Resolution of evolutionary relationships among some monocot orders remains problematic despite the application of various taxon and molecular locus sampling strategies. In this study we sequenced and analysed a fragment of the low‐copy, nuclear phytochrome C (PHYC) gene and combined these data with a previous multigene data set (four plastid, one mitochondrial, two nuclear ribosomal loci) to determine if adding this marker improved resolution and support of relationships among major lineages of monocots. Our results indicate the addition of PHYC to the multigene dataset increases support along the backbone of the monocot tree, although relationships among orders of commelinids remain elusive. We also estimated divergence times in monocots by applying newly evaluated fossil calibrations to our resolved phylogenetic tree. Inclusion of early‐diverging angiosperm lineages confirmed the origin of extant monocots c. 131 Mya and strengthened the hypothesis of recent divergence times for some lineages, although current divergence time estimation methods may inadequately model rate heterogeneity in monocots. We note significant shifts in diversification in at least two monocot orders, Poales and Asparagales. We describe patterns of diversification in the context of radiation of other relevant plant and animal lineages. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 178, 375–393.

The phylogeny of Chloridoideae (Gramineae) was inferred from parsimony analyses of DNA sequences from two genomes-the chloroplast trnL intron, trnL 3Ј exon, and trnL-F intergenic spacer, and the nuclear ribosomal internal transcribed spacer region (ITS1 ϩ 5.8S ϩ ITS2). Eighty species representing 66 chloridoid genera were sampled, including all but four of the native New World genera. Analyses of the individual and combined data sets were performed. The phylogenies were found to be highly congruent. Of the four tribes and seven subtribes of Chloridoideae sensu Clayton and Renvoize (1986) whose phylogenetic status could be tested with our taxon sample, only Orcuttieae and Uniolinae were monophyletic. The phylogenies suggested significant homoplasy in morphological traits, including inflorescence type, number of florets per spikelet, and number of lemma nerves. We propose a new classification based on the three main clades in the phylogenies-tribes Cynodonteae, Eragrostideae, and Zoysieae. The Eragrostideae clade is well resolved and supported and is further divided into three subtribes, Cotteinae, Eragrostidinae, and Uniolinae. Cynodonteae include most of the genera in our study, but the clade is poorly resolved. However, a clade formed of Muhlenbergia and nine other genera is present in both phylogenies and is well resolved and supported. A number of interesting, well-supported relationships are evident in the phylogenies, including Pappophorum-Tridens flavus, Tragus-Willkommia, and Gouinia-Tridens muticus-Triplasis-Vaseyochloa. Except for Bouteloua, no genus represented by multiple species proved to be monophyletic in the phylogenies.

Asparagus officinalis L. is a dioecious plant. A region called the M-locus located on a pair of homomorphic sex chromosomes controls the sexual dimorphism in asparagus. The aim of this work was to clone the region determining sex in asparagus from its position in the genome. The structure of the region encompassing M should be investigated and compared to the sex-determining regions in other dioecious model species. To establish an improved basis for physical mapping, a high-resolution genetic map was enriched with AFLP markers closely linked to the target locus by carrying out a bulked segregant analysis. By screening a BAC library with AFLP- and STS-markers followed by chromosome walking, a physical map with eight contigs could be established. However, the gaps between the contigs could not be closed due to a plethora of repetitive elements. Surprisingly, two of the contigs on one side of the M-locus did not overlap although they have been established with two markers, which mapped in a distance as low as 0.25 cM flanking the sex locus. Thus, the clustering of the markers indicates a reduced recombination frequency within the M-region. On the opposite side of the M-locus, a contig was mapped in a distance of 0.38 cM. Four closely linked BAC clones were partially sequenced and 64 putative ORFs were identified. Interestingly, only 25% of the ORFs showed sequence similarity to known proteins and ESTs. In addition, an accumulation of repetitive sequences and a low gene density was revealed in the sex-determining region of asparagus. Molecular cytogenetic and sequence analysis of BACs flanking the M-locus indicate that the BACs contain highly repetitive sequences that localize to centromeric and pericentromeric locations on all asparagus chromosomes, which hindered the localization of the M-locus to the single pair of sex chromosomes. We speculate that dioecious Silene, papaya and Asparagus species may represent three stages in the evolution of XX, XY sex determination systems. Given that asparagus still rarely produces hermaphroditic flowers and has homomorphic sex chromosomes, this species may be an ideal system to further investigates early sex chromosome evolution and the origins of dioecy.

