Free Book on Mixed and Phylogenetic Models

Ives, Anthony R. (2018) Mixed and Phylogenetic Models: A Conceptual Introduction to Correlated Data

You can download this for free at https://leanpub.com/correlateddata

This book introduces the concepts behind statistical methods used to analyze data with correlated error structures. While correlated data arise in many ways, the focus is on ecological and evolutionary data, and two types of correlations: correlations generated by the hierarchical nature of the sampling (e.g., plots sampled within sites) and correlations generated by the phylogenetic relationships among species. The book is integrated with R code that illustrates every point.

Chapter 1, Multiple Methods for Analyzing Hierarchical Data

Chapter 2, Good Statistical Properties

Chapter 3, Phylogenetic Comparative Methods

Chapter 4, Phylogenetic Community Ecology

Selected Research Publications

Here are selected publications corresponding to four research areas and a final selection of publications from the lab that do not include A. R. Ives as a co-author.

Lab members:

* postdoc
** graduate student
*** undergraduate student
**** high school student

Multispecies interactions

  • Ives, A. R., K. **Gross, and J. L. **Klug. 1999. Stability and variability in competitive communities. Science 286: 542-544.
  • **Klug, J. L., J. M. Fischer, A. R. Ives, and B. Dennis. 2000. Compensatory dynamics in planktonic community responses to pH perturbations. Ecology 81: 387-398.
  • Ives, A. R., J. L. **Klug, and K. **Gross. 2000. Stability and species richness in complex communities. Ecology Letters 3: 399-411.
  • Fischer, J. M., J. L. **Klug, A. R. Ives, and T. M. Frost. 2001. Ecological history and rapid evolution affect plankton community response to perturbation. Ecology 82: 2984-3000.
  • *Ripa, J., and A. R. Ives. 2003. Food web dynamics in correlated and autocorrelated environments. Theoretical Population Ecology 64: 369-384.
  • Ives, A. R., and B. J. *Cardinale. 2004. Food-web interactions govern the resistance of communities following non-random extinctions. Nature 429: 174-177.
  • Ives, A. R., and S. R. Carpenter. 2007. Stability and diversity of ecosystems. Science 317:58-62.
  • ***Ziebarth, N. L., K. C. *Abbott, and A. R. Ives. 2010. Weak population regulation in ecological time series. Ecology Letters 13:21-31.
  • Schooler, S. S., B. Salau, M. H. Julien, and A. R. Ives. 2011. Alternative stable states explain unpredictable biological control of salvinia in Kakadu. Nature 470:86-89.

Ecological and evolutionary dynamics

  • Ives, A. R., and W. H. Settle. 1997. Metapopulation dynamics and pest control in agricultural systems. American Naturalist 149: 220-246.
  • *Losey, J. E., A. R. Ives, J. ***Harmon, C. ***Brown, and F. ***Ballantyne. 1997. A polymorphism maintained by opposite patterns of parasitism and predation. Nature 388: 269-272.
  • **Gross, K., and A. R. Ives. 1999. Inferring host-parasitoid stability from patterns of parasitism among patches. American Naturalist 154: 489-496.
  • ***Olson, A. C., A. R. Ives, and K. **Gross. 2000. Spatially aggregated parasitism on pea aphids, Acyrthosiphon pisum, caused by random foraging behavior of the parasitoid Aphidius ervi. Oikos 91: 66-76.
  • ***Rauwald, K. S., and A. R. Ives. 2001. Biological control in disturbed agricultural systems and the rapid re-establishment of parasitoids. Ecological Applications 11: 1224-1234.
  • *Schellhorn, N. A., T. R. ***Kuhman, A. C. ***Olson, and A. R. Ives. 2002. Competition between native and introduced parasitoids of the pea aphid: implications for non-target effects and biological control. Ecology 83: 2745-2757.
  • *Snyder, W. E., and A. R. Ives. 2003. Interactions between specialist and generalist natural enemies: parasitoids, predators, and pea aphid biological control. Ecology 84: 91-107.
  • Ives, A. R., B. J. *Cardinale, and W. E. Snyder. 2005. A synthesis of subdisciplines: predator-prey interactions, and biodiversity and ecosystem functioning. Ecology Letters 8: 102-116.
  • *Harmon, J. P., N. A. Moran, and A. R. Ives. 2009. Species response to environmental change: impacts of food web interactions and evolution. Science 323:1347-1350.
  • ***Meisner, M. H. and A. R. Ives. 2013. Foraging efficiency and the fitness consequences of spatial marking by ladybeetle larvae. Oikos 122:1238-1246.
  • *Barton, B. T. and A. R. Ives. 2014. Species interactions and a chain of indirect effects driven by reduced precipitation. Ecology 95:486-494.
  • ***Meisner, M. H., J. P. *Harmon, and A. R. Ives. 2014. Temperature effects on long-term population dynamics in a parasitoid-host system. Ecological Monographs 84:457-476.
  • *Barton, B. T., and A. R. Ives. 2014. Direct and indirect effects of warming on aphids, their predators, and ant mutualists. Ecology 95:1479-1484.

