Joëlle Barido-Sottani

Joëlle Barido-Sottani

Permanent researcher (CRCN) at the Institute of Biology of the ENS

I am a computational biologist, specialised in the development and implementation of mathematical models for evolutionary processes. My research focuses on Bayesian phylogenetic inference, which aims to co-estimate a phylogeny and evolutionary parameters from an alignment of molecular and/or morphological information while explicitly accounting for uncertainty. I contribute actively to the software frameworks BEAST2 and RevBayes.

My main area of research is birth-death processes, particularly models which integrate clade-specific variations in diversification processes, as well as models which include fossil information in the phylogeny such as the Fossilized Birth-Death (FBD) process. I have developed several new models for the inference of lineage-specific birth and death rates from a phylogeny, including the packages MSBD and ClaDS for BEAST2. I use extensive simulations to test and evaluate the behaviour of both new and existing models, especially when their assumptions are violated, and establish guidelines for their use. In particular, I have studied how fossil age uncertainty and fossil placement information should be handled in FBD inferences.

In addition, I care about improving the reliability and usability of scientific software. I explore ways to improve both the developer and the user experience, as well as import best practices from other areas of software development. I am also an active contributor to the Taming the BEAST workshops and website, which aims to make BEAST2 analyses accessible to a broad community of biologists, epidemiologists and palaeontologists.

Interests: Bayesian phylogenetic inference, birth-death processes, scientific software

Programming languages: Java, C++, R, Python (beginner)

Selected publications

J. Barido-Sottani, D. Żyła, T.A. Heath. “Estimating the age of fossil deposits using a total-evidence approach” Systematic Biology, 2022. DOI: 10.1093/sysbio/syac073

A.M. Wright, D.W. Bapst, J. Barido-Sottani, R.C.M. Warnock. “Integrating Fossil Observations Into Phylogenetics Using the Fossilized Birth-Death Model” Annual Review of Ecology, Evolution, and Systematics, 2022. DOI: 10.1146/annurev-ecolsys-102220-030855

J. Barido-Sottani, J.A. Justison, et al. “Lessons learned from organizing and teaching virtual phylogenetics workshops” Bulletin of the Society of Systematic Biologists, 2022. DOI:10.18061/bssb.v1i2.8425

J. Barido-Sottani, T. G. Vaughan, T. Stadler. “A multi-types birth-death model for Bayesian inference of lineage-specific birth and death rates” Systematic Biology, 2020. DOI: 10.1093/sysbio/syaa016

J. Barido-Sottani, G. Aguirre-Fernández, M. J. Hopkins, T. Stadler, R. C. M. Warnock. “Ignoring stratigraphic age uncertainty leads to erroneous estimates of species divergence times under the fossilized birth-death process” Proceedings of the Royal Society B, 2019. DOI: 10.1098/rspb.2019.0685

J. Barido-Sottani, W. Pett, J. E. O’Reilly, R. C. M. Warnock. “FossilSim: an R package for simulating fossil occurrence data under mechanistic models of preservation and sampling” Methods in Ecology and Evolution, 2019. DOI: 10.1111/2041-210X.13170

A complete list of my publications can be found in my CV.

Software

Other contributions

  • Organizing and teaching online workshops “Bayesian phylogenetic inference with BEAST2” with Transmitting Science, next one in November 2024 - register here
  • Phyloseminar (part of a 3-part series on the Fossilized Birth-Death process), Youtube video

Internships

I am happy to supervise master students interested in evolution, paleontology and/or computational biology. A wide range of projects are possible, from model and software development to simulation studies to application to empirical datasets. I also have some smaller projects available for shorter internships.

Please don’t hesitate to contact me directly to discuss what you would like to do !

CV

CV_Barido-Sottani.pdf