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David A Baum

Publications and source records attributed to David A Baum.

13 recordsLinked to original sources
PubMed2007

Floral gigantism in Rafflesiaceae.

Species of Rafflesiaceae possess the world's largest flowers (up to 1 meter in diameter), yet their precise evolutionary relationships have been elusive, hindering our understanding of the evolution of their extraordinary reproductive morphology. We present results of phylogenetic analyses of mitochondrial, nuclear, and plastid data showing that Rafflesiaceae are derived from within Euphorbiaceae, the spurge family. Most euphorbs produce minute flowers, suggesting that the enormous flowers of Rafflesiaceae evolved from ancestors with tiny flowers. Given the inferred phylogeny, we estimate that there was a circa 79-fold increase in flower diameter on the stem lineage of Rafflesiaceae, making this one of the most dramatic cases of size evolution reported for eukaryotes.

Bayes Theorem↗
PubMed2006

Bayesian estimation of concordance among gene trees.

Multigene sequence data have great potential for elucidating important and interesting evolutionary processes, but statistical methods for extracting information from such data remain limited. Although various biological processes may cause different genes to have different genealogical histories (and hence different tree topologies), we also may expect that the number of distinct topologies among a set of genes is relatively small compared with the number of possible topologies. Therefore evidence about the tree topology for one gene should influence our inferences of the tree topology on a different gene, but to what extent? In this paper, we present a new approach for modeling and estimating concordance among a set of gene trees given aligned molecular sequence data. Our approach introduces a one-parameter probability distribution to describe the prior distribution of concordance among gene trees. We describe a novel 2-stage Markov chain Monte Carlo (MCMC) method that first obtains independent Bayesian posterior probability distributions for individual genes using standard methods. These posterior distributions are then used as input for a second MCMC procedure that estimates a posterior distribution of gene-to-tree maps (GTMs). The posterior distribution of GTMs can then be summarized to provide revised posterior probability distributions for each gene (taking account of concordance) and to allow estimation of the proportion of the sampled genes for which any given clade is true (the sample-wide concordance factor). Further, under the assumption that the sampled genes are drawn randomly from a genome of known size, we show how one can obtain an estimate, with credibility intervals, on the proportion of the entire genome for which a clade is true (the genome-wide concordance factor). We demonstrate the method on a set of 106 genes from 8 yeast species.

Algorithms↗
PubMed2005

Molecular evolution of the transcription factor LEAFY in Brassicaceae.

LEAFY (LFY) is a DNA-binding transcription factor that regulates floral meristem identity. LFY is unusual among angiosperm developmental regulators because it is not part of an extended gene family. Recent expression studies and transgenic experiments have suggested that changes at the LFY locus might have played a role in the evolution of rosette flowering, a modified plant architecture that has evolved at least three times in Brassicaceae. Here we examined the sequences of LFY genes from 16 species of Brassicaceae to evaluate whether gene duplication and/or the shift to rosette flowering correlate with changes in the molecular evolution of LFY. We found evidence of gene duplication in four taxa, but phylogenetic analysis suggested that duplicate genes have generally not persisted through multiple speciation events. This result can be explained if LFY is prone to be lost by drift due to a low probability of subfunctionalization or neofunctionalization. Despite great heterogeneity in dN/dS ratios, duplicate genes show a significant tendency to have elevated dN/dS ratios. Rosette-flowering lineages also show elevated dN/dS ratios and two of the rosette-flowering taxa, Idahoa and Leavenworthia, have some radical amino acid substitutions that are candidates for having played a causal role in the evolution of rosette flowering.

Arabidopsis Proteins↗
PubMed2005

Floral MADS box genes and homeotic gender dimorphism in Thalictrum dioicum (Ranunculaceae) - a new model for the study of dioecy.

In most dioecious angiosperm species, flowers are initially perfect but abort either stamens or carpels during their development, indicating that sex determination occurs after floral organ identity has been established. Dioecious members of the genus Thalictrum (meadow-rue), however, produce flowers that lack aborted organs. Examination of early flower development of T. dioicum confirms that flowers are male or female from inception, raising the possibility that genetic mechanisms working at or above the level of organ identity promote sex determination through a homeotic-like mechanism. In order to investigate this possibility, we identified homologs of the organ identity genes PISTILLATA (PI), APETALA3 (AP3) and AGAMOUS (AG) from T. dioicum and the hermaphroditic species T. thalictroides. A combination of early and late duplication events was uncovered in these gene lineages and expression analyses indicate that these events are generally associated with divergence in gene regulation. In light of these findings, we discuss the potential of T. dioicum as a new model for the study of sex determination in the basal eudicots.

