Bat Appreciation Day: The Latest Methodological Advances

Post provided by Kate Jones and the Biodiversity Modelling Research Group

The Funnel-eared bat (Natalus stramineus)

The Funnel-eared bat (Natalus stramineus) – © Veronica Zamora-Gutierrez

Today (17 April) is Bat Appreciation Day! Yes I know, a whole day to appreciate bats. Although my biodiversity modelling research group at University College London would argue that 24 hours is just not enough time to appreciate these cool, yet misunderstood animals, we wanted to mark the day by giving MEE a round-up of the latest methodological advances in bat monitoring and what we hope to see in the next few years.

Bat Detectives and Machine Learning

oisin_pictureOisin Mac Aodha PostDoc – If you have ever tried to spot bats flying around at night you will know that it can be very difficult. However, bats leak information about themselves into the environment in the form of the sounds they make while navigating and feeding. These calls are often too high for us to hear, but we can use devices known as bat detectors to transform them into a form that we can record and listen to. Monitoring bat populations over wide areas or long periods can result in huge amounts of data which is difficult to analyse though. To address this problem, our group, along with Zooniverse, have setup a citizen science project called Bat Detective which asks members of the public help us find bat calls in audio recordings that have been collected from all over Europe (the infographic below gives a bit more information on this). We have had an amazing response to date and our detectives have already located several thousand bat calls. However, to scale up monitoring, we need more automated methods of detecting calls. Using the analysis provided by our Bat Detectives, we are currently working on building algorithms that can automatically tell us if a recording contains a bat call.

In this video we see a visual representation of an audio signal called a spectrogram that features several bat calls. On top you see the result of an automated method we have developed for detecting bat calls. The larger the value, the more certain the algorithm is that there is a bat call at that point in time. Continue reading

Methods digest – update

A round up of recent methods-relevant research published recently: it is ages since we did this, largely because the journal has been so busy with papers coming in and being published. Do send through links to any new methods papers to me or to the journal, or post a comment below.

In Evolution, Werthelm & Sanderson look at how estimates of diversification rates are influenced by improved estimates of divergence times; Robert Lanfear introduces a new method for comparing rates of molecular evolution on trees.

In Systematic Biology Eric Stone has an extremely interesting article on why common comparative methods are robust to tree misspecification. Martin Linder et al. evaluate Bayesian models of substitution rate evoluton, whist Chung & Ané compare Bayesian methods for gene and species tree reconstructions. Simon Ho et al. have a short paper on Bayesian estimation of substitution rates from ancient DNA sequences.  Leaché & Rannala compare the accuracy of species tree estimation under different methods. Anne Kupczok explores the consequences of different null models for shape bias of supertree methods. John Huelsenbeck et al. compare phylogenetic models with the ‘No Common Mechanisms Model’.

In the Journal of Animal Ecology Andrew Jackson & co. have a paper on a new R package (SIBER) for comparing isotopic niche widths.

Sophie Smout et al. look at how heterogeneity of detection and mark loss affect estimates of survival in grey seals in Journal of Applied Ecology. Issue 1 of 2011 has a special profile introduced by Julia Jones on monitoring species abundance.

Eve McDonald-Madden et al. have a paper in Ecological Applications on how to allocate conservation resources when the persistence of a species in not certain. Mary Beth Rew and colleagues look at the problem of how many genetic markers should be used to tag an individual in the presence of close relatives.

A paper by Adam Algar et al. in Ecology looks at how it is possible to quantify the roles of trait-based filters in determining local and regional species composition. Florent Bled, Andy Royle & Emmanuelle Cam have a paper on testing hypotheses about nesting site dynamics by combining population and fitness data.

In Oikos, Sofia Berg et al. have a paper on the use of sensitivity analysis to identify keystones in foodwebs.

Finally for this update, in Ecography Simon Linke and co look at how multivariate analysis can produce conservation planning that addresses the needs of practitioners. Steinar Engen et al. describe a new approach to measuring the similarity of communities and Canrain Liu et al. have a paper on measuring the accuracy of species distribution models using presence absence data.

I’ll try to do another update in the next couple of weeks to cover some of the journals I have missed in this one.

Methods digest – June 2010

Here is the methods digest update for June 2010 – do let me know if there is anything that you think I should feature.

In Oikos Novak & Wooton have a paper on using indices to quantify the effects of comeptition and Landau & Ryan present new ‘null model tests for presence-absence data’ (NMTPAs).

A paper in Conservation Letters by Michael Kearney et al. evaluates species distribution models by comparing the output of correlative and mechanistic models.

In the Journal of Ecology the debate about how to measure the intensity and importance of competition continues to rage. Walker et al. also review the use of chronosequences in studies of succession. Hautier et al. look at how to model the growth of parasitic plants (see also the editorial commentary by Mark Rees).

In the current issue of Systematic Biology, Susana Magallón applies a method using fossils to break long branches to molecular dating of the angiosperm phylogeny. Carstens & Dewey have a new method for species delimitation. Haartman et al. have a paper on sampling trees from evolutionary models.Towsend & Lopez-Giraldez look at the optimal selection of gene and ingroup taxon sampling for resolving phylogenetic relationships.

Salvador Pueyo et al. in Ecology Letters look at the problem of testing for criticality in ecosystem dynamics. Kuhnert et al. review the use of expert knowledge in Bayesian modelling.

