This page contains papers from the Nielsen Lab starting in 2020. For earlier papers, please see Google Scholar.

2026

Selection-driven color variation in the aposematic strawberry poison frog, Oophaga pumilio

Aguilar-Gómez et al. 2026. Current Biology.

The genetics, evolution, and maintenance of a biological rock-paper-scissors game

Corl et al. 2026. Science.

2025

A general framework for branch length estimation in ancestral recombination graphs

Deng et al. 2025. PNAS.

Robust and accurate Bayesian inference of genome-wide genealogies for hundreds of genomes

Deng, Nielsen, and Song. 2025. Nature Genetics.

ASTER: a package for large-scale phylogenomic reconstructions

Zhang, Nielsen, and Mirarab. 2025. Molecular Biology and Evolution.

Genetic rescue of Florida panthers reduced homozygosity but did not swamp ancestral genotypes

Aguilar-Gómez et al. 2025. PNAS.

Genome sequencing reveals the Adgrl3 gene as a possible cause of cephalic hypersensitivity in the STA rat and migraine in humans

Nielsen et al. 2025. Cephalalgia.

A Framework for Archaeological Involvement with Human Genetic Data for European Prehistory

Sørensen et al. 2025. Open Archaeology.

Genetic and training adaptations in the Haenyeo divers of Jeju, Korea

Aguilar-Gómez et al. 2025. Cell Reports.

Occurrence of aneuploidy across the range of coast redwood (Sequoia sempervirens)

Nikolaeva et al. 2025. G3.

Challenges in Detecting Ecological Interactions Using Sedimentary Ancient DNA Data

Callahan et al. 2025. Environmental DNA.

vcfgl: a flexible genotype likelihood simulator for VCF/BCF files

Altinkaya et al. 2025. Bioinformatics.

A tale of two species: the origin of the Cantonese cancer in southern China

Nielsen. 2025. National Science Review.

Signatures of natural selection may indicate a genetic basis for the beneficial effects of oily fish intake in indigenous people from coastal Ecuador

Brandt et al. 2025. G3.

Genetic architecture in Greenland is shaped by demography, structure and selection

Staeger et al. 2025. Nature.

Revisiting the Briggs Ancient DNA Damage Model: A Fast Maximum Likelihood Method to Estimate Post-Mortem Damage

Zhao et al. 2025. Molecular Ecology Resources.

A previously reported bottleneck in human ancestry 900 kya is likely a statistical artifact

Deng, Nielsen, and Song. 2025. Genetics.

CASTER: Direct species tree inference from whole-genome alignments

Zhang, Nielsen, and Mirarab. 2025. Science.

Inference and applications of ancestral recombination graphs

Nielsen, Vaughn, and Deng. 2025. Nature Reviews Genetics.

2024

Elevated genetic risk for multiple sclerosis emerged in steppe pastoralist populations

Barrie et al. 2024. Nature.

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

Vaughn and Nielsen 2024. Molecular Biology and Evolution.

The selection landscape and genetic legacy of ancient Eurasians

Irving-Pease, Refoyo-Martínez, Barrie, Ingason, Pearson, and Fischer et al. 2024. Nature.

100 ancient genomes show repeated population turnovers in Neolithic Denmark

Allentoft, Sikora, and Fischer et al. 2024. Nature.

Deep ancestral introgressions between ovine species shape sheep genomes via argali-mediated gene flow

Lv et al. 2024. Molecular Biology and Evolution.

Population genomics of post-glacial western Eurasia

Allentoft, Sikora, Refoyo-Martínez, Irving-Pease, Fischer, Barrie, and Ingason et al. 2024. Nature.

Utilizing non-invasive prenatal test sequencing data for human genetic investigation

Liu et al. 2024. Cell Genomics.

A rapid phylogeny-based method for accurate community profiling of large-scale metabarcoding datasets

Pipes and Nielsen. 2024. eLife.

What Makes a Mimic? Orange, Red, and Black Color Production in the Mimic Poison Frog (Ranitomeya imitator)

Rubio et al. 2024. Genome Biology and Evolution.

Selfing promotes spread and introgression of segregation distorters in hermaphroditic plants

Wang et al. 2024. Molecular Biology and Evolution.

Plastic and genomic change of a newly established lizard population following a founder event

Sabolić et al. 2024. Molecular Ecology.

High-resolution African HLA resource uncovers HLA-DRB1 expression effects underlying vaccine response

Mentzer et al. 2024. Nature Medicine.

Transcriptomic analyses during development reveal mechanisms of integument structuring and color production

Stuckert et al. 2024. Evolutionary Ecology.

The evolutionary dynamics of local adaptations under genetic rescue is determined by mutational load and polygenicity

Zhang et al. 2024. Journal of Heredity.

Functional annotation of variants of the BRCA2 gene via locally haploid human pluripotent stem cells

Li et al. 2024. Nature Biomedical Engineering.

2023

North African fox genomes show signatures of repeated introgression and adaptation to life in deserts

Rocha et al. 2023. Nature Ecology and Evolution.

Bayesian inference of admixture graphs on Native American and Arctic populations

Nielsen and Vaughn et al. 2023. PLOS Genetics.

2022

The population genomic legacy of the second plague pandemic

Gopalakrishnan et al. 2022. Current Biology.

