Francisco Vergara-Silva

A Phylogeny of the Monocots, as Inferred from rbcL and atpA Sequence Variation, and a Comparison of Methods for Calculating Jackknife and Bootstrap Values

Abstract A phylogenetic analysis of the monocots was conducted on the basis of nucleotide sequence variation in two genes (atpA, encoded in the mitochondrial genome, and rbcL, encoded in the plastid genome). The taxon sample of 218 angiosperm terminals included 177 monocots and 41 dicots. Among the major results of the analysis are the resolution of a clade comprising four magnoliid lineages (Canellales, Piperales, Magnoliales, and Laurales) as sister of the monocots, with the deepest branch within the monocots between a clade consisting of Araceae, Tofieldiaceae, Acorus, and Alismatales, and a clade that includes all other monocots. Nartheciaceae are placed as the sister of Pandanales, and Corsiaceae as the sister of Liliales. The Triuridaceae, represented by three genera, including Lacandonia, are resolved as monophyletic and placed in a range of positions, generally within Pandanales. Dasypogonaceae and Arecaceae diverge sequentially from a clade that includes all other commelinid taxa, and within the latter group Poales s. lat. are sister of a clade in which Zingiberales and Commelinales are sisters. Within Poales s. lat., Trithuria (Hydatellaceae) and Mayaca appear to be closely related to some or all elements of Xyridaceae. A comparison was conducted of jackknife and bootstrap values, as computed using strict-consensus (SC) and frequency-within-replicates (FWR) approaches. Jackknife values tend to be higher than bootstrap values, and for each of these methods support values obtained with the FWR approach tend to exceed those obtained with the SC approach.

The key role of morphology in modelling inflorescence architecture

Emerging evidence suggests that certain key genes control the branching patterns of flower-bearing axes (i.e. inflorescences) in angiosperms. However, the terminology surrounding inflorescence architecture is heavily typological and suffers from radically divergent definitions of terms that together reduce the value of some recent predictive models. We attempt to resolve the paradox of conflicting definitions of the same terms and clarify the assumptions surrounding this complex subject. We argue in favour of uniform terminology and against over-simplification. The valid conceptual platforms for modelling should be clearly defined and should adequately reflect observed structural diversity.

Recurrent abnormalities in conifer cones and the evolutionary origins of flower-like structures

Conifer cones are reproductive structures that are typically of restricted growth and either exclusively pollen-bearing (male) or exclusively ovule-bearing (female). Here, we review two common spontaneous developmental abnormalities of conifer cones: proliferated cones, in which the apex grows vegetatively, and bisexual cones, which possess both male and female structures. Emerging developmental genetic data, combined with evidence from comparative morphology, ontogeny and palaeobotany, provide new insights into the evolution of both cones and flowers, and prompt novel strategies for understanding seed-plant evolution.

Molecular control of normal and acrocona mutant seed cone development in Norway spruce (Picea abies) and the evolution of conifer ovule‐bearing organs

Reproductive organs in seed plants are morphologically divergent and their evolutionary history is often unclear. The mechanisms controlling their development have been extensively studied in angiosperms but are poorly understood in conifers and other gymnosperms. Here, we address the molecular control of seed cone development in Norway spruce, Picea abies. We present expression analyses of five novel MADS-box genes in comparison with previously identified MADS and LEAFY genes at distinct developmental stages. In addition, we have characterized the homeotic transformation from vegetative shoot to female cone and associated changes in regulatory gene expression patterns occurring in the acrocona mutant. The analyses identified genes active at the onset of ovuliferous and ovule development and identified expression patterns marking distinct domains of the ovuliferous scale. The reproductive transformation in acrocona involves the activation of all tested genes normally active in early cone development, except for an AGAMOUS-LIKE6/SEPALLATA (AGL6/SEP) homologue. This absence may be functionally associated with the nondeterminate development of the acrocona ovule-bearing scales. Our morphological and gene expression analyses give support to the hypothesis that the modern cone is a complex structure, and the ovuliferous scale the result of reductions and compactions of an ovule-bearing axillary short shoot in cones of Paleozoic conifers.

