Algorithms for Phylogenetic Network Inference from DNA Sequence Data
Lead Research Organisation:
Earlham Institute
Department Name: Research Faculty
Abstract
United States
People |
ORCID iD |
| Richard Leggett (Principal Investigator) |
Publications
Gross E
(2023)
Dimensions of Level-1 Group-Based Phylogenetic Networks
in arXiv
Gross E
(2024)
Dimensions of Level-1 Group-Based Phylogenetic Networks.
in Bulletin of mathematical biology
| Description | A core goal of phylogenomics is to determine the evolutionary history of a set of species from biological sequence data. Phylogenetic networks are able to describe more complex evolutionary phenomena than phylogenetic trees but are more difficult to accurately reconstruct. Recently, there has been growing interest in developing methods to infer semi-directed phylogenetic networks. As computing such networks can be computationally intensive, one approach to building such networks is to puzzle together smaller networks. Thus, it is essential to have robust methods for inferring semi-directed phylogenetic networks on small numbers of taxa. Through this award, we developed an algebraic method for performing phylogenetic network inference from nucleotide sequence data on semi-directed phylogenetic networks by analysing the distribution of leaf-pattern probabilities. On simulated data, we found that we can correctly identify with high accuracy semi-directed networks and that we are able to use our approach to identify tree-like evolution and determine the underlying tree. |
| Exploitation Route | The results will be used by biologists and mathematicians researching evolutionary network theory or applying networks to understanding evolutionary biology. |
| Sectors | Agriculture Food and Drink Environment Healthcare Other |
| URL | https://www.biorxiv.org/content/10.1101/2023.09.11.557152v3.abstract |
| Description | Collaboration with Elizabeth Gross, University of Hawaii |
| Organisation | University of Hawaii |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | Research collaboration around phylogenetic network models. |
| Collaborator Contribution | Research collaboration around phylogenetic network models. |
| Impact | Sam Martin visited Elizabeth Gross in Hawaii and we are now working on two papers for publication. |
| Start Year | 2022 |
| Description | Talk at Algebraic Statistics 2022 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Talk at conference Algebraic Statistics 2022, held at the University of Hawai'i at Manoa, May 2022. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://sites.google.com/iit.edu/as2022 |
| Description | Talk at BAMC 2022 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | Contributed talk at conference "British Applied Mathematics Colloquium 2022". Audience consisted of academics working in various areas of applied mathematics. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://bamc2022.lboro.ac.uk/ |
| Description | Talk at Emerging Mathematical Frontiers in Molecular Evolution |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Contributed talk (online) at the conference Emerging Mathematical Frontiers in Molecular Evolution, held at the Institut Mittag-Leffler in Sweden, August 2022. |
| Year(s) Of Engagement Activity | 2022 |
| URL | http://www.mittag-leffler.se/konferens/emerging-mathematical-frontiers-molecular-evolution |