المؤلفون: Vladimir Mikryukov, Kessy Abarenkov, Shawn Laffan, Tim Robertson, Emily Jane McTavish, Thomas Stjernegaard Jeppesen, John Waller, Matthew Blissett, Urmas Kõljalg, Joseph T. Miller

المصدر: BMC Ecology and Evolution, Vol 24, Iss 1, Pp 1-13 (2024)

مصطلحات موضوعية: Big data, Biodiversity, Data cleaning, Derived datasets, GBIF, Open Tree of Life, Ecology, QH540-549.5, Evolution, QH359-425

وصف الملف: electronic resource

Relation: https://doaj.org/toc/2730-7182

URL الوصول: https://doaj.org/article/4ab69d1244e64a64ab1b9ccdde4eba85

المؤلفون: Luna L. Sanchez Reyes, Emily Jane McTavish

المصدر: Journal of Statistics and Data Science Education, Vol 30, Iss 3, Pp 304-310 (2022)

مصطلحات موضوعية: Datelife, Open science, Open Tree of Life, Pedagogy, Phylogenetics, R programming language, Probabilities. Mathematical statistics, QA273-280, Special aspects of education, LC8-6691

وصف الملف: electronic resource

Relation: https://doaj.org/toc/2693-9169

URL الوصول: https://doaj.org/article/023a67c55ad843aeaf606c0f400c81fc

المؤلفون: Ewers-Saucedo, Christine, Owen, Christopher L, Perez-Losada, Marcos, Høeg, Jens T., Glenner, Henrik, Chan, Benny K.K., Crandall, Keith A.

المصدر: PeerJ

مصطلحات موضوعية: Barnacles, Thecostraca, Synthesis tree, Open tree of life, Phylogenetic studies, Taxonomy, Morphology

وصف الملف: application/pdf

Relation: urn:issn:2167-8359; http://hdl.handle.net/1956/21665; https://doi.org/10.7717/peerj.7387; cristin:1764553

الاتاحة: http://hdl.handle.net/1956/21665
https://doi.org/10.7717/peerj.7387

المؤلفون: Buntrock,Lydia, Renard,Bernhard, Heitlinger,Emanuel

المصدر: Biodiversity Information Science and Standards 2: e25739

مصطلحات موضوعية: Ancestral state reconstruction, parasites, maximum parsimony, Castor, Global biotic interactions (GloBI), Open tree of life (OTL)

وصف الملف: text/html

Relation: info:eu-repo/semantics/altIdentifier/eissn/2535-0897

الاتاحة: https://doi.org/10.3897/biss.2.25739
https://biss.pensoft.net/article/25739/

المؤلفون: Vladimir Mikryukov, Kessy Abarenkov, Shawn Laffan, Tim Robertson, Emily Jane McTavish, Mark Holder, Thomas Stjernegaard Jeppesen, John Waller, Matthew Blissett, Urmas Kõljalg, Joseph T. Miller

مصطلحات موضوعية: docker, singularity, phylogenetic diversity, endemism, biodiversity, spatial phylogenetics, GBIF, Open Tree of Life, PhyloNext

Relation: https://doi.org/10.5281/zenodo.7973797; https://doi.org/10.5281/zenodo.7973798; oai:zenodo.org:7973798

الاتاحة: https://doi.org/10.5281/zenodo.7973798

المؤلفون: Vladimir Mikryukov, Kessy Abarenkov, Shawn Laffan, Tim Robertson, Emily Jane McTavish, Mark Holder, Thomas Stjernegaard Jeppesen, John Waller, Matthew Blissett, Urmas Kõljalg, Joseph T. Miller

مصطلحات موضوعية: biodiversity, phylogenetic diversity, endemism, GBIF, Open Tree of Life, PhyloNext

Relation: https://github.com/vmikk/PhyloNext/tree/1.3.0; https://doi.org/10.5281/zenodo.7973798; https://phylonext.github.io/; https://doi.org/10.5281/zenodo.7974080; https://doi.org/10.5281/zenodo.7974081; oai:zenodo.org:7974081

الاتاحة: https://doi.org/10.5281/zenodo.7974081

المؤلفون: Royal Botanic Gardens, Kew

مصطلحات موضوعية: Taxonomy Working Group, International Legume Conference, ILC 8, Phylogenomics, Legume Genome Sequencing Consortium, Occurrence Data Working Group, Flora do Brasil 2020, Legumes, New species, Advances in Legumes Systematics 14, Acacia, Bean Sprouts, Leguminosae, Bibliographies, Legume Phylogeny Working Group, Open Tree of Life, Lathyrus, Phylogenomic Working Group, Desert Legume Program, Traits Working Group, Rupert Barnaby Award (New York Botanical Garden), Legume Data Portal

Relation: The Bean Bag; https://www.kew.org/science/our-science/publications-and-reports/publications/the-bean-bag

الاتاحة: https://www.kew.org/science/our-science/publications-and-reports/publications/the-bean-bag

المؤلفون: Luna Luisa Sánchez-Reyes, Martha Kandziora, Emily Jane McTavish

المصدر: BMC Bioinformatics, Vol 22, Iss 1, Pp 1-13 (2021)
BMC Bioinformatics

مصطلحات موضوعية: 0106 biological sciences, Open science, Open Tree of Life, QH301-705.5, Gene tree, Computer applications to medicine. Medical informatics, Interoperability, R858-859.7, Tree of life, 010603 evolutionary biology, 01 natural sciences, Biochemistry, Field (computer science), 03 medical and health sciences, Gene phylogeny, Multilocus, Structural Biology, Phylogenetics, DNA alignment, Biology (General), Otol, Molecular Biology, Phylogeny, 030304 developmental biology, computer.programming_language, 0303 health sciences, Information retrieval, Phylogenetic tree, Applied Mathematics, Public database, Python (programming language), Reproducibility, Computer Science Applications, Workflow, computer, Software

