<?xml version="1.0" encoding="UTF-8"?><xml><records><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Xie, Lei</style></author><author><style face="normal" font="default" size="100%">Warren L. Wagner</style></author><author><style face="normal" font="default" size="100%">Richard H. Ree</style></author><author><style face="normal" font="default" size="100%">Berry, Paul E.</style></author><author><style face="normal" font="default" size="100%">Wen, Jun</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Molecular phylogeny, divergence time estimates, and historical biogeography of Circaea (Onagraceae) in the Northern Hemisphere</style></title><secondary-title><style face="normal" font="default" size="100%">Molecular Phylogenetics and Evolution</style></secondary-title><short-title><style face="normal" font="default" size="100%">Molecular Phylogenetics and Evolution</style></short-title></titles><dates><year><style  face="normal" font="default" size="100%">2009</style></year><pub-dates><date><style  face="normal" font="default" size="100%">12/2009</style></date></pub-dates></dates><urls><related-urls><url><style face="normal" font="default" size="100%">http://www.reelab.net/home/sites/default/files/Xie et al. - 2009 - Molecular phylogeny, divergence time estimates, an.pdf</style></url></related-urls></urls><volume><style face="normal" font="default" size="100%">53</style></volume><pages><style face="normal" font="default" size="100%">995 - 1009</style></pages><issue><style face="normal" font="default" size="100%">3</style></issue></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Zhang, Da-Cai</style></author><author><style face="normal" font="default" size="100%">Boufford, David E.</style></author><author><style face="normal" font="default" size="100%">Richard H. Ree</style></author><author><style face="normal" font="default" size="100%">Hang Sun</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">The 29°N latitudinal line: an important division in the Hengduan Mountains, a biodiversity hotspot in southwest China</style></title><secondary-title><style face="normal" font="default" size="100%">Nordic Journal of Botany</style></secondary-title><short-title><style face="normal" font="default" size="100%">Nordic Journal of Botany</style></short-title></titles><dates><year><style  face="normal" font="default" size="100%">2009</style></year><pub-dates><date><style  face="normal" font="default" size="100%">10/2009</style></date></pub-dates></dates><urls><related-urls><url><style face="normal" font="default" size="100%">http://www.reelab.net/home/sites/default/files/Zhang et al. - 2009 - The 29°N latitudinal line an important division i.PDF</style></url></related-urls></urls><volume><style face="normal" font="default" size="100%">27</style></volume><pages><style face="normal" font="default" size="100%">405 - 412</style></pages><issue><style face="normal" font="default" size="100%">5</style></issue></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Ji-Pei Yue</style></author><author><style face="normal" font="default" size="100%">Hang Sun</style></author><author><style face="normal" font="default" size="100%">Baum,David A.</style></author><author><style face="normal" font="default" size="100%">LI, Jian-Hua</style></author><author><style face="normal" font="default" size="100%">Al-Shebaz, Ihsan A.</style></author><author><style face="normal" font="default" size="100%">Richard H. Ree</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Molecular phylogeny of Solms-laubachia (Brassicaceae) s.l., based on multiple nuclear and plastid DNA sequences, and its biogeographic implications</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of Systematics and Evolution</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2009</style></year><pub-dates><date><style  face="normal" font="default" size="100%">09/2009</style></date></pub-dates></dates><urls><related-urls><url><style face="normal" font="default" size="100%">http://www.reelab.net/home/sites/default/files/Yue_et_al-2009-JSE.pdf</style></url></related-urls></urls><volume><style face="normal" font="default" size="100%">47</style></volume><pages><style face="normal" font="default" size="100%">402 - 415</style></pages><issue><style face="normal" font="default" size="100%">5</style></issue></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Richard H. Ree</style></author><author><style face="normal" font="default" size="100%">Isabel Sanmartín</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Prospects and challenges for parametric models in historical biogeographical inference</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of Biogeography</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2009</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://dx.doi.org/10.1111/j.1365-2699.2008.02068.x</style></url></web-urls><related-urls><url><style face="normal" font="default" size="100%">http://www.reelab.net/home/sites/default/files/Ree_and_Sanmartin-2009-JBiogeo.pdf</style></url></related-urls></urls><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">In historical biogeography, phylogenetic trees have long been used as tools for addressing a wide range of inference problems, from explaining common distribution patterns of species to reconstructing ancestral geographic ranges on branches of the tree of life. However, the potential utility of phylogenies for this purpose has yet to be fully realized, due in part to a lack of explicit conceptual links between processes underlying the evolution of geographic ranges and processes of phylogenetic tree growth. We suggest that statistical approaches that use parametric models to forge such links will stimulate integration and propel hypothesis-driven biogeographical inquiry in new directions. We highlight here two such approaches and describe how they represent early steps towards a more general framework for model-based historical biogeography that is based on likelihood as an optimality criterion, rather than having the traditional reliance on parsimony. The development of this framework will not be without significant challenges, particularly in balancing model complexity with statistical power, and these will be most apparent in studies of regions with many component areas and complex geological histories, such as the Mediterranean Basin.