MADS‐BOX GENES: DEVELOPMENT AND EVOLUTION OF PLANT BODY PLANS

We review functional data on MADS‐box genes, recent phylogenetic analyses of these coding regions, and their roles in the development and evolution of key morphological innovations in plants. We map the origin of important morphological structures in particular diverse stages of the life cycle in different plant clades onto organismal phylogenies, and present relevant molecular genetic aspects of development related to the MADS‐box genes. We focus on reproductive structures of the sporophyte because most functional characterizations have been done of MADS‐box genes involved in flower development. We discuss MADS‐box evolution in flowering plants, but we also review studies in the other nonflowering vascular plants, gymnosperms (conifers and gnetales), and ferns and preliminary data from the algae. We suggest that floral (e.g. flowering time, inflorescence, and flower meristem identity) MADS‐box and nonfloral plant MADS‐box genes should be the focus of future comparative research. Cloning and functional analyses of MADS‐box genes in bryophytes, particularly in the experimental system Physcomitrella patens (Hedw.) B.S.G., are needed. The ABC model of floral organ specification is an excellent general representation of an important network of genes; however, formal analytical tools are required to integrate data on complex gene interaction in comparative analyses. This and other analytical approaches to constructing gene network models will help to frame homology hypotheses in an evolutionary and developmental framework.

A character-based approach in the Mexican cycads supports diverse multigene combinations for DNA barcoding

A DNA barcoding study was conducted to determine the optimal combination of loci needed for successful species‐level molecular identification in three extant cycad genera—Ceratozamia, Dioon, and Zamia—that occur in Mexico. Based on conclusions of a previous multigene study in representative species of all genera in the Cycadales, we tested the DNA barcoding performance of seven chloroplast coding (matK, rpoB, rpoC1, and rbcL) and non‐coding (atpF/H, psbK/I, and trnH‐psbA) regions, plus sequences of the nuclear internal transcribed spacer. We analysed data under the assumptions of the “character attributes organization system” (CAOS), a character‐based approach in which species are identified through the presence of ‘DNA diagnostics’. In Ceratozamia, four chloroplast regions and one nuclear region were needed to achieve > 70% unique species identification. In contrast, the two‐gene combination atpF/H + psbK/I and the four‐gene combination atpF/H + psbK/I + rpoC1 + ITS2 were needed to reach 79% and 75% unique species identification in Dioon and Zamia, respectively. The combinations atpF/H + psbK/I and atpF/H + psbK/I + rpoC1 + ITS2 include loci previously considered by the international DNA barcoding community. However, none of the three combinations of potential DNA barcoding loci found to be optimal with a character‐based approach in the Mexican cycads coincides with the ‘core barcode’ of chloroplast markers (matK + rbcL) recently proposed for universal use in the plant kingdom.

Inside‐Out Flowers Characteristic of Lacandonia schismatica Evolved at Least before Its Divergence from a Closely Related Taxon, Triuris brevistylis

Lacandonia schismatica, a mycoheterotrophic, hermaphroditic monocotyledon endemic to the Lacandon rain forest of southeast Mexico, is the only flowering plant for which a spatial inversion (heterotopy, complete homeosis) of the reproductive floral whorls (stamens and carpels) is known to occur in natural populations. In order to investigate if this autapomorphic inside‐out arrangement of the reproductive organs is fixed in natural populations, we have undertaken extensive and intensive fieldwork spanning several years to locate new populations in addition to the type locality. In parallel, we have also searched for natural variation in floral organ arrangement in Triuris brevistylis, a closely related dioecious triurid that is found in nearby areas of the Lacandon forest. We have found that a small proportion of L. schismatica inflorescences bear unisexual flowers of both sexes, as well as bisexual flowers with differences in the number of reproductive organs. However, in all bisexual flowers, the stamens were always central and the carpels peripheral to them. More important, we have also found that a few T. brevistylis individuals have bisexual flowers with altered positions of stamens and carpels. Among these, flowers with an inside‐out L. schismatica–like floral organ arrangement were observed. We document our findings with scanning electron micrographs, histological sections, and dissection microscope views. The information presented implies that the developmental‐genetic mechanism putatively responsible for homeotic/heterotopic transformations involving floral reproductive organs in the two triurid species originated at least before these taxa diverged from each other. The Mexican triurids may be an example in which the molecular evolutionary events causally related to a major morphological change in plants can best be understood at the microevolutionary scale.

