Revisiting Past Biodiversity with the divDyn R Package

Posted on April 5, 2019 by Chris Grieves

Post provided by ÁDÁM T. KOCSIS

The source of occurrence data: fossil collections (Early Jurassic ammonites in the collection of the University of Erlangen-Nuremberg, photo by Konstantin Frisch)

The source of occurrence data: fossil collections (photo by Konstantin Frisch).

To find out about changes in ancient ecosystems we need to analyse fossil databases that register the taxonomy and stratigraphic (temporal) positions of fossils. These data can be used to detect changes of taxonomic diversity and to draft time series of originations and extinctions.

The story would be so simple if it wasn’t the effects of heterogeneous and incomplete sampling: the white spots in our understanding of where and when species lived exactly. This phenomenon decreases the fidelity of face-value patterns extracted from the fossil record, making them less reliable. It must be considered if we want to get a glimpse into the biology or the distribution of life in space and time. Naturally, several metrics have been proposed to overcome this problem, each claiming to accurately depict the patterns of ancient life. Continue reading →

Citizen Science Projects Have a Surprising New Partner – The Computer

Posted on February 28, 2019 by Chris Grieves

Below is a press release about the Methods in Ecology and Evolution article ‘Identifying animal species in camera trap images using deep learning and citizen science‘ taken from the University of Minnesota-Twin Cities.

The computer’s accuracy rates for identifying specific species, like this warthog, are between 88.7 percent and 92.7 percent. Image credit: ©Panthera

The computer’s accuracy rates for identifying specific species, like this warthog, are between 88.7 percent and 92.7 percent. ©Panthera

For more than a decade, citizen science projects have helped researchers use the power of thousands of volunteers who help sort through datasets that are too large for a small research team. Previously, this data generally couldn’t be processed by computers because the work required skills that only humans could accomplish.

Now, computer machine learning techniques that teach the computer specific image recognition skills can be used in crowdsourcing projects to deal with massively increasing amounts of data—making computers a surprising new partner in citizen science projects.

Continue reading →

Using Dual RNA-seq to Investigate Host-Pathogen Systems When Genomic Resources are Limited

Posted on February 20, 2019 by Chris Grieves

Post provided by KAYLEIGH O’KEEFFE

Tall fescue infected with fungal pathogen, Rhizoctonia solani. ©Brooklynn Newberry

Pathogens and the infectious diseases that they cause can have devastating impacts on host individuals and populations. To better understand how pathogens are able to cause disease, we can investigate the genetic mechanisms underlying the infection process. Hosts may respond to infection by upregulating defence pathways. Pathogens, in turn, evade these host immune responses as they infect and cause disease. As this process unfolds and each organism responds to the other, gene expression changes in both the host and the pathogen. These gene expression changes can be captured by dual RNA‐seq, which simultaneously captures the gene expression profiles of a host and of a pathogen during infection. Continue reading →

Advances in Modelling Demographic Processes: A New Cross-Journal Special Feature

Posted on February 5, 2019 by Chris Grieves

Analysis of datasets collected on marked individuals has spurred the development of statistical methodology to account for imperfect detection. This has relevance beyond the dynamics of marked populations. A couple of great examples of this are determining site occupancy or disease infection state.

EURING Meetings

The regular series of EURING-sponsored meetings (which began in 1986) have been key to this development. They’ve brought together biological practitioners, applied modellers and theoretical statisticians to encourage an exchange of ideas, data and methods.

This new cross-journal Special Feature between Methods in Ecology and Evolution and Ecology and Evolution, edited by Rob Robinson and Beth Gardner, brings together a collection of papers from the most recent EURING meeting. That meeting was held in Barcelona, Spain, 2017, and was hosted by the Museu de Ciènces Naturals de Barcelona. Although birds have provided a convenient focus, the methods are applicable to a wide range of taxa, from plants to large mammals. Continue reading →

The BES Macroecology (& Macroevolution) SIG: Who We Are, What We Do and What to Look Out for at #BES2018

Posted on December 13, 2018 by Chris Grieves

Post provided by Natalie Cooper

Defining macroecology should be easy; it’s just ecology at large spatial scales, right? In reality though, it’s a little more complex than that. No-one agrees on exactly how large the spatial scale should be, and many studies that could be macroecology may also be defined as biogeography, landscape ecology, community ecology etc. Working at large spatial scales can also mean working at large temporal scales, often in deep-time. So there’s a lot of overlap with studies of macroevolution both on living and extinct species too.

This breadth of definitions means the BES Macroecology Special Interest Group (or BES Macro as we usually call it) has members with interests across ecology, evolution and palaeontology. Probably the most common statement at any of our events is “I’m not a macroecologist but…”. So, if you’re interested in broad-scale ecology and evolution, in a living or palaeo context, the SIG is for you, even if you don’t identify as a macroecologist! Continue reading →

Speed Review at the BES Annual Meeting: Get a Senior Editor’s Opinion on YOUR Manuscript

Posted on December 13, 2018 by Chris Grieves

Coming to the BES Annual Meeting? Planning to submit a paper to a BES journal? Then you should sign up for the Speed Review Session on Monday 17 December! (sign-up sheets will be on the BES Stand in the Exhibition Hall.) Find out more about this session below.