</style></abstract></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Juan C. Santos</style></author><author><style face="normal" font="default" size="100%">Luis A. Coloma</style></author><author><style face="normal" font="default" size="100%">Kyle Summers</style></author><author><style face="normal" font="default" size="100%">Janalee P. Caldwell</style></author><author><style face="normal" font="default" size="100%">Richard H. Ree</style></author><author><style face="normal" font="default" size="100%">David C. Cannatella</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Amazonian Amphibian Diversity Is Primarily Derived from Late Miocene Andean Lineages</style></title><secondary-title><style face="normal" font="default" size="100%">PLoS Biology</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2009</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://dx.doi.org/10.1371%2Fjournal.pbio.1000056</style></url></web-urls></urls><number><style face="normal" font="default" size="100%">3</style></number><volume><style face="normal" font="default" size="100%">7</style></volume><pages><style face="normal" font="default" size="100%">e56</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The Neotropics contains half of remaining rainforests and Earth's largest reservoir of amphibian biodiversity. However, determinants of Neotropical biodiversity (i.e., vicariance, dispersals, extinctions, and radiations) earlier than the Quaternary are largely unstudied. Using a novel method of ancestral area reconstruction and relaxed Bayesian clock analyses, we reconstructed the biogeography of the poison frog clade {(Dendrobatidae).} We rejected an Amazonian center-of-origin in favor of a complex connectivity model expanding over the Neotropics. We inferred 14 dispersals into and 18 out of Amazonia to adjacent regions; the Andes were the major source of dispersals into Amazonia. We found three episodes of lineage dispersal with two interleaved periods of vicariant events between South and Central America. During the late Miocene, Amazonian, and Central {American-Chocoan} lineages significantly increased their diversity compared to the Andean and {Guianan-Venezuelan-Brazilian} Shield counterparts. Significant percentage of dendrobatid diversity in Amazonia and Chocó resulted from repeated immigrations, with radiations at {\textless}10.0 million years ago {(MYA),} rather than in situ diversification. In contrast, the Andes, Venezuelan Highlands, and Guiana Shield have undergone extended in situ diversification at near constant rate since the Oligocene. The effects of Miocene paleogeographic events on Neotropical diversification dynamics provided the framework under which Quaternary patterns of endemism evolved.</style></abstract></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Richard H. Ree</style></author><author><style face="normal" font="default" size="100%">Stephen A. Smith</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis</style></title><secondary-title><style face="normal" font="default" size="100%">Systematic Biology</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2008</style></year></dates><urls><related-urls><url><style face="normal" font="default" size="100%">http://www.reelab.net/home/sites/default/files/Ree_and_Smith-2008-SystBio.pdf</style></url></related-urls></urls><number><style face="normal" font="default" size="100%">1</style></number><volume><style face="normal" font="default" size="100%">57</style></volume><pages><style face="normal" font="default" size="100%">4–14</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">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 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.</style></abstract></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">John R. Clark</style></author><author><style face="normal" font="default" size="100%">Richard H. Ree</style></author><author><style face="normal" font="default" size="100%">Michael E. Alfaro</style></author><author><style face="normal" font="default" size="100%">Matthew G. King</style></author><author><style face="normal" font="default" size="100%">Warren L. Wagner</style></author><author><style face="normal" font="default" size="100%">Eric H. Roalson</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">A Comparative Study in Ancestral Range Reconstruction Methods: Retracing the Uncertain Histories of Insular Lineages</style></title><secondary-title><style face="normal" font="default" size="100%">Systematic Biology</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2008</style></year></dates><urls><related-urls><url><style face="normal" font="default" size="100%">http://www.reelab.net/home/sites/default/files/Clark_et_al-2008-SystBio.pdf</style></url></related-urls></urls><number><style face="normal" font="default" size="100%">5</style></number><volume><style face="normal" font="default" size="100%">57</style></volume><pages><style face="normal" font="default" size="100%">693–707</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">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. 