Populations and Evolution

Authors and titles for July 2013

[1] arXiv:1307.0202 (cross-list from q-bio.PE) [cn-pdf, pdf, other]

Title: Sensitivity Analysis in a Dengue Epidemiological Model Show Chinese title

Title: 登革热流行病学模型中的敏感性分析

Helena Sofia Rodrigues, M. Teresa T. Monteiro, Delfim F. M. Torres

Comments: Submitted 14-June-2013; accepted, after a minor revision, 30-June-2013; Conference Papers in Mathematics, Volume 2013, Article ID 721406, http://dx.doi.org/10.1155/2013/721406

Journal-ref: Conference Papers in Mathematics, Vol. 2013, Art. ID 721406, 7 pages, 2013

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

[2] arXiv:1307.0337 (cross-list from q-bio.PE) [cn-pdf, pdf, other]

Title: Demography-adjusted tests of neutrality based on genome-wide SNP data Show Chinese title

Title: 基于全基因组SNP数据的调整人口统计学中性检验

Marina Rafajlović (1), Alexander Klassmann (2), Anders Eriksson (3), Thomas Wiehe (2), Bernhard Mehlig (1) ((1) Department of Physics, University of Gothenburg, Sweden, (2) Institut für Genetik, Universität zu Köln, Germany, (3) Department of Zoology, University of Cambridge, U.K.)

Comments: 7 Figures. Supplemental material with 8 Tables and 7 Figures

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

[3] arXiv:1307.0343 (cross-list from q-bio.PE) [cn-pdf, pdf, other]

Title: Exponential growth of bifurcating processes with ancestral dependence Show Chinese title

Title: 分叉过程的指数增长与祖先依赖性

Sana Louhichi, Bernard Ycart

Comments: 25 pages, 1 figure

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

[4] arXiv:1307.0607 (cross-list from q-bio.PE) [cn-pdf, pdf, other]

Title: Structure of Intratumor Heterogeneity: Is Cancer Hedging Its Bets? Show Chinese title

Title: 肿瘤内异质性的结构：癌症是否在押注？

B. Brutovsky, D. Horvath

Comments: 10 pages, 2 figures

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

[5] arXiv:1307.0737 (cross-list from q-bio.PE) [cn-pdf, pdf, other]

Title: The rate of adaptation in large sexual populations with linear chromosomes Show Chinese title

Title: 大性种群中线性染色体的适应速率

D. B. Weissman, O. Hallatschek

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

[6] arXiv:1307.0968 (cross-list from q-bio.PE) [cn-pdf, pdf, other]

Title: Evolution on neutral networks accelerates the ticking rate of the molecular clock Show Chinese title

Title: 中性网络上的进化加速了分子钟的滴答速率

Susanna Manrubia, José A. Cuesta

Comments: 31 pages, 4 figures

Journal-ref: Journal of the Royal Society Interface 102, 20141010 (2015)

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

[7] arXiv:1307.1163 (cross-list from q-bio.PE) [cn-pdf, pdf, other]

Title: A mathematical model of kinetoplastid mitochondrial gene scrambling advantage Show Chinese title

Title: 一种动粒体线粒体基因打乱的优势数学模型

Harry Buhrman, Peter van der Gulik, Simone Severini, David Speijer

Comments: 22 pages, 2 figures

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

[8] arXiv:1307.1586 (cross-list from q-bio.PE) [cn-pdf, pdf, other]

Title: Evaluating strategies of phylogenetic analyses by the coherence of their results Show Chinese title

Title: 通过结果的一致性评估系统发育分析的策略

Blaise Li

Comments: 6 pages, 3 figures, accepted for publication in Comptes Rendus Palevol, based on a work presented at the "Journ\'ees d'automne 2012 de la Soci\'et\'e Fran\c{c}aise de Syst\'ematique" (http://www.normalesup.org/~bli/Papers/SFS_2012_BL.pdf)

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

[9] arXiv:1307.1736 (cross-list from q-bio.PE) [cn-pdf, pdf, other]

Title: Host mobility drives pathogen competition in spatially structured populations Show Chinese title

Title: 宿主移动性在空间结构种群中驱动病原体竞争

Chiara Poletto, Sandro Meloni, Vittoria Colizza, Yamir Moreno, Alessandro Vespignani