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2836105aa534cbf0e949f30b7fb0df16
https://doi.org/10.1186/s12859-021-04274-6

المؤلفون: Daijiang Li, Pamela S. Soltis, Douglas E. Soltis, Robert P. Guralnick, Lauren B. Trotta, Hannah E. Marx, Benjamin Baiser, Miao Sun, Julie M. Allen

المصدر: Ecology

مصطلحات موضوعية: 0106 biological sciences, Beta diversity, Tree of life, Biology, 010603 evolutionary biology, 01 natural sciences, Article, 03 medical and health sciences, community phylogenetic structure, Phylogenetics, Ecology, Evolution, Behavior and Systematics, Phylogeny, 030304 developmental biology, 0303 health sciences, Phylogenetic tree, open tree of life, trait, Ecology, 010604 marine biology & hydrobiology, phylogenetic signal, Articles, alpha diversity, Tree (graph theory), Phylogenetic diversity, Evolutionary biology, Trait, phylogenetic diversity, Pairwise comparison, Alpha diversity, beta diversity, Gene sequence

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8cf491a26c98819eb65be58fb2bebdd7
http://europepmc.org/articles/PMC7079099

المؤلفون: Li, Daijiang, Trotta, Lauren, Marx, Hannah E., Allen, Julie M., Sun, Miao, Soltis, Douglas E., Soltis, Pamela S., Guralnick, Robert P., Baiser, Benjamin

مصطلحات موضوعية: phylogenetic signal, trait, alpha diversity, open tree of life, community phylogenetic structure, beta diversity, phylogenetic diversity, Ecology and Evolutionary Biology, Science

