Reliability of map accuracy assessments: A comment on Hunter et al. (2016)

Map validation data that are ambiguously allocated to map units and collected via poorly designed sampling methods are not statistically reliable and will misrepresent map quality. A recent paper published in Ecological Management and Restoration (Ecological Management & Restoration, 17, 2016 and 40) reported that a map in south‐eastern Australia provided little or no predictive accuracy based on new field data, but the validation suffered from the aforementioned pitfalls. In this comment, we outline the basic guidelines for a robust, reliable and transparent accuracy assessment of thematic maps, pointing out where (Ecological Management & Restoration, 17, 2016 and 40) fails to meets these guidelines.     

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.     

Management implications of the Macquarie Island trophic cascade revisited: a reply to Dowding et al. (2009)

1. The management of non-indigenous species is not without its complications. In Bergstrom et al. 's (2009) study, we demonstrated that feral cats Felis catus on sub-Antarctic Macquarie Island were exerting top-down control on the feral rabbit Oryctolagus cuniculus population, and that the eradication of the cats led to a substantial increase in rabbit numbers and an associated trophic cascade.
2. Dowding et al. (2009) claim our modelling was flawed for various reasons, but primarily that a reduction in the application of the rabbit control agent, Myxoma virus, coinciding with cat removal, was a major driver of rabbit population release.
3. We explore this proposition (as well as others) by examining rates of Myxoma viral release between 1991 and 2006 (with an attenuation factor for the years, 2003–2006) in association with presence/absence of cats against two estimates of rabbit population size. Myxoma viral release was a significant factor in the lower estimates of rabbit population, but the effect was small, and was not significant for higher rabbit population estimates. By contrast, the presence or absence of cats remained highly significant for both estimates.
4. Synthesis and applications. We re-affirm our position that top-down control of rabbit numbers by cats, prior to their eradication, was occurring on Macquarie Island. Nonetheless, we agree with Dowding et al. (2009) that systems with multiple invasive species represent complex situations that require careful scrutiny. Such scrutiny should occur in advance of, during, and following management interventions.     

Predicting the distribution of non‐vagile taxa: a response to McNyset and Blackburn (2006) and re‐evaluation of Stockman et al. (2006)

This paper addresses the issues raised by McNyset and Blackburn (2006 ) in their response to Stockman et al. (2006 ). Re‐evaluation of our published GARP analyses by McNyset and Blackburn showed that a much improved ecological niche model is obtained for predicting the distribution of the trapdoor spider genus Promyrmekiaphila in central/northern California. The improved niche model results in a substantially reduced omission error rate and a predictive model comparable to models obtained using other methods (GLM and BIOCLIM). However, the improved GARP models have a high commission error rate (> 0.75); consequently, the inferences regarding difficulties in modelling non‐vagile taxa drawn by Stockman et al. remain valid. Finally, we discuss other relatively minor criticisms of our study raised by McNyset and Blackburn and issues related to the peer review of our original paper.     

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.