Issue 7.9

Issue 7.9 is now online!

The September issue of Methods is now online!

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

– Arborist Throw-Line Launcher: A cost-effective and simple alternative for collecting leaves and seeds from tall trees. The authors have also provided some tutorial videos on YouTube.

– ctmm: An R package which implements all of the continuous-time stochastic processes currently in use in the ecological literature and couples them with powerful statistical methods for autocorrelated data adapted from geostatistics and signal processing.

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New Associate Editors

Today we are welcoming two new Associate Editors to Methods in Ecology and Evolution: Samantha Price (University of California, Davis, USA) and Andrés Baselga (University of Santiago de Compostela, Spain).

Samantha Price

Samantha Price

Samantha Price

“My research seeks to answer the question ‘What regulates biodiversity?’. I use phylogenetic and comparative methods to investigate the abiotic and biotic drivers of global patterns of ecomorphological and lineage diversity over long periods of time and across large clades of vertebrates. To work at this macro-scale I tap the reserves of scientific data in museum collections, published literature, as well as online databases using data and techniques from across ecology, evolution, organismal biology, palaeobiology and data science. ”

Samantha will be joining the Board as our sixth Applications Editor. In July, she had an article titled ‘The Impact of Organismal Innovation on Functional and Ecological Diversification‘ published in Integrative and Comparative Biology. The paper introduces a framework for studying biological innovations in an evolutionary context. Earlier in the year, Sam was the first author of the article ‘A promising future for integrative biodiversity research: An increased role of scale-dependency and functional biology‘, published in Philosophical Transactions of The Royal Society B Biological Sciences. In this article, the authors argue that, given its direct relevance to the current biodiversity crisis, greater integration is needed across biodiversity research.

Andrés Baselga

Andres Baselga

Andres Baselga

“I am broadly interested in biodiversity. My background includes a PhD on beetle taxonomy. Later on I focused on biogeography and macroecology, particularly on beta diversity patterns and their underlying processes. This has led me to develop novel methods to quantify the dissimilarity between assemblages, aiming to improve our ability to infer the driving processes. With this objective, I am also interested in the integration of phylogenetic information to quantify macroecological patterns at multiple hierarchical levels (from genes to species, i.e. multi-hierarchical macroecology).”

Andrés has been an active author and reviewer for Methods in Ecology and Evolution over the past few years. He was the lead author of the article ‘Comparing methods to separate components of beta diversity‘,  which tested whether the replacement components derived from the BAS and POD frameworks are independent of richness difference. This article was also the basis for one of the most popular posts we have ever had on this blog: ‘What is Beta Diversity?‘. In addition to this, Andrés was the lead author of ‘Multi-hierarchical macroecology at species and genetic levels to discern neutral and non-neutral processes‘, published in Global Ecology and Biogeography in 2015. The paper proposed that the patterns emerging across multiple hierarchical levels can be used to discern the effects of neutral and non-neutral macroecological processes, which otherwise have proven difficult to separate.

We are thrilled to welcome Samantha and Andrés to the Associate Editor Board and we look forward to working with them over the coming years.

Exploring Microbial Diversity: From the Sequence to the Cell

Post provided by Ruben Props, Michelle Berry, Marian Schmidt, Frederiek-Maarten Kerckhof, Vincent Denef and Nico Boon

Searching Lake Michigan (USA) for uncharacterized microbial diversity. © Michelle Berry

Searching Lake Michigan (USA) for uncharacterized microbial diversity. © Michelle Berry

Exploring microbial diversity and relating it to ecosystem functions is one of the primary occupations of microbiologists and microbial ecologists worldwide. Unfortunately, recent studies have shown that the microbial census is far from complete and that it is heavily biased towards certain (host-associated) environments. With the Earth’s microbial diversity estimated at an impressive one trillion (1012) taxa, the search continues for new technologies and methodologies that may help us better describe, monitor and preserve the microbial diversity of our planet’s natural and engineered ecosystems.

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Biogeographic Regions: What Are They and What Can They Tell Us?