وصف الملف: application/pdf

Relation: Li, Daijiang; Trotta, Lauren; Marx, Hannah E.; Allen, Julie M.; Sun, Miao; Soltis, Douglas E.; Soltis, Pamela S.; Guralnick, Robert P.; Baiser, Benjamin (2019). "For common community phylogenetic analyses, go ahead and use synthesis phylogenies." Ecology 100(9): n/a-n/a.; https://hdl.handle.net/2027.42/151322; Ecology; Pons, J., T. G. Barraclough, J. Gomez‐Zurita, A. Cardoso, D. P. Duran, S. Hazell, S. Kamoun, W. D. Sumlin, and A. P. Vogler. 2006. Sequence‐based species delimitation for the DNA taxonomy of undescribed insects. Systematic Biology 55: 595 – 609.; Li, D., and D. M. Waller. 2017. Fire exclusion and climate change interact to affect long‐term changes in the functional composition of plant communities. Diversity and Distributions 23: 496 – 506.; Li, D., A. R. Ives, and D. M. Waller. 2017. Can functional traits account for phylogenetic signal in community composition? New Phytologist 214: 607 – 618.; Lozupone, C., and R. Knight. 2005. UniFrac: A new phylogenetic method for comparing microbial communities. Applied and Environmental Microbiology 71: 8228 – 8235.; Maherali, H., and J. N. Klironomos. 2007. Influence of phylogeny on fungal community assembly and ecosystem functioning. Science 316: 1746 – 1748.; Marx, H. E., C. Dentant, J. Renaud, R. Delunel, D. C. Tank, and S. Lavergne. 2017. Riders in the sky (islands): Using a mega‐phylogenetic approach to understand plant species distribution and coexistence at the altitudinal limits of angiosperm plant life. Journal of Biogeography 44: 2618 – 2630.; Miller, E. T., D. R. Farine, and C. H. Trisos. 2017. Phylogenetic community structure metrics and null models: A review with new methods and software. Ecography 40: 461 – 477.; Molina‐Venegas, R., and M. Á. Rodriguez. 2017. Revisiting phylogenetic signal; strong or negligible impacts of polytomies and branch length information? BMC Evolutionary Biology 17: 53.; Münkemüller, T., S. Lavergne, B. Bzeznik, S. Dray, T. Jombart, K. Schiffers, and W. Thuiller. 2012. How to measure and test phylogenetic signal. Methods in Ecology and Evolution 3: 743 – 756.; Pagel, M. 1999. Inferring the historical patterns of biological evolution. Nature 401: 877.; Paradis, E., J. Claude, and K. Strimmer. 2004. APE: Analyses of phylogenetics and evolution in R language. Bioinformatics 20: 289 – 290.; Park, D. S., S. Worthington, and Z. Xi. 2018. Taxon sampling effects on the quantification and comparison of community phylogenetic diversity. Molecular Ecology 27: 1296 – 1308.; Patrick, L. E., and R. D. Stevens. 2014. Investigating sensitivity of phylogenetic community structure metrics using North American desert bats. Journal of Mammalogy 95: 1240 – 1253.; Pearse, W. D., and A. Purvis. 2013. PhyloGenerator: An automated phylogeny generation tool for ecologists. Methods in Ecology and Evolution 4: 692 – 698.; Stamatakis, A. 2014. RAxML version 8: A tool for phylogenetic analysis and post‐analysis of large phylogenies. Bioinformatics 30: 1312 – 1313.; Qian, H., and J. Zhang. 2016. Are phylogenies derived from family‐level supertrees robust for studies on macroecological patterns along environmental gradients? Journal of Systematics and Evolution 54: 29 – 36.; R Core Team. 2017. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. www.r-project.org; Rabosky, D. L., F. Santini, J. Eastman, S. A. Smith, B. Sidlauskas, J. Chang, and M. E. Alfaro. 2013. Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation. Nature Communications 4: 1958.; Ronquist, F., and J. P. Huelsenbeck. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572 – 1574.; Smith, M. A., W. Hallwachs, and D. H. Janzen. 2014. Diversity and phylogenetic community structure of ants along a Costa Rican elevational gradient. Ecography 37: 720 – 731.; Smith, S. A., J. M. Beaulieu, and M. J. Donoghue. 2009. Mega‐phylogeny approach for comparative biology: An alternative to supertree and supermatrix approaches. BMC Evolutionary Biology 9: 37.; Smith, S. A., and J. W. Brown. 2018. Constructing a broadly inclusive seed plant phylogeny. American Journal of Botany 105: 302 – 314.; Swenson, N. G. 2009. Phylogenetic resolution and quantifying the phylogenetic diversity and dispersion of communities. PLoS ONE 4: e4390.; Trotta, L., B. Baiser, J. Possley, D. Li, J. Lange, S. Martin, and E. Sessa. 2018. Community phylogeny of the globally critically imperiled pine rockland ecosystem. American Journal of Botany 105: 1735 – 1747.; Tsirogiannis, C., and B. Sandel. 2016. PhyloMeasures: A package for computing phylogenetic biodiversity measures and their statistical moments. Ecography 39: 709 – 714.; Tucker, C. M., M. W. Cadotte, S. B. Carvalho, T. J. Davies, S. Ferrier, S. A. Fritz, R. Grenyer, M. R. Helmus, L. S. Jin, and A. O. Mooers. 2017. A guide to phylogenetic metrics for conservation, community ecology and macroecology. Biological Reviews 92: 698 – 715.; Vamosi, S., S. Heard, J. Vamosi, and C. Webb. 2009. Emerging patterns in the comparative analysis of phylogenetic community structure. Molecular Ecology 18: 572 – 592.; Webb, C. O., D. D. Ackerly, M. A. McPeek, and M. J. Donoghue. 2002. Phylogenies and community ecology. Annual Review of Ecology and Systematics 33: 475 – 505.; Webb, C. O., D. D. Ackerly, and S. W. Kembel. 2008. Phylocom: Software for the analysis of phylogenetic community structure and trait evolution. Bioinformatics 24: 2098 – 2100.; Webb, C. O., and M. J. Donoghue. 