Populations and Evolution

Authors and titles for q-bio.PE in Feb 2023

[1]  arXiv:2302.00582 [pdf, ps, other]

Title: Habitat transition in the evolution of bacteria and archaea

Authors: Alexander L. Jaffe, Cindy J. Castelle, Jillian F. Banfield

Comments: Accepted for publication in the Annual Review of Microbiology, Volume 77

Subjects: Populations and Evolution (q-bio.PE); Genomics (q-bio.GN)

[2]  arXiv:2302.00767 [pdf, other]

Title: ImageNomer: description of a functional connectivity and omics analysis tool and case study identifying a race confound

Authors: Anton Orlichenko, Grant Daly, Ziyu Zhou, Anqi Liu, Hui Shen, Hong-Wen Deng, Yu-Ping Wang

Comments: 11 pages

Subjects: Populations and Evolution (q-bio.PE); Machine Learning (cs.LG); Neurons and Cognition (q-bio.NC)

[3]  arXiv:2302.00826 [pdf, ps, other]

Title: Existence of exact solution of the Susceptible-Exposed-Infectious-Recovered (SEIR) epidemic model

Authors: Norio Yoshida

Comments: 40 pages, 9 figures

Journal-ref: J. Differential Equations 355(2023), 103-143

Subjects: Populations and Evolution (q-bio.PE)

[4]  arXiv:2302.00960 [pdf, other]

Title: Quantifying optimal resource allocation strategies for controlling epidemics

Authors: Biplab Maity, Swarnendu Banerjee, Abhishek Senapati, Joydev Chattopadhyay

Comments: 44 Pages, 10 Figures

Subjects: Populations and Evolution (q-bio.PE)

[5]  arXiv:2302.01076 [pdf, other]

Title: Convergence to the Equilibrium State in an Outbreak: When Can Growth Rates Accurately be Measured?

Authors: Adam Mielke, Lasse Engbo Christiansen

Comments: 4 pages, 1 figure

Subjects: Populations and Evolution (q-bio.PE)

[6]  arXiv:2302.02018 [pdf, other]

Title: Hierarchical Model with Allee Effect, Immigration, and Holling Type II Functional Response

Authors: Eddy Kwessi

Subjects: Populations and Evolution (q-bio.PE); Dynamical Systems (math.DS)

[7]  arXiv:2302.02263 [pdf, other]

Title: Vaccination in a two-strain model with cross-immunity and antibody-dependent enhancement

Authors: Lorena C. Bulhosa, Juliane F. Oliveira

Comments: Corrected typos. Revised figures, results unchanged

Subjects: Populations and Evolution (q-bio.PE)

[8]  arXiv:2302.02522 [pdf, other]

Title: Prior Density Learning in Variational Bayesian Phylogenetic Parameters Inference

Authors: Amine M. Remita, Golrokh Vitae, Abdoulaye Baniré Diallo

Comments: Accepted as a full paper for publication at RECOMB-CG 2023 (LNBI proof version). 15 pages (excluding references), 6 tables and 1 figure

Journal-ref: In Jahn, K., Vina\v{r}, T. (eds) Comparative Genomics. RECOMB-CG 2023. Lecture Notes in Computer Science, vol 13883. Springer, Cham

Subjects: Populations and Evolution (q-bio.PE); Machine Learning (cs.LG)

[9]  arXiv:2302.02812 [pdf, other]

Title: Simulation algorithms for Markovian and non-Markovian epidemics

Authors: Guohao Dou

Subjects: Populations and Evolution (q-bio.PE); Multiagent Systems (cs.MA); Biological Physics (physics.bio-ph)

[10]  arXiv:2302.03210 [pdf, other]

Title: Temporal and probabilistic comparisons of epidemic interventions

Authors: Mariah C. Boudreau, Andrea J. Allen, Nicholas J. Roberts, Antoine Allard, Laurent Hébert-Dufresne

Comments: 20 pages, 5 figures

Journal-ref: Bull. of Math. Biol. 85(2023)118

Subjects: Populations and Evolution (q-bio.PE)

[11]  arXiv:2302.03449 [pdf, other]

