RESEARCH ARTICLE Identifying genetic markers for a range of phylogenetic utility±From species to family level Bokyung Choi1, Michael D. Crisp1, Lyn G. Cook2, Karen Meusemann3,4, Robert 2,5 2 1,6 D. EdwardsID , Alicia Toon , Carsten KuÈ lheimID * 1 Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia, 2 The University of Queensland, School of Biological Sciences, Brisbane, Queensland, Australia, 3 Evolutionary Biology & Ecology, Institute for Biology, University a1111111111 of Freiburg, Freiburg (Brsg.), Germany, 4 Australian National Inset Collection, CSIRO National Research a1111111111 Collections Australia, Canberra, Australian Capital Territory, Australia, 5 Department of Botany, National a1111111111 Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America, 6 School of a1111111111 Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, a1111111111 United States of America *
[email protected] OPEN ACCESS Abstract Citation: Choi B, Crisp MD, Cook LG, Meusemann Resolving the phylogenetic relationships of closely related species using a small set of loci K, Edwards RD, Toon A, et al. (2019) Identifying genetic markers for a range of phylogenetic utility± is challenging as sufficient information may not be captured from a limited sample of the From species to family level. PLoS ONE 14(8): genome. Relying on few loci can also be problematic when conflict between gene-trees e0218995. https://doi.org/10.1371/journal. arises from incomplete lineage sorting and/or ongoing hybridization, problems especially pone.0218995 likely in recently diverged lineages. Here, we developed a method using limited genomic Editor: Michael Scott Brewer, East Carolina resources that allows identification of many low copy candidate loci from across the nuclear University, UNITED STATES and chloroplast genomes, design probes for target capture and sequence the captured loci.