2005. Phylomatic: Tree assembly for applied phylogenetics. Molecular Ecology Resources 5: 181 – 183.; Wikström, N., V. Savolainen, and M. W. Chase. 2001. Evolution of the angiosperms: Calibrating the family tree. Proceedings of the Royal Society B 268: 2211 – 2220.; Zanne, A. E., D. C. Tank, W. K. Cornwell, J. M. Eastman, S. A. Smith, R. G. FitzJohn, D. J. McGlinn, B. C. O’Meara, A. T. Moles, and P. B. Reich. 2014. Three keys to the radiation of angiosperms into freezing environments. Nature 506: 89 – 92.; Forest, F., R. Grenyer, M. Rouget, T. J. Davies, R. M. Cowling, D. P. Faith, A. Balmford, J. C. Manning, Ş. Procheş, and M. van der Bank. 2007. Preserving the evolutionary potential of floras in biodiversity hotspots. Nature 445: 757 – 760.; Fritz, S. A., O. R. Bininda‐Emonds, and A. Purvis. 2009. Geographical variation in predictors of mammalian extinction risk: Big is bad, but only in the tropics. Ecology Letters 12: 538 – 549.; Hebert, P. D., E. H. Penton, J. M. Burns, D. H. Janzen, and W. Hallwachs. 2004. Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly astraptes fulgerator. Proceedings of the National Academy of Sciences of the United States of America 101: 14812 – 14817.; Allen, J. M. et al. 2019. Spatial phylogenetics of florida vascular plants: The effects of calibration and uncertainty on diversity estimates. IScience 11: 57 – 70.; Antonelli, A., H. Hettling, F. L. Condamine, K. Vos, R. H. Nilsson, M. J. Sanderson, H. Sauquet, R. Scharn, D. Silvestro, and M. Töpel. 2017. Toward a self‐updating platform for estimating rates of speciation and migration, ages, and relationships of taxa. Systematic Biology 66: 152 – 166.; APG III. 2009. An update of the angiosperm phylogeny group classification for the orders and families of flowering plants: APG III. Botanical Journal of the Linnean Society 161: 105 – 121.; APG IV et al. 2016. An update of the angiosperm phylogeny group classification for the orders and families of flowering plants: APG IV. Botanical Journal of the Linnean Society 181: 1 – 20.; Baum, D. A., and S. D. Smith. 2012. Tree thinking: An introduction to phylogenetic biology. Roberts Co., Greenwood Village, Colorado, USA.; Bininda‐Emonds, O. R., M. Cardillo, K. E. Jones, R. D. MacPhee, R. M. Beck, R. Grenyer, S. A. Price, R. A. Vos, J. L. Gittleman, and A. Purvis. 2007. The delayed rise of present‐day mammals. Nature 446: 507.; Blomberg, S. P., T. Garland, and A. R. Ives. 2003. Testing for phylogenetic signal in comparative data: Behavioral traits are more labile. Evolution 57: 717 – 745.; Boyle, E. E., and S. J. Adamowicz. 2015. Community phylogenetics: Assessing tree reconstruction methods and the utility of DNA barcodes. PLoS ONE 10: e0126662.; Cadotte, M. W. 2015. Phylogenetic diversity–ecosystem function relationships are insensitive to phylogenetic edge lengths. Functional Ecology 29: 718 – 723.; Cardillo, M. 2011. Phylogenetic structure of mammal assemblages at large geographical scales: Linking phylogenetic community ecology with macroecology. Philosophical Transactions of the Royal Society B 366: 2545 – 2553.; Cavender‐Bares, J., and P. B. Reich. 2012. Shocks to the system: Community assembly of the oak savanna in a 40‐year fire frequency experiment. Ecology 93: S52 – S69.; Cavender‐Bares, J., A. Keen, and B. Miles. 2006. Phylogenetic structure of Floridian plant communities depends on taxonomic and spatial scale. Ecology 87: S109 – S122.; Cavender‐Bares, J., K. H. Kozak, P. V. Fine, and S. W. Kembel. 2009. The merging of community ecology and phylogenetic biology. Ecology Letters 12: 693 – 715.; Davies, T. J., N. J. Kraft, N. Salamin, and E. M. Wolkovich. 2012. Incompletely resolved phylogenetic trees inflate estimates of phylogenetic conservatism. Ecology 93: 242 – 247.; Drummond, A. J., and A. Rambaut. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology 7: 214.; Eastman, J. M., L. J. Harmon, and D. C. Tank. 2013. Congruification: Support for time scaling large phylogenetic trees. Methods in Ecology and Evolution 4: 688 – 691.; Edgar, R. C. 2004. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32: 1792 – 1797.; Faith, D. P. 1992. Conservation evaluation and phylogenetic diversity. Biological Conservation 61: 1 – 10.; Helmus, M. R., K. Savage, M. W. Diebel, J. T. Maxted, and A. R. Ives. 2007. Separating the determinants of phylogenetic community structure. Ecology Letters 10: 917 – 925.; Hinchliff, C. E., S. A. Smith, J. F. Allman, J. G. Burleigh, R. Chaudhary, L. M. Coghill, K. A. Crandall, J. Deng, B. T. Drew, and R. Gazis. 2015. Synthesis of phylogeny and taxonomy into a comprehensive tree of life. Proceedings of the National Academy of Sciences 112: 12764 – 12769.; Ives, A. R., and M. R. Helmus. 2010. Phylogenetic metrics of community similarity. American Naturalist 176: E128 – E142.; Jetz, W., G. Thomas, J. Joy, K. Hartmann, and A. Mooers. 2012. The global diversity of birds in space and time. Nature 491: 444 – 448.; Kumar, S., G. Stecher, M. Suleski, and S. B. Hedges. 2017. TimeTree: A resource for timelines, timetrees, and divergence times. Molecular Biology and Evolution 34: 1812 – 1819.; Lanfear, R., B. Calcott, S. Y. Ho, and S. Guindon. 2012. PartitionFinder: Combined selection of partitioning schemes and substitution models for phylogenetic analyses. Molecular Biology and Evolution 29: 1695 – 1701.; Lavergne, S., N. Mouquet, W. Thuiller, and O. Ronce. 2010. Biodiversity and climate change: Integrating evolutionary and ecological responses of species and communities. Annual Review of Ecology, Evolution, and Systematics 41: 321 – 350.

