Tag Archives: comparative methods

Conservation or Construction? Deciding Waterbird Hotspots

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Below is a press release about the Methods in Ecology and Evolution article ‘A comparative analysis of common methods to identify waterbird hotspots‘ taken from Michigan State University.

A mixed flock of waterbirds on the shore of Lake St. Clair. ©Michigan DNR

Imagine your favourite beach filled with thousands of ducks and gulls. Now envision coming back a week later and finding condos being constructed on that spot. This many ducks in one place surely should indicate this spot is exceptionally good for birds and must be protected from development, right?

It depends, say Michigan State University researchers.

In a new paper published in Methods in Ecology and Evolution, scientists show that conservation and construction decisions should rely on multiple approaches to determine waterbird “hotspots,” not just on one analysis method as is often done. Continue reading →

The Dark and Bright Sides of Phylogenetics and Comparative Methods

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Five years ago at Evolution 2014, ‘The Dark Side of Phylogenetics’ symposium (organised by Natalie Cooper) explored some of the issues with phylogenetic comparative methods (PCMs). This year at Evolution 2019, Michael Landis and Rosana Zenil-Ferguson are organising a contrasting ‘Bright Side of Phylogenetics‘ spotlight session (featuring Michael Matschiner). They aim to promote research that has overcome these pitfalls and that explores innovations in phylogenetics. Clearly they found our lack of faith disturbing.

Natalie and Michael have created a Virtual Issue to complement the spotlight session: Phylogenetics and Comparative Methods: The Bright and Dark Sides. It highlights recent Methods in Ecology and Evolution papers that feature either the ‘Bright Side’ or ‘Dark Side’ of phylogenetics and comparative methods. This Virtual Issue also highlights the diversity of researchers around the world working on these exciting questions. We hope you have a good feeling about it! Continue reading →

Issue 6.11

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Issue 6.11 is now online!

The November issue of Methods is now online!

This month’s issue contains two Applications articles and one Open Access article, all of which are freely available.

– mvMORPH: A package of multivariate phylogenetic comparative methods for the R statistical environment which allows fitting a range of multivariate evolutionary models under a maximum-likelihood criterion. Its use can be extended to any biological data set with one or multiple covarying continuous traits.

– Low-cost soil CO2 efflux and point concentration sensing systems: The authors use commercially available, low-cost and low-power non-dispersive infrared (NDIR) CO2 sensors to develop a soil CO2 efflux system and a point CO2 concentration system. Their methods enable terrestrial ecologists to substantially improve the characterization of CO2 fluxes and concentrations in heterogeneous environments.

This month’s Open Access article comes from Jolyon Troscianko and Martin Stevens. In ‘Image calibration and analysis toolbox – a free software suite for objectively measuring reflectance, colour and pattern‘ they introduce a toolbox that can convert images to correspond to the visual system (cone-catch values) of a wide range of animals, enabling human and non-human visual systems to be modelled. The toolbox is freely available as an addition to the open source ImageJ software and will considerably enhance the appropriate use of digital cameras across multiple areas of biology. In particular, researchers aiming to quantify animal and plant visual signals will find this useful. This article received some media attention upon Early View publication over the summer. You can read the Press Release about it here.

Our November issue also features articles on Population Genetics, Macroevolution, Modelling species turnover, Abundance modelling, Measuring stress and much more. Continue reading →

Methods Digest – February 2010

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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.

Phylogenetic comparative methods

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Phylogenetic comparative methods are always an area of hot discussion and lots of methodological development. So I thought it would be useful to highlight some recent papers that have developed new methods in the past year. Please email me or leave a comment if there is anything I have omitted or if something new comes out.

Thomas Hansen and colleagues have introduced a new method for studying adaptation using comparative methods. Their approach is a generalisation of the Ornstein-Uhlenbeck model that allows for adaptive constraints and phylogenetic intertia. They have an R-package SLOUCH which can be used to fit the model.

In Evolution Liam Revell has developed a new approach for data reduction and size correction using phylogenetic approaches – this is often done wrongly as the transformation is commonly applied before phylogenetic analysis, however it should be correctly done at the same time.

A new method in Functional Ecology allows one to test for phylogenetic dependence in complex multivariate data that also incorporate measurement error.

What will prove, I think, to be a very popular method is a new approach for testing for phylogenetic signal and analysing correlates of binary traits, basically a phylogenetic logistic regression by Anthony Ives and Ted Garland. The approach will allow linear modelling of correlates of a binary traits, which has been difficult before.

In a related area, another very important development is in the analysis of speciation and extinction rates when these are affected by a binary trait. FitzJohn et al. have shown how the BiSSE model, developed to do this, can be applied when phylogenies are incompletely resolved.

Likely to be of interest to many using comparative methods is a paper by Richard Smith on the use and misuse of Reduced Major Axis line fitting. He discusses the assumptions of this method, which are not widely appreciated.

In the American Naturalist Marc Lajeunesse has developed methods linking comparative analysis and meta-analysis, basically allowing meta-analysis to be corrected for phylogenetic non-independence.

In Proc B a new method for integrating spatial and phylogenetic dependence has been presented, and in JEB there has been a review of the ‘deadly sins of comparative analysis’ (apologies for self-promotion!).

Just to end with here is another method for explaining adaptation.