Post provided by Leonardo Dapporto, Gianni Ciolli, Roger L.H. Dennis, Richard Fox and Tim G. Shreeve

Every species in the world has a unique geographic distribution. But many species have similar ranges. There are many things that can cause two (or more) species to have similar ranges – for example shared evolutionary histories, physical obstacles (mountains, oceans etc.) or ecological barriers limiting their dispersal. As a consequence, different regions of the globe are inhabited by different sets of living organisms.

In the mid-19th century ecologists recognised that the earth could be divided into different biogeographic regions. Alfred Russel Wallace (1823–1913) played a key role in defining and recognising biogeographic regions. He improved the existing maps of  biogeographic regions and provided basic rules to identify them. His observation that some of these regions are home to similar species, despite being far away from each other and separated by significant barriers was the inspiration for Alfred Wegener’s theory of continental drift. In more recent years regionalisation has been used to understand the spatial drivers of biological evolution and to protect those regions characterised by particularly unique flora and fauna.

The biogeographic regions identified by Alfred Russel Wallace from The Geographical Distribution of Animals (1876)

The biogeographic regions identified by Alfred Russel Wallace from The Geographical Distribution of Animals (1876)

Despite the long history of biological regionalisation, the methods to identify biogeographic regions are still being improved. We are currently working in this exciting field of research and recently published ‘A new procedure for extrapolating turnover regionalization at mid-small spatial scales, tested on British butterflies’ in Methods in Ecology and Evolution. Continue reading

Celebrating Owl Research on International Owl Awareness Day

Post provided by LEANNE HEISLER

snowy-owl-981653_640Today, on International Owl Awareness Day (August 4), we celebrate the research we have done to better understand owls and their prey. There are over 200 extant species of owls, a handful of which have geographic distributions spanning several continents (i.e., barn owl, snowy owl, short-eared owl, long-eared owl). So no matter where you are in the world you’re probably not too far away from an owl.

Ecologists and paleontologists have taken advantage of this to study owls and their prey. One of the most widely used methods for this is collecting and dissecting owl pellets. We discuss some of the major benefits of studying owl pellets in our recent Methods in Ecology and Evolution Review article ‘Owl pellets: a more effective alternative to conventional trapping for broad-scale studies of small mammal communities’. Continue reading

Issue 7.6: Methods in Ecology and Evolution 5th Anniversary Special Feature

Issue 7.6 is now online!

The June issue of Methods, which includes our latest Special Feature – “5th Anniversary of Methods in Ecology and Evolution” – is now online!

Our 5th Anniversary Special Feature is a collection of six articles (plus an Editorial from Executive Editor Rob Freckleton) that highlights the breadth and depth of topics covered by the journal so far. It grew out of our 5th Anniversary Symposium – a joint event held in London, UK and Calgary, Canada and live-streamed around the world in April 2015 – and contains papers by Associate Editors, a former Robert May prize winner and regular contributors to the journal.

The six articles are based on talks given at last May’s Symposium. They focus on:

In his Editorial for the Special Feature, Rob Freckleton looks to the future. In his words: “we hope to continue to publish a wide range of papers on as diverse a range of topics as possible, exemplified by the diversity of the papers in this feature”.

All of the articles in the Special Feature will be freely available for a limited time. In addition to this, two of the articles (Shedding light on the ‘dark side’ of phylogenetic comparative methods and Perturbation analysis of transient population dynamics using matrix projection models) are Open Access.
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RPANDA: A Time Machine for Evolutionary Biologists

Post provided by HÉLÈNE MORLON

Yesterday saw the start of this year’s annual Evolution meeting and to celebrate Hélène Morlon has written a blog post discussing the amazingly versatile RPANDA package that she is developing with her research group. A description of RPANDA was published in the journal earlier this year and, like all our Applications papers, is freely available to read in full.

If you are attending Evolution, as well as attending the fabulous talks mentioned by Hélène below, do stop by booth 125 to see our BES colleague Simon Hoggart. Simon is the Assistant Editor of Journal of Animal Ecology and would be happy to answer your questions about any of our journals or any of the other work we do here at the BES.