الاتاحة: https://hdl.handle.net/2027.42/151322
https://doi.org/10.1002/ecy.2788

المؤلفون: Ewers-Saucedo, Christine, Owen, Christopher L, Perez-Losada, Marcos, Høeg, Jens T., Glenner, Henrik, Chan, Benny K.K., Crandall, Keith A.

الاتاحة: http://hdl.handle.net/1956/21665

المؤلفون: Smith, Stephen A., Brown, Joseph W.

مصطلحات موضوعية: clustering, divergence‐time estimation, diversification, GenBank, Open Tree of Life, phylogenetics, phylogenetic methods, plant tree of life, seed plants, Biology, Botany, Science

وصف الملف: application/pdf

Relation: Smith, Stephen A.; Brown, Joseph W. (2018). "Constructing a broadly inclusive seed plant phylogeny." American Journal of Botany 105(3): 302-314.; https://hdl.handle.net/2027.42/143673; American Journal of Botany; Sauquet, H., M. von Balthazar, S. Magallón, J. A. Doyle, P. K. Endress, E. J. Bailes, E. Barroso de Morais, et al. 2017. The ancestral flower of angiosperms and its early diversification. Nature Communications 8: 16047.; Rabosky, D. L., F. Santini, J. M. Eastman, S. A. Smith, B. Sidlauskas, J. Chang, and M. E. Alfaro. 2013. Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation. Nature Communications 4: 1958.; Redelings, B. D., and M. T. Holder. 2017. A supertree pipeline for summarizing phylogenetic and taxonomic information for millions of species. PeerJ 5: e3058.; Rees, J., and K. Cranston. 2017. Automated assembly of a reference taxonomy for phylogenetic data synthesis. Biodiversity Data Journal 5: e12581.; Salichos, L., A. Stamatakis, and A. Rokas. 2014. Novel information theory‐based measures for quantifying incongruence among phylogenetic trees. Molecular Biology and Evolution 31: 1261 – 1271.; Sanderson, M. J. 2002. Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Molecular Biology and Evolution 19: 101 – 109.; Sanderson, M. J. 2008. Phylogenetic signal in the eukaryotic tree of life. Science 321: 121 – 123.; Sanderson, M. J., D. Boss, D. Chen, K. A. Cranston, and A. Wehe. 2008. The PhyLoTA browser: processing GenBank for molecular phylogenetics research. Systematic Biology 57: 335 – 346.; Shen, X.‐ X., C. T. Hittinger, and A. Rokas. 2017. Contentious relationships in phylogenomic studies can be driven by a handful of genes. Nature Ecology & Evolution 1: 126.; Smith, S. A., and J. M. Beaulieu. 2009. Life history influences rates of climatic niche evolution in flowering plants. Proceedings of the Royal Society, B Biological Sciences 276: 4345 – 4352.; Smith, S. A., J. M. Beaulieu, and M. J. Donoghue. 2009. Mega‐phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches. BMC Evolutionary Biology 9: 37.; Smith, S. A., J. M. Beaulieu, A. Stamatakis, and M. J. Donoghue. 2011. Understanding angiosperm diversification using small and large phylogenetic trees. American Journal of Botany 98: 404 – 414.; Smith, S. A., J. W. Brown, and C. E. Hinchliff. 2013. Analyzing and synthesizing phylogenies using tree alignment graphs. PLoS computational Biology 9: e1003223.; Smith, S. A., J. W. Brown, Y. Yang, R. Bruenn, C. P. Drummond, S. F. Brockington, J. F. Walker, et al. 2017. Disparity, diversity, and duplications in the Caryophyllales. New Phytologist 217: 836 – 854.; Smith, S. A., and M. J. Donoghue. 2008. Rates of molecular evolution are linked to life history in flowering plants. Science 322: 86 – 89.; Smith, S. A., M. J. Moore, J. W. Brown, and Y. Yang. 2015. Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants. BMC Evolutionary Biology 15: 150.; Smith, S. A., and B. C. O’Meara. 2012. treePL: divergence time estimation using penalized likelihood for large phylogenies. Bioinformatics 28: 2689 – 2690.; Soltis, D. E., S. A. Smith, N. Cellinese, K. J. Wurdack, D. C. Tank, S. F. Brockington, N. F. Refulio‐Rodriguez, et al. 2011. Angiosperm phylogeny: 17 genes, 640 taxa. American Journal of Botany 98: 704 – 730.; Stamatakis, A. 2014. RAxML version 8: a tool for phylogenetic analysis and post‐analysis of large phylogenies. Bioinformatics 30: 1312 – 1313.; Tank, D. C., J. M. Eastman, M. W. Pennell, P. S. Soltis, D. E. Soltis, C. E. Hinchliff, J. W. Brown, et al. 2015. Nested radiations and the pulse of angiosperm diversification: increased diversification rates often follow whole genome duplications. New Phytologist 207: 454 – 467.; Walker, J. F., Y. Yang, M. J. Moore, J. Mikenas, A. Timoneda, S. F. Brockington, and S. A. Smith. 