megaModel.bib

@ARTICLE{carmel2017,
  title =	 "Using exclusion rate to unify niche and neutral
                  perspectives on coexistence",
  author =	 "Carmel, Yohay and Suprunenko, Yevhen F and Kunin,
                  William E and Kent, Rafi and Belmaker, Jonathan and
                  Bar-Massada, Avi and Cornell, Stephen J",
  journal =	 "Oikos",
  publisher =	 "Blackwell Publishing Ltd",
  volume =	 126,
  number =	 10,
  pages =	 "1451--1458",
  month =	 oct,
  year =	 2017,
  keywords =	 "continuousity\_simMethods;continuousity"
}

@ARTICLE{chisholm2009,
  title =	 "Linking dispersal, immigration and scale in the
                  neutral theory of biodiversity",
  author =	 "Chisholm, Ryan A and Lichstein, Jeremy W",
  affiliation =	 "Department of Ecology and Evolutionary Biology,
                  Princeton University, Princeton, NJ 08544,
                  USA. chisholm@princeton.edu",
  journal =	 "Ecol. Lett.",
  volume =	 12,
  number =	 12,
  pages =	 "1385--1393",
  month =	 dec,
  year =	 2009,
  keywords =	 "continuousity",
  language =	 "en"
}

@ARTICLE{dexter2012,
  title =	 "Historical effects on beta diversity and community
                  assembly in Amazonian trees",
  author =	 "Dexter, K G and Terborgh, J W and Cunningham, C W",
  journal =	 "Proceedings of the National Academy of Sciences",
  volume =	 109,
  number =	 20,
  pages =	 "7787--7792",
  month =	 may,
  year =	 2012,
  keywords =	 "Mendeley Import (Mar 20);continuousity"
}

@ARTICLE{engen1996gamma,
  title =	 "Population Dynamic Models Generating Species
                  Abundance Distributions of the Gamma Type",
  author =	 "Engen, Steinar and Lande, Russell",
  journal =	 "J. Theor. Biol.",
  publisher =	 "Elsevier",
  volume =	 178,
  number =	 3,
  pages =	 "325--331",
  month =	 feb,
  year =	 1996,
  keywords =	 "continuousity\_simMethods;continuousity"
}

@ARTICLE{engen1996lnorm,
  title =	 "Population dynamic models generating the lognormal
                  species abundance distribution",
  author =	 "Engen, S and Lande, R",
  affiliation =	 "Institute for Mathematics and Statistics, University
                  of Trondheim, Dragvoll, Norway.",
  journal =	 "Math. Biosci.",
  publisher =	 "Elsevier",
  volume =	 132,
  number =	 2,
  pages =	 "169--183",
  month =	 mar,
  year =	 1996,
  keywords =	 "continuousity\_simMethods;continuousity",
  language =	 "en"
}


@ARTICLE{etienne2005,
  title     = "A new sampling formula for neutral biodiversity",
  author    = "Etienne, Rampal S",
  journal   = "Ecol. Lett.",
  publisher = "Blackwell Science Ltd",
  volume    =  8,
  number    =  3,
  pages     = "253--260",
  month     =  feb,
  year      =  2005,
  keywords  = "Biodiversity; Ewens sampling formula; Hubbell; community;
               neutral model; urn scheme"
}

@ARTICLE{etienne2007,
  title =	 "A neutral sampling formula for multiple samples and
                  an 'exact' test of neutrality",
  author =	 "Etienne, Rampal S",
  journal =	 "Ecology Letters",
  volume =	 10,
  pages =	 "608--618",
  year =	 2007,
  keywords =	 "continuousity\_simMethods;continuousity"
}

@ARTICLE{etienne2009,
  title =	 "Maximum likelihood estimation of neutral model
                  parameters for multiple samples with different
                  degrees of dispersal limitation",
  author =	 "Etienne, Rampal S",
  affiliation =	 "Community and Conservation Ecology Group, Centre for
                  Ecological and Evolutionary Studies, University of
                  Groningen, P.O. Box 14, 9750 AA Haren, The
                  Netherlands.  r.s.etienne@rug.nl",
  journal =	 "J. Theor. Biol.",
  volume =	 257,
  number =	 3,
  pages =	 "510--514",
  month =	 apr,
  year =	 2009,
  keywords =	 "continuousity\_simMethods;continuousity",
  language =	 "en"
}

