Ecology, Field Methods, Methods 10th, Methods 10th Anniversary

10th Anniversary Volume 9: Acoustic Monitoring Editor’s Choice

To celebrate our 10th Anniversary, we are highlighting a key article from each of our volumes. For Volume 9 we selected ‘Estimating effective detection area of static passive acoustic data loggers from playback experiments with cetacean vocalisations’ by Nuuttila et al. (2018).

In this post, three of our Associate Editors with expertise in acoustic monitoring, Sarab Sethi, Camille Desjonquères and Lian Pin Koh, select their favourite MEE papers in this field.

India StephensonDecember 15, 2020December 15, 2020Leave a comment

Conservation and management, Methods 10th, Statistical methods

Anniversary Volume 9: Estimating Effective Detection Area of Static Passive Acoustic Data

Post provided by Hanna K Nuuttila

To celebrate the 10th Anniversary of the launch of Methods in Ecology and Evolution, we are highlighting an article from each volume to feature in the Methods.blog. For Volume 9, we have selected ‘Estimating effective detection area of static passive acoustic data loggers from playback experiments with cetacean vocalisations’ by Nuuttila et al. (2018). In this post, the authors discuss the background and key concepts of the article, and the application of the article for assessing abundance of cetaceans.

streamdnaDecember 14, 2020December 14, 2020Leave a comment

Methods 10th, Methods 10th Anniversary

10th Anniversary Volume 7: eDNA Editor’s Choice

To celebrate our 10th Anniversary, we are highlighting a key article from each of our volumes. For Volume 7 we selected ‘The ecologist’s field guide to sequence‐based identification of biodiversity’ by Creer et al. (2016).

In this post, two of our Associate Editors with expertise in eDNA, Lynsey Harper and Chloe Robinson, select their favourite MEE papers in this field.

India StephensonDecember 11, 2020December 11, 2020Leave a comment

Ecology, Methods 10th, Methods 10th Anniversary

10th Anniversary Volume 7: The ecologist’s field guide to sequence‐based identification of biodiversity

Post provided by Si Creer, Kristy Deiner, Serita Frey and Holly Bik

To celebrate the 10th Anniversary of the launch of Methods in Ecology and Evolution, we are highlighting an article from each volume to feature in the Methods.blog. For Volume 7, we have selected ‘The ecologist’s field guide to sequence‐based identification of biodiversity’ by Creer et al. (2016).

In this post, the authors share their motivation behind the paper and discuss advances in sequence‐based identification of biodiversity.

streamdnaDecember 10, 2020Leave a comment

Code and Applications, Ecology, Evolution, Methods papers, Statistical methods

Individual History and the Matrix Projection Model

Post provided by Rich Shefferson

A single time-step projection of a historical matrix projection model (hMPM), for a 7 life stage life history model of *Cypripedium parviflorum*, the small yellow lady’s slipper. In this case, the vector of biologically plausible stage pairs in time 2 is equal to the full projection matrix multiplied by the vector of biologically plausible stage pairs in time 1.

Matrix projection modeling is a mainstay of population ecology. Ecologists working in natural area management and conservation, as well as in theoretical and academic realms such as the study of life history evolution, develop and use these models routinely. Matrix projection models (MPMs) have advanced dramatically in complexity over the years, originating from age-based and stage-based matrix models parameterized directly from the data, to complex matrices developed from statistical models of vital rates such as integral projection models (IPMs) and age-by-stage models. We consider IPMs to be a class of function-based MPM, while age-by-stage MPMs may be raw or function-based, but are typically the latter due to a better ability to handle smaller dataset. The rapid development of these methods can leave many feeling bewildered if they need to use these methods but lack sufficient understanding of scientific programming and of the background theory to analyze them properly.

streamdnaDecember 4, 2020December 3, 2020Leave a comment

Journal Issues, Methods papers

December Issue Out Now!

The latest issue of Methods in Ecology and Evolution is now online!

Senior Editor Bob O’Hara has selected five Featured Articles this month, including methods for predicting pollinator abundance, evaluating species distribution modelling applications and accelerating image‐based ecological surveys using interactive machine learning – find out about all of them below.

We also have 12 articles that are free to read, including five Applications and two Practical Tools articles – no subscription required!

India StephensonDecember 3, 2020December 3, 2020Leave a comment

Code and Applications, Evolution, Methods 10th, Methods 10th Anniversary, Phylogenetic analysis

10th Anniversary Volume 8: Phylogenetics Editor’s Choice

To celebrate our 10th Anniversary, we are highlighting a key article from each of our volumes. For Volume 8, we selected ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data by Yu et al. (2016).

In this post, our Associate Editors Samantha Price and Francisco Balao share their favourite MEE papers in the field of phylogenetics.

India StephensonNovember 24, 2020November 24, 2020Leave a comment

Field Methods, Methods papers

DNA from Bite Marks: An Amplicon Sequencing Protocol for Attacker Identification

Post provided by Daniela C. Rößler

Understanding interactions between predators and prey is of interest to a variety of research fields. These interactions not only hold valuable information about ecological dynamics and food webs but are also crucial in understanding the evolution of predatory and anti-predator traits such as vision, visual signals and behavior. Thus, the “who attacks what and why” is key to approach broad evolutionary and ecological questions.

streamdnaNovember 23, 2020November 20, 2020Leave a comment

International Days

World Fisheries Day 2020: Cleaning up the Act of Salmon Fisheries?

Post provided by Ben Whittaker and Hannah L. Harrison

Juvenile lumpfish in hatchery facility. Credit: Emily Costello (UK).

World Fisheries Day is celebrated annually on 21^st November, to reflect on the ever-increasing knowledge about fishing, fishers, coastal communities, and the status of the oceans and fish stocks. This year, the Canadian Wildlife Federation are highlighting their work towards ending the current practice of salmon aquaculture, via the gradual phasing out of open-pen finfish aquaculture (OPFA) to prevent further negative impacts of the practice on wildlife and marine habitats. One of the major impacts of salmon aquaculture on wildlife, is the transmission of sea lice to wild salmonid populations, which has resulted in mass mortalities of wild fish. The most efficient control method to reduce sea-lice in farms is arguably the deployment of cleaner fish, however, there is little information on how this widely used method impacts individual welfare and worldwide sustainability of cleaner fish stocks. In this blog post, Dr Ben Whittaker and Dr Hannah L. Harrison, discuss the current status of cleaner fish fisheries.

streamdnaNovember 20, 2020November 20, 2020Leave a comment

Code and Applications, Evolution, Methods 10th, Methods 10th Anniversary, Phylogenetic analysis

10th Anniversary Volume 8: Phylogenetic tree visualization with multivariate data

Post provided by Guangchuang Yu and Tommy Tsan-Yuk Lam

To celebrate the 10th Anniversary of the launch of Methods in Ecology and Evolution, we are highlighting an article from each volume to feature in the Methods.blog. For Volume 8, we have selected ‘ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data‘ by Yu et al. (2016).

In this post, the authors share their inspiration behind the ggtree package for R and present new resources of ggtree and a series of other related packages.

The team publishing the ggtree paper is working in the field of emerging infectious diseases. Particularly the corresponding author Tommy Lam (TL) has been advocating the integration of different biological and epidemiological information in the studies of fast-evolving viral pathogens. The lead author Guangchuang Yu (GY) joined The University of Hong Kong to pursue his doctorate degree under the supervision of TL and Yi Guan (co-author in the paper), as he was very curious about the application of genomics and phylogenetics in the study of emerging infectious diseases.

Daniel CaetanoNovember 19, 2020November 17, 20202 Comments