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... {[ABSTRACT} {FROM} {AUTHOR]}</style></abstract></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Ji-Pei Yue</style></author><author><style face="normal" font="default" size="100%">Kevin Feldheim</style></author><author><style face="normal" font="default" size="100%">Hang Sun</style></author><author><style face="normal" font="default" size="100%">Richard H. Ree</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Ten microsatellite loci from Solms-laubachia eurycarpa (Brassicaceae)</style></title><secondary-title><style face="normal" font="default" size="100%">Molecular Ecology Resources</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2008</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://dx.doi.org/10.1111/j.1755-0998.2008.02141.x</style></url></web-urls></urls><number><style face="normal" font="default" size="100%">5</style></number><volume><style face="normal" font="default" size="100%">8</style></volume><pages><style face="normal" font="default" size="100%">1023–1025</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Solms-laubachia eurycarpa is a medicinal herb endemic to the Hengduan Mountains region of south-central China. We screened a partial genomic library enriched for microsatellites and characterized 10 polymorphic loci for S. eurycarpa. The number of alleles per locus ranged from five to 15, with an average of 9.6. The observed and expected heterozygosities ranged from 0.2 to 0.725 and from 0.585 to 0.871, respectively. Amplification in closely related taxa was successful for most loci. The results indicate significant potential for the utility of these markers in studying the population genetics of S. eurycarpa and related species.</style></abstract></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Sargent,Risa D.</style></author><author><style face="normal" font="default" size="100%">Goodwillie,Carol</style></author><author><style face="normal" font="default" size="100%">Kalisz,Susan</style></author><author><style face="normal" font="default" size="100%">Richard H. Ree</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Phylogenetic evidence for a flower size and number trade-off</style></title><secondary-title><style face="normal" font="default" size="100%">American Journal of Botany</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2007</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2007/12/01/</style></date></pub-dates></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.amjbot.org/cgi/content/abstract/94/12/2059</style></url></web-urls><related-urls><url><style face="normal" font="default" size="100%">http://www.reelab.net/home/sites/default/files/Sargent_et_al-2007-AmJBot.pdf</style></url></related-urls></urls><volume><style face="normal" font="default" size="100%">94</style></volume><pages><style face="normal" font="default" size="100%">2059-2062</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">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 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.</style></abstract><issue><style face="normal" font="default" size="100%">12</style></issue></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>13</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Kalisz,Susan</style></author><author><style face="normal" font="default" size="100%">Richard H. Ree</style></author><author><style face="normal" font="default" size="100%">Sargent,Risa D.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Linking floral symmetry genes to breeding system evolution</style></title><secondary-title><style face="normal" font="default" size="100%">Trends in Plant Science</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2006</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2006///</style></date></pub-dates></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.sciencedirect.com/science/article/B6TD1-4M9H8YB-1/2/ebf60ed78a7486871b4061797ff4b955</style></url></web-urls><related-urls><url><style face="normal" font="default" size="100%">http://www.reelab.net/home/sites/default/files/Kalisz_et_al-2006-TPS.pdf</style></url></related-urls></urls><volume><style face="normal" font="default" size="100%">11</style></volume><pages><style face="normal" font="default" size="100%">568 - 573</style></pages><isbn><style face="normal" font="default" size="100%">1360-1385</style></isbn><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Understanding 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.
</style></abstract><issue><style face="normal" font="default" size="100%">12</style></issue></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>13</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Blanco,Oscar</style></author><author><style face="normal" font="default" size="100%">Crespo,Ana</style></author><author><style face="normal" font="default" size="100%">Richard H. Ree</style></author><author><style face="normal" font="default" size="100%">Lumbsch,H. Thorsten</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Major clades of parmelioid lichens (Parmeliaceae, Ascomycota) and the evolution of their morphological and chemical diversity</style></title><secondary-title><style face="normal" font="default" size="100%">Molecular Phylogenetics and Evolution</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Ascomycota</style></keyword><keyword><style  face="normal" font="default" size="100%">Character evolution</style></keyword><keyword><style  