The primary goal of the study was to estimate the phylogeny of Boute/oua and relatives (Gramineae: Chloridoideae) employing cladistic parsimony analysis of nuclear ribosomal intern al transcribed spacer region (ITS I + 5. SS + ITS2) DNA sequences . In cluded were Aegopogon (2 of 4 species), Boute/oua (34 of 42) , Buchloe (I of I), Buch/omimus (I of I), Cathestecum (2 of 4), Cyclostachya (I of I), Griffithsoch/oa ( I of I), Hilaria (I of 7), Opizia (2 of 2), Pentarrhaphis (2 of 3), Pleuraphis (2 of 3) , Pringleochloa ( I of I), Soderstromia (I of I), and fi ve outgroup genera/species for a total of IS genera, 56 species, and ten varieties . In all , the ITS regio n of 72 plants was seque nced and analyzed utilizing PAUP. Aegopogon, the Hilaria-Pleuraphis clade, and Tragus (an outgro up represe ntative) formed a tetratomy with a clade containing the remaining ingroup taxa. Neither Bouteloua no r its two subgenera, Bouteloua and Chondrosium, were found to be monophyletic. B. eriostachya, B. hirsuta, and B. pectinata (subg. Chondrosium). Bouteloua j uncea, which has been included in the B. curtipendula complex, was not a member of that clade. No new circumscriptions were proposed, although recognition of Boute/oua in the broad sense, with Chondrosium reduced to synonymy, was advocated. The findings suggested homopl asy in morphol ogical, anato mical, and breeding syste m traits.

Unisexual flowers have evolved repeatedly in the angiosperms. In Poaceae, multiple transitions from bisexual to unisexual flowers are hypothesized. There appear to be at least three distinct developmental mechanisms for unisexual flower formation as found in members of three subfamilies (Ehrhartoideae, Panicoideae, Pharoideae). In this study, unisexual flower development is described for the first time in subfamily Chloridoideae, as exemplified by Bouteloua dimorpha. Scanning electron microscopy (SEM) and anatomy were used to characterize the development of male (staminate) and female (pistillate) flowers, spikelets, and inflorescences. We found the developmental pathway for staminate flowers in B. dimorpha to be distinct from that described in the other three subfamilies, showing gynoecial arrest occurs at a different stage with possible loss of some cellular contents. However, pistillate flowers of B. dimorpha had some similarity to those described in other unisexual-flowered grasses, with filament and anther differentiation in abortive stamens. Comparing our findings with previous reports, unisexual flowers seem to have evolved independently in the four examined grass subfamilies. This analysis suggests the action of different genetic mechanisms, which are consistent with previous observations that floral unisexuality is a homoplasious condition in angiosperms.

The New World grass genus Bouteloua (Chloridoideae: Cynodonteae) comprises 57 species, 13 of which produce unisexual spikelets and hence are diclinous. Andromonoecy, gynodioecy, monoecy, trimonoecy, and dioecy all occur in the genus, and ten species are known to express more than one of these breeding systems. Employing a phylogenetic estimate based on parsimony analysis of DNA sequences from the ITS (nrDNA) and trnL-F (cpDNA) regions representing 35 species of Bouteloua, including ten of 13 diclinous species, we used parsimony character state reconstructions to investigate the evolution of unisexual spikelets and breeding systems. Our specific goals were to estimate (1) the ancestral condition in the genus, (2) the number of times spikelet unisexuality has arisen and/or been lost, and (3) the evolutionary pathways leading to dioecy and the other breeding systems. Although a number of related genera are diclinous, the reconstructions suggest that the common ancestor of Bouteloua probably was not diclinous. Spikelet unisexuality appears to have evolved two to seven times in the genus, but precisely how many times is uncertain; zero to four reversals to hermaphroditism are inferred. The reconstructions show andromonoecy arising from monoecy, and gynodioecy arising from monocliny. Neither andromonoecy nor gynodioecy are implicated in the origin of monoecy or dioecy. Monoecy is shown to evolve from monocliny and dioecy, and dioecy from monocliny and monoecy. Polyploidy and arid environments are possible factors in the evolution and variability of breeding systems in Bouteloua.

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