Comments: 23 pages, 8 figures, 1 table. Final version to appear in PLoS Comp. Bio

Journal-ref: PLoS Comput Biol 9(8): e1003169 (2013)

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

[10] arXiv:1307.1917 (cross-list from q-bio.PE) [cn-pdf, pdf, other]

Title: Stabilizing spatially structured populations through Adaptive Limiter Control Show Chinese title

Title: 通过自适应限制器控制稳定空间结构种群

Pratha Sah, Sutirth Dey

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

[11] arXiv:1307.1918 (cross-list from q-bio.PE) [cn-pdf, pdf, other]

Title: The Changing Geometry of a Fitness Landscape Along an Adaptive Walk Show Chinese title

Title: 适应行走过程中适应度景观几何形状的变化

Devin Greene, Kristina Crona

Comments: 29 pages, 7 figures

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

[12] arXiv:1307.2404 (cross-list from q-bio.PE) [cn-pdf, pdf, other]

Title: Outbreaks of coinfections: the critical role of cooperativity Show Chinese title

Title: 共感染爆发：协同作用的关键作用

Li Chen, Fakhteh Ghanbarnejad, Weiran Cai, Peter Grassberger

Comments: 5 pages, including 5 figures

Journal-ref: EPL 104 (2013) 50001

Subjects: Populations and Evolution (q-bio.PE) ; Disordered Systems and Neural Networks (cond-mat.dis-nn)

[13] arXiv:1307.2461 (cross-list from q-bio.PE) [cn-pdf, pdf, other]

Title: Inference of chromosomal inversion dynamics from Pool-Seq data in natural and laboratory populations of Drosophila melanogaster Show Chinese title

Title: 从果蝇自然种群和实验室种群的Pool-Seq数据推断染色体倒位动力学

Martin Kapun, Hester van Schalkwyk, Bryant McAllister, Thomas Flatt, Christian Schlötterer

Comments: 31 pages, 4 main figures, 1 main table, 7 supporting figures, 11 supporting tables

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

[14] arXiv:1307.2506 (cross-list from q-bio.PE) [cn-pdf, pdf, other]

Title: Landscape construction in non-gradient dynamics: A case from evolution Show Chinese title

Title: 非梯度动力学中的景观构建：进化的一个案例

Song Xu, Xinan Wang, Shuyun Jiao

Comments: arXiv admin note: text overlap with arXiv:q-bio/0605020 by other authors

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

[15] arXiv:1307.3097 (cross-list from q-bio.PE) [cn-pdf, pdf, other]

Title: Extinction in four species cyclic competition Show Chinese title

Title: 四种物种的周期竞争中的灭绝

Ben Intoy, Michel Pleimling

Comments: 18 pages, 13 figures, submitted to J. Stat. Mech

Journal-ref: J. Stat. Mech (2013) P08011

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

[16] arXiv:1307.3434 (cross-list from q-bio.PE) [cn-pdf, pdf, other]

Title: Forecasts of Cancer and Chronic Patients: Big Data Metrics of Population Health Show Chinese title

Title: 癌症和慢性病患者的预测：人口健康的大数据指标

Jacob Kuriyan, Nathaniel Cobb

Comments: 26 pages, 6 figures and 6 tables

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

[17] arXiv:1307.4036 (cross-list from q-bio.PE) [cn-pdf, pdf, other]

Title: Population Dynamics with Infinite Leslie Matrices Show Chinese title

Title: 无限列文蒂矩阵的人口动力学

João Alves, António Bravo, Henrique Oliveira

Comments: 12 Pages

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

[18] arXiv:1307.4103 (cross-list from q-bio.PE) [cn-pdf, pdf, other]

Title: Migration-selection balance at multiple loci and selection on dominance and recombination Show Chinese title

Title: 多个位点的迁移-选择平衡以及对显性和重组的选择

Alexey Yanchukov, Stephen R. Proulx

Comments: includes 6 figures and a Supporting Information. Mathematica notebook where the numerical results were obtained is available upon request

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

[19] arXiv:1307.4118 (cross-list from q-bio.PE) [cn-pdf, pdf, other]

Title: Genomic identification of founding haplotypes reveals the history of the selfing species Capsella rubella Show Chinese title

