Creation of Diversity tutorial

topics/metagenomics/tutorials/diversity/images/test

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topics/metagenomics/tutorials/diversity/tutorial.bib

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+
+@article{Berger.1970,
+ abstract = {The diversity of a planktonic foraminiferal assemblage on the ocean floor depends on the state of preservation of that assemblage. As dissolution progresses, species diversity (number of species in the assemblage) decreases, but compound diversity (based on relative species abundance) first increases and then decreases; species dominance first decreases and then increases. The reason for these changes is that the species most susceptible to solution deliver moresediment to the ocean floor than do species with solution-resistant shells, possibly because the more soluble tests are produced in surface waters, where growth and production are greatest.},
+ author = {Berger, W. H. and Parker, F. L.},
+ year = {1970},
+ title = {Diversity of planktonic foraminifera in deep-sea sediments},
+ pages = {1345--1347},
+ volume = {168},
+ number = {3937},
+ issn = {0036-8075},
+ journal = {Science (New York, N.Y.)},
+ doi = {10.1126/science.168.3937.1345.}
+}
+
+
+@article{Bolyen.2019,
+ author = {Bolyen, Evan and Rideout, Jai Ram and Dillon, Matthew R. and Bokulich, Nicholas A. and Abnet, Christian C. and Al-Ghalith, Gabriel A. and Alexander, Harriet and Alm, Eric J. and Arumugam, Manimozhiyan and Asnicar, Francesco and Bai, Yang and Bisanz, Jordan E. and Bittinger, Kyle and Brejnrod, Asker and Brislawn, Colin J. and Brown, C. Titus and Callahan, Benjamin J. and Caraballo-Rodr{\'i}guez, Andr{\'e}s Mauricio and Chase, John and Cope, Emily K. and {Da Silva}, Ricardo and Diener, Christian and Dorrestein, Pieter C. and Douglas, Gavin M. and Durall, Daniel M. and Duvallet, Claire and Edwardson, Christian F. and Ernst, Madeleine and Estaki, Mehrbod and Fouquier, Jennifer and Gauglitz, Julia M. and Gibbons, Sean M. and Gibson, Deanna L. and Gonzalez, Antonio and Gorlick, Kestrel and Guo, Jiarong and Hillmann, Benjamin and Holmes, Susan and Holste, Hannes and Huttenhower, Curtis and Huttley, Gavin A. and Janssen, Stefan and Jarmusch, Alan K. and Jiang, Lingjing and Kaehler, Benjamin D. and Kang, Kyo Bin and Keefe, Christopher R. and Keim, Paul and Kelley, Scott T. and Knights, Dan and Koester, Irina and Kosciolek, Tomasz and Kreps, Jorden and Langille, Morgan G. I. and Lee, Joslynn and Ley, Ruth and Liu, Yong-Xin and Loftfield, Erikka and Lozupone, Catherine and Maher, Massoud and Marotz, Clarisse and Martin, Bryan D. and McDonald, Daniel and McIver, Lauren J. and Melnik, Alexey V. and Metcalf, Jessica L. and Morgan, Sydney C. and Morton, Jamie T. and Naimey, Ahmad Turan and Navas-Molina, Jose A. and Nothias, Louis Felix and Orchanian, Stephanie B. and Pearson, Talima and Peoples, Samuel L. and Petras, Daniel and Preuss, Mary Lai and Pruesse, Elmar and Rasmussen, Lasse Buur and Rivers, Adam and Robeson, Michael S. and Rosenthal, Patrick and Segata, Nicola and Shaffer, Michael and Shiffer, Arron and Sinha, Rashmi and Song, Se Jin and Spear, John R. and Swafford, Austin D. and Thompson, Luke R. and Torres, Pedro J. and Trinh, Pauline and Tripathi, Anupriya and Turnbaugh, Peter J. and Ul-Hasan, Sabah and {van der Hooft}, Justin J. J. and Vargas, Fernando and V{\'a}zquez-Baeza, Yoshiki and Vogtmann, Emily and von Hippel, Max and Walters, William and Wan, Yunhu and Wang, Mingxun and Warren, Jonathan and Weber, Kyle C. and Williamson, Charles H. D. and Willis, Amy D. and Xu, Zhenjiang Zech and Zaneveld, Jesse R. and Zhang, Yilong and Zhu, Qiyun and Knight, Rob and Caporaso, J. Gregory},