Phylogenetic analyses

  • Garland, T., and A. R. Ives. 2000. Using the past to predict the present: confidence intervals for regression equations in phylogenetic comparative methods. American Naturalist 155: 346-364.
  • **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.
  • Ives, A. R., P. E. Midford, and T. Garland Jr. 2007. Within-species variation and measurement error in phylogenetic comparative methods. Systematic Biology 56:252-270.
  • Zheng, L., A. R. Ives, T. Garland, Jr., B. R. Larget, Y. Yu, and K. Cao. 2009. Multivariate tests for phylogenetic signal and trait correlations applied to ecophysiological phenotypes of nine Manglietia species. Functional Ecology 23:1059-1069.
  • Ives, A. R., and T. Garland. 2010. Phylogenetic logistic regression for binary dependent variables. Systematic Biology 59:9-26.
  • Ives, A. R., and M. R. **Helmus. 2010. Phylogenetic metrics of community similarity. American Naturalist 176:E128-E142.
  • Ives, A. R., and M. R. Helmus. 2011. Generalized linear mixed models for phylogenetic analyses of community structure. Ecological Monographs 81:511-525.
  • **Rafferty, N. E. and A. R. Ives. 2013. Phylogenetic trait-based analyses of ecological networks. Ecology 94:2321-2333.
  • Li, D., A. R. Ives, and D. M. Waller. 2017. Can functional traits account for phylogenetic signal in community composition? New Phytologist.

Complex population dynamics

  • Ives, A. R., and V. A. A. Jansen. 1998. Complex dynamics in stochastic tritrophic models. Ecology 79: 1039-1052.
  • **Kilpatrick, A. M., and A. R. Ives. 2003. Species interactions can explain Taylor’s power law for time series. Nature 422: 65-68.
  • *Williams, C. K., A. R. Ives, R. D. Applegate, and J. *Ripa. 2004. The collapse of cycles in the dynamics of North American grouse populations. Ecology Letters 7: 1135-1142.
  • Ives, A. R., and J. Zhu. 2006. Statistics for correlated data: phylogenies, space, and time. Ecological Applications 16:16-32.
  • Ives, A. R., A. Einarsson, V. A. A. Jansen, and A. Gardarsson. 2008. High-amplitude fluctuations and alternative dynamical states of midges in Lake Myvatn. Nature 452:84-87.
  • *Duffy, M. A., S. R. Hall, C. E. Caceres, and A. R. Ives. 2009. Rapid evolution, seasonality, and the termination of parasite epidemics. Ecology 90:1441-1448.
  • Ives, A. R., P. R. ***Glaum, N. L. ***Ziebarth, and D. A. Andow. 2011. The evolution of resistance to two-toxin pyramid transgenic crops. Ecological Applications 21:503-515.
  • Strier, K. B. and A. R. Ives. 2012. Unexpected demography in the recovery of an endangered primate population. PLoS ONE 7.
  • *Northfield, T. D. and A. R. Ives. 2013. Coevolution and the effects of climate change on interacting species. PLoS Biology 11.
  • Ives, A. R. 2015. For testing the significance of regression coefficients, go ahead and log-transform count data. Methods in Ecology and Evolution 6:828-835.
  • **Fan, H., A. R. Ives, Y. Surget-Groba, and C. H. Cannon. 2015. An assembly and alignment-free method of phylogeny reconstruction from next-generation sequencing data. Bmc Genomics 16.
  • Warton, D. I., M. Lyons, J. Stoklosa, and A. R. Ives. 2016. Three points to consider when choosing a LM or GLM test for count data. Methods in Ecology and Evolution.
  • **Webert, K. C., C. M. Herren, Á. Einarsson, M. Bartrons, U. Hauptfleisch, and A. R. Ives. 2017. Midge‐stabilized sediment drives the composition of benthic cladoceran communities in Lake Mývatn, Iceland. Ecosphere 8.

