Early floral development and androecium organization in Fouquieriaceae (Ericales)

Early floral development with focus on the androecium was studied with the help of scanning electron microscopy and serial microtome sectioning in Fouquieria columnaris and F. splendens. Perianth organs appear in a spiral pattern on the floral apex. The spiral may be a clockwise or anti-clockwise. The androecium is best interpreted as two-whorled with all the stamens arranged in a single series. In F. splendens, two or more of the five epipetalous stamen positions are doubled, i.e. they are occupied by stamen pairs. Unusual features in the floral development of Fouquieriaceae include (1) a strong spiral component even in whorled organ categories and (2) a pronouncedly asymmetric floral apex during an early phase of floral development. From a phylogenetic point of view, it seems plausible that the common ancestor of Fouquieriaceae and its sister family Polemoniaceae was characterized by two alternating, pentamerous stamen-whorls.     

Phylogeny of the basal angiosperm genus Pseuduvaria (Annonaceae) inferred from five chloroplast DNA regions, with interpretation of morphological character evolution

Phylogenetic relationships within the magnoliid basal angiosperm genus Pseuduvaria (Annonaceae) are investigated using chloroplast DNA sequences from five regions: psbA-trnH spacer, trnL-F, matK, rbcL, and atpB-rbcL spacer. Over 4000 nucleotides from 51 species (of the total 53) were sequenced. The five cpDNA datasets were analyzed separately and in combination using maximum parsimony (MP), maximum likelihood (ML), and Bayesian methods. The phylogenetic trees constructed using all three phylogenetic methods, based on the combined data, strongly support the monophyly of Pseuduvaria following the inclusion of Craibella phuyensis. The trees generated using MP were less well resolved, but relationships are similar to those obtained using the other methods. ML and Bayesian analyses recovered trees with short branch lengths, showing five main clades. This study highlights the evolutionary changes in seven selected morphological characters (floral sex, stamen and carpel numbers, inner petal color, presence of inner petal glands, flowering peduncle length, and monocarp size). Although floral unisexuality is ancestral within the genus, several evolutionary lineages reveal reversal to bisexuality. Other phylogenetic transitions include the evolution of sapromyophily, and fruit-bat frugivory and seed dispersal, thus allowing a wide range of adaptations for species survival.     

Mycorrhizal characterization of the boojum tree, <Emphasis Type="Italic">Fouquieria columnaris</Emphasis>, an endemic ancient tree from the Baja California Peninsula,Mexico

The mycorrhizal association with the boojum tree, Fouquieria columnaris (=Idria columnaris), was studied. This unusual tree is almost exclusively endemic to granite and volcanic soils in highly arid areas of the Baja California Peninsula of Mexico. Soil and root samples from ten sites, covering the extent of geographic distribution of the tree on the peninsula, were analyzed. The roots of the boojum tree contained all structures of an arbuscular mycorrhizal (AM) association. Morphologically different species, 23 in number, were identified in close vicinity to the boojum tree indicating that F. columnaris is associated with a high number of AM species of several AM genera and families.     

GeneTRACE-reconstruction of gene content of ancestral species

While current computational methods allow the reconstruction of individual ancestral protein sequences, reconstruction of complete gene content of ancestral species is not yet an established task. In this paper, we describe GENETRACE, an efficient linear-time algorithm that allows the reconstruction of evolutionary history of individual protein families as well as the complete gene content of ancestral species. The performance of the method was validated with a simulated evolution program called SimulEv. Our results indicate that given a set of correct phylogenetic profiles and a correct species tree, ancestral gene content can be reconstructed with sensitivity and selectivity of more than 90%. SimulEv simulations were also used to evaluate performance of the reconstruction of gene content-based phylogenetic trees, suggesting that these trees may be accurate at the terminal branches but suffer from long branch attraction near the root of the tree.     

