Skills

R

90%

python

10%

git

linux

Science

Data analysis

Phylogenetics

Technical writing

Presenting

Affliations

Towards open, modular, phylogenetic pipelines in R

As part of my post-doc I’m devising and developing an automated pipeline for generating phylogenetic trees, supersmartR. This new program acts as an update to SUPERSMART and is comprised of a series of independent R packages.

All R packages developed as part of this project are aimed to be of the highest quality, and as a result they are all submitted to ROpenSci for thorough scrutiny, review and testing.

For the latest updates on supersmartR progress, check out the website.









Background photo credit: Asadalikhan1993

What, if anything, are “living fossils”?

“Living fossil” is a term coined by Darwin often used to describe organisms that appear to be ancient and have changed little. The term, however, is hugely controversial: it has multiple definitions and interpretations; it seems to recall the debunked Victorian science of “evolutionary progress”; and many, wrongly, use the term to argue that evolution can be halted.

In my PhD I attempted to take a new look at the term. I wanted to understand whether the term could be a real label: does it denote a unique category of biodiversity? I also attempted to clarify the concept by proposing a quantifiable definition. Additionally, I explored what the label means for conservation biologists (Are living fossils worth conserving?) and what potential factors may explain the “living fossil”-condition.

My entire PhD thesis is available here and the slides and recording of a Royal Society presentation I gave – that gives a brief overview of much of my thesis – can be downloaded here.


Which taxa are “living fossils”?

Below are the top “living fossil” birds and mammals according to their proximate “Evolutionary Performance Index” (pEPI) – the lower the less performant and the more likely the taxon is a living fossil. The table also holds key stats on over 20,000 other plants and animals. For more information see the paper, “Quantifying the Living Fossil Concept”

N.spp = Number of species, Age = Time since clade split, Success = number of species relative to sister, Change = observed morpholoical and ecological change relative to sister, pEPI = proximate evolutionary performance (excludes change) [plus % quartile], EPI = evolutionary performance (includes change), ED = Evolutionary distinctness Open table in a new window









Background photo credit: Patrick K59

Software

*

Divide and conquer phylogenetic supermatrices and supertrees in R.

Install and Run Programs, Outside of R, Inside of R.

Create and Query a Local Copy of GenBank in R.

Automated Retrieval of Orthologous DNA Sequences from GenBank.

An R package for manipulating phylogentic trees.

phyloGenerator-lite: generate phylogenies, lightly, in python (2013)

TaxonNamesResolver: Automatically search taxon names against the Global Names Resolver (2013)

Tools for manipulating ecological data – first ever R package! (2013).