Article
Genetics & Heredity
Brian C. Zhang, Arjun Biddanda, Arni Freyr Gunnarsson, Fergus Cooper, Pier Francesco Palamara
Summary: ARG-Needle is a method for inferring genome-wide genealogies from large-scale genotyping data and can be used in association analyses. When applied to UK Biobank data, genealogy-based testing shows more associations with traits compared to using imputed genotypes. Genome-wide genealogies provide a compact representation of the evolutionary history of genomes and inferring them from genetic data can facilitate various analyses. This study introduces the ARG-Needle method to accurately infer genealogies from sequencing or genotyping data in biobank-scale studies and explores the use of genealogies in complex trait analyses.
Article
Biochemistry & Molecular Biology
Zeqi Yao, Kehui Liu, Shanjun Deng, Xionglei He
Summary: The study introduces a new coalescent method, i-coalescent analysis, which computes the instantaneous coalescent rate by using a phylogenetic tree of sampled alleles. It accurately reconstructs population size dynamics of highly structured populations, although larger sample sizes are often required for structured populations.
JOURNAL OF GENETICS AND GENOMICS
(2021)
Article
Primary Health Care
Maria Yanes-Rodriguez, Maria Concepcion Cruz-Canovas, Enrique Jose Gamero-de-Luna
Summary: Agenogram and genealogical tree are graphic tools used to represent family structure and inheritance patterns. Although they have similarities, they serve different purposes. Family doctors need to have the necessary skills to effectively utilize these tools.
MEDICINA DE FAMILIA-SEMERGEN
(2022)
Article
Multidisciplinary Sciences
H. Christoph Liedtke, Karem Lopez-Hervas, Ismael Galvan, Nuria Polo-Cavia, Ivan Gomez-Mestre
Summary: Facultative colour change, primarily achieved through changes in eumelanin quantity in the skin, is rapid and reversible in western spadefoot toad larvae. This colour change allows them to track fine-grained differences in background brightness but not hue or saturation. Additionally, the increased eumelanin production and/or maintenance is correlated with changes in morphology and oxidative stress, leading to larger tail fins and improved redox status.
SCIENTIFIC REPORTS
(2023)
Article
Computer Science, Software Engineering
Youngmo Kim, Byeongchan Park, Seok-Yoon Kim
Summary: This article introduces an encryption/decryption method for protecting sensitive music usage history information, ensuring confidentiality and integrity in the theme, background, and signal music blockchain environment, and resolving potential disputes.
JOURNAL OF WEB ENGINEERING
(2022)
Article
Evolutionary Biology
Aki Jarl Laruson, Matthew C. Fitzpatrick, Stephen R. Keller, Benjamin C. Haller, Katie E. Lotterhos
Summary: This study explores the relationship between GF Offset and fitness in the Gradient Forest algorithm, and finds that GF Offset is correlated with fitness offsets under both single locus and polygenic architectures. However, neutral demography, genomic architecture, and the nature of the adaptive environment can confound this relationship.
EVOLUTIONARY APPLICATIONS
(2022)
Article
Biology
Manisha Munasinghe, Benjamin C. Haller, Andrew G. Clark
Summary: In this study, the consequences of sexually antagonistic mitochondrial-nuclear interactions in a subdivided population were investigated using computer simulations. Disrupting these interactions resulted in less-fit males, but the strength of these interactions was not enough to drive population isolation.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Multidisciplinary Sciences
Anthony Wilder Wohns, Yan Wong, Ben Jeffery, Ali Akbari, Swapan Mallick, Ron Pinhasi, Nick Patterson, David Reich, Jerome Kelleher, Gil McVean
Summary: The sequencing of modern and ancient genomes from around the world has revolutionized our understanding of human history and evolution. Although the problem of characterizing ancestral relationships from genomic variation remains unsolved, nonparametric methods have been used successfully to infer a unified genealogy of modern and ancient humans, identify descendants of ancient samples, and estimate geographical location of ancestors.
Article
Biochemical Research Methods
Ali Mahmoudi, Jere Koskela, Jerome Kelleher, Yao-ban Chan, David Balding
Summary: This article presents a novel algorithm, ARGinfer, for probabilistic inference of the Ancestral Recombination Graph under the Coalescent with Recombination. The algorithm uses the Succinct Tree Sequence data structure and accurately estimates evolutionary history properties of the sample, providing interpretable uncertainty assessments through posterior probability distributions.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Genetics & Heredity
Graham Gower, Aaron P. Ragsdale, Gertjan Bisschop, Ryan N. Gutenkunst, Matthew Hartfield, Ekaterina Noskova, Stephan Schiffels, Travis J. Struck, Jerome Kelleher, Kevin R. Thornton
Summary: Understanding the demographic history of populations is crucial in population genetics, but the lack of a standardized format to define population dynamic models hampers progress in the field. Therefore, we propose the Demes data model and file format to address these issues.
Article
Ecology
Benjamin C. Haller, Philipp W. Messer
Summary: The SLiM software framework, widely used in population genetics, has been restricted to modeling only a single species, limiting its broader application in evolutionary biology. The lack of a general-purpose, flexible modeling framework that supports simulating multiple species with explicit genetics and continuous space has hindered our ability to model higher biological levels, such as communities, ecosystems, coevolutionary and eco-evolutionary processes, and biodiversity. The release of SLiM 4 addresses this significant gap by adding support for multiple species and ecological interactions, and provides examples to showcase its new features.