+ year = {2019},
+ title = {Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2},
+ pages = {852--857},
+ volume = {37},
+ number = {8},
+ journal = {Nature biotechnology},
+ doi = {10.1038/s41587-019-0209-9}
+}
+
+
+@article{Bray.1957,
+ author = {Bray, J. Roger and Curtis, J. T.},
+ year = {1957},
+ title = {An Ordination of the Upland Forest Communities of Southern Wisconsin},
+ pages = {325--349},
+ volume = {27},
+ number = {4},
+ issn = {0012-9615},
+ journal = {Ecological Monographs},
+ doi = {10.2307/1942268}
+}
+
+
+@article{Chao.1992,
+ author = {Chao, Anne and Lee, Shen-Ming},
+ year = {1992},
+ title = {Estimating the Number of Classes via Sample Coverage},
+ pages = {210--217},
+ volume = {87},
+ number = {417},
+ issn = {0162-1459},
+ journal = {Journal of the American Statistical Association},
+ doi = {10.1080/01621459.1992.10475194}
+}
+
+
+@article{Fisher.1943,
+ author = {Fisher, R. A. and Corbet, A. Steven and Williams, C. B.},
+ year = {1943},
+ title = {The Relation Between the Number of Species and the Number of Individuals in a Random Sample of an Animal Population},
+ pages = {42},
+ volume = {12},
+ number = {1},
+ issn = {00218790},
+ journal = {The Journal of Animal Ecology},
+ doi = {10.2307/1411}
+}
+
+
+@article{Jaccard.1912,
+ author = {Jaccard, Paul},
+ year = {1912},
+ title = {THE DISTRIBUTION OF THE FLORA IN THE ALPINE ZONE.1},
+ pages = {37--50},
+ volume = {11},
+ number = {2},
+ issn = {0028-646X},
+ journal = {New Phytologist},
+ doi = {10.1111/j.1469-8137.1912.tb05611.x}
+}
+
+@article{Margalef.1969,
+ author = {Margalef, R.},
+ year = {1969},
+ title = {Perspectives in Ecological Theory},
+ pages = {571},
+ volume = {20},
+ number = {2},
+ issn = {00301299},
+ journal = {Oikos},
+ doi = {10.2307/3543237}
+}
+
+
+@article{Pielou.1966,
+ author = {Pielou, E. C.},
+ year = {1966},
+ title = {The measurement of diversity in different types of biological collections},
+ pages = {131--144},
+ volume = {13},
+ issn = {00225193},
+ journal = {Journal of Theoretical Biology},
+ doi = {10.1016/0022-5193(66)90013-0}
+}
+
+
+@article{Shannon.1948,
+ author = {Shannon, C. E.},
+ year = {1948},
+ title = {A Mathematical Theory of Communication},
+ pages = {379--423},
+ volume = {27},
+ number = {3},
+ issn = {00058580},
+ journal = {Bell System Technical Journal},
+ doi = {10.1002/j.1538-7305.1948.tb01338.x}
+}
+
+
+@article{SIMPSON.1949,
+ author = {SIMPSON, E. H.},
+ year = {1949},
+ title = {Measurement of Diversity},
+ pages = {688},
+ volume = {163},
+ number = {4148},
+ issn = {0028-0836},
+ journal = {Nature},
+ doi = {10.1038/163688a0}
+}
+
+
+@article{Srensen.1948,
+ author = {S{\o}rensen, T.},
+ year = {1948},
+ title = {A method of establishing groups of equal amplitude in plant sociology based on similarity of species and its application to analyses of the vegetation on Danish commons},
+ pages = {1--34},
+ number = {5},
+ journal = {Kongelige Danske Videnskabernes Selskab.}
+ link = {https://www.royalacademy.dk/Publications/High/295_S%C3%B8rensen,%20Thorvald.pdf}
+}
+
+
+@article{BonillaRosso.2012,