A MOLECULAR PHYLOGENY OF THE HETEROKONT ALGAE BASED ON ANALYSES OF CHLOROPLAST-ENCODED rbcL SEQUENCE DATA1

Nearly complete ribulose-1,5-bisphosphate carboxylase/ oxygenase (rbcL)sequences from 27 taxa of heterokont algae were determined and combined with rbcL sequences obtained from GenBank for four other heterokont algae and three red algae. The phylogeny of the morphologically diverse haterokont algae was inferred from an unambiguously aligned data matrix using the red algae as the root, Significantly higher levels of mutational saturation in third codon positions were found when plotting the pair-wise substitutions with and without corrections for multiple substitutions at the same site for first and second codon positions only and for third positions only. In light of this observation, third codon positions were excluded from phylogenetic analyses. Both weighted-parsimony and maximum-likelihood analyses supported with high bootstrap values the monophyly of the nine currently recognized classes of heterokont algae. The Eustigmatophyceae were the most basal group, and the Dictyochophyceae branched off as the second most basal group. The branching pattern for the other classes was well supported in terms of bootstrap values in the weightedparsimony analysis but was weakly supported in the maximum-likelihood analysis (<50%). In the parsimony analysis, the diatoms formed a sister group to the branch containing the Chrysophyceae and Synurophyceae. This clade, charactetized by siliceous structures (frustules, cysts, scales), was the sister group to the Pelagophyceae/Sarcinochrysidales and Phaeo-/Xantho-/ Raphidophyceae clades. In the latter clade, the raphido-phytes were sister to the Phaeophyceae and Xanthophyceae. A relative rate test revealed that the rbcL gene in the Chrysophyceae and Synurophyceae has experienced a significantly different rate of substitutions compared to other classes of heterokont algae. The branch lengths in the maximum-likelihood reconstruction suggest that these two classes have evolved at an accelerated rate. Six major carotenoids were analyzed cladistically to study the usefulness of carotenoid pigmentation as a class-level character in the heterokont algae. In addition, each carotenoid was mapped onto both the rbcL tree and a consensus tree derived from nuclear-encoded small-subunit ribosomal DNA (SSU rDNA) sequences. Carotenoid pigmentation does not provide unambiguous phylogenetic information, whether analyzed cladistically by itself or when mapped onto phylogenetic trees based upon molecular sequence data.     

Early evolutionary relationships among known life forms inferred from elongation factor EF-2/EF-G sequences: Phylogenetic coherence and structure of the archaeal domain

Summary Phylogenies were inferred from both the gene and the protein sequences of the translational elongation factor termed EF-2 (for Archaea and Eukarya) and EF-G (for Bacteria). All treeing methods used (distance-matrix, maximum likelihood, and parsimony), including evolutionary parsimony, support the archaeal tree and disprove the eocyte tree (i.e., the polyphyly and paraphyly of the Archaea). Distance-matrix trees derived from both the amino acid and the DNA sequence alignments (first and second codon positions) showed the Archaea to be a monophyletia-holophyletic grouping whose deepest bifurcation divides a Sulfolobus branch from a branch comprising Methanococcus, Halobacterium, and Thermoplasma. Bootstrapped distance-matrix treeing confirmed the monophyly-holophyly of Archaea in 100% of the samples and supported the bifurcation of Archaea into a Sulfolobus branch and a methanogen-halophile branch in 97% of the samples. Similar phylogenies were inferred by maximum likelihood and by maximum (protein and DNA) parsimony. DNA parsimony trees essentially identical to those inferred from first and second codon positions were derived from alternative DNA data sets comprising either the first or the second position of each codon. Bootstrapped DNA parsimony supported the monophyly-holophyly of Archaea in 100% of the bootstrap samples and confirmed the division of Archaea into a Sulfolobus branch and a methanogen-halophile branch in 93% of the bootstrap samples. Distance-matrix and maximum likelihood treeing under the constraint that branch lengths must be consistent with a molecular clock placed the root of the universal tree between the Bacteria and the bifurcation of Archaea and Eukarya. The results support the division of Archaea into the kingdoms Crenarchaeota (corresponding to the Sulfolobus branch and Euryarchaeota). This division was not confirmed by evolutionary parsimony, which identified Halobacterium rather than Sulfolobus as the deepest offspring within the Archaea.Offprint requests to: P. Cammarano     

