Target capture data resolve recalcitrant relationships in the coffee family (Rubioideae, Rubiaceae)

Abstract

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) + 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 concatenation- and 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.

New chromosome counts on Rubiaceae from Africa and the Western Indian Ocean islands

“…& C. Rydin and Urophylleae. The relationships of the basalmost tribes remain unsettled as analyses of mitochondrial, nuclear and plastid data lead to conflicting topologies, but Lasiantheae‐Perameae and Coussareeae are consistently resolved as successive sister groups to a clade comprising the Psychotrieae and Spermacoceae alliances (Wikström et al 2015, 2020, Rydin et al 2017, Razafimandimbison et al 2020, Thureborn et al 2022).…”

A target enrichment probe set for resolving phylogenetic relationships in the coffee family, Rubiaceae

“…The loci isolated using Rubiaceae2270x have properties that are desirable for phylogenomics, including high variability (Figure 2), long average length (Table 3), and a relatively low proportion of paralogs (the greatest average proportion of potential paralogs observed in a clade was 27% [MERs] for Hillieae). Comparing our Palicoureeae+ Psychotrieae (Rubioideae) data set to Thureborn et al (2022), which used Angiosperms353 to sequence taxa across Rubioideae, Rubiaceae2270x resulted in a similar proportion of total loci with paralog warnings (55% in our study vs. 53% in Thureborn et al, 2022). Here, these percentages refer to loci for which >1 contig covering a specified percentage of the length of the reference sequence was assembled by HybPiper (our study uses a 75% cutoff and Thureborn et al uses a less conservative cutoff of 85%).…”

Phylogenomics and topological conflicts in the tribe Anthospermeae (Rubiaceae)

“…We sampled herbarium or silica-dried specimens for one representative of each of the 12 currently recognized genera of Anthospermeae (Thureborn et al, 2019). A set of outgroups were selected based on the results in previous work (Antonelli et al, 2021;Rydin et al, 2017;Thureborn et al, 2019Thureborn et al, , 2022Wikström et al, 2020)…”

“…Two recent molecular phylogenetic studies have generated overall well-resolved relationships in Anthospermeae; the Anthospermeae-focused study by Thureborn et al (2019), which used selected chloroplast and nuclear ribosomal markers, and the Rubioideae-wide study by Thureborn et al (2022), in which hundreds of low-copy nuclear genes were used. However, while taxon Botany, Genomics, Phylogenetics sampling was dense in the former study, it was based on a restricted set of molecular markers (two nuclear ribosomal and five chloroplast loci), and some nodes were not statistically supported.…”