Free Book on Mixed and Phylogenetic Models
Ives, Anthony R. (2018) Mixed and Phylogenetic Models: A Conceptual Introduction to Correlated Data
You can download the book for free.
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 three 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 |
Species and community dynamics
- Ives, A. R., K. **Gross, and J. L. **Klug. 1999. Stability and variability in competitive communities. Science 286: 542-544.
- Ives, A. R., J. L. **Klug, and K. **Gross. 2000. Stability and species richness in complex communities. Ecology Letters 3: 399-411.
- ***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.
- *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.
- Ives, A. R., and S. R. Carpenter. 2007. Stability and diversity of ecosystems. Science 317:58-62.
- 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.
- ***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.
- Strier, K. B. and A. R. Ives. 2012. Unexpected demography in the recovery of an endangered primate population. PLoS ONE 7.
- *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.
- **Phillips, J. S., A. R. **McCormick, A. Einarsson, S. N. ***Grover, and A. R. Ives. 2019. Spatiotemporal variation in the sign and magnitude of ecosystem engineer effects on lake ecosystem production. Ecosphere 10.
- Ives, A. R., and C. Bozzuto. 2021. Estimating and explaining the spread of COVID-19 at the county level in the USA. Communications Biology 4:60.
- **Phillips, J. S., A. R. **McCormick, J. C. **Botsch, and A. R. Ives. 2021. Ecosystem engineering alters density-dependent feedbacks in an aquatic insect population. Ecology 102:e03513.
- **McCormick, A. R., J. S. **Phillips, J. C. **Botsch, and A. R. Ives. 2021. Shifts in the partitioning of benthic and pelagic primary production within and across summers in Lake Mývatn, Iceland. Inland Waters 11:13-28.
- **McCormick, A.R., **Phillips, J.S., **Botsch, J.C., Einarsson, Á., Gardarsson, A., & Ives, A.R. 2023. Reconstructing midge consumer–resource dynamics using carbon stable isotope signatures of archived specimens. Ecology, 104, e3901.
- **McCormick, A. R., J. S. **Phillips, J. C. **Botsch, J. S. Ólafsson, and A. R. Ives. 2024. Resource use differences of two coexisting chironomid species at localized scales. Oecologia 205:473-485. https://doi.org/10.1007/s00442-024-05584-1.
- **Botsch, J. C., A. N. ***Zaveri, L. A. **Nell, A. R. **McCormick, K. R. **Book, J. S. **Phillips, Á. Einarsson, and A. R. Ives. 2024. Disentangling the drivers of decadal body size decline in an insect population. Global Change Biology 30:e17014. https://doi.org/10.1111/gcb.17014.
Ecological and evolutionary interactions
- *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.
- Ives, A. R., and D. A. Andow. 2002. Evolution of resistance to Bt crops: directional selection in structured environments. Ecology Letters 5:792-801.
- *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.
- *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.
- *Northfield, T. D. and A. R. Ives. 2013. Coevolution and the effects of climate change on interacting species. PLoS Biology 11.
- Ives, A. R., C. Paull, A. Hulthen, S. Downes, D. A. Andow, R. Haygood, M. P. Zalucki, and N. A. Schellhorn. 2017. Spatio-temporal variation in landscape composition may speed resistance evolution of pests to Bt crops. Plos One 12.
- Bozzuto, C., I. Biebach, S. Muff, A. R. Ives, and L. F. Keller. 2019. Inbreeding reduces long-term growth of Alpine ibex populations. Nature Ecology & Evolution 3:1359-1364.
- Ives, A. R., B. T. Barton, R. M. Penczykowski, J. P. Harmon, K. L. Kim, K. Oliver, and V. C. Radeloff. 2020. Self-perpetuating ecological-evolutionary dynamics in an agricultural host-parasite system. Nature Ecology & Evolution 4:702-711.
