We introduce an R package, PCMBase, to rapidly calculate the likelihood for multivariate phylogenetic comparative methods. The package is not specific to particular models but offers the user the functionality to very easily implement a wide range of models where the transition along a branch is multivariate normal. We demonstrate the package's possibilities on the now standard, multitrait Ornstein-Uhlenbeck process as well as the novel multivariate punctuated equilibrium model. The package can handle trees of various types (e.g. ultrametric, nonultrametric, polytomies, e.t.c.), as well as measurement error, missing measurements or non-existing traits for some of the species in the tree.
Challenges of sampling and how phylogenetic comparative methods help: With a case study of the Pama-Nyungan laminal contrast
Surrey Morphology Group, University of Surrey（萨里大学萨里形态学组）；Ancient Language Lab, The University of Queensland（昆士兰大学古代语言实验室）；Max Planck Institute for the Science of Human History（马克斯·普朗克人类历史科学研究所）；Laboratoire Dynamique Du Langage (UMR 5596), CNRS / Université Lyon 2（法国国家科学研究中心/里昂第二大学语言动态实验室）
Evaluating Phylogenetic Comparative Methods under Reticulate Evolutionary Scenarios
Texas A&M University（德克萨斯农工大学）；Lakehead University（湖首大学）；IISD Experimental Lakes Area（国际可持续发展研究所实验湖区）；The Institute for Computational and Experimental Research in Mathematics, Brown University（布朗大学计算与实验数学研究所）；RIKEN iTHEMS（理化学研究所创新智能数学科学中心）
Revisiting a random model of lateral gene transfer in phylogenetics
The Ohio State University（俄亥俄州立大学）；National Institute for Theory and Mathematics in Biology, Northwestern University and The University of Chicago（西北大学和芝加哥大学生物数学理论国家研究所）；University of Auckland（奥克兰大学）；New Jersey Institute of Technology（新泽西理工学院）
Graph construction in QUBO-based recursive phylogenetic tree reconstruction
Graduate School of Media and Governance, Keio University（庆应义塾大学媒体治理研究生院）；Human Biology-Microbiome-Quantum Research Center (WPI-Bio2Q), Keio University（庆应义塾大学生物学-微生物组-量子研究中心 (WPI-Bio2Q)）；Keio University Sustainable Quantum Artificial Intelligence Center (KSQAIC), Keio University（庆应义塾大学可持续量子人工智能中心 (KSQAIC)）
