How to Assemble, Fill and Clean Metapopulation Microcosm Plates: Two Video Tutorials

Metapopulation Microcosm Plates (MMP) are devices which resemble 96-well microtiter plates in size and shape, but with corridors connecting the wells in any configuration desired. They can be used to culture microbial metapopulations or metacommunities with up to 96 habitat patches.

In these two video tutorials, Helen Kurkjian explains how you can assemble, fill and clean MMPs in your lab.

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Spatial Cross-Validation of Species Distribution Models in R: Introducing the blockCV Package

Post provided by Roozbeh Valavi

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Modelling species distributions involves relating a set of species occurrences to relevant environmental variables. An important step in this process is assessing how good your model is at figuring out where your target species is. We generally do this by evaluating the predictions made for a set of locations that aren’t included in the model fitting process (the ‘testing points’).

Random splitting of the species occurrence data into training and testing points

Random splitting of the species occurrence data into training and testing points

The normal, practical advice people give about this suggests that, for reliable validation, the testing points should be independent of the points used to train the model. But, truly independent data are often not available. Instead, modellers usually split their data into a training set (for model fitting) and a testing set (for model validation), and this can be done to produce multiple splits (e.g. for cross-validation). The splitting is typically done randomly. So testing points sometimes end up located close to training points. You can see this in the figure to the right: the testing points are in red and training points are in blue. But, could this cause any problem? Continue reading

اعتبارسنجی متقاطع مکانی در مدلسازی توزیع گونه‌‌ها

نویسنده: روزبه وَلَوی

This post is available in English

مدلسازی توزیع گونه‌ها به تخمین و برآورد ارتباط بین مجموعه‌ای از نقاط حضور گونه با متغیرهای زیست‌محیطی مرتبط می پردازد. یکی از مراحل اساسی این فرایند، ارزیابی قدرت مدل برای پیش­بینی مکان‌هایی است که احتمال حضورگونه در آنجا وجود دارد. این کار اغلب با ارزیابی پیش­بینی انجام شده در مجموعه‌ای ازنقاط که در فرآیند مدلسازی مورد استفاده قرار نگرفته اند (نقاط آزمایشی) صورت می‌گیرد.

تقسیم تصادفی داده‌های حضور گونه به نقاط آزمایشی و آموزشی

تقسیم تصادفی داده‌های حضور گونه به نقاط آزمایشی و آموزشی

مطالعات پیشین بر این نکته تاکید دارند که به منظور ارزیابی معتبر، نقاط آزمایشی باید مستقل از نقاط آموزشی باشند، این درحالیست که داده مستقل واقعی به ندرت در دسترس می باشد. به همین دلیل، در فرایند مدلسازی معمولا داده‌های موجود را به دو قسمت داده‌های آموزشی (برای کالیبره کردن مدل) و داده های آزمایشی (برای ارزیابی دقت مدل) تقسیم می‌کنند، این استراتژی می‌تواند چند قسمتی هم باشد (برای مثال اعتبارسنجی متقاطع یا cross-validation). از آنجاییکه این تقسیم بندی معمولا بصورت تصادفی انجام می‌شود، بنابراین گاهی اوقات نقاط آزمایشی در فواصل نزدیک به نقاط آموزشی قرار می‌گیرند. شکل زیر این مساله را به خوبی نشان می دهد که در آن نقاط آزمایشی به رنگ قرمز و نقاط آموزشی آبی هستند. اما آیا این مساله می‌تواند مشکلی ایجاد کند؟ Continue reading

New Associate Editors

Two new Associate Editors are joining the Methods in Ecology and Evolution Board today: Sydne Record (Bryn Mawr College, USA) and Hao Ye (University of Florida, USA). They have both joined on a three-year term and you can find out more about them below.

Sydne Record

“My research incorporates knowledge of field-based natural history, ecological theory, statistics, remote sensing, and computer modeling to ask how abiotic, biotic, and anthropogenic drivers structure biodiversity across a wide range of spatiotemporal scales. I am particularly interested in understanding how differences in scale (i.e., spatial, temporal, levels of biological organization) influence inferences about biological systems and contribute to uncertainty in models. I enjoy thinking about biota with different life histories.”

Sydne is currently working on understanding drivers of community assembly across several taxonomic groups including ants, trees, and small mammals. In many of these projects, she leverages spatially and/or temporally replicated data sets collected by networks of sites (e.g., the Long Term Ecological Research [LTER] and National Ecological Observatory Networks [NEON]).

Hao Ye

“I am a computational ecologist who dabbles in dynamical systems and software development. My research is centered around modeling change in ecosystems, using methods to infer the underlying processes that produce time series observations. Some specific areas that I work on include: population dynamics and forecasting, quantifying information flow and causality, and indicators of stability & resilience. I am also interested in reproducible research practices to both accelerate science and improve its accessibility.”