Estimating the relative proportions of SARS-CoV-2 haplotypes from wastewater samples

Pipes et al. 2022. Cell Reports Methods.

The genetic architecture of phenotypic diversity in the Betta fish (Betta splendens)

Zhang et al. 2022. Science Advances.

Predicting egg passage adaptations to design better vaccines for the H3N2 influenza virus

Liu et al. 2022. Viruses.

SCONCE2: jointly inferring single cell copy number profles and tumor evolutionary distances

Hui and Nielsen 2022. BMC Bioinformatics.

Overcoming Language Barriers in Academia: Machine Translation Tools and a Vision for a Multilingual Future

Steigerwald et al. 2022. BioScience.

Estimating the timing of multiple admixture events using 3-locus linkage disequilibrium

Liang et al. 2022. PLoS Genetics.

Population Genomics of Variegated Toad-Headed Lizard Phrynocephalus versicolor and Its Adaptation to the Colorful Sand of the Gobi Desert

Jin and Aguilar-Gómez et al. 2022. Genome Biology and Evolution.

Covariance of pairwise differences on a multi-species coalescent tree and implications for FST

Guerra and Nielsen. 2022. Philosophical Transactions of the Royal Society B.

distAngsd: Fast and accurate inference of genetic distances for next-generation sequencing data

Zhao et al. 2022. Molecular Biology and Evolution.

Evaluation of methods for estimating coalescence times using ancestral recombination graphs

Brandt et al. 2022. Genetics.

The Tibetan-Yi region is both a corridor and a barrier for human gene flow

Zhang et al. 2022. Cell Reports.

Inferring person-to-person networks of Plasmodium falciparum transmission: are analyses of routine surveillance data up to the task?

Huber et al. 2022. Malaria Journal.

SCONCE: a method for profiling copy number alterations in cancer evolution using single-cell whole genome sequencing

Hui and Nielsen 2022. Bioinformatics.

2021

AncestralClust: clustering of divergent nucleotide sequences by ancestral sequence reconstruction using phylogenetic trees

Pipes and Nielsen 2021. Bioinformatics.

Detecting selection in multiple populations by modelling ancestral admixture components

Cheng et al. 2021. Molecular Biology and Evolution.

Human-Mediated Admixture and Selection Shape the Diversity on the Modern Swine (Sus scrofa) Y Chromosomes

Ai et al. 2021. GigaScience.

The distribution of waiting distances in ancestral recombination graphs

Deng, Song, and Nielsen. 2021. Theoretical Population Biology.

Convergent evolution of increased urine-concentrating ability in desert mammals

Rocha et al. 2021. Mammal Review.

Whole-genome sequence analysis unveils different origins of European and Asiatic mouflon and domestication-related genes in sheep

Chen et al. 2021. Communications Biology.

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

Zhang et al. 2021. PNAS.

Investigate the origins of COVID-19

Bloom et al. 2021. Science.

Inferring adaptive introgression using hidden Markov models

Svedberg et al. 2021. Molecular Biology and Evolution.

Life in Deserts: The Genetic Basis of Mammalian Desert Adaptation

Rocha et al. 2021. Trends in Ecology and Evolution.

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

Pipes et al. 2021. Molecular Biology and Evolution.

The CALeDNA program: Citizen scientists and researchers inventory California's biodiversity

Meyer et al. 2021. California Agriculture.

Disentangling selection on genetically correlated polygenic traits via whole-genome genealogies

Stern et al. 2021. AJHG.

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

Wang, Pipes, and Nielsen. 2021. Virus Evolution.

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

Stuckert et al. 2021. Molecular Ecology.

2020

The genetic architecture of sporadic and multiple consecutive miscarriage

Laisk et al. 2020. Nature Communications.

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

Márquez et al. 2020. Molecular Ecology.

On the distribution of tract lengths during adaptive introgression

Shchur et al. 2020. G3: Genes, Genomes, Genetics.

Population genomics of the Viking world

Margaryan et al. 2020. Nature.

Inferring the ancestry of parents and grandparents from genetic data

Pei et al. 2020. PLoS Computational Biology.

Massive haplotypes underlie ecotypic differentiation in sunflowers

Todesco et al. 2020. Nature.

VolcanoFinder: genomic scans for adaptive introgression

Setter et al. 2020. PLoS Genetics.

Phenotypic convergence is not mirrored at the protein level in a lizard adaptive radiation

Corbett-Detig et al. 2020. Molecular Biology and Evolution.

Ancient hybridization with an unknown population facilitated high-altitude adaptation of canids

Wang et al. 2020. Molecular Biology and Evolution.

A Bayesian framework for inferring the influence of sequence context on point mutations

Ling et al. 2020. Molecular Biology and Evolution.

No statistical evidence for an effect of CCR5-Δ 32 on lifespan in the UK Biobank cohort

Maier et al. 2020. Nature Medicine.

A likelihood method for estimating present-day human contamination in ancient male samples using low-depth X-chromosome data

Moreno-Mayar et al. 2020. Bioinformatics.

Pronounced somatic bottleneck in mitochondrial DNA of human hair

Barrett et al. 2020. Philosophical Transactions of the Royal Society B.

A draft genome sequence of the elusive giant squid, Architeuthis dux

Da Fonseca et al. 2020. GigaScience.