@ARTICLE{etienne2011,
  title =	 "The spatial limitations of current neutral models of
                  biodiversity",
  author =	 "Etienne, Rampal S and Rosindell, James",
  affiliation =	 "Community and Conservation Ecology Group, Centre for
                  Ecological and Evolutionary Studies, University of
                  Groningen, Groningen, The
                  Netherlands. r.s.etienne@rug.nl",
  journal =	 "PLoS One",
  volume =	 6,
  number =	 3,
  pages =	 "e14717",
  month =	 mar,
  year =	 2011,
  keywords =	 "continuousity\_simMethods;continuousity",
  language =	 "en"
}

@ARTICLE{etienne2011fission,
  title =	 "The neutral theory of biodiversity with random
                  fission speciation",
  author =	 "Etienne, Rampal S and Haegeman, Bart",
  journal =	 "Theor. Ecol.",
  volume =	 4,
  number =	 1,
  pages =	 "87--109",
  month =	 feb,
  year =	 2011,
  keywords =	 "continuousity\_simMethods;Mendeley Import (Mar
                  20)/mol2ecol;continuousity"
}

@ARTICLE{gorelick2006,
  title =	 "Combining richness and abundance into a single
                  diversity index using matrix analogues of Shannon's
                  and Simpson's indices",
  author =	 "Gorelick, Root",
  journal =	 "Ecography",
  publisher =	 "Blackwell Publishing Ltd",
  volume =	 29,
  number =	 4,
  pages =	 "525--530",
  month =	 aug,
  year =	 2006,
  keywords =	 "continuousity"
}

@ARTICLE{green2007,
  title =	 "A statistical theory for sampling species
                  abundances",
  author =	 "Green, Jessica L and Plotkin, Joshua B",
  affiliation =	 "Center for Ecology and Evolutionary Biology,
                  University of Oregon, Eugene, OR, USA.",
  journal =	 "Ecol. Lett.",
  volume =	 10,
  number =	 11,
  pages =	 "1037--1045",
  month =	 nov,
  year =	 2007,
  keywords =	 "continuousity\_simMethods;continuousity",
  language =	 "en"
}

@ARTICLE{grilli2012,
  title =	 "Absence of detailed balance in ecology[No title]",
  author =	 "Grilli, Jacopo and Azaele, Sandro and Banavar,
                  Jayanth R and Maritan, Amos",
  journal =	 "EPL",
  volume =	 100,
  pages =	 38002,
  year =	 2012,
  keywords =	 "continuousity"
}

@ARTICLE{grilli2017,
  title =	 "Higher-order interactions stabilize dynamics in
                  competitive network models",
  author =	 "Grilli, Jacopo and Barab{\'a}s, Gy{\"o}rgy and
                  Michalska-Smith, Matthew J and Allesina, Stefano",
  journal =	 "Nature",
  volume =	 548,
  number =	 7666,
  pages =	 "210--213",
  month =	 aug,
  year =	 2017,
  keywords =	 "continuousity\_simMethods;continuousity",
  language =	 "en"
}

@ARTICLE{jabot2009,
  title =	 "Inferring the parameters of the neutral theory of
                  biodiversity using phylogenetic information and
                  implications for tropical forests",
  author =	 "Jabot, Franck and Chave, J{\'e}r{\^o}me",
  journal =	 "Ecol. Lett.",
  publisher =	 "Blackwell Publishing Ltd",
  volume =	 12,
  number =	 3,
  pages =	 "239--248",
  month =	 mar,
  year =	 2009,
  keywords =	 "Approximate Bayesian computation; community
                  phylogenetics; dispersal limitation; neutral theory;
                  parameter inference; phylogenetic imbalance;
                  regional species
                  pool;continuousity\_simMethods;Mendeley Import (Mar
                  20)/mol2ecol;Mendeley Import (Mar 20);continuousity"
}

@ARTICLE{kelleher2016,
  title =	 "Efficient Coalescent Simulation and Genealogical
                  Analysis for Large Sample Sizes",
  author =	 "Kelleher, Jerome and Etheridge, Alison M and McVean,
                  Gilean",
  affiliation =	 "Wellcome Trust Centre for Human Genetics, University
                  of Oxford, Oxford, United Kingdom. Department of
                  Statistics, University of Oxford, Oxford, United
                  Kingdom. Li Ka Shing Centre for Health Information
                  and Discovery, University of Oxford, Oxford, United
                  Kingdom.",
  journal =	 "PLoS Comput. Biol.",
  volume =	 12,
  number =	 5,
  pages =	 "e1004842",
  month =	 may,
  year =	 2016,
  keywords =	 "continuousity\_simMethods;continuousity",
  language =	 "en"
}

