Article
Biochemistry & Molecular Biology
Scott A. Martin, Gregory J. Lipps, H. Lisle Gibbs
Summary: Managing endangered species in fragmented landscapes requires estimating dispersal rates between populations. A new method using genetic pedigree data was developed to quantify recent dispersal, revealing limited contemporary connectivity among Eastern Massasauga rattlesnake populations but high rates within genetic clusters. This approach can provide insights into recent movement patterns and demographic isolation of conservation units.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Obstetrics & Gynecology
Tsegaselassie Workalemahu, Jessica M. Page, Huong Meeks, Zhe Yu, Emily Guinto, Alison Fraser, Michael W. Varner, Lauren H. Theilen, Aaron Quinlan, Hilary Coon, Daniel A. Enquobahrie, Cande V. Ananth, Fasil Tekola-Ayele, Lynn B. Jorde, Robert M. Silver
Summary: This study identifies familial aggregation of stillbirth and quantifies its familial risk. It also reveals gender-specific risks associated with affected parents. These findings suggest the need for research on genes related to stillbirth and large-scale studies to determine the genetic architecture of stillbirth.
BJOG-AN INTERNATIONAL JOURNAL OF OBSTETRICS AND GYNAECOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Lauren E. Petty, Kathrine Phillippi-Falkenstein, H. Michael Kubisch, Muthuswamy Raveendran, R. Alan Harris, Eric J. Vallender, Chad D. Huff, Rudolf P. Bohm, Jeffrey Rogers, Jennifer E. Below
Summary: The accurate estimation of relatedness among individuals is crucial in analyzing free-ranging animal populations. Methods developed for human genetic data have been applied and evaluated in the analysis of nonhuman primates, showing high concordance between expected and identified relationships for close relatives. These methods are valuable for determination of relatedness in various animal populations, with diverse applications to conservation biology, evolutionary and ecological research and biomedical studies.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Genetics & Heredity
Jennifer Irving McGrath, Wengang Zhang, Regina Hollar, Alison Collings, Roger Powell, Rob D. Foale, Nicola Thurley, Jeffrey A. Brockman, Richard J. Mellanby, Danielle A. Gunn-Moore, Jeffrey J. Schoenebeck
Summary: The study found that non-pedigree domestic cats in the UK, including DSH, DLH, and DSLH cats, are random-bred rather than crossbred or pedigree-admixed. While most of these cats have a lower proportion of HBD segments in their genome compared to pedigree cats, indicating older segments, there is also evidence of recent inbreeding events in a portion of the random-bred cat genomes, suggesting they are not completely immune to inbreeding and its associated health risks.
Review
Biodiversity Conservation
Teri B. Jones, Micheline Manseau
Summary: Network analysis is a flexible statistical framework widely used in ecology and other fields. This review article focuses on genetic-based networks and their applications in population structure, genetic connectivity, and individual genetic relatedness. The article categorizes the studies into population-level networks and individual-based genetic networks and discusses the similarities and differences between these approaches. The article also provides an overview of the current methods and software available for constructing and analyzing genetic networks. Additionally, the article highlights the importance of genetic networks in conservation biology, including defining population structure, understanding genetic connectivity, and studying individual or familial fitness.
BIOLOGICAL CONSERVATION
(2022)
Article
Biochemistry & Molecular Biology
Benedikt Kirsch-Gerweck, Leonard Bohnenkaemper, Michel T. Henrichs, Jarno N. Alanko, Hideo Bannai, Bastien Cazaux, Pierre Peterlongo, Joachim Burger, Jens Stoye, Yoan Diekmann
Summary: We developed an efficient haplotype-based approach to detect positive selection in large genomic datasets. By combining pattern matching and model-based inference, our method achieves high sensitivity and specificity with low computational resource requirements. Evaluation using UK Biobank data indicates scalability to population genomic datasets with millions of individuals. Our approach serves as an algorithmic blueprint for big data genomics, combining a combinatorial core with statistical inference in closed form.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Ecology
Shannon L. White, Nicholas M. Sard, Harold M. Brundage, Robin L. Johnson, Barbara A. Lubinski, Michael S. Eackles, Ian A. Park, Dewayne A. Fox, David C. Kazyak
Summary: This study evaluates the influence of bias in genetic pedigree reconstruction on the estimation of breeding population size using genetic-based approaches. The results indicate that pedigree errors can be minimized with adequate genetic data. Even with limited data, the simulation analysis can still provide informative estimates of population size, which can guide conservation decisions.
