Tag Archives: Ecosystem Services

New Associate Editors

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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.

Also of Interest… Journal of Applied Ecology

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Post provided by Aaron M. Ellison

The Struggle is Real: Finding Interesting and Relevant Articles

Where to start? We are awash in data, information, papers, and books. There are hundreds of ecological and environmental journals published regularly around the world; the British Ecological Society alone publishes five journals and is now accepting submissions for a sixth (more information on People and Nature here).

None of us has time even to click on the various articles flagged by alerts, feeds, or keywords, and few even browse tables of contents (which are becoming irrelevant as we move to DOIs and immediate-online publication). Increasingly, we rely on our friends, colleagues, students, and mentors to point us towards papers we might find interesting – further evidence, I suppose, of the importance of good networks for knowledge creation and scientific understanding.

Regular readers of Methods in Ecology and Evolution or this Methods blog may not realise how many methodological papers are published routinely in our BES sister journals. In this inaugural posting of Also of interest…, I highlight three papers recently published in Journal of Applied Ecology that introduce and apply new, model-based methodology to interesting ecological questions. The specific methods are like many seen in the pages of Methods in Ecology and Evolution and suggest general approaches for modelling and studying complex ecological and environmental phenomena. Continue reading →

Building Universal PCR Primers for Aquatic Ecosystem Assessments

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Post provided by Vasco Elbrecht

Many things can negatively affect stream ecosystems – water abstraction, eutrophication and fine sediment influx are just a few. However, only intact freshwater ecosystems can sustainably deliver the ecosystem services – such as particle filtration, food biomass production and the supply of drinking water – that we rely on. Because of this, stream management and restoration has often been in the focus of environmental legislation world-wide. Macrozoobenthic communities are often key biological components of stream ecosystems. As many taxa within these communities are sensitive to negative stressors introduced by humans, they’re ideal for assessing the quality of water.

Unfortunately, most macrozoobenthic taxa – such as stone-, may-, and caddisflies as well as most other invertebrates – are often found in juvenile larval life stages in these ecosystems, so they’re often difficult to identify based on morphology. With the DNA based metabarcoding method though, almost all taxa in a stream can be reliably identified up to species level using a standardised gene fragment. One key component of this strategy is the development of universal markers, which allow detection of the diverse macrozoobenthic groups.

Our new R package PrimerMiner provides a framework for obtaining sequence data from available reference databases and identifying suitable primer binding sites for marker amplification. The package makes this process quicker and easier. In the following pictures, we summarise the key steps of DNA metabarcoding.

Rivers are home to a wide range of macroinvertebrate species. These are often used to assess water quality as many respond sensitively to anthropogenic stressors, like organic pollution, eutrophication or fine sediment influx.
One macroinvertebrate sample can contain hundreds or even thousands of specimens.
Invertebrates are collected using standardised field sampling protocols and usually identified based on their morphology. The taxa lists obtained this way are then used to assess stream water quality based on associated bioindication values of the individual taxa. But identifying juvenile invertebrates by morphology isn’t possible for all collected taxa.
DNA based identification is a promising alternative to morphology based identification. Whole bulk samples with hundreds of organisms can be identified at once – often to species level – which can improve the accuracy of assessments.
All specimens in the sample have to be well homogenised for DNA extraction before we can move on to DNA metabarcoding. The specimens are easier to homogenise if they are dried first.
The dried samples are mechanically homogenised using a bead mill and sterile tubes (which are only used once).
After 30 minutes of grinding, all specimens are homogenised to fine powder, which can then used for DNA extraction.
The homogenized macroinvertebrate tissue is incubated in digestion buffer (a solution that dissolves cell membranes) to enable DNA extraction. Only a few mg (~10 – 20 mg) of the homogenate is used for DNA extraction, as the efficiency decreases when too much tissue is extracted at once.
We used the R package PrimerMiner to obtain sequences for the 15 most important freshwater invertebrates from reference databases. Edith Vamos and I are screening the sequence alignment for suitable primer binding sites in this picture.
The developed primers are tested and PCR optimised using both mock samples and complete communities.
After successful marker amplification, several uniquely tagged samples are pooled and then sent to an external service provider for high throughput sequencing. The sequences are then bioinformatically processed and compared to reference databases. These precisely identify the taxa in each sample and connect bioindication values to taxa lists and stream types.

To find out more about PrimerMiner, read our Methods in Ecology and Evolution article ‘PrimerMiner: an r package for development and in silico validation of DNA metabarcoding primers’. Like all Applications articles, this paper is freely available to everyone.

When Measuring Biodiversity, Do Individuals Matter?

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Post provided by Samuel RP-J Ross

Close up of a black-capped babbler (Pellorneum capistratum), one of the species included in our study.

Close up of a black-capped babbler (Pellorneum capistratum), one of the species in our study.

Our newly-developed method simulates intraspecific trait variation when measuring biodiversity. This gives us an understanding of how individual variation affects ecosystem processes and functioning. We were able to show that accounting for within-species variation when measuring functional diversity can reveal details about ecological communities which would otherwise remain unseen. Namely, we found a negative impact of selective-logging on birds in Borneo when accounting for intraspecific variation which we could not detect when ignoring intraspecific variation.