2017. Widespread paleopolyploidy, gene tree conflict, and recalcitrant relationships among the carnivorous Caryophyllales. American Journal of Botany 104: 858 – 867.; Wickett, N. J., S. Mirarab, N. Nguyen, T. Warnow, E. Carpenter, N. Matasci, S. Ayyampalayam, et al. 2014. Phylotranscriptomic analysis of the origin and early diversification of land plants. Proceedings of the National Academy of Sciences, USA 111: E4859 – E4868.; Yang, Y., and S. A. Smith. 2014. Orthology inference in nonmodel organisms using transcriptomes and low‐coverage genomes: improving accuracy and matrix occupancy for phylogenomics. Molecular Biology and Evolution 31: 3081 – 3092.; Yang, Y., M. J. Moore, S. F. Brockington, D. E. Soltis, G. K.‐S. Wong, E. J. Carpenter, Y. Zhang, et al. 2015. Dissecting molecular evolution in the highly diverse plant clade Caryophyllales using transcriptome sequencing. Molecular Biology and Evolution 32: 2001 – 2014.; Zanne, A. E., D. C. Tank, W. K. Cornwell, J. M. Eastman, S. A. Smith, R. G. FitzJohn, D. J. McGlinn, et al. 2014. Three keys to the radiation of angiosperms into freezing environments. Nature 506: 89 – 92.; Antonelli, A., H. Hettling, F. L. Condamine, K. Vos, R. H. Nilsson, M. J. Sanderson, H. Sauquet, et al. 2017. Toward a self‐updating platform for estimating rates of speciation and migration, ages, and relationships of taxa. Systematic Biology 66: 152 – 166.; Beaulieu, J. M., B. C. O’Meara, P. Crane, and M. J. Donoghue. 2015. Heterogeneous rates of molecular evolution and diversification could explain the Triassic age estimate for angiosperms. Systematic Biology 64: 869 – 878.; Beaulieu, J. M., R. H. Ree, J. Cavender‐Bares, G. D. Weiblen, and M. J. Donoghue. 2012. Synthesizing phylogenetic knowledge for ecological research. Ecology 93: S4 – S13.; Berger, S. A., D. Krompass, and A. Stamatakis. 2011. Performance, accuracy, and Web server for evolutionary placement of short sequence reads under maximum likelihood. Systematic Biology 60: 291 – 302.; Bocak, L., C. Barton, A. Crampton‐Platt, D. Chesters, D. Ahrens, and A. P. Vogler. 2013. Building the Coleoptera tree‐of‐life for >8000 species: composition of public DNA data and fit with Linnaean classification. Systematic Entomology 39: 97 – 110.; Brown, J. M., and R. C. Thomson. 2016. Bayes factors unmask highly variable information content, bias, and extreme influence in phylogenomic analyses. Systematic Biology 66: 517 – 530.; Chase, M. W., D. E. Soltis, R. G. Olmstead, D. Morgan, D. H. Les, B. D. Mishler, M. R. Duvall, et al. 1993. Phylogenetics of seed plants: An analysis of nucleotide sequences from the plastid gene rbcL. Annals of the Missouri Botanical Garden 80: 528 – 580.; Chesters, D. 2017. Construction of a Species‐level tree of life for the insects and utility in taxonomic profiling. Systematic Biology 66: 426 – 439.; Comer, J. R., W. B. Zomlefer, C. F. Barrett, D. W. Stevenson, K. Heyduk, and J. H. Leebens‐Mack. 2016. Nuclear phylogenomics of the palm subfamily Arecoideae (Arecaceae). Molecular Phylogenetics and Evolution 97: 32 – 42.; Cornwell, W. K., M. Westoby, D. S. Falster, R. G. FitzJohn, B. C. O’Meara, M. W. Pennell, D. J. McGlinn, et al. 2014. Functional distinctiveness of major plant lineages. Journal of Ecology 102: 345 – 356.; Dongen, S. M. V. 2000. Graph clustering by flow simulation. PhD dissertation, University of Utrecht, Utrecht, Netherlands.; Donoghue, M. J. 2005. Key innovations, convergence, and success: macroevolutionary lessons from plant phylogeny. Paleobiology 31: 77 – 93.; Donoghue, M. J., and J. A. Doyle. 2000. Seed plant phylogeny: Demise of the anthophyte hypothesis? Current Biology 10: R106 – R109.; Donoghue, M. J., and M. J. Sanderson. 2015. Confluence, synnovation, and depauperons in plant diversification. New Phytologist 207: 260 – 274.; Driskell, A. C., C. Ané, J. G. Burleigh, M. M. McMahon, B. C. O’Meara, and M. J. Sanderson. 2004. Prospects for building the tree of life from large sequence databases. Science 306: 1172 – 1174.; Eastman, J. M., L. J. Harmon, and D. C. Tank. 2013. Congruification: support for time scaling large phylogenetic trees. Methods in Ecology and Evolution 4: 688 – 691.; Edwards, E. J., J. M. de Vos, and M. J. Donoghue. 2015. Doubtful pathways to cold tolerance in plants. Nature 521: E5 – E6.; Edwards, E. J., C. P. Osborne, C. A. E. Strömberg, S. A. Smith, C4 Grasses Consortium, W. J. Bond, and P.‐ A. Christin, et al. 2010. The origins of C 4 grasslands: integrating evolutionary and ecosystem science. Science 328: 587 – 591.; Edwards, E. J., and S. A. Smith. 