face="normal" font="default" size="100%">Lichens</style></keyword><keyword><style  face="normal" font="default" size="100%">Parmeliaceae</style></keyword><keyword><style  face="normal" font="default" size="100%">Stochastic mapping</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2006</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2006///</style></date></pub-dates></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.sciencedirect.com/science/article/B6WNH-4J8D929-2/2/c9b98bd0af4936233e5281b21e32f64e</style></url></web-urls></urls><volume><style face="normal" font="default" size="100%">39</style></volume><pages><style face="normal" font="default" size="100%">52 - 69</style></pages><isbn><style face="normal" font="default" size="100%">1055-7903</style></isbn><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Parmelioid lichens comprise about 1500 species and have a worldwide distribution. Numerous species are widely distributed and well known, including important bioindicators for atmospheric pollution. The phylogeny and classification of parmelioid lichens has been a matter of debate for several decades. Previous studies using molecular data have helped to establish hypotheses of the phylogeny of certain clades within this group. In this study, we infer the phylogeny of major clades of parmelioid lichens using DNA sequence data from two nuclear loci and one mitochondrial locus from 145 specimens (117 species) that represent the morphological and chemical diversity in these taxa. Parmelioid lichens are not monophyletic; however, a core group is strongly supported as monophyletic, excluding Arctoparmelia and Melanelia s. str., and including Parmeliopsis and Parmelaria. Within this group, seven well-supported clades are found, but the relationships among them remain unresolved. Stochastic mapping on a MC/MCMC tree sampling was employed to infer the evolution of two morphological and two chemical traits believed to be important for the evolutionary success of these lichens, and have also been used as major characters for classification. The results suggest that these characters have been gained and lost multiple times during the diversification of parmelioid lichens.
</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Paul V. A. Fine</style></author><author><style face="normal" font="default" size="100%">Richard H. Ree</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Evidence for a time-Integrated species-area effect on the latitudinal gradient in tree diversity.</style></title><secondary-title><style face="normal" font="default" size="100%">The American Naturalist</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2006</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.journals.uchicago.edu/doi/abs/10.1086/508635</style></url></web-urls><related-urls><url><style face="normal" font="default" size="100%">http://www.reelab.net/home/sites/default/files/Fine_and_Ree-2006-AmNat.pdf</style></url></related-urls></urls><number><style face="normal" font="default" size="100%">6</style></number><volume><style face="normal" font="default" size="100%">168</style></volume><pages><style face="normal" font="default" size="100%">796–804</style></pages><language><style face="normal" font="default" size="100%">eng</style></language></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Richard H. Ree</style></author><author><style face="normal" font="default" size="100%">B R Moore</style></author><author><style face="normal" font="default" size="100%">C O Webb</style></author><author><style face="normal" font="default" size="100%">Donoghue,Michael J.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">A likelihood framework for inferring the evolution of geographic range on phylogenetic trees</style></title><secondary-title><style face="normal" font="default" size="100%">Evolution</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2005</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://apps.isiknowledge.com.proxy.uchicago.edu/full_record.do?product=WOS&search_mode=GeneralSearch&qid=10&SID=2D4gKmdhNOe7CMoeeiD&page=1&doc=5</style></url></web-urls><related-urls><url><style face="normal" font="default" size="100%">http://www.reelab.net/home/sites/default/files/Ree_et_al-2005-Evolution.pdf</style></url></related-urls></urls><number><style face="normal" font="default" size="100%">11</style></number><volume><style face="normal" font="default" size="100%">59</style></volume><pages><style face="normal" font="default" size="100%">2299–2311</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">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.</style></abstract></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Richard H. Ree</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Detecting the historical signature of key innovations using stochastic models of character evolution and cladogenesis</style></title><secondary-title><style face="normal" font="default" size="100%">Evolution</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2005</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://apps.isiknowledge.com.proxy.uchicago.edu/full_record.do?product=WOS&search_mode=GeneralSearch&qid=10&SID=2D4gKmdhNOe7CMoeeiD&page=1&doc=7</style></url></web-urls><related-urls><url><style face="normal" font="default" size="100%">http://www.reelab.net/home/sites/default/files/Ree-2005-Evolution.pdf</style></url></related-urls></urls><number><style face="normal" font="default" size="100%">2</style></number><volume><style face="normal" font="default" size="100%">59</style></volume><pages><style face="normal" font="default" size="100%">257–265</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">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 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.