Not Just N e N e -More: New Applications for SMC from Ecology to Phylogenies
Year: 2025
Type: article
Abstract: Genomes contain the mutational footprint of an organism's evolutionary history, shaped by diverse forces including ecological factors, selective pressures, and life history traits. The sequentially Markovian coalescent (SMC) is a versatile and tractable model for the genetic genealogy of a sample of genomes, which captures this shared history. Methods that utilize the SMC, such as PSMC and MSMC, have been widely used in evolution and ecology to infer demographic histories. However, these methods ignore common biological features, such as gene flow events and structural variation. Recently, there have been several advancements that widen the applicability of SMC-based methods: inclusion of an isolation with migration model, integration with the multi-species coalescent, incorporation of ecological life history traits (such as selfing and dormancy), and many computational advances in applying these models to data. We give an overview of the SMC model and its various recent extensions, discuss examples of biological discoveries through SMC-based inference, and comment on the assumptions, benefits and drawbacks of various methods.
Source: Genome Biology and Evolution
DOI: 10.1093/gbe/evaf229
Institutions: Brown University, University of Cambridge, University of Southern California, University of Oxford, The University of Sydney, Centre National de la Recherche Scientifique, École Pratique des Hautes Études, Université Paris Sciences et Lettres, Sorbonne Université, Institut de Systématique, Évolution, Biodiversité, Muséum national d'Histoire naturelle, Institut de Recherche pour le Développement, Université des Antilles, University of Memphis
Language: English
Subfield: Genetics
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $2,850
OpenAlex ID: W4416808231