Vanderpoorten, Alain ; Université de Liège - ULiège > Département de Biologie, Ecologie et Evolution > Biologie de l'évolution et de la conservation - aCREA-Ulg
Language :
English
Title :
Quantification of complex modular architecture in plants.
Biot E, Cortizo M, Burguet J, Kiss A, Oughou M, Maugarny-Calès A, Gonçalves B, Adroher B, Andrey P, Boudaoud A et al. 2016. Multiscale quantification of morphodynamics: MorphoLeaf software for 2D shape analysis. Development 143: 3417–3428.
Bouckaert R, Heled J, Kühnert D, Vaughan T, Wu C-H, Xie D, Suchard MA, Rambaut A, Drummond AJ. 2014. BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Computational Biology 10: e1003537.
CBOL Plant Working Group. 2009. A DNA barcode for plants. Proceedings of the National Academy of Sciences, USA 106: 12794–12797.
Carstens B, Pelletier T, Reid N, Satler J. 2013. How to fail in species delimitation. Molecular Ecology 22: 4369–4383.
Castro-Romero R, Montes MM, Martorelli SR, Sepulveda D, Tapia S, Martinez-Aquino A. 2016. Integrative taxonomy of Peniculus, Metapeniculus, and Trifur (Siphonostomatoida: Pennellidae), copepod parasites of marine fishes from Chile: species delimitation analyses using DNA barcoding and morphological evidence. Systematics and Biodiversity 14: 466–483.
Chatrand G. 1985. Introductory graph theory. Dover books on mathematics. New York, NY, USA: Dover Publications.
Cope JS, Corney D, Clark JY, Remagnino P, Wilkin P. 2012. Plant species identification using digital morphometrics: a review. Expert Systems with Applications 39: 7562–7573.
Corney D, Clark JY, Tang HL, Wilkin P. 2012. Automatic extraction of leaf characters from herbarium specimens. Taxon 61: 231–244.
Coudert Y, Bell NE, Edelin C, Harrison CJ. 2017. Multiple innovations underpinned branching form diversification in mosses. New Phytologist 215: 840–850.
Debortoli N, Li X, Eyres I, Fontaneto D, Hespeels B, Tang C, Flot JF, Van Doninck K. 2016. Genetic exchange among bdelloid rotifers is more likely due to horizontal gene transfer than to meiotic sex. Current Biology 26: 723–732.
Dellicour S, Flot JF. 2015. Delimiting species-poor data sets using single molecular markers: a study of barcode gaps, haplowebs and GMYC. Systematic Biology 64: 900–908.
Diestel R. 2010. Graph theory. Graduate texts in mathematics collection, 4th edn. New York, NY, USA: Springer.
Doyle J. 1995. The irrelevance of allele tree topologies for species delimitation and a non-topological alternative. Systematic Botany 20: 574–588.
Drummond AJ, Rambaut A. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology 7: 214.
Esteve-Altava B. 2017. In search of morphological modules: a systematic review. Biological Reviews 92: 1332–1347.
Ezard T, Fujisawa T, Barraclough T. 2009. splits: SPecies’ LImits by Threshold Statistics. R package version 1.0-11/r29. [WWW document] URL http://r-forge.r-project.org/projects/splits/
Ferreira T. 2016. hIPNAT: hIPNAT 1.0.1. doi 10.5281/zenodo.49399.
Flot JF. 2007. CHAMPURU 1.0: a computer software for unraveling mixtures of two DNA sequences of unequal lengths. Molecular Ecology Notes 7: 974–977.
Flot JF. 2010. SeqPHASE: a web tool for interconverting PHASE input/output files and FASTA sequence alignments. Molecular Ecology Resources 10: 162–166.
Flot JF. 2015. Species delimitation's coming of age. Systematic Biology 64: 897–899.
Flot JF, Couloux A, Tillier S. 2010. Haplowebs as a graphical tool for delimiting species: a revival of Doyle's “Field For Recombination” approach and its application to the coral genus Pocillopora in Clipperton. BMC Evolutionary Biology 10: 372–384.
Flot JF, Tillier A, Samadi S, Tillier S. 2006. Phase determination from direct sequencing of length-variable DNA regions. Molecular Ecology Notes 6: 627–630.
Fontaneto D, Flot JF, Cuong Q. 2015. Guidelines for DNA taxonomy, with a focus on the meiofauna. Marine Biodiversity 45: 433–451.
