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Markov Chain Nest Productivity Model

What is MCnest?

The Markov Chain Nest Productivity Model (or MCnest) quantitatively estimates the impact of pesticide-use scenarios on the annual reproductive success of bird populations. MCnest integrates existing toxicity information from three standardized avian toxicity tests with information on species life history and the timing of pesticide applications relative to the timing of avian breeding seasons. The model provides risk assessors with a tool to go beyond the current screening-level quotient method approaches for assessing reproductive effects by estimating the proportional change in reproductive success. MCnest translates toxicity information into the currency needed for conducting a population-level assessment of pesticide risks.


There are two versions of MCnest.  The first version, referred to as Basic MCnest, or MCnest v1.0, was publicly released in 2013.  The second version, referred to as TIM/MCnest, or MCnest v2.0, was publicly released in 2017.  MCnest v2.0 retains all the functionality of MCnest v1.0, but includes three important additional features. First, MCnest v2.0 allows users to choose between T-REX  or TIM  for simulating exposure.  Second, MCnest v2.0 allows users to directly enter data from standard toxicity tests on the MCnest graphical user interface for generating surrogate toxicity endpoints. In MCnest v1.0, surrogate endpoints must be pre-calculated.  Finally, MCnest v2.0 includes beta algorithms for exploring systematic variation in model parameters over the course of an avian breeding season.


The user's manuals (version-specific) provide an introduction and examples of MCnest features. The technical manual (applies equally to both versions) provides background on how the model functions and the scientific basis for its approach to estimating changes in reproductive success. It is intended to help MCnest users understand the strengths and limitations of the model and to interpret the results of MCnest simulations. The Avian Life-History Profiles for Use in MCnest document provides background information and rationale for selecting the default life history characteristics for a suite of avian species. Go to the MCnest Documentation  page to download PDF versions of these documents.

MCnest is written and compiled in Matlab ®.  Running MCnest requires installation of the Matlab® Compiler Runtime (MCR), which is version‑specific.  MCnest will not run without the MCR.  The MCR files are very large and are not hosted on our website.  You may download the MCR from the Mathworks  website.

MCnest v1.0 (basic version) consists of the following two self-extracting zip files, the contents of which must be placed in the same directory on your computer.  You must also download and install the MCR for Windows 32-bit for Matlab release 2012a .

MCnest v2.0 (TIM/MCnest) consists of the following two self-extracting zip files, the contents of which must be placed in the same directory on your computer.  You must also download and install the MCR for Windows 64-bit for Matlab release 2016b .

A MCnest revision history as well as a species library history can also be downloaded from the MCnest Documentation page.

Background References

Bennett, R. S. and M. A. Etterson.  2006.  Estimating pesticide effects on fecundity rates of wild birds using current laboratory reproduction tests.  Human and Ecological Risk Assessment 12(4): 762-781.

Bennett, R. S. and M. A. Etterson.  2007.  Incorporating results of avian toxicity tests into a model of annual reproductive success.  Integrated Environmental Assessment and Management  3(4): 498-507.

Bennett, R. S., I. C. Dewhurst, A. Fairbrother, A. D. M. Hart, M. J. Hooper, A. Leopold, P. Mineau, S. R. Mortensen, R. F. Shore, and T. A. Springer.  2005.  A new interpretation of avian and mammalian reproduction toxicity test data in ecological risk assessment.  Ecotoxicology 14(8): 801-815.

Bennett, R.S. and M.A. Etterson. 2013. On selecting surrogate endpoints for estimating pesticide effects on avian reproductive success. Integrated Environmental Assessment and Management 9:600-609.

Etterson, M., K. Garber, and E. Odenkirchen. 2017. Mechanistic modeling of insecticide risk to breeding birds in North American agroecosystems. PLoS One 12(5): e0176998.

Etterson, M. A. and R. S. Bennett.  2006.  On the use of published demographic data for population-level risk assessment in birds.  Human and Ecological Risk Assessment 12(6):1074-1093.

Etterson, M. A., R. S. Bennett, E. L. Kershner, and J. W. Walk.  2009.  Markov chain estimation of avian seasonal fecundity.  Ecological Applications  19(3): 622-630.

Etterson, M. A., S. N. Ellis-Felege, D. Evers, G. Gauthier, J. A. Grzybowski, B. J. Mattsson, L. R. Nagy, B. J. Olsen, C. M. Pease, M. P. van der Burg, and A. Potvien. 2011. Modeling fecundity in birds:  Conceptual overview, current models, and considerations for future developments. Ecological Modelling 222: 2178-2190.

Etterson, M.A. and R.S. Bennett, R.S. 2013. Quantifying the effects of pesticide exposure on annual reproductive success of birds. Integrated Environmental Assessment and Management 9:590-599.

Ruskin, K.J., M.A. Etterson. T.P. Hodgman, A.C. Borowske, J.B. Cohen, C.S. Elhphick, C.R Field, R.A. Kern, E. King, A.R. Kocek, A.I. Kovach, K.M. O’Brien, N. Pau, W.G. Shriver, J. Walsh, and B.J. Olsen. 2017. Seasonal fecundity is not related to geographic position across a species’ global range despite a central peak in abundance. Oecologia 183: 291-301.

For Further Information

For further information, please contact Matt Etterson, (218) 529-5158.