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David Winter

Evolution, computational biology and genomics

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After spending quite a long time with my head down working on various projects I am very happy to say that a number of them are coming to completion. At the moment I have three papers somewhere between submission and publication, so I thought I should briefly describe each one and provide links to the pre-print versions.

Population genomics of Plasmodium vivax from Córdoba Colombia

The first paper to come from my postdoc has just been accepted at PLOS Neglected Tropical Diseases. Briefly, we analysed whole genome sequencing data from 8 Colombian patients with P. vivax malaria. Our results show that there is considerable genetic diversity in this population, and that there has been strong selective pressure for drug-resistance alleles. We also use the whole-genome data to develop new microsatellite loci, which we hope will support epidemiological studies of this important disease.

The revised preprint for our manuscript is here, and I will be sure to write a more detailed post when the final article is published.

The nucleotide mutation rate in Tetrahymena thermophila is really low

The first of the papers from our Tetrahymena experiment is in review. In this experiment we accumulated mutations in Tetrahymena cell lines for 1 000 generations and identified mutations through a combination of traditional methods and our own probabilistic mutation caller. We didn’t find many mutations. In fact, we end up with mutation rate estimate of 7.61 x 10-12 mutations per site per generation. That’s among the lowest mutation rates known, and several orders of magnitude lower than the human mutation rate.

One of the few other species with a comparably low mutation is another ciliate, Paramecium tetraurelia. In the manuscript, we discuss why ciliates might have particularity low mutation rates, especially in view of theories about the evolution of mutation rate. The preprint it available from bioarxiv.

rotl connects the Open Tree of Life to your R session

Finally, I’m really pleased to say we have submitted a manuscript describing “rotl”, and R package for the Open Tree of Life project’s data. The Open Tree of Life aims to produce a phylogeny relating every species on earth, and our package let’s users make the most of that data in R.

This package is a result of a collaboration between Francois Michonneau, Joseph Brown and myself at the Open Tree’s hackathon in Ann Arbor last year. The package is here, the preprint describing it is here. We’d love to have comments about the paper, and especially feedback from anyone who uses the package in their research.