When?

Friday, 1 April 2022

10.00 - 11.00 h

Where?

https://stockholmuniversity.zoom.us/j/62208705509

Which paper are we discussing?

I will summarize a recent review article on the estimation of Ne (effective population size) with different resolutions for different time spans (contemporary vs. long-term evolutionary Ne):

Nadachowska-Brzyska, K., Konczal, M., & Babik, W. (2022). Navigating the temporal continuum of effective population size. Methods in Ecology and Evolution, 13(1), 22–41. https://doi.org/10.1111/2041-210X.13740

Abstract

Effective population size, Ne, is a key evolutionary parameter that determines the levels of genetic variation and efficacy of selection. Estimation and interpretation of Ne are essential in diverse areas of evolutionary and conservation biology, ranging from assessing the evolutionary potential or extinction risk to empowering research on the genomic basis of adaptation.
The diverse applications of the Ne concept resulted in largely independent methodological developments using different Ne definitions and focusing on the estimation of either contemporary or long-term Ne. Recently, several novel approaches appeared that allow the estimation of temporal Ne trends at various parts of the temporal Ne continuum.
Here, we provide an overview of the temporal aspects of Ne, asking whether the existing methods and available data provide Ne estimates for the entire temporal continuum. We outline the apparent division into contemporary and long-term Ne existing in the literature, review Ne estimation methods across the temporal continuum and navigate the reader through it pointing to the important biological and methodological limitations inherent to the estimation procedures. Finally, we provide examples of recent research and future perspectives.
We conclude that the entire temporal Ne continuum can now be inferred using several complementary approaches, bringing together contemporary and long-term perspectives. Further rapid progress in the field is expected from the wide adoption of machine learning and transition to haplotype-resolved population genomic data. The expected progress notwithstanding, interpretational difficulties are likely to remain, emphasising the need for a thorough understanding of the Ne theory behind the methods, their assumptions and inherent limitations.

Who is presenting?

Verena

Notes

Here are my presentation slides:

And here is some additional literature on PSMC:

A paper on site filtering (e.g. missingness), depth of coverage, and other technical issues affecting PSMC: https://doi.org/10.1111/mec.13540
A paper showing (in the supplement) how mutation rate and generation time affect the PSMC curves: http://dx.doi.org/10.1016/j.cub.2015.03.047

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