- Open Access
Horizons in evolutionary genomics: an interview with David Ferrier
© The Author(s). 2018
- Received: 9 October 2018
- Accepted: 9 October 2018
- Published: 1 November 2018
David Ferrier is a Reader at the University of St Andrews and Deputy Director of the Scottish Oceans Institute, where his lab studies how the diversity of form in the animal kingdom evolved, with an emphasis on using comparative genomics. In this interview, David shares his thoughts on how to escape the ‘straitjacket’ of traditional model systems, transparency in peer review, and the past and future of genome sequencing.
- Genome organization
The technical developments in DNA sequencing are progressing at a staggering rate, and costs are tumbling. This is a very exciting time to be working in fields associated with genomics. I think some of the key areas of progress that are happening (but that we need more of) are things like improved taxon sampling, to provide denser coverage of clades as well as wider coverage of the animal kingdom (speaking as a zoologist!); improvements to assembly pipelines, which are also being aided by things like long-molecule sequencing technologies; and developments in annotation tools and pipelines, as plenty of manual annotation is still required for those of us interested in the precise details of gene family evolution and organization.
CRISPR and RNAi techniques have also been truly revolutionary, and this now opens up biology to make use of broader taxon sampling so that we can start to move away from the straitjacket of a small handful of model organisms. Instead we can find the organism that has the interesting biology and do the experiments in that species, rather than having to adapt our research so that we have to do experiments in one of the big traditional systems like Drosophila, Caenorhabditis, or one of the few vertebrates that are usually worked on for functional genetics. The research funding bodies have a major role to play in this new era of using a diversity of species in biology involving functional genetics, and it is to be hoped that they do respond by broadening their horizons.
It is an essential element of science, and so a duty of all scientists to contribute. There are also more selfish sides to agreeing to review manuscripts, such as seeing interesting work before the community at large as well as helping to shape this work, hopefully for the benefit of the field.
There are interesting developments in more open peer review, exploring different forms of this (e.g. review reports published either with or without the reviewers’ names). There are pros and cons  and having experienced various versions of open review I’m not sure if there is one best option, but on balance this extra transparency is likely to lead to overall improvements.
I am wary about making this second point, because as an English speaker I am very lucky that the international language of science is English. And I recognize that things are much harder for those who have English as a second language. So this comment is certainly not meant as a criticism of those who might struggle to write well in English and I certainly do not want to give the impression that I am criticizing the writing of non-English speakers. Nothing could be further from the truth. My point though is that there is often a scope for manuscripts to be improved for written English before going out to academic editors and referees.
The aim must be to enable academic editors and reviewers to focus solely on the science, making the process more efficient. Time is precious, and it can be frustrating within the peer review process when one feels the need to provide lots of comments on sentence construction and appropriate vocabulary. Also, part of the problem is that the professional editing services that authors have to pay large sums of money for are of highly variable quality. Whether the burden for this extra language editing should be picked up more by the journals is a moot point, but there is certainly scope for more to be done by the universities and research institutions around the world, to develop further their in-house editing services.
Research in the author’s laboratory is funded by the Leverhulme Trust, BBSRC, EU Horizon2020 CORBEL and ASSEMBLE+, and the University of St Andrews, School of Biology.
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