树木不同着生位置1级根的形态、解剖结构和氮含量

树木根系中1级根在养分和水分吸收方面发挥着重要作用。研究1级根的形态结构与功能的联系,对了解1级根的生理功能和寿命,以及森林生态系统碳和养分的循环具有重要的理论意义。但是,1级根在根系统中,因着生的位置不同,可能表现出不同的生理生态功能。该研究以胡桃楸(Juglans mandshurica)、黄波罗(Phellodendron amurense)和水曲柳(Fraxinus mandshurica)人工林根系的1级根为研究对象,研究了不同着生位置的1级根的形态、解剖结构和组织化学特征。将1级根按着生位置的不同分成3类:Ar类根为2级根上的1级根;Br类根为2级–4级根的根尖;Cr类根为3级–5级根上的1级根。结果表明:不同着生位置的1级根,形态、解剖结构和组织化学方面都具有高度的异质性。3类1级根中,Ar类根数量多、根长较短、直径细,N含量高,皮层比例高、维根比低,主要由二原型原生木质部的根组成;Br类和Cr类根数量较少、单根较长、直径粗,N含量低,皮层比例低、维根比高,主要由多原型原生木质部的根组成。研究结果对了解不同着生位置的1级根的吸收功能和寿命具有重要的理论意义。     

Maximum parsimony on subsets of taxa

In this paper we investigate mathematical questions concerning the reliability (reconstruction accuracy) of Fitch's maximum parsimony algorithm for reconstructing the ancestral state given a phylogenetic tree and a character. In particular, we consider the question whether the maximum parsimony method applied to a subset of taxa can reconstruct the ancestral state of the root more accurately than when applied to all taxa, and we give an example showing that this indeed is possible. A surprising feature of our example is that ignoring a taxon closer to the root improves the reliability of the method. On the other hand, in the case of the two-state symmetric substitution model, we answer affirmatively a conjecture of Li, Steel and Zhang which states that under a molecular clock the probability that the state at a single taxon is a correct guess of the ancestral state is a lower bound on the reconstruction accuracy of Fitch's method applied to all taxa.     

Evolutionary transitions of style polymorphisms in Lithodora (Boraginaceae)

Floral polymorphisms provide suitable model systems to test hypotheses concerning the evolution of outbreeding in plants. Although heterostyly has evolved in more than 28 angiosperm families, the evolutionary pathways involving related floral conditions have not yet been fully resolved. In this study, the reconstruction of ancestral states of style polymorphism, with both parsimony and maximum likelihood methods, was carried out for Boraginaceae species in the tribe Lithospermeae, particularly in the genus Lithodora sensu lato, where species present a wide variety of stylar conditions. Detailed floral morphometric analysis confirm different types of style polymorphism within Lithodora. They also reveal a novel style polymorphism (relaxed style dimorphism) in which anther height is variable within a flower (each anther being at a different height), which contrasts to regular distyly (constant anther height within flowers). Style monomorphism is likely to be the ancestral condition in Lithospermeae where the evolution of distyly has occurred several times. Style dimorphism is probably ancestral to distyly, as predicted by certain evolutionary models proposed for heterostyly. However, a reversion from distyly to style dimorphism also appears to occur in this tribe. This is the first documented occurrence of such a transition. This secondary style dimorphism is of the relaxed type and demonstrates the labile nature of floral polymorphisms, which are not necessarily a transition towards heterostyly. We discuss the selective forces involved in the evolution, maintainance and loss of style polymorphisms.     

Time-Dependent-Asymmetric-Linear-Parsimonious Ancestral State Reconstruction

The time-dependent-asymmetric-linear parsimony is an ancestral state reconstruction method which extends the standard linear parsimony (a.k.a. Wagner parsimony) approach by taking into account both branch lengths and asymmetric evolutionary costs for reconstructing quantitative characters (asymmetric costs amount to assuming an evolutionary trend toward the direction with the lowest cost). A formal study of the influence of the asymmetry parameter shows that the time-dependent-asymmetric-linear parsimony infers states which are all taken among the known states, except for some degenerate cases corresponding to special values of the asymmetry parameter. This remarkable property holds in particular for the Wagner parsimony. This study leads to a polynomial algorithm which determines, and provides a compact representation of, the parametric reconstruction of a phylogenetic tree, that is for all the unknown nodes, the set of all the possible reconstructed states associated with the asymmetry parameters leading to them. The time-dependent-asymmetric-linear parsimony is finally illustrated with the parametric reconstruction of the body size of cetaceans.     

