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Michael J Donoghue

Publications and source records attributed to Michael J Donoghue.

16 recordsLinked to original sources
PubMed2006

Phylogenetic analysis of the "ECE" (CYC/TB1) clade reveals duplications predating the core eudicots.

Flower symmetry is of special interest in understanding angiosperm evolution and ecology. Evidence from the Antirrhineae (snapdragon and relatives) indicates that several TCP gene-family transcription factors, especially CYCLOIDEA (CYC) and DICHOTOMA (DICH), play a role in specifying dorsal identity in the corolla and androecium of monosymmetric (bilateral) flowers. Studies of rosid and asterid angiosperms suggest that orthologous TCP genes may be important in dorsal identity, but there has been no broad phylogenetic context to determine copy number or orthology. Here, we compare published data from rosids and asterids with newly collected data from ranunculids, caryophyllids, Saxifragales, and Asterales to ascertain the phylogenetic placement of major duplications in the "ECE" (CYC/TB1) clade of TCP transcription factors. Bayesian analyses indicate that there are three major copies of "CYC" in the ECE clade, and that duplications leading to these copies predate the core eudicots. CYC1 contains no subsequent duplications and may not be expressed in floral tissue. CYC3 exhibits similar patterns of duplication to CYC2 in several groups. Using RT-PCR, we show that, in flowers of Lonicera morrowii (Caprifoliaceae), DipsCYC2B is expressed in the four dorsal petals and not in the ventral petal. DipsCYC3B is expressed in flower and petal primordia, possibly most strongly in the ventral petal.

Antirrhinum↗
PubMed2006

Pereskia and the origin of the cactus life-form.

The cactus life-form is cited as an example of a tight relationship between organism form and function: a succulent, long-lived, photosynthetic stem allows cacti to survive long periods of drought while maintaining a positive tissue water status. Pereskia (Cactaceae) comprises 17 species of leafy shrubs and trees that are thought to represent the original cactus condition. Recent phylogenetic work has shown that there are two separate clades of Pereskia species, which are basal and paraphyletic with respect to the rest of the cacti. We selected seven Pereskia species, representing both clades, and characterized their water relations by measuring a suite of physiological traits in wild populations. Additionally, we estimated basic climate parameters from collection localities for all 17 Pereskia species. Extant Pereskia species exhibit ecological water use patterns that are very similar to those of the leafless, stem-succulent cacti. Ancestral trait reconstruction for the physiological and environmental data provides a preliminary assessment of the ecology and water relations of the earliest cacti and suggests that several key elements of the cactus ecological niche were established before the evolution of the cactus life-form. We interpret these ecological traits as potentially important drivers of evolutionary innovation in the cacti.

Biological Evolution↗
PubMed2006

Increasing data transparency and estimating phylogenetic uncertainty in supertrees: Approaches using nonparametric bootstrapping.

The estimation of ever larger phylogenies requires consideration of alternative inference strategies, including divide-and-conquer approaches that decompose the global inference problem to a set of smaller, more manageable component problems. A prominent locus of research in this area is the development of supertree methods, which estimate a composite tree by combining a set of partially overlapping component topologies. Although promising, the use of component tree topologies as the primary data dissociates supertrees from complexities within the underling character data and complicates the evaluation of phylogenetic uncertainty. We address these issues by exploring three approaches that variously incorporate nonparametric bootstrapping into a common supertree estimation algorithm (matrix representation with parsimony, although any algorithm might be used), including bootstrap-weighting, source-tree bootstrapping, and hierarchical bootstrapping. We illustrate these procedures by means of hypothetical and empirical examples. Our preliminary experiments suggest that these methods have the potential to improve the correspondence of supertree estimates to those derived from simultaneous analysis of the combined data and to allow uncertainty in supertree topologies to be quantified. The ability to increase the transparency of supertrees to the underlying character data has several practical implications and sheds new light on an old debate. These methods have been implemented in the freely available program, tREeBOOT.

Classification↗
PubMed2006

Phylodiversity-dependent seedling mortality, size structure, and disease in a Bornean rain forest.

