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

A Model Approach to Weed Management

Post provided by VANESSA ADAMS

Vanessa Adams in the field with gamba grass in the Batchelor region, NT. ©Amy Kimber (NERP Northern Australia Hub)

Vanessa Adams in the field with gamba grass in the Batchelor region, NT.
©Amy Kimber (NERP Northern Australia Hub)

Invasive weeds cause environmental and economic harm around the world. Land managers bear a heavy responsibility for the control of infestations in what is often a time-consuming and costly battle.

Fortunately, an increasing number of research-based solutions are giving land managers an advantage. This includes tools to determine the distribution of weeds and also the development of modelling approaches to predict their spread.

Understanding the current and future distribution of an invasive species allows managers to better direct their limited resources. However, the direct and strategic management of weeds is tricky and that’s why population models (in particular spatial dispersal models that can be applied without much data) are needed to inform and facilitate action on the ground. Continue reading

Inferring Extinction: When is a Species as Dead as a Dodo?

Post provided by ELIZABETH BOAKES

The indisputably extinct Dodo (Raphus cucullatus). ©Ballista

The indisputably extinct Dodo (Raphus cucullatus). ©Ballista

A species is either extant or extinct – it exists or it does not exist. Black and white, a binary choice. Surely it should not be difficult to assign species to one of these two categories? Well, in practice it can be extremely challenging and a plethora of methods have been developed to deal with the problem.  This of course leads to a second challenge – which of the plethora should you use?! (More on this later…)

There are a few well-studied cases where we can assert extinction confidently. For example, the chances of the Dodo (Raphus cucullatus) having existed undetected for upwards of 300 years on an island now densely populated by humans are infinitesimally small. However, many extinctions are far harder to diagnose. Species typically become extremely rare before becoming extinct. If taxa are particularly cryptic or are found across a huge geographic range it is quite plausible that the few remaining individuals may exist undetected for decades. An extreme illustration of this is the 1938 discovery of Latimeria chalumnae, a deep-sea member of the Coelacanths, the entire order of which was believed to have become extinct 80 million years earlier! Continue reading