Explanipedia

Exome Sequencing and Allele Dosage Analysis of Coast Redwood, a Hexaploid Conifer, Reveals a Major Population Break South of San Francisco Bay Open

Alexandra Sasha Nikolaeva, Richard S. Dodd, Rasmus Nielsen · 2025

The coast redwood ( Sequoia sempervirens ) is a long-lived, hexaploid conifer of high ecological, cultural, and economic value whose range has been greatly reduced by historical logging [1]. Effective restoration and conservation depend on…

Author Correction: Robust and accurate Bayesian inference of genome-wide genealogies for hundreds of genomes Open

Yun Deng, Rasmus Nielsen, Yun S. Song · 2025

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

Yun Deng, Rasmus Nielsen, Yun S. Song · 2025

The Ancestral Recombination Graph (ARG), which describes the genealogical history of a sample of genomes, is a vital tool in population genomics and biomedical research. Recent advancements have substantially increased ARG reconstruction s…

ASTER: A Package for Large-Scale Phylogenomic Reconstructions Open

Chao Zhang, Rasmus Nielsen, Siavash Mirarab · 2025

Many algorithms are available for inferring species trees from various input types while accounting for gene tree discordance. Several quartet-based species tree inference methods, collectively known as the ASTRAL family, are based on simi…

Genome sequencing reveals the Adgrl3 ( ADGRL3 ) gene as a possible cause of cephalic hypersensitivity in the STA rat and migraine in humans Open

Brian Skriver Nielsen, Hongru Wang, Tanya Ramdal Techlo, Lisette J. A. Kogelman, Sarah Louise Christensen , et al. · 2025

Background Migraine is a common primary headache disorder with a significant genetic component influencing its pathophysiology, in which the trigeminal system plays a central role. The spontaneous trigeminal allodynia (STA) inbred rat stra…

ngsAMOVA: A Probabilistic Framework for Analysis of Molecular Variance, dXY and Neighbor-Joining Trees with Low Depth Sequencing Data Open

Isin Altinkaya, Lei Zhao, Rasmus Nielsen, Thorfinn Sand Korneliussen · 2025

Motivation Next-generation sequencing (NGS) has transformed population genetics and evolutionary biology, but the data produced in studies of non-model organisms, ancient DNA, and environmental DNA often consist of low- or medium-depth seq…

Stochastic Phylogenetic Models of Shape Open

Sofia Stroustrup, Morten Akhoej Pedersen, Frank van der Meulen, Stefan Sommer, Rasmus Nielsen · 2025

Phylogenetic modeling of morphological shape in two or three dimensions is one of the most challenging statistical problems in evolutionary biology. As shape data are inherently correlated and non-linear, most naïve methods for phylogeneti…

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

Alexandra Sasha Nikolaeva, James S. Santangelo, Lydia L. Smith, Richard S. Dodd, Rasmus Nielsen · 2025

Aneuploidy, a condition characterized by an abnormal number of chromosomes, can have significant consequences for fitness of an organism, often manifesting in reduced fertility and other developmental challenges. In plants, aneuploidy is p…

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

Isin Altinkaya, Rasmus Nielsen, Thorfinn Sand Korneliussen · 2025

Motivation Accurate quantification of genotype uncertainty is pivotal in ensuring the reliability of genetic inferences drawn from NGS data. Genotype uncertainty is typically modeled using Genotype Likelihoods (GLs), which can help propaga…

Challenges in Detecting Ecological Interactions Using Sedimentary Ancient DNA Data Open

Fiona Margaret Callahan, Jacky Kaiyuan Li, Rasmus Nielsen · 2025

With increasing availability of ancient and modern environmental DNA technology, whole‐community species occurrence and abundance data over time and space is becoming more available. Sedimentary ancient DNA data can be used to infer associ…

A General Framework for Branch Length Estimation in Ancestral Recombination Graphs Open

Yun Deng, Yun S. Song, Rasmus Nielsen · 2025

Inference of Ancestral Recombination Graphs (ARGs) is of central interest in the analysis of genomic variation. ARGs can be specified in terms of topologies and coalescence times. The coalescence times are usually estimated using an inform…

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

Frederik Filip Stæger, Mette K. Andersen, Zilong Li, Jasmin Pernille Hjerresen, Shixu He , et al. · 2025

Greenlandic Inuit and other indigenous populations are underrepresented in genetic research^1,2, leading to inequity in healthcare opportunities. To address this, we performed analyses of sequenced or imputed genomes of 5,996 Gre…

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

Débora Y. C. Brandt, Óscar H. Del Brutto, Rasmus Nielsen · 2025

Atahualpa is a rural village located in coastal Ecuador, a region that has been inhabited by people as early as 10,000 years ago. The traditional diet of their indigenous inhabitants is rich in oily fish and they have, therefore, served as…

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

Rasmus Nielsen · 2025

WASTER: Practical de novo phylogenomics from low-coverage short reads Open

Chao Zhang, Rasmus Nielsen · 2025

The advent of affordable whole-genome sequencing has spurred numerous large-scale projects aimed at inferring the tree of life, yet achieving a complete species-level phylogeny remains a distant goal due to significant costs and computatio…