Title: 自交物种拟南芥属红花的奠基单倍型的基因组鉴定揭示了其历史

Yaniv Brandvain, Tanja Slotte, Khaled Hazzouri, Stephen Wright, Graham Coop

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

[20] arXiv:1307.4137 (cross-list from q-bio.PE) [cn-pdf, pdf, other]

Title: A model-based approach for identifying signatures of balancing selection in genetic data Show Chinese title

Title: 基于模型的方法在遗传数据中识别平衡选择的特征

Michael DeGiorgio, Kirk E. Lohmueller, Rasmus Nielsen

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

[21] arXiv:1307.4141 (cross-list from q-bio.PE) [cn-pdf, pdf, other]

Title: Evolution via imitation among like-minded individuals Show Chinese title

Title: 通过模仿的进化在志同道合的个体之间

Naoki Masuda

Comments: 3 figures

Journal-ref: Journal of Theoretical Biology, 349, 100-108 (2014)

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

[22] arXiv:1307.4327 (cross-list from q-bio.PE) [cn-pdf, pdf, other]

Title: Environmental vs demographic variability in stochastic predator-prey models Show Chinese title

Title: 环境与种群数量变异在随机捕食者-被捕食者模型中的比较

Ulrich Dobramysl, Uwe C. Tauber

Comments: 28 pages, 10 figures, Proceedings paper of the STATPHYS 25 conference

Journal-ref: J. Stat. Mech. (2013) P10001

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

[23] arXiv:1307.4375 (cross-list from q-bio.PE) [cn-pdf, pdf, other]

Title: Evolutionary games with facilitators: When does selection favor cooperation? Show Chinese title

Title: 有促进者的进化博弈：选择何时促进合作？

Mauro Mobilia

Comments: 12 pages, 5 figures. Version to be published (special issue on "collective behavior and evolutionary games")

Journal-ref: Chaos, Solitons & Fractals 56, 113 (2013)

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

[24] arXiv:1307.4415 (cross-list from q-bio.PE) [cn-pdf, pdf, other]

Title: No early warning signals for stochastic transitions: insights from large deviation theory Show Chinese title

Title: 对随机跃迁没有早期预警信号：来自大偏差理论的见解

Carl Boettiger, Alan Hastings

Journal-ref: 2013. Proceedings of the Royal Society B: Biological Sciences 280, 20131372-20131372

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

[25] arXiv:1307.4417 (cross-list from q-bio.PE) [cn-pdf, pdf, other]

Title: Re-imagining the Hardy-Weinberg Law Show Chinese title

Title: 重新构想哈迪-温伯格定律

Von Bing Yap

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

[26] arXiv:1307.4628 (cross-list from q-bio.PE) [cn-pdf, pdf, other]

Title: The structure of infectious disease outbreaks across the animal-human interface Show Chinese title

Title: 跨动物与人类界面的传染病爆发结构

Sarabjeet Singh, David J. Schneider, Christopher R. Myers

Comments: 18 pages (8 main text + 10 Appendix), 15 figures in total, currently submitted to a journal for review

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

[27] arXiv:1307.4789 (cross-list from q-bio.PE) [cn-pdf, pdf, other]

Title: Reproductive Value in Graph-structured Populations Show Chinese title

Title: 图结构种群中的繁殖价值

Wes Maciejewski

Journal-ref: Journal of Theoretical Biology, (2014), vol.340, pp.285-293

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

[28] arXiv:1307.4954 (cross-list from q-bio.PE) [cn-pdf, pdf, other]

Title: Guidelines for the design of evolve and resequencing studies Show Chinese title

Title: 演进和再测序研究的设计指南

Robert Kofler, Christian Schlötterer

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

[29] arXiv:1307.5050 (cross-list from q-bio.PE) [cn-pdf, pdf, other]

Title: Existence of periodic solutions for the periodically forced SIR model Show Chinese title

Title: 周期强迫SIR模型的周期解的存在性

Guy Katriel

Journal-ref: Neliniini Kolyvannya (Nonlinear Oscillations) 16 (2013), 359-366, Journal of Mathemarical Sciences 201 (2014) 335-342

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

[30] arXiv:1307.5147 (cross-list from q-bio.PE) [cn-pdf, pdf, other]

Title: An Arrow-type result for inferring a species tree from gene trees Show Chinese title

Title: 一种从基因树推断物种树的Arrow型结果

Mike Steel

Comments: 5 pages, 0 figures

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

[31] arXiv:1307.5300 (cross-list from q-bio.PE) [cn-pdf, pdf, other]

