andropogoneae are polyphyletic.

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“…HARLAN et al (1970) suggested that there are genes in Tripsacum that, when present in hybrids with maize, induces chromosomes to form pairs. Similarly, DE WET and HARLAN ( 1972) suggested that « genetically controlled preferential bivalent formation may result in diploid like cytological behavior even in true genomic autoploids ». CHHEDA and HARLAN (1962) also demonstrated that bivalent formation in the generic complex Dichanthium-Bothriochloa-Capillipedium is controlled by a simple dominant genetic system.…”

Section: In Tetraploid Tripsacum Dactyloidesmentioning

confidence: 99%

“…He was successful in producing this intergeneric hybrid, by fertilizing sugarcane (clone P.O.J.2725) flowers with sorghum (variety-' Periamanjal ') pollen (THOMAS and VENKATRAMAN 1930;VENKATRAMAN 1931;BRANDES 1935). The success of this intergeneric cross is due to the buffering effect polyploidy has on the sugarcane genotype (RAGHAVAN 1951;SuBBA RAo et al 1963;DE WET and HARLAN 1970;DE WET 1971;HARLAN and DE WET 1976). Cytogenetic studies indicate that reduced as well as unreduced gametes in both male and female parents may function sexually (MORIYA 1940;PRICE 1957;BHAT et al 1962).…”

Section: Introductionmentioning

confidence: 99%