Throughout March and April, we are featuring articles shortlisted for the 2024 Robert May Prize. The Robert May Prize is awarded by the British Ecological Society each year for the best paper in Methods in Ecology and Evolution written by an early career author. Nicolas Mongiardino Koch’s article ‘Chronospaces: An R package for the statistical exploration of divergence times promotes the assessment of methodological sensitivity‘ is one of those shortlisted for the award.

The paper

What is your shortlisted paper about, and what are you seeking to answer with your research?  

The paper describes new methods of exploring and visualizing the sensitivity associated with time calibrating phylogenies to the choice of modelling parameters, presents an R package that implements these approaches, and explores their use with three genome-scale datasets. Our main objective was to develop better tools to understand how divergence time estimation is impacted by methodological assumptions that are often chosen semi-arbitrarily by researchers. By developing novel ways of quantifying and visualizing the consequences of those choices, we hope we can assist researchers in disentangling results that are truly data-driven from those that are mostly consequence of human choices.

Were you surprised by anything when working on it?  Did you have any challenges to overcome? 

We had two major surprises while working on this. First, we soon realized that the different choices that researchers are confronted with have widely differing magnitudes of impact, with some decisions imparting effects hundreds to thousands of times larger than others. This heterogeneity had been so far overlooked. The second surprise was the realization that, no matter the age of the clade one is working with, whether one is timing a recent radiation or the deep structure of the tree of life, it is the same set of choices that one needs to be especially cautious with.  

What is the next step in this field going to be?  

As novel sequencing technologies emerged and costs came down, the field of molecular phylogenetics became quite suddenly free of data limitations. However, the efficiency of our analytical toolkit has not improved as dramatically, on the contrary, phylogenetic models have become increasingly more realistic, something that often means longer run times. As the pace of data acquisition keeps increasing, the gap between sequencing and publishing is likely going to keep widening. Decreasing the computational burden of phylogenetic tasks, especially complex ones such as time calibration, would be transformative in the era of phylogenomics.  

What are the broader impacts or implications of your research for policy or practice?   

Linked to my previous answer, the computation burden of phylogenetic analyses is not only challenging but also very expensive and environmentally damaging. A better understanding of the determinants of our results can be used to prioritize computational resources, as well as minimize the number of runs necessary to conclude that a given result is robust. In terms of common practices in the field, I think that highlighting the extent to which results can easily change based on decisions we make will help us recognize how uncertain we often are about reconstructing biological history. 

The author

How did you get involved in ecology?  

I have always thought of myself as a scientist, even from a very young age, and I remember becoming obsessed with understanding how the natural world operates when I was in elementary school. I think that everything I have done since has just been following that drive. As an undergrad, I joined a lab at the Department of Ecology, Genetics & Evolution of my local university as soon as I could, and had the luck of finding wonderful mentors and colleagues along the way that have made my professional journey everything I could have hoped for.

What is your current position? 

I am a Research Specialist at Princeton University, working remotely from my home country of Argentina for the Simões lab. When this manuscript was published, I was a postdoc at UC San Diego, a position I had to terminate early to fulfill with immigration regulations imposed by the Fulbright Program (which had awarded me a PhD scholarship). Research funding in Argentina has been stalled by the government, with no research positions open nationwide, a policy now sadly echoed in other countries. After fulfilling two years of residence here, I will begin a position as Assistant Professor at Colorado State University.  

Have you continued the research your paper is about? 

Yes! I have recently extended these results to other types of phylogenetic analyses, which further consolidates the extent to which our conclusions regarding the affinities and evolutionary history of lineages can be determined by aspects of the analytical pipeline. This research is currently accessible as a preprint here. I am also in the process of developing new software to improve the ways we visualize and manipulate phylogenetic data and results, as I believe that the field needs to be more accessible to non-specialists.  

What one piece of advice would you give to someone in your field?  

I once read that pretending that we know something that remains uncertain, robs us of the future joy of discovering the true answer. I think that in a world of scarce academic jobs, highly competitive funding opportunities, shifting political climates, impact factors, and other pressures that drive the publish-or-perish culture, we should all take an extra minute to ponder whether our results are truly definitive. Acknowledging uncertainty might seem less impactful, but reconstructing events that happened millions of years ago is not easy, and is best approached as an exercise in slowly and carefully weeding out less likely scenarios.