Details of Award
NERC Reference : NE/X003469/1
An introductory molecular phylogenetics course: integrating molecules with taxonomy and systematics
Training Grant Award
- Lead Supervisor:
- Dr S Williams, The Natural History Museum, Life Sciences
- Grant held at:
- The Natural History Museum, Life Sciences
- Science Area:
- Atmospheric
- Earth
- Freshwater
- Marine
- Terrestrial
- Overall Classification:
- Freshwater
- ENRIs:
- Biodiversity
- Environmental Risks and Hazards
- Global Change
- Natural Resource Management
- Pollution and Waste
- Science Topics:
- Animal ecology
- Applied ecology
- Aquatic ecology
- Bioclimatology
- Biodiversity
- Ecosystems
- Environmental genetics
- Marine studies
- Plant ecology
- Earth & environmental
- Evolution
- Species diversity
- Conservation Ecology
- Bioinform. for transcriptomics
- Bioinformatics for genomics
- Bioinformatics Taxonomy
- Bioinformatics
- Abstract:
- Lack of taxonomic skills is regularly highlighted as a "headline" concern by UK Research and Innovation (UKRI) and knowing how to produce a robust phylogeny is an indispensable tool for modern taxonomists, systematists and evolutionary and environmental biologists. A phylogeny is essential for defining species boundaries, species identifications, recognition of cryptic species, testing systematic hypotheses, identifying evolutionary and biogeographic patterns, and understanding the evolution of traits. They are foundational for studies on neglected tropical diseases, understanding community biodiversity, environmental monitoring, aquaculture and food security, origins and spread of disease, biodiversity inventories and evolution of drug resistance - all hot topics regularly funded by UKRI. There are a number of bioinformatic courses available at universities and offered by private companies, but courses that are designed for absolute beginners that establish firm foundations for a career as a molecularly confident taxonomist, environmental scientist or evolutionary biologist are rare. This one-week introductory-level course is designed to foster and develop strategically important and vulnerable research skills and capabilities by teaching participants the steps involved in the production of molecular phylogenies from traditional Sanger and next-generation sequence (NGS) data. By the time the participants have completed the course, they will have the necessary theoretical and practical knowledge to i) edit raw Sanger and NGS sequence data, ii) carry out multiple sequence alignments, iii) choose appropriate models of sequence evolution, iv) carry out phylogenetic analyses (including Bayesian inference, maximum likelihood), v) interpret tree topology and nodal support, vi) produce publication-ready trees, vii) work with public sequence repositories, vii) assemble and annotate next generation sequence data, viii) understand potential for phylogenomics, ix) understand methods used to assess community diversity with eDNA, x) recognise cryptic species and xi) have an awareness of complicating issues affecting lab work and analyses. This one-week course assumes no prior experience with DNA sequence data or any of the software. Lectures will be given to provide theoretical background prior to any practical applications. Each step, involving specific software, will be demonstrated, and practiced in hands-on computer lab sessions. During computer lab sessions, we aim to have three tutors present to ensure a high level of assistance for 12 in-person and 12 online participants (two courses to be run consecutively). On the last afternoon, participants will be able to analyse their own data or return to sections of the course of their own choice. In addition to the formal training, course participants also have the opportunity to meet and discuss their research with NHM scientists. Lectures will be pre-recorded for the online course and practicals can be worked on at an applicant's own pace. Tutors will be available for questions at set times on each day with the option for breakout groups for individual questions. We will provide datasets that will result in clean, quick analyses, but also discuss more challenging datasets to introduce participants to solutions to some of the most common problems encountered with molecular phylogenetics, such as sequence contamination, pseudogenes, and stochastic and systematic errors. We will also discuss the fallibility of public databases and online repositories (e.g. GenBank) due to sequence errors, contamination and incorrect species identification. The Natural History Museum is the perfect place to hold such a course. The lecturers and tutors are experienced in undertaking molecular systematic studies and work with a broad range of taxa and evolutionary questions. This course will leave the participants feeling empowered and capable of tackling independent analyses of their own data.
- NERC Reference:
- NE/X003469/1
- Grant Stage:
- Completed
- Scheme:
- Doctoral Training
- Grant Status:
- Closed
- Programme:
- Advanced Training
This training grant award has a total value of £50,769
FDAB - Financial Details (Award breakdown by headings)
| Total - Other Costs |
|---|
| £50,769 |
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