Patterns of host-plant choice in bees of the genus Chelostoma: the constraint hypothesis of host-range evolution in bees

To trace the evolution of host-plant choice in bees of the genus Chelostoma (Megachilidae), we assessed the host plants of 35 Palearctic, North American and Indomalayan species by microscopically analyzing the pollen loads of 634 females and reconstructed their phylogenetic history based on four genes and a morphological dataset, applying both parsimony and Bayesian methods. All species except two were found to be strict pollen specialists at the level of plant family or genus. These oligolectic species together exploit the flowers of eight different plant orders that are distributed among all major angiosperm lineages. Based on ancestral state reconstruction, we found that oligolecty is the ancestral state in Chelostoma and that the two pollen generalists evolved from oligolectic ancestors. The distinct pattern of host broadening in these two polylectic species, the highly conserved floral specializations within the different clades, the exploitation of unrelated hosts with a striking floral similarity as well as a recent report on larval performance on nonhost pollen in two Chelostoma species clearly suggest that floral host choice is physiologically or neurologically constrained in bees of the genus Chelostoma. Based on this finding, we propose a new hypothesis on the evolution of host range in bees.     

Ancestral sequence reconstruction in primate mitochondrial DNA: compositional bias and effect on functional inference

Reconstruction of ancestral DNA and amino acid sequences is an important means of inferring information about past evolutionary events. Such reconstructions suggest changes in molecular function and evolutionary processes over the course of evolution and are used to infer adaptation and convergence. Maximum likelihood (ML) is generally thought to provide relatively accurate reconstructed sequences compared to parsimony, but both methods lead to the inference of multiple directional changes in nucleotide frequencies in primate mitochondrial DNA (mtDNA). To better understand this surprising result, as well as to better understand how parsimony and ML differ, we constructed a series of computationally simple "conditional pathway" methods that differed in the number of substitutions allowed per site along each branch, and we also evaluated the entire Bayesian posterior frequency distribution of reconstructed ancestral states. We analyzed primate mitochondrial cytochrome b (Cyt-b) and cytochrome oxidase subunit I (COI) genes and found that ML reconstructs ancestral frequencies that are often more different from tip sequences than are parsimony reconstructions. In contrast, frequency reconstructions based on the posterior ensemble more closely resemble extant nucleotide frequencies. Simulations indicate that these differences in ancestral sequence inference are probably due to deterministic bias caused by high uncertainty in the optimization-based ancestral reconstruction methods (parsimony, ML, Bayesian maximum a posteriori). In contrast, ancestral nucleotide frequencies based on an average of the Bayesian set of credible ancestral sequences are much less biased. The methods involving simpler conditional pathway calculations have slightly reduced likelihood values compared to full likelihood calculations, but they can provide fairly unbiased nucleotide reconstructions and may be useful in more complex phylogenetic analyses than considered here due to their speed and flexibility. To determine whether biased reconstructions using optimization methods might affect inferences of functional properties, ancestral primate mitochondrial tRNA sequences were inferred and helix-forming propensities for conserved pairs were evaluated in silico. For ambiguously reconstructed nucleotides at sites with high base composition variability, ancestral tRNA sequences from Bayesian analyses were more compatible with canonical base pairing than were those inferred by other methods. Thus, nucleotide bias in reconstructed sequences apparently can lead to serious bias and inaccuracies in functional predictions.     