2010. Phylogenetic analyses reveal the shady history of C 4 grasses. Proceedings of the National Academy of Sciences, USA 107: 2532 – 2537.; Freyman, W. A. 2015. SUMAC: Constructing phylogenetic supermatrices and assessing partially decisive taxon coverage. Evolutionary Bioinformatics Online 11: 263 – 266.; Givnish, T. J., D. Spalink, M. Ames, S. P. Lyon, S. J. Hunter, A. Zuluaga, W. J. D. Iles, et al. 2015. Orchid phylogenomics and multiple drivers of their extraordinary diversification. Proceedings of the Royal Society, B, Biological Sciences 282: 20151553.; Goldberg, E. E., J. R. Kohn, R. Lande, K. A. Robertson, S. A. Smith, and B. Igić. 2010. Species selection maintains self‐incompatibility. Science 330: 493 – 495.; Goloboff, P. A., S. A. Catalano, J. Marcos Mirande, C. A. Szumik, J. Salvador Arias, M. Källersjö, and J. S. Farris. 2009. Phylogenetic analysis of 73 060 taxa corroborates major eukaryotic groups. Cladistics 25: 211 – 230.; Harmon, L. J., J. T. Weir, C. D. Brock, R. E. Glor, and W. Challenger. 2008. GEIGER: investigating evolutionary radiations. Bioinformatics 24: 129 – 131.; Hedges, S. B., J. Dudley, and S. Kumar. 2006. TimeTree: a public knowledge‐base of divergence times among organisms. Bioinformatics 22: 2971 – 2972.; Hibbett, D. S., R. H. Nilsson, M. Snyder, M. Fonseca, J. Costanzo, and M. Shonfeld. 2005. Automated phylogenetic taxonomy: an example in the homobasidiomycetes (mushroom‐forming fungi). Systematic Biology 54: 660 – 668.; Hinchliff, C. E., and S. A. Smith. 2014. Some limitations of public sequence data for phylogenetic inference (in plants). PloS One 9: e98986.; Hinchliff, C. E., S. A. Smith, J. F. Allman, J. G. Burleigh, R. Chaudhary, L. M. Coghill, K. A. Crandall, et al. 2015. Synthesis of phylogeny and taxonomy into a comprehensive tree of life. Proceedings of the National Academy of Sciences, USA 112: 12764 – 12769.; Izquierdo‐Carrasco, F., J. Cazes, S. A. Smith, and A. Stamatakis. 2014. PUmPER: phylogenies updated perpetually. Bioinformatics 30: 1476 – 1477.; Jetz, W., G. H. Thomas, J. B. Joy, K. Hartmann, and A. Ø. Mooers. 2012. The global diversity of birds in space and time. Nature 491: 444 – 448.; Katoh, K., and D. M. Standley. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution 30: 772 – 780.; Ksepka, D. T., J. F. Parham, J. F. Allman, M. J. Benton, M. T. Carrano, K. A. Cranston, P. C. J. Donoghue, et al. 2015. The fossil calibration database—a new resource for divergence dating. Systematic Biology 64: 853 – 859.; Kuhn, T. S., A. Ø. Mooers, and G. H. Thomas. 2011. A simple polytomy resolver for dated phylogenies. Methods in Ecology and Evolution 2: 427 – 436.; Magallón, S., S. Gómez‐Acevedo, L. L. Sánchez‐Reyes, and T. Hernández‐Hernández. 2015. A metacalibrated time‐tree documents the early rise of flowering plant phylogenetic diversity. New Phytologist 207: 437 – 453.; Matsen, F. A., R. B. Kodner, and E. V. Armbrust. 2010. pplacer: linear time maximum‐likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinformatics 11: 538.; McKain, M. R., H. Tang, J. R. McNeal, S. Ayyampalayam, J. I. Davis, C. W. dePamphilis, T. J. Givnish, et al. 2016. A phylogenomic assessment of ancient polyploidy and genome evolution across the Poales. Genome Biology and Evolution 8: 1150 – 1164.; McMahon, M. M., and M. J. Sanderson. 2006. Phylogenetic supermatrix analysis of GenBank sequences from 2228 papilionoid legumes. Systematic Biology 55: 818 – 836.; McTavish, E. J., C. E. Hinchliff, J. F. Allman, J. W. Brown, K. A. Cranston, M. T. Holder, J. A. Rees, and S. A. Smith. 2015. Phylesystem: a git‐based data store for community‐curated phylogenetic estimates. Bioinformatics 31: 2794 – 2800.; O’Meara, B. C., S. D. Smith, W. S. Armbruster, L. D. Harder, C. R. Hardy, L. C. Hileman, L. Hufford, et al. 2016. Non‐equilibrium dynamics and floral trait interactions shape extant angiosperm diversity. Proceedings of the Royal Society, B, Biological Sciences 283: 20152304.; Pennell, M. W., J. M. Eastman, G. J. Slater, J. W. Brown, J. C. Uyeda, R. G. FitzJohn, M. E. Alfaro, and L. J. Harmon. 2014. geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees. Bioinformatics 30: 2216 – 2218.; Rabosky, D. L. 2015. No substitute for real data: A cautionary note on the use of phylogenies from birth–death polytomy resolvers for downstream comparative analyses. Evolution 69: 3207 – 3216.