Hao Ye contributed to the BES Guide to Reproducible Code last year. He has recently been published in Regional Studies in Marine Science and Nature.

We’re delighted to welcome Hao Ye and Sydne to the Associate Editor Board and we look forward to working with them over the coming years.

Monitoring Ecosystems through Sound: The Present and Future of Passive Acoustics

Post provided by Ella Browning and Rory Gibb

AudioMoth low-cost, open-source acoustic sensor ©openacousticdevices.info

AudioMoth low-cost, open-source acoustic sensor ©openacousticdevices.info

As human impacts on the world accelerate, so does the need for tools to monitor the effects we have on species and ecosystems. Alongside technologies like camera traps and satellite remote sensing, passive acoustic monitoring (PAM) has emerged as an increasingly valuable and flexible tool in ecology. The idea behind PAM is straightforward: autonomous acoustic sensors are placed in the field to collect audio recordings. The wildlife sounds within those recordings are then used to calculate important ecological metrics – such as species occupancy and relative abundance, behaviour and phenology, or community richness and diversity.

The Pros and Cons of Passive Acoustic Monitoring

Using sound to monitor ecosystems, rather than traditional survey methods or visual media, has many advantages. For example, it’s much easier to survey vocalising animals that are nocturnal, underwater or otherwise difficult to see. Also, because acoustic sensors capture the entire soundscape, it’s possible to calculate acoustic biodiversity metrics that aim to describe the entire vocalising animal community, as well as abiotic elements in the environment.

The use of PAM in ecology has been steadily growing for a couple of decades, mainly in bat and cetacean studies. But with sensor costs dropping and audio processing tools improving, there’s currently a massive growth in interest in applying acoustic methods to large-scale or long-term monitoring projects. As very low-cost sensors such as AudioMoth start to emerge, it’s becoming easier to deploy large numbers of sensors in the field and start collecting data. Continue reading

New Associate Editor: Res Altwegg

Today, we are pleased to be welcoming a new member of the Methods in Ecology and Evolution Associate Editor Board. Res Altwegg joins us from the University of Cape Town, South Africa and you can find out a little more about him below.

Res Altwegg

“My interests lie at the intersection between ecology and statistics, particularly in demography, population ecology, species range dynamics and community ecology. My work addresses questions in conservation biology especially in relation to climate change. I’m particularly excited about the increasing availability of large data sets, such as those collected by citizen scientists, and the opportunities and challenges their analysis brings.”

Res is the founding director of the centre for Statistics in Ecology, Environment and Conservation at the University of Cape Town. The centre brings together ecologists and statisticians with the aim to address some of the most important questions in ecology and conservation using cutting-edge statistical methods. He has reviewed for Methods in Ecology and Evolution a number of times over the past few years and has had one article – ‘A general framework for animal density estimation from acoustic detections across a fixed microphone array‘ – published in the journal. Another of Res’ articles has recently been accepted for publication and will appear in an upcoming Special Feature.

We are thrilled to welcome Res as a new Associate Editor and we look forward to working with him on the journal.

In Conservation Planning, Some Data are More Important Than Others

Provided by Heini Kujala and José Lahoz-Monfort

Esta entrada de blog también está disponible en español

Spatial Conservation Planning and the Quest for Perfect Data

Conservation planners and managers often need to make decisions with imperfect information. When deciding what action to take or how to divide resources between candidate locations, we rarely have all the information we’d like on what species are present at a site or which areas are most critical for supporting their population viability. A large volume of ecological research focuses on answering these very questions.

To make conservation decisions, we need other types of data as well. These include information on things like the cost of carrying out a given conservation action, current condition of sites, the distribution and intensity of threats in a region, and much more. Many conservation problems are spatial, meaning that we often need to decide between multiple candidate locations and that there are spatial dependencies between sites that need to be accounted for. All these different pieces of information are needed to make cost-efficient and effective conservation decisions.

Ecologists and conservation biologists are usually concerned about the completeness and accuracy of the ecological data used to make these decisions (understandably). But less effort has been spent in researching and verifying the accuracy of the types of data mentioned above. At the same time, we have relatively poor understanding of how data gaps influence solutions optimised across multiple species and locations, and the relative importance of gaps in different types of data. This is what we set out to find in ‘Not all data are equal: Influence of data type and amount in spatial conservation prioritisation’. Continue reading

En la planificación de la conservación, algunos datos son más importantes que otros

Por Heini Kujala y José Lahoz-Monfort

This blog post is also available in English

La planificación espacial de la conservación y la búsqueda de datos perfectos

Los planificadores y administradores de la conservación a menudo necesitan tomar decisiones con información imperfecta. Al decidir qué acción tomar o cómo dividir recursos entre diferentes localizaciones, rara vez tenemos toda la información que nos gustaría sobre qué especies están presentes en un lugar o qué áreas son las más críticas para respaldar su viabilidad poblacional. Un gran volumen de investigación ecológica se focaliza en responder a estas preguntas.