Amino Acid Sequence↗
PubMed2005

Genealogical evidence of homoploid hybrid speciation in an adaptive radiation of Scaevola (goodeniaceae) in the Hawaiian Islands.

Although homoploid hybrid speciation is increasingly recognized as an important phenomenon in plant evolution, its role in adaptive radiations is poorly documented. We studied a clade of seven extant species of Scaevola that are endemic to the Hawaiian Islands and show substantial ecological and morphological diversity. We estimated the genealogies for alleles isolated from multiple accessions of each species at four nuclear loci: the ITS region, and the introns of three nuclear genes, LEAFY (LFY), NITRATE REDUCTASE (NIA), and GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE (G3PDH). For five of the seven species, there was complete concordance among the genealogies estimated from the four loci and, when all four regions were combined, the relationships among these five species were fully resolved. Inclusion of alleles from the remaining two species, S. procera and S. kilaueae, resulted in incongruence among loci, which appears to reflect a history of hybridization. Based on the distribution of alleles, we infer that S. procera is the result of a homoploid hybrid speciation event between S. gaudichaudii and S. mollis and that S. kilaueae is probably the result of hybrid speciation between S. coriacea and S. chamissoniana. In each case the inferred hybridization is consistent with morphological, ecological, and geographic information. We conclude that homoploid hybrid speciation may be more common than is perceived and may play a role in generating novel combinations of adaptive traits that arise during island radiations.

Adaptation, Physiological↗
PubMed2004

Transgenic study of parallelism in plant morphological evolution.

Developmental constraint is indicated when one finds that similar genetic mechanisms are responsible for independent origins of the same derived phenotype. We studied three independent origins of rosette flowering within the mustard family and attempted to evaluate the extent to which the same mechanisms were involved in each transition from the ancestral phenotype, inflorescence flowering. We used transformation to move a candidate gene, LFY, and its cis-regulatory sequences from rosette-flowering species into an inflorescence-flowering recipient, Arabidopsis thaliana, in place of its endogenous LFY gene. The transgenic phenotypes of experimental and control lines (containing an A. thaliana LFY transgene) and the expression driven by the cis-regulatory sequences show that changes at the LFY locus might have contributed to the evolution of rosette flowering in two of the three lineages. In the third case, changes upstream of LFY are implicated. Our data suggest that changes in a single developmental regulatory program were involved in multiple origins of the same derived trait but that the specific genetic changes were different in each case.

Arabidopsis Proteins↗
PubMed2004

Evolution of GCYC, a Gesneriaceae homolog of CYCLOIDEA, within Gesnerioideae (Gesneriaceae).

Through recent advances in molecular developmental biology it has become clear that similar morphological traits may sometimes arise from different genetic bases. The molecular developmental biology of floral symmetry has been examined recently in detail and several genes important in controlling floral symmetry in diverse Asteridae have been identified. One of the most important among these is the floral symmetry gene CYCLOIDEA (CYC). We compared GCYC (the Gesneriaceae homolog of CYC) sequences in Gesneriaceae genera with the typical bilaterally symmetric flowers and genera with radial or near radial symmetry. Parsimony, Bayesian and maximum likelihood analyses of GCYC sequences among members of Gesnerioideae are mostly congruent with previous phylogenetic hypotheses, but suggest two unexpected generic positions: Diastema as sister to Gesneria, and Bellonia within Gloxinieae. In order to evaluate whether these results might be artifactual we obtained new gene sequences from chloroplast and nuclear ribosomal regions. These data disagree with GCYC regarding the placement of Diastema, but agree with GCYC regarding Bellonia. We did not find any mutations in GCYC that could explain the shift in symmetry and there were no consistent differences in molecular evolution between taxa with bilaterally or radially symmetric flowers. Likewise taxa with radial floral symmetry are not sister to each other showing that the loss of bilateral symmetry has occurred multiple times in parallel. Further investigations of GCYC expression will be necessary to determine if any of these independent events involved changes in the regulation of GCYC.

Asteraceae↗
PubMed2004

Cryptic bracts exposed: insights into the regulation of leaf expansion.

