Issue 7.8

Issue 7.8 is now online!

The August issue of Methods is now online!

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

Plant-O-Matic: A free iOS application that combines the species distribution models with the location services built into a mobile device to provide users with a list of all plant species expected to occur in the 100 × 100 km geographic grid cell corresponding to the user’s location.

RClone: An R package built upon genclone software which includes functions to handle clonal data sets, allowing:

  • Checking for data set reliability to discriminate multilocus genotypes (MLGs)
  • Ascertainment of MLG and semi-automatic determination of clonal lineages (MLL)
  • Genotypic richness and evenness indices calculation based on MLGs or MLLs
  • Describing several spatial components of clonality

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European Bison, Rewilding and Dung Fungal Spore

Post provided by AMBROISE BAKER

In the US, July is National Bison Month but most people in Europe are totally oblivious to it. I wasn’t even aware of it before being asked to write this blog post in connection with our recent Methods in Ecology and Evolution paper about quantifying population sizes of large herbivores. Some will argue that it is because we don’t ‘do’ day, month, state or national animals on this side of the Atlantic as much as the Americans do.

The European bison survived from extinction thanks to about 50 individuals kept in zoos. The species has been reintroduced in the wild in several European countries but remains ‘Vulnerable’ according to the IUCN criteria.

The European bison survived extinction thanks to ~50 individuals kept in zoos. It has been reintroduced in several countries but remains ‘Vulnerable’. ©4028mdk09

But another reason is that the European bison, Bison bonasus bonasus, is simply not sufficiently well-known or associated with European nature in the public’s mind. This is particularly true in Western Europe where this species has been extinct since medieval times.

Early European accounts from North America reported huge bison populations – with estimates of up to 60 million – moving to and fro in the great bison belt. These past migratory movements across the Great Plains are familiar well beyond the US and feed our view of untamed wilderness prior to the impact of European ’civilisation’. In contrast, there are hardly any records of European bison numbers until just before the last wild one was reported killed in Poland in 1921. Continue reading

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

Ecological Transcriptomics for Endangered Species: Avoiding the “Successful Operation, but the Patient Died” Problem

Post provided by TILL CZYPIONKA, DANIEL GOEDBLOED, ARNE NOLTE and LEON BLAUSTEIN

Ecological Transcriptomics and Endangered Species

 The small size of the rockpool and the salamander population makes non-invasive sampling a necessity (from left: Tamar Krugman, Alan Templeton, Leon Blaustein). © Arne Nolte

The small size of the rockpool and the salamander population makes non-invasive sampling a necessity (from left: Tamar Krugman, Alan Templeton, Leon Blaustein). © Arne Nolte

Friday was Endangered Species Day – so this is a good time to reflect on what science and scientists can do to support conservation efforts and to reduce the rate of species extinctions. One obvious answer is that we need to study endangered species to understand their habitat requirements as well as their potential for acclimatization and adaptation to changing environmental conditions. This information is crucial to for the design of informed conservation planning. However, for most endangered species the relevant phenotypes are not known a priori, which leaves the well-intentioned scientist asking “which traits should I measure?”. Transcriptome analysis is often a good way to answer to this question.

Transcriptome analysis measures the expression levels of thousands of genes in parallel. This amount of data circumvents the need to decide on a reduced number of traits of unknown relevance and allows for a relatively unbiased phenotypic screen of many traits. In particular, physiological changes, which often influence a species’ distributional range, can be studied using transcriptome analysis. Also, transcriptomics provide a direct connection to the genetic level. This is essential for in-depth analyses of aspects of evolution and might even be helpful for a new kind of conservation planning, which aims to foster endangered species by promoting (supposedly) beneficial hybridization. The integration of transcriptomic analysis with ecological studies is known as ‘Ecological transcriptomics’. 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

National Wildlife Day 2015

Happy National Wildlife Day everyone!

Today is 10th National Wildlife Day. As we have done for a few awareness days this year (Bats, Biodiversity and Bees so far) we are marking the day by highlighting some of our favourite Methods in Ecology and Evolution articles on the subject. Obviously ‘wildlife’ is a pretty big topic, so we have narrowed our focus (slightly) to monitoring wildlife (with one or two additional papers that we didn’t want to leave out).

This list is certainly not exhaustive and there are many more wonderful articles on these topics in the journal. You can see more of them on the Wiley Online Library.

If you would like to learn more about National Wildlife Day, you may wish to visit the organisation’s website, follow them on Twitter and Facebook or check out today’s hashtag: #NationalWildlifeDay.

Without further ado though, please enjoy our selection of Methods articles for National Wildlife Day:

Integrating Demographic Data

Our National Wildlife Day celebration begins with an article from our EURING Special Feature. Robert Robinson et al. present an approach which allows important demographic parameters to be identified, even if they are not measured directly, in ‘Integrating demographic data: towards a framework for monitoring wildlife populations at large spatial scales‘. Using their approach they were able to retrieve known demographic signals both within and across species and identify the demographic causes of population decline in Song Thrush and Lawping.

 

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International Day for Biological Diversity 2015

Happy International Day for Biological Diversity everyone!

As you may know, today (Friday 22 May) is the United Nations Day for Biodiversity and we are celebrating by highlighting some of the best papers that have been published on biodiversity in Methods in Ecology and Evolution. This is by no means an exhaustive list and you can find many more articles on similar topics on the Wiley Online Library (remember, if you are a member of the BES, you can access all Methods articles free of charge).

If you would like to learn more about the International Day for Biological Diversity, you may wish to visit the Convention on Biological Diversity website, follow them on Twitter or check out today’s hashtag: #IBD2015.

Without further ado though, here are a few of the best Methods papers on Biological Diversity:

Methods Cover - August 2012Biodiversity Soup

We begin with an Open Access article from one of our Associate Editors, Douglas Yu (et al.). This article was published in the August issue of 2012 and focuses on the metabarcoding of arthropods. The authors present protocols for the extraction of ecological, taxonomic and phylogenetic information from bulk samples of arthropods. They also demonstrate that metabarcoding allows for the precise estimation of pairwise community dissimilarity (beta diversity) and within-community phylogenetic diversity (alpha diversity), despite the inevitable loss of taxonomic information.

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