Density-dependent models that partition neighbors into conspecifics and heterospecifics ignore the great variation in effect of heterospecifics on focal plants. Both evolutionary theory and empirical results suggest that the negative effect of other plants on a focal plant should be higher for closely related neighbors than for less related neighbors. Using community-wide seedling mortality data from a forest where density dependence has previously been found, we searched for significant phylogenetic neighborhood effects (the "phylodiversity" neighborhood) on seedling (<50 cm tall) survival at various spatial scales. Logistic regression models were used, with 19-mo survival of individual seedlings as the response. We found a significant positive effect of nearest taxon phylodiversity on seedling survival at the 36-m2 scale and the 4-m2 scale, indicating that seedling survival is enhanced by being in a neighborhood where heterospecifics are not closely related. At all scales there was a strong negative effect of conspecific seedling density on focal survival, and at small scales there was also an effect of heterospecific density, indicating generalized competition. We place these results (for seedling dynamics over a relatively short period of time) in the context of changes in phylodiversity between different size classes of plants in the same forest, which integrate the effects of dynamics of all size classes over long time periods. At the 36-m2 scale, there was an increase in nearest taxon phylodiversity (i.e., a decrease in phylogenetic clustering) from the seedlings (<50 cm tall) to the poles (1-5 cm diameter), consistent with the positive effect of local phylodiversity on seedling survival. In contrast, there was a marked decrease in average phylodiversity from seedlings to saplings at the same scale. The trees in the 1600 m2 surrounding the seedling plots had much lower phylodiversity than either the seedlings or saplings. Taken together, these results suggest that (1) over short time and spatial scales, local seedling phylodiversity has a positive effect on seedling survival, possibly via interaction with pathogens (which we discuss in detail), but (2) over longer time periods and larger spatial scales the effect of abiotic-related mortality results in habitat filtering for phylogenetically conserved traits.

Biodiversity↗
PubMed2005

Explosive radiation of Malpighiales supports a mid-cretaceous origin of modern tropical rain forests.

Fossil data have been interpreted as indicating that Late Cretaceous tropical forests were open and dry adapted and that modern closed-canopy rain forest did not originate until after the Cretaceous-Tertiary (K/T) boundary. However, some mid-Cretaceous leaf floras have been interpreted as rain forest. Molecular divergence-time estimates within the clade Malpighiales, which constitute a large percentage of species in the shaded, shrub, and small tree layer in tropical rain forests worldwide, provide new tests of these hypotheses. We estimate that all 28 major lineages (i.e., traditionally recognized families) within this clade originated in tropical rain forest well before the Tertiary, mostly during the Albian and Cenomanian (112-94 Ma). Their rapid rise in the mid-Cretaceous may have resulted from the origin of adaptations to survive and reproduce under a closed forest canopy. This pattern may also be paralleled by other similarly diverse lineages and supports fossil indications that closed-canopy tropical rain forests existed well before the K/T boundary. This case illustrates that dated phylogenies can provide an important new source of evidence bearing on the timing of major environmental changes, which may be especially useful when fossil evidence is limited or controversial.

Biological Evolution↗
PubMed2005

A likelihood framework for inferring the evolution of geographic range on phylogenetic trees.

At a time when historical biogeography appears to be again expanding its scope after a period of focusing primarily on discerning area relationships using cladograms, new inference methods are needed to bring more kinds of data to bear on questions about the geographic history of lineages. Here we describe a likelihood framework for inferring the evolution of geographic range on phylogenies that models lineage dispersal and local extinction in a set of discrete areas as stochastic events in continuous time. Unlike existing methods for estimating ancestral areas, such as dispersal-vicariance analysis, this approach incorporates information on the timing of both lineage divergences and the availability of connections between areas (dispersal routes). Monte Carlo methods are used to estimate branch-specific transition probabilities for geographic ranges, enabling the likelihood of the data (observed species distributions) to be evaluated for a given phylogeny and parameterized paleogeographic model. We demonstrate how the method can be used to address two biogeographic questions: What were the ancestral geographic ranges on a phylogenetic tree? How were those ancestral ranges affected by speciation and inherited by the daughter lineages at cladogenesis events? For illustration we use hypothetical examples and an analysis of a Northern Hemisphere plant clade (Cercis), comparing and contrasting inferences to those obtained from dispersal-vicariance analysis. Although the particular model we implement is somewhat simplistic, the framework itself is flexible and could readily be modified to incorporate additional sources of information and also be extended to address other aspects of historical biogeography.

Biological Evolution↗
PubMed2004

Patterns in the assembly of temperate forests around the Northern Hemisphere.

Recent studies of Northern Hemisphere biogeography have highlighted potentially significant differences between disjunction patterns in plants versus animals. To assess such differences, we compiled a larger sample of relevant plant phylogenies from which disjunction patterns, ancestral areas and directions of movement could be inferred. We considered 66 plant clades with species variously endemic today to eastern Asia (EA), Europe (including southwestern Asia), eastern North America (ENA), and/or western North America (WNA). Within these clades we focused on 100 disjunctions among these major areas, for 33 of which absolute divergence times have also been inferred. Our analyses uphold the view that disjunctions between EA and ENA are exceptionally common in plants, apparently more so than in animals. Compared with animals, we find few disjunctions between EA and WNA, consistent with increased extinction in WNA or failure of some groups to colonize that region. Taken at face value, our data also support the view that many temperate forest plant groups originated and diversified within EA, followed by movement out of Asia at different times, but mostly during the last 30 Myr. This favours Beringia over a North Atlantic land bridge as the primary path between the Old World and the New World. Additional studies are needed, especially to evaluate the impacts of differential extinction on these patterns, to more confidently establish divergence times, and to assess the statistical significance of these findings. Fortunately, many more plant groups show relevant disjunction patterns and could soon be added to such analyses.