Publications by lab members

  • **Palmer, T. M. 1995. The influence of spatial heterogeneity on the behavior and growth of two herbivorous stream insects. Oecologia 104:476-486.
  • Fisher, M. M., J. L. **Klug, G. Lauster, M. Newton, and E. W. Triplett. 2000. Effects of resources and trophic interactions on freshwater bacterioplankton diversity. Microbial Ecology 40:125-138.
  • Fisher, M. M., J. L. **Klug, G. Lauster, M. Newton, and E. W. Triplett. 2001. Effects of resources and trophic interactions on freshwater bacterioplankton (vol 40, pg 125, 2000). Microbial Ecology 41:82-82.
  • **Klug, J. L., and K. L. Cottingham. 2001. Interactions among environmental drivers: Community responses to changing nutrients and dissolved organic carbon. Ecology 82:3390-3403.
  • **Gross, K. 2002. Efficient data collection for estimating growth rates of structured populations. Ecology 83:1762-1767.
  • **Gross, K., B. A. Craig, and W. D. Hutchinson. 2002. Bayesian estimation of a demographic matrix model from stage-frequency data. Ecology 83:3285-3298.
  • **Klug, J. L. 2002. Positive and negative effects of allochthonous dissolved organic matter and inorganic nutrients on phytoplankton growth. Canadian Journal of Fisheries and Aquatic Sciences 59:85-95.
  • Dodson, S. I., A. K. Grishanin, K. **Gross, and G. A. Wyngaard. 2003. Morphological analysis of some cryptic species in the Acanthocyclops vernalis species complex from North America. Hydrobiologia 500:131-143.
  • Rooney, T. P., and K. **Gross. 2003. A demographic study of deer browsing impacts on Trillium grandiflorum. Plant Ecology 168:267-277.
  • **Forbes, A. E. 2005. Spines and natural history of three cenchrus species. American Midland Naturalist 153:80-86.
  • **Forbes, A. E., C. T. **Harvey, and K. J. *Tilmon. 2005. Variation in the responses of spotted Alfalfa Aphids, Therioaphis maculata Buckton (Homoptera : Aphididae) and pea aphids, Acythosiphon pisum Harris (Homoptera : Aphididae) to drought conditions in Alfalfa (Medicago sativa L., Fabaceae). Journal of the Kansas Entomological Society 78:387-389.
  • **Klug, J. L. 2005. Bacterial response to dissolved organic matter affects resource availability for algae. Canadian Journal of Fisheries and Aquatic Sciences 62:472-481.
  • Gratton, C., and A. E. **Forbes. 2006. Changes in delta C-13 stable isotopes in multiple tissues of insect predators fed isotopically distinct prey. Oecologia 147:615-624.
  • **Foufopoulos, J., and G. C. Mayer. 2007. Turnover of passerine birds on islands in the Aegean Sea (Greece). Journal of Biogeography 34:1113-1123.
  • Newton, R. J., S. E. Jones, M. R. **Helmus, and K. D. McMahon. 2007. Phylogenetic ecology of the freshwater Actinobacteria acI lineage. Applied and Environmental Microbiology 73:7169-7176.
  • **Helmus, M. R., and G. G. Sass. 2008. The rapid effects of a whole-lake reduction of coarse woody debris on fish and benthic macroinvertebrates. Freshwater Biology 53:1423-1433.
  • Ahrenstorff, T. D., G. G. Sass, and M. R. **Helmus. 2009. The influence of littoral zone coarse woody habitat on home range size, spatial distribution, and feeding ecology of largemouth bass (Micropterus salmoides). Hydrobiologia 623:223-233.
  • **Helmus, M. R., L. B. ***Allen, O. Dominguez-Dominguez, E. D. Pardo, P. Gesundheit, J. Lyons, and N. M. Silva. 2009. Threatened fishes of the world: Allotoca goslinei Smith and Miller, 1987 (Goodeidae). Environmental Biology of Fishes 84:197-198.
  • ***Fabina, N. S., K. C. *Abbott, and R. T. **Gilman. 2010. Sensitivity of plant-pollinator-herbivore communities to changes in phenology. Ecological Modelling 221:453-458.
  • **Helmus, M. R., W. Keller, M. J. Paterson, N. D. Yan, C. H. Cannon, and J. A. Rusak. 2010. Communities contain closely related species during ecosystem disturbance. Ecology Letters 13:162-174.
  • Mercado-Silva, N., M. R. **Helmus, and M. J. Vander Zanden. 2009. The effects of impoundment and non-native species on a river food web in Mexico’s central plateau. River Research and Applications 25:1090-1108.
  • **Gilman, R. T., N. E. Mathews, B. G. Skinner, V. L. Julis, E. S. Frank, and J. Paul-Murphy. 2010. Effects of Maternal Status on the Movement and Mortality of Sterilized Female White-Tailed Deer. Journal of Wildlife Management 74:1484-1491.
  • Cooper, I. A., R. T. **Gilman, and J. W. Boughman. 2011. Sexual dimorphism and speciation on two ecological coins: patterns from nature and theoretical predictions. Evolution 65:2553-2571.
  • **Gilman, R. T., and J. E. **Behm. 2011. Hybridization, species collapse, and species reemergence after disturbance to premating mechanisms of reproductive isolation. Evolution 65:2592-2605.
  • Quan, R.-C., G. Ren, J. E. **Behm, L. Wang, Y. Huang, Y. Long, and J. Zhu. 2011. Why does rhinopithecus bieti prefer the highest elevation range in winter? A test of the sunshine hypothesis. Plos One 6.
  • **Gilman, R. T., N. S. ***Fabina, K. C. *Abbott, and N. E. **Rafferty. 2012. Evolution of plant-pollinator mutualisms in response to climate change. Evolutionary Applications 5:2-16.
  • Harmon, J. P., and B. T. *Barton. 2013. On their best behavior: how animal behavior can help determine the combined effects of species interactions and climate change. Climate Change and Species Interactions: Ways Forward 1297:139-147.
  • *Barton, B. T. 2014. Reduced wind strengthens top-down control of an insect herbivore. Ecology 95:2375-2381.
  • **Usinowicz, J. 2015. Limited dispersal drives clustering and reduces coexistence by the storage effect. American Naturalist 186:634-648.