Why Biodiversity Matters

Biodiversity is important for many reasons. One of the main reasons is its contribution to the range of goods and services provided by ecosystems (i.e. ecosystem services) that we can take advantage of, such as natural food resources or climatic regulation. It’s generally believed that biodiversity contributes to these services by increasing and maintaining ‘ecosystem functioning’ – often defined as the rate at which ecosystems are turning input energy (e.g. sunlight) into outputs (e.g. plant biomass). Continue reading →

Celebrating Wetlands Today, Protecting Them for Tomorrow

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Post Provided by JULIA CHERRY, UNIVERSITY OF ALABAMA

Today is World Wetlands Day, a day to raise awareness about wetlands and the many ecosystem services that they provide. Wetlands are broadly defined as areas saturated or inundated with water for periods long enough to generate anaerobic soils and support water-loving plants. They include bogs, swamps, floodplain forests, marshes and mangroves.

Some may wonder why these habitats deserve their own day of recognition, as wetlands can evoke images of the soggy, unpleasant wild places– the “ghast pools” of Dante’s Divine Comedy or the “waste places” of Beowulf. Unfortunately, these descriptions overshadow the true beauty and value of the world’s diverse wetland ecosystems. For those of us dedicated to researching and enjoying wetlands, these areas are worth appreciating every day of the year for numerous reasons.

In honor of World Wetlands Day, I will make the case for wetlands and highlight an example of a new research tool designed to understand how coastal wetlands may respond to sea-level rise.

Wetland habitats, including (A) a marine-dominated coastal marsh and maritime pine island complex (Grand Bay National Estuarine Research Reserve, Mississippi, USA), (B) a freshwater floodplain marsh (Hale County, Alabama, USA), (C) a cypress-tupelo swamp (Perry Lakes, Alabama, USA), and (D) a Gulf of Mexico salt marsh (Rockefeller Wildlife Refuge, Louisiana, USA). ©Julia Cherry

Wetland habitats, including (A) a marine-dominated coastal marsh and maritime pine island complex (Grand Bay National Estuarine Research Reserve, Mississippi, USA), (B) a freshwater floodplain marsh (Hale County, Alabama, USA), (C) a cypress-tupelo swamp (Perry Lakes, Alabama, USA), and (D) a Gulf of Mexico salt marsh (Rockefeller Wildlife Refuge, Louisiana, USA). ©Julia Cherry

Continue reading →

New Associate Editors

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Over the next few weeks we will be welcoming three new Associate Editors to Methods in Ecology and Evolution. Susan Johnston (University of Edinburgh, UK) became a member of the Associate Editor Board on Monday 5 October. She will be joined on 19 October by Natalie Cooper (Natural History Museum, London, UK) and finally by Luísa Carvalheiro (University of Brasília, Brazil) on 2 November. You can find out more about all three of our new Associate Editors below.

Susan Johnston

Susan Johnston“My research focuses on using genomic information to understand evolution in natural populations. I adapt mixed model approaches to determine the genetic architecture of interesting traits (e.g. estimating heritability, genome-wide association studies, outlier analyses) to examine its relationship with fitness or importance in local adaptation. I am interested in the potential of affordable genomics to answer evolutionary and ecological questions in wild systems, and how to deal with various statistical issues arising from such studies in small and/or structured populations.”

Susan’s most recently published article is ‘Low but significant genetic differentiation underlies biologically meaningful phenotypic divergence in a large Atlantic salmon population‘, co-authored with T. Aykanat, P. Orell, E. Niemelä, J. Erkinaro and C.R. Primmer. The findings suggest that different evolutionary processes affect sub-populations of Atlantic salmon and that hybridization and subsequent selection may maintain low genetic differentiation without hindering adaptive divergence. This article was published in Molecular Ecology.

Natalie Cooper

Natalie Cooper“I am an evolutionary biologist, focusing mainly on macroevolution and macroecology. My interests include phylogenetic comparative methods, morphological evolution, using museum specimens in research, and integrating neontological and palaeontological data and approaches for understanding broad-scale patterns of biodiversity.”

Natalie has recently been published in Molecular Phylogenetics and Evolution (‘Effects of missing data on topological inference using a Total Evidence approach‘ with T. Guillerme) and in Evolution (‘Investigating evolutionary lag using the species-pairs evolutionary lag test (SPELT)‘ with C.L. Nunn). She was also a speaker at the Methods in Ecology and Evolution 5th Anniversary Symposium. Her presentation, ‘Limitations of Phylogenetic Comparative Methods‘, is freely available on YouTube.

Luísa Carvalheiro

Luisa Carvalheiro“My research focuses on community ecology & conservation. I have particular interest in the study of dynamics of biodiversity through time and space; and on the evaluation of how such biotic changes affect ecosystem functioning and ecosystem services, considering how the complex network of ecological interactions in which species are integrated mediates such changes.”

Earlier this year Luísa’s article ‘Susceptibility of pollinators to ongoing landscape changes depends on landscape history‘ (with J. Aguirre-Gutiérrez, J.C. Biesmeijer, E.E. van Loon, M. Reemer, and M.F. Wallis De Vries) was published in Diversity and Distributions. The article emphasizes the limited value of a one-size-fits-all biodiversity conservation measures and highlights the importance of considering landscape history when planning biodiversity conservation actions. This article is Open Access. Luísa was also the lead author of ‘The potential for indirect effects between co-flowering plants via shared pollinators depends on resource abundance, accessibility and relatedness‘ an Open Access article published in Ecology Letters last year.

We are thrilled to welcome Susan, Natalie and Luísa to the Associate Editor Board and we look forward to working with them over the coming years.