In the latest issue of Ecology Bailey et al. look at estimation in multistate models with unobservable states. Mérigot et al. look at goodness of fit measures for dendrogram analyses.

Hines et al in Ecological Applications present a new approach for occupancy modelling for cluster sampling. In the same issue Waddle et al. present a new approach for estimating co-occurrence of interacting species.

Finally, in the American Naturalist Hamilton et al. look at the problem of estimating the uncertainty in estimates of species richness, and Solow & Smith look at how to estimate abundance from occupancy.

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 – March 2010

The first thing to point out this month is that issue 1 of the journal is now online here. To accompany the issue we have a podcast and a videocast. There is also now a  journal correspondence site to host feedback and discussion of published papers, more on this soon.

The one day journal launch symposium is accepting bookings, with a good response so far. However places are still available, and the booking form is here.

We hope that Methods in Ecology and Evolution will be listed on ISI as soon as possible – if you have 2 minutes to spare we would be really grateful if you would fill out the nomination form. This will help us get noticed by them.

To begin this month’s round up of recent methods papers, Ecological Monographs has a paper  by James Grace and colleagues on structural equation modelling. In this paper they outline how meta-models can be used to aid the translation of theory into SEMs.

In Ecological Applications, Lester Yuan describes how observational data and propensity scores can be used to estimate the effects of excessive nutrients on stream invertebrates.

In Ecology Fitsum Abadi and colleagues perform an analysis of the performance of integrated population models, particularly focussing on the issue of independence of data. Pierre Legendre et al. look at how ‘space-for-time’ experiments can be analysed in the absence of replication. Toby Patterson et al. look at how state space methods can be used to correct telemetry data and the limits to this approach. Etienne Laliberté & Pierre Legendre present a new approach for measuring functional diversity, along with R code.

Richard P. Brown and Ziheng Yang in Systematic Biology look at the problem of dating shallow phylogenies with relaxed clocks using Bayesian methods. Jeremy Brown et al. discuss the problem of very long branch length estimates in trees generated using Bayesian methods, compared with ML alternatives. R. Alexander Pyron presents a Likelihood method for assessing molecular divergence time estimates with the placement of fossils.

In Ecology Letters Colleen Webb et al. present a new approach to develop trait based theory for predicting community composition and ecosystem function.

The latest issue of the Journal of Applied Ecology has a section on ‘Modelling Distributions’. This includes methods papers on the use of proxy-based methods for mapping ecosystem services,  estimating individual survival using occupancy data, estimation of immigration rates using integrated population models, and the ability of habitat suitability models to predict the recovery of threatened species.

In the American Naturalist Bart Haegeman and Rampal Etienne look at the relationship between entropy maxization and species distributions.

Thanks to Rua Mordecai for pointing out an interesting paper in the Auk by Jason Riddle and colleagues on incorporating estimates of prior detections in estimating occupancy, abundance and probability of detection.

Please let me know if there are any papers that could be featured in the next month’s digest update.

Science Blogs - Blog Rankings

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 – December 2009

A round-up of methods papers published in the last month. If there are any papers that you think should be featured, email me or leave a comment and I will add them.

Liam Revell has a paper in Evolution on size correction and principal components analysis of phylogenetic comparative data. Olivier Gimenez and colleagues also have a paper in the same issue on generating fitness landscapes using mark-recapture data.

Systematic Biology has a number of papers with interesting methods: Campbell & Lapointe have a paper on the use and validity of composite taxa in phylogenetic analysis; Fitzjohn et al. have a nice paper on estimating trait-dependent speciation and extinction rates in phylogenies that are not complete; Bui Quang Minh and colleages present an algorithm for efficiently estimating phylogenetic diversity; Michael D. Pirie, Aelys M. Humphreys, Nigel P. Barker, and H. Peter Linder present an approach for dealing with implications of conflicting gene trees on inferences of evolutionary history above the species level.

In Conservation Biology, Angelia Vanderlaan and Christopher Tagaart describe how a voluntary scheme for ships to avoid cetain areas has worked in preventing lethal strikes on right whales.

In Ecological Applications, Cang Hui and colleagues compare approaches for extrapolating population sizes from abundance-occupancy relationships. Matthew Etterson et al. look at the problem of estimating population trends when there is detection heterogeneity and overdipsersion in the data. Paul Beier and co-workers use a case study to examine the use of least-cost modelling to design wildlife corridors.

Oscar Puebla and colleagues describe in Ecology a study that estimates dispersal using genetic distances in a coral reef fish. Sean Connolly et al. have a new bootstrap approach for testing species abudance models in the same issue. Andy Royle et al. present Bayesian method for estimating population sizes using camera trap data. David G. Angeler, Olga Viedma, and JoséM. Moreno present a critique of time lag analysis in time series modelling. David Carslake et al. have a paper presenting useful review of constraints and rules for elasticity analysis in matrix modelling. Finally in that same issue Paul Stapp and Daniel J. Salkeld look at the use of stable isotopes in studying host-parasite interactions.

Finally for this month in Animal Conservation, Heidy Kikillus et al. look at minimising false negatives in predicting distributions of invasive species. (Thanks to Andrew Tyre for pointing this one out).

Phylogenetic comparative methods

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.