Friedland G, Jantz K, Lentz T, Rojas R. 2006. Extending the SIOX algorithm: alternative clustering methods, sub-pixel accurate object extraction from still images, and generic video segmentation. Berlin, Germany: Free University of Berlin, Department of Computer Science.
Fujisawa T, Barraclough TG. 2013. Delimiting species using single-locus data and the generalized mixed yule coalescent approach: a revised method and evaluation on simulated data sets. Systematic Biology 62: 707–724.
Fujita M, Leaché A, Burbrink F, McGuire J, Moritz C. 2012. Coalescent-based species delimitation in an integrative taxonomy. Trends in Ecology and Evolution 27: 480–488.
Harper JB, Rosen B, White J. 1986. The growth and form of modular organisms. Philosophical Transactions of the Royal Society B 313: 1–5.
Horton R. 1945. Erosional development of streams and their drainage basins, hydrophysical approach to quantitative morphology. Geological Society of America Bulletin 53: 275–370.
Ishizaki K, Nishihama R, Yamato KT, Kohchi T. 2016. Molecular genetic tools and techniques for Marchantia polymorpha research. Plant Cell Physiology 57: 262–270.
Johnston EC, Forsman ZH, Flot J-F, Schmidt-Roach S, Pinzón JH, Knapp ISS, Toonen RJ. 2017. A genomic glance through the fog of plasticity and diversification in Pocillopora. Scientific Reports 7: 5991.
Kaandorp JA. 1999. Morphological analysis of growth forms of branching marine sessile organisms along environmental gradients. Marine Biology 134: 295–306.
Kaandorp JA, Koopman EA, Sloot PMA, Bak RPM, Vermeij MJ, Lampmann LEH. 2003. Simulation and analysis of flow patterns around the scleractinian coral Madracis mirabilis (Duchassaing and Michelotti). Philosophical Transactions of the Royal Society B 358: 1551–1157.
Kaandorp JA, Kübler J. 2001. The algorithmic beauty of seaweeds, sponges and corals. New York, NY, USA: Springer.
Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C et al. 2012. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28: 1647–1649.
Konglerd P, Reeb C, Jansson F, Kaandorp JA. 2017. Quantitative morphological analysis of 2D images of complex-shaped branching biological growth forms: the example of branching thalli of liverworts. BMC Research Notes 10: 103.
Kruszyński KJ, Kaandorp JA, van Liere RA. 2007. Computational method for quantifying morphological variation in scleractinian corals. Coral Reefs 26: 831–840.
Liong CY, Foo SF. 2013. Comparison of linear discriminant analysis and logistic regression for data classification. Proceedings of the 20th National Symposium on Mathematical Sciences 1522: 1159–1165.
Lobet G. 2017. Image analysis in plant sciences: publish then perish. Trends in Plant Science 22: 559–566.
Lobet G, Pagès L, Draye X. 2011. A novel image analysis toolbox enabling quantitative analysis of root system architecture. Plant Physiology 157: 29–39.
Lobet G, Pound MP, Diener J, Pradal C, Draye X, Godin C, Javaux M, Leitner D, Meunier F, Nacry P et al. 2015. Root System Markup Language: toward a unified root architecture description language. Plant Physiology 167: 617–627.
Matsumoto A. 2004. Heterogeneous and compensatory growth in Melithaea flabellifera (Octocorallia: Melithaeidae) in Japan. Hydrobiologia 530: 389–397.
Mishler B, De Luna E. 1991. The use of ontogenetic data in phylogenetic analysis. Advances in Bryology 4: 123–167.
Monaghan M, Wild R, Elliot M, Fujisawa T, Balke M, Inward D, Lees D, Ranaivosolo R, Eggleton P, Barraclough T et al. 2009. Accelerated species inventory on Madagascar using coalescent-based models of species delineation. Systematic Biology 58: 298–311.
Montagna M, Mereghetti V, Lencioni V, Rossaro B. 2016. Integrated taxonomy and DNA barcoding of Alpine midges (Diptera: Chironomidae). PLoS ONE 11: e0149673.
Oliver P, Lee M. 2010. The botanical and zoological code impede biodiversity research by discouiraging publicatIon of unamed species. Taxon 59: 1201–1205.
Pante E, Schoelinck C, Puillandre N. 2015. From integrative taxonomy to species description: one step beyond. Systematic Biology 64: 152–160.
Pohar M, Blas M, Turk S. 2004. Comparison of logistic regression and linear discriminant analysis: a simulation study. Metodološki zvezki 1: 143–161.
