Molecular Phylogenetics and Evolution

Molecular Phylogenetics and Evolution
Title	Molecular Phylogenetics and Evolution
Discipline	Evolutionary biology
Abbreviation	Mol. Phylogenet. Evol.
Publisher	Elsevier
Country	Netherlands
History	1992–present
Frequency	Monthly
ISSN	1055-7903

Contents

Molecular Phylogenetics and Evolution Molecular Phylogenetics and Evolution is a peer-reviewed scientific journal that publishes research on the genetic reconstruction of evolutionary relationships using molecular data. The journal interfaces with topics relevant to researchers associated with National Center for Biotechnology Information, Smithsonian Institution, Max Planck Society, University of Cambridge, and Harvard University while engaging authors from institutions such as Stanford University, University of California, Berkeley, University of Oxford, University of Tokyo, and Imperial College London. Contributions often reference landmark projects and collections like the Human Genome Project, Tree of Life Web Project, Barcode of Life Data System, Museum of Natural History, London, and Smithsonian National Museum of Natural History.

Introduction

The journal addresses the intersection of empirical studies and theoretical advances that stem from work by investigators linked to Nobel Prize in Physiology or Medicine, Royal Society, National Academy of Sciences, European Molecular Biology Laboratory, and laboratories at Cold Spring Harbor Laboratory, Sanger Institute, Broad Institute, Wellcome Trust, and Howard Hughes Medical Institute. Early influential authors published alongside names affiliated with Francis Crick, James Watson, Carl Woese, Allan Wilson, and groups connected to Linnean Society of London and American Society of Naturalists. The scope integrates data types and methodological frameworks developed in contexts such as the International Barcode of Life, Genome Australia, Chinese Academy of Sciences, and the European Research Council.

Articles describe empirical pipelines that draw on sequence repositories and specimen archives maintained by GenBank, European Nucleotide Archive, DNA Data Bank of Japan, Museum of Comparative Zoology, and Natural History Museum, Vienna. Typical datasets derive from studies performed in facilities like W.M. Keck Observatory, Max Planck Institute for Evolutionary Anthropology, Royal Botanic Gardens, Kew, Australian National University, and field programs tied to Borneo Rainforest Research Partnership, Smithsonian Tropical Research Institute, and Scripps Institution of Oceanography. Molecular markers discussed include loci characterized in collaborations with Human Microbiome Project, 1000 Genomes Project, EcoGene, and regional efforts such as African Genome Variation Project and Pan-Asian SNP Consortium. Authors routinely use laboratory methods refined at Cold Spring Harbor Laboratory, using reagents and protocols from companies linked to Thermo Fisher Scientific and Roche.

Theoretical advances reported often build on statistical foundations from scholars associated with Ronald Fisher, J.B.S. Haldane, Sewall Wright, and institutions like Princeton University, University of Chicago, University of Edinburgh, and Columbia University. Model frameworks include substitution models whose development traces to work at University of California, Los Angeles, State University of New York at Stony Brook, University of Washington, and collaborators at University of Michigan. Algorithms for tree search and support estimation are described with reference to software origins from teams at University of Oslo, University of Vienna, ETH Zurich, Université Paris-Saclay, and Technical University of Munich. Bayesian methods and coalescent-based approaches cite innovations associated with groups at University of Toronto, Yale University, Duke University, University of British Columbia, and research networks funded by Wellcome Trust and National Institutes of Health.

Research published applies molecular phylogenetic approaches to taxonomic revision projects undertaken by curators at Natural History Museum, London, American Museum of Natural History, Field Museum, and botanical programs at Royal Botanic Gardens, Kew. Case studies include phylogeographic reconstructions tied to expeditions with National Geographic Society, conservation genetics reports used by International Union for Conservation of Nature, and coevolution studies linked to collaborations with World Wildlife Fund and Conservation International. Paleogenomic and ancient DNA studies engage laboratories at Max Planck Institute for Evolutionary Anthropology, University College Dublin, and University of Copenhagen and interface with fossil collections from Smithsonian Institution and Natural History Museum, Vienna.

Discussions of methodological bias and reproducibility cite debates centering on practices promoted by journals like Nature, Science, Proceedings of the National Academy of Sciences, and controversies involving high-profile consortia such as the ENCODE Project. Concerns about taxon sampling, model misspecification, and horizontal gene transfer are contextualized with reference to case histories from Darwin College, Galápagos Islands research programs, and datasets produced by the Global Biodiversity Information Facility. Ethical and legal dimensions of genomic sampling reference policy frameworks from Convention on Biological Diversity, Nagoya Protocol, Convention on International Trade in Endangered Species of Wild Fauna and Flora, and institutional review boards at World Health Organization and United Nations Educational, Scientific and Cultural Organization.

The journal reports on software, databases, and computational platforms developed or maintained by groups at University of California, San Diego, Carnegie Mellon University, University of Pittsburgh, University of Illinois Urbana-Champaign, Johns Hopkins University, and tech partners including Google Research and Microsoft Research. Commonly cited tools and infrastructures are associated with projects like CyVerse, HPC centers at Lawrence Berkeley National Laboratory, XSEDE, and cloud initiatives by Amazon Web Services used in collaborations with European Bioinformatics Institute and National Institutes of Health. Training and community resources described involve workshops hosted by Gordon Research Conferences, Society for Molecular Biology and Evolution, European Society for Evolutionary Biology, and summer schools at EMBL-EBI and Wellcome Trust Sanger Institute.

Category:Evolutionary biology journals