@ARTICLE{kendall1948,
  title =	 "On the Generalized ``{Birth-and-Death}'' Process",
  author =	 "Kendall, David G",
  journal =	 "Ann. Math. Stat.",
  volume =	 19,
  number =	 1,
  pages =	 "1--15",
  month =	 mar,
  year =	 1948,
  keywords =	 "birth-death process;species abundance
                  distribution;continuousity\_simMethods;Mendeley
                  Import (Mar 20);continuousity"
}

@ARTICLE{kendall1948fisher,
  title =	 "On Some Modes of Population Growth Leading to
                  R. A. Fisher's Logarithmic Series Distribution",
  author =	 "Kendall, David G",
  journal =	 "Biometrika",
  volume =	 35,
  number =	 1,
  pages =	 "6--15",
  year =	 1948,
  keywords =	 "birth-death process;immigration;logseries;species
                  abundance
                  distribution;continuousity\_simMethods;Mendeley
                  Import (Mar 20);continuousity"
}

@ARTICLE{kendall1949,
  title =	 "Stochastic Processes and Population Growth",
  author =	 "Kendall, David G",
  volume =	 11,
  number =	 2,
  pages =	 "230--282",
  year =	 1949,
  keywords =	 "birth-death process;immigration;logseries;negative
                  binomial;species abundance
                  distribution;continuousity\_simMethods;Mendeley
                  Import (Mar 20);continuousity"
}

@ARTICLE{kessler2014,
  title =	 "Neutral-like abundance distributions in the presence
                  of selection in a continuous fitness landscape",
  author =	 "Kessler, David A and Shnerb, Nadav M",
  affiliation =	 "Department of Physics, Bar-Ilan University,
                  Ramat-Gan IL52900, Israel. Electronic address:
                  kessler@dave.ph.biu.ac.il.  Department of Physics,
                  Bar-Ilan University, Ramat-Gan IL52900,
                  Israel. Electronic address: Nadav.Shnerb@gmail.com.",
  journal =	 "J. Theor. Biol.",
  volume =	 345,
  pages =	 "1--11",
  month =	 mar,
  year =	 2014,
  keywords =	 "Fisher log-series; Neutral theory; Selection;
                  Species abundance
                  distribution;continuousity\_simMethods;continuousity",
  language =	 "en"
}

@ARTICLE{laroche2015,
  title =	 "A neutral theory for interpreting correlations
                  between species and genetic diversity in
                  communities",
  author =	 "Laroche, Fabien and Jarne, Philippe and Lamy, Thomas
                  and David, Patrice and Massol, Francois",
  journal =	 "Am. Nat.",
  volume =	 185,
  number =	 1,
  pages =	 "59--69",
  month =	 jan,
  year =	 2015,
  keywords =	 "continuousity\_simMethods;continuousity",
  language =	 "en"
}

@ARTICLE{manceau2015-qb,
  title =	 "Phylogenies support out‐of‐equilibrium models of
                  biodiversity",
  author =	 "Manceau, M and Lambert, A and Morlon, H",
  journal =	 "Ecol. Lett.",
  publisher =	 "Wiley Online Library",
  year =	 2015,
  keywords =	 "continuousity"
}

@ARTICLE{mcgaughran2015,
  title =	 "Integrating a Population Genomics Focus into
                  Biogeographic and Macroecological Research",
  author =	 "McGaughran, Angela",
  journal =	 "Frontiers in Ecology and Evolution",
  publisher =	 "Frontiers",
  volume =	 3,
  pages =	 132,
  month =	 nov,
  year =	 2015,
  keywords =	 "Adaptive potential; Population Genomics;
                  biogeography; integration; macroecology; phenotypic
                  plasticity;Mendeley Import (Mar 20);continuousity"
}

@ARTICLE{odwyer2010,
  title =	 "Field theory for biogeography: a spatially explicit
                  model for predicting patterns of biodiversity",
  author =	 "O'Dwyer, James P and Green, Jessica L",
  journal =	 "Ecol. Lett.",
  volume =	 13,
  number =	 1,
  pages =	 "87--95",
  month =	 jan,
  year =	 2010,
  keywords =	 "continuousity\_simMethods;Mendeley Import (Mar
                  20);continuousity"
}

@ARTICLE{odwyer2017,
  title =	 "Cross-scale neutral ecology and the maintenance of
                  biodiversity",
  author =	 "O'Dwyer, James P and Cornell, Stephen J",
  month =	 may,
  year =	 2017,
  keywords =	 "continuousity\_simMethods;continuousity",
  archivePrefix ="arXiv",
  primaryClass = "q-bio.PE",
  eprint =	 "1705.07856"
}

