Subfamily Rubioideae is the largest of the main lineages in the coffee family

(Rubiaceae), with over 8,000 species and 29 tribes. Phylogenetic relationships

among tribes and other major clades within this group of plants are still

only partly resolved despite considerable efforts. While previous studies have

mainly utilized data from the organellar genomes and nuclear ribosomal DNA,

we here use a large number of low-copy nuclear genes obtained via a target

capture approach to infer phylogenetic relationships within Rubioideae. We

included 101 Rubioideae species representing all but two (the monogeneric

tribes Foonchewieae and Aitchinsonieae) of the currently recognized tribes,

and all but one non-monogeneric tribe were represented by more than

one genus. Using data from the 353 genes targeted with the universal

Angiosperms353 probe set we investigated the impact of data type, analytical

approach, and potential paralogs on phylogenetic reconstruction. We inferred

a robust phylogenetic hypothesis of Rubioideae with the vast majority (or

all) nodes being highly supported across all analyses and datasets and few

incongruences between the inferred topologies. The results were similar to

those of previous studies but novel relationships were also identified. We

found that supercontigs [coding sequence (CDS) C non-coding sequence]

clearly outperformed CDS data in levels of support and gene tree congruence.

The full datasets (353 genes) outperformed the datasets with potentially

paralogous genes removed (186 genes) in levels of support but increased

gene tree incongruence slightly. The pattern of gene tree conflict at short

internal branches were often consistent with high levels of incomplete lineage

sorting (ILS) due to rapid speciation in the group. While concatenationand

coalescence-based trees mainly agreed, the observed phylogenetic

discordance between the two approaches may be best explained by

their differences in accounting for ILS. The use of target capture data 

greatly improved our confidence and understanding of the Rubioideae

phylogeny, highlighted by the increased support for previously uncertain

relationships and the increased possibility to explore sources of underlying

phylogenetic discordance.