Rasmus Nielsen and Ziheng Yang

Through collaborative and complementary work, Rasmus Nielsen and Ziheng Yang have transformed molecular evolution by creating statistical methods and computational tools that reveal how genomes change over time. Their contributions have made it possible to distinguish the effects of natural selection from those of demography and genetic drift, and thereby to leverage the rapidly expanding volume of genomic data for inference of evolutionary adaptation. Together, they helped establish a rigorous quantitative framework for studying adaptation, demography, and speciation. Their methods are now used throughout evolutionary biology, human genetics, and comparative genomics, allowing researchers to test questions that were previously accessible only through qualitative interpretation, and to assess uncertainty explicitly.

Yang and Nielsen jointly developed likelihood-based codon models for detecting molecular adaptation. These models describe how changes occur between the three-letter codons that encode amino acids, while accounting for the structure of the genetic code and for differences in evolutionary rates among sites and lineages. They allow researchers to distinguish neutral or negative selection from positive selection at particular positions in a protein and along particular evolutionary branches. These methods have become standard tools for identifying adaptive molecular change across a wide range of organisms. Nielsen and Yang also contributed to statistical frameworks that separate the effects of population structure, migration, and shared ancestry from those of natural selection.

Ziheng Yang established key theoretical and computational foundations for modern phylogenetic analysis. He is the principal developer of PAML, one of the most widely used software packages for analysing molecular evolution by maximum likelihood. He pioneered models that account for variation in evolutionary rates across sequence sites, developed methods based on the multispecies coalescent to explain differences between gene trees and species trees, and devised algorithms for estimating phylogenies and divergence times when evolutionary rates vary among lineages. His work placed the statistical inference of molecular evolutionary processes on a firm and widely applicable basis and made advanced evolutionary analysis available to researchers across the life sciences.

Rasmus Nielsen extended statistical evolutionary methods to population genomics and applied them to major empirical questions. He developed powerful approaches for detecting selective sweeps, in which a beneficial mutation rises rapidly in frequency and alters patterns of genetic variation in the surrounding region. He used such methods to uncover important examples of human adaptation, including the role of a Denisovan-derived EPAS1 variant in high-altitude adaptation among Tibetans and genetic changes related to fatty-acid metabolism in Greenlandic Inuit.

Together, Yang and Nielsen have linked evolutionary theory, statistical inference, and genomic data in a uniquely productive way. Their work has provided both the conceptual foundations and the practical tools needed to identify the molecular basis of adaptation, reconstruct the evolutionary history of species and populations, and understand how selection has shaped biodiversity across the tree of life and in our own species.