Target sequence capture of Barnadesioideae (Compositae) demonstrates the utility of low coverage loci in phylogenomic analyses.

Target sequence capture has emerged as a powerful method to sequence hundreds or thousands of genomic regions in a cost- and time-efficient approach. In most cases, however, targeted regions lack full sequence information for certain samples, due to taxonomic, laboratory, or stochastic factors. Loci lacking molecular data for a large number of samples are commonly excluded from downstream analyses, even though they may still contain valuable information. On the other hand, including data-poor loci may bias phylogenetic analyses. Here we use a target sequence capture dataset of an ecologically and taxonomically diverse group of spiny sunflowers (Asteraceae, or Compositae: Barnadesioideae) to test how the inclusion or exclusion of such data-poor loci affects phylogenetic inference. We investigate the sensitivity of concatenation and coalescent approaches to missing data with matrices of varying taxonomic completeness by filtering loci with different proportions of missing samples prior to data analysis. We find that missing data affect both the topology and branch support of the resulting phylogenies. The matrix containing all loci yielded the overall highest node support values, independently of the amount of missing nucleotides. These results provide empirical support to earlier suggestions based on single genes and data simulations that taxa with high amounts of missing data should not be readily dismissed as they can provide essential information for phylogenomic reconstruction.

Phylogeny and circumscription of Dasyphyllum (Asteraceae: Barnadesioideae) based on molecular data with the recognition of a new genus, Archidasyphyllum.

Dasyphyllum Kunth is the most diverse genus of the South American subfamily Barnadesioideae (Asteraceae), comprising 33 species that occur in tropical Andes, Atlantic Forest, Caatinga, Cerrado, and Chaco. Based on distribution, variation in anther apical appendages, and leaf venation pattern, it has traditionally been divided into two subgenera, namely, Archidasyphyllum and Dasyphyllum. Further, based on involucre size and capitula arrangement, two sections have been recognized within subgenus Dasyphyllum: Macrocephala and Microcephala (=Dasyphyllum). Here, we report a phylogenetic analysis performed to test the monophyly of Dasyphyllum and its infrageneric classification based on molecular data from three non-coding regions (trnL-trnF, psbA-trnH, and ITS), using a broad taxonomic sampling of Dasyphyllum and representatives of all nine genera of Barnadesioideae. Moreover, we used a phylogenetic framework to investigate the evolution of the morphological characters traditionally used to recognize its infrageneric groups. Our results show that neither Dasyphyllum nor its infrageneric classification are currently monophyletic. Based on phylogenetic, morphological, and biogeographical evidence, we propose a new circumscription for Dasyphyllum, elevating subgenus Archidasyphyllum to generic rank and doing away with the infrageneric classification. Ancestral states reconstruction shows that the ancestor of Dasyphyllum probably had acrodromous leaf venation, bifid anther apical appendages, involucres up to 18 mm in length, and capitula arranged in synflorescence.