ECOLOGICAL APPLICATIONS
(2022)
Article
Computer Science, Interdisciplinary Applications
Pavan K. Inguva, Kaylee C. Schickel, Richard D. Braatz
Summary: This study introduces a finite difference scheme at the limit of numerical stability, which has very low computational cost and zero discretization error for certain classes of PBMs, showing good performance in various applications.
COMPUTERS & CHEMICAL ENGINEERING
(2022)
Article
Agriculture, Dairy & Animal Science
O. Jarnecka, E. A. Bauer, W. Jagusiak
Summary: This study described the population structure and inbreeding level of Polish Red Cattle (PRC), with an average inbreeding of 4% and 23.8% inbred animals. The results indicate the potential disruption of the balance in small populations like PRC, highlighting the need for continuous monitoring of endangered populations.
Article
Biochemistry & Molecular Biology
Remi Matthey-Doret
Summary: SimBit is a high-performance population genetics simulator that can simulate various selection, demographic and mating scenarios, track QTLs and model ecological relationships among multiple species. It comes with a convenient R wrapper for project management and outperforms other simulators in most benchmarks.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Agriculture, Dairy & Animal Science
Yutaka Masuda, Shogo Tsuruta, Matias Bermann, Heather L. Bradford, Ignacy Misztal
Summary: In this study, genetic trends were compared among models with UPG and MF H-inverses, showing that EUPG and MF H-inverses are preferred for their lack of genetic trend biases.
JOURNAL OF ANIMAL SCIENCE
(2021)
Article
Chemistry, Multidisciplinary
Alexander Kuprava, Michael Huth
Summary: Focused electron-beam-induced deposition (FEBID) is a versatile direct-write approach for 3D nanofabrication of functional materials. A new numerical simulation approach is described to study the influence of growth parameters on the shape of the 3D structures. The modular nature of the simulation method allows for future performance improvements using parallelization or graphics cards. Combining the simulation approach with beam-control pattern generation will optimize shape transfer for 3D FEBID.
Article
Computer Science, Interdisciplinary Applications
Pavan K. Inguva, Richard D. Braatz
Summary: Multidimensional population balance models (PBMs) are used to describe chemical and biological processes with distribution over multiple intrinsic properties. We propose a low-cost finite difference scheme based on operator splitting that achieves a discretization error of zero for certain classes of PBMs. The scheme exploits the commutative property of the differential operators and can be computationally efficient.
COMPUTERS & CHEMICAL ENGINEERING
(2023)
Article
Agronomy
Yongjun Li, Sukhjiwan Kaur, Luke W. Pembleton, Hossein Valipour-Kahrood, Garry M. Rosewarne, Hans D. Daetwyler
Summary: Genomic selection can increase genetic gain by shortening the breeding cycle, but it also leads to higher genetic diversity loss. Selecting segregating parents in the early stages of the breeding cycle can result in higher genetic gain. Increasing the number of F-1 intercross families increases genetic diversity, while increasing the number of progeny per family increases genetic gain but decreases genetic diversity. Adding F-2 family phenotypes to the training population improves the accuracy of genomic breeding values and genetic gain, while reducing the rate of genetic diversity loss.
THEORETICAL AND APPLIED GENETICS
(2022)
Article
Mechanics
Alessandro Monti, Vikram Rathee, Amy Q. Shen, Marco E. Rosti
Summary: The cutting-edge software presented in this study adopts an optimized searching algorithm to tackle the dynamics of dense suspensions in Newtonian fluids. The emphasis is on reducing computational cost and memory efficiency, while allowing efficient parallelization and handling of non-monodispersed particles with high size-ratio. Validations and verifications of the numerical procedure are also provided, along with new software capabilities.
Article
Genetics & Heredity
Peter Ralph, Kevin Thornton, Jerome Kelleher
Article
Ecology
Joshua S. Schiffman, Peter L. Ralph
Summary: Even if a species' phenotype remains unchanged, the underlying molecular mechanism may change. This study uses linear system theory to explore how the gene network supporting a conserved phenotype evolves, and how the exploration of distinct mechanisms can lead to reproductive incompatibility between independently evolving populations.
