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Abstract— Artocarpus bergii , named for the late C. C. Berg, is from Halmahera in the Moluccas, and is a close ally of breadfruit ( A. altilis ). The species resembles the Micronesian A. mariannensis but with generally smaller parts. Because it is known from only a small area and the type locality is a potential mining site, A. bergii is likely of conservation concern, particularly given its status as a crop wild relative. 

Recent taxonomic work on Artoarpus has revealed two undescribed species from Thailand and Vietnam. Artocarpus rubrosoccatus, endemic to peninsular Thailand, resembles A. lacucha but is distinguished by its deep red clavate staminate inflorescences. Artocarpus montanus is found in the montane regions of southern and central Vietnam, and perhaps also in Thailand. This species resembles the vegetative parts of A. lowii and A. excelsus, but A. montanus differs in its longer syncarp processes and its geographic distribution. The vast majority of Artocarpus species are found in tropical lowlands, and A. montanus, along with A. excelsus, represent the only known members of the genus that are restricted to montane habitats. The provisional conservation assessment of both new species is Near Threatened, because although their known areas of occupancy are restricted, both occur in protected areas. 

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.] 

The reduced cost of high‐throughput sequencing and the development of gene sets with wide phylogenetic applicability has led to the rise of sequence capture methods as a plausible platform for both phylogenomics and population genomics in plants. An important consideration in large targeted sequencing projects is the per‐sample cost, which can be inflated when using off‐the‐shelf kits or reagents not purchased in bulk. Here, we discuss methods to reduce per‐sample costs in high‐throughput targeted sequencing projects. We review the minimal equipment and consumable requirements for targeted sequencing while comparing several alternatives to reduce bulk costs inDNAextraction, library preparation, target enrichment, and sequencing. We consider how each of the workflow alterations may be affected byDNAquality (e.g., fresh vs. herbarium tissue), genome size, and the phylogenetic scale of the project. We provide a cost calculator for researchers considering targeted sequencing to use when designing projects, and identify challenges for future development of low‐cost sequencing in non‐model plant systems.