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Abstract PremiseCentropogonsubgenusCentropogoncomprises 55 species found primarily in midelevation Andean forests featuring some of the most curved flowers among angiosperms. Floral curvature is linked to coevolution with the sicklebill hummingbird, which pollinates most species. Despite charismatic flowers, there is limited knowledge about the phylogenetic relationships and floral evolution. MethodsWe conducted the first densely sampled phylogenomic analysis of the clade using methods that account for incomplete lineage sorting on a sequence capture dataset generated with a lineage‐specific probe set. Using phylogenetic comparative methods, we test for correlated evolution of two traits central to sicklebill pollination. ResultsWe improve understanding of species relationships by more than doubling past taxon sampling. We confirm the monophyly of the subgenus and two sections, and the non‐monophyly of remaining sections. The subgenus is characterized by high gene tree discordance. Three widespread species display contrasting phylogenetic dynamics, withC. cornutusforming a clade andC. granulosusandC. solanifoliusforming non‐monophyletic, biogeographically clustered lineages. Correlated evolution of floral curvature and inflorescence structure has led to multiple putative losses of sicklebill pollination. ConclusionsCentropogonsubgenusCentropogonadds to a growing body of literature of Andean plant clades with high gene tree discordance. This phylogeny serves as a foundational framework for further macroevolutionary investigations into the environmental and biogeographic factors shaping the evolution of pollination‐related traits. 

Abstract The Andes mountains of western South America are a globally important biodiversity hotspot, yet there is a paucity of resolved phylogenies for plant clades from this region. Filling an important gap in our understanding of the World’s richest flora, we present the first phylogeny of Freziera (Pentaphylacaceae), an Andean-centered, cloud forest radiation. Our dataset was obtained via hybrid-enriched target sequence capture of Angiosperms353 universal loci for 50 of the ca. 75 spp., obtained almost entirely from herbarium specimens. We identify high phylogenomic complexity in Freziera, including the presence of data artifacts. Via by-eye observation of gene trees, detailed examination of warnings from recently improved assembly pipelines, and gene tree filtering, we identified that artifactual orthologs (i.e., the presence of only one copy of a multicopy gene due to differential assembly) were an important source of gene tree heterogeneity that had a negative impact on phylogenetic inference and support. These artifactual orthologs may be common in plant phylogenomic datasets, where multiple instances of genome duplication are common. After accounting for artifactual orthologs as source of gene tree error, we identified a significant, but nonspecific signal of introgression using Patterson’s D and f4 statistics. Despite phylogenomic complexity, we were able to resolve Freziera into 9 well-supported subclades whose evolution has been shaped by multiple evolutionary processes, including incomplete lineage sorting, historical gene flow, and gene duplication. Our results highlight the complexities of plant phylogenomics, which are heightened in Andean radiations, and show the impact of filtering data processing artifacts and standard filtering approaches on phylogenetic inference.