R. Nielsen

Recent effective population size of the snowy owl (Bubo scandiacus) tracks historical climate variation

This study uses whole-genome resequencing to show that the snowy owl's effective population size has declined over the past 1,600 years, linked to historical climate changes.

Acyl-CoA Binding Protein in White and Brown Adipose Tissue is Dispensable for Systemic Energy Metabolism

This study shows that ACBP is not essential for adipose tissue function or systemic energy metabolism in mice, as knockout mice show no significant metabolic changes.

Transcriptomic responses of sponge holobionts to in situ, seasonal anoxia and hypoxia

This study examines the transcriptomic responses of two sponge species and their microbial symbionts to seasonal anoxia and hypoxia, revealing species-specific adaptations and limited metabolic changes under low oxygen conditions.

Fast and accurate estimation of selection coefficients and allele histories from ancient and modern DNA

CLUES2 estimates selection coefficients and allele histories from ancient and modern DNA, showing changing selective pressures in genes related to agriculture and diet in ancient Europe.

CASTER: Direct species tree inference from whole-genome alignments

CASTER infers species trees directly from whole-genome alignments by addressing discordance without predefining recombination-free loci, showing scalability and accuracy in simulations and real data.

Genetic basis of aposematic coloration in a mimetic radiation of poison frogs

This study identifies genes underlying Mullerian mimicry in poison frogs and shows that mimicry evolved through independent selective sweeps on color and pattern loci.

Symbiotic acacia ants drive nesting behavior by birds in an African savanna

The paper investigates whether acacia ants influence tree-nesting birds' nest site selection in an African savanna by assessing ant defense behavior against browsing mammals.

Elevated genetic risk for multiple sclerosis originated in Steppe Pastoralist populations

This study identifies the origin of genetic risk variants for multiple sclerosis in Steppe pastoralist populations and traces their spread into Europe through migration.

The Selection Landscape and Genetic Legacy of Ancient Eurasians

This study models ancient Eurasian selection landscapes and shows ancestry-specific genetic risk associations with modern phenotypes.

Estimating population split times and migration rates from historical effective population sizes

The paper estimates population split times and migration rates by adjusting for changes in effective population sizes, showing divergence between San and Dinka populations occurred around 108 kya instead of 255 kya.

Convergent evolution of increased urine concentrating ability in desert mammals

This study tests whether desert mammals have evolved increased urine concentrating ability compared to non-desert species, finding that aridity index better predicts this ability than body mass or metabolic rate.

The distribution of waiting distances in ancestral recombination graphs and its applications

The paper derives an analytic expression for waiting distances in ancestral recombination graphs and identifies biases in existing tree inference methods.

Assessing uncertainty in the rooting of the SARS-CoV-2 phylogeny

This study evaluates different methods for rooting the SARS-CoV-2 phylogeny and finds they produce statistically incompatible results, suggesting caution in interpreting the origin and early spread of the virus.

COAL_PHYRE: A Composite Likelihood Method for Estimating Species Tree Parameters from Genomic Data Using Coalescent Theory

COAL_PHYRE estimates species tree parameters using a composite likelihood method, offering faster and more accurate results than existing methods for large genomic datasets.

The genomics of mimicry: gene expression throughout development provides insights into convergent and divergent phenotypes in a Mullerian mimicry system

The paper investigates the genetic mechanisms of color and pattern variation in poison frogs using genome and gene expression analyses across developmental stages.

The history and evolution of the Denisovan-EPAS1 haplotype in Tibetans

The paper investigates the origin and timing of Denisovan introgression into Tibetans at the EPAS1 locus, finding an East Asian-specific introgression event around 43,000 years ago followed by selection 12,000 years ago.

Inferring Adaptive Introgression Using Hidden Markov Models

This paper introduces Ancestry_HMM-S, a Hidden Markov Model method for detecting adaptive introgression, and applies it to a Drosophila population to identify 17 loci with adaptive introgression signatures.

Non-additive polygenic models improve predictions of fitness traits in three eukaryote model species

The paper develops a non-additive polygenic model to predict fitness traits in three eukaryote species and finds non-additive models better explain fitness in some cases.

VolcanoFinder: genomic scans for adaptive introgression

VolcanoFinder detects adaptive introgression using polymorphism data from a single population, identifying volcano-shaped patterns of increased variability around beneficial alleles.

Synonymous mutations and the molecular evolution of SARS-Cov-2 origins

The paper analyzes synonymous divergence in SARS-CoV-2 to assess recombination and selection, finding evidence supporting recombination into RaTG13 and a fitness cost of non-synonymous mutations.

Divergence, gene flow and the origin of leapfrog geographic distributions: The history of color pattern variation in Phyllobates poison-dart frogs

This study examines the role of divergence and gene flow in shaping leapfrog geographic distributions of color patterns in Phyllobates poison frogs, finding evidence for gene flow between neighboring populations but not over long distances.

Massive haplotypes underlie ecotypic differentiation in sunflowers

The paper identifies large haplotype blocks associated with ecotypic differentiation in sunflowers, showing how structural variation maintains adaptive alleles despite hybridization.

Deviations from Hardy Weinberg Equilibrium at CCR5-Δ32 in Large Sequencing Data Sets?

The paper examines deviations from Hardy-Weinberg Equilibrium at CCR5-Δ32 in UKB WES and gnomAD data, finding a deficiency of homozygotes and supporting a deleterious effect of the deletion mutation.

A map of climate change-driven natural selection in Arabidopsis thaliana

The paper assesses climate change-driven natural selection in Arabidopsis thaliana by analyzing fitness impacts of rainfall manipulation across different geographic regions.

The California Environmental DNA \"CALeDNA\" Program

The paper describes the CALeDNA program, a community science initiative that uses environmental DNA to monitor biodiversity in California, providing public access to biodiversity data and analysis tools.

Estimating the timing of multiple admixture pulses during local ancestry inference.

This paper introduces a method to estimate multiple admixture events using coalescent theory and applies it to Drosophila melanogaster data, finding evidence for both recent and ancient admixture pulses.

On The Number Of Siblings And p-th Cousins In A Large Population Sample

The paper derives expressions for the distribution and expectation of p-th cousins in a population sample, showing that relatedness is common in large cohorts.

A hidden Markov model approach for simultaneously estimating local ancestry and admixture time using next generation sequence data in samples of arbitrary ploidy

This paper introduces a hidden Markov model for estimating local ancestry and admixture time using next-generation sequence data in samples of arbitrary ploidy, demonstrating its accuracy on high-ploidy samples and applying it to Drosophila melanogaster populations.

Archaic adaptive introgression in TBX15/WARS2

The paper identifies an archaic adaptive introgression in the TBX15/WARS2 region in Greenlandic Inuit, showing its association with gene expression and DNA methylation changes.