Richard H Ree

Publications of Richard H Ree

• Analysis of inbreeding depression in mixed-mating plants provides evidence for selective interference and stable mixed mating.

  Authors: Alice A Winn, Elizabeth Elle, Susan Kalisz, Pierre-Olivier Cheptou, Christopher G Eckert, Carol Goodwillie, Mark O Johnston, David A Moeller, Richard H Ree, Risa D Sargent, Mario Vallejo-Marín

  Evolution; international journal of organic evolution. 12/2011; 65(12):3339-59.

  Hermaphroditic individuals can produce both selfed and outcrossed progeny, termed mixed mating. General theory predicts that mixed-mating populations should evolve quickly toward high rates ofHermaphroditic individuals can produce both selfed and outcrossed progeny, termed mixed mating. General theory predicts that mixed-mating populations should evolve quickly toward high rates of selfing, driven by rapid purging of genetic load and loss of inbreeding depression (ID), but the substantial number of mixed-mating species observed in nature calls this prediction into question. Lower average ID reported for selfing than for outcrossing populations is consistent with purging and suggests that mixed-mating taxa in evolutionary transition will have intermediate ID. We compared the magnitude of ID from published estimates for highly selfing (r > 0.8), mixed-mating (0.2 ≤ r ≥ 0.8), and highly outcrossing (r < 0.2) plant populations across 58 species. We found that mixed-mating and outcrossing taxa have equally high average lifetime ID (δ= 0.58 and 0.54, respectively) and similar ID at each of four life-cycle stages. These results are not consistent with evolution toward selfing in most mixed-mating taxa. We suggest that prevention of purging by selective interference could explain stable mixed mating in many natural populations. We identify critical gaps in the empirical data on ID and outline key approaches to filling them.

• Phylogenetic inference of reciprocal effects between geographic range evolution and diversification.

  Authors: Emma E Goldberg, Lesley T Lancaster, Richard H Ree

  Systematic biology. 07/2011; 60(4):451-65.

  Geographic characters--traits describing the spatial distribution of a species-may both affect and be affected by processes associated with lineage birth and death. This is potentially confounding toGeographic characters--traits describing the spatial distribution of a species-may both affect and be affected by processes associated with lineage birth and death. This is potentially confounding to comparative analyses of species distributions because current models do not allow reciprocal interactions between the evolution of ranges and the growth of phylogenetic trees. Here, we introduce a likelihood-based approach to estimating region-dependent rates of speciation, extinction, and range evolution from a phylogeny, using a new model in which these processes are interdependent. We demonstrate the method with simulation tests that accurately recover parameters relating to the mode of speciation and source-sink dynamics. We then apply it to the evolution of habitat occupancy in Californian plant communities, where we find higher rates of speciation in chaparral than in forests and evidence for expanding habitat tolerances.

• Serpentine soils do not limit mycorrhizal fungal diversity.

  Authors: Sara Branco, Richard H Ree

  PloS one. 01/2010; 5(7):e11757.

  Physiologically stressful environments tend to host depauperate and specialized biological communities. Serpentine soils exemplify this phenomenon by imposing well-known constraints on plants;Physiologically stressful environments tend to host depauperate and specialized biological communities. Serpentine soils exemplify this phenomenon by imposing well-known constraints on plants; however, their effect on other organisms is still poorly understood. We used a combination of field and molecular approaches to test the hypothesis that serpentine fungal communities are species-poor and specialized. We conducted surveys of ectomycorrhizal fungal diversity from adjacent serpentine and non-serpentine sites, described fungal communities using nrDNA Internal Transcribed Spacer (ITS) fragment and sequence analyses, and compared their phylogenetic community structure. Although we detected low fungal overlap across the two habitats, we found serpentine soils to support rich fungal communities that include representatives from all major fungal lineages. We failed to detect the phylogenetic signature of endemic clades that would result from specialization and adaptive radiation within this habitat. Our results indicate that serpentine soils do not constitute an extreme environment for ectomycorrhizal fungi, and raise important questions about the role of symbioses in edaphic tolerance and the maintenance of biodiversity.