+ abstract = {Metagenomics holds the promise of greatly advancing the study of diversity in natural communities, but novel theoretical and methodological approaches must first be developed and adjusted for these data sets. We evaluated widely used macroecological metrics of taxonomic diversity on a simulated set of metagenomic samples, using phylogenetically meaningful protein-coding genes as ecological proxies. To our knowledge, this is the first approach of this kind to evaluate taxonomic diversity metrics derived from metagenomic data sets. We demonstrate that abundance matrices derived from protein-coding marker genes reproduce more faithfully the structure of the original community than those derived from SSU-rRNA gene. We also found that the most commonly used diversity metrics are biased estimators of community structure and differ significantly from their corresponding real parameters and that these biases are most likely caused by insufficient sampling and differences in community phylogenetic composition. Our results suggest that the ranking of samples using multidimensional metrics makes a good qualitative alternative for contrasting community structure and that these comparisons can be greatly improved with the incorporation of metrics for both community structure and phylogenetic diversity. These findings will help to achieve a standardized framework for community diversity comparisons derived from metagenomic data sets.},
+ author = {Bonilla-Rosso, Germ{\'a}n and Eguiarte, Luis E. and Romero, David and Travisano, Michael and Souza, Valeria},
+ year = {2012},
+ title = {Understanding microbial community diversity metrics derived from metagenomes: performance evaluation using simulated data sets},
+ pages = {37--49},
+ volume = {82},
+ number = {1},
+ journal = {FEMS microbiology ecology},
+ doi = {10.1111/j.1574-6941.2012.01405.x}
+}
+
+
+@article{Chao.2015,
+ author = {Chao, Anne and Jost, Lou},
+ year = {2015},
+ title = {Estimating diversity and entropy profiles via discovery rates of new species},
+ pages = {873--882},
+ volume = {6},
+ number = {8},
+ issn = {2041-210X},
+ journal = {Methods in Ecology and Evolution},
+ doi = {10.1111/2041-210X.12349}
+}
+
+
+@article{Hill.1973,
+ author = {Hill, M. O.},
+ year = {1973},
+ title = {Diversity and Evenness: A Unifying Notation and Its Consequences},
+ pages = {427--432},
+ volume = {54},
+ number = {2},
+ issn = {00129658},
+ journal = {Ecology},
+ doi = {10.2307/1934352}
+}
+
+@article{Finotello.2018,
+ abstract = {The human microbiota is a complex ecological community of commensal, symbiotic and pathogenic microorganisms harboured by the human body. Next-generation sequencing (NGS) technologies, in particular targeted amplicon sequencing of the 16S ribosomal RNA gene (16S-seq), are enabling the identification and quantification of human-resident microorganisms at unprecedented resolution, providing novel insights into the role of the microbiota in health and disease. Once microbial abundances are quantified through NGS data analysis, diversity indices provide valuable mathematical tools to describe the ecological complexity of a single sample or to detect species differences between samples. However, diversity is not a determined physical quantity for which a consensus definition and unit of measure have been established, and several diversity indices are currently available. Furthermore, they were originally developed for macroecology and their robustness to the possible bias introduced by sequencing has not been characterized so far. To assist the reader with the selection and interpretation of diversity measures, we review a panel of broadly used indices, describing their mathematical formulations, purposes and properties, and characterize their behaviour and criticalities in dependence of the data features using simulated data as ground truth. In addition, we make available an R package, DiversitySeq, which implements in a unified framework the full panel of diversity indices and a simulator of 16S-seq data, and thus represents a valuable resource for the analysis of diversity from NGS count data and for the benchmarking of computational methods for 16S-seq.},