Para tomar decisiones de conservación, también necesitamos otros tipos de datos, incluyendo, entre otros, información sobre el costo de llevar a cabo una acción de conservación determinada, la condición actual de los diferentes sitios, y la distribución e intensidad de las amenazas en una región. Muchos problemas de conservación son espaciales, es decir que a menudo tenemos que decidir entre varias ubicaciones candidatas, con dependencias espaciales entre ellas. Todas estas diferentes piezas de información son necesarias para tomar decisiones de conservación rentables y efectivas.

Los ecólogos y los biólogos de la conservación suelen estar preocupados por la integridad y exactitud de los datos ecológicos utilizados para tomar estas decisiones (comprensiblemente). Pero se ha dedicado menos esfuerzo a investigar y verificar la exactitud de los otros tipos de datos mencionados anteriormente. Además, tenemos una comprensión relativamente pobre de cómo las lagunas en los datos influyen en las soluciones optimizadas en múltiples especies y ubicaciones, y la importancia relativa de las lagunas en los diferentes tipos de datos. Es esto precisamente lo que nos propusimos investigar en el artículo ‘Not all data are equal: Influence of data type and amount in spatial conservation prioritisation’. Continue reading

New Associate Editors

Today we are welcoming two new Associate Editors to Methods in Ecology and Evolution: Huijie Qiao (Chinese Academy of Sciences, China) and Veronica Zamora-Gutierrez (Unidad Durango, Mexico and University of Southampton, UK). They have both joined on a three-year term and you can find out more about them below.

Huijie Qiao

Huijie Qiao

Huijie Qiao

“My research is focused broadly on macroecology. I work to clarify the theory and methodology behind ecological niche modelling and species distribution modelling. In this realm, I have worked to improve our understanding of those modelling algorithms that perform best under different model configuration scenarios, and examined how spatial bias affects model outcomes. I have also developed a simulation framework designed to understand the causal mechanisms that structure biodiversity on both long and short timescales in a virtual world.”

Huijie had an article published in last December’s issue of Methods in Ecology and Evolution. In ‘Using data from related species to overcome spatial sampling bias and associated limitations in ecological niche modelling‘ the authors assess how useful it is to integrate occurrence data for closely related species with varying degrees of niche overlap into Ecological niche models of focal species. In recent years, Huijie has also had articles published in Global Ecology and Biogeography, American Naturalist and Ecography.

Veronica Zamora-Gutierrez

Veronica Zamora Gutierrez

Veronica Zamora Gutierrez

“I am an ecologist and my research interests range from mammal´s conservation, bioacoustics and species interactions to ecosystem services in both natural areas and human-dominated landscapes like cities and agroecosistems. At present, my work focuses mainly on bats to answer question related to their importance as pollinators and suppressors of insects’ population, their echolocation behaviour and how global change is and might affect them. Deepening our understanding of these questions is crucial for developing effective conservation strategies in this anthropozoic era.”

In 2016, Veronica was the lead author on ‘Acoustic identification of Mexican bats based on taxonomic and ecological constraints on call design‘ which was published in the September issue of Methods in Ecology and Evolution. The article collated a reference call library for bat species that occur in a megadiverse country (Mexico) and is now freely available. More recently, she has published articles on the effects of climate change on bats and the importance of vertebrate pollinators.

We’re delighted to welcome Huijie and Veronica to the Associate Editor Board and we look forward to working with them over the coming years.

Balance: Time for Your Life and Your Career

Post Provided by Stacy De Ruiter

There’s an Impostor Behind this Post

The premise of this post is that it might provide some useful advice on how to achieve a tenable work-life balance and find a satisfying, successful career in science.

©Paul VanDerWerf

I’m writing this post, but there is no way that I would hold myself up as an example of success. I have a job that’s a great fit for me, but there was probably no-one else who wanted it, and there are so many others with more prestigious and high-profile jobs. I sometimes manage to divide my time well between my family and my work goals, but I actually feel like I am shortchanging both of them, basically all the time. And how long ago was the last time I got enough sleep, enough exercise, enough personal time? I often feel like someday very soon everyone is going to realise that I really don’t have it all together.

But here’s the thing: almost all the successful, self-aware people I know feel this way, at least some of the time. Impostor syndrome seems to be incredibly common, and I think at least partly it grows out of a genuine awareness of the privilege and luck that helped pave the way to your achievements. Impostor syndrome that interferes with your mental health or limits your potential is clearly unhealthy, and the part where you refuse to believe in your own competence must go immediately. But if it can peacefully coexist with confidence in your own abilities and healthy ambition, it might even be a good thing (or at least, an honest thing). Continue reading