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

Marie Louise Stig Sørensen, Daniela Hofmann, Kristian Kristiansen, Fabrice Demeter, Rasmus Nielsen , et al. · 2025

A concern with ethics and commitments to ethical conduct and standards has increasingly been raised within archaeology, recently also concerning aDNA data. We suggest that codes, whether for working with ancient DNA or other archaeological…

Runners with a high body mass index and previous running‐related problems is a high‐risk population for sustaining a new running‐related injury: A 18‐month cohort study Open

Ida Lindman, Josefin Abrahamson, Rasmus Nielsen · 2024

High body mass index (BMI) and a previous running‐related injury (RRI) have been highlighted as two risk factors for sustaining an RRI. However, a critical gap exists in the knowledge of whether runners with both elevated BMI and a previou…

Ancient genomics support deep divergence between Eastern and Western Mediterranean Indo-European languages Open

Fulya Eylem Yediay, Guus Kroonen, Serena Sabatini, Karin Margarita Frei, Anja B. Frank , et al. · 2024

Summary The Indo-European languages are among the most widely spoken in the world, yet their early diversification remains contentious 1–5 . It is widely accepted that the spread of this language family across Europe from the 5th millenniu…

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

Siyang Liu, Yanhong Liu, Yuqin Gu, Xingchen Lin, Huanhuan Zhu , et al. · 2024

Non-invasive prenatal testing (NIPT) employs ultra-low-pass sequencing of maternal plasma cell-free DNA to detect fetal trisomy. Its global adoption has established NIPT as a large human genetic resource for exploring genetic variations an…

Challenges in detecting ecological interactions using sedimentary ancient DNA data Open

Fiona Margaret Callahan, Jacky Kaiyuan Li, Rasmus Nielsen · 2024

With increasing availability of ancient and modern environmental DNA technology, whole-community species occurrence and abundance data over time and space is becoming more available. Sedimentary ancient DNA data can be used to infer associ…

Author response: A rapid phylogeny-based method for accurate community profiling of large-scale metabarcoding datasets Open

Lenore Pipes, Rasmus Nielsen · 2024

Evolution and Diversification of the Aposematic Poison Frog,Oophaga pumilio,in Bocas del Toro Open

Diana Aguilar‐Gómez, Layla Freeborn, Lin Yuan, Lydia L. Smith, Alex Guzmán , et al. · 2024

The aposematic strawberry poison frog, Oophaga pumilio , is an iconic model system for studying the evolution and maintenance of color variation. Through most of its range, this frog is red with blue limbs. However, frogs from the Bocas de…

Fast and Accurate Estimation of Selection Coefficients and Allele Histories from Ancient and Modern DNA Open

Andrew H. Vaughn, Rasmus Nielsen · 2024

We here present CLUES2, a full-likelihood method to infer natural selection from sequence data that is an extension of the method CLUES. We make several substantial improvements to the CLUES method that greatly increases both its applicabi…

Evolutionary new centromeres in the snowy owl genome putatively seeded from a transposable element Open

Helle Tessand Baalsrud, Benedicte Garmann-Aarhus, Emily Louise Gilbert Enevoldsen, Anders K. Krabberød, Dominik Fischer , et al. · 2024

Comparative genomic studies in birds have revealed that bird genomes are relatively repeat-poor and stable in terms of karyotype, size, and gene synteny/collinearity compared to other vertebrates. One notable exception is the owls, with cy…

Selfing Promotes Spread and Introgression of Segregation Distorters in Hermaphroditic Plants Open

Hongru Wang, Léo Planche, Vladimir Shchur, Rasmus Nielsen · 2024

Segregation distorters (SDs) are genetic elements that distort the Mendelian segregation ratio to favor their own transmission and are able to spread even when they incur fitness costs on organisms carrying them. Depending on the biology o…

Robust and Accurate Bayesian Inference of Genome-Wide Genealogies for Large Samples Open

Yun Deng, Rasmus Nielsen, Yun S. Song · 2024

The Ancestral Recombination Graph (ARG), which describes the full genealogical history of a sample of genomes, is a vital tool in population genomics and biomedical research. Recent advancements have increased ARG reconstruction scalabilit…

Elevated genetic risk for multiple sclerosis emerged in steppe pastoralist populations Open

William Barrie, Yaoling Yang, Evan K. Irving-Pease, Kathrine E. Attfield, Gabriele Scorrano , et al. · 2024

The selection landscape and genetic legacy of ancient Eurasians Open

Evan K. Irving-Pease, Alba Refoyo-Martínez, William Barrie, Andrés Ingason, Alice Pearson , et al. · 2024

100 ancient genomes show repeated population turnovers in Neolithic Denmark Open

Morten E. Allentoft, Martin Sikora, Anders Fischer, Karl-Göran Sjögren, Andrés Ingason , et al. · 2024

Major migration events in Holocene Eurasia have been characterized genetically at broad regional scales 1–4 . However, insights into the population dynamics in the contact zones are hampered by a lack of ancient genomic data sampled at hig…

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

Andrew H. Vaughn, Rasmus Nielsen · 2023

We here present CLUES2, a full-likelihood method to infer natural selection from sequence data that is an extension of the method CLUES. We make several substantial improvements to the CLUES method that greatly increases both its applicabi…

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