</style></abstract></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Richard H. Ree</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Phylogeny and the Evolution of Floral Diversity in Pedicularis (Orobanchaceae)</style></title><secondary-title><style face="normal" font="default" size="100%">International Journal of Plant Sciences</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2005</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://dx.doi.org.proxy.uchicago.edu/10.1086/430191</style></url></web-urls><related-urls><url><style face="normal" font="default" size="100%">http://www.reelab.net/home/sites/default/files/Ree-2005-IJPS.pdf</style></url></related-urls></urls><number><style face="normal" font="default" size="100%">4</style></number><volume><style face="normal" font="default" size="100%">166</style></volume><pages><style face="normal" font="default" size="100%">595–613</style></pages><language><style face="normal" font="default" size="100%">eng</style></language></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Richard H. Ree</style></author><author><style face="normal" font="default" size="100%">Citerne,Helene L.</style></author><author><style face="normal" font="default" size="100%">Lavin,Matt</style></author><author><style face="normal" font="default" size="100%">Cronk,Quentin C. B.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Heterogeneous Selection on LEGCYC Paralogs in Relation to Flower Morphology and the Phylogeny of Lupinus (Leguminosae)</style></title><secondary-title><style face="normal" font="default" size="100%">Mol Biol Evol</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2004</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2004/02/01/</style></date></pub-dates></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://mbe.oxfordjournals.org/cgi/content/abstract/21/2/321</style></url></web-urls><related-urls><url><style face="normal" font="default" size="100%">http://www.reelab.net/home/sites/default/files/Ree_et_al-2004-MBE.pdf</style></url></related-urls></urls><volume><style face="normal" font="default" size="100%">21</style></volume><pages><style face="normal" font="default" size="100%">321 - 331</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">An analysis of the molecular evolution of two LEGCYC paralogs in Lupinus (Genisteae: Leguminosae) reveals a varied history of site-specific and lineage-specific evolutionary rates and selection both within and between loci. LEGCYC genes are homologous to regulatory loci known to control floral symmetry and adaxial flower organ identity in Antirrhinum and its relatives. Within Lupinus, L. densiflorus is unusual in having flowers with a proportionally smaller standard (fused adaxial petals) and larger wings (lateral petals) than other lupin species. Phylogenetic estimates of the nonsynonymous/synonymous substitution rate ratio, {omega}, suggest that along the L. densiflorus lineage, positive selection ([IMG]f1.gif&quot; BORDER=&quot;0&quot;&gt; &gt; 1) acted at some codon sites of one paralog, LEGCYC1B, and greater purifying selection ([IMG]f1.gif&quot; BORDER=&quot;0&quot;&gt; &lt; 1) acted at some sites of the other paralog, LEGCYC1A. Overall, LEGCYC1A appears to be evolving faster than LEGCYC1B, and both paralogs are evolving faster than the internal transcribed spacer (ITS) region of nr DNA. The predominant historical pattern inferred is a highly heterogeneous &quot;selectional mosaic&quot; which we suggest may be typical of the teosinte branched 1-cycloidea-PCF (TCP) class of transcriptional activators, and possibly other genes. Codon models that do not account for both site-specific and lineage-specific variation in {omega} do not detect positive selection at these loci. We suggest a modification of existing branch-site models involving an additional {omega} parameter along the foreground branch, to account for the effects of both greater positive selection and greater purifying selection at different codon sites along a particular branch. The higher rates of evolution and congruent phylogenetic signal of both LEGCYC paralogs show promise for the use of these genes as markers for phylogeny reconstruction at low taxonomic levels in Genisteae.</style></abstract><issue><style face="normal" font="default" size="100%">2</style></issue></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Sanderson,Michael J.</style></author><author><style face="normal" font="default" size="100%">Driskell,Amy C.</style></author><author><style face="normal" font="default" size="100%">Richard H. Ree</style></author><author><style face="normal" font="default" size="100%">Eulenstein,Oliver</style></author><author><style face="normal" font="default" size="100%">Langley,Sasha</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Obtaining Maximal Concatenated Phylogenetic Data Sets from Large Sequence Databases</style></title><secondary-title><style face="normal" font="default" size="100%">Mol Biol Evol</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2003</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2003/07/01/</style></date></pub-dates></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://mbe.oxfordjournals.org/cgi/content/abstract/20/7/1036</style></url></web-urls></urls><volume><style face="normal" font="default" size="100%">20</style></volume><pages><style face="normal" font="default" size="100%">1036 - 1042</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">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 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.