Title: Turing patterns in a Leslie-Gower predator prey model

Authors: Florinda Capone, Roberta De Luca, Isabella Torcicollo

Subjects: Populations and Evolution (q-bio.PE); Mathematical Physics (math-ph)

[12]  arXiv:2302.03471 [pdf, ps, other]

Title: How a simple chloroplast psbA gene mutation changed world agriculture

Authors: Jack Dekker

Subjects: Populations and Evolution (q-bio.PE)

[13]  arXiv:2302.04223 [pdf, other]

Title: On the redundancy of birth and death rates in homogenous epidemic SIR models

Authors: Florian Nill

Comments: 9 pages, 3 figures, 2 tables. arXiv admin note: text overlap with arXiv:2301.00159

Journal-ref: Fractal Fract. 2023, 7, 313

Subjects: Populations and Evolution (q-bio.PE); Dynamical Systems (math.DS)

[14]  arXiv:2302.04594 [pdf, ps, other]

Title: Ecological system with fear induced group defence and prey refuge

Authors: Shivam Yadav, Jai Prakash Tripathi, Shrichand Bhuria, Satish Kumar Tiwari, Deepak Tripathi, Vandana Tiwari, Ranjit Kumar Upadhyay, Yun Kang

Subjects: Populations and Evolution (q-bio.PE)

[15]  arXiv:2302.06261 [pdf, other]

Title: An Algebraic Discussion of Bisexual Populations with Wolbachia Infection I: Discrete Dynamical System Approach

Authors: Barış Özdinç, Songül Esin, Müge Kanuni

Comments: 17 pages, 11 figures

Subjects: Populations and Evolution (q-bio.PE)

[16]  arXiv:2302.06573 [pdf, ps, other]

Title: Propagation of weakly advantageous mutations in cancer cell population

Authors: Andrzej Polanski, Mateusz Kania, Jarosław Gil, Wojciech Łabaj, Ewa Lach, Agnieszka Szczęsna

Comments: Removed Figure 6, corrections

Subjects: Populations and Evolution (q-bio.PE); Numerical Analysis (math.NA)

[17]  arXiv:2302.07820 [pdf, other]

Title: Equilibria of large random Lotka-Volterra systems with vanishing species: a mathematical approach

Authors: Imane Akjouj, Walid Hachem, Mylène Maïda, Jamal Najim

Subjects: Populations and Evolution (q-bio.PE); Probability (math.PR)

[18]  arXiv:2302.07955 [src]

Title: Mathematical models for order of mutation problem in myeloproliferative neoplasm: non-additivity and non-commutativity

Authors: Yue Wang

Comments: Highly incomplete work that needs extensive revision

Subjects: Populations and Evolution (q-bio.PE); Molecular Networks (q-bio.MN)

[19]  arXiv:2302.08071 [pdf, other]

Title: Statistical Theory of Asymmetric Damage Segregation in Clonal Cell Populations

Authors: Arkady Pikovsky, Lev S. Tsimring

Comments: Mathematical Biosciences, 2023 (in press)

Subjects: Populations and Evolution (q-bio.PE); Adaptation and Self-Organizing Systems (nlin.AO); Biological Physics (physics.bio-ph)

[20]  arXiv:2302.08695 [pdf, other]

Title: A Countable-Type Branching Process Model for the Tug-of-War Cancer Cell Dynamics

Authors: Ren-Yi Wang, Marek Kimmel

Subjects: Populations and Evolution (q-bio.PE); Probability (math.PR)

[21]  arXiv:2302.09076 [pdf, ps, other]

Title: Nowcasting the 2022 mpox outbreak in England

Authors: Christopher E. Overton, Sam Abbott, Rachel Christie, Fergus Cumming, Julie Day, Owen Jones, Rob Paton, Charlie Turner, Thomas Ward

Subjects: Populations and Evolution (q-bio.PE)

[22]  arXiv:2302.09402 [pdf, other]

Title: CRP-Tree: A phylogenetic association test for binary traits

Authors: Julie Zhang, Gabriel A. Preising, Molly Schumer, Julia A. Palacios

Comments: 40 pages, 23 figures

Subjects: Populations and Evolution (q-bio.PE); Applications (stat.AP)

[23]  arXiv:2302.10015 [pdf, ps, other]

