Issue 7.7 is now online!

The July issue of Methods is now online!

This month’s issue contains two Applications articles and two Open Access articles, all of which are freely available.

– MO-Phylogenetics: A software tool to infer phylogenetic trees optimising two reconstruction criteria simultaneously and integrating a framework for multi-objective optimisation with two phylogenetic software packages.

– PHYLOMETRICS: An efficient algorithm to construct the null distributions (by generating phylogenies under a trait state-dependent speciation and extinction model) and a pipeline for estimating the false-positive rate and the statistical power of tests on phylogenetic metrics..

This month’s Open Access article comes from Laura D. Williamson et al. In ‘Echolocation detections and digital video surveys provide reliable estimates of the relative density of harbour porpoises‘, the authors compare methods of obtaining robust estimates of the density or abundance of cetaceans. These results provide confidence in the emerging use of digital video and acoustic surveys for studying the density of small cetaceans and their responses to environmental and anthropogenic change.

Increasing the power of genome wide association studies in natural populations using repeated measures – evaluation and implementation‘ by Lars Rönnegård et al. is our second Open Access article in this issue. In this article, the authors present a new method that was successful in estimating permanent environmental effects from simulated repeated measures data. The method is available in the R package RepeatABEL. It increases the power in Genome wide association studies having repeated measures, especially for long-term studies of natural populations, and the R implementation is expected to facilitate modelling of longitudinal data for studies of both animal and human populations.

Our July issue also features articles on Community Ecology, Evolution, Monitoring, Conservation and more.

This month’s cover image shows a leaf of a grape vine (vitis vinifera) in the region of Las Alpujarras, Spain. The veins of the leaf form a complex tree which tapers out towards extremes. We can view this as an analogy with the process of inferring phylogenetic trees: the strong veins represent clear relationships, but as we approach the edges it is more difficult to make accurate connections.

The associated article, ‘MO-Phylogenetics: a phylogenetic inference software tool with multi-objective evolutionary metaheuristics‘ is about a software tool for phylogenetic inference. The tool searches for the best phylogenetic tree to explain the evolutionary relationships among different species. It is a NP-hard problem, so finding the optimal tree among all the possible solutions is computationally expensive. MO-Phylogenetics includes a number of non-exact multi-objective techniques known as metaheuristics, which produce satisfactory solutions in a reasonable amount of time.

Photo © Antonio J. Nebro

To keep up to date with Methods newest content, have a look at our Accepted Articles and Early View articles, which will be included in forthcoming issues.