Asia↗
PubMed2004

Historical biogeography, ecology and species richness.

Ecology and historical (phylogeny-based) biogeography have much to offer one another, but exchanges between these fields have been limited. Historical biogeography has become narrowly focused on using phylogenies to discover the history of geological connections among regions. Conversely, ecologists often ignore historical biogeography, even when its input can be crucial. Both historical biogeographers and ecologists have more-or-less abandoned attempts to understand the processes that determine the large-scale distribution of clades. Here, we describe the chasm that has developed between ecology and historical biogeography, some of the important questions that have fallen into it and how it might be bridged. To illustrate the benefits of an integrated approach, we expand on a model that can help explain the latitudinal gradient of species richness.

Journal Article↗
PubMed2004

Viburnum phylogeny: evidence from the duplicated nuclear gene GBSSI.

DNA sequencing studies of the granule-bound starch synthase gene (GBSSI) indicate the presence of two loci in Viburnum. Gene trees from separate and combined phylogenetic analyses of the GBSSI paralogues are generally congruent with each other and with trees from previous analyses, especially those of Donoghue et al. [Syst. Bot. 29 (2004) 188] based on nuclear ribosomal ITS and chloroplast trnK intron DNA sequences. Specifically, our GBSSI trees confirm (i) the monophyly of some and non-monophyly of other traditionally recognized taxonomic sections, (ii) the presence of three major supra-sectional lineages within Viburnum, and (iii) the resolution of many species relationships within the section-level clades. Analyses of GBSSI also provide greater resolution of relationships within the largest supra-sectional lineage. Relationships at the base of the Viburnum phylogeny remain uncertain; in particular, the position of the root, relationships among the supra-sectional clades, and the exact placement of several smaller groups (e.g., Viburnum clemensiae, Viburnum urceolatum, and section Pseudotinus). In two lineages each GBSSI paralogue is represented by two distinct sequences. The presence of additional copies appears to be correlated with polyploidy in these clades. Placement of the homoeologues in our gene trees suggests the possibility of a hybrid origin for these polyploids.

Base Sequence↗
PubMed2003

The small-world dynamics of tree networks and data mining in phyloinformatics.

MOTIVATION: A noble and ultimate objective of phyloinformatic research is to assemble, synthesize, and explore the evolutionary history of life on earth. Data mining methods for performing these tasks are not yet well developed, but one avenue of research suggests that network connectivity dynamics will play an important role in future methods. Analysis of disordered networks, such as small-world networks, has applications as diverse as disease propagation, collaborative networks, and power grids. Here we apply similar analyses to networks of phylogenetic trees in order to understand how synthetic information can emerge from a database of phylogenies. RESULTS: Analyses of tree network connectivity in TreeBASE show that a collection of phylogenetic trees behaves as a small-world network-while on the one hand the trees are clustered, like a non-random lattice, on the other hand they have short characteristic path lengths, like a random graph. Tree connectivities follow a dual-scale power-law distribution (first power-law exponent approximately 1.87; second approximately 4.82). This unusual pattern is due, in part, to the presence of alternative tree topologies that enter the database with each published study. As expected, small collections of trees decrease connectivity as new trees are added, while large collections of trees increase connectivity. However, the inflection point is surprisingly low: after about 600 trees the network suddenly jumps to a higher level of coherence. More stringent definitions of 'neighbour' greatly delay the threshold whence a database achieves sufficient maturity for a coherent network to emerge. However, more stringent definitions of 'neighbour' would also likely show improved focus in data mining. AVAILABILITY: http://treebase.org

Algorithms↗
PubMed2003

Adaptive evolution in the photosensory domain of phytochrome A in early angiosperms.

Flowering plant diversity now far exceeds the combined diversity of all other plant groups. Recently identified extant remnants of the earliest-diverging lines suggest that the first angiosperms may have lived in shady, disturbed, and moist understory habitats, and that the aquatic habit also arose early. This would have required the capacity to begin life in dimly lit environments. If so, evolution in light-sensing mechanisms may have been crucial to their success. The photoreceptor phytochrome A is unique among angiosperm phytochromes in its capacity to serve a transient role under conditions where an extremely high sensitivity is required. We present evidence of altered functional constraints between phytochrome A (PHYA) and its paralog, PHYC. Tests for selection suggest that an elevation in nonsynonymous rates resulted from an episode of selection along the branch leading to all angiosperm PHYA sequences. Most nucleotide sites (95%) are selectively constrained, and the ratio of nonsynonymous to synonymous substitutions on branches within the PHYA clade does not differ from the ratio on the branches in the PHYC clade. Thus, positive selection at a handful of sites, rather than relaxation of selective constraints, apparently has played a major role in the evolution of the photosensory domain of phytochrome A. The episode of selection occurred very early in the history of flowering plants, suggesting that innovation in phyA may have given the first angiosperms some adaptive advantage.