Title: Comparison of orchard networks using their extended $μ$-representation

Authors: Gabriel Cardona, Joan Carles Pons, Gerard Ribas, Tomás Martínez Coronado

Subjects: Populations and Evolution (q-bio.PE); Discrete Mathematics (cs.DM)

[24]  arXiv:2302.11438 [pdf, ps, other]

Title: On the scope of applicability of the models of Darwinian dynamics

Authors: Georgiy Karev

Comments: 39 pages, 11 figures

Subjects: Populations and Evolution (q-bio.PE)

[25]  arXiv:2302.12381 [pdf, other]

Title: Optimal interruption of P. vivax malaria transmission using mass drug administration

Authors: Md Nurul Anwar, Roslyn I. Hickson, Somya Mehra, David J. Price, James M. McCaw, Mark B. Flegg, Jennifer A. Flegg

Comments: 39 pages, 14 figures

Subjects: Populations and Evolution (q-bio.PE)

[26]  arXiv:2302.13384 [pdf, other]

Title: Trade-off between reproduction and mobility prolongs organisms' survival in rock-paper-scissors models

Authors: J. Menezes, E. Rangel

Comments: 7 pages, 5 figures

Journal-ref: Europhysics Letters 142, 47002 (2023)

Subjects: Populations and Evolution (q-bio.PE); Statistical Mechanics (cond-mat.stat-mech); Adaptation and Self-Organizing Systems (nlin.AO); Pattern Formation and Solitons (nlin.PS); Biological Physics (physics.bio-ph)

[27]  arXiv:2302.13897 [pdf, ps, other]

Title: Resistance Maintained in Digital Organisms despite Guanine/Cytosine-Based Fitness Cost and Extended De-Selection: Implications to Microbial Antibiotics Resistance

Authors: Clarence FG Castillo, Zhu En Chay, Maurice HT Ling

Journal-ref: MOJ Proteomics & Bioinformatics 2(2): 00039 (2015)

Subjects: Populations and Evolution (q-bio.PE); Neural and Evolutionary Computing (cs.NE)

[28]  arXiv:2302.14573 [pdf, ps, other]

Title: On a kinetic description of Lotka-Volterra dynamics

Authors: Giuseppe Toscani, Mattia Zanella

Subjects: Populations and Evolution (q-bio.PE); Adaptation and Self-Organizing Systems (nlin.AO); Physics and Society (physics.soc-ph)

[29]  arXiv:2302.14700 [pdf, other]

Title: Natural selection for collective action

Authors: Benjamin Allen, Abdur-Rahman Khwaja, James L. Donahue, Cassidy Lattanzio, Yulia A. Dementieva, Christine Sample

Comments: 86 pages, 9 figures

Subjects: Populations and Evolution (q-bio.PE)

[30]  arXiv:2302.14778 [pdf, other]

Title: The self-organization of selfishness: Reinforcement Learning shows how selfish behavior can emerge from agent-environment interaction dynamics

Authors: Aamir Sahil Chandroth, Nithya Ramakrishnan, Sanjay Chandrasekharan

Comments: 9 pages, 16 figs, 1 table. Reinforcement Learning - Parametric Analysis, Social Behavior

Subjects: Populations and Evolution (q-bio.PE); Quantitative Methods (q-bio.QM)

[31]  arXiv:2302.02470 (cross-list from q-bio.QM) [pdf, other]

Title: Towards inferring network properties from epidemic data

Authors: István Z. Kiss, Luc Berthouze, Wasiur R. KhudaBukhsh

Comments: 23 pages, 15 figures

Subjects: Quantitative Methods (q-bio.QM); Populations and Evolution (q-bio.PE)

[32]  arXiv:2302.05338 (cross-list from q-bio.MN) [pdf, ps, other]

Title: Algebraic structure of hierarchic first-order reaction networks applicable to models of clone size distribution and stochastic gene expression

Authors: Ximo Pechuan-Jorge, Raymond S. Puzio, Cameron Smith

Comments: 9 pages

Subjects: Molecular Networks (q-bio.MN); Mathematical Physics (math-ph); Probability (math.PR); Populations and Evolution (q-bio.PE); Quantitative Methods (q-bio.QM)

[33]  arXiv:2302.08796 (cross-list from q-bio.QM) [pdf, other]

