Research Expertise and Interest
evolution, molecular evolution, population genetics, human variation, human genetics, phylogenetics, applied statistics, genetics, evolutionary processes, evolutionary biology
Research Description
Dr. Nielsen received his Ph.D. from UC-Berkeley in 1998, did postdoctoral research at Harvard University and worked as an assistant professor at Cornell University from 2000-2004. From 2004 he has been a Professor of Biology at the University of Copenhagen and he joined the faculty at the departments of Integrative Biology and Statistics at Berkeley in Jan. 2008.
His work is on statistical and population genetic analyses of genomic data, in particular methods for detecting natural selection, describing population genetic variation, inferring demography, and methods for association mapping. Much of his current research concerns statistical analysis of next-generation sequencing data, both in the context of medical genetics and population genetics. Many of the methods he has developed are heavily used by other researchers, including the phylogeny based methods for detecting positive selection implemented in PAML, the methods for inferring demographic histories implemented in the IM and IMa programs, the method for detecting selective sweeps implemented in SweepFinder, and the methods for analysing Next Generation Sequencing (NGS) data implemented in ANGSD.
One of the central problems he has been interested in is the molecular basis of evolutionary adaptation. What happens at the molecular levels as one species is transformed into another over evolutionary time? To address this question he has developed a number of computational methods and applied them to large scale genomic data, such as genomic comparisons of humans and chimpanzees.
He has also worked on understanding human genetic variation. He uses both classical statistical methods and evolutionary inferences to identify genetic variants that affect phenotypic variability in humans, including genetic adaptations to diet and local environmental factors. He has studied the genetic basis of human adaption to high altitude, changes in diet, and cold climates. He has also worked extensively on analyses of ancient DNA derived from fossils to understand human origins and diversification.
He teaches courses in human biological variation, population genetics, human genetics, and statistics.
Example publications:
- E Huerta-Sánchez, X Jin, Z Bianba, BM Peter, N Vinckenbosch, Y Liang, X Yi, M He, M Somel, P Ni, B Wang, X Ou, J Luosang, Z Xi Ping Cuo, K Li, G Gao, Y Yin, W Wang, X Zhang, X Xu, H Yang, Y Li, J Wang, J Wang, R Nielsen (2014). Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA. Nature 512: 194-197.
- I Moltke, N Grarup, ME Jørgensen, et al. (2014). A common Greenlandic TBC1D4 variant confers muscle insulin resistance and type 2 diabetes. Nature 512: 190-193
- R Nielsen, JS Paul, A Albrechtsen, YS Song (2011). Genotype and SNP calling from next-generation sequencing data. Nat. Rev. Genet. 12 (6): 443-451.
- Hey J. and R. Nielsen. 2007. Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics. Proc Natl Acad Sci U S A. 104: 2785–2790.
For more information see: https://nielsen-lab.github.io
In the News
Six Berkeley Faculty Members Elected to National Academy of Sciences
Tales from 141,430 and one genomes
Enlarged spleen key to diving endurance of ‘sea nomads’
What the Inuit can tell us about omega-3 fats and ‘paleo’ diets
The traditional diet of Greenland natives – the Inuit – is held up as an example of how high levels of omega-3 fatty acids can counterbalance the bad health effects of a high-fat diet, but a new study hints that what’s true for the Inuit may not be true for everyone else.
Genome Analysis Pinpoints Arrival and Spread of First Americans
The original Americans came from Siberia in a single wave no more than 23,000 years ago, at the height of the last Ice Age, and apparently hung out in the north – perhaps for thousands of years – before spreading in two distinct populations throughout North and South America, according to a new genomic analysis.
Extinct human cousin gave Tibetans advantage at high elevation
Tens of thousands of years ago, the common ancestors of Han Chinese and Tibetans interbred with a mysterious human-like group known as Denisovans and picked up a unique variant of a gene for hemoglobin regulation that later helped them adapt to a low-oxygen environment on the high Tibetan plateau, reports UC Berkeley professor of integrative biology Rasmus Nielsen
Polar bear genome gives new insight into adaptations to high-fat diet
A comparison of the genomes of polar bears and brown bears reveals that the polar bear is a much younger species than previously believed. Also uncovered were several genes that may be involved in the polar bears’ extreme adaptations to life in the high Arctic.
Study dispels theories of Y chromosome’s demise
A comparison of Y chromosomes in eight African and eight European men dispels the common notion that the Y‘s genes are mostly unimportant and that the chromosome is destined to dwindle and disappear.
Scientists look to Hawaii’s bugs for clues to origins of biodiversity
The Hawaiian Islands are a unique and ongoing series of evolutionary and ecological experiments. As each volcano rises above the waves, it is colonized by life from neighboring volcanoes and develops its own flora and fauna.
Tibetans adapted to high altitude in less than 3,000 years
UC Berkeley's Rasmus Nielsen teamed up with Chinese researchers to compare the genomes of Tibetans living above 14,000 feet to Han Chinese living at essentially sea level. They found that within the last 3,000 years, Tibetans evolved genetic mutations in a number of genes having to do with how the body deals with oxygen, making it possible for Tibetans to thrive at high altitudes while their Han relatives cannot.