Methods Digest – May 2010

Here is the latest methods digest:-

In Evolution Marta Szulkin, Nicolas Bierne and Patrice David have  perspective piece on measuring correlations between fitness and heterozygosity. Günter Wagner introduces a new approach to measuring fitness. Max Shpak and colleagues introduce an approach to coalescent modelling in populations that are structured and fluctuate seasonally. Richard Reynolds and colleagues look at the problem of measuring selection gradients.

Valério Pillar and Leandro Duarte present in Ecology Letters a new approach to analysing phylogenetic structure in metacommunities. Andy Fenton and colleagues look at the the problem of detecting interspecific interactions between macroparasites from ecological data. Johan Dahlgren has a contribution to the debate on regression methods.

In Proceedings B Peter Henderson and Anne Magurran present a new method for plotting species abundance distributions and linking to biomass. Tatsuya Amano et al. present a new approach for developing phenological indices.

William Morris and colleagues have in Ecology a paper looking at cost-benefit curves for pollination mutualisms. Michael Greenacre considers the problem of correspondance analysis of unstandardised data. Stephanie Carlson, Athanasios Kottas and Marc Mangel describe how Bayesian methods can be used to analyse size-dependent over-winter survival.

In Ecological Monographs Dennis Heisey et al. look at the problem of estimating spatio-temporal dynamics from cross-sectional data. Kyle Dexter and colleagues ask how accurate are identifications of tropical trees, using DNA data to test accuracy.

In Systematic Biology Christian Klingenberg and Nelly Gidaszewski describe new methods for measuring phylogenetic signal and homoplasy in morphometric data.  Thomas White et al. describe a network approach to studying karyotypic evolution. Liat Grievink et al. consider phylogenetic reconstruction when the proportional of variable sites varies across a tree. Stéphane Guindon and colleagues assess the performance of PhyML.

Finally for this month, in Journal of Applied Ecology, Jim Hone et al. look at estimates of maximal rates of population growth of mammals and applications in management, and Thomas Ezard and colleagues deal with the issue of transient dynamics in population management.

If there are any papers that you think should be featured, please do contact me.

Methods Digest – February 2010

This monthly digest is a bit late as we have been busy writing an editorial and finalizing the running order for the first issue of the journal. That should be online in a couple of weeks. Pre-publication versions of papers are here, whilst an up-to-date list of accepted papers is here. The very latest updates are also available via Twitter and Facebook.

In Ecology Letters, Colin Beale et al. review problems in the regression analysis of spatial data. This review deals with some of the practical considerations in dealing with spatially referenced ecological data.

In Conservation Biology, Jared Underwood and colleagues look at the difficulties of identifying conservation area using different distribution data sets: this is a tricky methodological issue and they identify novel tools for addressing such problems. The problem of how to build an efficient conservation fence is dealt with in a paper by Michael Bode and Brendan Wintle in the same issue and also Wolfgang Nentwig et al. propose a new method for scoring the impact of invasive species.

Andrew Solow and Woollcott Smith describe in Evolution a new test for Cope’s Rule, the tendency for body size to increase along an evolutionary lineage.

In the Journal of Evolutionary Biology Klug et al. review problems in the measurement of sexual selection. Jarrod Hadfield and Shinichi Nakagawa present a new approach that synthesizes comparative analysis with meta-analysis and quantitative genetics, and shows the formal equivalence between some commonly employed methods.

In the Journal of Applied Ecology there are several papers of interest: Devictor et al. consider the problem of defining and measuring ecological specialization; Ward et al. consider the issue of inferring spatial structure in time series data; Obbard et al. compare density estimators for large carnivores; Firn et al. apply alternative state models to invasive species control; De Barba et al. commpare opportunistic and systematic approaches for genetic monitoring; finally Parris et al. consider how to assess ethical trade-offs in ecological field studies.

Andy Hector and colleagues review the analysis of variance with unbalanced data in the latest Journal of Animal Ecology. In the same issue Marc Kéry and Andy Royle present a method for modelling and estimating abundance and trends in metapopulations.

In Global Ecology and Biogeography, Peres-Neto and Legendre look at how to estimate and control for spatial structure in ecological communities. Mellin et al. look at the problem of developing estimators for predicting species and abundance in coral reef fishes.

In Ecological Modelling David Bausch and colleagues compare three statistical methods for modelling resource selection.

Please do email if there are any papers that you think should be featured in the next digest.

Methods Digest – January 2010

A belated happy new year! Here is this month’s round-up of methods papers published in the last month. Do let me know if there are any papers that I have missed that could be featured.

In Systematic Biology Brian O’Meara presents new heuristics for joint species delimitation and tree inference. A new comparative method for logistic regression controlling for phylogeny is outlined by Ives & Garland, and Wertheim et al. publish an analysis of the use of relaxed clocks in phylogenetic inference.

Marc Cadotte and colleagues outline in the latest issue of Ecology Letters new metrics for measuring phylogenetic diversity in ecological communities.

In the Journal of Applied Ecology Len Thomas and colleagues present a review of distance sampling and its use in estimating population size; Marc Kéry and co-workers illustrate a method for estimating trends from replicated count data when detection is imperfect; Deanna Dawson and Murray Efford demonstrate a new method for estimating bird densities from acoustic data. William Kendall and Gary White have a cautionary note on substituting spatial subnits for temporally replicated sampling in estimating site occupancy.

A ‘how to’ paper in Journal of Animal Ecology by Alastair Wilson et al. presents a review and guide to using the ‘animal model’ in quantitative genetics.

In Global Ecology and Biogeography Cabral & Schurr have a paper illustrating a method for linking range dynamics and demographic models in the Fynbos. Andrés Baselga has a paper in the same issue illustrating a method for disentangling the contributions of spatial turnover and nestedness to beta diversity.

Tommaso Zillion and Fangliang He publish in Oikos a new method for linking species abundance distributions across scales.

In Journal of Ecology Damgaard & Fayolle present a new method for estimating the influence of competition in plants.

A mini-review by Gavin Stewart and colleagues in Conservation Letters reviews the design of temperate marine reserves from a analytic perspective. In the same issue Kyle Van Houtan et al. look at the effectiveness of translocations in conserving endangered species.

Methods Digest, October 2009

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.