</style></abstract><issue><style face="normal" font="default" size="100%">7</style></issue></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Donoghue,Michael J.</style></author><author><style face="normal" font="default" size="100%">Richard H. Ree</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Homoplasy and Developmental Constraint: A Model and an Example from Plants1</style></title><secondary-title><style face="normal" font="default" size="100%">American Zoologist</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2000</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2000///</style></date></pub-dates></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.bioone.org.proxy.uchicago.edu/doi/full/10.1668/0003-1569%282000%29040%5B0759%3AHADCAM%5D2.0.CO%3B2</style></url></web-urls></urls><volume><style face="normal" font="default" size="100%">40</style></volume><pages><style face="normal" font="default" size="100%">759 - 769</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Much attention has been paid to the role of developmental information in estimating phylogenetic relationships and, more recently, to the use of phylogenies in understanding the evolution of development. At the moment, however, we lack a sufficiently general theory connecting phylogenetic patterns of character evolution to properties of developmental systems. Here we outline a simple model relating homoplasy to the rate of character change and the number of evolvable states, both of which may reflect developmental constraints. Given a particular rate of character change, the fewer the evolvable states the more homoplasy is expected, and vice versa. The repeated evolution of a limited number of forms of bilateral flower symmetry may reflect constraints imposed by overall flower orientation and underlying mechanisms of differentiation.</style></abstract><issue><style face="normal" font="default" size="100%">5</style></issue></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Richard H. Ree</style></author><author><style face="normal" font="default" size="100%">Donoghue,Michael J.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Inferring Rates of Change in Flower Symmetry in Asterid Angiosperms</style></title><secondary-title><style face="normal" font="default" size="100%">Systematic Biology</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">1999</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.informaworld.com/10.1080/106351599260201</style></url></web-urls><related-urls><url><style face="normal" font="default" size="100%">http://www.reelab.net/home/sites/default/files/Ree_and_Donoghue-1999-SystBio.pdf</style></url></related-urls></urls><number><style face="normal" font="default" size="100%">3</style></number><volume><style face="normal" font="default" size="100%">48</style></volume><pages><style face="normal" font="default" size="100%">633</style></pages><language><style face="normal" font="default" size="100%">eng</style></language></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Richard H. Ree</style></author><author><style face="normal" font="default" size="100%">Donoghue,Michael J.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Step Matrices and the Interpretation of Homoplasy..</style></title><secondary-title><style face="normal" font="default" size="100%">Systematic Biology</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">1998</style></year><pub-dates><date><style  face="normal" font="default" size="100%">1998/12//</style></date></pub-dates></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://proxy.uchicago.edu/login?url=http://search.ebscohost.com/login.aspx?direct=true&db=hch&AN=1454164&loginpage=Login.asp&site=ehost-live&scope=site</style></url></web-urls><related-urls><url><style face="normal" font="default" size="100%">http://www.reelab.net/home/sites/default/files/Ree_and_Donoghue-1998-SystBio.pdf</style></url></related-urls></urls><volume><style face="normal" font="default" size="100%">47</style></volume><pages><style face="normal" font="default" size="100%">582 - 588</style></pages><isbn><style face="normal" font="default" size="100%">10635157</style></isbn><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Assumptions about the costs of character change, coded in the form of a step matrix, determine most-parsimonious inferences of character evolution on phylogenies. We present a graphical approach to exploring the relationship between cost assumptions and evolutionary inferences from character data. The number of gains and losses of a binary trait on a phylogeny can be plotted over a range of cost assumptions, to reveal the inflection point at which there is a switch from more gains to more losses and the point at which all changes are inferred to be in one direction or the other. Phylogenetic structure in the data, the tree shape, and the relative frequency of states among the taxa influence the shape of such graphs and complicate the interpretation of possible permutationbased tests for directionality of change. The costs at which the most-parsimonious state of each internal node switches from one state to another can also be quantified by iterative ancestral-state reconstruction over a range of costs. This procedure helps identify the most robust inferences of change in each direction, which should be of use in designing comparative studies. [Ancestral states; character evolution; homoplasy; parsimony; phylogenetic inference.]