• 1 Chicago Botanic Garden, Negaunee Institute for Plant Conservation Science and Action, 1000 Lake Cook Road, Glencoe, IL, USA
  • 2 Forest Research Centre, Sabah Forestry Department, P.O. Box 1407, Sandakan, Sabah, Malaysia
  • 3 Faculty of Resource Science & Technology, Universiti Malaysia Sarawak, Kota Samarahan, Sarawak, Malaysia
  • 4 Herbarium Bogoriense, Research Center for Biology, Indonesian Institute of Sciences, Cibinong, Jawa Barat, Indonesia
Syst Biol, 2020 Sep 24.
PMID: 32970819 DOI: 10.1093/sysbio/syaa073


We present a 517-gene phylogenetic framework for the breadfruit genus Artocarpus (ca. 70 spp., Moraceae), making use of silica-dried leaves from recent fieldwork and herbarium specimens (some up to 106 years old) to achieve 96% taxon sampling. We explore issues relating to assembly, paralogous loci, partitions, and analysis method to reconstruct a phylogeny that is robust to variation in data and available tools. While codon partitioning did not result in any substantial topological differences, the inclusion of flanking non-coding sequence in analyses significantly increased the resolution of gene trees. We also found that increasing the size of datasets increased convergence between analysis methods but did not reduce gene tree conflict. We optimized the HybPiper targeted-enrichment sequence assembly pipeline for short sequences derived from degraded DNA extracted from museum specimens. While the subgenera of Artocarpus were monophyletic, revision is required at finer scales, particularly with respect to widespread species. We expect our results to provide a basis for further studies in Artocarpus and provide guidelines for future analyses of datasets based on target enrichment data, particularly those using sequences from both fresh and museum material, counseling careful attention to the potential of off-target sequences to improve resolution.

* Title and MeSH Headings from MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.