Vegetation formations and associations of the zonobiomes along the North American Pacific coast

This phytosociological study, carried out according to the Braun-Blanquet method and supported by cluster analysis, describes Walter's zonobiomes along the North American Pacific coast between British Columbia (Canada) and Baja California Sur (Mexico). Fourteen floristic associations have been identified and each is characterized by a unique floristic combination, a distinctive geographical range and particular bioclimatic conditions.Abbreviations of the associations that appear in table and figures AE Fraxino trifoliatae-Aesculetum parryi - AM Ambrosio chenopodifoliae-Larreetum tridentatae - BE Bergerocacto emoryi-Agavetum shawii - CA Calystegio intermediae-Ceanothetum megacarpi - CE Cercidio praecocis-Prosopidetum palmeri - CY Antigono leptopi-Cyrtocarpetum edulis - DU Malosmo laurinae-Quercetum dumosae - ID Agavo cerulatae-Idrietum columnaris - LO Lonicero denudatae-Quercetum agrifoliae - OX Oxalido oreganae-Sequoietum sempervirentis - RO Roso minutifoliae-Aesculetum parryi - TH Thujo plicatae-Tsugetum heterophyllae - UM Umbellulario californicae-Quercetum agrifoliae - YU Yucco validae-Fouquierietum diguetii     

A method for molecular phylogeny construction by direct use of nucleotide sequence data

Summary A method for molecular phylogeny construction is newly developed. The method, called the stepwise ancestral sequence method, estimates molecular phylogenetic trees and ancestral sequences simultaneously on the basis of parsimony and sequence homology. For simplicity the emphasis is placed more on parsiomony than on sequence homology in the present study, though both are certainly important. Because parsimony alone will sometimes generate plural candidate trees, the method retains not one but five candidates from which one can then single out the final tree taking other criteria into account.The properties and performance of the method are then examined by simulating an evolving gene along a model phylogenetic tree. The estimated trees are found to lie in a narrow range of the parsimony criteria used in the present study. Thus, other criteria such as biological evidence and likelihood are necessary to single out the correct tree among them, with biological evidence taking precedence over any other criterion. The computer simulation also reveals that the method satisfactorily estimates both tree topology and ancestral sequences, at least for the evolutionary model used in the present study.     

Mapping uncertainty and phylogenetic uncertainty in ancestral character state reconstruction: an example in the moss genus Brachytheciastrum

The evolution of species traits along a phylogeny can be examined through an increasing number of possible, but not necessarily complementary, approaches. In this paper, we assess whether deriving ancestral states of discrete morphological characters from a model whose parameters are (i) optimized by ML on a most likely tree; (II) optimized by ML onto each of a Bayesian sample of trees; and (III) sampled by a MCMC visiting the space of a Bayesian sample of trees affects the reconstruction of ancestral states in the moss genus Brachytheciastrum. In the first two methods, the choice of a single- or two-rate model and of a genetic distance (wherein branch lengths are used to determine the probabilities of change) or speciational (wherein changes are only driven by speciation events) model based upon a likelihood-ratio test strongly depended on the sampled trees. Despite these differences in model selection, reconstructions of ancestral character states were strongly correlated to each others across nodes, often at r > 0.9, for all the characters. The Bayesian approach of ancestral character state reconstruction offers, however, a series of advantages over the single-tree approach or the ML model optimization on a Bayesian sample of trees because it does not involve restricting model parameters prior to reconstructing ancestral states, but rather allows a range of model parameters and ancestral character states to be sampled according to their posterior probabilities. From the distribution of the latter, conclusions on trait evolution can be made in a more satisfactorily way than when a substantial part of the uncertainty of the results is obscured by the focus on a single set of model parameters and associated ancestral states. The reconstructions of ancestral character states in Brachytheciastrum reveal rampant parallel morphological evolution. Most species previously described based on phenetic grounds are thus resolved of polyphyletic origin. Species polyphylly has been increasingly reported among mosses, raising severe reservations regarding current species definition.     

Branch length mediates flower production and inflorescence architecture of Fouquieria splendens (ocotillo)

The capacity of individual branches to store water and fix carbon can have profound effects on inflorescence size and architecture, thus on floral display, pollination, and fecundity. Mixed regression was used to investigate the relation between branch length, a proxy for plant resources, and floral display of Fouquieria splendens (ocotillo), a woody, candelabraform shrub of wide distribution in arid North America. Long branches produced three times as many flowers as short branches, regardless of overall plant size. Long branches also had more complex panicles with more cymes and cyme types than short branches; thus, branch length also influenced inflorescence architecture. Within panicles, increasing the number of cymes by one unit added about two flowers, whereas increasing the number of cyme types by one unit added about 21 flowers. Because flower production is mediated by branch length, and because most plants have branches of various lengths, the floral display of individual plants necessarily encompasses a wide range of inflorescence size and structure.     