Article
Genetics & Heredity
Franz Baumdicker, Gertjan Bisschop, Daniel Goldstein, Graham Gower, Aaron P. Ragsdale, Georgia Tsambos, Sha Zhu, Bjarki Eldon, E. Castedo Ellerman, Jared G. Galloway, Ariella L. Gladstein, Gregor Gorjanc, Bing Guo, Ben Jeffery, Warren W. Kretzschumar, Konrad Lohse, Michael Matschiner, Dominic Nelson, Nathaniel S. Pope, Consuelo D. Quinto-Cortes, Murillo F. Rodrigues, Kumar Saunack, Thibaut Sellinger, Kevin Thornton, Hugo van Kemenade, Anthony W. Wohns, Yan Wong, Simon Gravel, Andrew D. Kern, Jere Koskela, Peter L. Ralph, Jerome Kelleher
Summary: This article introduces the release of msprime 1.0 and summarizes its numerous features and advantages through a collaborative open source development model. Compared to specialized alternatives, msprime demonstrates excellent performance with faster speed and higher memory efficiency, making it a commonly used simulation tool in population genetics.
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.
Review
Ecology
Maria R. Felipe-Lucia, Angela M. Guerrero, Steven M. Alexander, Jaime Ashander, Jacopo A. Baggio, Michele L. Barnes, Orjan Bodin, Aletta Bonn, Marie-Josee Fortin, Rachel S. Friedman, Jessica A. Gephart, Kate J. Helmstedt, Aislyn A. Keyes, Kailin Kroetz, Francois Massol, Michael J. O. Pocock, Jesse Sayles, Ross M. Thompson, Spencer A. Wood, Laura E. Dee
Summary: This article discusses the challenges and opportunities of using social-ecological networks (SENs) in ecosystem service research, and proposes a typology to represent ecosystem services in SENs. The typology provides guidance for improving research design and addressing a wider range of questions regarding human-nature interdependencies.
TRENDS IN ECOLOGY & EVOLUTION
(2022)
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
Ecology
Abigail S. L. Lewis, Christine R. Rollinson, Andrew J. Allyn, Jaime Ashander, Stephanie Brodie, Cole B. Brookson, Elyssa Collins, Michael C. Dietze, Amanda S. Gallinat, Noel Juvigny-Khenafou, Gerbrand Koren, Daniel J. McGlinn, Hassan Moustahfid, Jody A. Peters, Nicholas R. Record, Caleb J. Robbins, Jonathan Tonkin, Glenda M. Wardle
Summary: This article introduces a conceptual framework that describes how ecological forecasting can energize and advance ecological theory. The authors emphasize the potential for future progress through increased forecast development, comparison, and synthesis. They envision a future where forecasting is integrated as part of the toolset used in fundamental ecology, and aim to decrease barriers to entry and broaden the community of researchers using forecasting for fundamental ecological insight.
METHODS IN ECOLOGY AND EVOLUTION
(2023)
Article
Green & Sustainable Science & Technology
Jaime Ashander, Kailin Kroetzt, Rebecca Epanchin-Niell, Nicholas B. D. Phelps, Robert G. Haight, Laura E. Dee
Summary: Using network metrics to guide management can effectively address the challenges of biological invasions. The study evaluates the performance of network-guided invasive species management compared to optimal management and finds that the network-guided approach achieves high performance, even with incomplete information. This research highlights the potential of network approaches for sustainable resource management.
NATURE SUSTAINABILITY
(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
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
Biochemical Research Methods
Frederick A. Matsen, Peter L. Ralph
Summary: This article presents a method for computing the likelihoods of genome mutations using bounds on the propagation of dependency. It also discusses protocols for examining residuals and iterative model refinement. The method provides an R package for efficient analysis and can be used to examine the context dependence of mutations.
JOURNAL OF COMPUTATIONAL BIOLOGY
(2022)
Article
Genetics & Heredity
Katja R. Kasimatis, Abin Abraham, Peter L. Ralph, Andrew D. Kern, John A. Capra, Patrick C. Phillips
Summary: Sex and sexual differentiation are common in various species, leading to different selection pressures between sexes. However, studies on autosomal loci in humans did not find clear evidence of sexually antagonistic viability selection, possibly due to cross-hybridization with sex chromosome regions at these loci.