Morphological “primary homology” and expression of AG -subfamily MADS-box genes in pines, podocarps, and yews

SUMMARY The morphological variation among reproductive organs of extant gymnosperms is remarkable, especially among conifers. Several hypotheses concerning morphological homology between various conifer reproductive organs have been put forward, in particular in relation to the pine ovuliferous scale. Here, we use the expression patterns of orthologs of the ABC‐model MADS‐box gene AGAMOUS (AG) for testing morphological homology hypotheses related to organs of the conifer female cone. To this end, we first developed a tailored 3′RACE procedure that allows reliable amplification of partial sequences highly similar to gymnosperm‐derived members of the AG‐subfamily of MADS‐box genes. Expression patterns of two novel conifer AG orthologs cloned with this procedure—namely PodAG and TgAG, obtained from the podocarp Podocarpus reichei and the yew Taxus globosa, respectively—are then further characterized in the morphologically divergent female cones of these species. The expression patterns of PodAG and TgAG are compared with those of DAL2, a previously discovered Picea abies (Pinaceae) AG ortholog. By treating the expression patterns of DAL2, PodAG, and TgAG as character states mapped onto currently accepted cladogram topologies, we suggest that the epimatium—that is, the podocarp female cone organ previously postulated as a “modified” ovuliferous scale—and the canonical Pinaceae ovuliferous scale can be legitimally conceptualized as “primary homologs.” Character state mapping for TgAG suggests in turn that the aril of Taxaceae should be considered as a different type of organ. This work demonstrates how the interaction between developmental‐genetic data and formal cladistic theory could fruitfully contribute to gymnosperm systematics.

AGAMOUS subfamily MADS-box genes and the evolution of seed cone morphology in Cupressaceae and Taxodiaceae

SUMMARY In this comparative developmental genetics study, we test hypotheses based on fossil and morphological data on reproductive organ morphology and evolution in conifers—specifically, the ovule‐bearing organ in Cupressaceae and Taxodiaceae. Genes homologous to the Arabidopsis gene AGAMOUS are expressed in ovuliferous scales of spruces (Picea) throughout development. Previous studies have shown that the AGAMOUS subfamily of MADS‐box genes predates the split between angiosperms and gymnosperms, and that these genes have in part conserved functions in reproductive development among seed plants, especially in the specification of identity of the ovule‐bearing organs. These data indicate that their expression in conifer families other than Pinaceae might be used as markers for organs homologous to the Pinaceae ovuliferous scale. Here we have isolated putative AGAMOUS orthologs from Cupressaceae and Taxodiaceae and analyzed their expression pattern in seed cones to test for the presence of morphological homologs of ovuliferous scales. Our results were not congruent with the hypothesis that the tooth of the Cryptomeria seed cone is homologous to the Picea ovuliferous scale. Likewise, the hypothesis that the bracts of Thujopsis and Juniperus contain fused ovuliferous scales was not supported. However, we found expression of AGAMOUS homologs in the sterile bracts of Cupressaceae seed cones at late developmental stages. This expression probably represents a novel gene function in these conifer families, since no corresponding expression has been identified in Pinaceae. Our study suggests that the evolutionary history of modern conifer cones is more diverse than previously thought.

Character-based, population-level DNA barcoding in Mexican species of Zamia L. (Zamiaceae: Cycadales)

Background and aims: With the recent proposal of matK and rbcL as core plant DNA barcoding regions by the Consortium for the Barcoding of Life Plant Working Group, the construction of reference libraries in the botanical DNA barcoding initiative has entered a new phase. However, in a recent DNA barcoding study in the three Mexican genera of the gymnosperm order Cycadales, we found that neither matK nor rbcL allow high levels of molecular identification of previously established species. Materials and methods: Our data analysis in that study rested on the “Characteristic Attributes Organization System” (CAOS), a character-based algorithm for the definition of “DNA diagnostics.” Here, we use CAOS to analyze a population-level molecular data set in Zamia, one of the three cycad genera occurring in Mexico, whose populations display contrasting biogeographic patterns. Our population-level study, which includes all species in the region formally known as Megamexico, is restricted to the genome region, which showed the best single-locus molecular identification performance in our previous study—namely, the noncoding intergenic chloroplast spacer psbK-I. Results: Our comparison of single-individual vs. population-level psbK-I datasets in Zamia indicates that CAOS analyses are sensitive to slight alignment changes, which in turn derive from the different amounts of molecular variation present in each matrix type. Conclusion: We, therefore, suggest that character-based studies that involve population-level data should contemplate this type of comparison between data matrices, before a set of DNA diagnostics in a given DNA barcoding reference library is considered definitive.