Title: Approaching epidemiological dynamics of COVID-19 with physics-informed neural networks

Authors: Shuai Han, Lukas Stelz, Horst Stoecker, Lingxiao Wang, Kai Zhou

Comments: 23 pages, 14 figures

Subjects: Quantitative Methods (q-bio.QM); Machine Learning (cs.LG); Dynamical Systems (math.DS); Physics and Society (physics.soc-ph); Populations and Evolution (q-bio.PE)

[34]  arXiv:2302.11345 (cross-list from q-bio.CB) [pdf, other]

Title: Travelling waves in a coarse-grained model of volume-filling cell invasion: Simulations and comparisons

Authors: Rebecca M. Crossley, Philip K. Maini, Tommaso Lorenzi, Ruth E. Baker

Comments: 28 pages, 12 figures

Subjects: Cell Behavior (q-bio.CB); Analysis of PDEs (math.AP); Populations and Evolution (q-bio.PE); Tissues and Organs (q-bio.TO)

[35]  arXiv:2302.01528 (cross-list from stat.ME) [pdf, ps, other]

Title: Four principles for improved statistical ecology

Authors: Gordana Popovic, Tanya J. Mason, Tiago A. Marques, Joanne Potts, Szymon M. Drobniak, Rocío Joo, Res Altwegg, Carolyn C. I. Burns, Michael A. McCarthy, Alison Johnston, Shinichi Nakagawa, Louise McMillan, Kadambari Devarajan, Patrick l. Taggart, Alison C. Wunderlich, Magdalena M. Mair, Juan Andrés Martínez-Lanfranco, Malgorzata Lagisz, Patrice P. Pottier

Comments: 19 pages, 2 figures

Subjects: Methodology (stat.ME); Populations and Evolution (q-bio.PE); Applications (stat.AP)

[36]  arXiv:2302.02488 (cross-list from stat.AP) [pdf, other]

Title: A three-state coupled Markov switching model for COVID-19 outbreaks across Quebec based on hospital admissions

Authors: Dirk Douwes-Schultz, Alexandra M. Schmidt, Yannan Shen, David Buckeridge

Comments: First revision

Subjects: Applications (stat.AP); Populations and Evolution (q-bio.PE)

[37]  arXiv:2302.02826 (cross-list from math.PR) [pdf, other]

Title: Extinction time in growth models subject to binomial catastrophes

Authors: F. Duque, V. V. Junior, F. P. Machado, A. Roldan-Correa

Comments: 16 pages, 2 figures. arXiv admin note: substantial text overlap with arXiv:2109.10997

Subjects: Probability (math.PR); Populations and Evolution (q-bio.PE)

[38]  arXiv:2302.03096 (cross-list from cs.NE) [pdf, ps, other]

Title: The Struggle for Existence: Time, Memory and Bloat

Authors: John C Stevenson

Comments: 1 table, 4 figures, 1 PDL

Subjects: Neural and Evolutionary Computing (cs.NE); Physics and Society (physics.soc-ph); Populations and Evolution (q-bio.PE)

[39]  arXiv:2302.07542 (cross-list from math.PR) [pdf, other]

Title: A Wright-Fisher graph model and the impact of directional selection on genetic variation

Authors: Ingemar Kaj, Carina F. Mugal, Rebekka Müller

Subjects: Probability (math.PR); Populations and Evolution (q-bio.PE)

[40]  arXiv:2302.08062 (cross-list from cs.CV) [pdf, ps, other]

Title: Fossil Image Identification using Deep Learning Ensembles of Data Augmented Multiviews

Authors: Chengbin Hou, Xinyu Lin, Hanhui Huang, Sheng Xu, Junxuan Fan, Yukun Shi, Hairong Lv

Comments: published in Methods in Ecology and Evolution

Journal-ref: Methods in Ecology and Evolution, 14, 3020-3034 (2023)

Subjects: Computer Vision and Pattern Recognition (cs.CV); Artificial Intelligence (cs.AI); Populations and Evolution (q-bio.PE)

[41]  arXiv:2302.08194 (cross-list from math.PR) [pdf, other]

Title: Sterile versus prolific individuals pertaining to linear-fractional Bienaym{é}-Galton-Watson trees