Evolution, Molecular↗
PubMed2002

The root of the angiosperms revisited.

Most recent phylogenetic analyses of basal angiosperms have converged on the placement of Amborella as sister to all other extant angiosperms. However, certain recent studies suggest that Amborella and Nymphaeales (water lilies) form a clade sister to all remaining angiosperms or that Nymphaeales alone are the sister to the remaining angiosperms. We report here (i) maximum parsimony, maximum likelihood, and Bayesian phylogenetic analyses of 11 genes (>15,000 bp per taxon) for 16 taxa, (ii) maximum parsimony analysis for a subset of these genes for 104 taxa, and (iii) tests of alternative rootings with the nonparametric bootstrap and the likelihood ratio test with the parametric bootstrap. In addition, we use simulation analyses to examine the amount of bias that may be present in our methods of phylogeny estimation. Amborella continues to receive strong bootstrap support as the sister to all other extant angiosperms, and three of four tests reject alternative hypotheses of the angiosperm root. Although we cannot conclusively choose between Amborella vs. Amborella + Nymphaeales as sister to all other angiosperms, most analyses favor the former rooting.

Evolution, Molecular↗
PubMed2002

Laurasian migration explains Gondwanan disjunctions: evidence from Malpighiaceae.

Explanations for biogeographic disjunctions involving South America and Africa typically invoke vicariance of western Gondwanan biotas or long distance dispersal. These hypotheses are problematical because many groups originated and diversified well after the last known connection between Africa and South America (approximately 105 million years ago), and it is unlikely that "sweepstakes" dispersal accounts for many of these disjunctions. Phylogenetic analyses of the angiosperm clade Malpighiaceae, combined with fossil evidence and molecular divergence-time estimates, suggest an alternative hypothesis to account for such distributions. We propose that Malpighiaceae originated in northern South America, and that members of several clades repeatedly migrated into North America and subsequently moved via North Atlantic land connections into the Old World during episodes starting in the Eocene, when climates supported tropical forests. This Laurasian migration route may explain many other extant lineages that exhibit western Gondwanan distributions.

Arabidopsis Proteins↗
PubMed2002

Recreating a functional ancestral archosaur visual pigment.

The ancestors of the archosaurs, a major branch of the diapsid reptiles, originated more than 240 MYA near the dawn of the Triassic Period. We used maximum likelihood phylogenetic ancestral reconstruction methods and explored different models of evolution for inferring the amino acid sequence of a putative ancestral archosaur visual pigment. Three different types of maximum likelihood models were used: nucleotide-based, amino acid-based, and codon-based models. Where possible, within each type of model, likelihood ratio tests were used to determine which model best fit the data. Ancestral reconstructions of the ancestral archosaur node using the best-fitting models of each type were found to be in agreement, except for three amino acid residues at which one reconstruction differed from the other two. To determine if these ancestral pigments would be functionally active, the corresponding genes were chemically synthesized and then expressed in a mammalian cell line in tissue culture. The expressed artificial genes were all found to bind to 11-cis-retinal to yield stable photoactive pigments with lambda(max) values of about 508 nm, which is slightly redshifted relative to that of extant vertebrate pigments. The ancestral archosaur pigments also activated the retinal G protein transducin, as measured in a fluorescence assay. Our results show that ancestral genes from ancient organisms can be reconstructed de novo and tested for function using a combination of phylogenetic and biochemical methods.

Amino Acid Sequence↗
PubMed2000

Phylogenetic Analysis of Dioecy in Monocotyledons.

Surveys of plant breeding systems in angiosperm families have shown a significant association between monoecy and dioecy, and researchers have proposed that dioecy has tended to evolve from monoecy. We evaluated this hypothesis in the context of a phylogeny of 918 monocotyledons assembled from 19 published trees. Binary and multistate breeding system characters were mapped onto a set of composite trees, and alternative models of character change were compared using maximum likelihood. Over a range of tree topologies and optimizations, we found three to eight times as many changes from hermaphroditism to dioecy as we did from monoecy to dioecy. Also, the rate at which monoecy gave rise to dioecy was not significantly higher than the rate at which hermaphroditism gave rise to dioecy. Our analysis implies that the correlation of monoecy and dioecy in angiosperm families does not reflect a preponderance of changes from monoecy to dioecy. Instead, we postulate that the family-level correlation results from the clustering of breeding system changes in the underlying phylogeny. Our results suggest renewed attention to modeling the transition from hermaphroditism to dioecy, possibly involving transient intermediates such as gynodioecy.

breeding systems↗