Here is a round-up of some interesting methods papers published in the past few weeks. If you see any more papers that you would like to see flagged up, leave a comment below or email me.

In PLoS Biology Wayne Getz presents a thoughtful review of the models and modelling approaches that might be useful in predicting the consequences of multiple threats to ecosystems from a food web / ecosystem perspective.

Ecology has several interesting methods papers: Murray Efford and colleagues show how it is possible to use likelihood methods to estimate densities of animals from arrays of passive detectors (such as arrays of microphones). Michael Neubert et al. present a new method for estimating the rate of growth of perturbations in transient dynamics. Jessica Metcalf et al. apply integral projection models to the problem of estimating flux of individuals in tropical forests. And Grosbois et al. demonstrate a new approach for estimating individual survival / mortality rates from mult-population data.

In Conservation Biology Berlund et al. show how Bayesian methods can be used to understand habitat association of trees from presence records and environmental data. Finn et al. compare methods for estimating population size variability with a view to priortising populations that are more risk to extinction from variability. And Christopher Grouios & Lisa Manne ask whether occupancy or abundance data are more useful in predicting population persistence and how this impacts on reserve design.

Ecology Letters has a paper by Paul Murtaugh comparing model selection methods that is likely to be of general interest. Mosser et al argue that density may not be a generally good measure of habitat quality (in terms of food/ resources), particularly if low quality habitat provides a refuge for non-reproductive  individuals.

Finally, in Systematic Biology Sennblad & Lagergren show how probabilistic orthology analysis can be used to overcome some of the problems in identifying orthologous genes and gene products. And there is some debate about the use of barcodes in taxonomy centring on the effects of sampling error on the model used to delimit species.