• Correlated evolution of mating system and floral display traits in flowering plants and its implications for the distribution of mating system variation.

  Authors: Carol Goodwillie, Risa D Sargent, Christopher G Eckert, Elizabeth Elle, Monica A Geber, Mark O Johnston, Susan Kalisz, David A Moeller, Richard H Ree, Mario Vallejo-Marin, Alice A Winn

  The New phytologist. 10/2009;

  New Phytologist (2009)Summary * Reduced allocation to structures for pollinator attraction is predicted in selfing species. We explored the association between outcrossing and floral display in aNew Phytologist (2009)Summary * Reduced allocation to structures for pollinator attraction is predicted in selfing species. We explored the association between outcrossing and floral display in a broad sample of angiosperms. We used the demonstrated relationship to test for bias against selfing species in the outcrossing rate distribution, the shape of which has relevance for the stability of mixed mating. * Relationships between outcrossing rate, flower size, flower number and floral display, measured as the product of flower size and number, were examined using phylogenetically independent contrasts. The distribution of floral displays among species in the outcrossing rate database was compared with that of a random sample of the same flora. * The outcrossing rate was positively associated with the product of flower size and number; individually, components of display were less strongly related to outcrossing. Compared with a random sample, species in the outcrossing rate database showed a deficit of small floral display sizes. * We found broad support for reduced allocation to attraction in selfing species. We suggest that covariation between mating systems and total allocation to attraction can explain the deviation from expected trade-offs between flower size and number. Our results suggest a bias against estimating outcrossing rates in the lower half of the distribution, but not specifically against highly selfing species.

• Plant mating systems in a changing world.

  Authors: Christopher G Eckert, Susan Kalisz, Monica A Geber, Risa Sargent, Elizabeth Elle, Pierre-Olivier Cheptou, Carol Goodwillie, Mark O Johnston, John K Kelly, David A Moeller, Emmanuelle Porcher, Richard H Ree, Mario Vallejo-Marín, Alice A Winn

  Trends in ecology & evolution (Personal edition). 09/2009;

  There is increasing evidence that human disturbance can negatively impact plant-pollinator interactions such as outcross pollination. We present a meta-analysis of 22 studies involving 27 plantThere is increasing evidence that human disturbance can negatively impact plant-pollinator interactions such as outcross pollination. We present a meta-analysis of 22 studies involving 27 plant species showing a significant reduction in the proportion of seeds outcrossed in response to anthropogenic habitat modifications. We discuss the evolutionary consequences of disturbance on plant mating systems, and in particular whether reproductive assurance through selfing effectively compensates for reduced outcrossing. The extent to which disturbance reduces pollinator versus mate availability could generate diverse selective forces on reproductive traits. Investigating how anthropogenic change influences plant mating will lead to new opportunities for better understanding of how mating systems evolve, as well as of the ecological and evolutionary consequences of human activities and how to mitigate them.

• A comparative study in ancestral range reconstruction methods: retracing the uncertain histories of insular lineages.

  Authors: John R Clark, Richard H Ree, Michael E Alfaro, Matthew G King, Warren L Wagner, Eric H Roalson

  Systematic biology. 11/2008; 57(5):693-707.

