Making research accessible is core to Open Research Europe’s publishing model. Open access articles allow authors to reach the widest possible audience. Anyone can freely access articles on Open Research Europe without paywalls. This includes fellow researchers, students, policymakers and the public. Making research open is especially important for authors who have developed bespoke software tools for the scientific community to freely use and apply to their research.
Openness was the deciding factor for Joëlle Barido-Sottani, co-author of the Method Article “Practical guidelines for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC)”, published on Open Research Europe. Read on to learn more about their work and why they chose to publish with Open Research Europe.
How would you summarize your Method Article?
Phylogenies show how different organisms or species are related through the process of evolution. They can be used in a wide range of applications, from studying the links between extinctions and environmental changes, to following the progression of epidemics. Thus, the methods for reconstructing phylogenies are a major area of research in evolutionary biology. Several different software frameworks are available for biologists to infer phylogenies from genetic or morphological information, but their complexity and the number of models and options available can make it very confusing for users. In this Method Article, we aim to give detailed, concrete advice for users of phylogenetic inference tools, focusing on MCMC. We draw on our experience as developers, users and teachers of these methods to demonstrate issues commonly encountered by researchers and present guidelines for good practices.
What inspired you to investigate the topic of your recent publication?
As developers and teachers of phylogenetic inference tools, we’ve noticed that most of the available materials focus on the theoretical details of the models and methods, which are often introduced on toy datasets with little complexity. On the other hand, students and researchers who apply these methods to real datasets very often have much more practical concerns, such as how long the software will need to run or what to do when faced with errors or unexpected results. Obtaining practical advice on these questions often requires asking developers directly, which is very inefficient (for both researchers and developers) and means that useful information does not spread easily or widely through the phylogenetic community. These observations directly led us to writing this article to collect and summarize our combined knowledge and advice, to make it more openly accessible.
What key findings came from your article and what are their impacts?
The primary goal of our Method Article is to share good practices and troubleshooting advice with users of phylogenetic inference tools, which will lead directly to more efficient and more accurate phylogenies being built. We also hope that the publication of this article will increase the community awareness around practical obstacles to phylogenetic inference and inspire other developers to contribute their own knowledge and experience on these matters.
Why is open science important to you?
As developers of open software, the entire principle of our work is to build tools which are freely accessible to the scientific community and can be easily reused. Open science is therefore a natural extension of this. In addition, since this research was funded primarily by public funding sources, we believe that the public in general should be able to access and benefit from the results of their investment.
This Method Article in particular presents guidelines and advice to build efficient and accurate phylogenies, and thus it is in the interest of the global phylogenetic community that this information is spread as widely as possible. Making this article open access also helps bridge the knowledge gap between students and researchers from Western institutions, who have easier access to training workshops or even direct contact with developers, and students and users who lack these opportunities.
What motivated you to publish with Open Research Europe & how did you find the submission process?
The open access and the rapid publication motivated us to publish through Open Research Europe, since our aim was to make this information as accessible as possible to a wide audience. We also liked that reviews are public, as our reviewers brought substantial expertise to their commentary. The submission process for both the initial submission and the revision was straightforward, and similar to other journals in our field.
What are your next steps?
Our article demonstrates that some common issues currently lack robust, widely applicable solutions, and that troubleshooting frequently relies on trial and error to find an analysis setup which performs adequately. Our next step will thus be to encourage a community effort to discuss and hopefully find better solutions for these issues. Further studies should also be launched to systematically evaluate the performance and applicability of the different techniques presented in the article and elsewhere, to provide more accurate advice in the future.
Read the full Method Article on Open Research Europe to learn more about the method and findings.
