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.]

中文翻译：

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旁系同源物和脱靶序列提高了面包果属（面包果，桑科）的密集采样研究中的系统发育分辨率。

摘要

我们提出了一个517基因进化框架的面包果属桂（桑科植物，约70 pppp），利用最近田野调查所得的二氧化硅干燥叶片和标本室标本（有些长达106年）来实现96％的分类群采样。我们探索与装配，旁系基因座，分区和分析方法有关的问题，以重建对数据和可用工具的变化都具有鲁棒性的系统发育。尽管密码子分配没有导致任何实质性的拓扑差异，但分析中包含侧翼非编码序列显着提高了基因树的分辨率。我们还发现，增加数据集的大小可以提高分析方法之间的收敛性，但并不能减少基因树冲突。我们针对从博物馆标本中提取的降解DNA衍生的短序列优化了HybPiper靶向富集序列组装管道。虽然是面包果是单生的，需要在较小的规模上进行修订，特别是对于广泛的物种。我们希望我们的结果将为面包果的进一步研究提供依据，并为将来基于靶标富集数据的数据集分析提供指导，尤其是那些使用来自新鲜和博物馆材料的序列的数据集，建议谨慎注意脱靶序列的潜力以提高分辨率。[面包果; 桑科; 非编码序列；系统基因组学 目标富集。]