  Island systems have long been useful models for understanding lineage diversification in a geographic context, especially pertaining to the importance of dispersal in the origin of new clades. HereIsland systems have long been useful models for understanding lineage diversification in a geographic context, especially pertaining to the importance of dispersal in the origin of new clades. Here we use a well-resolved phylogeny of the flowering plant genus Cyrtandra (Gesneriaceae) from the Pacific Islands to compare four methods of inferring ancestral geographic ranges in islands: two developed for character-state reconstruction that allow only single-island ranges and do not explicitly associate speciation with range evolution (Fitch parsimony [FP; parsimony-based] and stochastic mapping [SM; likelihood-based]) and two methods developed specifically for ancestral range reconstruction, in which widespread ranges (spanning islands) are integral to inferences about speciation scenarios (dispersal-vicariance analysis [DIVA; parsimony-based] and dispersal-extinction-cladogenesis [DEC; likelihood-based]). The methods yield conflicting results, which we interpret in light of their respective assumptions. FP exhibits the least power to unequivocally reconstruct ranges, likely due to a combination of having flat (uninformative) transition costs and not using branch length information. SM reconstructions generally agree with a prior hypothesis about dispersal-driven speciation across the Pacific, despite the conceptual mismatch between its character-based model and this mode of range evolution. In contrast with narrow extant ranges for species of Cyrtandra, DIVA reconstructs broad ancestral ranges at many nodes. DIVA results also conflict with geological information on island ages; we attribute these conflicts to the parsimony criterion not considering branch lengths or time, as well as vicariance being the sole means of divergence for widespread ancestors. DEC analyses incorporated geological information on island ages and allowed prior hypotheses about range size and dispersal rates to be evaluated in a likelihood framework and gave more nuanced inferences about range evolution and the geography of speciation than other methods tested. However, ancestral ranges at several nodes could not be conclusively resolved, due possibly to uncertainty in the phylogeny or the relative complexity of the underlying model. Of the methods tested, SM and DEC both converge on plausible hypotheses for area range histories in Cyrtandra, due in part to the consideration of branch lengths and/or timing of events. We suggest that DEC model-based methods for ancestral range inference could be improved by adopting a Bayesian SM approach, in which stochastic sampling of complete geographic histories could be integrated over alternative phylogenetic topologies. Likelihood-based estimates of ancestral ranges for Cyrtandra suggest a major dispersal route into the Pacific through the islands of Fiji and Samoa, motivating future biogeographic investigation of this poorly known region.

• Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis.

  Authors: Richard H Ree, Stephen A Smith

  Systematic biology. 03/2008; 57(1):4-14.

  In historical biogeography, model-based inference methods for reconstructing the evolution of geographic ranges on phylogenetic trees are poorly developed relative to the diversity of analogousIn historical biogeography, model-based inference methods for reconstructing the evolution of geographic ranges on phylogenetic trees are poorly developed relative to the diversity of analogous methods available for inferring character evolution. We attempt to rectify this deficiency by constructing a dispersal-extinction-cladogenesis (DEC) model for geographic range evolution that specifies instantaneous transition rates between discrete states (ranges) along phylogenetic branches and apply it to estimating likelihoods of ancestral states (range inheritance scenarios) at cladogenesis events. Unlike an earlier version of this approach, the present model allows for an analytical solution to probabilities of range transitions as a function of time, enabling free parameters in the model, rates of dispersal, and local extinction to be estimated by maximum likelihood. Simulation results indicate that accurate parameter estimates may be difficult to obtain in practice but also show that ancestral range inheritance scenarios nevertheless can be correctly recovered with high success if rates of range evolution are low relative to the rate of cladogenesis. We apply the DEC model to a previously published, exemplary case study of island biogeography involving Hawaiian endemic angiosperms in Psychotria (Rubiaceae), showing how the DEC model can be iteratively refined from inspecting inferences of range evolution and also how geological constraints involving times of island origin may be imposed on the likelihood function. The DEC model is sufficiently similar to character models that it might serve as a gateway through which many existing comparative methods for characters could be imported into the realm of historical biogeography; moreover, it might also inspire the conceptual expansion of character models toward inclusion of evolutionary change as directly coincident, either as cause or consequence, with cladogenesis events. The DEC model is thus an incremental advance that highlights considerable potential in the nascent field of model-based historical biogeographic inference.

• Phylogenetic evidence for a flower size and number trade-off.

  Authors: Risa D Sargent, Carol Goodwillie, Susan Kalisz, Richard H Ree

  American journal of botany. 12/2007; 94(12):2059-62.