Arabidopsis is unusual in producing flowers that are not subtended by specialized leaves, called floral bracts. Writing in Development, Dinneny et al. and Ohno et al. show that gain-of-function mutations of the JAGGED transcription factor produce bracts, and provide evidence that this gene plays a key role in a developmental program that regulates the size and shape of all leaves and leaf-homologs.

Arabidopsis↗
PubMed2003

Differential regulation of symmetry genes and the evolution of floral morphologies.

Shifts in flower symmetry have occurred frequently during the diversification of angiosperms, and it is thought that such shifts play important roles in plant-pollinator interactions. In the model developmental system Antirrhinum majus (snapdragon), the closely related genes CYCLOIDEA (CYC) and DICHOTOMA (DICH) are needed for the development of zygomorphic flowers and the determination of adaxial (dorsal) identity of floral organs, including adaxial stamen abortion and asymmetry of adaxial petals. However, it is not known whether these genes played a role in the divergence of species differing in flower morphology and pollination mode. We compared A. majus with a close relative, Mohavea confertiflora (desert ghost flower), which differs from Antirrhinum in corolla (petal) symmetry and pollination mode. In addition, Mohavea has undergone a homeotic-like transformation in stamen number relative to Antirrhinum, aborting the lateral and adaxial stamens during flower development. Here we show that the patterns of expression of CYC and DICH orthologs have shifted in concert with changes in floral morphology. Specifically, lateral stamen abortion in Mohavea is correlated with an expansion of CYC and DICH expression, and internal symmetry of Mohavea adaxial petals is correlated with a reduction in DICH expression during petal differentiation. We propose that changes in the pattern of CYC and DICH expression have contributed to the derived flower morphology of Mohavea and may reflect adaptations to a pollination strategy resulting from a mimetic relationship, linking the genetic basis for morphological evolution to the ecological context in which the morphology arose.

Antirrhinum↗
PubMed2003

Why do paralogs persist? Molecular evolution of CYCLOIDEA and related floral symmetry genes in Antirrhineae (Veronicaceae).

CYCLOIDEA (CYC) and DICHOTOMA (DICH) are paralogous genes that determine adaxial (dorsal) flower identity in the bilaterally symmetric flowers of Antirrhinum majus (snapdragon). We show here that the duplication leading to the existence of both CYC and DICH in Antirrhinum occurred before the radiation of the Antirrhineae (the tribe to which snapdragon belongs). We find no additional gene duplications within Antirrhineae. Using explicit codon-based models of evolution in a likelihood framework, we show that patterns of molecular evolution after the duplication that gave rise to CYC and DICH are consistent with purifying selection acting at both loci, despite their known functional redundancy in snapdragon. However, for specific gene regions, purifying selection is significantly relaxed across DICH lineages, relative to CYC lineages. In addition, we find evidence for relaxed purifying selection along the lineage leading to snapdragon in one of two putative functional domains of DICH. A model of selection accounting for the persistence of paralogous genes in the absence of diversifying selection is presented. This model takes into account differences in the degree of purifying selection acting at the two loci and is consistent with subfunctionalization models of paralogous gene evolution.

Antirrhinum↗
PubMed2002

Early Tertiary out-of-India dispersal of Crypteroniaceae: evidence from phylogeny and molecular dating.

Phylogenetic analyses and molecular dating estimates based on chloroplast DNA sequences were used to establish the relationships of the southern and Southeast Asian Crypteroniaceae and elucidate their biogeographic history. Maximum parsimony and likelihood analyses of rbcL sequences suggested that Crypteroniaceae should be restricted to Crypteronia, Axinandra, and Dactylocladus and that Crypteroniaceae, so defined, are sister to a clade formed by three small African taxa (Oliniaceae, Penaeaceae, and Rhynchocalycaceae) and the monotypic Central and South American Alzateaceae. Three molecular dating approaches (maximum-likelihood under a molecular clock, Langley-Fitch, and penalized-likelihood) were used to infer the age of Crypteroniaceae using both paleobotanic and geologic calibrations. Comparisons among these three methods revealed significant lineage effects in rbcL sequences. Clock-independent dating estimates suggested that divergence of Crypteroniaceae from its African and South American relatives coincided with the breakup of Gondwana, and that India likely served as a "raft" transporting Crypteroniaceae to Asia, with later expansion to Southeast Asia. To our knowledge, Crypteroniaceae are the first plant group for which the out-of-India hypothesis is well corroborated by molecular-based estimates of divergence times.

Biological Evolution↗