Title: Detecting a trend change in cross-border epidemic transmission Show Chinese title

Title: 检测跨境流行病传播中的趋势变化

Yoshiharu Maeno

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

[32] arXiv:1307.5335 (cross-list from q-bio.PE) [cn-pdf, pdf, other]

Title: Mean Field Approximation to a Spatial Host-Pathogen Model Show Chinese title

Title: 平均场近似用于空间宿主-病原体模型

M.A.M. de Aguiar, E. Rauch, B.C. Stacey, Y. Bar-Yam

Comments: 7 pages (1 of errata), 1 figure; original paper by MdA, ER and YB; errata by MdA, BCS and YB. v2: additional misprints corrected and docketed

Journal-ref: Physical Review E 67, 047102 (2003)

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

[33] arXiv:1307.5364 (cross-list from q-bio.PE) [cn-pdf, pdf, other]

Title: No complexity-stability relationship in natural communities Show Chinese title

Title: 自然群落中不存在复杂性-稳定性关系

Claire Jacquet, Charlotte Moritz, Lyne Morissette, Pierre Legagneux, François Massol, Phillippe Archambault, Dominique Gravel

Comments: Main text: 9 pages, 4 figures. Supplementary Information: 14 pages, 3 figures

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

[34] arXiv:1307.5574 (cross-list from q-bio.PE) [cn-pdf, pdf, other]

Title: Matrix group structure and Markov invariants in the strand symmetric phylogenetic substitution model Show Chinese title

Title: 矩阵群结构和链对称系统进化替换模型中的马尔可夫不变量

Peter D Jarvis, Jeremy G Sumner

Comments: v2: Major revision now includes explicit forms for quadratic and cubic Markov invariants

Journal-ref: J Mathematical Biology (Online First, Dec 2015)

Subjects: Populations and Evolution (q-bio.PE) ; Representation Theory (math.RT) ; Statistics Theory (math.ST) ; Quantitative Methods (q-bio.QM)

[35] arXiv:1307.5747 (cross-list from q-bio.PE) [cn-pdf, pdf, other]

Title: Reply to Hartig et al. [arXiv:1305.3544]: The "true model" myth Show Chinese title

Title: 回复Hartig等人。 [arXiv:1305.3544]："真实模型"的神话

Charles T. Perretti, Stephan B. Munch, George Sugihara

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

[36] arXiv:1307.5908 (cross-list from q-bio.PE) [cn-pdf, pdf, other]

Title: Distance-based phylogenetic methods around a polytomy Show Chinese title

Title: 基于距离的多分支点系统发育方法

Ruth Davidson, Seth Sullivant

Comments: 21 pages, 9 figures

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

[37] arXiv:1307.6043 (cross-list from q-bio.PE) [cn-pdf, pdf, other]

Title: New outcomes in mutation rates analysis Show Chinese title

Title: 突变率分析的新成果

Valentina Agoni

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

[38] arXiv:1307.6071 (cross-list from q-bio.PE) [cn-pdf, pdf, other]

Title: Bacterial chemotaxis without gradient-sensing Show Chinese title

Title: 细菌趋化作用无需梯度感知

Changwook Yoon, Yong-Jung Kim

Comments: 19 pages, 4 figures

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

[39] arXiv:1307.6177 (cross-list from q-bio.PE) [cn-pdf, pdf, other]

Title: Nonlinear group survival in Kimura's model for the evolution of altruism Show Chinese title

Title: 非线性群体生存在基姆拉模型中对利他主义进化的描述

Jose F. Fontanari, Maurizio Serva

Journal-ref: Mathematical Biosciences 249 (2014), 18-26

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

[40] arXiv:1307.6436 (cross-list from q-bio.PE) [cn-pdf, pdf, other]

Title: Birth and death of links control disease spreading in empirical contact networks Show Chinese title

Title: 链接的生成与消失控制实际接触网络中的疾病传播

Petter Holme, Fredrik Liljeros

Journal-ref: Scientific Reports 4, 4999 (2014)

Subjects: Populations and Evolution (q-bio.PE) ; Social and Information Networks (cs.SI) ; Physics and Society (physics.soc-ph)

[41] arXiv:1307.6594 (cross-list from q-bio.PE) [cn-pdf, pdf, other]