What is a Speed Review Session?

©schlagzahluhren.de

Essentially, Speed Review is a chance for you to get a Senior Editor’s opinion on your manuscript. All you need to do is sign-up and bring along a figure or a key finding from your research to centre the discussion on. Each session will be limited to five minutes, so try to have a succinct summary of your manuscript ready as well. The Editor you speak to will let you know what they think of your paper and try to give you some advice about any areas to highlight or any potential concerns that they might have about it. Continue reading →

Biodiversity Monitoring by Plant Proxy is Cheap and Easy: Here’s How and Why

Posted on October 8, 2018 by Chris Grieves

Post provided by Rasmus Ejrnæs, Ane Kirstine Brunbjerg & Hans Henrik Bruun

Could we use the plants in this swamp forest to predict the diversity of other species?

Local communities and regional biotas are built of hundreds, if not thousands, of species. Most of these species are small-bodied and discreet lifeforms. So it’s no wonder that naturalists have almost always focused their attention on conspicuous species of their particular liking. Why plants then? Well, plants are practical and efficient. They “stand still and wait to be counted”, as the eminent population biologist John Harper put it. No matter the weather, from spring to autumn. There are enough plant species to show contrasts between sites, and yet they can usually be identified to species level in the field.

You Can’t Predict the Diversity of Beetles from Lichens… Can You?

Unfortunately, the overwhelming scientific consensus seems to be that any particular taxonomic group won’t adequately represent the biodiversity of other taxonomic groups. The idea of surrogacy seems to hit the same hard wall as most attempts to provide generally working models for variation in biodiversity at local and regional scales. Biodiversity remains one of the largest scientific research questions without good general answers. Continue reading →

Crossing the Palaeontological-Ecological Gap

Posted on August 30, 2018 by Chris Grieves

Today is the first day of the Crossing the Palaeontological-Ecological Gap (CPEG) conference. The aim of the conference is to open a dialogue between palaeontologists and ecologists who work on similar questions but across vastly different timescales. This splitting of temporal scales tends to make communication, data integration and synthesis in ecology harder. A lot of this comes from the fact that palaeontologists and ecologists tend to publish in different journals and attend different meetings.

Methods in Ecology and Evolution is one of few ecological journals that attracts submissions from both ecologists and palaeontologists. To highlight this, we’ve released a Virtual Issue, also called Crossing the Palaeontological-Ecological Gap. Continue reading →

Editor Recommendation: The Ecologist’s Field Guide to Sequence-Based Identification of Biodiversity

Posted on May 17, 2018 by Chris Grieves

Post provided by Pierre M Durand

A fossilized species of the diatom Thalassiosira. B. A species of the dinoflagellate Prorocentrum. (Image provided by A. Ndhlovu).

As any reader of Methods in Ecology and Evolution will know, advances in technologies and methodologies used by ecologists and evolutionary biologists are never-ending. Coupled with the tendency for researchers to become ever more specialised, this means that keeping up to date with all the advances is challenging at best. Occasionally, new advances revolutionise the kinds of questions we ask and encourage us to develop new approaches to answer them. One of these huge advances emerged from the ‘-omics’ revolution.

The application of -omics methodologies to evolution and ecology has been particularly rapid. These technologies usually aren’t part of the basic science education in these fields – it’s more usual for computational biologists to cross over to ecology and evolution than the other way around. The review by Simon Creer and colleagues ’The ecologist’s field guide to sequence-based identification of biodiversity’ helps bridge this gap. It’s not too technical, but sufficiently detailed, and it provides a very handy overview of how genomics, transcriptomics and their meta-analyses can be applied to evolutionary ecology. The paper is filled with enormously helpful workflows, pointers, examples and, as the title suggests, is a guide for those who are not experts in sequence based technologies. Continue reading →

Resolving Conservation Conflicts: The Nominal Group Technique

Posted on February 16, 2018 by Chris Grieves

Post provided by Jean Hugé

Conservation conflicts are actually conflicts among people with different priorities.

Conservation issues seem to be getting ever more complex and challenging. Practitioners and society at large agree on the need to gather – and somehow use – as much information as possible before making any conservation-related decisions. Talking to all kinds of people, ranging from local villagers, fishermen and hunters to international experts, community leaders and environmentalists, is now common practice in conservation research. Not everyone will agree on the eventual conservation decisions, but the idea is that decisions should only be made after (almost) everyone’s opinion has been heard.

So far so good. The calls for inclusive conservation are being acknowledged, and we should be ready to move on and make better decisions, right? Well, it’s not always that easy. Conservation conflicts are actually conflicts among people with different priorities and values. Just calling for dialogue and hoping that consensus and effective conservation action will just follow isn’t enough. Continue reading →

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