@ARTICLE{pigot2015,
  title =	 "A new dynamic null model for phylogenetic community
                  structure",
  author =	 "Pigot, Alex L and Etienne, Rampal S",
  journal =	 "Ecol. Lett.",
  volume =	 18,
  number =	 2,
  pages =	 "153--163",
  month =	 feb,
  year =	 2015,
  keywords =	 "Colonisation; community assembly; extinction; null
                  model; phylogeny; speciation;
                  traits;continuousity\_simMethods;continuousity",
  language =	 "en"
}

@INPROCEEDINGS{purtan2013,
  title =	 "A Modified Stochastic Simulation Algorithm for
                  {Time-Dependent} Intensity Rates",
  booktitle =	 "2013 19th International Conference on Control
                  Systems and Computer Science",
  author =	 "Purtan, R R P and Udrea, A",
  pages =	 "365--369",
  month =	 may,
  year =	 2013,
  keywords =	 "Markov processes;algorithm theory;chemical
                  reactions;differential equations;Gillespie
                  algorithm;biochemical reaction;biochemical
                  system;continuous time-discrete state Markov
                  process;differential equation;first reaction
                  method;master equation approach;stochastic
                  process;stochastic simulation algorithm;tau-leaping
                  algorithm;time-dependent intensity
                  rate;Chemicals;Computational
                  modeling;Equations;Mathematical model;Stochastic
                  processes;Vectors;chemical kinetics;stochastic
                  simulation algorithm;time-dependent intensity
                  rates;continuousity\_simMethods;continuousity"
}

@ARTICLE{rosenberg2002,
  title =	 "Genealogical trees, coalescent theory and the
                  analysis of genetic polymorphisms",
  author =	 "Rosenberg, Noah A and Nordborg, Magnus",
  journal =	 "Nat. Rev. Genet.",
  volume =	 3,
  number =	 5,
  pages =	 "380--390",
  month =	 may,
  year =	 2002,
  keywords =	 "continuousity\_simMethods;continuousity",
  language =	 "en"
}

@ARTICLE{rosindell2007,
  title =	 "Species-area relationships from a spatially explicit
                  neutral model in an infinite landscape",
  author =	 "Rosindell, James and Cornell, Stephen J",
  journal =	 "Ecol. Lett.",
  volume =	 10,
  number =	 7,
  pages =	 "586--595",
  month =	 jul,
  year =	 2007,
  keywords =	 "continuousity\_simMethods;continuousity",
  language =	 "en"
}

@ARTICLE{rosindell2008ecoInfo,
  title =	 "A coalescence approach to spatial neutral ecology",
  author =	 "Rosindell, James and Wong, Yan and Etienne, Rampal
                  S",
  journal =	 "Ecol. Inform.",
  volume =	 3,
  number =	 3,
  pages =	 "259--271",
  month =	 jul,
  year =	 2008,
  keywords =	 "Coalescence; Neutral; Spatial ecology; Simulation
                  models;continuousity\_simMethods;continuousity"
}

@ARTICLE{rosindell2010,
  title =	 "Protracted speciation revitalizes the neutral theory
                  of biodiversity",
  author =	 "Rosindell, James and Cornell, Stephen J and Hubbell,
                  Stephen P and Etienne, Rampal S",
  journal =	 "Ecol. Lett.",
  volume =	 13,
  number =	 6,
  pages =	 "716--727",
  month =	 may,
  year =	 2010,
  keywords =	 "continuousity\_simMethods;Mendeley Import (Mar
                  20);continuousity"
}

@ARTICLE{rosindell2011,
  title =	 "A unified model of island biogeography sheds light
                  on the zone of radiation",
  author =	 "Rosindell, James and Phillimore, Albert B",
  journal =	 "Ecol. Lett.",
  publisher =	 "Blackwell Publishing Ltd",
  volume =	 14,
  number =	 6,
  pages =	 "552--560",
  month =	 jun,
  year =	 2011,
  keywords =	 "Endemicity; island biogeography; neutral
                  theory;adaptive radiation;eco-evo
                  dynamics;equilibrium;island
                  biogeography;macroecology;neutral theory;species
                  abundance
                  distribution;continuousity\_simMethods;Mendeley
                  Import (Mar 20);continuousity"
}