Press SJ, Wilson S. 1978. Choosing between logistic regression and discriminant analysis. Journal of the American Statistical Association 73: 699–705.
Preußing M, Olsson S, Schäfer-Verkimp A, Wickett N, Wicke D, Nebel M. 2010. New insights of the evolution of the liverwort family Aneuraceae (Metzgeriales, Marchantiophyta), with emphasis on the genus Lobatiriccardia. Taxon 59: 1424–1240.
Puillandre N, Baylac M, Boisselier-Dubayle MC, Cruaud C, Samadi S. 2009. An integrative approach to species delimitation in Benthomangelia (Mollusca: Conoidea). Biological Journal of the Linnean Society 96: 696–708.
Puillandre N, Lambert A, Brouillet S, Achaz G. 2012. ABGD Automatic Barcode Gap Discovery for primary species delimitation. Molecular Ecology 21: 1864–1877.
Rabeau L, Gradstein R, Dubuisson JY, Nebel M, Quandt D, Reeb C. 2017. New insights into the phylogeny and relationships among the worldwide genus Riccardia (Aneuraceae, Marchantiophytina). European Journal of Taxonomy 273: 1–6.
Raftery A, Newton M, Satagopan J, Krivitsky P. 2007. Estimating the integrated likelihood via posterior simulation using the harmonic mean identity. In: Bernardo JM, Bayarri MJ, Berger JO, eds. Bayesian statistics. New York, NY, USA: Oxford University Press, 1–45.
Rambaut A, Suchard MA, Xie D, Drummond AJ. 2014. Tracer v1.6. [WWW document] URL http://tree.bio.ed.ac.uk/software/tracer/
Reeb C, Bardat J. 2014. Studies on African types and related materials. Cryptogamie Bryologie 35: 47–75.
Renner MAM, Heslewood MM, Patzak SDF, Schäfer-Verwimp A, Heinrichs J. 2017. By how much do we underestimate species diversity of liverworts using morphological evidence? An example from Australasian Plagiochila (Plagiochilaceae: Jungermanniopsida). Molecular Phylogenetics and Evolution 107: 576–593.
Saïd AH, Hennequin S, Rouhan G, Dubuisson J-Y. 2017. Disentangling the diversity and taxonomy of Hymenophyllaceae (Hymenophyllales, polypodiidae) in the Comoros. European Journal of Taxonomy 313: 1–53.
Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, Preibisch S, Rueden C, Saalfeld S, Schmid B et al. 2012. Fiji: an open-source platform for biological-image analysis. Nature Methods 9: 676–682.
Schneider CA, Rasband WS, Eliceiri KW. 2012. NIH Image to ImageJ: 25 years of image analysis. Nature Methods 9: 671–675.
Song S, Zhao J, Li C. 2017. Species delimitation and phylogenetic reconstruction of the Sinipercids (Perciformes: Sinipercidae) based on target enrichment of thousands of nuclear coding sequences. Molecular Phylogenetics and Evolution 111: 44–55.
Stanton D, Reeb C. 2016. Morphogeometric approaches to non-vascular plants. Frontiers in Plant Sciences 7: 916.
Strahler A. 1952. Hypsometria (area-altitude) analysis of erosional topography. Bulletin of the Geological Society of America 63: 1167–1177.
Talavera G, Dincă V, Vila R. 2013. Factors affecting species delimitations with the GMYC model: insights from a butterfly survey. Methods in Ecology and Evolution 4: 1101–1110.
Tomlinson P. 1987. Branching is a process, not a concept. Taxon 36: 54–57.
Unger J, Merhof D, Renner S. 2016. Computer vision applied to herbarium specimens of German trees: testing the future utility of the millions of herbarium specimen images for automated identification. BMC Evolutionary Biology 16: 248.
Zanardo S, Zaliapin I, Foulafoula-Giorgio E. 2013. Are American rivers Tokunaga self-similar? New results on fluvial network topology and its climatic dependence. Journal of Geophysical Research 118: 1–18.
Zhang J, Kapli P, Pavlidis P, Stamatakis A. 2013. A general species delimitation method with applications to phylogenetic placements. Bioinformatics 29: 2869–2876.
Zhang TY, Suen CY. 1984. A fast parallel algorithm for thinning digital patterns. Communication of the ACM 27: 236–239.
Zhao S, Guo Y, Sheng Q, Shyr Y. 2014. Heatmap3: an improved heatmap package with more powerful and convenient features. BMC Bioinformatics 15: P16.