  The size and number of flowers displayed together on an inflorescence (floral display) influences pollinator attraction and pollen transfer and receipt, and is integral to plant reproductive successThe size and number of flowers displayed together on an inflorescence (floral display) influences pollinator attraction and pollen transfer and receipt, and is integral to plant reproductive success and fitness. Life history theory predicts that the evolution of floral display is constrained by trade-offs between the size and number of flowers and inflorescences. Indeed, a trade-off between flower size and flower number is a key assumption of models of inflorescence architecture and the evolution of floral display. Surprisingly, however, empirical evidence for the trade-off is limited. In particular, there is a lack of phylogenetic evidence for a trade-off between flower size and number. Analyses of phylogenetic independent contrasts (PICs) of 251 angiosperm species spanning 63 families yielded a significant negative correlation between flower size and flower number. At smaller phylogenetic scales, analyses of individual genera did not always find evidence of a trade-off, a result consistent with previous studies that have examined the trade-off for a single species or genus. Ours is the first study to support an angiosperm-wide trade-off between flower size and number and supports the theory that life history constraints have influenced the evolution of floral display.

• Linking floral symmetry genes to breeding system evolution.

  Authors: Susan Kalisz, Richard H Ree, Risa D Sargent

  Trends in plant science. 01/2007; 11(12):568-73.

  Understanding the genetic basis of ecologically important traits is a major focus of evolutionary research. Recent advances in molecular genetic techniques should significantly increase ourUnderstanding the genetic basis of ecologically important traits is a major focus of evolutionary research. Recent advances in molecular genetic techniques should significantly increase our understanding of how regulatory genes function. By contrast, our understanding of the broader macro-evolutionary implications of developmental gene function lags behind. Here we review published data on the floral symmetry gene network (FSGN), and conduct phylogenetic analyses that provide evidence of a link between floral symmetry and breeding systems in angiosperms via dichogamy. Our results suggest that known genes in the FSGN and those yet to be described underlie this association. We posit that the integration of floral symmetry and the roles of other regulatory genes in plant breeding system evolution will provide new insights about macro-evolutionary patterns and processes in flowering plants.

• Evidence for a time-integrated species-area effect on the latitudinal gradient in tree diversity.

  Authors: Paul V A Fine, Richard H Ree

  The American naturalist. 01/2007; 168(6):796-804.

  The greater area of tropical forest biomes has been proposed as a factor that drives the latitudinal gradient in species diversity by modulating speciation and extinction rates. But speciation andThe greater area of tropical forest biomes has been proposed as a factor that drives the latitudinal gradient in species diversity by modulating speciation and extinction rates. But speciation and extinction are processes that operate over millions of years, so an adequate test of area's contribution to diversity patterns must take into consideration that biome areas have changed through time in response to climate. Here we correlate estimates of current tree species diversity with a composite parameter integrating area over geological time for each continent's tropical, temperate, and boreal biomes. We find significant positive correlations between current tree diversity and area-time for periods since the Eocene, Oligocene, and Miocene, which we take as evidence for a time-integrated species-area effect on current patterns of species richness across biomes. These results contribute to explanations for why most lineages have tropical origins and why tropical forests are more diverse than extratropical forests.

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

  Authors: Richard H. Ree, Brian R Moore, Campbell O Webb, Michael J Donoghue

  Evolution; international journal of organic evolution. 12/2005; 59(11):2299-311.

  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 neededAt 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.

• Detecting the historical signature of key innovations using stochastic models of character evolution and cladogenesis.

  Authors: Richard H Ree

  Evolution; international journal of organic evolution. 03/2005; 59(2):257-65.

  Phylogenetic evidence for biological traits that increase the net diversification rate of lineages (key innovations) is most commonly drawn from comparisons of clade size. This can work well forPhylogenetic evidence for biological traits that increase the net diversification rate of lineages (key innovations) is most commonly drawn from comparisons of clade size. This can work well for ancient, unreversed traits and for correlating multiple trait origins with higher diversification rates, but it is less suitable for unique events, recently evolved innovations, and traits that exhibit homoplasy. Here I present a new method for detecting the phylogenetic signature of key innovations that tests whether the evolutionary history of the candidate trait is associated with shorter waiting times between cladogenesis events. The method employs stochastic models of character evolution and cladogenesis and integrates well into a Bayesian framework in which uncertainty in historical inferences (such as phylogenetic relationships) is allowed. Applied to a well-known example in plants, nectar spurs in columbines, the method gives much stronger support to the key innovation hypothesis than previous tests.

• Obtaining maximal concatenated phylogenetic data sets from large sequence databases.