+ author = {Finotello, Francesca and Mastrorilli, Eleonora and {Di Camillo}, Barbara},
+ year = {2018},
+ title = {Measuring the diversity of the human microbiota with targeted next-generation sequencing},
+ pages = {679--692},
+ volume = {19},
+ number = {4},
+ journal = {Briefings in bioinformatics},
+ doi = {10.1093/bib/bbw119}
+}
+
+@article{Bolyen.2019,
+ author = {Bolyen, Evan and Rideout, Jai Ram and Dillon, Matthew R. and Bokulich, Nicholas A. and Abnet, Christian C. and Al-Ghalith, Gabriel A. and Alexander, Harriet and Alm, Eric J. and Arumugam, Manimozhiyan and Asnicar, Francesco and Bai, Yang and Bisanz, Jordan E. and Bittinger, Kyle and Brejnrod, Asker and Brislawn, Colin J. and Brown, C. Titus and Callahan, Benjamin J. and Caraballo-Rodr{\'i}guez, Andr{\'e}s Mauricio and Chase, John and Cope, Emily K. and {Da Silva}, Ricardo and Diener, Christian and Dorrestein, Pieter C. and Douglas, Gavin M. and Durall, Daniel M. and Duvallet, Claire and Edwardson, Christian F. and Ernst, Madeleine and Estaki, Mehrbod and Fouquier, Jennifer and Gauglitz, Julia M. and Gibbons, Sean M. and Gibson, Deanna L. and Gonzalez, Antonio and Gorlick, Kestrel and Guo, Jiarong and Hillmann, Benjamin and Holmes, Susan and Holste, Hannes and Huttenhower, Curtis and Huttley, Gavin A. and Janssen, Stefan and Jarmusch, Alan K. and Jiang, Lingjing and Kaehler, Benjamin D. and Kang, Kyo Bin and Keefe, Christopher R. and Keim, Paul and Kelley, Scott T. and Knights, Dan and Koester, Irina and Kosciolek, Tomasz and Kreps, Jorden and Langille, Morgan G. I. and Lee, Joslynn and Ley, Ruth and Liu, Yong-Xin and Loftfield, Erikka and Lozupone, Catherine and Maher, Massoud and Marotz, Clarisse and Martin, Bryan D. and McDonald, Daniel and McIver, Lauren J. and Melnik, Alexey V. and Metcalf, Jessica L. and Morgan, Sydney C. and Morton, Jamie T. and Naimey, Ahmad Turan and Navas-Molina, Jose A. and Nothias, Louis Felix and Orchanian, Stephanie B. and Pearson, Talima and Peoples, Samuel L. and Petras, Daniel and Preuss, Mary Lai and Pruesse, Elmar and Rasmussen, Lasse Buur and Rivers, Adam and Robeson, Michael S. and Rosenthal, Patrick and Segata, Nicola and Shaffer, Michael and Shiffer, Arron and Sinha, Rashmi and Song, Se Jin and Spear, John R. and Swafford, Austin D. and Thompson, Luke R. and Torres, Pedro J. and Trinh, Pauline and Tripathi, Anupriya and Turnbaugh, Peter J. and Ul-Hasan, Sabah and {van der Hooft}, Justin J. J. and Vargas, Fernando and V{\'a}zquez-Baeza, Yoshiki and Vogtmann, Emily and von Hippel, Max and Walters, William and Wan, Yunhu and Wang, Mingxun and Warren, Jonathan and Weber, Kyle C. and Williamson, Charles H. D. and Willis, Amy D. and Xu, Zhenjiang Zech and Zaneveld, Jesse R. and Zhang, Yilong and Zhu, Qiyun and Knight, Rob and Caporaso, J. Gregory},
+ year = {2019},
+ title = {Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2},
+ pages = {852--857},
+ volume = {37},
+ number = {8},
+ journal = {Nature biotechnology},
+ doi = {10.1038/s41587-019-0209-9}
+}
+
+
+
+