Authors: Thierry Huillet (LPTM - UMR 8089), Servet Martinez (CMM)

Subjects: Probability (math.PR); Statistical Mechanics (cond-mat.stat-mech); Populations and Evolution (q-bio.PE)

[42]  arXiv:2302.08218 (cross-list from math.DS) [pdf, ps, other]

Title: A statistical interpretation of biologically inspired growth models

Authors: A. Samoletov, B. Vasiev

Comments: 18 pages, 4 figures

Subjects: Dynamical Systems (math.DS); Populations and Evolution (q-bio.PE)

[43]  arXiv:2302.08840 (cross-list from stat.ML) [pdf, other]

Title: Learnable Topological Features for Phylogenetic Inference via Graph Neural Networks

Authors: Cheng Zhang

Comments: ICLR 2023

Subjects: Machine Learning (stat.ML); Machine Learning (cs.LG); Populations and Evolution (q-bio.PE)

[44]  arXiv:2302.10340 (cross-list from cs.SD) [pdf, ps, other]

Title: pykanto: a python library to accelerate research on wild bird song

Authors: Nilo Merino Recalde

Comments: 9 pages, 3 figures

Journal-ref: Methods in Ecology and Evolution, 00, 1-9

Subjects: Sound (cs.SD); Audio and Speech Processing (eess.AS); Populations and Evolution (q-bio.PE); Quantitative Methods (q-bio.QM)

[45]  arXiv:2302.10375 (cross-list from physics.soc-ph) [pdf, other]

Title: Cultural transmission of move choice in chess

Authors: Egor Lappo, Noah A. Rosenberg, Marcus W. Feldman

Comments: 25 pages

Subjects: Physics and Society (physics.soc-ph); Populations and Evolution (q-bio.PE)

[46]  arXiv:2302.10662 (cross-list from math.CO) [pdf, other]

Title: Snakes and Ladders: a Treewidth Story

Authors: Steven Chaplick, Steven Kelk, Ruben Meuwese, Matus Mihalak, Georgios Stamoulis

Comments: Compared to the earlier arXiv/WG version we have added analytical (as opposed to empirical) tightness bounds, and an extended discussion. See also Authors note 2 at the end of the introduction about earlier work in this area by Marchand et al

Subjects: Combinatorics (math.CO); Data Structures and Algorithms (cs.DS); Populations and Evolution (q-bio.PE)

[47]  arXiv:2302.11904 (cross-list from stat.AP) [pdf, ps, other]

Title: Forecasting influenza hospital admissions within English sub-regions using hierarchical generalised additive models

Authors: Jonathon Mellor, Rachel Christie, Christopher E Overton, Robert S Paton, Rhianna Leslie, Maria Tang, Sarah Deeny, Thomas Ward

Subjects: Applications (stat.AP); Populations and Evolution (q-bio.PE)

[48]  arXiv:2302.12121 (cross-list from cs.MA) [pdf, other]

Title: Decentralized core-periphery structure in social networks accelerates cultural innovation in agent-based model

Authors: Jesse Milzman, Cody Moser

Comments: 9 pages, 5 figures, AAMAS 2023 (accepted)

Subjects: Multiagent Systems (cs.MA); Populations and Evolution (q-bio.PE)

[49]  arXiv:2302.12790 (cross-list from stat.AP) [pdf, ps, other]

Title: Estimating the severity of COVID-19 Omicron Variant in USA, India, Brazil, France, Germany and UK

Authors: Tulio Eduardo Rodrigues, Otaviano Helene

Comments: 13 pages, 4 figures and 2 tables

Subjects: Applications (stat.AP); Physics and Society (physics.soc-ph); Populations and Evolution (q-bio.PE)

[50]  arXiv:2302.13358 (cross-list from physics.soc-ph) [pdf, other]

Title: Nonlinear bias toward complex contagion in uncertain transmission settings

Authors: Guillaume St-Onge, Laurent Hébert-Dufresne, Antoine Allard

Comments: 19 pages, 5 figures

Journal-ref: Proc. Natl. Acad. Sci. U.S.A., 121, e2312202121 (2023)

Subjects: Physics and Society (physics.soc-ph); Populations and Evolution (q-bio.PE)