. [ABSTRACT FROM AUTHOR] Copyright of Systematic Biology is the property of Taylor &amp; Francis Ltd and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts)</style></abstract><issue><style face="normal" font="default" size="100%">4</style></issue><notes><style face="normal" font="default" size="100%">Accession Number: 1454164; Ree, Richard H.; Donoghue, Michael J.; Source Information: Dec98, Vol. 47 Issue 4, p582; Number of Pages: 7p; Document Type: Article</style></notes></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Donoghue,Michael J.</style></author><author><style face="normal" font="default" size="100%">Richard H. Ree</style></author><author><style face="normal" font="default" size="100%">Baum,David A.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Phylogeny and the evolution of flower symmetry in the Asteridae</style></title><secondary-title><style face="normal" font="default" size="100%">Trends in Plant Science</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">evolution</style></keyword><keyword><style  face="normal" font="default" size="100%">flower</style></keyword><keyword><style  face="normal" font="default" size="100%">symmetry</style></keyword><keyword><style  face="normal" font="default" size="100%">systematics</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">1998</style></year><pub-dates><date><style  face="normal" font="default" size="100%">1998/08/01/</style></date></pub-dates></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.sciencedirect.com/science/article/B6TD1-3VCR1N6-9/2/8f40798f05a963fd3470fab0d1e0b198</style></url></web-urls><related-urls><url><style face="normal" font="default" size="100%">http://www.reelab.net/home/sites/default/files/Donoghue_et_al-1998-TPS.pdf</style></url></related-urls></urls><volume><style face="normal" font="default" size="100%">3</style></volume><pages><style face="normal" font="default" size="100%">311 - 317</style></pages><isbn><style face="normal" font="default" size="100%">1360-1385</style></isbn><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Phylogenetic 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.
</style></abstract><issue><style face="normal" font="default" size="100%">8</style></issue></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Richard H. Ree</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Pollen Flow, Fecundity, and the Adaptive Significance of Heterostyly in Palicourea padifolia (Rubiaceae)</style></title><secondary-title><style face="normal" font="default" size="100%">Biotropica</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">1997</style></year><pub-dates><date><style  face="normal" font="default" size="100%">1997/09//</style></date></pub-dates></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.jstor.org/stable/2389145</style></url></web-urls></urls><volume><style face="normal" font="default" size="100%">29</style></volume><pages><style face="normal" font="default" size="100%">298 - 308</style></pages><isbn><style face="normal" font="default" size="100%">00063606</style></isbn><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Palicourea padifolia is a distylous shrub visited primarily by hummingbirds and bees in mid-elevation rain forests in Costa Rica. At Las Cruces Biological Station, the population of P. padifolia is composed of equal numbers of pin and thrum plants and morphs are randomly distributed. Like the majority of distylous species, P. padifolia exhibits a self- and intramorph-incompatible mating system. The analysis of stigmatic pollen loads obtained from emasculated flowers shows that pollen flow between floral morphs is disassortative, which supports the Darwinian hypothesis concerning the adaptive significance of heterostyly. Pins experience greater disassortative pollination than thrums. Pins also set more seed than thrums, suggesting that the higher frequency of compatible pollen deposited on pin stigmas results in greater fecundity; alternatively, greater seed set in pins could be due to the differential allocation of resources to male and female function between morphs. Overall, seed set for the Las Cruces population of P. padifolia is much lower than the potential maximum. Factors which could contribute to seed set limitation include the frequency and/or spatial pattern of pollinator visits, pollen availability, and resource availability.</style></abstract><issue><style face="normal" font="default" size="100%">3</style></issue><notes><style face="normal" font="default" size="100%">Palicourea padifolia is a distylous shrub visited primarily by hummingbirds and bees in mid-elevation rain forests in Costa Rica. At Las Cruces Biological Station, the population of P. padifolia is composed of equal numbers of pin and thrum plants and morphs are randomly distributed. Like the majority of distylous species, P. padifolia exhibits a self- and intramorph-incompatible mating system. The analysis of stigmatic pollen loads obtained from emasculated flowers shows that pollen flow between floral morphs is disassortative, which supports the Darwinian hypothesis concerning the adaptive significance of heterostyly. Pins experience greater disassortative pollination than thrums. Pins also set more seed than thrums, suggesting that the higher frequency of compatible pollen deposited on pin stigmas results in greater fecundity; alternatively, greater seed set in pins could be due to the differential allocation of resources to male and female function between morphs. Overall, seed set for the Las Cruces population of P. padifolia is much lower than the potential maximum. Factors which could contribute to seed set limitation include the frequency and/or spatial pattern of pollinator visits, pollen availability, and resource availability.</style></notes></record></records></xml>