AMERICAN NATURALIST
(2023)
Article
Evolutionary Biology
Mathieu Fourment, Christiaan J. Swanepoel, Jared G. Galloway, Xiang Ji, Karthik Gangavarapu, Marc A. Suchard, Frederick A. Matsen
Summary: Gradients of probabilistic model likelihoods are crucial for computational statistics and machine learning. General-purpose machine-learning libraries like TensorFlow and PyTorch offer automatic differentiation for arbitrary models. However, for phylogenetic cases, these libraries may be slower compared to specialized code. This paper compares six gradient implementations and finds that automatic differentiation is slower than carefully implemented methods. A mixed approach combining phylogenetic libraries and machine learning libraries is recommended for optimal speed and model flexibility.
GENOME BIOLOGY AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Bea Angelica Andersson, Wei Zhao, Benjamin C. Haller, Ake Braennstrom, Xiao-Ru Wang
Summary: The distribution of fitness effects (DFE) of new mutations has been a topic of interest for evolutionary biologists. However, little is known about how data processing, sample size, and population structure impact the accuracy of DFE inference. This study demonstrates that the choice of missing-data treatment, sample size, SNP quantity, and population structure can affect DFE estimation accuracy and variance. Downsampling proves to be the most effective method, while small samples and limited SNPs can lead to unreliable DFE estimates. Moreover, population structure may bias the inferred DFE towards more deleterious mutations.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Multidisciplinary Sciences
Luke Anderson-Trocme, Dominic Nelson, Shadi Zabad, Alex Diaz-Papkovich, Ivan Kryukov, Nikolas Baya, Mathilde Touvier, Ben Jeffery, Christian Dina, Helene Vezina, Jerome Kelleher, Simon Gravel
Summary: Population genetic models provide coarse representations of real-world ancestry, but this study used a large pedigree and genotype data to finely model and trace French Canadian ancestry. The loss of ancestral population structure and the emergence of spatial and regional structure highlights various population expansion models. Migration, genetic, and genealogical patterns were found within river networks in different regions of Quebec. The study also provides a simulated whole-genome sequence dataset for investigating population genetics at a high resolution.
Article
Biology
M. Elise Lauterbur, Maria Izabel A. Cavassim, Ariella L. Gladstein, Graham Gower, Nathaniel S. Pope, Georgia Tsambos, Jeffrey Adrion, Saurabh Belsare, Arjun Biddanda, Victoria Caudill, Jean Cury, Ignacio Echevarria, Benjamin C. Haller, Ahmed R. Hasan, Xin Huang, Leonardo Nicola Martin Iasi, Ekaterina Noskova, Jana Obsteter, Vitor Antonio Correa Pavinato, Alice Pearson, David Peede, Manolo F. Perez, Murillo F. Rodrigues, Chris C. R. Smith, Jeffrey P. Spence, Anastasia Teterina, Silas Tittes, Per Unneberg, Juan Manuel Vazquez, Ryan K. Waples, Anthony Wilder Wohns, Yan Wong, Franz Baumdicker, Reed A. Cartwright, Gregor Gorjanc, Ryan N. Gutenkunst, Jerome Kelleher, Andrew D. Kern, Aaron P. Ragsdale, Peter L. Ralph, Daniel R. Schrider, Ilan Gronau
Summary: Simulation is crucial for population genetics research, but it remains a challenge to produce simulations that accurately represent genomic datasets. The development of more realistic simulations has become possible with advances in genetic data and simulation software. However, it still requires significant time and specialized knowledge.
Article
Genetics & Heredity
Chris C. R. Smith, Silas Tittes, Peter L. Ralph, Andrew D. Kern
Summary: The geographic nature of biological dispersal shapes genetic variation patterns, allowing the estimation of dispersal properties from genetic data. This study presents a deep learning approach called disperseNN, which utilizes geographically distributed genotype data and convolutional neural network to estimate the mean per-generation dispersal distance. Through extensive simulations, disperseNN is shown to outperform or be competitive with existing methods, especially for small sample sizes. It also proves effective in estimating dispersal distance when other model parameters are unknown, without relying on local population density or accurate inference of identity-by-descent tracts.
Article
Ecology
Jaehee Kim, Keith D. Harris, Isabel K. Kim, Shahar Shemesh, Philipp W. Messer, Gili Greenbaum
Summary: Gene drive technology is a promising tool in fighting vector-borne diseases, agricultural pests, and invasive species. It is important to incorporate ecological features into gene drive models and evaluate its dynamics, potential outcomes, and risks realistically.
Article
Multidisciplinary Sciences
Caitlin I. Stoddard, Kevin Sung, Zak A. Yaffe, Haidyn Weight, Guillaume Beaudoin-Bussieres, Jared Galloway, Soren Gantt, Judith Adhiambo, Emily R. Begnel, Ednah Ojee, Jennifer Slyker, Dalton Wamalwa, John Kinuthia, Andres Finzi, Frederick A. Matsen IV, Dara A. Lehman, Julie Overbaugh
Summary: Limited data is available on the antibody response to SARS-CoV-2 in infants compared to their mothers. This study found that infants have distinct antibody profiles, including elevated levels of antibody binding to Spike and elevated ADCC, as well as convergent antibody binding escape profiles in the Spike fusion peptide. These findings suggest that infants develop different antibody responses to viral infection compared to adults.
NATURE COMMUNICATIONS
(2023)
Article
Biochemical Research Methods
Jared G. Galloway, Kevin Sung, Samuel S. Minot, Meghan E. Garrett, Caitlin Stoddard, Alexandra C. Willcox, Zak A. Yaffe, Ryan Yucha, Julie Overbaugh, Frederick A. Matsen
Summary: We present the phippery software suite, which consists of a Nextflow pipeline, a Python API, and a Streamlit application, for analyzing data from PhIP-Seq methods. It enables processing of raw sequencing data, calculation of enrichment, and visualization of data as a heatmap.