Title: Robust forward simulations of recurrent hitchhiking Show Chinese title

Title: 稳健的递归劫持前向模拟

Lawrence H. Uricchio, Ryan D. Hernandez

Journal-ref: Genetics May 2014 197:221-236

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

[42] arXiv:1307.6692 (cross-list from q-bio.PE) [cn-pdf, pdf, other]

Title: A General Formula for the Generation Time Show Chinese title

Title: 生成时间的通用公式

François Bienvenu, Lloyd Demetrius, Stéphane Legendre

Comments: 13 pages, 3 figures

Journal-ref: The American Naturalist, 185(6), 834-843 (2015)

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

[43] arXiv:1307.6729 (cross-list from q-bio.PE) [cn-pdf, pdf, other]

Title: Speed of adaptation and genomic footprints of host-parasite coevolution under arms race and trench warfare dynamics Show Chinese title

Title: 适应速度和宿主-寄生虫协同进化下的基因组足迹在军备竞赛和阵地战动力学下

Aurelien Tellier, Stefany Moreno-Gamez, Wolfgang Stephan

Comments: Supplementary Information available upon request

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

[44] arXiv:1307.6914 (cross-list from q-bio.PE) [cn-pdf, pdf, other]

Title: Edge effects in game theoretic dynamics of spatially structured tumours Show Chinese title

Title: 空间结构肿瘤博弈论动态中的边缘效应

Artem Kaznatcheev, Jacob G. Scott, David Basanta

Comments: 14 pages, 3 figures; restructured abstract, added histology to fig. 1, added fig. 3, discussion of EMT introduced and cancer biology expanded

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

[45] arXiv:1307.7313 (cross-list from q-bio.PE) [cn-pdf, pdf, other]

Title: The genomic impacts of drift and selection for hybrid performance in maize Show Chinese title

Title: 玉米杂交性能中遗传漂变和选择的基因组影响

Justin P. Gerke, Jode W. Edwards, Katherine E. Guill, Jeffrey Ross-Ibarra, Michael D. McMullen

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

[46] arXiv:1307.7678 (cross-list from q-bio.PE) [cn-pdf, pdf, other]

Title: Comprehensive analysis of imprinted genes in maize reveals limited conservation with other species and allelic variation for imprinting Show Chinese title

Title: 玉米印记基因的综合分析揭示了与其他物种的有限保守性以及印记的等位基因变异

Amanda J. Waters, Paul Bilinski, Steve R. Eichten, Matthew W. Vaughn, Jeffrey Ross-Ibarra, Mary Gehring, Nathan M. Springer

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

[47] arXiv:1307.7756 (cross-list from q-bio.PE) [cn-pdf, pdf, other]

Title: A path integral formulation of the Wright-Fisher process with genic selection Show Chinese title

Title: 基因选择的Wright-Fisher过程的路径积分表述

Joshua G. Schraiber

Comments: 22 pages, 3 figures

Journal-ref: Theoretical Population Biology 92, 2013, pp 30-35

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

[48] arXiv:1307.7759 (cross-list from q-bio.PE) [cn-pdf, pdf, other]

Title: The Population Genetic Signature of Polygenic Local Adaptation Show Chinese title

Title: 多基因局部适应的种群遗传特征

Jeremy J. Berg, Graham Coop

Comments: 42 pages including 8 figures and 3 tables; supplementary figures and tables not included on this upload, but are mostly unchanged from v1

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

[49] arXiv:1307.8014 (cross-list from q-bio.PE) [cn-pdf, pdf, other]

Title: Ancient west Eurasian ancestry in southern and eastern Africa Show Chinese title

Title: 古代西欧亚血统在非洲南部和东部

Joseph K. Pickrell, Nick Patterson, Po-Ru Loh, Mark Lipson, Bonnie Berger, Mark Stoneking, Brigitte Pakendorf, David Reich

Comments: Added additional simulations, some additional discussion

Journal-ref: Proc Natl Acad Sci U S A. 2014 Feb 18;111(7):2632-7

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

[50] arXiv:1307.8143 (cross-list from q-bio.PE) [cn-pdf, pdf, other]

Title: Constructing Lower-Bounds for CTL Escape Rates in Early HIV and SIV Infection Show Chinese title

Title: 构建早期HIV和SIV感染中CTL逃逸率的下限

Sivan Leviyang

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