@ARTICLE{rosindell2013island,
  title =	 "A unified model of species immigration, extinction
                  and abundance on islands",
  author =	 "Rosindell, James and Harmon, Luke J",
  editor =	 "Burns, K C",
  journal =	 "J. Biogeogr.",
  volume =	 40,
  number =	 6,
  pages =	 "1107--1118",
  month =	 jun,
  year =	 2013,
  keywords =	 "continuousity\_simMethods;Mendeley Import (Mar
                  20);continuousity"
}

@ARTICLE{rosindell2013sadScaling,
  title =	 "Universal scaling of species-abundance distributions
                  across multiple scales",
  author =	 "Rosindell, James and Cornell, Stephen J",
  abstract =	 "The scale-dependent species abundance distribution
                  (SAD) is fundamental in ecology, but few spatially
                  explicit models of this pattern have thus far been
                  studied. Here we show spatially explicit neutral
                  model predictions for SADs over a wide range of
                  spatial scales, which appear to match empirical
                  patterns qualitatively. We find that the assumption
                  of a log-series SAD in the metacommunity made by
                  spatially implicit neutral models can be justified
                  with a spatially explicit model in the large area
                  limit. Furthermore, our model predicts that SADs on
                  multiple scales are characterized by a single,
                  compound parameter that represents the ratio of the
                  survey area to the species’ average biogeographic
                  range (which is in turn set by the speciation rate
                  and the dispersal distance). This intriguing
                  prediction is in line with recent empirical evidence
                  for a universal scaling of the species-area
                  curve. Hence we hypothesize that empirical SAD
                  patterns will show a similar universal scaling for
                  many different taxa and across multiple spatial
                  scales.",
  journal =	 "Oikos",
  publisher =	 "Blackwell Publishing Ltd",
  volume =	 122,
  number =	 7,
  pages =	 "1101--1111",
  month =	 jul,
  year =	 2013,
  keywords =	 "continuousity\_simMethods;continuousity"
}

@ARTICLE{rosindell2015,
  title =	 "Unifying ecology and macroevolution with
                  individual-based theory",
  author =	 "Rosindell, James and Harmon, Luke J and Etienne,
                  Rampal S",
  editor =	 "Mooers, Arne",
  journal =	 "Ecol. Lett.",
  volume =	 18,
  number =	 5,
  pages =	 "472--482",
  month =	 may,
  year =	 2015,
  keywords =	 "continuousity\_simMethods;Mendeley Import (Mar
                  20)/mol2ecol;continuousity"
}

@ARTICLE{schoener2011,
  title =	 "The newest synthesis: understanding the interplay of
                  evolutionary and ecological dynamics",
  author =	 "Schoener, Thomas W",
  journal =	 "Science",
  volume =	 331,
  number =	 6016,
  pages =	 "426--429",
  month =	 jan,
  year =	 2011,
  keywords =	 "continuousity",
  language =	 "en"
}

@ARTICLE{stone2012,
  title =	 "Reconstructing community assembly in time and space
                  reveals enemy escape in a Western Palearctic insect
                  community",
  author =	 "Stone, Graham N and Lohse, Konrad and Nicholls,
                  James A and Fuentes-Utrilla, Pablo and Sinclair,
                  Frazer and Sch{\"o}nrogge, Karsten and Cs{\'o}ka,
                  Gy{\"o}rgy and Melika, George and Nieves-Aldrey,
                  Jose-Luis and Pujade-Villar, Juli and Tavakoli,
                  Majide and Askew, Richard R and Hickerson, Michael
                  J",
  journal =	 "Curr. Biol.",
  volume =	 22,
  number =	 6,
  pages =	 "532--537",
  month =	 mar,
  year =	 2012,
  keywords =	 "continuousity",
  language =	 "en"
}

@ARTICLE{tilman2004,
  title =	 "Niche tradeoffs, neutrality, and community
                  structure: a stochastic theory of resource
                  competition, invasion, and community assembly",
  author =	 "Tilman, David",
  journal =	 "Proc. Natl. Acad. Sci. U. S. A.",
  publisher =	 "National Acad Sciences",
  volume =	 101,
  number =	 30,
  pages =	 "10854--10861",
  month =	 jul,
  year =	 2004,
  keywords =	 "continuousity\_simMethods;Mendeley Import (Mar
                  20);continuousity"
}

@ARTICLE{wakeley2004,
  title =	 "Metapopulation models for historical inference",
  author =	 "Wakeley, John",
  journal =	 "Mol. Ecol.",
  volume =	 13,
  number =	 4,
  pages =	 "865--875",
  month =	 apr,
  year =	 2004,
  keywords =	 "continuousity\_simMethods;continuousity",
  language =	 "en"
}