Bayesian analysis of Douglas-fir hydraulic architecture at multiple scales

We used a Bayesian hierarchical model to analyze the variation in xylem anatomy, hydraulic properties, and the relationship between anatomy and properties within Douglas-fir trees. The hierarchical scales in our study included fertilization treatments (fertilized and unfertilized), trees within the treatments, and positions within the trees. We measured tracheid diameter, tracheid length, percent latewood, number of pits per cell, density, and specific conductivity (K _s) on seven positions in each of 16 fertilized and 16 unfertilized trees: the trunk at cambial age 52 (breast height), 25, and 5; a branch at cambial age 20 and 7; and a root at cambial age 42 and 22. Vulnerability to embolism was also measured on the oldest trunk, branch, and root positions. For any measurement, there was little variation between treatments, however, there was great variation among positions. Tracheid diameter, tracheid length, number of pits per cell, K _s, and vulnerability to embolism decreased vertically from the roots to the branches. Correlations were evident between some positions for tracheid diameter, percent earlywood, pits per cell, and vulnerability to embolism, mostly in the fertilized treatment. We found evidence for large-scale relationships (among all observations from all trees) between density and tracheid diameter, K _s and diameter, vulnerability and diameter, K _s and pits per cell, and vulnerability and pits per cell. At a smaller scale of within position, however, usually only the branches and roots maintained the relationship.     

Evaluation of phylogenetic relationships between five polyploid Aegilops L. species of the U-genome cluster by means of chromosomal analysis

Four tetraploid (Aegilops ovata, Ae. biuncialis, Ae. columnaris, and Ae. triaristata) and one hexaploid (Ae. recta) species of the U-genome cluster were studied using C-banding technique. All species displayed broad C-banding polymorphism and high frequency of chromosomal rearrangements. Chromosomal rearrangements were represented by paracentric inversions and intragenomic and intergenomic translocations. We found that the processes of intraspecific divergence of Ae. ovata, Ae. biuncialis, and Ae. columnaris were probably associated with introgression of genetic material from other species. The results obtained confirmed that tetraploid species Ae. ovata and Ae. biuncialis occurred as a result of hybridization of a diploid Ae. umbellulata with Ae. comosa and Ae. heldreichii, respectively. The dissimilarity of the C-banding patterns of several chromosomes of these tetraploid species and their ancestral diploid forms indicated that chromosomal aberrations might have taken place during their speciation. Significant differences of karyotype structure, total amount and distribution of C-heterochromatin found between Ae. columnaris and Ae. triaristata, on the one hand, and Ae. ovata and Ae. biuncialis, on the other, evidenced in favor of different origin of these groups of species. In turn, similarity of the C-banding patterns of Ae. columnaris and Ae. triaristata chromosomes suggested that they were derived from a common ancestor. A diploid species Ae. umbellulata was the U-genome donor of Ae. columnaris and Ae. triaristata; however, the donor of the second genome of these species was not determined. We assumed that these tetraploid species occurred as a result of introgressive hybridization. Similarity of the C-banding patterns of chromosomes of Ae. recta and its parental species Ae. triaristata and Ae. uniaristata indicated that the formation of the hexaploid form was not associated with large modifications of the parental genomes.     

Anthocyanins of the Fouquieriaceae

Species of the Fouquieriaceae cluster into four groups on the basis of floral anthocyanin content. The four clusters agree with species groupings based on morphological characters. Floral anthocyanins support a close relationship between the Fouquieriaceae and the Solanales.     

Approximate Maximum Parsimony and Ancestral Maximum Likelihood

We explore the maximum parsimony (MP) and ancestral maximum likelihood (AML) criteria in phylogenetic tree reconstruction. Both problems are NP-hard, so we seek approximate solutions. We formulate the two problems as Steiner tree problems under appropriate distances. The gist of our approach is the succinct characterization of Steiner trees for a small number of leaves for the two distances. This enables the use of known Steiner tree approximation algorithms. The approach leads to a 16/9 approximation ratio for AML and asymptotically to a 1.55 approximation ratio for MP.