RPANDA: a time machine for evolutionary biologists

Imagine “Doc”, Marty’s friend in Back to the Future, trying to travel back millions of years in an attempt to understand the history of life. Instead of building a time machine from a DeLorean sports car powered by plutonium, he could dig fossils, or more likely, he would use molecular phylogenies.

Molecular phylogenies are family trees of species that can be built from data collected today: the genes (molecules) of present-day species (Fig 1). They are often thought of as trees, in reference to Darwin’s tree of life. The leaves represent the present: species that can be found on Earth today. The branches represent the past: ancestral species, which from time to time split, giving rise to two independent species. The structure of the tree tells us which species descend from which ancestors, and when their divergence happened.

birds_phylog

Fig 1: The phylogenetic tree of all birds (adapted from Jetz et al. 2012). Each bird order is represented by a single bird silloutter and a specific colour (the most abundant order of Passeriformes, for example is represented in dark orange). Each terminal leaf represents a present-day bird species, while internal branches represent the evolutionary relationships among these species.

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A New Modelling Strategy for Conservation Practice? Ensembles of Small Models (ESMS) for Modelling Rare Species

Post provided by FRANK BREINER, ARIEL BERGAMINI, MICHAEL NOBIS and ANTOINE GUISAN

Rare Species and their Protection

Erythronium dens-canis L. – a rare and threatened species used for modelling in Switzerland. ©Michael Nobis

Erythronium dens-canis L. – a rare and threatened species used for modelling in Switzerland. ©Michael Nobis

Rare species can be important for ecosystem functioning and there is also a high intrinsic interest to protect them as they are often the most original and unique components of local biodiversity. However, rare species are usually those most threatened with extinction.

In order to help prioritizing conservation efforts, the International Union for Conservation of Nature (IUCN) has published criteria to categorize the status of threatened species, which are then published in Red Lists. Changes in a species’ geographical distribution is one of the several criteria used to assign a threat status. For rare species, however, the exact distribution is often inadequately known. In conservation science, Species Distribution Models (SDMs) have recurrently been used to estimate the potential distribution of rare or insufficiently sampled species. Continue reading

What is Dark Diversity?

Post provided by ROB LEWIS & MEELIS PÄRTEL

Our understanding of how biological diversity works has been advanced by a long history of observing species and linking patterns to ecological processes. However, we generally don’t focus as much on those species that aren’t observed, or in other words ‘absent species’. But, can absent species provide valuable information?

Dark diversity – a set of species absent from a particular site but which belong to its species pool – has the potential to be as ecologically meaningful as observed diversity. Part of the species pool concept, understanding dark diversity is relatively straightforward.

The Basic Theory of Dark Diversity

To begin learning about dark diversity, there are two important terms that we need to define: ‘species pool’ and ‘focal community’. A ‘species pool’ is a set of species present in a particular region or landscape that can potentially inhabit a particular observed community because of suitable local ecological conditions.

A ‘focal community’ is the set of species that have been observed in a particular region or landscape (this is the ‘observed community’ and can also be referred to as alpha diversity). For a given focal community to become established, the species within it must have overcome dispersal pressures as well as environmental and biotic filters.

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Biggest Library of Bat Sounds Compiled

Below is a press release about the Methods paper ‘Acoustic identification of Mexican bats based on taxonomic and ecological constraints on call design‘ taken from the University College London.

The Funnel-eared bat (Natalus stramineus)

The Funnel-eared bat (Natalus stramineus)

The biggest library of bat sounds has been compiled to detect bats in Mexico – a country which harbours many of the Earth’s species and has one of the highest rates of species extinction and habitat loss.

An international team led by scientists from UCL, University of Cambridge and the Zoological Society of London, developed the reference call library and a new way of classifying calls to accurately and quickly identify and differentiate between bat species.

It is the first time automatic classification for bat calls has been attempted for a large variety of species, most of them previously noted as hard to identify acoustically. Continue reading