Improving Bayesian isotope mixing models: a response to Jackson et al. (2009)

We recently described a Bayesian framework for stable isotope mixing models and provided a software tool, MixSIR, for conducting such analyses (Ecol. Lett., 2008; 11 :470). Jackson et al. (Ecol. Lett., 2009; 12:E1) criticized the performance of our software based on tests using simulated data. However, their simulation data were flawed, rendering claims of erroneous behaviour inaccurate. A re‐evaluation of the MixSIR source code did, however, uncover two minor coding errors, which we have fixed. When data are correctly simulated according to eqns  (1)–(4) in Jackson et al. (2009) , MixSIR consistently and accurately estimated the proportional contribution of prey to a predator diet, and was surprisingly robust to additional unquantified error. Jackson et al. (2009) also suggested we use a Dirichlet prior on the source proportion parameters, which we agree with. Finally, Jackson et al. (2009) propose adding additional error parameters to our mixing model framework. We caution that such increases in model complexity should be evaluated based on data support.     

Fire as a dimension of historical ecology: a response to Bowman et al. (2011)

Bowman et al. (Journal of Biogeography, 2011, 38 , 2223–2236) attempt a synthesis of the current status of study into human use of fire as an ecosystem management tool and provide a framework for guiding research on the human dimensions of global fire. While we applaud this ambitious effort, we believe the proposed ‘pyric phase and transition’ model to be too deterministic and simplistic to account for the complexity and diversity in human–fire relationships. After reviewing theoretical problems with the proposed framework, we question policy implications of their conclusions concerning tropical forest systems. We suggest that a theoretically informed perspective should build on an historical fire ecology framework for investigating social and ecological aspects of human–environment interactions.     

Response to Collins et al. (2011)

We note serious problems in Collins et al. (Journal of Biogeography, 2011, doi: 10.1111/j.1365‐2699.2011.02506.x ): failure to use over 80% of the available data; failure to use one of the two available archipelagoes; mistaken inclusion of four species; and reliance on a grossly inadequate number of null matrices. Curing the paper of these problems would have strengthened the evidence for checkerboards and the role of competition.     

Demystifying the marine‐terrestrial biodiversity gradient: response to Vermeij et al.

We respond to seven criticisms made by Vermeij et al. ( 2018 ) regarding Miller & Wiens ( 2017 ). Their criticisms generally reflect misunderstandings, unsupported speculations, and topics that were explicitly addressed in our paper.     

Evidence for epistasis: reply to Trouve et al.

Salathé and Ebert (2003, J. Evol. Biol. 16: 976–985) have shown that the mean logarithmic fitness of Daphnia magna clones declined faster than linearly with increasing inbreeding coefficient F. They interpreted this result as evidence for synergistic epistasis. Trouve et al. (2004, J. Evol. Biol., doi: 10.1111/j.1420‐9101.2004.00755.x) suggested that hybrid vigour could be an alternative explanation for this finding. We use a population genetic model to support the original claim that the marked deviation from linearity cannot be explained without epistasis. We further argue that the relevant reference population is the metapopulation and not the subpopulation. Taken together, we believe that synergistic epistasis between recessive deleterious alleles segregating in the D. magna metapopulation is the most likely explanation for the finding of Salathé and Ebert.