الاتاحة: https://hdl.handle.net/2027.42/143673
https://doi.org/10.1002/ajb2.1019

المؤلفون: Michonneau, Franéois, Brown, Joseph W., Winter, David J.

مصطلحات موضوعية: phylogenetics, Open Tree of Life, macroevolution, comparative methods, Ecology and Evolutionary Biology, Science

وصف الملف: application/pdf

Relation: Michonneau, François; Brown, Joseph W.; Winter, David J. (2016). "rotl: an R package to interact with the Open Tree of Life data." Methods in Ecology and Evolution 7(12): 1476-1481.; https://hdl.handle.net/2027.42/135519; Methods in Ecology and Evolution; Revell, L.J. ( 2012 ) phytools: an R package for phylogenetic comparative biology (and other things). Methods in Ecology and Evolution, 3, 217 – 223.; Ksepka, D.T., Parham, J.F., Allman, J.F., Benton, M.J., Carrano, M.T., Cranston, K.A. et al. ( 2015 ) The fossil calibration database—a new resource for divergence dating. Systematic Biology, 64, 853 – 859.; Lewis, P.O. ( 2003 ) NCL: A C++ class library for interpreting data files in NEXUS format. Bioinformatics, 19, 2330 – 2331.; Maddison, D.R., Swofford, D.L. & Maddison, W.P. ( 1997 ) NEXUS: an extensible file format for systematic information. Systematic Biology, 46, 590 – 621.; Magee, A.F., May, M.R. & Moore, B.R. ( 2014 ) The dawn of open access to phylogenetic data.; O’Meara, B.C. ( 2012 ) Evolutionary inferences from phylogenies: a review of methods. Annual Review of Ecology, Evolution, and Systematics, 43, 267 – 285.; Paradis, E., Claude, J. & Strimmer, K. ( 2004 ) APE: Analyses of Phylogenetics and Evolution in R language. Bioinformatics, 20, 289 – 290.; Pearse, W.D. & Purvis, A. ( 2013 ) phyloGenerator: an automated phylogeny generation tool for ecologists. Methods in Ecology and Evolution, 4, 692 – 698.; Pearse, W.D., Cadotte, M.W., Cavender‐Bares, J., Ives, A.R., Tucker, C.M., Walker, S.C. & Helmus, M.R. ( 2015 ) pez: phylogenetics for the environmental sciences. Bioinformatics, 31, 2888 – 2890.; Pennell, M.W., FitzJohn, R.G. & Cornell, W.K. ( 2016 ) A simple approach for maximizing the overlap of phylogenetic and comparative data. Methods in Ecology and Evolution, in press.; Pennell, M.W. & Harmon, L.J. ( 2013 ) An integrative view of phylogenetic comparative methods: connections to population genetics, community ecology, and paleobiology. Annals of the New York Academy of Sciences, 1289, 90 – 105.; Pennell, M.W., Eastman, J.M., Slater, G.J., Brown, J.W., Uyeda, J.C., FitzJohn, R.G., Alfaro, M.E. & Harmon, L.J. ( 2014 ) Geiger V2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees. Bioinformatics, 30, 2216 – 2218.; Schliep, K.P. ( 2011 ) phangorn: phylogenetic analysis in R. Bioinformatics, 27, 592 – 593.; Stoltzfus, A., O’Meara, B., Whitacre, J., Mounce, R., Gillespie, E.L., Kumar, S., Rosauer, D.F. & Vos, R.A. ( 2012 ) Sharing and re‐use of phylogenetic trees (and associated data) to facilitate synthesis. BMC Research Notes, 5, 574.; Varela, S., González‐Hernández, J., Casabella, E. & Barrientos, R. ( 2014 ) rAvis: an R‐package for downloading information stored in proyecto AVIS, a citizen science bird project. PLoS ONE, 9, e91650.; Varela, S., González‐Hernández, J., Sgarbi, L.F., Marshall, C., Uhen, M.D., Peters, S. & Mcclennen, M. ( 2015 ) paleobioDB: an R package for downloading, visualizing and processing data from the Paleobiology Database. Ecography, 38, 419 – 425.; Vos, R.A., Balhoff, J.P., Caravas, J.A., Holder, M.T., Lapp, H., Maddison, W.P. et al. ( 2012 ) NeXML: rich, extensible, and verifiable representation of comparative data and metadata. Systematic Biology, 61, 675 – 689.; Webb, C.O., Ackerly, D.D. & Kembel, S.W. ( 2008 ) Phylocom: software for the analysis of phylogenetic community structure and trait evolution. Bioinformatics, 24, 2098 – 2100.; Webb, C.O., Ackerly, D.D., McPeek, M.A. & Donoghue, M.J. ( 2002 ) Phylogenies and community ecology. Annual Review of Ecology and Systematics, 33, 475 – 505.; Xie, Y. ( 2015 ) Dynamic Documents with R and knitr, 2nd edn. Chapman and Hall/CRC, Boca Raton, FL.; Boettiger, C., Lang, D.T. & Wainwright, P.C. ( 2012 ) Rfishbase: exploring, manipulating and visualizing FishBase data from R. Journal of Fish Biology, 81, 2030 – 2039.; Boettiger, C. & Temple Lang, D. ( 2012 ) Treebase: an R package for discovery, access and manipulation of online phylogenies. Methods in Ecology and Evolution, 3, 1060 – 1066.; Boettiger, C., Chamberlain, S., Hart, E. & Ram, K. ( 2015a ) Building software, building community: lessons from the rOpenSci project. Journal of Open Research Software, 3, p.e8.; Boettiger, C., Chamberlain, S., Vos, R. & Lapp, H. ( 2015b ) RNeXML: a package for reading and writing richly annotated phylogenetic, character, and trait data in R. Methods in Ecology and Evolution, 7, 352 – 357.; Bolker, B., Butler, M., Cowan, P., de Vienne, D., Eddelbuettel, D., Holder, M. et al. ( 2015 ) phylobase: Base Package for Phylogenetic Structures and Comparative Data.; Chamberlain, S., Foster, Z., Bartomeus, I., LeBauer, D. & Harris, D. ( 2016 ) traits: Species Trait Data from Around the Web.; Cranston, K., Harmon, L.J., O’Leary, M.A. & Lisle, C. ( 2014 ) Best practices for data sharing in phylogenetic research. PLoS Currents, 6, 1 – 8.; Drew, B.T., Gazis, R., Cabezas, P., Swithers, K.S., Deng, J., Rodriguez, R. et al. ( 2013 ) Lost branches on the tree of life. PLoS Biology, 11, e1001636.; Hinchliff, C.E., Smith, S.A., Allman, J.F., Burleigh, J.G., Chaudhary, R., Coghill, L.M. et al. ( 2015 ) Synthesis of phylogeny and taxonomy into a comprehensive tree of life. Proceedings of the National Academy of Sciences, 112, 12764 – 12769.; Johnson, W.E., Eizirik, E., Pecon‐Slattery, J., Murphy, W.J., Antunes, A., Teeling, E. & O’Brien, S.J. ( 2006 ) The late Miocene radiation of modern Felidae: a genetic assessment. Science, 311, 73 – 77.; Kembel, S.W., Cowan, P.D., Helmus, M.R., Cornwell, W.K., Morlon, H., Ackerly, D.D., Blomberg, S.P. & Webb, C.O. ( 2010 ) Picante: R tools for integrating phylogenies and ecology. Bioinformatics, 26, 1463 – 1464.; Knuth, D.E. ( 1984 ) Literate programming. The Computer Journal (British Computer Society), 27, 97 – 111.

الاتاحة: https://hdl.handle.net/2027.42/135519
https://doi.org/10.1111/2041-210X.12593

المؤلفون: Ewers-Saucedo, Christine, Owen, Christopher L., Pérez-Losada, Marcos, Høeg, Jens T., Glenner, Henrik, Chan, Benny K. K., Crandall, Keith A.

المصدر: Ewers-Saucedo , C , Owen , C L , Pérez-Losada , M , Høeg , J T , Glenner , H , Chan , B K K & Crandall , K A 2019 , ' Towards a barnacle tree of life : integrating diverse phylogenetic efforts into a comprehensive hypothesis of thecostracan evolution ' , PeerJ , vol. 7 , e7387 .

مصطلحات الفهرس: Barnacles, Thecostraca, Synthesis tree, Open tree of life, Phylogenetic studies, Taxonomy, Morphology, article

URL: https://curis.ku.dk/portal/da/publications/towards-a-barnacle-tree-of-life(30324300-9430-456a-859a-71bf574c92a6).html
https://doi.org/10.7717/peerj.7387
https://curis.ku.dk/ws/files/227195448/Towards_a_barnacle_tree_of_life.pdf