  Authors: Michael J Sanderson, Amy C Driskell, Richard H Ree, Oliver Eulenstein, Sasha Langley

  Molecular biology and evolution. 08/2003; 20(7):1036-42.

  To improve the accuracy of tree reconstruction, phylogeneticists are extracting increasingly large multigene data sets from sequence databases. Determining whether a database contains at least kTo improve the accuracy of tree reconstruction, phylogeneticists are extracting increasingly large multigene data sets from sequence databases. Determining whether a database contains at least k genes sampled from at least m species is an NP-complete problem. However, the skewed distribution of sequences in these databases permits all such data sets to be obtained in reasonable computing times even for large numbers of sequences. We developed an exact algorithm for obtaining the largest multigene data sets from a collection of sequences. The algorithm was then tested on a set of 100,000 protein sequences of green plants and used to identify the largest multigene ortholog data sets having at least 3 genes and 6 species. The distribution of sizes of these data sets forms a hollow curve, and the largest are surprisingly small, ranging from 62 genes by 6 species, to 3 genes by 65 species, with more symmetrical data sets of around 15 taxa by 15 genes. These upper bounds to sequence concatenation have important implications for building the tree of life from large sequence databases.

• Inferring Rates of Change in Flower Symmetry in Asterid Angiosperms

  Authors: Richard H. Ree, Michael J Donoghue

• Phylogeny and the evolution of flower symmetry in the Asteridae

  Authors: Michael J Donoghue, Richard H Ree, David A Baum

  Trends in Plant Science.

  Phylogenetic trees imply that flowers with a single plane of symmetry (zygomorphic flowers) have evolved several times independently from radially symmetrical (actinomorphic) ancestors within thePhylogenetic trees imply that flowers with a single plane of symmetry (zygomorphic flowers) have evolved several times independently from radially symmetrical (actinomorphic) ancestors within the Asteridae. However, there also appear to have been reversals to actinomorphy. A few evolutionarily derived actinomorphic flowers resemble mutants caused by loss-of-function mutations in genes such as CYCLOIDEA. However, a majority of the shifts from zygomorphy to actinomorphy appear to have entailed a reduction in petal number and flower size, implying a mechanism other than loss of CYCLOIDEA function. Within the Asteridae there appear to be three common forms of zygomorphy. An explanation for the virtual absence of other forms rests on the near universality of the basic orientation of the flower in the Asteridae.

• Molecular phylogeny, divergence time estimates, and historical biogeography of Circaea (Onagraceae) in the Northern Hemisphere

  Authors: Lei Xie, Warren L. Wagner, Richard H. Ree, Paul E. Berry, Jun Wen

  Molecular Phylogenetics and Evolution.

  Circaea (Onagraceae) consists of eight species and six subspecies distributed in Eurasia and North America. The sister group of Circaea was recently shown to be Fuchsia, which comprises 107 speciesCircaea (Onagraceae) consists of eight species and six subspecies distributed in Eurasia and North America. The sister group of Circaea was recently shown to be Fuchsia, which comprises 107 species primarily distributed in montane Central and South America, including four species occurring in the South Pacific islands. Three plastid markers (petB–petD, rpl16, and trnL-F) and nrITS sequences from 13 of the 14 taxa of Circaea were sequenced and used to reconstruct the phylogenetic and biogeographic history of the genus. Parsimony and Bayesian analyses support that (1) Circaea is monophyletic; (2) the bilocular group is a weakly supported clade nested within the unilocular grade; (3) neither the C. alpina complex nor the C. canadensis complex is monophyletic; and (4) the western North American C. alpina subsp. pacifica diverged first in the genus. Divergence time estimates based on the Bayesian “relaxed” clock methods suggest that the earliest Circaea divergence occurred minimally at 16.17 mya (95% HPD: 7.69–24.53 mya). Biogeographic analyses using divergence–vicariance analysis (DIVA) and a likelihood method support the New World origin of Circaea. Three independent dispersal events between Eurasia and North America via the Bering land bridge were inferred within Circaea. Higher taxon diversity of Circaea in eastern Asia was probably caused by geologic and ecological changes during the late Tertiary in the Northern Hemisphere.