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The breadfruit genus Artocarpus J.R.Forst. & G.Forst. (Moraceae) has sixteen species in Singapore, fourteen of them native. In this precursory study to the treatment of Artocarpus for the Flora of Singapore, we present updated phylogenomic analyses of Artocarpus subgenus Artocarpus based on 517 nuclear genes. The following taxonomic changes based on recent phylogenetic analyses, review of herbarium specimens, and field observations, are proposed. Artocarpus subg. Cauliflori (F.M.Jarrett) Zerega is reduced to a section within Artocarpus subg. Artocarpus, and Artocarpus sect. Glandulifolium F.M.Jarrett is raised to subgenus status. The new monotypic subgenus Artocarpus subg. Aenigma E.M.Gardner & Zerega is proposed for Artocarpus sepicanus Diels, whose phylogenetic position remains uncertain and may be of ancient hybrid origin. Artocarpus elasticus Reinw. ex Blume, A. scortechinii King and A. corneri Kochummen are recognised as distinct species. Artocarpus clementis Merr. is reinstated as distinct from A. lanceifolius Roxb. Artocarpus calophyllus Kurz and A. melinoxylus Gagnep. are reinstated as distinct from both A. chama Buch.-Ham. and A. rigidus Blume. Artocarpus nigrescens Elmer is reinstated as distinct from A. treculianus Elmer. Keys to the subgenera, the sections of Artocarpus subg. Artocarpus and to the species found in Singapore are presented. A nomenclatural synopsis of subgenera Artocarpus, Aenigma and Glandulifolium is presented with taxonomic notes to aid in identification. Seventeen lectotypes, six of them in a second step, and two neotypes are designated. 

Abstract 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. Although codon partitioning did not result in any substantial topological differences, the inclusion of flanking noncoding sequence in analyses significantly increased the resolution of gene trees. We also found that increasing the size of data sets 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. Although 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 data sets 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. [Artocarpus; Moraceae; noncoding sequences; phylogenomics; target enrichment.]