- Northfield, T. D., J. Ripa, L. A. Nell, and A. R. Ives. 2021. Coevolution, diversification and alternative states in two-trophic communities. Ecology Letters 24:269-278.
- *Kishinevsky, M., & Ives, A.R. 2022. The success of a habitat specialist biological control agent in the face of disturbance. Ecosphere, 13, e4050.
- **Nell, L. A., M. *Kishinevsky, M. J. **Bosch, C. ***Sinclair, K. ***Bhat, N. ***Ernst, H. ***Boulaleh, K. M. Oliver, and A. R. Ives. 2024. Dispersal stabilizes coupled ecological and evolutionary dynamics in a host-parasitoid system. Science 383:1240-1244. https://doi.org/10.1126/science.adg4602.
- *Kishinevsky, M., and A. R. Ives. 2024. Longevity of hymenopteran parasitoids in natural vs. agricultural habitats and implications for biological control. Ecological Applications 34(6): e3009. https://doi.org/10.1002/eap.3009.
Statistics for ecology and evolution
- Ives, A. R., and J. Zhu. 2006. Statistics for correlated data: phylogenies, space, and time. Ecological Applications 16:16-32.
- **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.
- **Helmus, M. R., T. J. ***Bland, C. K. *Williams, and A. R. Ives. 2007. Phylogenetic measures of biodiversity. American Naturalist 169:E68-E83.
- 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.
- 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.
- Li, D., A. R. Ives, and D. M. Waller. 2017. Can functional traits account for phylogenetic signal in community composition? New Phytologist.
- Li, D., and A. R. Ives. 2017. The statistical need to include phylogeny in trait-based analyses of community composition. Methods in Ecology and Evolution 8:1192-1199.
- Ives, A. R., and D. Li. 2018. rr2: An R package to calculate R2s for regression models. Journal of Open Source Software 3:1028.
- Ives, A. R. 2019. R2s for correlated data: phylogenetic models, LMMs, and GLMMs. Systematic Biology 68:234-251.
- Li, D., R. Dinnage, L. A. Nell, M. R. Helmus, and A. R. Ives. 2020. phyr: An r package for phylogenetic species-distribution modelling in ecological communities. Methods in Ecology and Evolution 11:1455-1463.
- Ives, A. R., L. Zhu, F. Wang, J. Zhu, C. J. Morrow, and V. C. Radeloff. 2021. Statistical inference for trends in spatiotemporal data. Remote Sensing of Environment 266:112678.
- Ives, A. R., L. Zhu, F. Wang, J. Zhu, C. J. Morrow, and V. C. Radeloff. 2022. Statistical tests for non-independent partitions of large autocorrelated datasets. MethodsX 9.
- Ives, A. R. 2022. Random errors are neither: On the interpretation of correlated data. Methods in Ecology and Evolution 13:2092-2105.
- Bozzuto, C., and A. R. Ives. 2023. Differences in COVID-19 cyclicity and predictability among U.S. counties and states reflect the effectiveness of protective measures. Scientific Reports 13:14277. https://doi.org/10.1038/s41598-023-40990-0.
- Bozzuto, C., and A. R. Ives. 2024. Predictability of ecological and evolutionary dynamics in a changing world. Proceedings of the Royal Society B: Biological Sciences https://doi.org/10.1098/rspb.2024.0980.
Publications by lab members
This is a selection of papers writen by lab members not including A. R. Ives.
- **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.
- **Nell, L. A. 2020. jackalope: A swift, versatile phylogenomic and high-throughput sequencing simulator. Molecular Ecology Resources 20:1132-1140.
- **Phillips, J. S. 2020. Time-varying responses of lake metabolism to light and temperature. Limnology and Oceanography 65:652-666.
- McCary, M. A., J. S. **Phillips, T. *Ramiadantsoa, L. A. **Nell, A. R. **McCormick, and J. C. **Botsch. 2021. Transient top-down and bottom-up effects of resources pulsed to multiple trophic levels. Ecology 102:e03197.