Building Universal PCR Primers for Aquatic Ecosystem Assessments

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.

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?

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

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

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.